ggbio 1.12.0 autoplot() with txdb example is broken
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Hello Tengfei + bioc list, >From http://www.bioconductor.org/packages/release/bioc/vignettes/ggbi o/inst/doc/ggbio.pdf page 4 (complied on april 11 2014), the following example loads to an error as shown below. I wasn't seeing this error before (aka, last week). The only guess that comes to mind is the recent update to GenomicRanges (1.16.2) although that doesn't seem to be related from the traceback() output, well... maybe it's related to the ignore.strand = TRUE part as described in the error. I'll create a GitHub issue just for completeness. Thank you, Leonardo > library(ggbio) ## Removed the output, nothing out of ordinary > library(TxDb.Hsapiens.UCSC.hg19.knownGene) ## Removed the output > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > data(genesymbol, package = "biovizBase") > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) Aggregating TranscriptDb... Parsing transcripts... Parsing exons... Parsing cds... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done Constructing graphics... Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : error in evaluating the argument 'X' in selecting a method for function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = TRUE))) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in .local(x, ...) : unused argument (ignore.strand = TRUE) > traceback() 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) 13: endoapply(obj.lst, function(x) { if (!is.nullgroup.name)) { if (!group.selfish) { x.n <- split(x, values(x)[, group.name]) irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) irs.new <- resize(irs, fix = fix, width = width(irs) + extend.size) irs.new <- sort(irs.new) .lvs <- disjointBins(irs.new) values(x)$stepping <- .lvs[as.character(values(x)[, group.name])] x } else { values(x)$stepping <- as.numeric(as.factor(values(x)[, group.name])) x } } else { irs <- ranges(x) values(x)$stepping <- as.numeric(disjointBins(resize(irs, fix = "center", width = width(irs) + extend.size))) x } }) 12: endoapply(obj.lst, function(x) { if (!is.nullgroup.name)) { if (!group.selfish) { x.n <- split(x, values(x)[, group.name]) irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) irs.new <- resize(irs, fix = fix, width = width(irs) + extend.size) irs.new <- sort(irs.new) .lvs <- disjointBins(irs.new) values(x)$stepping <- .lvs[as.character(values(x)[, group.name])] x } else { values(x)$stepping <- as.numeric(as.factor(values(x)[, group.name])) x } } else { irs <- ranges(x) values(x)$stepping <- as.numeric(disjointBins(resize(irs, fix = "center", width = width(irs) + extend.size))) x } }) 11: .local(obj, ...) 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, fix = "start", extend.size = es) 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, fix = "start", extend.size = es) 8: .local(data, ...) 7: (function (data, ...) standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="" "transcriptdb"="">, truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", stat = "identity", names.expr = "tx_name", label = TRUE, which = <s4 object="" of="" class="" "granges"="">, list()) 6: (function (data, ...) standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="" "transcriptdb"="">, truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", stat = "identity", names.expr = "tx_name", label = TRUE, which = <s4 object="" of="" class="" "granges"="">, list()) 5: do.call(geom_alignment, args.res) 4: do.call(geom_alignment, args.res) 3: .local(object, ...) 2: autoplot(txdb, which = genesymbol["BRCA1"]) 1: autoplot(txdb, which = genesymbol["BRCA1"]) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 [4] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.2 [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 ggbio_1.12.0 [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.5 BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 cluster_1.15.2 [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 GenomicAlignments_1.0.0 grid_3.1.0 [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 labeling_0.2 [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 munsell_0.4.2 plyr_1.8.1 [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 reshape2_1.2.2 [36] Rsamtools_1.16.0 RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >
TranscriptDb TranscriptDb • 1.6k views
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Tengfei Yin ▴ 490
@tengfei-yin-6162
Last seen 6.6 years ago
Hi Leonardo, Frankly speaking, the vignette is still in progress, and there are some known bugs in ggbio I need to fix (still trying to find a time to do that ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my new MBP with OSX 10.9, but fails, probably binary build is not ready for maverick yet, maybe available by the end of April? Thanks for reporting the bug, I will keep you posted on this when I successfully get it on my laptop and start fixing the problems. cheers Tengfei On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < lcollado@jhsph.edu> wrote: > Hello Tengfei + bioc list, > > From > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > page 4 (complied on april 11 2014), the following example loads to an > error as shown below. I wasn't seeing this error before (aka, last > week). The only guess that comes to mind is the recent update to > GenomicRanges (1.16.2) although that doesn't seem to be related from > the traceback() output, well... maybe it's related to the > ignore.strand = TRUE part as described in the error. > > I'll create a GitHub issue just for completeness. > > Thank you, > Leonardo > > > library(ggbio) > ## Removed the output, nothing out of ordinary > > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > ## Removed the output > > > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > data(genesymbol, package = "biovizBase") > > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > Aggregating TranscriptDb... > Parsing transcripts... > Parsing exons... > Parsing cds... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > Constructing graphics... > Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : > error in evaluating the argument 'X' in selecting a method for > function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = > TRUE))) : > error in evaluating the argument 'x' in selecting a method for > function 'unlist': Error in .local(x, ...) : unused argument > (ignore.strand = TRUE) > > > traceback() > 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) > 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > 13: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)$stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 12: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)$stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 11: .local(obj, ...) > 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 8: .local(data, ...) > 7: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 6: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 5: do.call(geom_alignment, args.res) > 4: do.call(geom_alignment, args.res) > 3: .local(object, ...) > 2: autoplot(txdb, which = genesymbol["BRCA1"]) > 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > GenomicRanges_1.16.2 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > ggbio_1.12.0 > [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.5 > BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 > [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > BSgenome_1.32.0 cluster_1.15.2 > [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > dichromat_2.0-0 digest_0.6.4 > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > GenomicAlignments_1.0.0 grid_3.1.0 > [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > iterators_1.0.7 labeling_0.2 > [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > munsell_0.4.2 plyr_1.8.1 > [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > RCurl_1.95-4.1 reshape2_1.2.2 > [36] Rsamtools_1.16.0 RSQLite_0.11.4 > rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > survival_2.37-7 tools_3.1.0 > [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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btw, based on the error, let me try to debug it. On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > Frankly speaking, the vignette is still in progress, and there are some > known bugs in ggbio I need to fix (still trying to find a time to do that > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my new MBP > with OSX 10.9, but fails, probably binary build is not ready for maverick > yet, maybe available by the end of April? > > Thanks for reporting the bug, I will keep you posted on this when I > successfully get it on my laptop and start fixing the problems. > > cheers > > Tengfei > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Hello Tengfei + bioc list, >> >> From >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf >> page 4 (complied on april 11 2014), the following example loads to an >> error as shown below. I wasn't seeing this error before (aka, last >> week). The only guess that comes to mind is the recent update to >> GenomicRanges (1.16.2) although that doesn't seem to be related from >> the traceback() output, well... maybe it's related to the >> ignore.strand = TRUE part as described in the error. >> >> I'll create a GitHub issue just for completeness. >> >> Thank you, >> Leonardo >> >> > library(ggbio) >> ## Removed the output, nothing out of ordinary >> >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> ## Removed the output >> >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> > data(genesymbol, package = "biovizBase") >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) >> Aggregating TranscriptDb... >> Parsing transcripts... >> Parsing exons... >> Parsing cds... >> Parsing utrs... >> ------exons... >> ------cdss... >> ------introns... >> ------utr... >> aggregating... >> Done >> Constructing graphics... >> Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : >> error in evaluating the argument 'X' in selecting a method for >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = >> TRUE))) : >> error in evaluating the argument 'x' in selecting a method for >> function 'unlist': Error in .local(x, ...) : unused argument >> (ignore.strand = TRUE) >> >> > traceback() >> 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) >> 13: endoapply(obj.lst, function(x) { >> if (!is.nullgroup.name)) { >> if (!group.selfish) { >> x.n <- split(x, values(x)[, group.name]) >> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >> irs.new <- resize(irs, fix = fix, width = width(irs) + >> extend.size) >> irs.new <- sort(irs.new) >> .lvs <- disjointBins(irs.new) >> values(x)$stepping <- .lvs[as.character(values(x)[, >> group.name])] >> x >> } >> else { >> values(x)$stepping <- as.numeric(as.factor(values(x)[, >> group.name])) >> x >> } >> } >> else { >> irs <- ranges(x) >> values(x)$stepping <- as.numeric(disjointBins(resize(irs, >> fix = "center", width = width(irs) + extend.size))) >> x >> } >> }) >> 12: endoapply(obj.lst, function(x) { >> if (!is.nullgroup.name)) { >> if (!group.selfish) { >> x.n <- split(x, values(x)[, group.name]) >> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >> irs.new <- resize(irs, fix = fix, width = width(irs) + >> extend.size) >> irs.new <- sort(irs.new) >> .lvs <- disjointBins(irs.new) >> values(x)$stepping <- .lvs[as.character(values(x)[, >> group.name])] >> x >> } >> else { >> values(x)$stepping <- as.numeric(as.factor(values(x)[, >> group.name])) >> x >> } >> } >> else { >> irs <- ranges(x) >> values(x)$stepping <- as.numeric(disjointBins(resize(irs, >> fix = "center", width = width(irs) + extend.size))) >> x >> } >> }) >> 11: .local(obj, ...) >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >> fix = "start", extend.size = es) >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >> fix = "start", extend.size = es) >> 8: .local(data, ...) >> 7: (function (data, ...) >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">> "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name", label = TRUE, >> which = <s4 object="" of="" class="" "granges"="">, list()) >> 6: (function (data, ...) >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">> "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name", label = TRUE, >> which = <s4 object="" of="" class="" "granges"="">, list()) >> 5: do.call(geom_alignment, args.res) >> 4: do.call(geom_alignment, args.res) >> 3: .local(object, ...) >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] XVector_0.4.0 >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> GenomicRanges_1.16.2 >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> ggbio_1.12.0 >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BatchJobs_1.2 BBmisc_1.5 >> BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> BSgenome_1.32.0 cluster_1.15.2 >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> dichromat_2.0-0 digest_0.6.4 >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >> GenomicAlignments_1.0.0 grid_3.1.0 >> [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 >> iterators_1.0.7 labeling_0.2 >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >> munsell_0.4.2 plyr_1.8.1 >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> RCurl_1.95-4.1 reshape2_1.2.2 >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 >> survival_2.37-7 tools_3.1.0 >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >> > >> > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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Hi Tengfei, ----- Original Message ----- > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > To: lcollado at jhu.edu > Cc: bioconductor at r-project.org > Sent: Wednesday, April 23, 2014 7:52:11 AM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > btw, based on the error, let me try to debug it. > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > <tengfei.yin at="" sbgenomics.com="">wrote: > > > Hi Leonardo, > > > > Frankly speaking, the vignette is still in progress, and there are > > some > > known bugs in ggbio I need to fix (still trying to find a time to > > do that > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my > > new MBP > > with OSX 10.9, but fails, probably binary build is not ready for > > maverick > > yet, maybe available by the end of April? > > > > Thanks for reporting the bug, I will keep you posted on this when I > > successfully get it on my laptop and start fixing the problems. > > You can install the Snow Leopard build of R and should have no problems, binary packages are available for that version. It will run fine on Mavericks. Dan > > cheers > > > > Tengfei > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > lcollado at jhsph.edu> wrote: > > > >> Hello Tengfei + bioc list, > >> > >> From > >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio /inst/doc/ggbio.pdf > >> page 4 (complied on april 11 2014), the following example loads to > >> an > >> error as shown below. I wasn't seeing this error before (aka, last > >> week). The only guess that comes to mind is the recent update to > >> GenomicRanges (1.16.2) although that doesn't seem to be related > >> from > >> the traceback() output, well... maybe it's related to the > >> ignore.strand = TRUE part as described in the error. > >> > >> I'll create a GitHub issue just for completeness. > >> > >> Thank you, > >> Leonardo > >> > >> > library(ggbio) > >> ## Removed the output, nothing out of ordinary > >> > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> ## Removed the output > >> > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> > data(genesymbol, package = "biovizBase") > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > >> Aggregating TranscriptDb... > >> Parsing transcripts... > >> Parsing exons... > >> Parsing cds... > >> Parsing utrs... > >> ------exons... > >> ------cdss... > >> ------introns... > >> ------utr... > >> aggregating... > >> Done > >> Constructing graphics... > >> Error in sapply(listData, function(Xi) extends(class(Xi), > >> elementTypeX)) : > >> error in evaluating the argument 'X' in selecting a method for > >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand > >> = > >> TRUE))) : > >> error in evaluating the argument 'x' in selecting a method for > >> function 'unlist': Error in .local(x, ...) : unused argument > >> (ignore.strand = TRUE) > >> > >> > traceback() > >> 15: sapply(listData, function(Xi) extends(class(Xi), > >> elementTypeX)) > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > >> 13: endoapply(obj.lst, function(x) { > >> if (!is.nullgroup.name)) { > >> if (!group.selfish) { > >> x.n <- split(x, values(x)[, group.name]) > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> TRUE))) > >> irs.new <- resize(irs, fix = fix, width = > >> width(irs) + > >> extend.size) > >> irs.new <- sort(irs.new) > >> .lvs <- disjointBins(irs.new) > >> values(x)$stepping <- > >> .lvs[as.character(values(x)[, > >> group.name])] > >> x > >> } > >> else { > >> values(x)$stepping <- > >> as.numeric(as.factor(values(x)[, > >> group.name])) > >> x > >> } > >> } > >> else { > >> irs <- ranges(x) > >> values(x)$stepping <- > >> as.numeric(disjointBins(resize(irs, > >> fix = "center", width = width(irs) + > >> extend.size))) > >> x > >> } > >> }) > >> 12: endoapply(obj.lst, function(x) { > >> if (!is.nullgroup.name)) { > >> if (!group.selfish) { > >> x.n <- split(x, values(x)[, group.name]) > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> TRUE))) > >> irs.new <- resize(irs, fix = fix, width = > >> width(irs) + > >> extend.size) > >> irs.new <- sort(irs.new) > >> .lvs <- disjointBins(irs.new) > >> values(x)$stepping <- > >> .lvs[as.character(values(x)[, > >> group.name])] > >> x > >> } > >> else { > >> values(x)$stepping <- > >> as.numeric(as.factor(values(x)[, > >> group.name])) > >> x > >> } > >> } > >> else { > >> irs <- ranges(x) > >> values(x)$stepping <- > >> as.numeric(disjointBins(resize(irs, > >> fix = "center", width = width(irs) + > >> extend.size))) > >> x > >> } > >> }) > >> 11: .local(obj, ...) > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > >> fix = "start", extend.size = es) > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > >> fix = "start", extend.size = es) > >> 8: .local(data, ...) > >> 7: (function (data, ...) > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> >> "TranscriptDb">, > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > >> stat = "identity", names.expr = "tx_name", label = TRUE, > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> 6: (function (data, ...) > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> >> "TranscriptDb">, > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > >> stat = "identity", names.expr = "tx_name", label = TRUE, > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> 5: do.call(geom_alignment, args.res) > >> 4: do.call(geom_alignment, args.res) > >> 3: .local(object, ...) > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >> > >> > sessionInfo() > >> R version 3.1.0 (2014-04-10) > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >> locale: > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >> attached base packages: > >> [1] parallel stats graphics grDevices utils datasets > >> methods base > >> > >> other attached packages: > >> [1] XVector_0.4.0 > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> GenomicRanges_1.16.2 > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> ggbio_1.12.0 > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> > >> loaded via a namespace (and not attached): > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> Biostrings_2.32.0 > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> BSgenome_1.32.0 cluster_1.15.2 > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> dichromat_2.0-0 digest_0.6.4 > >> [16] fail_1.2 foreach_1.4.2 > >> Formula_1.1-1 > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> Hmisc_3.14-4 > >> iterators_1.0.7 labeling_0.2 > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > >> munsell_0.4.2 plyr_1.8.1 > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> [41] splines_3.1.0 stats4_3.1.0 > >> stringr_0.6.2 > >> survival_2.37-7 tools_3.1.0 > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> zlibbioc_1.10.0 > >> > > >> > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > > > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
0
Entering edit mode
Hi Dan, Thanks a lot! I will try this! cheers Tengfei On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Tengfei, > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > To: lcollado@jhu.edu > > Cc: bioconductor@r-project.org > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > btw, based on the error, let me try to debug it. > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > <tengfei.yin@sbgenomics.com>wrote: > > > > > Hi Leonardo, > > > > > > Frankly speaking, the vignette is still in progress, and there are > > > some > > > known bugs in ggbio I need to fix (still trying to find a time to > > > do that > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my > > > new MBP > > > with OSX 10.9, but fails, probably binary build is not ready for > > > maverick > > > yet, maybe available by the end of April? > > > > > > Thanks for reporting the bug, I will keep you posted on this when I > > > successfully get it on my laptop and start fixing the problems. > > > > > You can install the Snow Leopard build of R and should have no problems, > binary packages are available for that version. It will run fine on > Mavericks. > > Dan > > > > > cheers > > > > > > Tengfei > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > lcollado@jhsph.edu> wrote: > > > > > >> Hello Tengfei + bioc list, > > >> > > >> From > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > >> page 4 (complied on april 11 2014), the following example loads to > > >> an > > >> error as shown below. I wasn't seeing this error before (aka, last > > >> week). The only guess that comes to mind is the recent update to > > >> GenomicRanges (1.16.2) although that doesn't seem to be related > > >> from > > >> the traceback() output, well... maybe it's related to the > > >> ignore.strand = TRUE part as described in the error. > > >> > > >> I'll create a GitHub issue just for completeness. > > >> > > >> Thank you, > > >> Leonardo > > >> > > >> > library(ggbio) > > >> ## Removed the output, nothing out of ordinary > > >> > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > >> ## Removed the output > > >> > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >> > data(genesymbol, package = "biovizBase") > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > >> Aggregating TranscriptDb... > > >> Parsing transcripts... > > >> Parsing exons... > > >> Parsing cds... > > >> Parsing utrs... > > >> ------exons... > > >> ------cdss... > > >> ------introns... > > >> ------utr... > > >> aggregating... > > >> Done > > >> Constructing graphics... > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) : > > >> error in evaluating the argument 'X' in selecting a method for > > >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand > > >> = > > >> TRUE))) : > > >> error in evaluating the argument 'x' in selecting a method for > > >> function 'unlist': Error in .local(x, ...) : unused argument > > >> (ignore.strand = TRUE) > > >> > > >> > traceback() > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > > >> 13: endoapply(obj.lst, function(x) { > > >> if (!is.nullgroup.name)) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 12: endoapply(obj.lst, function(x) { > > >> if (!is.nullgroup.name)) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 11: .local(obj, ...) > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 8: .local(data, ...) > > >> 7: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 6: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 5: do.call(geom_alignment, args.res) > > >> 4: do.call(geom_alignment, args.res) > > >> 3: .local(object, ...) > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> > > >> > > >> > sessionInfo() > > >> R version 3.1.0 (2014-04-10) > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > >> > > >> locale: > > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >> > > >> attached base packages: > > >> [1] parallel stats graphics grDevices utils datasets > > >> methods base > > >> > > >> other attached packages: > > >> [1] XVector_0.4.0 > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > >> GenomicRanges_1.16.2 > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > >> ggbio_1.12.0 > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > >> > > >> loaded via a namespace (and not attached): > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > >> Biostrings_2.32.0 > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > >> BSgenome_1.32.0 cluster_1.15.2 > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > >> dichromat_2.0-0 digest_0.6.4 > > >> [16] fail_1.2 foreach_1.4.2 > > >> Formula_1.1-1 > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > >> Hmisc_3.14-4 > > >> iterators_1.0.7 labeling_0.2 > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > >> munsell_0.4.2 plyr_1.8.1 > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > >> [41] splines_3.1.0 stats4_3.1.0 > > >> stringr_0.6.2 > > >> survival_2.37-7 tools_3.1.0 > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > >> zlibbioc_1.10.0 > > >> > > > >> > > > > > > > > > > > > -- > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866-0446 > > > > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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Entering edit mode
Hi Dan, So you mean I install R 3.1 for snow leopard and it should work? Is there a way to build from source using biocLite, like type = "source", this is what I got > library(BiocInstaller) Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help > biocLite("GenomicRanges") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version 3.1.0. Installing package(s) 'GenomicRanges' package âGenomicRangesâ is available as a source package but not as a binary Warning message: package âGenomicRangesâ is not available (for R version 3.1.0) Just wondering is there a solution without re-install R for snow leopard. And what's the plan for maverick? Thanks Tengfei On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Tengfei, > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > To: lcollado@jhu.edu > > Cc: bioconductor@r-project.org > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > btw, based on the error, let me try to debug it. > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > <tengfei.yin@sbgenomics.com>wrote: > > > > > Hi Leonardo, > > > > > > Frankly speaking, the vignette is still in progress, and there are > > > some > > > known bugs in ggbio I need to fix (still trying to find a time to > > > do that > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my > > > new MBP > > > with OSX 10.9, but fails, probably binary build is not ready for > > > maverick > > > yet, maybe available by the end of April? > > > > > > Thanks for reporting the bug, I will keep you posted on this when I > > > successfully get it on my laptop and start fixing the problems. > > > > > You can install the Snow Leopard build of R and should have no problems, > binary packages are available for that version. It will run fine on > Mavericks. > > Dan > > > > > cheers > > > > > > Tengfei > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > lcollado@jhsph.edu> wrote: > > > > > >> Hello Tengfei + bioc list, > > >> > > >> From > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > >> page 4 (complied on april 11 2014), the following example loads to > > >> an > > >> error as shown below. I wasn't seeing this error before (aka, last > > >> week). The only guess that comes to mind is the recent update to > > >> GenomicRanges (1.16.2) although that doesn't seem to be related > > >> from > > >> the traceback() output, well... maybe it's related to the > > >> ignore.strand = TRUE part as described in the error. > > >> > > >> I'll create a GitHub issue just for completeness. > > >> > > >> Thank you, > > >> Leonardo > > >> > > >> > library(ggbio) > > >> ## Removed the output, nothing out of ordinary > > >> > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > >> ## Removed the output > > >> > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >> > data(genesymbol, package = "biovizBase") > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > >> Aggregating TranscriptDb... > > >> Parsing transcripts... > > >> Parsing exons... > > >> Parsing cds... > > >> Parsing utrs... > > >> ------exons... > > >> ------cdss... > > >> ------introns... > > >> ------utr... > > >> aggregating... > > >> Done > > >> Constructing graphics... > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) : > > >> error in evaluating the argument 'X' in selecting a method for > > >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand > > >> = > > >> TRUE))) : > > >> error in evaluating the argument 'x' in selecting a method for > > >> function 'unlist': Error in .local(x, ...) : unused argument > > >> (ignore.strand = TRUE) > > >> > > >> > traceback() > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > > >> 13: endoapply(obj.lst, function(x) { > > >> if (!is.nullgroup.name)) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 12: endoapply(obj.lst, function(x) { > > >> if (!is.nullgroup.name)) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 11: .local(obj, ...) > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 8: .local(data, ...) > > >> 7: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 6: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 5: do.call(geom_alignment, args.res) > > >> 4: do.call(geom_alignment, args.res) > > >> 3: .local(object, ...) > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> > > >> > > >> > sessionInfo() > > >> R version 3.1.0 (2014-04-10) > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > >> > > >> locale: > > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >> > > >> attached base packages: > > >> [1] parallel stats graphics grDevices utils datasets > > >> methods base > > >> > > >> other attached packages: > > >> [1] XVector_0.4.0 > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > >> GenomicRanges_1.16.2 > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > >> ggbio_1.12.0 > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > >> > > >> loaded via a namespace (and not attached): > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > >> Biostrings_2.32.0 > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > >> BSgenome_1.32.0 cluster_1.15.2 > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > >> dichromat_2.0-0 digest_0.6.4 > > >> [16] fail_1.2 foreach_1.4.2 > > >> Formula_1.1-1 > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > >> Hmisc_3.14-4 > > >> iterators_1.0.7 labeling_0.2 > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > >> munsell_0.4.2 plyr_1.8.1 > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > >> [41] splines_3.1.0 stats4_3.1.0 > > >> stringr_0.6.2 > > >> survival_2.37-7 tools_3.1.0 > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > >> zlibbioc_1.10.0 > > >> > > > >> > > > > > > > > > > > > -- > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866-0446 > > > > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
0
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----- Original Message ----- > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, lcollado at jhu.edu > Sent: Wednesday, April 23, 2014 9:24:42 AM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > Hi Dan, > > > So you mean I install R 3.1 for snow leopard and it should work? Yes. ? Is > there a way to build from source using biocLite, like type = > "source", this is what I got > > > > > library(BiocInstaller) > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help > > biocLite("GenomicRanges") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > 3.1.0. > Installing package(s) 'GenomicRanges' > > > package ?GenomicRanges? is available as a source package but not as a > binary > > > Warning message: > package ?GenomicRanges? is not available (for R version 3.1.0) > > > Just wondering is there a solution without re-install R for snow > leopard. And what's the plan for maverick? > You can do biocLite("GenomicRanges", type="source") but you need to have the appropriate compilers, etc. I *STRONGLY* recommend using the Snow Leopard build. You can have multiple installations of R on your Mac and switch between them using Rswitch (http://r.research.att.com/#other) or another easy mechanism. We are building packages for Mavericks now, we just have to resolve a few build issues and test the resulting packages, we still hope to have them available by the end of the month. But since you can install the Snow Leopard build without needing to remove your Mavericks build, you should do that. Dan > > Thanks > > > Tengfei > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < dtenenba at fhcrc.org > > wrote: > > > Hi Tengfei, > > > ----- Original Message ----- > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > To: lcollado at jhu.edu > > Cc: bioconductor at r-project.org > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > broken > > > > btw, based on the error, let me try to debug it. > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > < tengfei.yin at sbgenomics.com >wrote: > > > > > Hi Leonardo, > > > > > > Frankly speaking, the vignette is still in progress, and there > > > are > > > some > > > known bugs in ggbio I need to fix (still trying to find a time to > > > do that > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my > > > new MBP > > > with OSX 10.9, but fails, probably binary build is not ready for > > > maverick > > > yet, maybe available by the end of April? > > > > > > Thanks for reporting the bug, I will keep you posted on this when > > > I > > > successfully get it on my laptop and start fixing the problems. > > > > > You can install the Snow Leopard build of R and should have no > problems, binary packages are available for that version. It will > run fine on Mavericks. > > Dan > > > > > > > cheers > > > > > > Tengfei > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > lcollado at jhsph.edu > wrote: > > > > > >> Hello Tengfei + bioc list, > > >> > > >> From > > >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggb io/inst/doc/ggbio.pdf > > >> page 4 (complied on april 11 2014), the following example loads > > >> to > > >> an > > >> error as shown below. I wasn't seeing this error before (aka, > > >> last > > >> week). The only guess that comes to mind is the recent update to > > >> GenomicRanges (1.16.2) although that doesn't seem to be related > > >> from > > >> the traceback() output, well... maybe it's related to the > > >> ignore.strand = TRUE part as described in the error. > > >> > > >> I'll create a GitHub issue just for completeness. > > >> > > >> Thank you, > > >> Leonardo > > >> > > >> > library(ggbio) > > >> ## Removed the output, nothing out of ordinary > > >> > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > >> ## Removed the output > > >> > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >> > data(genesymbol, package = "biovizBase") > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > >> Aggregating TranscriptDb... > > >> Parsing transcripts... > > >> Parsing exons... > > >> Parsing cds... > > >> Parsing utrs... > > >> ------exons... > > >> ------cdss... > > >> ------introns... > > >> ------utr... > > >> aggregating... > > >> Done > > >> Constructing graphics... > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) : > > >> error in evaluating the argument 'X' in selecting a method for > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > >> ignore.strand > > >> = > > >> TRUE))) : > > >> error in evaluating the argument 'x' in selecting a method for > > >> function 'unlist': Error in .local(x, ...) : unused argument > > >> (ignore.strand = TRUE) > > >> > > >> > traceback() > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > >> elementTypeX)) > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > > >> 13: endoapply(obj.lst, function(x) { > > >> if (!is.null( group.name )) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name ]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name ])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name ])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 12: endoapply(obj.lst, function(x) { > > >> if (!is.null( group.name )) { > > >> if (!group.selfish) { > > >> x.n <- split(x, values(x)[, group.name ]) > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> TRUE))) > > >> irs.new <- resize(irs, fix = fix, width = > > >> width(irs) + > > >> extend.size) > > >> irs.new <- sort(irs.new) > > >> .lvs <- disjointBins(irs.new) > > >> values(x)$stepping <- > > >> .lvs[as.character(values(x)[, > > >> group.name ])] > > >> x > > >> } > > >> else { > > >> values(x)$stepping <- > > >> as.numeric(as.factor(values(x)[, > > >> group.name ])) > > >> x > > >> } > > >> } > > >> else { > > >> irs <- ranges(x) > > >> values(x)$stepping <- > > >> as.numeric(disjointBins(resize(irs, > > >> fix = "center", width = width(irs) + > > >> extend.size))) > > >> x > > >> } > > >> }) > > >> 11: .local(obj, ...) > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > >> fix = "start", extend.size = es) > > >> 8: .local(data, ...) > > >> 7: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 6: (function (data, ...) > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > >> "TranscriptDb">, > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> 5: do.call(geom_alignment, args.res) > > >> 4: do.call(geom_alignment, args.res) > > >> 3: .local(object, ...) > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> > > >> > > >> > sessionInfo() > > >> R version 3.1.0 (2014-04-10) > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > >> > > >> locale: > > >> [1] > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >> > > >> attached base packages: > > >> [1] parallel stats graphics grDevices utils datasets > > >> methods base > > >> > > >> other attached packages: > > >> [1] XVector_0.4.0 > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > >> GenomicRanges_1.16.2 > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > >> ggbio_1.12.0 > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > >> > > >> loaded via a namespace (and not attached): > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > >> Biostrings_2.32.0 > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > >> BSgenome_1.32.0 cluster_1.15.2 > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > >> dichromat_2.0-0 digest_0.6.4 > > >> [16] fail_1.2 foreach_1.4.2 > > >> Formula_1.1-1 > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > >> Hmisc_3.14-4 > > >> iterators_1.0.7 labeling_0.2 > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > >> munsell_0.4.2 plyr_1.8.1 > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > >> [41] splines_3.1.0 stats4_3.1.0 > > >> stringr_0.6.2 > > >> survival_2.37-7 tools_3.1.0 > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > >> zlibbioc_1.10.0 > > >> > > > >> > > > > > > > > > > > > -- > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866-0446 > > > > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > -- > > > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866- 0446 >
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Thanks a lot Dan! it's clear to me now, sorry that I am still a newbie to OSX ... I got R-devel running and I will try Rswitcher, I also want to do that switch easily in emacs too. cheers Tengfei On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, > lcollado@jhu.edu > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > > > Hi Dan, > > > > > > So you mean I install R 3.1 for snow leopard and it should work? > > Yes. > > > ? Is > > there a way to build from source using biocLite, like type = > > "source", this is what I got > > > > > > > > > library(BiocInstaller) > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help > > > biocLite("GenomicRanges") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > > 3.1.0. > > Installing package(s) 'GenomicRanges' > > > > > > package ‘GenomicRanges’ is available as a source package but not as a > > binary > > > > > > Warning message: > > package ‘GenomicRanges’ is not available (for R version 3.1.0) > > > > > > Just wondering is there a solution without re-install R for snow > > leopard. And what's the plan for maverick? > > > > You can do > biocLite("GenomicRanges", type="source") > > but you need to have the appropriate compilers, etc. > > I *STRONGLY* recommend using the Snow Leopard build. You can have multiple > installations of R on your Mac and switch between them using Rswitch ( > http://r.research.att.com/#other) or another easy mechanism. > > We are building packages for Mavericks now, we just have to resolve a few > build issues and test the resulting packages, we still hope to have them > available by the end of the month. But since you can install the Snow > Leopard build without needing to remove your Mavericks build, you should do > that. > > Dan > > > > > > > Thanks > > > > > > Tengfei > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < dtenenba@fhcrc.org > > > wrote: > > > > > > Hi Tengfei, > > > > > > ----- Original Message ----- > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > To: lcollado@jhu.edu > > > Cc: bioconductor@r-project.org > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > broken > > > > > > btw, based on the error, let me try to debug it. > > > > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > > < tengfei.yin@sbgenomics.com >wrote: > > > > > > > Hi Leonardo, > > > > > > > > Frankly speaking, the vignette is still in progress, and there > > > > are > > > > some > > > > known bugs in ggbio I need to fix (still trying to find a time to > > > > do that > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my > > > > new MBP > > > > with OSX 10.9, but fails, probably binary build is not ready for > > > > maverick > > > > yet, maybe available by the end of April? > > > > > > > > Thanks for reporting the bug, I will keep you posted on this when > > > > I > > > > successfully get it on my laptop and start fixing the problems. > > > > > > > > You can install the Snow Leopard build of R and should have no > > problems, binary packages are available for that version. It will > > run fine on Mavericks. > > > > Dan > > > > > > > > > > > > cheers > > > > > > > > Tengfei > > > > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > > lcollado@jhsph.edu > wrote: > > > > > > > >> Hello Tengfei + bioc list, > > > >> > > > >> From > > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > > >> page 4 (complied on april 11 2014), the following example loads > > > >> to > > > >> an > > > >> error as shown below. I wasn't seeing this error before (aka, > > > >> last > > > >> week). The only guess that comes to mind is the recent update to > > > >> GenomicRanges (1.16.2) although that doesn't seem to be related > > > >> from > > > >> the traceback() output, well... maybe it's related to the > > > >> ignore.strand = TRUE part as described in the error. > > > >> > > > >> I'll create a GitHub issue just for completeness. > > > >> > > > >> Thank you, > > > >> Leonardo > > > >> > > > >> > library(ggbio) > > > >> ## Removed the output, nothing out of ordinary > > > >> > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > > >> ## Removed the output > > > >> > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > >> > data(genesymbol, package = "biovizBase") > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> Aggregating TranscriptDb... > > > >> Parsing transcripts... > > > >> Parsing exons... > > > >> Parsing cds... > > > >> Parsing utrs... > > > >> ------exons... > > > >> ------cdss... > > > >> ------introns... > > > >> ------utr... > > > >> aggregating... > > > >> Done > > > >> Constructing graphics... > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > > >> elementTypeX)) : > > > >> error in evaluating the argument 'X' in selecting a method for > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > > >> ignore.strand > > > >> = > > > >> TRUE))) : > > > >> error in evaluating the argument 'x' in selecting a method for > > > >> function 'unlist': Error in .local(x, ...) : unused argument > > > >> (ignore.strand = TRUE) > > > >> > > > >> > traceback() > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > > >> elementTypeX)) > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > > > >> 13: endoapply(obj.lst, function(x) { > > > >> if (!is.null( group.name )) { > > > >> if (!group.selfish) { > > > >> x.n <- split(x, values(x)[, group.name ]) > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > >> TRUE))) > > > >> irs.new <- resize(irs, fix = fix, width = > > > >> width(irs) + > > > >> extend.size) > > > >> irs.new <- sort(irs.new) > > > >> .lvs <- disjointBins(irs.new) > > > >> values(x)$stepping <- > > > >> .lvs[as.character(values(x)[, > > > >> group.name ])] > > > >> x > > > >> } > > > >> else { > > > >> values(x)$stepping <- > > > >> as.numeric(as.factor(values(x)[, > > > >> group.name ])) > > > >> x > > > >> } > > > >> } > > > >> else { > > > >> irs <- ranges(x) > > > >> values(x)$stepping <- > > > >> as.numeric(disjointBins(resize(irs, > > > >> fix = "center", width = width(irs) + > > > >> extend.size))) > > > >> x > > > >> } > > > >> }) > > > >> 12: endoapply(obj.lst, function(x) { > > > >> if (!is.null( group.name )) { > > > >> if (!group.selfish) { > > > >> x.n <- split(x, values(x)[, group.name ]) > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > >> TRUE))) > > > >> irs.new <- resize(irs, fix = fix, width = > > > >> width(irs) + > > > >> extend.size) > > > >> irs.new <- sort(irs.new) > > > >> .lvs <- disjointBins(irs.new) > > > >> values(x)$stepping <- > > > >> .lvs[as.character(values(x)[, > > > >> group.name ])] > > > >> x > > > >> } > > > >> else { > > > >> values(x)$stepping <- > > > >> as.numeric(as.factor(values(x)[, > > > >> group.name ])) > > > >> x > > > >> } > > > >> } > > > >> else { > > > >> irs <- ranges(x) > > > >> values(x)$stepping <- > > > >> as.numeric(disjointBins(resize(irs, > > > >> fix = "center", width = width(irs) + > > > >> extend.size))) > > > >> x > > > >> } > > > >> }) > > > >> 11: .local(obj, ...) > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > > >> fix = "start", extend.size = es) > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > > >> fix = "start", extend.size = es) > > > >> 8: .local(data, ...) > > > >> 7: (function (data, ...) > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > >> "TranscriptDb">, > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > >> 6: (function (data, ...) > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > >> "TranscriptDb">, > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > >> 5: do.call(geom_alignment, args.res) > > > >> 4: do.call(geom_alignment, args.res) > > > >> 3: .local(object, ...) > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> > > > >> > > > >> > sessionInfo() > > > >> R version 3.1.0 (2014-04-10) > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > >> > > > >> locale: > > > >> [1] > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > >> > > > >> attached base packages: > > > >> [1] parallel stats graphics grDevices utils datasets > > > >> methods base > > > >> > > > >> other attached packages: > > > >> [1] XVector_0.4.0 > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > > >> GenomicRanges_1.16.2 > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > > >> ggbio_1.12.0 > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > >> > > > >> loaded via a namespace (and not attached): > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > > >> Biostrings_2.32.0 > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > > >> BSgenome_1.32.0 cluster_1.15.2 > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > > >> dichromat_2.0-0 digest_0.6.4 > > > >> [16] fail_1.2 foreach_1.4.2 > > > >> Formula_1.1-1 > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > > >> Hmisc_3.14-4 > > > >> iterators_1.0.7 labeling_0.2 > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > > >> munsell_0.4.2 plyr_1.8.1 > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > > >> [41] splines_3.1.0 stats4_3.1.0 > > > >> stringr_0.6.2 > > > >> survival_2.37-7 tools_3.1.0 > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > > >> zlibbioc_1.10.0 > > > >> > > > > >> > > > > > > > > > > > > > > > > -- > > > > Tengfei Yin, PhD > > > > Seven Bridges Genomics > > > > sbgenomics.com > > > > 625 Mt. Auburn St. Suite #208 > > > > Cambridge, MA 02138 > > > > (617) 866-0446 > > > > > > > > > > > > > > > > -- > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866-0446 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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Hi Tengfei, ----- Original Message ----- > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, lcollado at jhu.edu > Sent: Wednesday, April 23, 2014 10:46:02 AM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > Thanks a lot Dan! it's clear to me now, sorry that I am still a > newbie to OSX ... I got R-devel running and I will try Rswitcher, I > also want to do that switch easily in emacs too. > > You don't want to use R-devel. Both BioC release (2.14) and BioC devel (3.0) are meant to work with R-3.1.0, the released version of R. I think the Rswitch app just sets a symbolic link, so you should be able to do that within emacs. Run it and see what it does to /Library/Frameworks/R.framework. Dan > > cheers > > > Tengfei > > > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org > > wrote: > > > > > > ----- Original Message ----- > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >, > > lcollado at jhu.edu > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > broken > > > > > > > Hi Dan, > > > > > > So you mean I install R 3.1 for snow leopard and it should work? > > Yes. > > > > ? Is > > there a way to build from source using biocLite, like type = > > "source", this is what I got > > > > > > > > > library(BiocInstaller) > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for > > help > > > biocLite("GenomicRanges") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > > 3.1.0. > > Installing package(s) 'GenomicRanges' > > > > > > package ?GenomicRanges? is available as a source package but not as > > a > > binary > > > > > > Warning message: > > package ?GenomicRanges? is not available (for R version 3.1.0) > > > > > > Just wondering is there a solution without re-install R for snow > > leopard. And what's the plan for maverick? > > > > You can do > biocLite("GenomicRanges", type="source") > > but you need to have the appropriate compilers, etc. > > I *STRONGLY* recommend using the Snow Leopard build. You can have > multiple installations of R on your Mac and switch between them > using Rswitch ( http://r.research.att.com/#other ) or another easy > mechanism. > > We are building packages for Mavericks now, we just have to resolve a > few build issues and test the resulting packages, we still hope to > have them available by the end of the month. But since you can > install the Snow Leopard build without needing to remove your > Mavericks build, you should do that. > > Dan > > > > > > > > > Thanks > > > > > > Tengfei > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > dtenenba at fhcrc.org > > > wrote: > > > > > > Hi Tengfei, > > > > > > ----- Original Message ----- > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > > To: lcollado at jhu.edu > > > Cc: bioconductor at r-project.org > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > broken > > > > > > btw, based on the error, let me try to debug it. > > > > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > > < tengfei.yin at sbgenomics.com >wrote: > > > > > > > Hi Leonardo, > > > > > > > > Frankly speaking, the vignette is still in progress, and there > > > > are > > > > some > > > > known bugs in ggbio I need to fix (still trying to find a time > > > > to > > > > do that > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on > > > > my > > > > new MBP > > > > with OSX 10.9, but fails, probably binary build is not ready > > > > for > > > > maverick > > > > yet, maybe available by the end of April? > > > > > > > > Thanks for reporting the bug, I will keep you posted on this > > > > when > > > > I > > > > successfully get it on my laptop and start fixing the problems. > > > > > > > > You can install the Snow Leopard build of R and should have no > > problems, binary packages are available for that version. It will > > run fine on Mavericks. > > > > Dan > > > > > > > > > > > > cheers > > > > > > > > Tengfei > > > > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > > lcollado at jhsph.edu > wrote: > > > > > > > >> Hello Tengfei + bioc list, > > > >> > > > >> From > > > >> http://www.bioconductor.org/packages/release/bioc/vignettes/g gbio/inst/doc/ggbio.pdf > > > >> page 4 (complied on april 11 2014), the following example > > > >> loads > > > >> to > > > >> an > > > >> error as shown below. I wasn't seeing this error before (aka, > > > >> last > > > >> week). The only guess that comes to mind is the recent update > > > >> to > > > >> GenomicRanges (1.16.2) although that doesn't seem to be > > > >> related > > > >> from > > > >> the traceback() output, well... maybe it's related to the > > > >> ignore.strand = TRUE part as described in the error. > > > >> > > > >> I'll create a GitHub issue just for completeness. > > > >> > > > >> Thank you, > > > >> Leonardo > > > >> > > > >> > library(ggbio) > > > >> ## Removed the output, nothing out of ordinary > > > >> > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > > >> ## Removed the output > > > >> > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > >> > data(genesymbol, package = "biovizBase") > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> Aggregating TranscriptDb... > > > >> Parsing transcripts... > > > >> Parsing exons... > > > >> Parsing cds... > > > >> Parsing utrs... > > > >> ------exons... > > > >> ------cdss... > > > >> ------introns... > > > >> ------utr... > > > >> aggregating... > > > >> Done > > > >> Constructing graphics... > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > > >> elementTypeX)) : > > > >> error in evaluating the argument 'X' in selecting a method for > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > > >> ignore.strand > > > >> = > > > >> TRUE))) : > > > >> error in evaluating the argument 'x' in selecting a method for > > > >> function 'unlist': Error in .local(x, ...) : unused argument > > > >> (ignore.strand = TRUE) > > > >> > > > >> > traceback() > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > > >> elementTypeX)) > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, > > > >> ...)) > > > >> 13: endoapply(obj.lst, function(x) { > > > >> if (!is.null( group.name )) { > > > >> if (!group.selfish) { > > > >> x.n <- split(x, values(x)[, group.name ]) > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > >> TRUE))) > > > >> irs.new <- resize(irs, fix = fix, width = > > > >> width(irs) + > > > >> extend.size) > > > >> irs.new <- sort(irs.new) > > > >> .lvs <- disjointBins(irs.new) > > > >> values(x)$stepping <- > > > >> .lvs[as.character(values(x)[, > > > >> group.name ])] > > > >> x > > > >> } > > > >> else { > > > >> values(x)$stepping <- > > > >> as.numeric(as.factor(values(x)[, > > > >> group.name ])) > > > >> x > > > >> } > > > >> } > > > >> else { > > > >> irs <- ranges(x) > > > >> values(x)$stepping <- > > > >> as.numeric(disjointBins(resize(irs, > > > >> fix = "center", width = width(irs) + > > > >> extend.size))) > > > >> x > > > >> } > > > >> }) > > > >> 12: endoapply(obj.lst, function(x) { > > > >> if (!is.null( group.name )) { > > > >> if (!group.selfish) { > > > >> x.n <- split(x, values(x)[, group.name ]) > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > >> TRUE))) > > > >> irs.new <- resize(irs, fix = fix, width = > > > >> width(irs) + > > > >> extend.size) > > > >> irs.new <- sort(irs.new) > > > >> .lvs <- disjointBins(irs.new) > > > >> values(x)$stepping <- > > > >> .lvs[as.character(values(x)[, > > > >> group.name ])] > > > >> x > > > >> } > > > >> else { > > > >> values(x)$stepping <- > > > >> as.numeric(as.factor(values(x)[, > > > >> group.name ])) > > > >> x > > > >> } > > > >> } > > > >> else { > > > >> irs <- ranges(x) > > > >> values(x)$stepping <- > > > >> as.numeric(disjointBins(resize(irs, > > > >> fix = "center", width = width(irs) + > > > >> extend.size))) > > > >> x > > > >> } > > > >> }) > > > >> 11: .local(obj, ...) > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = > > > >> FALSE, > > > >> fix = "start", extend.size = es) > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = > > > >> FALSE, > > > >> fix = "start", extend.size = es) > > > >> 8: .local(data, ...) > > > >> 7: (function (data, ...) > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > >> "TranscriptDb">, > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > >> 6: (function (data, ...) > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > >> "TranscriptDb">, > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > >> 5: do.call(geom_alignment, args.res) > > > >> 4: do.call(geom_alignment, args.res) > > > >> 3: .local(object, ...) > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > >> > > > >> > > > >> > sessionInfo() > > > >> R version 3.1.0 (2014-04-10) > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > >> > > > >> locale: > > > >> [1] > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > >> > > > >> attached base packages: > > > >> [1] parallel stats graphics grDevices utils datasets > > > >> methods base > > > >> > > > >> other attached packages: > > > >> [1] XVector_0.4.0 > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > > >> GenomicFeatures_1.16.0 > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > > >> GenomicRanges_1.16.2 > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > > >> ggbio_1.12.0 > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > >> > > > >> loaded via a namespace (and not attached): > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > > >> Biostrings_2.32.0 > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > > >> BSgenome_1.32.0 cluster_1.15.2 > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > > >> dichromat_2.0-0 digest_0.6.4 > > > >> [16] fail_1.2 foreach_1.4.2 > > > >> Formula_1.1-1 > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > > >> Hmisc_3.14-4 > > > >> iterators_1.0.7 labeling_0.2 > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > > >> munsell_0.4.2 plyr_1.8.1 > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > > >> [41] splines_3.1.0 stats4_3.1.0 > > > >> stringr_0.6.2 > > > >> survival_2.37-7 tools_3.1.0 > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > > >> zlibbioc_1.10.0 > > > >> > > > > >> > > > > > > > > > > > > > > > > -- > > > > Tengfei Yin, PhD > > > > Seven Bridges Genomics > > > > sbgenomics.com > > > > 625 Mt. Auburn St. Suite #208 > > > > Cambridge, MA 02138 > > > > (617) 866-0446 > > > > > > > > > > > > > > > > -- > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866-0446 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at r-project.org > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > > > > > -- > > > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866- 0446 >
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Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R 3.1? And do some sort of switch for bioc? The website you send to me also have a R-devel build, my plan is to install bioc 3.0 on R-devel and bioc 2.14 on R 3.1, and do some tricks with emacs for R only to switch bioc, so that I could debug and maintain released and devel version. On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Tengfei, > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, > lcollado@jhu.edu > > Sent: Wednesday, April 23, 2014 10:46:02 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > > > Thanks a lot Dan! it's clear to me now, sorry that I am still a > > newbie to OSX ... I got R-devel running and I will try Rswitcher, I > > also want to do that switch easily in emacs too. > > > > > > You don't want to use R-devel. Both BioC release (2.14) and BioC devel > (3.0) are meant to work with R-3.1.0, the released version of R. > > I think the Rswitch app just sets a symbolic link, so you should be able > to do that within emacs. Run it and see what it does to > /Library/Frameworks/R.framework. > > Dan > > > > > > cheers > > > > > > Tengfei > > > > > > > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba@fhcrc.org > > > wrote: > > > > > > > > > > > > ----- Original Message ----- > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > > > Cc: "Bioconductor mailing list" < bioconductor@r-project.org >, > > > lcollado@jhu.edu > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > broken > > > > > > > > > > > Hi Dan, > > > > > > > > > So you mean I install R 3.1 for snow leopard and it should work? > > > > Yes. > > > > > > > > ? Is > > > there a way to build from source using biocLite, like type = > > > "source", this is what I got > > > > > > > > > > > > > library(BiocInstaller) > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for > > > help > > > > biocLite("GenomicRanges") > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > > > 3.1.0. > > > Installing package(s) 'GenomicRanges' > > > > > > > > > package âGenomicRangesâ is available as a source package but not as > > > a > > > binary > > > > > > > > > Warning message: > > > package âGenomicRangesâ is not available (for R version 3.1.0) > > > > > > > > > Just wondering is there a solution without re-install R for snow > > > leopard. And what's the plan for maverick? > > > > > > > You can do > > biocLite("GenomicRanges", type="source") > > > > but you need to have the appropriate compilers, etc. > > > > I *STRONGLY* recommend using the Snow Leopard build. You can have > > multiple installations of R on your Mac and switch between them > > using Rswitch ( http://r.research.att.com/#other ) or another easy > > mechanism. > > > > We are building packages for Mavericks now, we just have to resolve a > > few build issues and test the resulting packages, we still hope to > > have them available by the end of the month. But since you can > > install the Snow Leopard build without needing to remove your > > Mavericks build, you should do that. > > > > Dan > > > > > > > > > > > > > > > > Thanks > > > > > > > > > Tengfei > > > > > > > > > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > > dtenenba@fhcrc.org > > > > wrote: > > > > > > > > > Hi Tengfei, > > > > > > > > > ----- Original Message ----- > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > > To: lcollado@jhu.edu > > > > Cc: bioconductor@r-project.org > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > > broken > > > > > > > > btw, based on the error, let me try to debug it. > > > > > > > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > > > < tengfei.yin@sbgenomics.com >wrote: > > > > > > > > > Hi Leonardo, > > > > > > > > > > Frankly speaking, the vignette is still in progress, and there > > > > > are > > > > > some > > > > > known bugs in ggbio I need to fix (still trying to find a time > > > > > to > > > > > do that > > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on > > > > > my > > > > > new MBP > > > > > with OSX 10.9, but fails, probably binary build is not ready > > > > > for > > > > > maverick > > > > > yet, maybe available by the end of April? > > > > > > > > > > Thanks for reporting the bug, I will keep you posted on this > > > > > when > > > > > I > > > > > successfully get it on my laptop and start fixing the problems. > > > > > > > > > > > You can install the Snow Leopard build of R and should have no > > > problems, binary packages are available for that version. It will > > > run fine on Mavericks. > > > > > > Dan > > > > > > > > > > > > > > > > > cheers > > > > > > > > > > Tengfei > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > > > lcollado@jhsph.edu > wrote: > > > > > > > > > >> Hello Tengfei + bioc list, > > > > >> > > > > >> From > > > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > > > >> page 4 (complied on april 11 2014), the following example > > > > >> loads > > > > >> to > > > > >> an > > > > >> error as shown below. I wasn't seeing this error before (aka, > > > > >> last > > > > >> week). The only guess that comes to mind is the recent update > > > > >> to > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be > > > > >> related > > > > >> from > > > > >> the traceback() output, well... maybe it's related to the > > > > >> ignore.strand = TRUE part as described in the error. > > > > >> > > > > >> I'll create a GitHub issue just for completeness. > > > > >> > > > > >> Thank you, > > > > >> Leonardo > > > > >> > > > > >> > library(ggbio) > > > > >> ## Removed the output, nothing out of ordinary > > > > >> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > > > >> ## Removed the output > > > > >> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > > >> > data(genesymbol, package = "biovizBase") > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> Aggregating TranscriptDb... > > > > >> Parsing transcripts... > > > > >> Parsing exons... > > > > >> Parsing cds... > > > > >> Parsing utrs... > > > > >> ------exons... > > > > >> ------cdss... > > > > >> ------introns... > > > > >> ------utr... > > > > >> aggregating... > > > > >> Done > > > > >> Constructing graphics... > > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > > > >> elementTypeX)) : > > > > >> error in evaluating the argument 'X' in selecting a method for > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > > > >> ignore.strand > > > > >> = > > > > >> TRUE))) : > > > > >> error in evaluating the argument 'x' in selecting a method for > > > > >> function 'unlist': Error in .local(x, ...) : unused argument > > > > >> (ignore.strand = TRUE) > > > > >> > > > > >> > traceback() > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > > > >> elementTypeX)) > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, > > > > >> ...)) > > > > >> 13: endoapply(obj.lst, function(x) { > > > > >> if (!is.null( group.name )) { > > > > >> if (!group.selfish) { > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > >> TRUE))) > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > >> width(irs) + > > > > >> extend.size) > > > > >> irs.new <- sort(irs.new) > > > > >> .lvs <- disjointBins(irs.new) > > > > >> values(x)$stepping <- > > > > >> .lvs[as.character(values(x)[, > > > > >> group.name ])] > > > > >> x > > > > >> } > > > > >> else { > > > > >> values(x)$stepping <- > > > > >> as.numeric(as.factor(values(x)[, > > > > >> group.name ])) > > > > >> x > > > > >> } > > > > >> } > > > > >> else { > > > > >> irs <- ranges(x) > > > > >> values(x)$stepping <- > > > > >> as.numeric(disjointBins(resize(irs, > > > > >> fix = "center", width = width(irs) + > > > > >> extend.size))) > > > > >> x > > > > >> } > > > > >> }) > > > > >> 12: endoapply(obj.lst, function(x) { > > > > >> if (!is.null( group.name )) { > > > > >> if (!group.selfish) { > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > >> TRUE))) > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > >> width(irs) + > > > > >> extend.size) > > > > >> irs.new <- sort(irs.new) > > > > >> .lvs <- disjointBins(irs.new) > > > > >> values(x)$stepping <- > > > > >> .lvs[as.character(values(x)[, > > > > >> group.name ])] > > > > >> x > > > > >> } > > > > >> else { > > > > >> values(x)$stepping <- > > > > >> as.numeric(as.factor(values(x)[, > > > > >> group.name ])) > > > > >> x > > > > >> } > > > > >> } > > > > >> else { > > > > >> irs <- ranges(x) > > > > >> values(x)$stepping <- > > > > >> as.numeric(disjointBins(resize(irs, > > > > >> fix = "center", width = width(irs) + > > > > >> extend.size))) > > > > >> x > > > > >> } > > > > >> }) > > > > >> 11: .local(obj, ...) > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = > > > > >> FALSE, > > > > >> fix = "start", extend.size = es) > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = > > > > >> FALSE, > > > > >> fix = "start", extend.size = es) > > > > >> 8: .local(data, ...) > > > > >> 7: (function (data, ...) > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > > >> "TranscriptDb">, > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > >> 6: (function (data, ...) > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > > > >> "TranscriptDb">, > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > >> 5: do.call(geom_alignment, args.res) > > > > >> 4: do.call(geom_alignment, args.res) > > > > >> 3: .local(object, ...) > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> > > > > >> > > > > >> > sessionInfo() > > > > >> R version 3.1.0 (2014-04-10) > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > >> > > > > >> locale: > > > > >> [1] > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > >> > > > > >> attached base packages: > > > > >> [1] parallel stats graphics grDevices utils datasets > > > > >> methods base > > > > >> > > > > >> other attached packages: > > > > >> [1] XVector_0.4.0 > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > > > >> GenomicFeatures_1.16.0 > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > > > >> GenomicRanges_1.16.2 > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > > > >> ggbio_1.12.0 > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > > >> > > > > >> loaded via a namespace (and not attached): > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > > > >> Biostrings_2.32.0 > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > > > >> BSgenome_1.32.0 cluster_1.15.2 > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > > > >> dichromat_2.0-0 digest_0.6.4 > > > > >> [16] fail_1.2 foreach_1.4.2 > > > > >> Formula_1.1-1 > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > > > >> Hmisc_3.14-4 > > > > >> iterators_1.0.7 labeling_0.2 > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > > > >> munsell_0.4.2 plyr_1.8.1 > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > > > >> [41] splines_3.1.0 stats4_3.1.0 > > > > >> stringr_0.6.2 > > > > >> survival_2.37-7 tools_3.1.0 > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > > > >> zlibbioc_1.10.0 > > > > >> > > > > > >> > > > > > > > > > > > > > > > > > > > > -- > > > > > Tengfei Yin, PhD > > > > > Seven Bridges Genomics > > > > > sbgenomics.com > > > > > 625 Mt. Auburn St. Suite #208 > > > > > Cambridge, MA 02138 > > > > > (617) 866-0446 > > > > > > > > > > > > > > > > > > > > > -- > > > > Tengfei Yin, PhD > > > > Seven Bridges Genomics > > > > sbgenomics.com > > > > 625 Mt. Auburn St. Suite #208 > > > > Cambridge, MA 02138 > > > > (617) 866-0446 > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor@r-project.org > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866- 0446 > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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Hi Tengfei, ----- Original Message ----- > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, lcollado at jhu.edu > Sent: Wednesday, April 23, 2014 11:01:18 AM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R 3.1? Yes, install two copies of R 3.1 and switch between them. > And do some sort of switch for bioc? The website you send to me also > have a R-devel build, my plan is to install bioc 3.0 on R-devel and > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to > switch bioc, so that I could debug and maintain released and devel > version. PLEASE don't use R-devel at all. Just use R-3.1.0. You can use the Rswitch app but as you point out it won't work within emacs. This is what I do: Every time I download a new version of R, I run its installer. The installer always puts it in /Library/Frameworks/R.framework So after I install each version of R, I rename the R.framework directory to something like R.framework.bioc214_snowleopard And then I make a symlink from R.framework.bioc214_snowleopard to R.framework. I have a little script at https://github.com/dtenenba/renv which lets me see what the various installed Rs are: $renv 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 This tells me that the currently active R is nicknamed "releaseMav" (this means there is a link from /Library/Frameworks/R.framework.releaseMav to /Library/Frameworks/R.framework. It shows the versions, svn revisions, dates, and architectures of each version. (darwin10.8.0 is Snow Leopard; darwin13.1.0 is Mavericks). Note that in my nomenclature devel means BioC devel, not R-devel. So if I wanted to switch to the "develSL" version I would do: sudo renv develSL HTH Dan > > > > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < dtenenba at fhcrc.org > > wrote: > > > > Hi Tengfei, > > ----- Original Message ----- > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >, > > lcollado at jhu.edu > > > Sent: Wednesday, April 23, 2014 10:46:02 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > broken > > > > > > > Thanks a lot Dan! it's clear to me now, sorry that I am still a > > newbie to OSX ... I got R-devel running and I will try Rswitcher, I > > also want to do that switch easily in emacs too. > > > > > > You don't want to use R-devel. Both BioC release (2.14) and BioC > devel (3.0) are meant to work with R-3.1.0, the released version of > R. > > I think the Rswitch app just sets a symbolic link, so you should be > able to do that within emacs. Run it and see what it does to > /Library/Frameworks/R.framework. > > Dan > > > > > > cheers > > > > > > Tengfei > > > > > > > > > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org > > > > > wrote: > > > > > > > > > > > > ----- Original Message ----- > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >, > > > lcollado at jhu.edu > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > broken > > > > > > > > > > > Hi Dan, > > > > > > > > > So you mean I install R 3.1 for snow leopard and it should work? > > > > Yes. > > > > > > > > ? Is > > > there a way to build from source using biocLite, like type = > > > "source", this is what I got > > > > > > > > > > > > > library(BiocInstaller) > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for > > > help > > > > biocLite("GenomicRanges") > > > BioC_mirror: http://bioconductor.org > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > > > 3.1.0. > > > Installing package(s) 'GenomicRanges' > > > > > > > > > package ?GenomicRanges? is available as a source package but not > > > as > > > a > > > binary > > > > > > > > > Warning message: > > > package ?GenomicRanges? is not available (for R version 3.1.0) > > > > > > > > > Just wondering is there a solution without re-install R for snow > > > leopard. And what's the plan for maverick? > > > > > > > You can do > > biocLite("GenomicRanges", type="source") > > > > but you need to have the appropriate compilers, etc. > > > > I *STRONGLY* recommend using the Snow Leopard build. You can have > > multiple installations of R on your Mac and switch between them > > using Rswitch ( http://r.research.att.com/#other ) or another easy > > > > mechanism. > > > > We are building packages for Mavericks now, we just have to resolve > > a > > few build issues and test the resulting packages, we still hope to > > have them available by the end of the month. But since you can > > install the Snow Leopard build without needing to remove your > > Mavericks build, you should do that. > > > > Dan > > > > > > > > > > > > > > > > Thanks > > > > > > > > > Tengfei > > > > > > > > > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > > dtenenba at fhcrc.org > > > > wrote: > > > > > > > > > Hi Tengfei, > > > > > > > > > ----- Original Message ----- > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > > > To: lcollado at jhu.edu > > > > Cc: bioconductor at r-project.org > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > > > > is > > > > broken > > > > > > > > btw, based on the error, let me try to debug it. > > > > > > > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > > > < tengfei.yin at sbgenomics.com >wrote: > > > > > > > > > Hi Leonardo, > > > > > > > > > > Frankly speaking, the vignette is still in progress, and > > > > > there > > > > > are > > > > > some > > > > > known bugs in ggbio I need to fix (still trying to find a > > > > > time > > > > > to > > > > > do that > > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on > > > > > my > > > > > new MBP > > > > > with OSX 10.9, but fails, probably binary build is not ready > > > > > for > > > > > maverick > > > > > yet, maybe available by the end of April? > > > > > > > > > > Thanks for reporting the bug, I will keep you posted on this > > > > > when > > > > > I > > > > > successfully get it on my laptop and start fixing the > > > > > problems. > > > > > > > > > > > You can install the Snow Leopard build of R and should have no > > > problems, binary packages are available for that version. It will > > > run fine on Mavericks. > > > > > > Dan > > > > > > > > > > > > > > > > > cheers > > > > > > > > > > Tengfei > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > > > lcollado at jhsph.edu > wrote: > > > > > > > > > >> Hello Tengfei + bioc list, > > > > >> > > > > >> From > > > > >> http://www.bioconductor.org/packages/release/bioc/vignettes /ggbio/inst/doc/ggbio.pdf > > > > >> page 4 (complied on april 11 2014), the following example > > > > >> loads > > > > >> to > > > > >> an > > > > >> error as shown below. I wasn't seeing this error before > > > > >> (aka, > > > > >> last > > > > >> week). The only guess that comes to mind is the recent > > > > >> update > > > > >> to > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be > > > > >> related > > > > >> from > > > > >> the traceback() output, well... maybe it's related to the > > > > >> ignore.strand = TRUE part as described in the error. > > > > >> > > > > >> I'll create a GitHub issue just for completeness. > > > > >> > > > > >> Thank you, > > > > >> Leonardo > > > > >> > > > > >> > library(ggbio) > > > > >> ## Removed the output, nothing out of ordinary > > > > >> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > > > >> ## Removed the output > > > > >> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > > >> > data(genesymbol, package = "biovizBase") > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> Aggregating TranscriptDb... > > > > >> Parsing transcripts... > > > > >> Parsing exons... > > > > >> Parsing cds... > > > > >> Parsing utrs... > > > > >> ------exons... > > > > >> ------cdss... > > > > >> ------introns... > > > > >> ------utr... > > > > >> aggregating... > > > > >> Done > > > > >> Constructing graphics... > > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > > > >> elementTypeX)) : > > > > >> error in evaluating the argument 'X' in selecting a method > > > > >> for > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > > > >> ignore.strand > > > > >> = > > > > >> TRUE))) : > > > > >> error in evaluating the argument 'x' in selecting a method > > > > >> for > > > > >> function 'unlist': Error in .local(x, ...) : unused argument > > > > >> (ignore.strand = TRUE) > > > > >> > > > > >> > traceback() > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > > > >> elementTypeX)) > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, > > > > >> ...)) > > > > >> 13: endoapply(obj.lst, function(x) { > > > > >> if (!is.null( group.name )) { > > > > >> if (!group.selfish) { > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > >> TRUE))) > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > >> width(irs) + > > > > >> extend.size) > > > > >> irs.new <- sort(irs.new) > > > > >> .lvs <- disjointBins(irs.new) > > > > >> values(x)$stepping <- > > > > >> .lvs[as.character(values(x)[, > > > > >> group.name ])] > > > > >> x > > > > >> } > > > > >> else { > > > > >> values(x)$stepping <- > > > > >> as.numeric(as.factor(values(x)[, > > > > >> group.name ])) > > > > >> x > > > > >> } > > > > >> } > > > > >> else { > > > > >> irs <- ranges(x) > > > > >> values(x)$stepping <- > > > > >> as.numeric(disjointBins(resize(irs, > > > > >> fix = "center", width = width(irs) + > > > > >> extend.size))) > > > > >> x > > > > >> } > > > > >> }) > > > > >> 12: endoapply(obj.lst, function(x) { > > > > >> if (!is.null( group.name )) { > > > > >> if (!group.selfish) { > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > >> TRUE))) > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > >> width(irs) + > > > > >> extend.size) > > > > >> irs.new <- sort(irs.new) > > > > >> .lvs <- disjointBins(irs.new) > > > > >> values(x)$stepping <- > > > > >> .lvs[as.character(values(x)[, > > > > >> group.name ])] > > > > >> x > > > > >> } > > > > >> else { > > > > >> values(x)$stepping <- > > > > >> as.numeric(as.factor(values(x)[, > > > > >> group.name ])) > > > > >> x > > > > >> } > > > > >> } > > > > >> else { > > > > >> irs <- ranges(x) > > > > >> values(x)stepping <- > > > > >> as.numeric(disjointBins(resize(irs, > > > > >> fix = "center", width = width(irs) + > > > > >> extend.size))) > > > > >> x > > > > >> } > > > > >> }) > > > > >> 11: .local(obj, ...) > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = > > > > >> FALSE, > > > > >> fix = "start", extend.size = es) > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = > > > > >> FALSE, > > > > >> fix = "start", extend.size = es) > > > > >> 8: .local(data, ...) > > > > >> 7: (function (data, ...) > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> > > > >> class > > > > >> "TranscriptDb">, > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > >> 6: (function (data, ...) > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> > > > >> class > > > > >> "TranscriptDb">, > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > >> 5: do.call(geom_alignment, args.res) > > > > >> 4: do.call(geom_alignment, args.res) > > > > >> 3: .local(object, ...) > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > >> > > > > >> > > > > >> > sessionInfo() > > > > >> R version 3.1.0 (2014-04-10) > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > >> > > > > >> locale: > > > > >> [1] > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > >> > > > > >> attached base packages: > > > > >> [1] parallel stats graphics grDevices utils datasets > > > > >> methods base > > > > >> > > > > >> other attached packages: > > > > >> [1] XVector_0.4.0 > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > > > >> GenomicFeatures_1.16.0 > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > > > >> GenomicRanges_1.16.2 > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > > > >> ggbio_1.12.0 > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > > >> > > > > >> loaded via a namespace (and not attached): > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > > > >> Biostrings_2.32.0 > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > > > >> BSgenome_1.32.0 cluster_1.15.2 > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > > > >> dichromat_2.0-0 digest_0.6.4 > > > > >> [16] fail_1.2 foreach_1.4.2 > > > > >> Formula_1.1-1 > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > > > >> Hmisc_3.14-4 > > > > >> iterators_1.0.7 labeling_0.2 > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > > > >> munsell_0.4.2 plyr_1.8.1 > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > > > >> [41] splines_3.1.0 stats4_3.1.0 > > > > >> stringr_0.6.2 > > > > >> survival_2.37-7 tools_3.1.0 > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > > > >> zlibbioc_1.10.0 > > > > >> > > > > > >> > > > > > > > > > > > > > > > > > > > > -- > > > > > Tengfei Yin, PhD > > > > > Seven Bridges Genomics > > > > > sbgenomics.com > > > > > 625 Mt. Auburn St. Suite #208 > > > > > Cambridge, MA 02138 > > > > > (617) 866-0446 > > > > > > > > > > > > > > > > > > > > > -- > > > > Tengfei Yin, PhD > > > > Seven Bridges Genomics > > > > sbgenomics.com > > > > 625 Mt. Auburn St. Suite #208 > > > > Cambridge, MA 02138 > > > > (617) 866-0446 > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor at r-project.org > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866- 0446 > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > > > > > -- > > > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866- 0446 > ADD REPLY 0 Entering edit mode Hi Dan, It works like a charm, thanks! I use your method, then I changed /Library/Framework/ folder and R.Framework folder ownership to myself so I don't have to sudo it, then I just add alias to "emacs2" and "emacs3" to run your renv to switch the R first. This solves my problem. Try to customize variable for R hooks in emacs as alternative solution, but may need more time. Thanks again! Tengfei On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > Hi Tengfei, > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, > lcollado@jhu.edu > > Sent: Wednesday, April 23, 2014 11:01:18 AM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > > > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R 3.1? > > Yes, install two copies of R 3.1 and switch between them. > > > And do some sort of switch for bioc? The website you send to me also > > have a R-devel build, my plan is to install bioc 3.0 on R-devel and > > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to > > switch bioc, so that I could debug and maintain released and devel > > version. > > PLEASE don't use R-devel at all. > > Just use R-3.1.0. > > You can use the Rswitch app but as you point out it won't work within > emacs. > > This is what I do: > > Every time I download a new version of R, I run its installer. The > installer always puts it in > > /Library/Frameworks/R.framework > > So after I install each version of R, I rename the R.framework directory > to something like > R.framework.bioc214_snowleopard > > And then I make a symlink from R.framework.bioc214_snowleopard to > R.framework. > > I have a little script at https://github.com/dtenenba/renv which lets me > see what the various installed Rs are: > > renv > 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > > This tells me that the currently active R is nicknamed "releaseMav" (this > means there is a link from /Library/Frameworks/R.framework.releaseMav to > /Library/Frameworks/R.framework. It shows the versions, svn revisions, > dates, and architectures of each version. (darwin10.8.0 is Snow Leopard; > darwin13.1.0 is Mavericks). > > Note that in my nomenclature devel means BioC devel, not R-devel. > > So if I wanted to switch to the "develSL" version I would do: > > sudo renv develSL > > HTH > Dan > > > > > > > > > > > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < dtenenba@fhcrc.org > > > wrote: > > > > > > > > Hi Tengfei, > > > > ----- Original Message ----- > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > > > Cc: "Bioconductor mailing list" < bioconductor@r-project.org >, > > > lcollado@jhu.edu > > > > > Sent: Wednesday, April 23, 2014 10:46:02 AM > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > broken > > > > > > > > > > > Thanks a lot Dan! it's clear to me now, sorry that I am still a > > > newbie to OSX ... I got R-devel running and I will try Rswitcher, I > > > also want to do that switch easily in emacs too. > > > > > > > > > > You don't want to use R-devel. Both BioC release (2.14) and BioC > > devel (3.0) are meant to work with R-3.1.0, the released version of > > R. > > > > I think the Rswitch app just sets a symbolic link, so you should be > > able to do that within emacs. Run it and see what it does to > > /Library/Frameworks/R.framework. > > > > Dan > > > > > > > > > > cheers > > > > > > > > > Tengfei > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba@fhcrc.org > > > > > > > wrote: > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > > > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > > > > Cc: "Bioconductor mailing list" < bioconductor@r-project.org >, > > > > lcollado@jhu.edu > > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > > > broken > > > > > > > > > > > > > > > Hi Dan, > > > > > > > > > > > > So you mean I install R 3.1 for snow leopard and it should work? > > > > > > Yes. > > > > > > > > > > > > ? Is > > > > there a way to build from source using biocLite, like type = > > > > "source", this is what I got > > > > > > > > > > > > > > > > > library(BiocInstaller) > > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for > > > > help > > > > > biocLite("GenomicRanges") > > > > BioC_mirror: http://bioconductor.org > > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version > > > > 3.1.0. > > > > Installing package(s) 'GenomicRanges' > > > > > > > > > > > > package âGenomicRangesâ is available as a source package but not > > > > as > > > > a > > > > binary > > > > > > > > > > > > Warning message: > > > > package âGenomicRangesâ is not available (for R version 3.1.0) > > > > > > > > > > > > Just wondering is there a solution without re-install R for snow > > > > leopard. And what's the plan for maverick? > > > > > > > > > > You can do > > > biocLite("GenomicRanges", type="source") > > > > > > but you need to have the appropriate compilers, etc. > > > > > > I *STRONGLY* recommend using the Snow Leopard build. You can have > > > multiple installations of R on your Mac and switch between them > > > using Rswitch ( http://r.research.att.com/#other ) or another easy > > > > > > > mechanism. > > > > > > We are building packages for Mavericks now, we just have to resolve > > > a > > > few build issues and test the resulting packages, we still hope to > > > have them available by the end of the month. But since you can > > > install the Snow Leopard build without needing to remove your > > > Mavericks build, you should do that. > > > > > > Dan > > > > > > > > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > Tengfei > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > > > dtenenba@fhcrc.org > > > > > wrote: > > > > > > > > > > > > Hi Tengfei, > > > > > > > > > > > > ----- Original Message ----- > > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > > > > To: lcollado@jhu.edu > > > > > Cc: bioconductor@r-project.org > > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > > > > > is > > > > > broken > > > > > > > > > > btw, based on the error, let me try to debug it. > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > > > > < tengfei.yin@sbgenomics.com >wrote: > > > > > > > > > > > Hi Leonardo, > > > > > > > > > > > > Frankly speaking, the vignette is still in progress, and > > > > > > there > > > > > > are > > > > > > some > > > > > > known bugs in ggbio I need to fix (still trying to find a > > > > > > time > > > > > > to > > > > > > do that > > > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on > > > > > > my > > > > > > new MBP > > > > > > with OSX 10.9, but fails, probably binary build is not ready > > > > > > for > > > > > > maverick > > > > > > yet, maybe available by the end of April? > > > > > > > > > > > > Thanks for reporting the bug, I will keep you posted on this > > > > > > when > > > > > > I > > > > > > successfully get it on my laptop and start fixing the > > > > > > problems. > > > > > > > > > > > > > > You can install the Snow Leopard build of R and should have no > > > > problems, binary packages are available for that version. It will > > > > run fine on Mavericks. > > > > > > > > Dan > > > > > > > > > > > > > > > > > > > > > > cheers > > > > > > > > > > > > Tengfei > > > > > > > > > > > > > > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < > > > > > > lcollado@jhsph.edu > wrote: > > > > > > > > > > > >> Hello Tengfei + bioc list, > > > > > >> > > > > > >> From > > > > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > > > > >> page 4 (complied on april 11 2014), the following example > > > > > >> loads > > > > > >> to > > > > > >> an > > > > > >> error as shown below. I wasn't seeing this error before > > > > > >> (aka, > > > > > >> last > > > > > >> week). The only guess that comes to mind is the recent > > > > > >> update > > > > > >> to > > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be > > > > > >> related > > > > > >> from > > > > > >> the traceback() output, well... maybe it's related to the > > > > > >> ignore.strand = TRUE part as described in the error. > > > > > >> > > > > > >> I'll create a GitHub issue just for completeness. > > > > > >> > > > > > >> Thank you, > > > > > >> Leonardo > > > > > >> > > > > > >> > library(ggbio) > > > > > >> ## Removed the output, nothing out of ordinary > > > > > >> > > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > > > > >> ## Removed the output > > > > > >> > > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > > > >> > data(genesymbol, package = "biovizBase") > > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > > > > >> Aggregating TranscriptDb... > > > > > >> Parsing transcripts... > > > > > >> Parsing exons... > > > > > >> Parsing cds... > > > > > >> Parsing utrs... > > > > > >> ------exons... > > > > > >> ------cdss... > > > > > >> ------introns... > > > > > >> ------utr... > > > > > >> aggregating... > > > > > >> Done > > > > > >> Constructing graphics... > > > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), > > > > > >> elementTypeX)) : > > > > > >> error in evaluating the argument 'X' in selecting a method > > > > > >> for > > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > > > > >> ignore.strand > > > > > >> = > > > > > >> TRUE))) : > > > > > >> error in evaluating the argument 'x' in selecting a method > > > > > >> for > > > > > >> function 'unlist': Error in .local(x, ...) : unused argument > > > > > >> (ignore.strand = TRUE) > > > > > >> > > > > > >> > traceback() > > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > > > > >> elementTypeX)) > > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, > > > > > >> ...)) > > > > > >> 13: endoapply(obj.lst, function(x) { > > > > > >> if (!is.null( group.name )) { > > > > > >> if (!group.selfish) { > > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > > >> TRUE))) > > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > > >> width(irs) + > > > > > >> extend.size) > > > > > >> irs.new <- sort(irs.new) > > > > > >> .lvs <- disjointBins(irs.new) > > > > > >> values(x)$stepping <- > > > > > >> .lvs[as.character(values(x)[, > > > > > >> group.name ])] > > > > > >> x > > > > > >> } > > > > > >> else { > > > > > >> values(x)$stepping <- > > > > > >> as.numeric(as.factor(values(x)[, > > > > > >> group.name ])) > > > > > >> x > > > > > >> } > > > > > >> } > > > > > >> else { > > > > > >> irs <- ranges(x) > > > > > >> values(x)$stepping <- > > > > > >> as.numeric(disjointBins(resize(irs, > > > > > >> fix = "center", width = width(irs) + > > > > > >> extend.size))) > > > > > >> x > > > > > >> } > > > > > >> }) > > > > > >> 12: endoapply(obj.lst, function(x) { > > > > > >> if (!is.null( group.name )) { > > > > > >> if (!group.selfish) { > > > > > >> x.n <- split(x, values(x)[, group.name ]) > > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > > > > >> TRUE))) > > > > > >> irs.new <- resize(irs, fix = fix, width = > > > > > >> width(irs) + > > > > > >> extend.size) > > > > > >> irs.new <- sort(irs.new) > > > > > >> .lvs <- disjointBins(irs.new) > > > > > >> values(x)$stepping <- > > > > > >> .lvs[as.character(values(x)[, > > > > > >> group.name ])] > > > > > >> x > > > > > >> } > > > > > >> else { > > > > > >> values(x)$stepping <- > > > > > >> as.numeric(as.factor(values(x)[, > > > > > >> group.name ])) > > > > > >> x > > > > > >> } > > > > > >> } > > > > > >> else { > > > > > >> irs <- ranges(x) > > > > > >> values(x)$stepping <- > > > > > >> as.numeric(disjointBins(resize(irs, > > > > > >> fix = "center", width = width(irs) + > > > > > >> extend.size))) > > > > > >> x > > > > > >> } > > > > > >> }) > > > > > >> 11: .local(obj, ...) > > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = > > > > > >> FALSE, > > > > > >> fix = "start", extend.size = es) > > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = > > > > > >> FALSE, > > > > > >> fix = "start", extend.size = es) > > > > > >> 8: .local(data, ...) > > > > > >> 7: (function (data, ...) > > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> > > > > >> class > > > > > >> "TranscriptDb">, > > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > > >> 6: (function (data, ...) > > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> > > > > >> class > > > > > >> "TranscriptDb">, > > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, > > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > > > > >> 5: do.call(geom_alignment, args.res) > > > > > >> 4: do.call(geom_alignment, args.res) > > > > > >> 3: .local(object, ...) > > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > > >> > > > > > >> > > > > > >> > sessionInfo() > > > > > >> R version 3.1.0 (2014-04-10) > > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > > >> > > > > > >> locale: > > > > > >> [1] > > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > > >> > > > > > >> attached base packages: > > > > > >> [1] parallel stats graphics grDevices utils datasets > > > > > >> methods base > > > > > >> > > > > > >> other attached packages: > > > > > >> [1] XVector_0.4.0 > > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > > > > >> GenomicFeatures_1.16.0 > > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > > > > >> GenomicRanges_1.16.2 > > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > > > > >> ggbio_1.12.0 > > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > > > >> > > > > > >> loaded via a namespace (and not attached): > > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > > > > >> Biostrings_2.32.0 > > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > > > > >> BSgenome_1.32.0 cluster_1.15.2 > > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > > > > >> dichromat_2.0-0 digest_0.6.4 > > > > > >> [16] fail_1.2 foreach_1.4.2 > > > > > >> Formula_1.1-1 > > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > > > > >> Hmisc_3.14-4 > > > > > >> iterators_1.0.7 labeling_0.2 > > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > > > > >> munsell_0.4.2 plyr_1.8.1 > > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > > > > >> [41] splines_3.1.0 stats4_3.1.0 > > > > > >> stringr_0.6.2 > > > > > >> survival_2.37-7 tools_3.1.0 > > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > > > > >> zlibbioc_1.10.0 > > > > > >> > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > > > > > Seven Bridges Genomics > > > > > > sbgenomics.com > > > > > > 625 Mt. Auburn St. Suite #208 > > > > > > Cambridge, MA 02138 > > > > > > (617) 866-0446 > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Tengfei Yin, PhD > > > > > Seven Bridges Genomics > > > > > sbgenomics.com > > > > > 625 Mt. Auburn St. Suite #208 > > > > > Cambridge, MA 02138 > > > > > (617) 866-0446 > > > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > > > _______________________________________________ > > > > > Bioconductor mailing list > > > > > Bioconductor@r-project.org > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > Search the archives: > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > Tengfei Yin, PhD > > > > Seven Bridges Genomics > > > > sbgenomics.com > > > > 625 Mt. Auburn St. Suite #208 > > > > Cambridge, MA 02138 > > > > (617) 866- 0446 > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > Tengfei Yin, PhD > > > Seven Bridges Genomics > > > sbgenomics.com > > > 625 Mt. Auburn St. Suite #208 > > > Cambridge, MA 02138 > > > (617) 866- 0446 > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
0
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Hello again, Looking back, I have a file from 2014-04-15 with ggbio 1.12.0 where autoplot() with a txdb was working. The code is not the same from the example I reported above, but it uses the same ggbio functionality. You can see the working output at https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExplor ation/basicExploration.html#Best_region_clusters while the R session is at the end of https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExplor ation/basicExploration.html#Details In particular, the working version used: * GenomicRanges 1.16.0 instead of 1.16.2 * IRanges 1.22.2 instead of 1.22.3 * GenomeInfoDb 1.0.1 instead of 1.0.2 So, it seems that the problem is indeed related to recent updates to GenomicRanges (or maybe IRanges, GenomeInfoDb). On a different topic, there is no equivalent to using devtools::install_github(ref), right? With it, I can install a version of a GitHub-hosted package for a specific reference (which can be a specific commit). Thanks, Leonardo On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres <lcollado at="" jhsph.edu=""> wrote: > Hello Tengfei + bioc list, > > From http://www.bioconductor.org/packages/release/bioc/vignettes/ggb io/inst/doc/ggbio.pdf > page 4 (complied on april 11 2014), the following example loads to an > error as shown below. I wasn't seeing this error before (aka, last > week). The only guess that comes to mind is the recent update to > GenomicRanges (1.16.2) although that doesn't seem to be related from > the traceback() output, well... maybe it's related to the > ignore.strand = TRUE part as described in the error. > > I'll create a GitHub issue just for completeness. > > Thank you, > Leonardo > >> library(ggbio) > ## Removed the output, nothing out of ordinary > >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) > ## Removed the output > >> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> data(genesymbol, package = "biovizBase") >> p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > Aggregating TranscriptDb... > Parsing transcripts... > Parsing exons... > Parsing cds... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > Constructing graphics... > Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : > error in evaluating the argument 'X' in selecting a method for > function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = > TRUE))) : > error in evaluating the argument 'x' in selecting a method for > function 'unlist': Error in .local(x, ...) : unused argument > (ignore.strand = TRUE) > >> traceback() > 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) > 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > 13: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)$stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 12: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)$stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 11: .local(obj, ...) > 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 8: .local(data, ...) > 7: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 6: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 5: do.call(geom_alignment, args.res) > 4: do.call(geom_alignment, args.res) > 3: .local(object, ...) > 2: autoplot(txdb, which = genesymbol["BRCA1"]) > 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > GenomicRanges_1.16.2 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > ggbio_1.12.0 > [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.5 > BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 > [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > BSgenome_1.32.0 cluster_1.15.2 > [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > dichromat_2.0-0 digest_0.6.4 > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > GenomicAlignments_1.0.0 grid_3.1.0 > [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > iterators_1.0.7 labeling_0.2 > [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > munsell_0.4.2 plyr_1.8.1 > [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > RCurl_1.95-4.1 reshape2_1.2.2 > [36] Rsamtools_1.16.0 RSQLite_0.11.4 > rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > survival_2.37-7 tools_3.1.0 > [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >>
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Entering edit mode
I suspect it's probably problem from ggbio itself, I didn't check frequently with new update from dependencies, as soon as I got snow leopard binary on my laptop today, I will start debugging! On Wed, Apr 23, 2014 at 10:51 AM, Leonardo Collado Torres < lcollado@jhsph.edu> wrote: > Hello again, > > Looking back, I have a file from 2014-04-15 with ggbio 1.12.0 where > autoplot() with a txdb was working. > > The code is not the same from the example I reported above, but it > uses the same ggbio functionality. You can see the working output at > > https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExpl oration/basicExploration.html#Best_region_clusters > while the R session is at the end of > > https://rawgit.com/lcolladotor/derfinderReport/master/inst/basicExpl oration/basicExploration.html#Details > > In particular, the working version used: > * GenomicRanges 1.16.0 instead of 1.16.2 > * IRanges 1.22.2 instead of 1.22.3 > * GenomeInfoDb 1.0.1 instead of 1.0.2 > > So, it seems that the problem is indeed related to recent updates to > GenomicRanges (or maybe IRanges, GenomeInfoDb). > > > On a different topic, there is no equivalent to using > devtools::install_github(ref), right? With it, I can install a version > of a GitHub-hosted package for a specific reference (which can be a > specific commit). > > Thanks, > Leonardo > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres > <lcollado@jhsph.edu> wrote: > > Hello Tengfei + bioc list, > > > > From > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > page 4 (complied on april 11 2014), the following example loads to an > > error as shown below. I wasn't seeing this error before (aka, last > > week). The only guess that comes to mind is the recent update to > > GenomicRanges (1.16.2) although that doesn't seem to be related from > > the traceback() output, well... maybe it's related to the > > ignore.strand = TRUE part as described in the error. > > > > I'll create a GitHub issue just for completeness. > > > > Thank you, > > Leonardo > > > >> library(ggbio) > > ## Removed the output, nothing out of ordinary > > > >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > ## Removed the output > > > >> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> data(genesymbol, package = "biovizBase") > >> p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > > Aggregating TranscriptDb... > > Parsing transcripts... > > Parsing exons... > > Parsing cds... > > Parsing utrs... > > ------exons... > > ------cdss... > > ------introns... > > ------utr... > > aggregating... > > Done > > Constructing graphics... > > Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) > : > > error in evaluating the argument 'X' in selecting a method for > > function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = > > TRUE))) : > > error in evaluating the argument 'x' in selecting a method for > > function 'unlist': Error in .local(x, ...) : unused argument > > (ignore.strand = TRUE) > > > >> traceback() > > 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) > > 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > > 13: endoapply(obj.lst, function(x) { > > if (!is.nullgroup.name)) { > > if (!group.selfish) { > > x.n <- split(x, values(x)[, group.name]) > > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > > irs.new <- resize(irs, fix = fix, width = width(irs) + > > extend.size) > > irs.new <- sort(irs.new) > > .lvs <- disjointBins(irs.new) > > values(x)$stepping <- .lvs[as.character(values(x)[, > > group.name])] > > x > > } > > else { > > values(x)$stepping <- as.numeric(as.factor(values(x)[, > > group.name])) > > x > > } > > } > > else { > > irs <- ranges(x) > > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > > fix = "center", width = width(irs) + extend.size))) > > x > > } > > }) > > 12: endoapply(obj.lst, function(x) { > > if (!is.nullgroup.name)) { > > if (!group.selfish) { > > x.n <- split(x, values(x)[, group.name]) > > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > > irs.new <- resize(irs, fix = fix, width = width(irs) + > > extend.size) > > irs.new <- sort(irs.new) > > .lvs <- disjointBins(irs.new) > > values(x)$stepping <- .lvs[as.character(values(x)[, > > group.name])] > > x > > } > > else { > > values(x)$stepping <- as.numeric(as.factor(values(x)[, > > group.name])) > > x > > } > > } > > else { > > irs <- ranges(x) > > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > > fix = "center", width = width(irs) + extend.size))) > > x > > } > > }) > > 11: .local(obj, ...) > > 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > fix = "start", extend.size = es) > > 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > > fix = "start", extend.size = es) > > 8: .local(data, ...) > > 7: (function (data, ...) > > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > "TranscriptDb">, > > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > stat = "identity", names.expr = "tx_name", label = TRUE, > > which = <s4 object="" of="" class="" "granges"="">, list()) > > 6: (function (data, ...) > > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> > "TranscriptDb">, > > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > > stat = "identity", names.expr = "tx_name", label = TRUE, > > which = <s4 object="" of="" class="" "granges"="">, list()) > > 5: do.call(geom_alignment, args.res) > > 4: do.call(geom_alignment, args.res) > > 3: .local(object, ...) > > 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > > >> sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets > > methods base > > > > other attached packages: > > [1] XVector_0.4.0 > > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > > [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > GenomicRanges_1.16.2 > > [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > ggbio_1.12.0 > > [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > > > loaded via a namespace (and not attached): > > [1] BatchJobs_1.2 BBmisc_1.5 > > BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 > > [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > BSgenome_1.32.0 cluster_1.15.2 > > [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > dichromat_2.0-0 digest_0.6.4 > > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > > GenomicAlignments_1.0.0 grid_3.1.0 > > [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > > iterators_1.0.7 labeling_0.2 > > [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > munsell_0.4.2 plyr_1.8.1 > > [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > RCurl_1.95-4.1 reshape2_1.2.2 > > [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > > survival_2.37-7 tools_3.1.0 > > [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 > >> > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. 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Dan Tenenbaum ★ 8.2k
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----- Original Message ----- > From: "Leonardo Collado Torres" <lcollado at="" jhu.edu=""> > To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Wednesday, April 23, 2014 3:32:20 PM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > Hi Dan, > > I got RSwitch to work with a second installation of R 3.1. Basically, > I downloaded the leopard tarball, expanded it, renamed the folder 3.1 > to 3.1patched (which is the version I downloaded, but well, anything > except for 3.1 would work), compressed it again, and then expanded it > at the root location. > > So it would be something like this: > > wget > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > tar -xvf R-*gz > mv Library/Frameworks/R.framework/Versions/3.1 > Library/Frameworks/R.framework/Versions/3.1patched > tar -cvzf Rlib.tgz Library > sudo tar fvxz Rlib.tgz -C / > > Then used RSwitch, and was able to install BioC-devel. > That's good to know. I usually install from the installer (.pkg file) not the tarball, so I didn't think of this approach. Dan > I might try out your renv at a different time. It's great to know > that it exists =) > > Cheers, > Leo > > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > <tengfei.yin at="" sbgenomics.com=""> wrote: > > Hi Dan, > > > > It works like a charm, thanks! > > > > I use your method, then I changed /Library/Framework/ folder and > > R.Framework > > folder ownership to myself so I don't have to sudo it, then I just > > add alias > > to "emacs2" and "emacs3" to run your renv to switch the R first. > > This solves > > my problem. > > > > Try to customize variable for R hooks in emacs as alternative > > solution, but > > may need more time. > > > > Thanks again! > > > > Tengfei > > > > > > On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > > wrote: > >> > >> Hi Tengfei, > >> > >> ----- Original Message ----- > >> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > >> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > >> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, > >> > lcollado at jhu.edu > >> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > >> > broken > >> > > >> > > >> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R > >> > 3.1? > >> > >> Yes, install two copies of R 3.1 and switch between them. > >> > >> > And do some sort of switch for bioc? The website you send to me > >> > also > >> > have a R-devel build, my plan is to install bioc 3.0 on R-devel > >> > and > >> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to > >> > switch bioc, so that I could debug and maintain released and > >> > devel > >> > version. > >> > >> PLEASE don't use R-devel at all. > >> > >> Just use R-3.1.0. > >> > >> You can use the Rswitch app but as you point out it won't work > >> within > >> emacs. > >> > >> This is what I do: > >> > >> Every time I download a new version of R, I run its installer. The > >> installer always puts it in > >> > >> /Library/Frameworks/R.framework > >> > >> So after I install each version of R, I rename the R.framework > >> directory > >> to something like > >> R.framework.bioc214_snowleopard > >> > >> And then I make a symlink from R.framework.bioc214_snowleopard to > >> R.framework. > >> > >> I have a little script at https://github.com/dtenenba/renv which > >> lets me > >> see what the various installed Rs are: > >> > >> $renv > >> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >> This tells me that the currently active R is nicknamed > >> "releaseMav" (this > >> means there is a link from > >> /Library/Frameworks/R.framework.releaseMav to > >> /Library/Frameworks/R.framework. It shows the versions, svn > >> revisions, > >> dates, and architectures of each version. (darwin10.8.0 is Snow > >> Leopard; > >> darwin13.1.0 is Mavericks). > >> > >> Note that in my nomenclature devel means BioC devel, not R-devel. > >> > >> So if I wanted to switch to the "develSL" version I would do: > >> > >> sudo renv develSL > >> > >> HTH > >> Dan > >> > >> > >> > >> > > >> > > >> > > >> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >> > dtenenba at fhcrc.org > > >> > wrote: > >> > > >> > > >> > > >> > Hi Tengfei, > >> > > >> > ----- Original Message ----- > >> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > > >> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >> > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org > >> > > >, > >> > > lcollado at jhu.edu > >> > > >> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >> > > is > >> > > broken > >> > > > >> > > > >> > > >> > > Thanks a lot Dan! it's clear to me now, sorry that I am still > >> > > a > >> > > newbie to OSX ... I got R-devel running and I will try > >> > > Rswitcher, I > >> > > also want to do that switch easily in emacs too. > >> > > > >> > > > >> > > >> > You don't want to use R-devel. Both BioC release (2.14) and BioC > >> > devel (3.0) are meant to work with R-3.1.0, the released version > >> > of > >> > R. > >> > > >> > I think the Rswitch app just sets a symbolic link, so you should > >> > be > >> > able to do that within emacs. Run it and see what it does to > >> > /Library/Frameworks/R.framework. > >> > > >> > Dan > >> > > >> > > >> > > > >> > > cheers > >> > > > >> > > > >> > > Tengfei > >> > > > >> > > > >> > > > >> > > >> > > >> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >> > > dtenenba at fhcrc.org > >> > > > > >> > > wrote: > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > ----- Original Message ----- > >> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > > > >> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >> > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org > >> > > > >, > >> > > > lcollado at jhu.edu > >> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > > > example is > >> > > > broken > >> > > > > >> > > > > >> > > > >> > > > Hi Dan, > >> > > > > >> > > > > >> > > > So you mean I install R 3.1 for snow leopard and it should > >> > > > work? > >> > > > >> > > Yes. > >> > > > >> > > > >> > > > >> > > ? Is > >> > > > there a way to build from source using biocLite, like type = > >> > > > "source", this is what I got > >> > > > > >> > > > > >> > > > > >> > > > > library(BiocInstaller) > >> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite > >> > > > for > >> > > > help > >> > > > > biocLite("GenomicRanges") > >> > > > BioC_mirror: http://bioconductor.org > >> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R > >> > > > version > >> > > > 3.1.0. > >> > > > Installing package(s) 'GenomicRanges' > >> > > > > >> > > > > >> > > > package ?GenomicRanges? is available as a source package but > >> > > > not > >> > > > as > >> > > > a > >> > > > binary > >> > > > > >> > > > > >> > > > Warning message: > >> > > > package ?GenomicRanges? is not available (for R version > >> > > > 3.1.0) > >> > > > > >> > > > > >> > > > Just wondering is there a solution without re-install R for > >> > > > snow > >> > > > leopard. And what's the plan for maverick? > >> > > > > >> > > > >> > > You can do > >> > > biocLite("GenomicRanges", type="source") > >> > > > >> > > but you need to have the appropriate compilers, etc. > >> > > > >> > > I *STRONGLY* recommend using the Snow Leopard build. You can > >> > > have > >> > > multiple installations of R on your Mac and switch between > >> > > them > >> > > using Rswitch ( http://r.research.att.com/#other ) or another > >> > > easy > >> > > >> > > >> > > mechanism. > >> > > > >> > > We are building packages for Mavericks now, we just have to > >> > > resolve > >> > > a > >> > > few build issues and test the resulting packages, we still > >> > > hope to > >> > > have them available by the end of the month. But since you can > >> > > install the Snow Leopard build without needing to remove your > >> > > Mavericks build, you should do that. > >> > > > >> > > Dan > >> > > > >> > > > >> > > > >> > > > >> > > > >> > > > > >> > > > Thanks > >> > > > > >> > > > > >> > > > Tengfei > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >> > > > dtenenba at fhcrc.org > >> > > > > wrote: > >> > > > > >> > > > > >> > > > Hi Tengfei, > >> > > > > >> > > > > >> > > > ----- Original Message ----- > >> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > > > > To: lcollado at jhu.edu > >> > > > > Cc: bioconductor at r-project.org > >> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > > > > example > >> > > > > is > >> > > > > broken > >> > > > > > >> > > > > btw, based on the error, let me try to debug it. > >> > > > > > >> > > > > > >> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >> > > > > < tengfei.yin at sbgenomics.com >wrote: > >> > > > > > >> > > > > > Hi Leonardo, > >> > > > > > > >> > > > > > Frankly speaking, the vignette is still in progress, and > >> > > > > > there > >> > > > > > are > >> > > > > > some > >> > > > > > known bugs in ggbio I need to fix (still trying to find > >> > > > > > a > >> > > > > > time > >> > > > > > to > >> > > > > > do that > >> > > > > > ... ), I am recently trying to install R 3.1 and Bioc > >> > > > > > 2.14 on > >> > > > > > my > >> > > > > > new MBP > >> > > > > > with OSX 10.9, but fails, probably binary build is not > >> > > > > > ready > >> > > > > > for > >> > > > > > maverick > >> > > > > > yet, maybe available by the end of April? > >> > > > > > > >> > > > > > Thanks for reporting the bug, I will keep you posted on > >> > > > > > this > >> > > > > > when > >> > > > > > I > >> > > > > > successfully get it on my laptop and start fixing the > >> > > > > > problems. > >> > > > > > > >> > > > > >> > > > You can install the Snow Leopard build of R and should have > >> > > > no > >> > > > problems, binary packages are available for that version. It > >> > > > will > >> > > > run fine on Mavericks. > >> > > > > >> > > > Dan > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > > cheers > >> > > > > > > >> > > > > > Tengfei > >> > > > > > > >> > > > > > > >> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado > >> > > > > > Torres < > >> > > > > > lcollado at jhsph.edu > wrote: > >> > > > > > > >> > > > > >> Hello Tengfei + bioc list, > >> > > > > >> > >> > > > > >> From > >> > > > > >> > >> > > > > >> http://www.bioconductor.org/packages/release/bioc/vign ettes/ggbio/inst/doc/ggbio.pdf > >> > > > > >> page 4 (complied on april 11 2014), the following > >> > > > > >> example > >> > > > > >> loads > >> > > > > >> to > >> > > > > >> an > >> > > > > >> error as shown below. I wasn't seeing this error before > >> > > > > >> (aka, > >> > > > > >> last > >> > > > > >> week). The only guess that comes to mind is the recent > >> > > > > >> update > >> > > > > >> to > >> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be > >> > > > > >> related > >> > > > > >> from > >> > > > > >> the traceback() output, well... maybe it's related to > >> > > > > >> the > >> > > > > >> ignore.strand = TRUE part as described in the error. > >> > > > > >> > >> > > > > >> I'll create a GitHub issue just for completeness. > >> > > > > >> > >> > > > > >> Thank you, > >> > > > > >> Leonardo > >> > > > > >> > >> > > > > >> > library(ggbio) > >> > > > > >> ## Removed the output, nothing out of ordinary > >> > > > > >> > >> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> > > > > >> ## Removed the output > >> > > > > >> > >> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> > > > > >> > data(genesymbol, package = "biovizBase") > >> > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > >> > > > > >> Aggregating TranscriptDb... > >> > > > > >> Parsing transcripts... > >> > > > > >> Parsing exons... > >> > > > > >> Parsing cds... > >> > > > > >> Parsing utrs... > >> > > > > >> ------exons... > >> > > > > >> ------cdss... > >> > > > > >> ------introns... > >> > > > > >> ------utr... > >> > > > > >> aggregating... > >> > > > > >> Done > >> > > > > >> Constructing graphics... > >> > > > > >> Error in sapply(listData, function(Xi) > >> > > > > >> extends(class(Xi), > >> > > > > >> elementTypeX)) : > >> > > > > >> error in evaluating the argument 'X' in selecting a > >> > > > > >> method > >> > > > > >> for > >> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > >> > > > > >> ignore.strand > >> > > > > >> = > >> > > > > >> TRUE))) : > >> > > > > >> error in evaluating the argument 'x' in selecting a > >> > > > > >> method > >> > > > > >> for > >> > > > > >> function 'unlist': Error in .local(x, ...) : unused > >> > > > > >> argument > >> > > > > >> (ignore.strand = TRUE) > >> > > > > >> > >> > > > > >> > traceback() > >> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > >> > > > > >> elementTypeX)) > >> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, > >> > > > > >> FUN, > >> > > > > >> ...)) > >> > > > > >> 13: endoapply(obj.lst, function(x) { > >> > > > > >> if (!is.null( group.name )) { > >> > > > > >> if (!group.selfish) { > >> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > > > > >> TRUE))) > >> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > > > > >> width(irs) + > >> > > > > >> extend.size) > >> > > > > >> irs.new <- sort(irs.new) > >> > > > > >> .lvs <- disjointBins(irs.new) > >> > > > > >> values(x)$stepping <- > >> > > > > >> .lvs[as.character(values(x)[, > >> > > > > >> group.name ])] > >> > > > > >> x > >> > > > > >> } > >> > > > > >> else { > >> > > > > >> values(x)$stepping <- > >> > > > > >> as.numeric(as.factor(values(x)[, > >> > > > > >> group.name ])) > >> > > > > >> x > >> > > > > >> } > >> > > > > >> } > >> > > > > >> else { > >> > > > > >> irs <- ranges(x) > >> > > > > >> values(x)$stepping <- > >> > > > > >> as.numeric(disjointBins(resize(irs, > >> > > > > >> fix = "center", width = width(irs) + > >> > > > > >> extend.size))) > >> > > > > >> x > >> > > > > >> } > >> > > > > >> }) > >> > > > > >> 12: endoapply(obj.lst, function(x) { > >> > > > > >> if (!is.null( group.name )) { > >> > > > > >> if (!group.selfish) { > >> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > > > > >> TRUE))) > >> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > > > > >> width(irs) + > >> > > > > >> extend.size) > >> > > > > >> irs.new <- sort(irs.new) > >> > > > > >> .lvs <- disjointBins(irs.new) > >> > > > > >> values(x)$stepping <- > >> > > > > >> .lvs[as.character(values(x)[, > >> > > > > >> group.name ])] > >> > > > > >> x > >> > > > > >> } > >> > > > > >> else { > >> > > > > >> values(x)$stepping <- > >> > > > > >> as.numeric(as.factor(values(x)[, > >> > > > > >> group.name ])) > >> > > > > >> x > >> > > > > >> } > >> > > > > >> } > >> > > > > >> else { > >> > > > > >> irs <- ranges(x) > >> > > > > >> values(x)stepping <- > >> > > > > >> as.numeric(disjointBins(resize(irs, > >> > > > > >> fix = "center", width = width(irs) + > >> > > > > >> extend.size))) > >> > > > > >> x > >> > > > > >> } > >> > > > > >> }) > >> > > > > >> 11: .local(obj, ...) > >> > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish > >> > > > > >> = > >> > > > > >> FALSE, > >> > > > > >> fix = "start", extend.size = es) > >> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish > >> > > > > >> = > >> > > > > >> FALSE, > >> > > > > >> fix = "start", extend.size = es) > >> > > > > >> 8: .local(data, ...) > >> > > > > >> 7: (function (data, ...) > >> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> >> > > > > >> class > >> > > > > >> "TranscriptDb">, > >> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > > > > >> "alignment", > >> > > > > >> stat = "identity", names.expr = "tx_name", label = > >> > > > > >> TRUE, > >> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > > > > >> 6: (function (data, ...) > >> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of=""> >> > > > > >> class > >> > > > > >> "TranscriptDb">, > >> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > > > > >> "alignment", > >> > > > > >> stat = "identity", names.expr = "tx_name", label = > >> > > > > >> TRUE, > >> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > > > > >> 5: do.call(geom_alignment, args.res) > >> > > > > >> 4: do.call(geom_alignment, args.res) > >> > > > > >> 3: .local(object, ...) > >> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > > > > >> > >> > > > > >> > >> > > > > >> > sessionInfo() > >> > > > > >> R version 3.1.0 (2014-04-10) > >> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > > > > >> > >> > > > > >> locale: > >> > > > > >> [1] > >> > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > > > > >> > >> > > > > >> attached base packages: > >> > > > > >> [1] parallel stats graphics grDevices utils datasets > >> > > > > >> methods base > >> > > > > >> > >> > > > > >> other attached packages: > >> > > > > >> [1] XVector_0.4.0 > >> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> > > > > >> GenomicFeatures_1.16.0 > >> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> > > > > >> GenomicRanges_1.16.2 > >> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> > > > > >> ggbio_1.12.0 > >> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> > > > > >> > >> > > > > >> loaded via a namespace (and not attached): > >> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> > > > > >> Biostrings_2.32.0 > >> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> > > > > >> dichromat_2.0-0 digest_0.6.4 > >> > > > > >> [16] fail_1.2 foreach_1.4.2 > >> > > > > >> Formula_1.1-1 > >> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> > > > > >> Hmisc_3.14-4 > >> > > > > >> iterators_1.0.7 labeling_0.2 > >> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > >> > > > > >> munsell_0.4.2 plyr_1.8.1 > >> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >> > > > > >> stringr_0.6.2 > >> > > > > >> survival_2.37-7 tools_3.1.0 > >> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> > > > > >> zlibbioc_1.10.0 > >> > > > > >> > > >> > > > > >> > >> > > > > > > >> > > > > > > >> > > > > > > >> > > > > > -- > >> > > > > > Tengfei Yin, PhD > >> > > > > > Seven Bridges Genomics > >> > > > > > sbgenomics.com > >> > > > > > 625 Mt. Auburn St. Suite #208 > >> > > > > > Cambridge, MA 02138 > >> > > > > > (617) 866-0446 > >> > > > > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > -- > >> > > > > Tengfei Yin, PhD > >> > > > > Seven Bridges Genomics > >> > > > > sbgenomics.com > >> > > > > 625 Mt. Auburn St. Suite #208 > >> > > > > Cambridge, MA 02138 > >> > > > > (617) 866-0446 > >> > > > > > >> > > > > [[alternative HTML version deleted]] > >> > > > > > >> > > > > _______________________________________________ > >> > > > > Bioconductor mailing list > >> > > > > Bioconductor at r-project.org > >> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > > > > Search the archives: > >> > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > -- > >> > > > > >> > > > > >> > > > Tengfei Yin, PhD > >> > > > Seven Bridges Genomics > >> > > > sbgenomics.com > >> > > > 625 Mt. Auburn St. Suite #208 > >> > > > Cambridge, MA 02138 > >> > > > (617) 866- 0446 > >> > > > > >> > > > >> > > > >> > > > >> > > > >> > > -- > >> > > > >> > > > >> > > Tengfei Yin, PhD > >> > > Seven Bridges Genomics > >> > > sbgenomics.com > >> > > 625 Mt. Auburn St. Suite #208 > >> > > Cambridge, MA 02138 > >> > > (617) 866- 0446 > >> > > > >> > > >> > > >> > > >> > > >> > -- > >> > > >> > > >> > Tengfei Yin, PhD > >> > Seven Bridges Genomics > >> > sbgenomics.com > >> > 625 Mt. Auburn St. Suite #208 > >> > Cambridge, MA 02138 > >> > (617) 866- 0446 > >> > > > > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > ADD COMMENT 0 Entering edit mode Tengfei Yin ▴ 490 @tengfei-yin-6162 Last seen 6.6 years ago Hi I just fixed the bug in bioc 2.14 and checked in the fix, fixed in biovizbase 1.12.1 and ggbio 1.12.2, please update later and let me know if that doesn't work. Because in biovizBase, I am using ignore.strand in the wrong function ranges,GRangesList, sorry about this. thanks Tengfei On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < lcollado@jhsph.edu> wrote: > Hello Tengfei + bioc list, > > From > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > page 4 (complied on april 11 2014), the following example loads to an > error as shown below. I wasn't seeing this error before (aka, last > week). The only guess that comes to mind is the recent update to > GenomicRanges (1.16.2) although that doesn't seem to be related from > the traceback() output, well... maybe it's related to the > ignore.strand = TRUE part as described in the error. > > I'll create a GitHub issue just for completeness. > > Thank you, > Leonardo > > > library(ggbio) > ## Removed the output, nothing out of ordinary > > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > ## Removed the output > > > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > data(genesymbol, package = "biovizBase") > > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > Aggregating TranscriptDb... > Parsing transcripts... > Parsing exons... > Parsing cds... > Parsing utrs... > ------exons... > ------cdss... > ------introns... > ------utr... > aggregating... > Done > Constructing graphics... > Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : > error in evaluating the argument 'X' in selecting a method for > function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = > TRUE))) : > error in evaluating the argument 'x' in selecting a method for > function 'unlist': Error in .local(x, ...) : unused argument > (ignore.strand = TRUE) > > > traceback() > 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) > 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > 13: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)$stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 12: endoapply(obj.lst, function(x) { > if (!is.nullgroup.name)) { > if (!group.selfish) { > x.n <- split(x, values(x)[, group.name]) > irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) > irs.new <- resize(irs, fix = fix, width = width(irs) + > extend.size) > irs.new <- sort(irs.new) > .lvs <- disjointBins(irs.new) > values(x)$stepping <- .lvs[as.character(values(x)[, > group.name])] > x > } > else { > values(x)$stepping <- as.numeric(as.factor(values(x)[, > group.name])) > x > } > } > else { > irs <- ranges(x) > values(x)stepping <- as.numeric(disjointBins(resize(irs, > fix = "center", width = width(irs) + extend.size))) > x > } > }) > 11: .local(obj, ...) > 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > fix = "start", extend.size = es) > 8: .local(data, ...) > 7: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 6: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 5: do.call(geom_alignment, args.res) > 4: do.call(geom_alignment, args.res) > 3: .local(object, ...) > 2: autoplot(txdb, which = genesymbol["BRCA1"]) > 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > GenomicRanges_1.16.2 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > ggbio_1.12.0 > [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.5 > BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 > [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > BSgenome_1.32.0 cluster_1.15.2 > [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > dichromat_2.0-0 digest_0.6.4 > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > GenomicAlignments_1.0.0 grid_3.1.0 > [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 > iterators_1.0.7 labeling_0.2 > [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > munsell_0.4.2 plyr_1.8.1 > [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > RCurl_1.95-4.1 reshape2_1.2.2 > [36] Rsamtools_1.16.0 RSQLite_0.11.4 > rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > survival_2.37-7 tools_3.1.0 > [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]] ADD COMMENT 0 Entering edit mode @lcolladotor Last seen 9 days ago United States See the email below. I forgot to send it with my registered email for the BioC list. On Wed, Apr 23, 2014 at 3:45 PM, Leonardo Collado Torres <lcollado at="" jhu.edu=""> wrote: > Awesome, thank you Tengfei! > > Also, Dan, your https://github.com/dtenenba/renv/blob/master/renv > script looks interesting. I'm curious if what you described of > installing a new R version and creating a symlink (like from > R.framework.bioc214_snowleopard to R.framework) works with Rswitch. > I'm not an emacs user, so Rswitch has been working pretty well for me. > Yet this is the first time that I need two R installations from the > same version (thanks for the trick suggestion!): basically I've been > using my own derfinder package but I want to test it for submitting > it to Bioc. > > Cheers, > Leo > > > > On Wed, Apr 23, 2014 at 3:35 PM, Tengfei Yin <tengfei.yin at="" sbgenomics.com=""> wrote: >> Hi >> >> I just fixed the bug in bioc 2.14 and checked in the fix, fixed in >> biovizbase 1.12.1 and ggbio 1.12.2, please update later and let me know if >> that doesn't work. >> >> Because in biovizBase, I am using ignore.strand in the wrong function >> ranges,GRangesList, sorry about this. >> >> thanks >> >> Tengfei >> >> >> On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres >> <lcollado at="" jhsph.edu=""> wrote: >>> >>> Hello Tengfei + bioc list, >>> >>> From >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf >>> page 4 (complied on april 11 2014), the following example loads to an >>> error as shown below. I wasn't seeing this error before (aka, last >>> week). The only guess that comes to mind is the recent update to >>> GenomicRanges (1.16.2) although that doesn't seem to be related from >>> the traceback() output, well... maybe it's related to the >>> ignore.strand = TRUE part as described in the error. >>> >>> I'll create a GitHub issue just for completeness. >>> >>> Thank you, >>> Leonardo >>> >>> > library(ggbio) >>> ## Removed the output, nothing out of ordinary >>> >>> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>> ## Removed the output >>> >>> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >>> > data(genesymbol, package = "biovizBase") >>> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) >>> Aggregating TranscriptDb... >>> Parsing transcripts... >>> Parsing exons... >>> Parsing cds... >>> Parsing utrs... >>> ------exons... >>> ------cdss... >>> ------introns... >>> ------utr... >>> aggregating... >>> Done >>> Constructing graphics... >>> Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : >>> error in evaluating the argument 'X' in selecting a method for >>> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand = >>> TRUE))) : >>> error in evaluating the argument 'x' in selecting a method for >>> function 'unlist': Error in .local(x, ...) : unused argument >>> (ignore.strand = TRUE) >>> >>> > traceback() >>> 15: sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) >>> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) >>> 13: endoapply(obj.lst, function(x) { >>> if (!is.nullgroup.name)) { >>> if (!group.selfish) { >>> x.n <- split(x, values(x)[, group.name]) >>> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >>> irs.new <- resize(irs, fix = fix, width = width(irs) + >>> extend.size) >>> irs.new <- sort(irs.new) >>> .lvs <- disjointBins(irs.new) >>> values(x)stepping <- .lvs[as.character(values(x)[, >>> group.name])] >>> x >>> } >>> else { >>> values(x)$stepping <- as.numeric(as.factor(values(x)[, >>> group.name])) >>> x >>> } >>> } >>> else { >>> irs <- ranges(x) >>> values(x)$stepping <- as.numeric(disjointBins(resize(irs, >>> fix = "center", width = width(irs) + extend.size))) >>> x >>> } >>> }) >>> 12: endoapply(obj.lst, function(x) { >>> if (!is.nullgroup.name)) { >>> if (!group.selfish) { >>> x.n <- split(x, values(x)[, group.name]) >>> irs <- unlist(range(ranges(x.n, ignore.strand = TRUE))) >>> irs.new <- resize(irs, fix = fix, width = width(irs) + >>> extend.size) >>> irs.new <- sort(irs.new) >>> .lvs <- disjointBins(irs.new) >>> values(x)$stepping <- .lvs[as.character(values(x)[, >>> group.name])] >>> x >>> } >>> else { >>> values(x)$stepping <- as.numeric(as.factor(values(x)[, >>> group.name])) >>> x >>> } >>> } >>> else { >>> irs <- ranges(x) >>> values(x)stepping <- as.numeric(disjointBins(resize(irs, >>> fix = "center", width = width(irs) + extend.size))) >>> x >>> } >>> }) >>> 11: .local(obj, ...) >>> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >>> fix = "start", extend.size = es) >>> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, >>> fix = "start", extend.size = es) >>> 8: .local(data, ...) >>> 7: (function (data, ...) >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">>> "TranscriptDb">, >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> stat = "identity", names.expr = "tx_name", label = TRUE, >>> which = <s4 object="" of="" class="" "granges"="">, list()) >>> 6: (function (data, ...) >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">>> "TranscriptDb">, >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> stat = "identity", names.expr = "tx_name", label = TRUE, >>> which = <s4 object="" of="" class="" "granges"="">, list()) >>> 5: do.call(geom_alignment, args.res) >>> 4: do.call(geom_alignment, args.res) >>> 3: .local(object, ...) >>> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >>> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >>> >>> >>> > sessionInfo() >>> R version 3.1.0 (2014-04-10) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] XVector_0.4.0 >>> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 >>> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >>> GenomicRanges_1.16.2 >>> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >>> ggbio_1.12.0 >>> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] BatchJobs_1.2 BBmisc_1.5 >>> BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 >>> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >>> BSgenome_1.32.0 cluster_1.15.2 >>> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >>> dichromat_2.0-0 digest_0.6.4 >>> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >>> GenomicAlignments_1.0.0 grid_3.1.0 >>> [21] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 >>> iterators_1.0.7 labeling_0.2 >>> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >>> munsell_0.4.2 plyr_1.8.1 >>> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >>> RCurl_1.95-4.1 reshape2_1.2.2 >>> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >>> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >>> [41] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 >>> survival_2.37-7 tools_3.1.0 >>> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >>> > >> >> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446 ADD COMMENT 0 Entering edit mode ----- Original Message ----- > From: "Leonardo Collado Torres" <lcollado at="" jhsph.edu=""> > To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > Cc: bioconductor at r-project.org > Sent: Wednesday, April 23, 2014 12:58:37 PM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > See the email below. I forgot to send it with my registered email for > the BioC list. > > On Wed, Apr 23, 2014 at 3:45 PM, Leonardo Collado Torres > <lcollado at="" jhu.edu=""> wrote: > > Awesome, thank you Tengfei! > > > > Also, Dan, your https://github.com/dtenenba/renv/blob/master/renv > > script looks interesting. I'm curious if what you described of > > installing a new R version and creating a symlink (like from > > R.framework.bioc214_snowleopard to R.framework) works with Rswitch. It's meant to be a replacement for Rswitch. I think Rswitch does things in a different way. So you'd need to pick either 'renv' or Rswitch and stick with it. But I'm not sure if Rswitch will let you install two identical copies of R. One would have to experiment... > > I'm not an emacs user, so Rswitch has been working pretty well for > > me. If Rswitch is working for you, I'd suggest sticking with it. My script was motivated by the fact that I have many copies of R on my machine and needed a way to manage them, and that I find it quicker to do things from the command line. Dan > > Yet this is the first time that I need two R installations from the > > same version (thanks for the trick suggestion!): basically I've > > been > > using my own derfinder package but I want to test it for > > submitting > > it to Bioc. > > > > Cheers, > > Leo > > > > > > > > On Wed, Apr 23, 2014 at 3:35 PM, Tengfei Yin > > <tengfei.yin at="" sbgenomics.com=""> wrote: > >> Hi > >> > >> I just fixed the bug in bioc 2.14 and checked in the fix, fixed in > >> biovizbase 1.12.1 and ggbio 1.12.2, please update later and let me > >> know if > >> that doesn't work. > >> > >> Because in biovizBase, I am using ignore.strand in the wrong > >> function > >> ranges,GRangesList, sorry about this. > >> > >> thanks > >> > >> Tengfei > >> > >> > >> On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres > >> <lcollado at="" jhsph.edu=""> wrote: > >>> > >>> Hello Tengfei + bioc list, > >>> > >>> From > >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbi o/inst/doc/ggbio.pdf > >>> page 4 (complied on april 11 2014), the following example loads > >>> to an > >>> error as shown below. I wasn't seeing this error before (aka, > >>> last > >>> week). The only guess that comes to mind is the recent update to > >>> GenomicRanges (1.16.2) although that doesn't seem to be related > >>> from > >>> the traceback() output, well... maybe it's related to the > >>> ignore.strand = TRUE part as described in the error. > >>> > >>> I'll create a GitHub issue just for completeness. > >>> > >>> Thank you, > >>> Leonardo > >>> > >>> > library(ggbio) > >>> ## Removed the output, nothing out of ordinary > >>> > >>> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >>> ## Removed the output > >>> > >>> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >>> > data(genesymbol, package = "biovizBase") > >>> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) > >>> Aggregating TranscriptDb... > >>> Parsing transcripts... > >>> Parsing exons... > >>> Parsing cds... > >>> Parsing utrs... > >>> ------exons... > >>> ------cdss... > >>> ------introns... > >>> ------utr... > >>> aggregating... > >>> Done > >>> Constructing graphics... > >>> Error in sapply(listData, function(Xi) extends(class(Xi), > >>> elementTypeX)) : > >>> error in evaluating the argument 'X' in selecting a method for > >>> function 'sapply': Error in unlist(range(ranges(x.n, > >>> ignore.strand = > >>> TRUE))) : > >>> error in evaluating the argument 'x' in selecting a method for > >>> function 'unlist': Error in .local(x, ...) : unused argument > >>> (ignore.strand = TRUE) > >>> > >>> > traceback() > >>> 15: sapply(listData, function(Xi) extends(class(Xi), > >>> elementTypeX)) > >>> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...)) > >>> 13: endoapply(obj.lst, function(x) { > >>> if (!is.nullgroup.name)) { > >>> if (!group.selfish) { > >>> x.n <- split(x, values(x)[, group.name]) > >>> irs <- unlist(range(ranges(x.n, ignore.strand = > >>> TRUE))) > >>> irs.new <- resize(irs, fix = fix, width = > >>> width(irs) + > >>> extend.size) > >>> irs.new <- sort(irs.new) > >>> .lvs <- disjointBins(irs.new) > >>> values(x)stepping <- > >>> .lvs[as.character(values(x)[, > >>> group.name])] > >>> x > >>> } > >>> else { > >>> values(x)$stepping <- > >>> as.numeric(as.factor(values(x)[, > >>> group.name])) > >>> x > >>> } > >>> } > >>> else { > >>> irs <- ranges(x) > >>> values(x)$stepping <- > >>> as.numeric(disjointBins(resize(irs, > >>> fix = "center", width = width(irs) + > >>> extend.size))) > >>> x > >>> } > >>> }) > >>> 12: endoapply(obj.lst, function(x) { > >>> if (!is.nullgroup.name)) { > >>> if (!group.selfish) { > >>> x.n <- split(x, values(x)[, group.name]) > >>> irs <- unlist(range(ranges(x.n, ignore.strand = > >>> TRUE))) > >>> irs.new <- resize(irs, fix = fix, width = > >>> width(irs) + > >>> extend.size) > >>> irs.new <- sort(irs.new) > >>> .lvs <- disjointBins(irs.new) > >>> values(x)$stepping <- > >>> .lvs[as.character(values(x)[, > >>> group.name])] > >>> x > >>> } > >>> else { > >>> values(x)$stepping <- > >>> as.numeric(as.factor(values(x)[, > >>> group.name])) > >>> x > >>> } > >>> } > >>> else { > >>> irs <- ranges(x) > >>> values(x)stepping <- > >>> as.numeric(disjointBins(resize(irs, > >>> fix = "center", width = width(irs) + > >>> extend.size))) > >>> x > >>> } > >>> }) > >>> 11: .local(obj, ...) > >>> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > >>> fix = "start", extend.size = es) > >>> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE, > >>> fix = "start", extend.size = es) > >>> 8: .local(data, ...) > >>> 7: (function (data, ...) > >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> >>> "TranscriptDb">, > >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > >>> stat = "identity", names.expr = "tx_name", label = TRUE, > >>> which = <s4 object="" of="" class="" "granges"="">, list()) > >>> 6: (function (data, ...) > >>> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> >>> "TranscriptDb">, > >>> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > >>> stat = "identity", names.expr = "tx_name", label = TRUE, > >>> which = <s4 object="" of="" class="" "granges"="">, list()) > >>> 5: do.call(geom_alignment, args.res) > >>> 4: do.call(geom_alignment, args.res) > >>> 3: .local(object, ...) > >>> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >>> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >>> > >>> > >>> > sessionInfo() > >>> R version 3.1.0 (2014-04-10) > >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >>> > >>> locale: > >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >>> > >>> attached base packages: > >>> [1] parallel stats graphics grDevices utils datasets > >>> methods base > >>> > >>> other attached packages: > >>> [1] XVector_0.4.0 > >>> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 > >>> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >>> GenomicRanges_1.16.2 > >>> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >>> ggbio_1.12.0 > >>> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >>> > >>> loaded via a namespace (and not attached): > >>> [1] BatchJobs_1.2 BBmisc_1.5 > >>> BiocParallel_0.6.0 biomaRt_2.20.0 > >>> Biostrings_2.32.0 > >>> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >>> BSgenome_1.32.0 cluster_1.15.2 > >>> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >>> dichromat_2.0-0 digest_0.6.4 > >>> [16] fail_1.2 foreach_1.4.2 > >>> Formula_1.1-1 > >>> GenomicAlignments_1.0.0 grid_3.1.0 > >>> [21] gridExtra_0.9.1 gtable_0.1.2 > >>> Hmisc_3.14-4 > >>> iterators_1.0.7 labeling_0.2 > >>> [26] lattice_0.20-29 latticeExtra_0.6-26 > >>> MASS_7.3-31 > >>> munsell_0.4.2 plyr_1.8.1 > >>> [31] proto_0.3-10 RColorBrewer_1.0-5 > >>> Rcpp_0.11.1 > >>> RCurl_1.95-4.1 reshape2_1.2.2 > >>> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >>> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >>> [41] splines_3.1.0 stats4_3.1.0 > >>> stringr_0.6.2 > >>> survival_2.37-7 tools_3.1.0 > >>> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >>> zlibbioc_1.10.0 > >>> > > >> > >> > >> > >> > >> -- > >> Tengfei Yin, PhD > >> Seven Bridges Genomics > >> sbgenomics.com > >> 625 Mt. Auburn St. Suite #208 > >> Cambridge, MA 02138 > >> (617) 866-0446 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > ADD REPLY 0 Entering edit mode @lcolladotor Last seen 9 days ago United States Dang it, forgot again to send with my @jhsph.edu account. See below again >.< On the email topic, is it possible to be subscribed with 2 emails accounts to the BioC mailing list but only get emails with one? I believe that I have to choose to either get the daily digest or get a single for every message sent. If not, I'll probably just drop my @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail I got (our university is pushing these mails). On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres <lcollado at="" jhu.edu=""> wrote: > Hi Dan, > > I got RSwitch to work with a second installation of R 3.1. Basically, > I downloaded the leopard tarball, expanded it, renamed the folder 3.1 > to 3.1patched (which is the version I downloaded, but well, anything > except for 3.1 would work), compressed it again, and then expanded it > at the root location. > > So it would be something like this: > > wget http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1 -branch-snowleopard-sa-x86_64.tar.gz > tar -xvf R-*gz > mv Library/Frameworks/R.framework/Versions/3.1 > Library/Frameworks/R.framework/Versions/3.1patched > tar -cvzf Rlib.tgz Library > sudo tar fvxz Rlib.tgz -C / > > Then used RSwitch, and was able to install BioC-devel. > > I might try out your renv at a different time. It's great to know > that it exists =) > > Cheers, > Leo > > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin <tengfei.yin at="" sbgenomics.com=""> wrote: >> Hi Dan, >> >> It works like a charm, thanks! >> >> I use your method, then I changed /Library/Framework/ folder and R.Framework >> folder ownership to myself so I don't have to sudo it, then I just add alias >> to "emacs2" and "emacs3" to run your renv to switch the R first. This solves >> my problem. >> >> Try to customize variable for R hooks in emacs as alternative solution, but >> may need more time. >> >> Thanks again! >> >> Tengfei >> >> >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >>> >>> Hi Tengfei, >>> >>> ----- Original Message ----- >>> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >>> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >>> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, >>> > lcollado at jhu.edu >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken >>> > >>> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the R 3.1? >>> >>> Yes, install two copies of R 3.1 and switch between them. >>> >>> > And do some sort of switch for bioc? The website you send to me also >>> > have a R-devel build, my plan is to install bioc 3.0 on R-devel and >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to >>> > switch bioc, so that I could debug and maintain released and devel >>> > version. >>> >>> PLEASE don't use R-devel at all. >>> >>> Just use R-3.1.0. >>> >>> You can use the Rswitch app but as you point out it won't work within >>> emacs. >>> >>> This is what I do: >>> >>> Every time I download a new version of R, I run its installer. The >>> installer always puts it in >>> >>> /Library/Frameworks/R.framework >>> >>> So after I install each version of R, I rename the R.framework directory >>> to something like >>> R.framework.bioc214_snowleopard >>> >>> And then I make a symlink from R.framework.bioc214_snowleopard to >>> R.framework. >>> >>> I have a little script at https://github.com/dtenenba/renv which lets me >>> see what the various installed Rs are: >>> >>> renv >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >>> >>> This tells me that the currently active R is nicknamed "releaseMav" (this >>> means there is a link from /Library/Frameworks/R.framework.releaseMav to >>> /Library/Frameworks/R.framework. It shows the versions, svn revisions, >>> dates, and architectures of each version. (darwin10.8.0 is Snow Leopard; >>> darwin13.1.0 is Mavericks). >>> >>> Note that in my nomenclature devel means BioC devel, not R-devel. >>> >>> So if I wanted to switch to the "develSL" version I would do: >>> >>> sudo renv develSL >>> >>> HTH >>> Dan >>> >>> >>> >>> > >>> > >>> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < dtenenba at fhcrc.org > >>> > wrote: >>> > >>> > >>> > >>> > Hi Tengfei, >>> > >>> > ----- Original Message ----- >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >>> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >>> > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >, >>> > > lcollado at jhu.edu >>> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >>> > > broken >>> > > >>> > > >>> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am still a >>> > > newbie to OSX ... I got R-devel running and I will try Rswitcher, I >>> > > also want to do that switch easily in emacs too. >>> > > >>> > > >>> > >>> > You don't want to use R-devel. Both BioC release (2.14) and BioC >>> > devel (3.0) are meant to work with R-3.1.0, the released version of >>> > R. >>> > >>> > I think the Rswitch app just sets a symbolic link, so you should be >>> > able to do that within emacs. Run it and see what it does to >>> > /Library/Frameworks/R.framework. >>> > >>> > Dan >>> > >>> > >>> > > >>> > > cheers >>> > > >>> > > >>> > > Tengfei >>> > > >>> > > >>> > > >>> > >>> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org >>> > > > >>> > > wrote: >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > ----- Original Message ----- >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >>> > > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >>> > > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org >, >>> > > > lcollado at jhu.edu >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >>> > > > broken >>> > > > >>> > > > >>> > > >>> > > > Hi Dan, >>> > > > >>> > > > >>> > > > So you mean I install R 3.1 for snow leopard and it should work? >>> > > >>> > > Yes. >>> > > >>> > > >>> > > >>> > > ? Is >>> > > > there a way to build from source using biocLite, like type = >>> > > > "source", this is what I got >>> > > > >>> > > > >>> > > > >>> > > > > library(BiocInstaller) >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for >>> > > > help >>> > > > > biocLite("GenomicRanges") >>> > > > BioC_mirror: http://bioconductor.org >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version >>> > > > 3.1.0. >>> > > > Installing package(s) 'GenomicRanges' >>> > > > >>> > > > >>> > > > package ?GenomicRanges? is available as a source package but not >>> > > > as >>> > > > a >>> > > > binary >>> > > > >>> > > > >>> > > > Warning message: >>> > > > package ?GenomicRanges? is not available (for R version 3.1.0) >>> > > > >>> > > > >>> > > > Just wondering is there a solution without re-install R for snow >>> > > > leopard. And what's the plan for maverick? >>> > > > >>> > > >>> > > You can do >>> > > biocLite("GenomicRanges", type="source") >>> > > >>> > > but you need to have the appropriate compilers, etc. >>> > > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You can have >>> > > multiple installations of R on your Mac and switch between them >>> > > using Rswitch ( http://r.research.att.com/#other ) or another easy >>> > >>> > >>> > > mechanism. >>> > > >>> > > We are building packages for Mavericks now, we just have to resolve >>> > > a >>> > > few build issues and test the resulting packages, we still hope to >>> > > have them available by the end of the month. But since you can >>> > > install the Snow Leopard build without needing to remove your >>> > > Mavericks build, you should do that. >>> > > >>> > > Dan >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > > >>> > > > Thanks >>> > > > >>> > > > >>> > > > Tengfei >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < >>> > > > dtenenba at fhcrc.org >>> > > > > wrote: >>> > > > >>> > > > >>> > > > Hi Tengfei, >>> > > > >>> > > > >>> > > > ----- Original Message ----- >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >>> > > > > To: lcollado at jhu.edu >>> > > > > Cc: bioconductor at r-project.org >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >>> > > > > is >>> > > > > broken >>> > > > > >>> > > > > btw, based on the error, let me try to debug it. >>> > > > > >>> > > > > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin >>> > > > > < tengfei.yin at sbgenomics.com >wrote: >>> > > > > >>> > > > > > Hi Leonardo, >>> > > > > > >>> > > > > > Frankly speaking, the vignette is still in progress, and >>> > > > > > there >>> > > > > > are >>> > > > > > some >>> > > > > > known bugs in ggbio I need to fix (still trying to find a >>> > > > > > time >>> > > > > > to >>> > > > > > do that >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on >>> > > > > > my >>> > > > > > new MBP >>> > > > > > with OSX 10.9, but fails, probably binary build is not ready >>> > > > > > for >>> > > > > > maverick >>> > > > > > yet, maybe available by the end of April? >>> > > > > > >>> > > > > > Thanks for reporting the bug, I will keep you posted on this >>> > > > > > when >>> > > > > > I >>> > > > > > successfully get it on my laptop and start fixing the >>> > > > > > problems. >>> > > > > > >>> > > > >>> > > > You can install the Snow Leopard build of R and should have no >>> > > > problems, binary packages are available for that version. It will >>> > > > run fine on Mavericks. >>> > > > >>> > > > Dan >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > > > cheers >>> > > > > > >>> > > > > > Tengfei >>> > > > > > >>> > > > > > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres < >>> > > > > > lcollado at jhsph.edu > wrote: >>> > > > > > >>> > > > > >> Hello Tengfei + bioc list, >>> > > > > >> >>> > > > > >> From >>> > > > > >> >>> > > > > >> http://www.bioconductor.org/packages/release/bioc/vigne ttes/ggbio/inst/doc/ggbio.pdf >>> > > > > >> page 4 (complied on april 11 2014), the following example >>> > > > > >> loads >>> > > > > >> to >>> > > > > >> an >>> > > > > >> error as shown below. I wasn't seeing this error before >>> > > > > >> (aka, >>> > > > > >> last >>> > > > > >> week). The only guess that comes to mind is the recent >>> > > > > >> update >>> > > > > >> to >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to be >>> > > > > >> related >>> > > > > >> from >>> > > > > >> the traceback() output, well... maybe it's related to the >>> > > > > >> ignore.strand = TRUE part as described in the error. >>> > > > > >> >>> > > > > >> I'll create a GitHub issue just for completeness. >>> > > > > >> >>> > > > > >> Thank you, >>> > > > > >> Leonardo >>> > > > > >> >>> > > > > >> > library(ggbio) >>> > > > > >> ## Removed the output, nothing out of ordinary >>> > > > > >> >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>> > > > > >> ## Removed the output >>> > > > > >> >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >>> > > > > >> > data(genesymbol, package = "biovizBase") >>> > > > > >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"]) >>> > > > > >> Aggregating TranscriptDb... >>> > > > > >> Parsing transcripts... >>> > > > > >> Parsing exons... >>> > > > > >> Parsing cds... >>> > > > > >> Parsing utrs... >>> > > > > >> ------exons... >>> > > > > >> ------cdss... >>> > > > > >> ------introns... >>> > > > > >> ------utr... >>> > > > > >> aggregating... >>> > > > > >> Done >>> > > > > >> Constructing graphics... >>> > > > > >> Error in sapply(listData, function(Xi) extends(class(Xi), >>> > > > > >> elementTypeX)) : >>> > > > > >> error in evaluating the argument 'X' in selecting a method >>> > > > > >> for >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, >>> > > > > >> ignore.strand >>> > > > > >> = >>> > > > > >> TRUE))) : >>> > > > > >> error in evaluating the argument 'x' in selecting a method >>> > > > > >> for >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused argument >>> > > > > >> (ignore.strand = TRUE) >>> > > > > >> >>> > > > > >> > traceback() >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), >>> > > > > >> elementTypeX)) >>> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, >>> > > > > >> ...)) >>> > > > > >> 13: endoapply(obj.lst, function(x) { >>> > > > > >> if (!is.null( group.name )) { >>> > > > > >> if (!group.selfish) { >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >>> > > > > >> TRUE))) >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >>> > > > > >> width(irs) + >>> > > > > >> extend.size) >>> > > > > >> irs.new <- sort(irs.new) >>> > > > > >> .lvs <- disjointBins(irs.new) >>> > > > > >> values(x)$stepping <- >>> > > > > >> .lvs[as.character(values(x)[, >>> > > > > >> group.name ])] >>> > > > > >> x >>> > > > > >> } >>> > > > > >> else { >>> > > > > >> values(x)$stepping <- >>> > > > > >> as.numeric(as.factor(values(x)[, >>> > > > > >> group.name ])) >>> > > > > >> x >>> > > > > >> } >>> > > > > >> } >>> > > > > >> else { >>> > > > > >> irs <- ranges(x) >>> > > > > >> values(x)$stepping <- >>> > > > > >> as.numeric(disjointBins(resize(irs, >>> > > > > >> fix = "center", width = width(irs) + >>> > > > > >> extend.size))) >>> > > > > >> x >>> > > > > >> } >>> > > > > >> }) >>> > > > > >> 12: endoapply(obj.lst, function(x) { >>> > > > > >> if (!is.null( group.name )) { >>> > > > > >> if (!group.selfish) { >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >>> > > > > >> TRUE))) >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >>> > > > > >> width(irs) + >>> > > > > >> extend.size) >>> > > > > >> irs.new <- sort(irs.new) >>> > > > > >> .lvs <- disjointBins(irs.new) >>> > > > > >> values(x)$stepping <- >>> > > > > >> .lvs[as.character(values(x)[, >>> > > > > >> group.name ])] >>> > > > > >> x >>> > > > > >> } >>> > > > > >> else { >>> > > > > >> values(x)$stepping <- >>> > > > > >> as.numeric(as.factor(values(x)[, >>> > > > > >> group.name ])) >>> > > > > >> x >>> > > > > >> } >>> > > > > >> } >>> > > > > >> else { >>> > > > > >> irs <- ranges(x) >>> > > > > >> values(x)$stepping <- >>> > > > > >> as.numeric(disjointBins(resize(irs, >>> > > > > >> fix = "center", width = width(irs) + >>> > > > > >> extend.size))) >>> > > > > >> x >>> > > > > >> } >>> > > > > >> }) >>> > > > > >> 11: .local(obj, ...) >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", group.selfish = >>> > > > > >> FALSE, >>> > > > > >> fix = "start", extend.size = es) >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish = >>> > > > > >> FALSE, >>> > > > > >> fix = "start", extend.size = es) >>> > > > > >> 8: .local(data, ...) >>> > > > > >> 7: (function (data, ...) >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="">>> > > > > >> class >>> > > > > >> "TranscriptDb">, >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >>> > > > > >> 6: (function (data, ...) >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="" of="">>> > > > > >> class >>> > > > > >> "TranscriptDb">, >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >>> > > > > >> stat = "identity", names.expr = "tx_name", label = TRUE, >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >>> > > > > >> 5: do.call(geom_alignment, args.res) >>> > > > > >> 4: do.call(geom_alignment, args.res) >>> > > > > >> 3: .local(object, ...) >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >>> > > > > >> >>> > > > > >> >>> > > > > >> > sessionInfo() >>> > > > > >> R version 3.1.0 (2014-04-10) >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> > > > > >> >>> > > > > >> locale: >>> > > > > >> [1] >>> > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> > > > > >> >>> > > > > >> attached base packages: >>> > > > > >> [1] parallel stats graphics grDevices utils datasets >>> > > > > >> methods base >>> > > > > >> >>> > > > > >> other attached packages: >>> > > > > >> [1] XVector_0.4.0 >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >>> > > > > >> GenomicFeatures_1.16.0 >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >>> > > > > >> GenomicRanges_1.16.2 >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >>> > > > > >> ggbio_1.12.0 >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >>> > > > > >> >>> > > > > >> loaded via a namespace (and not attached): >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 >>> > > > > >> Biostrings_2.32.0 >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >>> > > > > >> dichromat_2.0-0 digest_0.6.4 >>> > > > > >> [16] fail_1.2 foreach_1.4.2 >>> > > > > >> Formula_1.1-1 >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 >>> > > > > >> Hmisc_3.14-4 >>> > > > > >> iterators_1.0.7 labeling_0.2 >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >>> > > > > >> munsell_0.4.2 plyr_1.8.1 >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 >>> > > > > >> stringr_0.6.2 >>> > > > > >> survival_2.37-7 tools_3.1.0 >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 >>> > > > > >> zlibbioc_1.10.0 >>> > > > > >> > >>> > > > > >> >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > -- >>> > > > > > Tengfei Yin, PhD >>> > > > > > Seven Bridges Genomics >>> > > > > > sbgenomics.com >>> > > > > > 625 Mt. Auburn St. Suite #208 >>> > > > > > Cambridge, MA 02138 >>> > > > > > (617) 866-0446 >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > -- >>> > > > > Tengfei Yin, PhD >>> > > > > Seven Bridges Genomics >>> > > > > sbgenomics.com >>> > > > > 625 Mt. Auburn St. Suite #208 >>> > > > > Cambridge, MA 02138 >>> > > > > (617) 866-0446 >>> > > > > >>> > > > > [[alternative HTML version deleted]] >>> > > > > >>> > > > > _______________________________________________ >>> > > > > Bioconductor mailing list >>> > > > > Bioconductor at r-project.org >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > > > > Search the archives: >>> > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > -- >>> > > > >>> > > > >>> > > > Tengfei Yin, PhD >>> > > > Seven Bridges Genomics >>> > > > sbgenomics.com >>> > > > 625 Mt. Auburn St. Suite #208 >>> > > > Cambridge, MA 02138 >>> > > > (617) 866- 0446 >>> > > > >>> > > >>> > > >>> > > >>> > > >>> > > -- >>> > > >>> > > >>> > > Tengfei Yin, PhD >>> > > Seven Bridges Genomics >>> > > sbgenomics.com >>> > > 625 Mt. Auburn St. Suite #208 >>> > > Cambridge, MA 02138 >>> > > (617) 866- 0446 >>> > > >>> > >>> > >>> > >>> > >>> > -- >>> > >>> > >>> > Tengfei Yin, PhD >>> > Seven Bridges Genomics >>> > sbgenomics.com >>> > 625 Mt. Auburn St. Suite #208 >>> > Cambridge, MA 02138 >>> > (617) 866- 0446 >>> > >> >> >> >> >> -- >> Tengfei Yin, PhD >> Seven Bridges Genomics >> sbgenomics.com >> 625 Mt. Auburn St. Suite #208 >> Cambridge, MA 02138 >> (617) 866-0446
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----- Original Message ----- > From: "Leonardo Collado Torres" <lcollado at="" jhsph.edu=""> > To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Wednesday, April 23, 2014 3:38:11 PM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > Dang it, forgot again to send with my @jhsph.edu account. See below > again >.< > > On the email topic, is it possible to be subscribed with 2 emails > accounts to the BioC mailing list but only get emails with one? I > believe that I have to choose to either get the daily digest or get a > single for every message sent. If not, I'll probably just drop my > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail I > got (our university is pushing these mails). > I don't know; you could try it. Another option would be to configure your mail client with a filter to drop the undesired bioc emails. Dan > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > <lcollado at="" jhu.edu=""> wrote: > > Hi Dan, > > > > I got RSwitch to work with a second installation of R 3.1. > > Basically, > > I downloaded the leopard tarball, expanded it, renamed the folder > > 3.1 > > to 3.1patched (which is the version I downloaded, but well, > > anything > > except for 3.1 would work), compressed it again, and then expanded > > it > > at the root location. > > > > So it would be something like this: > > > > wget > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > > tar -xvf R-*gz > > mv Library/Frameworks/R.framework/Versions/3.1 > > Library/Frameworks/R.framework/Versions/3.1patched > > tar -cvzf Rlib.tgz Library > > sudo tar fvxz Rlib.tgz -C / > > > > Then used RSwitch, and was able to install BioC-devel. > > > > I might try out your renv at a different time. It's great to know > > that it exists =) > > > > Cheers, > > Leo > > > > > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > > <tengfei.yin at="" sbgenomics.com=""> wrote: > >> Hi Dan, > >> > >> It works like a charm, thanks! > >> > >> I use your method, then I changed /Library/Framework/ folder and > >> R.Framework > >> folder ownership to myself so I don't have to sudo it, then I just > >> add alias > >> to "emacs2" and "emacs3" to run your renv to switch the R first. > >> This solves > >> my problem. > >> > >> Try to customize variable for R hooks in emacs as alternative > >> solution, but > >> may need more time. > >> > >> Thanks again! > >> > >> Tengfei > >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > >> <dtenenba at="" fhcrc.org=""> wrote: > >>> > >>> Hi Tengfei, > >>> > >>> ----- Original Message ----- > >>> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > >>> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > >>> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, > >>> > lcollado at jhu.edu > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >>> > is broken > >>> > > >>> > > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the > >>> > R 3.1? > >>> > >>> Yes, install two copies of R 3.1 and switch between them. > >>> > >>> > And do some sort of switch for bioc? The website you send to me > >>> > also > >>> > have a R-devel build, my plan is to install bioc 3.0 on R-devel > >>> > and > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to > >>> > switch bioc, so that I could debug and maintain released and > >>> > devel > >>> > version. > >>> > >>> PLEASE don't use R-devel at all. > >>> > >>> Just use R-3.1.0. > >>> > >>> You can use the Rswitch app but as you point out it won't work > >>> within > >>> emacs. > >>> > >>> This is what I do: > >>> > >>> Every time I download a new version of R, I run its installer. > >>> The > >>> installer always puts it in > >>> > >>> /Library/Frameworks/R.framework > >>> > >>> So after I install each version of R, I rename the R.framework > >>> directory > >>> to something like > >>> R.framework.bioc214_snowleopard > >>> > >>> And then I make a symlink from R.framework.bioc214_snowleopard to > >>> R.framework. > >>> > >>> I have a little script at https://github.com/dtenenba/renv which > >>> lets me > >>> see what the various installed Rs are: > >>> > >>> $renv > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >>> > >>> This tells me that the currently active R is nicknamed > >>> "releaseMav" (this > >>> means there is a link from > >>> /Library/Frameworks/R.framework.releaseMav to > >>> /Library/Frameworks/R.framework. It shows the versions, svn > >>> revisions, > >>> dates, and architectures of each version. (darwin10.8.0 is Snow > >>> Leopard; > >>> darwin13.1.0 is Mavericks). > >>> > >>> Note that in my nomenclature devel means BioC devel, not R-devel. > >>> > >>> So if I wanted to switch to the "develSL" version I would do: > >>> > >>> sudo renv develSL > >>> > >>> HTH > >>> Dan > >>> > >>> > >>> > >>> > > >>> > > >>> > > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >>> > dtenenba at fhcrc.org > > >>> > wrote: > >>> > > >>> > > >>> > > >>> > Hi Tengfei, > >>> > > >>> > ----- Original Message ----- > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >>> > > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >>> > > Cc: "Bioconductor mailing list" < bioconductor at r-project.org > >>> > > >, > >>> > > lcollado at jhu.edu > >>> > > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >>> > > is > >>> > > broken > >>> > > > >>> > > > >>> > > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am still > >>> > > a > >>> > > newbie to OSX ... I got R-devel running and I will try > >>> > > Rswitcher, I > >>> > > also want to do that switch easily in emacs too. > >>> > > > >>> > > > >>> > > >>> > You don't want to use R-devel. Both BioC release (2.14) and > >>> > BioC > >>> > devel (3.0) are meant to work with R-3.1.0, the released > >>> > version of > >>> > R. > >>> > > >>> > I think the Rswitch app just sets a symbolic link, so you > >>> > should be > >>> > able to do that within emacs. Run it and see what it does to > >>> > /Library/Frameworks/R.framework. > >>> > > >>> > Dan > >>> > > >>> > > >>> > > > >>> > > cheers > >>> > > > >>> > > > >>> > > Tengfei > >>> > > > >>> > > > >>> > > > >>> > > >>> > > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >>> > > dtenenba at fhcrc.org > >>> > > > > >>> > > wrote: > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > ----- Original Message ----- > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >>> > > > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >>> > > > Cc: "Bioconductor mailing list" < > >>> > > > bioconductor at r-project.org >, > >>> > > > lcollado at jhu.edu > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >>> > > > example is > >>> > > > broken > >>> > > > > >>> > > > > >>> > > > >>> > > > Hi Dan, > >>> > > > > >>> > > > > >>> > > > So you mean I install R 3.1 for snow leopard and it should > >>> > > > work? > >>> > > > >>> > > Yes. > >>> > > > >>> > > > >>> > > > >>> > > ? Is > >>> > > > there a way to build from source using biocLite, like type > >>> > > > = > >>> > > > "source", this is what I got > >>> > > > > >>> > > > > >>> > > > > >>> > > > > library(BiocInstaller) > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite > >>> > > > for > >>> > > > help > >>> > > > > biocLite("GenomicRanges") > >>> > > > BioC_mirror: http://bioconductor.org > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R > >>> > > > version > >>> > > > 3.1.0. > >>> > > > Installing package(s) 'GenomicRanges' > >>> > > > > >>> > > > > >>> > > > package ?GenomicRanges? is available as a source package > >>> > > > but not > >>> > > > as > >>> > > > a > >>> > > > binary > >>> > > > > >>> > > > > >>> > > > Warning message: > >>> > > > package ?GenomicRanges? is not available (for R version > >>> > > > 3.1.0) > >>> > > > > >>> > > > > >>> > > > Just wondering is there a solution without re-install R for > >>> > > > snow > >>> > > > leopard. And what's the plan for maverick? > >>> > > > > >>> > > > >>> > > You can do > >>> > > biocLite("GenomicRanges", type="source") > >>> > > > >>> > > but you need to have the appropriate compilers, etc. > >>> > > > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You can > >>> > > have > >>> > > multiple installations of R on your Mac and switch between > >>> > > them > >>> > > using Rswitch ( http://r.research.att.com/#other ) or another > >>> > > easy > >>> > > >>> > > >>> > > mechanism. > >>> > > > >>> > > We are building packages for Mavericks now, we just have to > >>> > > resolve > >>> > > a > >>> > > few build issues and test the resulting packages, we still > >>> > > hope to > >>> > > have them available by the end of the month. But since you > >>> > > can > >>> > > install the Snow Leopard build without needing to remove your > >>> > > Mavericks build, you should do that. > >>> > > > >>> > > Dan > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > > >>> > > > Thanks > >>> > > > > >>> > > > > >>> > > > Tengfei > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >>> > > > dtenenba at fhcrc.org > >>> > > > > wrote: > >>> > > > > >>> > > > > >>> > > > Hi Tengfei, > >>> > > > > >>> > > > > >>> > > > ----- Original Message ----- > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >>> > > > > To: lcollado at jhu.edu > >>> > > > > Cc: bioconductor at r-project.org > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >>> > > > > example > >>> > > > > is > >>> > > > > broken > >>> > > > > > >>> > > > > btw, based on the error, let me try to debug it. > >>> > > > > > >>> > > > > > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: > >>> > > > > > >>> > > > > > Hi Leonardo, > >>> > > > > > > >>> > > > > > Frankly speaking, the vignette is still in progress, > >>> > > > > > and > >>> > > > > > there > >>> > > > > > are > >>> > > > > > some > >>> > > > > > known bugs in ggbio I need to fix (still trying to find > >>> > > > > > a > >>> > > > > > time > >>> > > > > > to > >>> > > > > > do that > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc > >>> > > > > > 2.14 on > >>> > > > > > my > >>> > > > > > new MBP > >>> > > > > > with OSX 10.9, but fails, probably binary build is not > >>> > > > > > ready > >>> > > > > > for > >>> > > > > > maverick > >>> > > > > > yet, maybe available by the end of April? > >>> > > > > > > >>> > > > > > Thanks for reporting the bug, I will keep you posted on > >>> > > > > > this > >>> > > > > > when > >>> > > > > > I > >>> > > > > > successfully get it on my laptop and start fixing the > >>> > > > > > problems. > >>> > > > > > > >>> > > > > >>> > > > You can install the Snow Leopard build of R and should have > >>> > > > no > >>> > > > problems, binary packages are available for that version. > >>> > > > It will > >>> > > > run fine on Mavericks. > >>> > > > > >>> > > > Dan > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > > cheers > >>> > > > > > > >>> > > > > > Tengfei > >>> > > > > > > >>> > > > > > > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado > >>> > > > > > Torres < > >>> > > > > > lcollado at jhsph.edu > wrote: > >>> > > > > > > >>> > > > > >> Hello Tengfei + bioc list, > >>> > > > > >> > >>> > > > > >> From > >>> > > > > >> > >>> > > > > >> http://www.bioconductor.org/packages/release/bioc/vig nettes/ggbio/inst/doc/ggbio.pdf > >>> > > > > >> page 4 (complied on april 11 2014), the following > >>> > > > > >> example > >>> > > > > >> loads > >>> > > > > >> to > >>> > > > > >> an > >>> > > > > >> error as shown below. I wasn't seeing this error > >>> > > > > >> before > >>> > > > > >> (aka, > >>> > > > > >> last > >>> > > > > >> week). The only guess that comes to mind is the recent > >>> > > > > >> update > >>> > > > > >> to > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to > >>> > > > > >> be > >>> > > > > >> related > >>> > > > > >> from > >>> > > > > >> the traceback() output, well... maybe it's related to > >>> > > > > >> the > >>> > > > > >> ignore.strand = TRUE part as described in the error. > >>> > > > > >> > >>> > > > > >> I'll create a GitHub issue just for completeness. > >>> > > > > >> > >>> > > > > >> Thank you, > >>> > > > > >> Leonardo > >>> > > > > >> > >>> > > > > >> > library(ggbio) > >>> > > > > >> ## Removed the output, nothing out of ordinary > >>> > > > > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >>> > > > > >> ## Removed the output > >>> > > > > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >>> > > > > >> > data(genesymbol, package = "biovizBase") > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > >>> > > > > >> > genesymbol["BRCA1"]) > >>> > > > > >> Aggregating TranscriptDb... > >>> > > > > >> Parsing transcripts... > >>> > > > > >> Parsing exons... > >>> > > > > >> Parsing cds... > >>> > > > > >> Parsing utrs... > >>> > > > > >> ------exons... > >>> > > > > >> ------cdss... > >>> > > > > >> ------introns... > >>> > > > > >> ------utr... > >>> > > > > >> aggregating... > >>> > > > > >> Done > >>> > > > > >> Constructing graphics... > >>> > > > > >> Error in sapply(listData, function(Xi) > >>> > > > > >> extends(class(Xi), > >>> > > > > >> elementTypeX)) : > >>> > > > > >> error in evaluating the argument 'X' in selecting a > >>> > > > > >> method > >>> > > > > >> for > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > >>> > > > > >> ignore.strand > >>> > > > > >> = > >>> > > > > >> TRUE))) : > >>> > > > > >> error in evaluating the argument 'x' in selecting a > >>> > > > > >> method > >>> > > > > >> for > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused > >>> > > > > >> argument > >>> > > > > >> (ignore.strand = TRUE) > >>> > > > > >> > >>> > > > > >> > traceback() > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > >>> > > > > >> elementTypeX)) > >>> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, > >>> > > > > >> FUN, > >>> > > > > >> ...)) > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > >>> > > > > >> if (!is.null( group.name )) { > >>> > > > > >> if (!group.selfish) { > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >>> > > > > >> TRUE))) > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >>> > > > > >> width(irs) + > >>> > > > > >> extend.size) > >>> > > > > >> irs.new <- sort(irs.new) > >>> > > > > >> .lvs <- disjointBins(irs.new) > >>> > > > > >> values(x)$stepping <- > >>> > > > > >> .lvs[as.character(values(x)[, > >>> > > > > >> group.name ])] > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> else { > >>> > > > > >> values(x)$stepping <- > >>> > > > > >> as.numeric(as.factor(values(x)[, > >>> > > > > >> group.name ])) > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> } > >>> > > > > >> else { > >>> > > > > >> irs <- ranges(x) > >>> > > > > >> values(x)$stepping <- > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >>> > > > > >> fix = "center", width = width(irs) + > >>> > > > > >> extend.size))) > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> }) > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > >>> > > > > >> if (!is.null( group.name )) { > >>> > > > > >> if (!group.selfish) { > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >>> > > > > >> TRUE))) > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >>> > > > > >> width(irs) + > >>> > > > > >> extend.size) > >>> > > > > >> irs.new <- sort(irs.new) > >>> > > > > >> .lvs <- disjointBins(irs.new) > >>> > > > > >> values(x)$stepping <- > >>> > > > > >> .lvs[as.character(values(x)[, > >>> > > > > >> group.name ])] > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> else { > >>> > > > > >> values(x)$stepping <- > >>> > > > > >> as.numeric(as.factor(values(x)[, > >>> > > > > >> group.name ])) > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> } > >>> > > > > >> else { > >>> > > > > >> irs <- ranges(x) > >>> > > > > >> values(x)stepping <- > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >>> > > > > >> fix = "center", width = width(irs) + > >>> > > > > >> extend.size))) > >>> > > > > >> x > >>> > > > > >> } > >>> > > > > >> }) > >>> > > > > >> 11: .local(obj, ...) > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > >>> > > > > >> group.selfish = > >>> > > > > >> FALSE, > >>> > > > > >> fix = "start", extend.size = es) > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish > >>> > > > > >> = > >>> > > > > >> FALSE, > >>> > > > > >> fix = "start", extend.size = es) > >>> > > > > >> 8: .local(data, ...) > >>> > > > > >> 7: (function (data, ...) > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> >>> > > > > >> of > >>> > > > > >> class > >>> > > > > >> "TranscriptDb">, > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >>> > > > > >> "alignment", > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > >>> > > > > >> TRUE, > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >>> > > > > >> 6: (function (data, ...) > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> >>> > > > > >> of > >>> > > > > >> class > >>> > > > > >> "TranscriptDb">, > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >>> > > > > >> "alignment", > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > >>> > > > > >> TRUE, > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >>> > > > > >> 5: do.call(geom_alignment, args.res) > >>> > > > > >> 4: do.call(geom_alignment, args.res) > >>> > > > > >> 3: .local(object, ...) > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > sessionInfo() > >>> > > > > >> R version 3.1.0 (2014-04-10) > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >>> > > > > >> > >>> > > > > >> locale: > >>> > > > > >> [1] > >>> > > > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >>> > > > > >> > >>> > > > > >> attached base packages: > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets > >>> > > > > >> methods base > >>> > > > > >> > >>> > > > > >> other attached packages: > >>> > > > > >> [1] XVector_0.4.0 > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >>> > > > > >> GenomicFeatures_1.16.0 > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >>> > > > > >> GenomicRanges_1.16.2 > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >>> > > > > >> ggbio_1.12.0 > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >>> > > > > >> > >>> > > > > >> loaded via a namespace (and not attached): > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >>> > > > > >> Biostrings_2.32.0 > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > >>> > > > > >> Formula_1.1-1 > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >>> > > > > >> Hmisc_3.14-4 > >>> > > > > >> iterators_1.0.7 labeling_0.2 > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >>> > > > > >> stringr_0.6.2 > >>> > > > > >> survival_2.37-7 tools_3.1.0 > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >>> > > > > >> zlibbioc_1.10.0 > >>> > > > > >> > > >>> > > > > >> > >>> > > > > > > >>> > > > > > > >>> > > > > > > >>> > > > > > -- > >>> > > > > > Tengfei Yin, PhD > >>> > > > > > Seven Bridges Genomics > >>> > > > > > sbgenomics.com > >>> > > > > > 625 Mt. Auburn St. Suite #208 > >>> > > > > > Cambridge, MA 02138 > >>> > > > > > (617) 866-0446 > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > -- > >>> > > > > Tengfei Yin, PhD > >>> > > > > Seven Bridges Genomics > >>> > > > > sbgenomics.com > >>> > > > > 625 Mt. Auburn St. Suite #208 > >>> > > > > Cambridge, MA 02138 > >>> > > > > (617) 866-0446 > >>> > > > > > >>> > > > > [[alternative HTML version deleted]] > >>> > > > > > >>> > > > > _______________________________________________ > >>> > > > > Bioconductor mailing list > >>> > > > > Bioconductor at r-project.org > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > > > > Search the archives: > >>> > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > -- > >>> > > > > >>> > > > > >>> > > > Tengfei Yin, PhD > >>> > > > Seven Bridges Genomics > >>> > > > sbgenomics.com > >>> > > > 625 Mt. Auburn St. Suite #208 > >>> > > > Cambridge, MA 02138 > >>> > > > (617) 866- 0446 > >>> > > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > -- > >>> > > > >>> > > > >>> > > Tengfei Yin, PhD > >>> > > Seven Bridges Genomics > >>> > > sbgenomics.com > >>> > > 625 Mt. Auburn St. Suite #208 > >>> > > Cambridge, MA 02138 > >>> > > (617) 866- 0446 > >>> > > > >>> > > >>> > > >>> > > >>> > > >>> > -- > >>> > > >>> > > >>> > Tengfei Yin, PhD > >>> > Seven Bridges Genomics > >>> > sbgenomics.com > >>> > 625 Mt. Auburn St. Suite #208 > >>> > Cambridge, MA 02138 > >>> > (617) 866- 0446 > >>> > > >> > >> > >> > >> > >> -- > >> Tengfei Yin, PhD > >> Seven Bridges Genomics > >> sbgenomics.com > >> 625 Mt. Auburn St. Suite #208 > >> Cambridge, MA 02138 > >> (617) 866-0446 > ADD REPLY 0 Entering edit mode Is there any reason why ggbio 1.12.2 hasn't made it to BioC release? http://master.bioconductor.org/packages/release/bioc/html/ggbio.html still points to 1.12.0 On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Leonardo Collado Torres" <lcollado@jhsph.edu> > > To: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing list" < > bioconductor@r-project.org> > > Sent: Wednesday, April 23, 2014 3:38:11 PM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > Dang it, forgot again to send with my @jhsph.edu account. See below > > again >.< > > > > On the email topic, is it possible to be subscribed with 2 emails > > accounts to the BioC mailing list but only get emails with one? I > > believe that I have to choose to either get the daily digest or get a > > single for every message sent. If not, I'll probably just drop my > > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail I > > got (our university is pushing these mails). > > > > I don't know; you could try it. Another option would be to configure your > mail client with a filter to drop the undesired bioc emails. > > Dan > > > > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > > <lcollado@jhu.edu> wrote: > > > Hi Dan, > > > > > > I got RSwitch to work with a second installation of R 3.1. > > > Basically, > > > I downloaded the leopard tarball, expanded it, renamed the folder > > > 3.1 > > > to 3.1patched (which is the version I downloaded, but well, > > > anything > > > except for 3.1 would work), compressed it again, and then expanded > > > it > > > at the root location. > > > > > > So it would be something like this: > > > > > > wget > > > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > > > tar -xvf R-*gz > > > mv Library/Frameworks/R.framework/Versions/3.1 > > > Library/Frameworks/R.framework/Versions/3.1patched > > > tar -cvzf Rlib.tgz Library > > > sudo tar fvxz Rlib.tgz -C / > > > > > > Then used RSwitch, and was able to install BioC-devel. > > > > > > I might try out your renv at a different time. It's great to know > > > that it exists =) > > > > > > Cheers, > > > Leo > > > > > > > > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > > > <tengfei.yin@sbgenomics.com> wrote: > > >> Hi Dan, > > >> > > >> It works like a charm, thanks! > > >> > > >> I use your method, then I changed /Library/Framework/ folder and > > >> R.Framework > > >> folder ownership to myself so I don't have to sudo it, then I just > > >> add alias > > >> to "emacs2" and "emacs3" to run your renv to switch the R first. > > >> This solves > > >> my problem. > > >> > > >> Try to customize variable for R hooks in emacs as alternative > > >> solution, but > > >> may need more time. > > >> > > >> Thanks again! > > >> > > >> Tengfei > > >> > > >> > > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > > >> <dtenenba@fhcrc.org> wrote: > > >>> > > >>> Hi Tengfei, > > >>> > > >>> ----- Original Message ----- > > >>> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > > >>> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > > >>> > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, > > >>> > lcollado@jhu.edu > > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > > >>> > is broken > > >>> > > > >>> > > > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on the > > >>> > R 3.1? > > >>> > > >>> Yes, install two copies of R 3.1 and switch between them. > > >>> > > >>> > And do some sort of switch for bioc? The website you send to me > > >>> > also > > >>> > have a R-devel build, my plan is to install bioc 3.0 on R-devel > > >>> > and > > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only to > > >>> > switch bioc, so that I could debug and maintain released and > > >>> > devel > > >>> > version. > > >>> > > >>> PLEASE don't use R-devel at all. > > >>> > > >>> Just use R-3.1.0. > > >>> > > >>> You can use the Rswitch app but as you point out it won't work > > >>> within > > >>> emacs. > > >>> > > >>> This is what I do: > > >>> > > >>> Every time I download a new version of R, I run its installer. > > >>> The > > >>> installer always puts it in > > >>> > > >>> /Library/Frameworks/R.framework > > >>> > > >>> So after I install each version of R, I rename the R.framework > > >>> directory > > >>> to something like > > >>> R.framework.bioc214_snowleopard > > >>> > > >>> And then I make a symlink from R.framework.bioc214_snowleopard to > > >>> R.framework. > > >>> > > >>> I have a little script at https://github.com/dtenenba/renv which > > >>> lets me > > >>> see what the various installed Rs are: > > >>> > > >>> renv > > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > > >>> > > >>> This tells me that the currently active R is nicknamed > > >>> "releaseMav" (this > > >>> means there is a link from > > >>> /Library/Frameworks/R.framework.releaseMav to > > >>> /Library/Frameworks/R.framework. It shows the versions, svn > > >>> revisions, > > >>> dates, and architectures of each version. (darwin10.8.0 is Snow > > >>> Leopard; > > >>> darwin13.1.0 is Mavericks). > > >>> > > >>> Note that in my nomenclature devel means BioC devel, not R-devel. > > >>> > > >>> So if I wanted to switch to the "develSL" version I would do: > > >>> > > >>> sudo renv develSL > > >>> > > >>> HTH > > >>> Dan > > >>> > > >>> > > >>> > > >>> > > > >>> > > > >>> > > > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > > >>> > dtenenba@fhcrc.org > > > >>> > wrote: > > >>> > > > >>> > > > >>> > > > >>> > Hi Tengfei, > > >>> > > > >>> > ----- Original Message ----- > > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > >>> > > > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > > >>> > > Cc: "Bioconductor mailing list" < bioconductor@r-project.org > > >>> > > >, > > >>> > > lcollado@jhu.edu > > >>> > > > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > > >>> > > is > > >>> > > broken > > >>> > > > > >>> > > > > >>> > > > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am still > > >>> > > a > > >>> > > newbie to OSX ... I got R-devel running and I will try > > >>> > > Rswitcher, I > > >>> > > also want to do that switch easily in emacs too. > > >>> > > > > >>> > > > > >>> > > > >>> > You don't want to use R-devel. Both BioC release (2.14) and > > >>> > BioC > > >>> > devel (3.0) are meant to work with R-3.1.0, the released > > >>> > version of > > >>> > R. > > >>> > > > >>> > I think the Rswitch app just sets a symbolic link, so you > > >>> > should be > > >>> > able to do that within emacs. Run it and see what it does to > > >>> > /Library/Frameworks/R.framework. > > >>> > > > >>> > Dan > > >>> > > > >>> > > > >>> > > > > >>> > > cheers > > >>> > > > > >>> > > > > >>> > > Tengfei > > >>> > > > > >>> > > > > >>> > > > > >>> > > > >>> > > > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > > >>> > > dtenenba@fhcrc.org > > >>> > > > > > >>> > > wrote: > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > ----- Original Message ----- > > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > >>> > > > > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > > >>> > > > Cc: "Bioconductor mailing list" < > > >>> > > > bioconductor@r-project.org >, > > >>> > > > lcollado@jhu.edu > > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > > >>> > > > example is > > >>> > > > broken > > >>> > > > > > >>> > > > > > >>> > > > > >>> > > > Hi Dan, > > >>> > > > > > >>> > > > > > >>> > > > So you mean I install R 3.1 for snow leopard and it should > > >>> > > > work? > > >>> > > > > >>> > > Yes. > > >>> > > > > >>> > > > > >>> > > > > >>> > > ? Is > > >>> > > > there a way to build from source using biocLite, like type > > >>> > > > = > > >>> > > > "source", this is what I got > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > library(BiocInstaller) > > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite > > >>> > > > for > > >>> > > > help > > >>> > > > > biocLite("GenomicRanges") > > >>> > > > BioC_mirror: http://bioconductor.org > > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R > > >>> > > > version > > >>> > > > 3.1.0. > > >>> > > > Installing package(s) 'GenomicRanges' > > >>> > > > > > >>> > > > > > >>> > > > package ‘GenomicRanges’ is available as a source package > > >>> > > > but not > > >>> > > > as > > >>> > > > a > > >>> > > > binary > > >>> > > > > > >>> > > > > > >>> > > > Warning message: > > >>> > > > package ‘GenomicRanges’ is not available (for R version > > >>> > > > 3.1.0) > > >>> > > > > > >>> > > > > > >>> > > > Just wondering is there a solution without re-install R for > > >>> > > > snow > > >>> > > > leopard. And what's the plan for maverick? > > >>> > > > > > >>> > > > > >>> > > You can do > > >>> > > biocLite("GenomicRanges", type="source") > > >>> > > > > >>> > > but you need to have the appropriate compilers, etc. > > >>> > > > > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You can > > >>> > > have > > >>> > > multiple installations of R on your Mac and switch between > > >>> > > them > > >>> > > using Rswitch ( http://r.research.att.com/#other ) or another > > >>> > > easy > > >>> > > > >>> > > > >>> > > mechanism. > > >>> > > > > >>> > > We are building packages for Mavericks now, we just have to > > >>> > > resolve > > >>> > > a > > >>> > > few build issues and test the resulting packages, we still > > >>> > > hope to > > >>> > > have them available by the end of the month. But since you > > >>> > > can > > >>> > > install the Snow Leopard build without needing to remove your > > >>> > > Mavericks build, you should do that. > > >>> > > > > >>> > > Dan > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > > >>> > > > Thanks > > >>> > > > > > >>> > > > > > >>> > > > Tengfei > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > >>> > > > dtenenba@fhcrc.org > > >>> > > > > wrote: > > >>> > > > > > >>> > > > > > >>> > > > Hi Tengfei, > > >>> > > > > > >>> > > > > > >>> > > > ----- Original Message ----- > > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > > >>> > > > > To: lcollado@jhu.edu > > >>> > > > > Cc: bioconductor@r-project.org > > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > > >>> > > > > example > > >>> > > > > is > > >>> > > > > broken > > >>> > > > > > > >>> > > > > btw, based on the error, let me try to debug it. > > >>> > > > > > > >>> > > > > > > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > >>> > > > > < tengfei.yin@sbgenomics.com >wrote: > > >>> > > > > > > >>> > > > > > Hi Leonardo, > > >>> > > > > > > > >>> > > > > > Frankly speaking, the vignette is still in progress, > > >>> > > > > > and > > >>> > > > > > there > > >>> > > > > > are > > >>> > > > > > some > > >>> > > > > > known bugs in ggbio I need to fix (still trying to find > > >>> > > > > > a > > >>> > > > > > time > > >>> > > > > > to > > >>> > > > > > do that > > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc > > >>> > > > > > 2.14 on > > >>> > > > > > my > > >>> > > > > > new MBP > > >>> > > > > > with OSX 10.9, but fails, probably binary build is not > > >>> > > > > > ready > > >>> > > > > > for > > >>> > > > > > maverick > > >>> > > > > > yet, maybe available by the end of April? > > >>> > > > > > > > >>> > > > > > Thanks for reporting the bug, I will keep you posted on > > >>> > > > > > this > > >>> > > > > > when > > >>> > > > > > I > > >>> > > > > > successfully get it on my laptop and start fixing the > > >>> > > > > > problems. > > >>> > > > > > > > >>> > > > > > >>> > > > You can install the Snow Leopard build of R and should have > > >>> > > > no > > >>> > > > problems, binary packages are available for that version. > > >>> > > > It will > > >>> > > > run fine on Mavericks. > > >>> > > > > > >>> > > > Dan > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > cheers > > >>> > > > > > > > >>> > > > > > Tengfei > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado > > >>> > > > > > Torres < > > >>> > > > > > lcollado@jhsph.edu > wrote: > > >>> > > > > > > > >>> > > > > >> Hello Tengfei + bioc list, > > >>> > > > > >> > > >>> > > > > >> From > > >>> > > > > >> > > >>> > > > > >> > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > > >>> > > > > >> page 4 (complied on april 11 2014), the following > > >>> > > > > >> example > > >>> > > > > >> loads > > >>> > > > > >> to > > >>> > > > > >> an > > >>> > > > > >> error as shown below. I wasn't seeing this error > > >>> > > > > >> before > > >>> > > > > >> (aka, > > >>> > > > > >> last > > >>> > > > > >> week). The only guess that comes to mind is the recent > > >>> > > > > >> update > > >>> > > > > >> to > > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to > > >>> > > > > >> be > > >>> > > > > >> related > > >>> > > > > >> from > > >>> > > > > >> the traceback() output, well... maybe it's related to > > >>> > > > > >> the > > >>> > > > > >> ignore.strand = TRUE part as described in the error. > > >>> > > > > >> > > >>> > > > > >> I'll create a GitHub issue just for completeness. > > >>> > > > > >> > > >>> > > > > >> Thank you, > > >>> > > > > >> Leonardo > > >>> > > > > >> > > >>> > > > > >> > library(ggbio) > > >>> > > > > >> ## Removed the output, nothing out of ordinary > > >>> > > > > >> > > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > >>> > > > > >> ## Removed the output > > >>> > > > > >> > > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >>> > > > > >> > data(genesymbol, package = "biovizBase") > > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > > >>> > > > > >> > genesymbol["BRCA1"]) > > >>> > > > > >> Aggregating TranscriptDb... > > >>> > > > > >> Parsing transcripts... > > >>> > > > > >> Parsing exons... > > >>> > > > > >> Parsing cds... > > >>> > > > > >> Parsing utrs... > > >>> > > > > >> ------exons... > > >>> > > > > >> ------cdss... > > >>> > > > > >> ------introns... > > >>> > > > > >> ------utr... > > >>> > > > > >> aggregating... > > >>> > > > > >> Done > > >>> > > > > >> Constructing graphics... > > >>> > > > > >> Error in sapply(listData, function(Xi) > > >>> > > > > >> extends(class(Xi), > > >>> > > > > >> elementTypeX)) : > > >>> > > > > >> error in evaluating the argument 'X' in selecting a > > >>> > > > > >> method > > >>> > > > > >> for > > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > > >>> > > > > >> ignore.strand > > >>> > > > > >> = > > >>> > > > > >> TRUE))) : > > >>> > > > > >> error in evaluating the argument 'x' in selecting a > > >>> > > > > >> method > > >>> > > > > >> for > > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused > > >>> > > > > >> argument > > >>> > > > > >> (ignore.strand = TRUE) > > >>> > > > > >> > > >>> > > > > >> > traceback() > > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > > >>> > > > > >> elementTypeX)) > > >>> > > > > >> 14: .updateCompressedList(X, lapply_CompressedList(X, > > >>> > > > > >> FUN, > > >>> > > > > >> ...)) > > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > > >>> > > > > >> if (!is.null( group.name )) { > > >>> > > > > >> if (!group.selfish) { > > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >>> > > > > >> TRUE))) > > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > > >>> > > > > >> width(irs) + > > >>> > > > > >> extend.size) > > >>> > > > > >> irs.new <- sort(irs.new) > > >>> > > > > >> .lvs <- disjointBins(irs.new) > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> .lvs[as.character(values(x)[, > > >>> > > > > >> group.name ])] > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> else { > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> as.numeric(as.factor(values(x)[, > > >>> > > > > >> group.name ])) > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> } > > >>> > > > > >> else { > > >>> > > > > >> irs <- ranges(x) > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> as.numeric(disjointBins(resize(irs, > > >>> > > > > >> fix = "center", width = width(irs) + > > >>> > > > > >> extend.size))) > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> }) > > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > > >>> > > > > >> if (!is.null( group.name )) { > > >>> > > > > >> if (!group.selfish) { > > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >>> > > > > >> TRUE))) > > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > > >>> > > > > >> width(irs) + > > >>> > > > > >> extend.size) > > >>> > > > > >> irs.new <- sort(irs.new) > > >>> > > > > >> .lvs <- disjointBins(irs.new) > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> .lvs[as.character(values(x)[, > > >>> > > > > >> group.name ])] > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> else { > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> as.numeric(as.factor(values(x)[, > > >>> > > > > >> group.name ])) > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> } > > >>> > > > > >> else { > > >>> > > > > >> irs <- ranges(x) > > >>> > > > > >> values(x)$stepping <- > > >>> > > > > >> as.numeric(disjointBins(resize(irs, > > >>> > > > > >> fix = "center", width = width(irs) + > > >>> > > > > >> extend.size))) > > >>> > > > > >> x > > >>> > > > > >> } > > >>> > > > > >> }) > > >>> > > > > >> 11: .local(obj, ...) > > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > > >>> > > > > >> group.selfish = > > >>> > > > > >> FALSE, > > >>> > > > > >> fix = "start", extend.size = es) > > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", group.selfish > > >>> > > > > >> = > > >>> > > > > >> FALSE, > > >>> > > > > >> fix = "start", extend.size = es) > > >>> > > > > >> 8: .local(data, ...) > > >>> > > > > >> 7: (function (data, ...) > > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> > >>> > > > > >> of > > >>> > > > > >> class > > >>> > > > > >> "TranscriptDb">, > > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > > >>> > > > > >> "alignment", > > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > > >>> > > > > >> TRUE, > > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >>> > > > > >> 6: (function (data, ...) > > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> > >>> > > > > >> of > > >>> > > > > >> class > > >>> > > > > >> "TranscriptDb">, > > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > > >>> > > > > >> "alignment", > > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > > >>> > > > > >> TRUE, > > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >>> > > > > >> 5: do.call(geom_alignment, args.res) > > >>> > > > > >> 4: do.call(geom_alignment, args.res) > > >>> > > > > >> 3: .local(object, ...) > > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >>> > > > > >> > > >>> > > > > >> > > >>> > > > > >> > sessionInfo() > > >>> > > > > >> R version 3.1.0 (2014-04-10) > > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > >>> > > > > >> > > >>> > > > > >> locale: > > >>> > > > > >> [1] > > >>> > > > > >> > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >>> > > > > >> > > >>> > > > > >> attached base packages: > > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets > > >>> > > > > >> methods base > > >>> > > > > >> > > >>> > > > > >> other attached packages: > > >>> > > > > >> [1] XVector_0.4.0 > > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > >>> > > > > >> GenomicFeatures_1.16.0 > > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > >>> > > > > >> GenomicRanges_1.16.2 > > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > >>> > > > > >> ggbio_1.12.0 > > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > >>> > > > > >> > > >>> > > > > >> loaded via a namespace (and not attached): > > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > >>> > > > > >> Biostrings_2.32.0 > > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > > >>> > > > > >> Formula_1.1-1 > > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > >>> > > > > >> Hmisc_3.14-4 > > >>> > > > > >> iterators_1.0.7 labeling_0.2 > > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > > >>> > > > > >> stringr_0.6.2 > > >>> > > > > >> survival_2.37-7 tools_3.1.0 > > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > >>> > > > > >> zlibbioc_1.10.0 > > >>> > > > > >> > > > >>> > > > > >> > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > -- > > >>> > > > > > Tengfei Yin, PhD > > >>> > > > > > Seven Bridges Genomics > > >>> > > > > > sbgenomics.com > > >>> > > > > > 625 Mt. Auburn St. Suite #208 > > >>> > > > > > Cambridge, MA 02138 > > >>> > > > > > (617) 866-0446 > > >>> > > > > > > > >>> > > > > > > >>> > > > > > > >>> > > > > > > >>> > > > > -- > > >>> > > > > Tengfei Yin, PhD > > >>> > > > > Seven Bridges Genomics > > >>> > > > > sbgenomics.com > > >>> > > > > 625 Mt. Auburn St. Suite #208 > > >>> > > > > Cambridge, MA 02138 > > >>> > > > > (617) 866-0446 > > >>> > > > > > > >>> > > > > [[alternative HTML version deleted]] > > >>> > > > > > > >>> > > > > _______________________________________________ > > >>> > > > > Bioconductor mailing list > > >>> > > > > Bioconductor@r-project.org > > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >>> > > > > Search the archives: > > >>> > > > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > -- > > >>> > > > > > >>> > > > > > >>> > > > Tengfei Yin, PhD > > >>> > > > Seven Bridges Genomics > > >>> > > > sbgenomics.com > > >>> > > > 625 Mt. Auburn St. Suite #208 > > >>> > > > Cambridge, MA 02138 > > >>> > > > (617) 866- 0446 > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > -- > > >>> > > > > >>> > > > > >>> > > Tengfei Yin, PhD > > >>> > > Seven Bridges Genomics > > >>> > > sbgenomics.com > > >>> > > 625 Mt. Auburn St. Suite #208 > > >>> > > Cambridge, MA 02138 > > >>> > > (617) 866- 0446 > > >>> > > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > -- > > >>> > > > >>> > > > >>> > Tengfei Yin, PhD > > >>> > Seven Bridges Genomics > > >>> > sbgenomics.com > > >>> > 625 Mt. Auburn St. Suite #208 > > >>> > Cambridge, MA 02138 > > >>> > (617) 866- 0446 > > >>> > > > >> > > >> > > >> > > >> > > >> -- > > >> Tengfei Yin, PhD > > >> Seven Bridges Genomics > > >> sbgenomics.com > > >> 625 Mt. Auburn St. Suite #208 > > >> Cambridge, MA 02138 > > >> (617) 866-0446 > > > [[alternative HTML version deleted]]
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Leonardo Collado Torres <lcollado at="" jhsph.edu=""> wrote: >Is there any reason why ggbio 1.12.2 hasn't made it to BioC release? >http://master.bioconductor.org/packages/release/bioc/html/ggbio.html >still >points to 1.12.0 > It's failing to build: http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html Dan > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >wrote: > >> >> >> ----- Original Message ----- >> > From: "Leonardo Collado Torres" <lcollado at="" jhsph.edu=""> >> > To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing >list" < >> bioconductor at r-project.org> >> > Sent: Wednesday, April 23, 2014 3:38:11 PM >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >broken >> > >> > Dang it, forgot again to send with my @jhsph.edu account. See below >> > again >.< >> > >> > On the email topic, is it possible to be subscribed with 2 emails >> > accounts to the BioC mailing list but only get emails with one? I >> > believe that I have to choose to either get the daily digest or get >a >> > single for every message sent. If not, I'll probably just drop my >> > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail >I >> > got (our university is pushing these mails). >> > >> >> I don't know; you could try it. Another option would be to configure >your >> mail client with a filter to drop the undesired bioc emails. >> >> Dan >> >> >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres >> > <lcollado at="" jhu.edu=""> wrote: >> > > Hi Dan, >> > > >> > > I got RSwitch to work with a second installation of R 3.1. >> > > Basically, >> > > I downloaded the leopard tarball, expanded it, renamed the folder >> > > 3.1 >> > > to 3.1patched (which is the version I downloaded, but well, >> > > anything >> > > except for 3.1 would work), compressed it again, and then >expanded >> > > it >> > > at the root location. >> > > >> > > So it would be something like this: >> > > >> > > wget >> > > >> >http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz >> > > tar -xvf R-*gz >> > > mv Library/Frameworks/R.framework/Versions/3.1 >> > > Library/Frameworks/R.framework/Versions/3.1patched >> > > tar -cvzf Rlib.tgz Library >> > > sudo tar fvxz Rlib.tgz -C / >> > > >> > > Then used RSwitch, and was able to install BioC-devel. >> > > >> > > I might try out your renv at a different time. It's great to >know >> > > that it exists =) >> > > >> > > Cheers, >> > > Leo >> > > >> > > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin >> > > <tengfei.yin at="" sbgenomics.com=""> wrote: >> > >> Hi Dan, >> > >> >> > >> It works like a charm, thanks! >> > >> >> > >> I use your method, then I changed /Library/Framework/ folder and >> > >> R.Framework >> > >> folder ownership to myself so I don't have to sudo it, then I >just >> > >> add alias >> > >> to "emacs2" and "emacs3" to run your renv to switch the R first. >> > >> This solves >> > >> my problem. >> > >> >> > >> Try to customize variable for R hooks in emacs as alternative >> > >> solution, but >> > >> may need more time. >> > >> >> > >> Thanks again! >> > >> >> > >> Tengfei >> > >> >> > >> >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum >> > >> <dtenenba at="" fhcrc.org=""> wrote: >> > >>> >> > >>> Hi Tengfei, >> > >>> >> > >>> ----- Original Message ----- >> > >>> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> > >>> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> > >>> > Cc: "Bioconductor mailing list" <bioconductor at="" r-project.org="">, >> > >>> > lcollado at jhu.edu >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >> > >>> > is broken >> > >>> > >> > >>> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on >the >> > >>> > R 3.1? >> > >>> >> > >>> Yes, install two copies of R 3.1 and switch between them. >> > >>> >> > >>> > And do some sort of switch for bioc? The website you send to >me >> > >>> > also >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on >R-devel >> > >>> > and >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only >to >> > >>> > switch bioc, so that I could debug and maintain released and >> > >>> > devel >> > >>> > version. >> > >>> >> > >>> PLEASE don't use R-devel at all. >> > >>> >> > >>> Just use R-3.1.0. >> > >>> >> > >>> You can use the Rswitch app but as you point out it won't work >> > >>> within >> > >>> emacs. >> > >>> >> > >>> This is what I do: >> > >>> >> > >>> Every time I download a new version of R, I run its installer. >> > >>> The >> > >>> installer always puts it in >> > >>> >> > >>> /Library/Frameworks/R.framework >> > >>> >> > >>> So after I install each version of R, I rename the R.framework >> > >>> directory >> > >>> to something like >> > >>> R.framework.bioc214_snowleopard >> > >>> >> > >>> And then I make a symlink from R.framework.bioc214_snowleopard >to >> > >>> R.framework. >> > >>> >> > >>> I have a little script at https://github.com/dtenenba/renv >which >> > >>> lets me >> > >>> see what the various installed Rs are: >> > >>> >> > >>> $renv >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> > >>> >> > >>> This tells me that the currently active R is nicknamed >> > >>> "releaseMav" (this >> > >>> means there is a link from >> > >>> /Library/Frameworks/R.framework.releaseMav to >> > >>> /Library/Frameworks/R.framework. It shows the versions, svn >> > >>> revisions, >> > >>> dates, and architectures of each version. (darwin10.8.0 is Snow >> > >>> Leopard; >> > >>> darwin13.1.0 is Mavericks). >> > >>> >> > >>> Note that in my nomenclature devel means BioC devel, not >R-devel. >> > >>> >> > >>> So if I wanted to switch to the "develSL" version I would do: >> > >>> >> > >>> sudo renv develSL >> > >>> >> > >>> HTH >> > >>> Dan >> > >>> >> > >>> >> > >>> >> > >>> > >> > >>> > >> > >>> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < >> > >>> > dtenenba at fhcrc.org > >> > >>> > wrote: >> > >>> > >> > >>> > >> > >>> > >> > >>> > Hi Tengfei, >> > >>> > >> > >>> > ----- Original Message ----- >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >>> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> > >>> > > Cc: "Bioconductor mailing list" < >bioconductor at r-project.org >> > >>> > > >, >> > >>> > > lcollado at jhu.edu >> > >>> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >example >> > >>> > > is >> > >>> > > broken >> > >>> > > >> > >>> > > >> > >>> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am >still >> > >>> > > a >> > >>> > > newbie to OSX ... I got R-devel running and I will try >> > >>> > > Rswitcher, I >> > >>> > > also want to do that switch easily in emacs too. >> > >>> > > >> > >>> > > >> > >>> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) and >> > >>> > BioC >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released >> > >>> > version of >> > >>> > R. >> > >>> > >> > >>> > I think the Rswitch app just sets a symbolic link, so you >> > >>> > should be >> > >>> > able to do that within emacs. Run it and see what it does to >> > >>> > /Library/Frameworks/R.framework. >> > >>> > >> > >>> > Dan >> > >>> > >> > >>> > >> > >>> > > >> > >>> > > cheers >> > >>> > > >> > >>> > > >> > >>> > > Tengfei >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > >> > >>> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < >> > >>> > > dtenenba at fhcrc.org >> > >>> > > > >> > >>> > > wrote: >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > ----- Original Message ----- >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >>> > > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> > >>> > > > Cc: "Bioconductor mailing list" < >> > >>> > > > bioconductor at r-project.org >, >> > >>> > > > lcollado at jhu.edu >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> > >>> > > > example is >> > >>> > > > broken >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > > > Hi Dan, >> > >>> > > > >> > >>> > > > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it >should >> > >>> > > > work? >> > >>> > > >> > >>> > > Yes. >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > ? Is >> > >>> > > > there a way to build from source using biocLite, like >type >> > >>> > > > = >> > >>> > > > "source", this is what I got >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > > library(BiocInstaller) >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), >?biocLite >> > >>> > > > for >> > >>> > > > help >> > >>> > > > > biocLite("GenomicRanges") >> > >>> > > > BioC_mirror: http://bioconductor.org >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R >> > >>> > > > version >> > >>> > > > 3.1.0. >> > >>> > > > Installing package(s) 'GenomicRanges' >> > >>> > > > >> > >>> > > > >> > >>> > > > package ?GenomicRanges? is available as a source package >> > >>> > > > but not >> > >>> > > > as >> > >>> > > > a >> > >>> > > > binary >> > >>> > > > >> > >>> > > > >> > >>> > > > Warning message: >> > >>> > > > package ?GenomicRanges? is not available (for R version >> > >>> > > > 3.1.0) >> > >>> > > > >> > >>> > > > >> > >>> > > > Just wondering is there a solution without re-install R >for >> > >>> > > > snow >> > >>> > > > leopard. And what's the plan for maverick? >> > >>> > > > >> > >>> > > >> > >>> > > You can do >> > >>> > > biocLite("GenomicRanges", type="source") >> > >>> > > >> > >>> > > but you need to have the appropriate compilers, etc. >> > >>> > > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You >can >> > >>> > > have >> > >>> > > multiple installations of R on your Mac and switch between >> > >>> > > them >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or >another >> > >>> > > easy >> > >>> > >> > >>> > >> > >>> > > mechanism. >> > >>> > > >> > >>> > > We are building packages for Mavericks now, we just have to >> > >>> > > resolve >> > >>> > > a >> > >>> > > few build issues and test the resulting packages, we still >> > >>> > > hope to >> > >>> > > have them available by the end of the month. But since you >> > >>> > > can >> > >>> > > install the Snow Leopard build without needing to remove >your >> > >>> > > Mavericks build, you should do that. >> > >>> > > >> > >>> > > Dan >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > > >> > >>> > > > Thanks >> > >>> > > > >> > >>> > > > >> > >>> > > > Tengfei >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < >> > >>> > > > dtenenba at fhcrc.org >> > >>> > > > > wrote: >> > >>> > > > >> > >>> > > > >> > >>> > > > Hi Tengfei, >> > >>> > > > >> > >>> > > > >> > >>> > > > ----- Original Message ----- >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >>> > > > > To: lcollado at jhu.edu >> > >>> > > > > Cc: bioconductor at r-project.org >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> > >>> > > > > example >> > >>> > > > > is >> > >>> > > > > broken >> > >>> > > > > >> > >>> > > > > btw, based on the error, let me try to debug it. >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: >> > >>> > > > > >> > >>> > > > > > Hi Leonardo, >> > >>> > > > > > >> > >>> > > > > > Frankly speaking, the vignette is still in progress, >> > >>> > > > > > and >> > >>> > > > > > there >> > >>> > > > > > are >> > >>> > > > > > some >> > >>> > > > > > known bugs in ggbio I need to fix (still trying to >find >> > >>> > > > > > a >> > >>> > > > > > time >> > >>> > > > > > to >> > >>> > > > > > do that >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc >> > >>> > > > > > 2.14 on >> > >>> > > > > > my >> > >>> > > > > > new MBP >> > >>> > > > > > with OSX 10.9, but fails, probably binary build is >not >> > >>> > > > > > ready >> > >>> > > > > > for >> > >>> > > > > > maverick >> > >>> > > > > > yet, maybe available by the end of April? >> > >>> > > > > > >> > >>> > > > > > Thanks for reporting the bug, I will keep you posted >on >> > >>> > > > > > this >> > >>> > > > > > when >> > >>> > > > > > I >> > >>> > > > > > successfully get it on my laptop and start fixing the >> > >>> > > > > > problems. >> > >>> > > > > > >> > >>> > > > >> > >>> > > > You can install the Snow Leopard build of R and should >have >> > >>> > > > no >> > >>> > > > problems, binary packages are available for that version. >> > >>> > > > It will >> > >>> > > > run fine on Mavericks. >> > >>> > > > >> > >>> > > > Dan >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > > > cheers >> > >>> > > > > > >> > >>> > > > > > Tengfei >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado >> > >>> > > > > > Torres < >> > >>> > > > > > lcollado at jhsph.edu > wrote: >> > >>> > > > > > >> > >>> > > > > >> Hello Tengfei + bioc list, >> > >>> > > > > >> >> > >>> > > > > >> From >> > >>> > > > > >> >> > >>> > > > > >> >> >http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ins t/doc/ggbio.pdf >> > >>> > > > > >> page 4 (complied on april 11 2014), the following >> > >>> > > > > >> example >> > >>> > > > > >> loads >> > >>> > > > > >> to >> > >>> > > > > >> an >> > >>> > > > > >> error as shown below. I wasn't seeing this error >> > >>> > > > > >> before >> > >>> > > > > >> (aka, >> > >>> > > > > >> last >> > >>> > > > > >> week). The only guess that comes to mind is the >recent >> > >>> > > > > >> update >> > >>> > > > > >> to >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to >> > >>> > > > > >> be >> > >>> > > > > >> related >> > >>> > > > > >> from >> > >>> > > > > >> the traceback() output, well... maybe it's related >to >> > >>> > > > > >> the >> > >>> > > > > >> ignore.strand = TRUE part as described in the error. >> > >>> > > > > >> >> > >>> > > > > >> I'll create a GitHub issue just for completeness. >> > >>> > > > > >> >> > >>> > > > > >> Thank you, >> > >>> > > > > >> Leonardo >> > >>> > > > > >> >> > >>> > > > > >> > library(ggbio) >> > >>> > > > > >> ## Removed the output, nothing out of ordinary >> > >>> > > > > >> >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> > >>> > > > > >> ## Removed the output >> > >>> > > > > >> >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = >> > >>> > > > > >> > genesymbol["BRCA1"]) >> > >>> > > > > >> Aggregating TranscriptDb... >> > >>> > > > > >> Parsing transcripts... >> > >>> > > > > >> Parsing exons... >> > >>> > > > > >> Parsing cds... >> > >>> > > > > >> Parsing utrs... >> > >>> > > > > >> ------exons... >> > >>> > > > > >> ------cdss... >> > >>> > > > > >> ------introns... >> > >>> > > > > >> ------utr... >> > >>> > > > > >> aggregating... >> > >>> > > > > >> Done >> > >>> > > > > >> Constructing graphics... >> > >>> > > > > >> Error in sapply(listData, function(Xi) >> > >>> > > > > >> extends(class(Xi), >> > >>> > > > > >> elementTypeX)) : >> > >>> > > > > >> error in evaluating the argument 'X' in selecting a >> > >>> > > > > >> method >> > >>> > > > > >> for >> > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, >> > >>> > > > > >> ignore.strand >> > >>> > > > > >> = >> > >>> > > > > >> TRUE))) : >> > >>> > > > > >> error in evaluating the argument 'x' in selecting a >> > >>> > > > > >> method >> > >>> > > > > >> for >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused >> > >>> > > > > >> argument >> > >>> > > > > >> (ignore.strand = TRUE) >> > >>> > > > > >> >> > >>> > > > > >> > traceback() >> > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), >> > >>> > > > > >> elementTypeX)) >> > >>> > > > > >> 14: .updateCompressedList(X, >lapply_CompressedList(X, >> > >>> > > > > >> FUN, >> > >>> > > > > >> ...)) >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { >> > >>> > > > > >> if (!is.null( group.name )) { >> > >>> > > > > >> if (!group.selfish) { >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> > >>> > > > > >> TRUE))) >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> > >>> > > > > >> width(irs) + >> > >>> > > > > >> extend.size) >> > >>> > > > > >> irs.new <- sort(irs.new) >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> > >>> > > > > >> values(x)$stepping <- >> > >>> > > > > >> .lvs[as.character(values(x)[, >> > >>> > > > > >> group.name ])] >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> else { >> > >>> > > > > >> values(x)$stepping <- >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> > >>> > > > > >> group.name ])) >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> } >> > >>> > > > > >> else { >> > >>> > > > > >> irs <- ranges(x) >> > >>> > > > > >> values(x)$stepping <- >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> > >>> > > > > >> fix = "center", width = width(irs) + >> > >>> > > > > >> extend.size))) >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> }) >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { >> > >>> > > > > >> if (!is.null( group.name )) { >> > >>> > > > > >> if (!group.selfish) { >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> > >>> > > > > >> TRUE))) >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> > >>> > > > > >> width(irs) + >> > >>> > > > > >> extend.size) >> > >>> > > > > >> irs.new <- sort(irs.new) >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> > >>> > > > > >> values(x)$stepping <- >> > >>> > > > > >> .lvs[as.character(values(x)[, >> > >>> > > > > >> group.name ])] >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> else { >> > >>> > > > > >> values(x)$stepping <- >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> > >>> > > > > >> group.name ])) >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> } >> > >>> > > > > >> else { >> > >>> > > > > >> irs <- ranges(x) >> > >>> > > > > >> values(x)stepping <- >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> > >>> > > > > >> fix = "center", width = width(irs) + >> > >>> > > > > >> extend.size))) >> > >>> > > > > >> x >> > >>> > > > > >> } >> > >>> > > > > >> }) >> > >>> > > > > >> 11: .local(obj, ...) >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", >> > >>> > > > > >> group.selfish = >> > >>> > > > > >> FALSE, >> > >>> > > > > >> fix = "start", extend.size = es) >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", >group.selfish >> > >>> > > > > >> = >> > >>> > > > > >> FALSE, >> > >>> > > > > >> fix = "start", extend.size = es) >> > >>> > > > > >> 8: .local(data, ...) >> > >>> > > > > >> 7: (function (data, ...) >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="">> > >>> > > > > >> of >> > >>> > > > > >> class >> > >>> > > > > >> "TranscriptDb">, >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> > >>> > > > > >> "alignment", >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = >> > >>> > > > > >> TRUE, >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> > >>> > > > > >> 6: (function (data, ...) >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="">> > >>> > > > > >> of >> > >>> > > > > >> class >> > >>> > > > > >> "TranscriptDb">, >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> > >>> > > > > >> "alignment", >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = >> > >>> > > > > >> TRUE, >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) >> > >>> > > > > >> 3: .local(object, ...) >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> > >>> > > > > >> >> > >>> > > > > >> >> > >>> > > > > >> > sessionInfo() >> > >>> > > > > >> R version 3.1.0 (2014-04-10) >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> > >>> > > > > >> >> > >>> > > > > >> locale: >> > >>> > > > > >> [1] >> > >>> > > > > >> >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> > >>> > > > > >> >> > >>> > > > > >> attached base packages: >> > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets >> > >>> > > > > >> methods base >> > >>> > > > > >> >> > >>> > > > > >> other attached packages: >> > >>> > > > > >> [1] XVector_0.4.0 >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> > >>> > > > > >> GenomicFeatures_1.16.0 >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> > >>> > > > > >> GenomicRanges_1.16.2 >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> > >>> > > > > >> ggbio_1.12.0 >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> > >>> > > > > >> >> > >>> > > > > >> loaded via a namespace (and not attached): >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 >> > >>> > > > > >> Biostrings_2.32.0 >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 >> > >>> > > > > >> Formula_1.1-1 >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 >> > >>> > > > > >> Hmisc_3.14-4 >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 >> > >>> > > > > >> stringr_0.6.2 >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 >> > >>> > > > > >> zlibbioc_1.10.0 >> > >>> > > > > >> > >> > >>> > > > > >> >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > -- >> > >>> > > > > > Tengfei Yin, PhD >> > >>> > > > > > Seven Bridges Genomics >> > >>> > > > > > sbgenomics.com >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 >> > >>> > > > > > Cambridge, MA 02138 >> > >>> > > > > > (617) 866-0446 >> > >>> > > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > -- >> > >>> > > > > Tengfei Yin, PhD >> > >>> > > > > Seven Bridges Genomics >> > >>> > > > > sbgenomics.com >> > >>> > > > > 625 Mt. Auburn St. Suite #208 >> > >>> > > > > Cambridge, MA 02138 >> > >>> > > > > (617) 866-0446 >> > >>> > > > > >> > >>> > > > > [[alternative HTML version deleted]] >> > >>> > > > > >> > >>> > > > > _______________________________________________ >> > >>> > > > > Bioconductor mailing list >> > >>> > > > > Bioconductor at r-project.org >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >>> > > > > Search the archives: >> > >>> > > > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >>> > > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > -- >> > >>> > > > >> > >>> > > > >> > >>> > > > Tengfei Yin, PhD >> > >>> > > > Seven Bridges Genomics >> > >>> > > > sbgenomics.com >> > >>> > > > 625 Mt. Auburn St. Suite #208 >> > >>> > > > Cambridge, MA 02138 >> > >>> > > > (617) 866- 0446 >> > >>> > > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > -- >> > >>> > > >> > >>> > > >> > >>> > > Tengfei Yin, PhD >> > >>> > > Seven Bridges Genomics >> > >>> > > sbgenomics.com >> > >>> > > 625 Mt. Auburn St. Suite #208 >> > >>> > > Cambridge, MA 02138 >> > >>> > > (617) 866- 0446 >> > >>> > > >> > >>> > >> > >>> > >> > >>> > >> > >>> > >> > >>> > -- >> > >>> > >> > >>> > >> > >>> > Tengfei Yin, PhD >> > >>> > Seven Bridges Genomics >> > >>> > sbgenomics.com >> > >>> > 625 Mt. Auburn St. Suite #208 >> > >>> > Cambridge, MA 02138 >> > >>> > (617) 866- 0446 >> > >>> > >> > >> >> > >> >> > >> >> > >> >> > >> -- >> > >> Tengfei Yin, PhD >> > >> Seven Bridges Genomics >> > >> sbgenomics.com >> > >> 625 Mt. Auburn St. Suite #208 >> > >> Cambridge, MA 02138 >> > >> (617) 866-0446 >> > >> ADD REPLY 0 Entering edit mode Oh ok. Thanks for the info On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC release? > >http://master.bioconductor.org/packages/release/bioc/html/ggbio.html > >still > >points to 1.12.0 > > > > It's failing to build: > > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > > Dan > > > > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > >wrote: > > > >> > >> > >> ----- Original Message ----- > >> > From: "Leonardo Collado Torres" <lcollado@jhsph.edu> > >> > To: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing > >list" < > >> bioconductor@r-project.org> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > >broken > >> > > >> > Dang it, forgot again to send with my @jhsph.edu account. See below > >> > again >.< > >> > > >> > On the email topic, is it possible to be subscribed with 2 emails > >> > accounts to the BioC mailing list but only get emails with one? I > >> > believe that I have to choose to either get the daily digest or get > >a > >> > single for every message sent. If not, I'll probably just drop my > >> > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail > >I > >> > got (our university is pushing these mails). > >> > > >> > >> I don't know; you could try it. Another option would be to configure > >your > >> mail client with a filter to drop the undesired bioc emails. > >> > >> Dan > >> > >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > >> > <lcollado@jhu.edu> wrote: > >> > > Hi Dan, > >> > > > >> > > I got RSwitch to work with a second installation of R 3.1. > >> > > Basically, > >> > > I downloaded the leopard tarball, expanded it, renamed the folder > >> > > 3.1 > >> > > to 3.1patched (which is the version I downloaded, but well, > >> > > anything > >> > > except for 3.1 would work), compressed it again, and then > >expanded > >> > > it > >> > > at the root location. > >> > > > >> > > So it would be something like this: > >> > > > >> > > wget > >> > > > >> > > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > >> > > tar -xvf R-*gz > >> > > mv Library/Frameworks/R.framework/Versions/3.1 > >> > > Library/Frameworks/R.framework/Versions/3.1patched > >> > > tar -cvzf Rlib.tgz Library > >> > > sudo tar fvxz Rlib.tgz -C / > >> > > > >> > > Then used RSwitch, and was able to install BioC-devel. > >> > > > >> > > I might try out your renv at a different time. It's great to > >know > >> > > that it exists =) > >> > > > >> > > Cheers, > >> > > Leo > >> > > > >> > > > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > >> > > <tengfei.yin@sbgenomics.com> wrote: > >> > >> Hi Dan, > >> > >> > >> > >> It works like a charm, thanks! > >> > >> > >> > >> I use your method, then I changed /Library/Framework/ folder and > >> > >> R.Framework > >> > >> folder ownership to myself so I don't have to sudo it, then I > >just > >> > >> add alias > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R first. > >> > >> This solves > >> > >> my problem. > >> > >> > >> > >> Try to customize variable for R hooks in emacs as alternative > >> > >> solution, but > >> > >> may need more time. > >> > >> > >> > >> Thanks again! > >> > >> > >> > >> Tengfei > >> > >> > >> > >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > >> > >> <dtenenba@fhcrc.org> wrote: > >> > >>> > >> > >>> Hi Tengfei, > >> > >>> > >> > >>> ----- Original Message ----- > >> > >>> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> > >>> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> > >> > >>> > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, > >> > >>> > lcollado@jhu.edu > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >> > >>> > is broken > >> > >>> > > >> > >>> > > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on > >the > >> > >>> > R 3.1? > >> > >>> > >> > >>> Yes, install two copies of R 3.1 and switch between them. > >> > >>> > >> > >>> > And do some sort of switch for bioc? The website you send to > >me > >> > >>> > also > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on > >R-devel > >> > >>> > and > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only > >to > >> > >>> > switch bioc, so that I could debug and maintain released and > >> > >>> > devel > >> > >>> > version. > >> > >>> > >> > >>> PLEASE don't use R-devel at all. > >> > >>> > >> > >>> Just use R-3.1.0. > >> > >>> > >> > >>> You can use the Rswitch app but as you point out it won't work > >> > >>> within > >> > >>> emacs. > >> > >>> > >> > >>> This is what I do: > >> > >>> > >> > >>> Every time I download a new version of R, I run its installer. > >> > >>> The > >> > >>> installer always puts it in > >> > >>> > >> > >>> /Library/Frameworks/R.framework > >> > >>> > >> > >>> So after I install each version of R, I rename the R.framework > >> > >>> directory > >> > >>> to something like > >> > >>> R.framework.bioc214_snowleopard > >> > >>> > >> > >>> And then I make a symlink from R.framework.bioc214_snowleopard > >to > >> > >>> R.framework. > >> > >>> > >> > >>> I have a little script at https://github.com/dtenenba/renv > >which > >> > >>> lets me > >> > >>> see what the various installed Rs are: > >> > >>> > >> > >>> renv > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >>> > >> > >>> This tells me that the currently active R is nicknamed > >> > >>> "releaseMav" (this > >> > >>> means there is a link from > >> > >>> /Library/Frameworks/R.framework.releaseMav to > >> > >>> /Library/Frameworks/R.framework. It shows the versions, svn > >> > >>> revisions, > >> > >>> dates, and architectures of each version. (darwin10.8.0 is Snow > >> > >>> Leopard; > >> > >>> darwin13.1.0 is Mavericks). > >> > >>> > >> > >>> Note that in my nomenclature devel means BioC devel, not > >R-devel. > >> > >>> > >> > >>> So if I wanted to switch to the "develSL" version I would do: > >> > >>> > >> > >>> sudo renv develSL > >> > >>> > >> > >>> HTH > >> > >>> Dan > >> > >>> > >> > >>> > >> > >>> > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >> > >>> > dtenenba@fhcrc.org > > >> > >>> > wrote: > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > Hi Tengfei, > >> > >>> > > >> > >>> > ----- Original Message ----- > >> > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >>> > > >> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> > >>> > > Cc: "Bioconductor mailing list" < > >bioconductor@r-project.org > >> > >>> > > >, > >> > >>> > > lcollado@jhu.edu > >> > >>> > > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >example > >> > >>> > > is > >> > >>> > > broken > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am > >still > >> > >>> > > a > >> > >>> > > newbie to OSX ... I got R-devel running and I will try > >> > >>> > > Rswitcher, I > >> > >>> > > also want to do that switch easily in emacs too. > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) and > >> > >>> > BioC > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released > >> > >>> > version of > >> > >>> > R. > >> > >>> > > >> > >>> > I think the Rswitch app just sets a symbolic link, so you > >> > >>> > should be > >> > >>> > able to do that within emacs. Run it and see what it does to > >> > >>> > /Library/Frameworks/R.framework. > >> > >>> > > >> > >>> > Dan > >> > >>> > > >> > >>> > > >> > >>> > > > >> > >>> > > cheers > >> > >>> > > > >> > >>> > > > >> > >>> > > Tengfei > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >> > >>> > > dtenenba@fhcrc.org > >> > >>> > > > > >> > >>> > > wrote: > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > ----- Original Message ----- > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >>> > > > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> > >>> > > > Cc: "Bioconductor mailing list" < > >> > >>> > > > bioconductor@r-project.org >, > >> > >>> > > > lcollado@jhu.edu > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >>> > > > example is > >> > >>> > > > broken > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > >> > >>> > > > Hi Dan, > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it > >should > >> > >>> > > > work? > >> > >>> > > > >> > >>> > > Yes. > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > ? Is > >> > >>> > > > there a way to build from source using biocLite, like > >type > >> > >>> > > > = > >> > >>> > > > "source", this is what I got > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > library(BiocInstaller) > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), > >?biocLite > >> > >>> > > > for > >> > >>> > > > help > >> > >>> > > > > biocLite("GenomicRanges") > >> > >>> > > > BioC_mirror: http://bioconductor.org > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R > >> > >>> > > > version > >> > >>> > > > 3.1.0. > >> > >>> > > > Installing package(s) 'GenomicRanges' > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > package âGenomicRangesâ is available as a source package > >> > >>> > > > but not > >> > >>> > > > as > >> > >>> > > > a > >> > >>> > > > binary > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Warning message: > >> > >>> > > > package âGenomicRangesâ is not available (for R version > >> > >>> > > > 3.1.0) > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Just wondering is there a solution without re-install R > >for > >> > >>> > > > snow > >> > >>> > > > leopard. And what's the plan for maverick? > >> > >>> > > > > >> > >>> > > > >> > >>> > > You can do > >> > >>> > > biocLite("GenomicRanges", type="source") > >> > >>> > > > >> > >>> > > but you need to have the appropriate compilers, etc. > >> > >>> > > > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You > >can > >> > >>> > > have > >> > >>> > > multiple installations of R on your Mac and switch between > >> > >>> > > them > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or > >another > >> > >>> > > easy > >> > >>> > > >> > >>> > > >> > >>> > > mechanism. > >> > >>> > > > >> > >>> > > We are building packages for Mavericks now, we just have to > >> > >>> > > resolve > >> > >>> > > a > >> > >>> > > few build issues and test the resulting packages, we still > >> > >>> > > hope to > >> > >>> > > have them available by the end of the month. But since you > >> > >>> > > can > >> > >>> > > install the Snow Leopard build without needing to remove > >your > >> > >>> > > Mavericks build, you should do that. > >> > >>> > > > >> > >>> > > Dan > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > > >> > >>> > > > Thanks > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Tengfei > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >> > >>> > > > dtenenba@fhcrc.org > >> > >>> > > > > wrote: > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Hi Tengfei, > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > ----- Original Message ----- > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >>> > > > > To: lcollado@jhu.edu > >> > >>> > > > > Cc: bioconductor@r-project.org > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >>> > > > > example > >> > >>> > > > > is > >> > >>> > > > > broken > >> > >>> > > > > > >> > >>> > > > > btw, based on the error, let me try to debug it. > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >> > >>> > > > > < tengfei.yin@sbgenomics.com >wrote: > >> > >>> > > > > > >> > >>> > > > > > Hi Leonardo, > >> > >>> > > > > > > >> > >>> > > > > > Frankly speaking, the vignette is still in progress, > >> > >>> > > > > > and > >> > >>> > > > > > there > >> > >>> > > > > > are > >> > >>> > > > > > some > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying to > >find > >> > >>> > > > > > a > >> > >>> > > > > > time > >> > >>> > > > > > to > >> > >>> > > > > > do that > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc > >> > >>> > > > > > 2.14 on > >> > >>> > > > > > my > >> > >>> > > > > > new MBP > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build is > >not > >> > >>> > > > > > ready > >> > >>> > > > > > for > >> > >>> > > > > > maverick > >> > >>> > > > > > yet, maybe available by the end of April? > >> > >>> > > > > > > >> > >>> > > > > > Thanks for reporting the bug, I will keep you posted > >on > >> > >>> > > > > > this > >> > >>> > > > > > when > >> > >>> > > > > > I > >> > >>> > > > > > successfully get it on my laptop and start fixing the > >> > >>> > > > > > problems. > >> > >>> > > > > > > >> > >>> > > > > >> > >>> > > > You can install the Snow Leopard build of R and should > >have > >> > >>> > > > no > >> > >>> > > > problems, binary packages are available for that version. > >> > >>> > > > It will > >> > >>> > > > run fine on Mavericks. > >> > >>> > > > > >> > >>> > > > Dan > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > > cheers > >> > >>> > > > > > > >> > >>> > > > > > Tengfei > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado > >> > >>> > > > > > Torres < > >> > >>> > > > > > lcollado@jhsph.edu > wrote: > >> > >>> > > > > > > >> > >>> > > > > >> Hello Tengfei + bioc list, > >> > >>> > > > > >> > >> > >>> > > > > >> From > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > >> > >>> > > > > >> page 4 (complied on april 11 2014), the following > >> > >>> > > > > >> example > >> > >>> > > > > >> loads > >> > >>> > > > > >> to > >> > >>> > > > > >> an > >> > >>> > > > > >> error as shown below. I wasn't seeing this error > >> > >>> > > > > >> before > >> > >>> > > > > >> (aka, > >> > >>> > > > > >> last > >> > >>> > > > > >> week). The only guess that comes to mind is the > >recent > >> > >>> > > > > >> update > >> > >>> > > > > >> to > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to > >> > >>> > > > > >> be > >> > >>> > > > > >> related > >> > >>> > > > > >> from > >> > >>> > > > > >> the traceback() output, well... maybe it's related > >to > >> > >>> > > > > >> the > >> > >>> > > > > >> ignore.strand = TRUE part as described in the error. > >> > >>> > > > > >> > >> > >>> > > > > >> I'll create a GitHub issue just for completeness. > >> > >>> > > > > >> > >> > >>> > > > > >> Thank you, > >> > >>> > > > > >> Leonardo > >> > >>> > > > > >> > >> > >>> > > > > >> > library(ggbio) > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary > >> > >>> > > > > >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> > >>> > > > > >> ## Removed the output > >> > >>> > > > > >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > >> > >>> > > > > >> > genesymbol["BRCA1"]) > >> > >>> > > > > >> Aggregating TranscriptDb... > >> > >>> > > > > >> Parsing transcripts... > >> > >>> > > > > >> Parsing exons... > >> > >>> > > > > >> Parsing cds... > >> > >>> > > > > >> Parsing utrs... > >> > >>> > > > > >> ------exons... > >> > >>> > > > > >> ------cdss... > >> > >>> > > > > >> ------introns... > >> > >>> > > > > >> ------utr... > >> > >>> > > > > >> aggregating... > >> > >>> > > > > >> Done > >> > >>> > > > > >> Constructing graphics... > >> > >>> > > > > >> Error in sapply(listData, function(Xi) > >> > >>> > > > > >> extends(class(Xi), > >> > >>> > > > > >> elementTypeX)) : > >> > >>> > > > > >> error in evaluating the argument 'X' in selecting a > >> > >>> > > > > >> method > >> > >>> > > > > >> for > >> > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, > >> > >>> > > > > >> ignore.strand > >> > >>> > > > > >> = > >> > >>> > > > > >> TRUE))) : > >> > >>> > > > > >> error in evaluating the argument 'x' in selecting a > >> > >>> > > > > >> method > >> > >>> > > > > >> for > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused > >> > >>> > > > > >> argument > >> > >>> > > > > >> (ignore.strand = TRUE) > >> > >>> > > > > >> > >> > >>> > > > > >> > traceback() > >> > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), > >> > >>> > > > > >> elementTypeX)) > >> > >>> > > > > >> 14: .updateCompressedList(X, > >lapply_CompressedList(X, > >> > >>> > > > > >> FUN, > >> > >>> > > > > >> ...)) > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >>> > > > > >> if (!group.selfish) { > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >>> > > > > >> TRUE))) > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >>> > > > > >> width(irs) + > >> > >>> > > > > >> extend.size) > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >>> > > > > >> group.name ])] > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >>> > > > > >> group.name ])) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> irs <- ranges(x) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >>> > > > > >> extend.size))) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> }) > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >>> > > > > >> if (!group.selfish) { > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >>> > > > > >> TRUE))) > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >>> > > > > >> width(irs) + > >> > >>> > > > > >> extend.size) > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >>> > > > > >> group.name ])] > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >>> > > > > >> group.name ])) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> irs <- ranges(x) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >>> > > > > >> extend.size))) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> }) > >> > >>> > > > > >> 11: .local(obj, ...) > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > >> > >>> > > > > >> group.selfish = > >> > >>> > > > > >> FALSE, > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", > >group.selfish > >> > >>> > > > > >> = > >> > >>> > > > > >> FALSE, > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >>> > > > > >> 8: .local(data, ...) > >> > >>> > > > > >> 7: (function (data, ...) > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> >> > >>> > > > > >> of > >> > >>> > > > > >> class > >> > >>> > > > > >> "TranscriptDb">, > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >>> > > > > >> "alignment", > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > >> > >>> > > > > >> TRUE, > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >>> > > > > >> 6: (function (data, ...) > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object=""> >> > >>> > > > > >> of > >> > >>> > > > > >> class > >> > >>> > > > > >> "TranscriptDb">, > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >>> > > > > >> "alignment", > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = > >> > >>> > > > > >> TRUE, > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) > >> > >>> > > > > >> 3: .local(object, ...) > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > sessionInfo() > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >>> > > > > >> > >> > >>> > > > > >> locale: > >> > >>> > > > > >> [1] > >> > >>> > > > > >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >>> > > > > >> > >> > >>> > > > > >> attached base packages: > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets > >> > >>> > > > > >> methods base > >> > >>> > > > > >> > >> > >>> > > > > >> other attached packages: > >> > >>> > > > > >> [1] XVector_0.4.0 > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> > >>> > > > > >> GenomicFeatures_1.16.0 > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> > >>> > > > > >> GenomicRanges_1.16.2 > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> > >>> > > > > >> ggbio_1.12.0 > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> > >>> > > > > >> > >> > >>> > > > > >> loaded via a namespace (and not attached): > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> > >>> > > > > >> Biostrings_2.32.0 > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > >> > >>> > > > > >> Formula_1.1-1 > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> > >>> > > > > >> Hmisc_3.14-4 > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >> > >>> > > > > >> stringr_0.6.2 > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> > >>> > > > > >> zlibbioc_1.10.0 > >> > >>> > > > > >> > > >> > >>> > > > > >> > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > -- > >> > >>> > > > > > Tengfei Yin, PhD > >> > >>> > > > > > Seven Bridges Genomics > >> > >>> > > > > > sbgenomics.com > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > > > Cambridge, MA 02138 > >> > >>> > > > > > (617) 866-0446 > >> > >>> > > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > -- > >> > >>> > > > > Tengfei Yin, PhD > >> > >>> > > > > Seven Bridges Genomics > >> > >>> > > > > sbgenomics.com > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > > Cambridge, MA 02138 > >> > >>> > > > > (617) 866-0446 > >> > >>> > > > > > >> > >>> > > > > [[alternative HTML version deleted]] > >> > >>> > > > > > >> > >>> > > > > _______________________________________________ > >> > >>> > > > > Bioconductor mailing list > >> > >>> > > > > Bioconductor@r-project.org > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >>> > > > > Search the archives: > >> > >>> > > > > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >>> > > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > -- > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Tengfei Yin, PhD > >> > >>> > > > Seven Bridges Genomics > >> > >>> > > > sbgenomics.com > >> > >>> > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > Cambridge, MA 02138 > >> > >>> > > > (617) 866- 0446 > >> > >>> > > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > -- > >> > >>> > > > >> > >>> > > > >> > >>> > > Tengfei Yin, PhD > >> > >>> > > Seven Bridges Genomics > >> > >>> > > sbgenomics.com > >> > >>> > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > Cambridge, MA 02138 > >> > >>> > > (617) 866- 0446 > >> > >>> > > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > -- > >> > >>> > > >> > >>> > > >> > >>> > Tengfei Yin, PhD > >> > >>> > Seven Bridges Genomics > >> > >>> > sbgenomics.com > >> > >>> > 625 Mt. Auburn St. Suite #208 > >> > >>> > Cambridge, MA 02138 > >> > >>> > (617) 866- 0446 > >> > >>> > > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> -- > >> > >> Tengfei Yin, PhD > >> > >> Seven Bridges Genomics > >> > >> sbgenomics.com > >> > >> 625 Mt. Auburn St. Suite #208 > >> > >> Cambridge, MA 02138 > >> > >> (617) 866-0446 > >> > > >> > > [[alternative HTML version deleted]]
0
Entering edit mode
right, it's failing to build and I am trying to figure out why now, because it passes check/build and works on my laptop, but it doesn't pass bioc build for both release and devel, let me dig into it tonight. thanks for your patience Tengfei On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Oh ok. Thanks for the info > > > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum <dtenenba@fhcrc.org>wrote: > >> >> >> Leonardo Collado Torres <lcollado@jhsph.edu> wrote: >> >Is there any reason why ggbio 1.12.2 hasn't made it to BioC release? >> >http://master.bioconductor.org/packages/release/bioc/html/ggbio.html >> >still >> >points to 1.12.0 >> > >> >> It's failing to build: >> >> >> http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> >> Dan >> >> > >> >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum <dtenenba@fhcrc.org> >> >wrote: >> > >> >> >> >> >> >> ----- Original Message ----- >> >> > From: "Leonardo Collado Torres" <lcollado@jhsph.edu> >> >> > To: "Tengfei Yin" <tengfei.yin@sbgenomics.com> >> >> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing >> >list" < >> >> bioconductor@r-project.org> >> >> > Sent: Wednesday, April 23, 2014 3:38:11 PM >> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >> >broken >> >> > >> >> > Dang it, forgot again to send with my @jhsph.edu account. See below >> >> > again >.< >> >> > >> >> > On the email topic, is it possible to be subscribed with 2 emails >> >> > accounts to the BioC mailing list but only get emails with one? I >> >> > believe that I have to choose to either get the daily digest or get >> >a >> >> > single for every message sent. If not, I'll probably just drop my >> >> > @jhsph.edu subscription and re-subscribe with the new @jhu.edu mail >> >I >> >> > got (our university is pushing these mails). >> >> > >> >> >> >> I don't know; you could try it. Another option would be to configure >> >your >> >> mail client with a filter to drop the undesired bioc emails. >> >> >> >> Dan >> >> >> >> >> >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres >> >> > <lcollado@jhu.edu> wrote: >> >> > > Hi Dan, >> >> > > >> >> > > I got RSwitch to work with a second installation of R 3.1. >> >> > > Basically, >> >> > > I downloaded the leopard tarball, expanded it, renamed the folder >> >> > > 3.1 >> >> > > to 3.1patched (which is the version I downloaded, but well, >> >> > > anything >> >> > > except for 3.1 would work), compressed it again, and then >> >expanded >> >> > > it >> >> > > at the root location. >> >> > > >> >> > > So it would be something like this: >> >> > > >> >> > > wget >> >> > > >> >> >> > >> http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz >> >> > > tar -xvf R-*gz >> >> > > mv Library/Frameworks/R.framework/Versions/3.1 >> >> > > Library/Frameworks/R.framework/Versions/3.1patched >> >> > > tar -cvzf Rlib.tgz Library >> >> > > sudo tar fvxz Rlib.tgz -C / >> >> > > >> >> > > Then used RSwitch, and was able to install BioC-devel. >> >> > > >> >> > > I might try out your renv at a different time. It's great to >> >know >> >> > > that it exists =) >> >> > > >> >> > > Cheers, >> >> > > Leo >> >> > > >> >> > > >> >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin >> >> > > <tengfei.yin@sbgenomics.com> wrote: >> >> > >> Hi Dan, >> >> > >> >> >> > >> It works like a charm, thanks! >> >> > >> >> >> > >> I use your method, then I changed /Library/Framework/ folder and >> >> > >> R.Framework >> >> > >> folder ownership to myself so I don't have to sudo it, then I >> >just >> >> > >> add alias >> >> > >> to "emacs2" and "emacs3" to run your renv to switch the R first. >> >> > >> This solves >> >> > >> my problem. >> >> > >> >> >> > >> Try to customize variable for R hooks in emacs as alternative >> >> > >> solution, but >> >> > >> may need more time. >> >> > >> >> >> > >> Thanks again! >> >> > >> >> >> > >> Tengfei >> >> > >> >> >> > >> >> >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum >> >> > >> <dtenenba@fhcrc.org> wrote: >> >> > >>> >> >> > >>> Hi Tengfei, >> >> > >>> >> >> > >>> ----- Original Message ----- >> >> > >>> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> >> >> > >>> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org> >> >> > >>> > Cc: "Bioconductor mailing list" <bioconductor@r-project.org>, >> >> > >>> > lcollado@jhu.edu >> >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >> >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >> >> > >>> > is broken >> >> > >>> > >> >> > >>> > >> >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on >> >the >> >> > >>> > R 3.1? >> >> > >>> >> >> > >>> Yes, install two copies of R 3.1 and switch between them. >> >> > >>> >> >> > >>> > And do some sort of switch for bioc? The website you send to >> >me >> >> > >>> > also >> >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on >> >R-devel >> >> > >>> > and >> >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R only >> >to >> >> > >>> > switch bioc, so that I could debug and maintain released and >> >> > >>> > devel >> >> > >>> > version. >> >> > >>> >> >> > >>> PLEASE don't use R-devel at all. >> >> > >>> >> >> > >>> Just use R-3.1.0. >> >> > >>> >> >> > >>> You can use the Rswitch app but as you point out it won't work >> >> > >>> within >> >> > >>> emacs. >> >> > >>> >> >> > >>> This is what I do: >> >> > >>> >> >> > >>> Every time I download a new version of R, I run its installer. >> >> > >>> The >> >> > >>> installer always puts it in >> >> > >>> >> >> > >>> /Library/Frameworks/R.framework >> >> > >>> >> >> > >>> So after I install each version of R, I rename the R.framework >> >> > >>> directory >> >> > >>> to something like >> >> > >>> R.framework.bioc214_snowleopard >> >> > >>> >> >> > >>> And then I make a symlink from R.framework.bioc214_snowleopard >> >to >> >> > >>> R.framework. >> >> > >>> >> >> > >>> I have a little script at https://github.com/dtenenba/renv >> >which >> >> > >>> lets me >> >> > >>> see what the various installed Rs are: >> >> > >>> >> >> > >>> $renv >> >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >> >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> > >>> >> >> > >>> This tells me that the currently active R is nicknamed >> >> > >>> "releaseMav" (this >> >> > >>> means there is a link from >> >> > >>> /Library/Frameworks/R.framework.releaseMav to >> >> > >>> /Library/Frameworks/R.framework. It shows the versions, svn >> >> > >>> revisions, >> >> > >>> dates, and architectures of each version. (darwin10.8.0 is Snow >> >> > >>> Leopard; >> >> > >>> darwin13.1.0 is Mavericks). >> >> > >>> >> >> > >>> Note that in my nomenclature devel means BioC devel, not >> >R-devel. >> >> > >>> >> >> > >>> So if I wanted to switch to the "develSL" version I would do: >> >> > >>> >> >> > >>> sudo renv develSL >> >> > >>> >> >> > >>> HTH >> >> > >>> Dan >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> > >> >> > >>> > >> >> > >>> > >> >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < >> >> > >>> > dtenenba@fhcrc.org > >> >> > >>> > wrote: >> >> > >>> > >> >> > >>> > >> >> > >>> > >> >> > >>> > Hi Tengfei, >> >> > >>> > >> >> > >>> > ----- Original Message ----- >> >> > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > >> >> > >>> > >> >> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > >> >> > >>> > > Cc: "Bioconductor mailing list" < >> >bioconductor@r-project.org >> >> > >>> > > >, >> >> > >>> > > lcollado@jhu.edu >> >> > >>> > >> >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM >> >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >example >> >> > >>> > > is >> >> > >>> > > broken >> >> > >>> > > >> >> > >>> > > >> >> > >>> > >> >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am >> >still >> >> > >>> > > a >> >> > >>> > > newbie to OSX ... I got R-devel running and I will try >> >> > >>> > > Rswitcher, I >> >> > >>> > > also want to do that switch easily in emacs too. >> >> > >>> > > >> >> > >>> > > >> >> > >>> > >> >> > >>> > You don't want to use R-devel. Both BioC release (2.14) and >> >> > >>> > BioC >> >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released >> >> > >>> > version of >> >> > >>> > R. >> >> > >>> > >> >> > >>> > I think the Rswitch app just sets a symbolic link, so you >> >> > >>> > should be >> >> > >>> > able to do that within emacs. Run it and see what it does to >> >> > >>> > /Library/Frameworks/R.framework. >> >> > >>> > >> >> > >>> > Dan >> >> > >>> > >> >> > >>> > >> >> > >>> > > >> >> > >>> > > cheers >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > Tengfei >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > >> >> > >>> > >> >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < >> >> > >>> > > dtenenba@fhcrc.org >> >> > >>> > > > >> >> > >>> > > wrote: >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > ----- Original Message ----- >> >> > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > >> >> > >>> > > >> >> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > >> >> > >>> > > > Cc: "Bioconductor mailing list" < >> >> > >>> > > > bioconductor@r-project.org >, >> >> > >>> > > > lcollado@jhu.edu >> >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM >> >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >> > >>> > > > example is >> >> > >>> > > > broken >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > >> >> > >>> > > > Hi Dan, >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > So you mean I install R 3.1 for snow leopard and it >> >should >> >> > >>> > > > work? >> >> > >>> > > >> >> > >>> > > Yes. >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > ? Is >> >> > >>> > > > there a way to build from source using biocLite, like >> >type >> >> > >>> > > > = >> >> > >>> > > > "source", this is what I got >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > > library(BiocInstaller) >> >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), >> >?biocLite >> >> > >>> > > > for >> >> > >>> > > > help >> >> > >>> > > > > biocLite("GenomicRanges") >> >> > >>> > > > BioC_mirror: http://bioconductor.org >> >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R >> >> > >>> > > > version >> >> > >>> > > > 3.1.0. >> >> > >>> > > > Installing package(s) 'GenomicRanges' >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > package âGenomicRangesâ is available as a source package >> >> > >>> > > > but not >> >> > >>> > > > as >> >> > >>> > > > a >> >> > >>> > > > binary >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > Warning message: >> >> > >>> > > > package âGenomicRangesâ is not available (for R version >> >> > >>> > > > 3.1.0) >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > Just wondering is there a solution without re- install R >> >for >> >> > >>> > > > snow >> >> > >>> > > > leopard. And what's the plan for maverick? >> >> > >>> > > > >> >> > >>> > > >> >> > >>> > > You can do >> >> > >>> > > biocLite("GenomicRanges", type="source") >> >> > >>> > > >> >> > >>> > > but you need to have the appropriate compilers, etc. >> >> > >>> > > >> >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You >> >can >> >> > >>> > > have >> >> > >>> > > multiple installations of R on your Mac and switch between >> >> > >>> > > them >> >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or >> >another >> >> > >>> > > easy >> >> > >>> > >> >> > >>> > >> >> > >>> > > mechanism. >> >> > >>> > > >> >> > >>> > > We are building packages for Mavericks now, we just have to >> >> > >>> > > resolve >> >> > >>> > > a >> >> > >>> > > few build issues and test the resulting packages, we still >> >> > >>> > > hope to >> >> > >>> > > have them available by the end of the month. But since you >> >> > >>> > > can >> >> > >>> > > install the Snow Leopard build without needing to remove >> >your >> >> > >>> > > Mavericks build, you should do that. >> >> > >>> > > >> >> > >>> > > Dan >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > > >> >> > >>> > > > Thanks >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > Tengfei >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < >> >> > >>> > > > dtenenba@fhcrc.org >> >> > >>> > > > > wrote: >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > Hi Tengfei, >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > ----- Original Message ----- >> >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > >> >> > >>> > > > > To: lcollado@jhu.edu >> >> > >>> > > > > Cc: bioconductor@r-project.org >> >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM >> >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >> > >>> > > > > example >> >> > >>> > > > > is >> >> > >>> > > > > broken >> >> > >>> > > > > >> >> > >>> > > > > btw, based on the error, let me try to debug it. >> >> > >>> > > > > >> >> > >>> > > > > >> >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin >> >> > >>> > > > > < tengfei.yin@sbgenomics.com >wrote: >> >> > >>> > > > > >> >> > >>> > > > > > Hi Leonardo, >> >> > >>> > > > > > >> >> > >>> > > > > > Frankly speaking, the vignette is still in progress, >> >> > >>> > > > > > and >> >> > >>> > > > > > there >> >> > >>> > > > > > are >> >> > >>> > > > > > some >> >> > >>> > > > > > known bugs in ggbio I need to fix (still trying to >> >find >> >> > >>> > > > > > a >> >> > >>> > > > > > time >> >> > >>> > > > > > to >> >> > >>> > > > > > do that >> >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and Bioc >> >> > >>> > > > > > 2.14 on >> >> > >>> > > > > > my >> >> > >>> > > > > > new MBP >> >> > >>> > > > > > with OSX 10.9, but fails, probably binary build is >> >not >> >> > >>> > > > > > ready >> >> > >>> > > > > > for >> >> > >>> > > > > > maverick >> >> > >>> > > > > > yet, maybe available by the end of April? >> >> > >>> > > > > > >> >> > >>> > > > > > Thanks for reporting the bug, I will keep you posted >> >on >> >> > >>> > > > > > this >> >> > >>> > > > > > when >> >> > >>> > > > > > I >> >> > >>> > > > > > successfully get it on my laptop and start fixing the >> >> > >>> > > > > > problems. >> >> > >>> > > > > > >> >> > >>> > > > >> >> > >>> > > > You can install the Snow Leopard build of R and should >> >have >> >> > >>> > > > no >> >> > >>> > > > problems, binary packages are available for that version. >> >> > >>> > > > It will >> >> > >>> > > > run fine on Mavericks. >> >> > >>> > > > >> >> > >>> > > > Dan >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > > > cheers >> >> > >>> > > > > > >> >> > >>> > > > > > Tengfei >> >> > >>> > > > > > >> >> > >>> > > > > > >> >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado >> >> > >>> > > > > > Torres < >> >> > >>> > > > > > lcollado@jhsph.edu > wrote: >> >> > >>> > > > > > >> >> > >>> > > > > >> Hello Tengfei + bioc list, >> >> > >>> > > > > >> >> >> > >>> > > > > >> From >> >> > >>> > > > > >> >> >> > >>> > > > > >> >> >> >> > >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf >> >> > >>> > > > > >> page 4 (complied on april 11 2014), the following >> >> > >>> > > > > >> example >> >> > >>> > > > > >> loads >> >> > >>> > > > > >> to >> >> > >>> > > > > >> an >> >> > >>> > > > > >> error as shown below. I wasn't seeing this error >> >> > >>> > > > > >> before >> >> > >>> > > > > >> (aka, >> >> > >>> > > > > >> last >> >> > >>> > > > > >> week). The only guess that comes to mind is the >> >recent >> >> > >>> > > > > >> update >> >> > >>> > > > > >> to >> >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem to >> >> > >>> > > > > >> be >> >> > >>> > > > > >> related >> >> > >>> > > > > >> from >> >> > >>> > > > > >> the traceback() output, well... maybe it's related >> >to >> >> > >>> > > > > >> the >> >> > >>> > > > > >> ignore.strand = TRUE part as described in the error. >> >> > >>> > > > > >> >> >> > >>> > > > > >> I'll create a GitHub issue just for completeness. >> >> > >>> > > > > >> >> >> > >>> > > > > >> Thank you, >> >> > >>> > > > > >> Leonardo >> >> > >>> > > > > >> >> >> > >>> > > > > >> > library(ggbio) >> >> > >>> > > > > >> ## Removed the output, nothing out of ordinary >> >> > >>> > > > > >> >> >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> >> > >>> > > > > >> ## Removed the output >> >> > >>> > > > > >> >> >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") >> >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = >> >> > >>> > > > > >> > genesymbol["BRCA1"]) >> >> > >>> > > > > >> Aggregating TranscriptDb... >> >> > >>> > > > > >> Parsing transcripts... >> >> > >>> > > > > >> Parsing exons... >> >> > >>> > > > > >> Parsing cds... >> >> > >>> > > > > >> Parsing utrs... >> >> > >>> > > > > >> ------exons... >> >> > >>> > > > > >> ------cdss... >> >> > >>> > > > > >> ------introns... >> >> > >>> > > > > >> ------utr... >> >> > >>> > > > > >> aggregating... >> >> > >>> > > > > >> Done >> >> > >>> > > > > >> Constructing graphics... >> >> > >>> > > > > >> Error in sapply(listData, function(Xi) >> >> > >>> > > > > >> extends(class(Xi), >> >> > >>> > > > > >> elementTypeX)) : >> >> > >>> > > > > >> error in evaluating the argument 'X' in selecting a >> >> > >>> > > > > >> method >> >> > >>> > > > > >> for >> >> > >>> > > > > >> function 'sapply': Error in unlist(range(ranges(x.n, >> >> > >>> > > > > >> ignore.strand >> >> > >>> > > > > >> = >> >> > >>> > > > > >> TRUE))) : >> >> > >>> > > > > >> error in evaluating the argument 'x' in selecting a >> >> > >>> > > > > >> method >> >> > >>> > > > > >> for >> >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : unused >> >> > >>> > > > > >> argument >> >> > >>> > > > > >> (ignore.strand = TRUE) >> >> > >>> > > > > >> >> >> > >>> > > > > >> > traceback() >> >> > >>> > > > > >> 15: sapply(listData, function(Xi) extends(class(Xi), >> >> > >>> > > > > >> elementTypeX)) >> >> > >>> > > > > >> 14: .updateCompressedList(X, >> >lapply_CompressedList(X, >> >> > >>> > > > > >> FUN, >> >> > >>> > > > > >> ...)) >> >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { >> >> > >>> > > > > >> if (!is.null( group.name )) { >> >> > >>> > > > > >> if (!group.selfish) { >> >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> >> > >>> > > > > >> TRUE))) >> >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> >> > >>> > > > > >> width(irs) + >> >> > >>> > > > > >> extend.size) >> >> > >>> > > > > >> irs.new <- sort(irs.new) >> >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> >> > >>> > > > > >> values(x)$stepping <- >> >> > >>> > > > > >> .lvs[as.character(values(x)[, >> >> > >>> > > > > >> group.name ])] >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> else { >> >> > >>> > > > > >> values(x)$stepping <- >> >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> >> > >>> > > > > >> group.name ])) >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> } >> >> > >>> > > > > >> else { >> >> > >>> > > > > >> irs <- ranges(x) >> >> > >>> > > > > >> values(x)$stepping <- >> >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> >> > >>> > > > > >> fix = "center", width = width(irs) + >> >> > >>> > > > > >> extend.size))) >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> }) >> >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { >> >> > >>> > > > > >> if (!is.null( group.name )) { >> >> > >>> > > > > >> if (!group.selfish) { >> >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> >> > >>> > > > > >> TRUE))) >> >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> >> > >>> > > > > >> width(irs) + >> >> > >>> > > > > >> extend.size) >> >> > >>> > > > > >> irs.new <- sort(irs.new) >> >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> >> > >>> > > > > >> values(x)$stepping <- >> >> > >>> > > > > >> .lvs[as.character(values(x)[, >> >> > >>> > > > > >> group.name ])] >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> else { >> >> > >>> > > > > >> values(x)$stepping <- >> >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> >> > >>> > > > > >> group.name ])) >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> } >> >> > >>> > > > > >> else { >> >> > >>> > > > > >> irs <- ranges(x) >> >> > >>> > > > > >> values(x)stepping <- >> >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> >> > >>> > > > > >> fix = "center", width = width(irs) + >> >> > >>> > > > > >> extend.size))) >> >> > >>> > > > > >> x >> >> > >>> > > > > >> } >> >> > >>> > > > > >> }) >> >> > >>> > > > > >> 11: .local(obj, ...) >> >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", >> >> > >>> > > > > >> group.selfish = >> >> > >>> > > > > >> FALSE, >> >> > >>> > > > > >> fix = "start", extend.size = es) >> >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", >> >group.selfish >> >> > >>> > > > > >> = >> >> > >>> > > > > >> FALSE, >> >> > >>> > > > > >> fix = "start", extend.size = es) >> >> > >>> > > > > >> 8: .local(data, ...) >> >> > >>> > > > > >> 7: (function (data, ...) >> >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="">> >> > >>> > > > > >> of >> >> > >>> > > > > >> class >> >> > >>> > > > > >> "TranscriptDb">, >> >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> >> > >>> > > > > >> "alignment", >> >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = >> >> > >>> > > > > >> TRUE, >> >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> >> > >>> > > > > >> 6: (function (data, ...) >> >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4 object="">> >> > >>> > > > > >> of >> >> > >>> > > > > >> class >> >> > >>> > > > > >> "TranscriptDb">, >> >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> >> > >>> > > > > >> "alignment", >> >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label = >> >> > >>> > > > > >> TRUE, >> >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) >> >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) >> >> > >>> > > > > >> 3: .local(object, ...) >> >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> > >>> > > > > >> >> >> > >>> > > > > >> >> >> > >>> > > > > >> > sessionInfo() >> >> > >>> > > > > >> R version 3.1.0 (2014-04-10) >> >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> > >>> > > > > >> >> >> > >>> > > > > >> locale: >> >> > >>> > > > > >> [1] >> >> > >>> > > > > >> >> >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> > >>> > > > > >> >> >> > >>> > > > > >> attached base packages: >> >> > >>> > > > > >> [1] parallel stats graphics grDevices utils datasets >> >> > >>> > > > > >> methods base >> >> > >>> > > > > >> >> >> > >>> > > > > >> other attached packages: >> >> > >>> > > > > >> [1] XVector_0.4.0 >> >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> >> > >>> > > > > >> GenomicFeatures_1.16.0 >> >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> >> > >>> > > > > >> GenomicRanges_1.16.2 >> >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> >> > >>> > > > > >> ggbio_1.12.0 >> >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> >> > >>> > > > > >> >> >> > >>> > > > > >> loaded via a namespace (and not attached): >> >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 >> >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 >> >> > >>> > > > > >> Biostrings_2.32.0 >> >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 >> >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 >> >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 >> >> > >>> > > > > >> Formula_1.1-1 >> >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 >> >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 >> >> > >>> > > > > >> Hmisc_3.14-4 >> >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 >> >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31 >> >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 >> >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 >> >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 >> >> > >>> > > > > >> stringr_0.6.2 >> >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 >> >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 >> >> > >>> > > > > >> zlibbioc_1.10.0 >> >> > >>> > > > > >> > >> >> > >>> > > > > >> >> >> > >>> > > > > > >> >> > >>> > > > > > >> >> > >>> > > > > > >> >> > >>> > > > > > -- >> >> > >>> > > > > > Tengfei Yin, PhD >> >> > >>> > > > > > Seven Bridges Genomics >> >> > >>> > > > > > sbgenomics.com >> >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 >> >> > >>> > > > > > Cambridge, MA 02138 >> >> > >>> > > > > > (617) 866-0446 >> >> > >>> > > > > > >> >> > >>> > > > > >> >> > >>> > > > > >> >> > >>> > > > > >> >> > >>> > > > > -- >> >> > >>> > > > > Tengfei Yin, PhD >> >> > >>> > > > > Seven Bridges Genomics >> >> > >>> > > > > sbgenomics.com >> >> > >>> > > > > 625 Mt. Auburn St. Suite #208 >> >> > >>> > > > > Cambridge, MA 02138 >> >> > >>> > > > > (617) 866-0446 >> >> > >>> > > > > >> >> > >>> > > > > [[alternative HTML version deleted]] >> >> > >>> > > > > >> >> > >>> > > > > _______________________________________________ >> >> > >>> > > > > Bioconductor mailing list >> >> > >>> > > > > Bioconductor@r-project.org >> >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > >>> > > > > Search the archives: >> >> > >>> > > > > >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >>> > > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > -- >> >> > >>> > > > >> >> > >>> > > > >> >> > >>> > > > Tengfei Yin, PhD >> >> > >>> > > > Seven Bridges Genomics >> >> > >>> > > > sbgenomics.com >> >> > >>> > > > 625 Mt. Auburn St. Suite #208 >> >> > >>> > > > Cambridge, MA 02138 >> >> > >>> > > > (617) 866- 0446 >> >> > >>> > > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > -- >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > Tengfei Yin, PhD >> >> > >>> > > Seven Bridges Genomics >> >> > >>> > > sbgenomics.com >> >> > >>> > > 625 Mt. Auburn St. Suite #208 >> >> > >>> > > Cambridge, MA 02138 >> >> > >>> > > (617) 866- 0446 >> >> > >>> > > >> >> > >>> > >> >> > >>> > >> >> > >>> > >> >> > >>> > >> >> > >>> > -- >> >> > >>> > >> >> > >>> > >> >> > >>> > Tengfei Yin, PhD >> >> > >>> > Seven Bridges Genomics >> >> > >>> > sbgenomics.com >> >> > >>> > 625 Mt. Auburn St. Suite #208 >> >> > >>> > Cambridge, MA 02138 >> >> > >>> > (617) 866- 0446 >> >> > >>> > >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> -- >> >> > >> Tengfei Yin, PhD >> >> > >> Seven Bridges Genomics >> >> > >> sbgenomics.com >> >> > >> 625 Mt. Auburn St. Suite #208 >> >> > >> Cambridge, MA 02138 >> >> > >> (617) 866-0446 >> >> > >> >> >> >> > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]] ADD REPLY 0 Entering edit mode ----- Original Message ----- > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > To: lcollado at jhu.edu > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Saturday, April 26, 2014 1:58:01 PM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > right, it's failing to build and I am trying to figure out why now, > because it passes check/build and works on my laptop, but it doesn't > pass bioc build for both release and devel, let me dig into it > tonight. > Seems like this could be fixed if you just add library(ggbio) to your vignette before the ggbio() function is called on line 557 of vignettes/realvignettes/ggbio.Rnw. Dan > > thanks for your patience > > > Tengfei > > > > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < > lcollado at jhsph.edu > wrote: > > > > Oh ok. Thanks for the info > > > > > > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < dtenenba at fhcrc.org > > wrote: > > > > > > Leonardo Collado Torres < lcollado at jhsph.edu > wrote: > > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC release? > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html > >still > >points to 1.12.0 > > > > It's failing to build: > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > > > > Dan > > > > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < dtenenba at fhcrc.org > >> > >wrote: > > > >> > >> > >> ----- Original Message ----- > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu > > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor > >> > mailing > >list" < > >> bioconductor at r-project.org > > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > >broken > >> > > >> > Dang it, forgot again to send with my @ jhsph.edu account. See > >> > below > >> > again >.< > >> > > >> > On the email topic, is it possible to be subscribed with 2 > >> > emails > >> > accounts to the BioC mailing list but only get emails with one? > >> > I > >> > believe that I have to choose to either get the daily digest or > >> > get > >a > >> > single for every message sent. If not, I'll probably just drop > >> > my > >> > @ jhsph.edu subscription and re-subscribe with the new @ jhu.edu > >> > mail > >I > >> > got (our university is pushing these mails). > >> > > >> > >> I don't know; you could try it. Another option would be to > >> configure > >your > >> mail client with a filter to drop the undesired bioc emails. > >> > >> Dan > >> > >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > >> > < lcollado at jhu.edu > wrote: > >> > > Hi Dan, > >> > > > >> > > I got RSwitch to work with a second installation of R 3.1. > >> > > Basically, > >> > > I downloaded the leopard tarball, expanded it, renamed the > >> > > folder > >> > > 3.1 > >> > > to 3.1patched (which is the version I downloaded, but well, > >> > > anything > >> > > except for 3.1 would work), compressed it again, and then > >expanded > >> > > it > >> > > at the root location. > >> > > > >> > > So it would be something like this: > >> > > > >> > > wget > >> > > > >> > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > >> > > tar -xvf R-*gz > >> > > mv Library/Frameworks/R.framework/Versions/3.1 > >> > > Library/Frameworks/R.framework/Versions/3.1patched > >> > > tar -cvzf Rlib.tgz Library > >> > > sudo tar fvxz Rlib.tgz -C / > >> > > > >> > > Then used RSwitch, and was able to install BioC-devel. > >> > > > >> > > I might try out your renv at a different time. It's great to > >know > >> > > that it exists =) > >> > > > >> > > Cheers, > >> > > Leo > >> > > > >> > > > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > >> > > < tengfei.yin at sbgenomics.com > wrote: > >> > >> Hi Dan, > >> > >> > >> > >> It works like a charm, thanks! > >> > >> > >> > >> I use your method, then I changed /Library/Framework/ folder > >> > >> and > >> > >> R.Framework > >> > >> folder ownership to myself so I don't have to sudo it, then I > >just > >> > >> add alias > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R > >> > >> first. > >> > >> This solves > >> > >> my problem. > >> > >> > >> > >> Try to customize variable for R hooks in emacs as alternative > >> > >> solution, but > >> > >> may need more time. > >> > >> > >> > >> Thanks again! > >> > >> > >> > >> Tengfei > >> > >> > >> > >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > >> > >> < dtenenba at fhcrc.org > wrote: > >> > >>> > >> > >>> Hi Tengfei, > >> > >>> > >> > >>> ----- Original Message ----- > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >> > >>> > Cc: "Bioconductor mailing list" < > >> > >>> > bioconductor at r-project.org >, > >> > >>> > lcollado at jhu.edu > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >>> > example > >> > >>> > is broken > >> > >>> > > >> > >>> > > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on > >the > >> > >>> > R 3.1? > >> > >>> > >> > >>> Yes, install two copies of R 3.1 and switch between them. > >> > >>> > >> > >>> > And do some sort of switch for bioc? The website you send > >> > >>> > to > >me > >> > >>> > also > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on > >R-devel > >> > >>> > and > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R > >> > >>> > only > >to > >> > >>> > switch bioc, so that I could debug and maintain released > >> > >>> > and > >> > >>> > devel > >> > >>> > version. > >> > >>> > >> > >>> PLEASE don't use R-devel at all. > >> > >>> > >> > >>> Just use R-3.1.0. > >> > >>> > >> > >>> You can use the Rswitch app but as you point out it won't > >> > >>> work > >> > >>> within > >> > >>> emacs. > >> > >>> > >> > >>> This is what I do: > >> > >>> > >> > >>> Every time I download a new version of R, I run its > >> > >>> installer. > >> > >>> The > >> > >>> installer always puts it in > >> > >>> > >> > >>> /Library/Frameworks/R.framework > >> > >>> > >> > >>> So after I install each version of R, I rename the > >> > >>> R.framework > >> > >>> directory > >> > >>> to something like > >> > >>> R.framework.bioc214_snowleopard > >> > >>> > >> > >>> And then I make a symlink from > >> > >>> R.framework.bioc214_snowleopard > >to > >> > >>> R.framework. > >> > >>> > >> > >>> I have a little script at https://github.com/dtenenba/renv > >which > >> > >>> lets me > >> > >>> see what the various installed Rs are: > >> > >>> > >> > >>> renv > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >>> > >> > >>> This tells me that the currently active R is nicknamed > >> > >>> "releaseMav" (this > >> > >>> means there is a link from > >> > >>> /Library/Frameworks/R.framework.releaseMav to > >> > >>> /Library/Frameworks/R.framework. It shows the versions, svn > >> > >>> revisions, > >> > >>> dates, and architectures of each version. (darwin10.8.0 is > >> > >>> Snow > >> > >>> Leopard; > >> > >>> darwin13.1.0 is Mavericks). > >> > >>> > >> > >>> Note that in my nomenclature devel means BioC devel, not > >R-devel. > >> > >>> > >> > >>> So if I wanted to switch to the "develSL" version I would > >> > >>> do: > >> > >>> > >> > >>> sudo renv develSL > >> > >>> > >> > >>> HTH > >> > >>> Dan > >> > >>> > >> > >>> > >> > >>> > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >> > >>> > dtenenba at fhcrc.org > > >> > >>> > wrote: > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > Hi Tengfei, > >> > >>> > > >> > >>> > ----- Original Message ----- > >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > >>> > > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >> > >>> > > Cc: "Bioconductor mailing list" < > > bioconductor at r-project.org > >> > >>> > > >, > >> > >>> > > lcollado at jhu.edu > >> > >>> > > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >example > >> > >>> > > is > >> > >>> > > broken > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I am > >still > >> > >>> > > a > >> > >>> > > newbie to OSX ... I got R-devel running and I will try > >> > >>> > > Rswitcher, I > >> > >>> > > also want to do that switch easily in emacs too. > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) > >> > >>> > and > >> > >>> > BioC > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released > >> > >>> > version of > >> > >>> > R. > >> > >>> > > >> > >>> > I think the Rswitch app just sets a symbolic link, so you > >> > >>> > should be > >> > >>> > able to do that within emacs. Run it and see what it does > >> > >>> > to > >> > >>> > /Library/Frameworks/R.framework. > >> > >>> > > >> > >>> > Dan > >> > >>> > > >> > >>> > > >> > >>> > > > >> > >>> > > cheers > >> > >>> > > > >> > >>> > > > >> > >>> > > Tengfei > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > >> > >>> > > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >> > >>> > > dtenenba at fhcrc.org > >> > >>> > > > > >> > >>> > > wrote: > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > ----- Original Message ----- > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > >>> > > > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > >> > >>> > > > Cc: "Bioconductor mailing list" < > >> > >>> > > > bioconductor at r-project.org >, > >> > >>> > > > lcollado at jhu.edu > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >>> > > > example is > >> > >>> > > > broken > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > >> > >>> > > > Hi Dan, > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it > >should > >> > >>> > > > work? > >> > >>> > > > >> > >>> > > Yes. > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > ? Is > >> > >>> > > > there a way to build from source using biocLite, like > >type > >> > >>> > > > = > >> > >>> > > > "source", this is what I got > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > library(BiocInstaller) > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), > >?biocLite > >> > >>> > > > for > >> > >>> > > > help > >> > >>> > > > > biocLite("GenomicRanges") > >> > >>> > > > BioC_mirror: http://bioconductor.org > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller > >> > >>> > > > 1.14.1), R > >> > >>> > > > version > >> > >>> > > > 3.1.0. > >> > >>> > > > Installing package(s) 'GenomicRanges' > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > package ?GenomicRanges? is available as a source > >> > >>> > > > package > >> > >>> > > > but not > >> > >>> > > > as > >> > >>> > > > a > >> > >>> > > > binary > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Warning message: > >> > >>> > > > package ?GenomicRanges? is not available (for R > >> > >>> > > > version > >> > >>> > > > 3.1.0) > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Just wondering is there a solution without re-install > >> > >>> > > > R > >for > >> > >>> > > > snow > >> > >>> > > > leopard. And what's the plan for maverick? > >> > >>> > > > > >> > >>> > > > >> > >>> > > You can do > >> > >>> > > biocLite("GenomicRanges", type="source") > >> > >>> > > > >> > >>> > > but you need to have the appropriate compilers, etc. > >> > >>> > > > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. You > >can > >> > >>> > > have > >> > >>> > > multiple installations of R on your Mac and switch > >> > >>> > > between > >> > >>> > > them > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or > >another > >> > >>> > > easy > >> > >>> > > >> > >>> > > >> > >>> > > mechanism. > >> > >>> > > > >> > >>> > > We are building packages for Mavericks now, we just have > >> > >>> > > to > >> > >>> > > resolve > >> > >>> > > a > >> > >>> > > few build issues and test the resulting packages, we > >> > >>> > > still > >> > >>> > > hope to > >> > >>> > > have them available by the end of the month. But since > >> > >>> > > you > >> > >>> > > can > >> > >>> > > install the Snow Leopard build without needing to remove > >your > >> > >>> > > Mavericks build, you should do that. > >> > >>> > > > >> > >>> > > Dan > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > > >> > >>> > > > Thanks > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Tengfei > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >> > >>> > > > dtenenba at fhcrc.org > >> > >>> > > > > wrote: > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Hi Tengfei, > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > ----- Original Message ----- > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > >> > >>> > > > > To: lcollado at jhu.edu > >> > >>> > > > > Cc: bioconductor at r-project.org > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > >> > >>> > > > > txdb > >> > >>> > > > > example > >> > >>> > > > > is > >> > >>> > > > > broken > >> > >>> > > > > > >> > >>> > > > > btw, based on the error, let me try to debug it. > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: > >> > >>> > > > > > >> > >>> > > > > > Hi Leonardo, > >> > >>> > > > > > > >> > >>> > > > > > Frankly speaking, the vignette is still in > >> > >>> > > > > > progress, > >> > >>> > > > > > and > >> > >>> > > > > > there > >> > >>> > > > > > are > >> > >>> > > > > > some > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying to > >find > >> > >>> > > > > > a > >> > >>> > > > > > time > >> > >>> > > > > > to > >> > >>> > > > > > do that > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and > >> > >>> > > > > > Bioc > >> > >>> > > > > > 2.14 on > >> > >>> > > > > > my > >> > >>> > > > > > new MBP > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build is > >not > >> > >>> > > > > > ready > >> > >>> > > > > > for > >> > >>> > > > > > maverick > >> > >>> > > > > > yet, maybe available by the end of April? > >> > >>> > > > > > > >> > >>> > > > > > Thanks for reporting the bug, I will keep you > >> > >>> > > > > > posted > >on > >> > >>> > > > > > this > >> > >>> > > > > > when > >> > >>> > > > > > I > >> > >>> > > > > > successfully get it on my laptop and start fixing > >> > >>> > > > > > the > >> > >>> > > > > > problems. > >> > >>> > > > > > > >> > >>> > > > > >> > >>> > > > You can install the Snow Leopard build of R and should > >have > >> > >>> > > > no > >> > >>> > > > problems, binary packages are available for that > >> > >>> > > > version. > >> > >>> > > > It will > >> > >>> > > > run fine on Mavericks. > >> > >>> > > > > >> > >>> > > > Dan > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > > cheers > >> > >>> > > > > > > >> > >>> > > > > > Tengfei > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado > >> > >>> > > > > > Torres < > >> > >>> > > > > > lcollado at jhsph.edu > wrote: > >> > >>> > > > > > > >> > >>> > > > > >> Hello Tengfei + bioc list, > >> > >>> > > > > >> > >> > >>> > > > > >> From > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf > >> > >>> > > > > >> page 4 (complied on april 11 2014), the following > >> > >>> > > > > >> example > >> > >>> > > > > >> loads > >> > >>> > > > > >> to > >> > >>> > > > > >> an > >> > >>> > > > > >> error as shown below. I wasn't seeing this error > >> > >>> > > > > >> before > >> > >>> > > > > >> (aka, > >> > >>> > > > > >> last > >> > >>> > > > > >> week). The only guess that comes to mind is the > >recent > >> > >>> > > > > >> update > >> > >>> > > > > >> to > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't seem > >> > >>> > > > > >> to > >> > >>> > > > > >> be > >> > >>> > > > > >> related > >> > >>> > > > > >> from > >> > >>> > > > > >> the traceback() output, well... maybe it's > >> > >>> > > > > >> related > >to > >> > >>> > > > > >> the > >> > >>> > > > > >> ignore.strand = TRUE part as described in the > >> > >>> > > > > >> error. > >> > >>> > > > > >> > >> > >>> > > > > >> I'll create a GitHub issue just for completeness. > >> > >>> > > > > >> > >> > >>> > > > > >> Thank you, > >> > >>> > > > > >> Leonardo > >> > >>> > > > > >> > >> > >>> > > > > >> > library(ggbio) > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary > >> > >>> > > > > >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> > >>> > > > > >> ## Removed the output > >> > >>> > > > > >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > >> > >>> > > > > >> > genesymbol["BRCA1"]) > >> > >>> > > > > >> Aggregating TranscriptDb... > >> > >>> > > > > >> Parsing transcripts... > >> > >>> > > > > >> Parsing exons... > >> > >>> > > > > >> Parsing cds... > >> > >>> > > > > >> Parsing utrs... > >> > >>> > > > > >> ------exons... > >> > >>> > > > > >> ------cdss... > >> > >>> > > > > >> ------introns... > >> > >>> > > > > >> ------utr... > >> > >>> > > > > >> aggregating... > >> > >>> > > > > >> Done > >> > >>> > > > > >> Constructing graphics... > >> > >>> > > > > >> Error in sapply(listData, function(Xi) > >> > >>> > > > > >> extends(class(Xi), > >> > >>> > > > > >> elementTypeX)) : > >> > >>> > > > > >> error in evaluating the argument 'X' in selecting > >> > >>> > > > > >> a > >> > >>> > > > > >> method > >> > >>> > > > > >> for > >> > >>> > > > > >> function 'sapply': Error in > >> > >>> > > > > >> unlist(range(ranges(x.n, > >> > >>> > > > > >> ignore.strand > >> > >>> > > > > >> = > >> > >>> > > > > >> TRUE))) : > >> > >>> > > > > >> error in evaluating the argument 'x' in selecting > >> > >>> > > > > >> a > >> > >>> > > > > >> method > >> > >>> > > > > >> for > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : > >> > >>> > > > > >> unused > >> > >>> > > > > >> argument > >> > >>> > > > > >> (ignore.strand = TRUE) > >> > >>> > > > > >> > >> > >>> > > > > >> > traceback() > >> > >>> > > > > >> 15: sapply(listData, function(Xi) > >> > >>> > > > > >> extends(class(Xi), > >> > >>> > > > > >> elementTypeX)) > >> > >>> > > > > >> 14: .updateCompressedList(X, > >lapply_CompressedList(X, > >> > >>> > > > > >> FUN, > >> > >>> > > > > >> ...)) > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >>> > > > > >> if (!group.selfish) { > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >>> > > > > >> TRUE))) > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >>> > > > > >> width(irs) + > >> > >>> > > > > >> extend.size) > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >>> > > > > >> group.name ])] > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >>> > > > > >> group.name ])) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> irs <- ranges(x) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >>> > > > > >> extend.size))) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> }) > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >>> > > > > >> if (!group.selfish) { > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >>> > > > > >> TRUE))) > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >>> > > > > >> width(irs) + > >> > >>> > > > > >> extend.size) > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >>> > > > > >> group.name ])] > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >>> > > > > >> group.name ])) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> } > >> > >>> > > > > >> else { > >> > >>> > > > > >> irs <- ranges(x) > >> > >>> > > > > >> values(x)$stepping <- > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >>> > > > > >> extend.size))) > >> > >>> > > > > >> x > >> > >>> > > > > >> } > >> > >>> > > > > >> }) > >> > >>> > > > > >> 11: .local(obj, ...) > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > >> > >>> > > > > >> group.selfish = > >> > >>> > > > > >> FALSE, > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", > >group.selfish > >> > >>> > > > > >> = > >> > >>> > > > > >> FALSE, > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >>> > > > > >> 8: .local(data, ...) > >> > >>> > > > > >> 7: (function (data, ...) > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> > >>> > > > > >> object > >> > >>> > > > > >> of > >> > >>> > > > > >> class > >> > >>> > > > > >> "TranscriptDb">, > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >>> > > > > >> "alignment", > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label > >> > >>> > > > > >> = > >> > >>> > > > > >> TRUE, > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >>> > > > > >> 6: (function (data, ...) > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> > >>> > > > > >> object > >> > >>> > > > > >> of > >> > >>> > > > > >> class > >> > >>> > > > > >> "TranscriptDb">, > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >>> > > > > >> "alignment", > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", label > >> > >>> > > > > >> = > >> > >>> > > > > >> TRUE, > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) > >> > >>> > > > > >> 3: .local(object, ...) > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > sessionInfo() > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >>> > > > > >> > >> > >>> > > > > >> locale: > >> > >>> > > > > >> [1] > >> > >>> > > > > >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >>> > > > > >> > >> > >>> > > > > >> attached base packages: > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils > >> > >>> > > > > >> datasets > >> > >>> > > > > >> methods base > >> > >>> > > > > >> > >> > >>> > > > > >> other attached packages: > >> > >>> > > > > >> [1] XVector_0.4.0 > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> > >>> > > > > >> GenomicFeatures_1.16.0 > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> > >>> > > > > >> GenomicRanges_1.16.2 > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> > >>> > > > > >> ggbio_1.12.0 > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> > >>> > > > > >> > >> > >>> > > > > >> loaded via a namespace (and not attached): > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> > >>> > > > > >> Biostrings_2.32.0 > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > >> > >>> > > > > >> Formula_1.1-1 > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> > >>> > > > > >> Hmisc_3.14-4 > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 > >> > >>> > > > > >> MASS_7.3-31 > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >> > >>> > > > > >> stringr_0.6.2 > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> > >>> > > > > >> zlibbioc_1.10.0 > >> > >>> > > > > >> > > >> > >>> > > > > >> > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > -- > >> > >>> > > > > > Tengfei Yin, PhD > >> > >>> > > > > > Seven Bridges Genomics > >> > >>> > > > > > sbgenomics.com > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > > > Cambridge, MA 02138 > >> > >>> > > > > > (617) 866-0446 > >> > >>> > > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > -- > >> > >>> > > > > Tengfei Yin, PhD > >> > >>> > > > > Seven Bridges Genomics > >> > >>> > > > > sbgenomics.com > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > > Cambridge, MA 02138 > >> > >>> > > > > (617) 866-0446 > >> > >>> > > > > > >> > >>> > > > > [[alternative HTML version deleted]] > >> > >>> > > > > > >> > >>> > > > > _______________________________________________ > >> > >>> > > > > Bioconductor mailing list > >> > >>> > > > > Bioconductor at r-project.org > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >>> > > > > Search the archives: > >> > >>> > > > > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >>> > > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > -- > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > Tengfei Yin, PhD > >> > >>> > > > Seven Bridges Genomics > >> > >>> > > > sbgenomics.com > >> > >>> > > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > > Cambridge, MA 02138 > >> > >>> > > > (617) 866- 0446 > >> > >>> > > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > -- > >> > >>> > > > >> > >>> > > > >> > >>> > > Tengfei Yin, PhD > >> > >>> > > Seven Bridges Genomics > >> > >>> > > sbgenomics.com > >> > >>> > > 625 Mt. Auburn St. Suite #208 > >> > >>> > > Cambridge, MA 02138 > >> > >>> > > (617) 866- 0446 > >> > >>> > > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > -- > >> > >>> > > >> > >>> > > >> > >>> > Tengfei Yin, PhD > >> > >>> > Seven Bridges Genomics > >> > >>> > sbgenomics.com > >> > >>> > 625 Mt. Auburn St. Suite #208 > >> > >>> > Cambridge, MA 02138 > >> > >>> > (617) 866- 0446 > >> > >>> > > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> -- > >> > >> Tengfei Yin, PhD > >> > >> Seven Bridges Genomics > >> > >> sbgenomics.com > >> > >> 625 Mt. Auburn St. Suite #208 > >> > >> Cambridge, MA 02138 > >> > >> (617) 866-0446 > >> > > >> > > > > > > > -- > > > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866- 0446 >
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----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > Cc: lcollado at jhu.edu, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> > Sent: Saturday, April 26, 2014 7:33:41 PM > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > > > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> > > To: lcollado at jhu.edu > > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing > > list" <bioconductor at="" r-project.org=""> > > Sent: Saturday, April 26, 2014 1:58:01 PM > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > > broken > > > > > > right, it's failing to build and I am trying to figure out why now, > > because it passes check/build and works on my laptop, but it > > doesn't > > pass bioc build for both release and devel, let me dig into it > > tonight. > > > > Seems like this could be fixed if you just add > > library(ggbio) > > to your vignette before the ggbio() function is called on line 557 of > vignettes/realvignettes/ggbio.Rnw. > Sorry, I spoke too soon; that just changes the error message you receive. Dan > Dan > > > > > > thanks for your patience > > > > > > Tengfei > > > > > > > > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < > > lcollado at jhsph.edu > wrote: > > > > > > > > Oh ok. Thanks for the info > > > > > > > > > > > > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < > > dtenenba at fhcrc.org > > > wrote: > > > > > > > > > > > > Leonardo Collado Torres < lcollado at jhsph.edu > wrote: > > > > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC > > >release? > > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html > > >still > > >points to 1.12.0 > > > > > > > It's failing to build: > > > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > > > > > > > > Dan > > > > > > > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < > > >dtenenba at fhcrc.org > > >> > > >wrote: > > > > > >> > > >> > > >> ----- Original Message ----- > > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu > > > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor > > >> > mailing > > >list" < > > >> bioconductor at r-project.org > > > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM > > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > > >> > is > > >broken > > >> > > > >> > Dang it, forgot again to send with my @ jhsph.edu account. See > > >> > below > > >> > again >.< > > >> > > > >> > On the email topic, is it possible to be subscribed with 2 > > >> > emails > > >> > accounts to the BioC mailing list but only get emails with > > >> > one? > > >> > I > > >> > believe that I have to choose to either get the daily digest > > >> > or > > >> > get > > >a > > >> > single for every message sent. If not, I'll probably just drop > > >> > my > > >> > @ jhsph.edu subscription and re-subscribe with the new @ > > >> > jhu.edu > > >> > mail > > >I > > >> > got (our university is pushing these mails). > > >> > > > >> > > >> I don't know; you could try it. Another option would be to > > >> configure > > >your > > >> mail client with a filter to drop the undesired bioc emails. > > >> > > >> Dan > > >> > > >> > > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > > >> > < lcollado at jhu.edu > wrote: > > >> > > Hi Dan, > > >> > > > > >> > > I got RSwitch to work with a second installation of R 3.1. > > >> > > Basically, > > >> > > I downloaded the leopard tarball, expanded it, renamed the > > >> > > folder > > >> > > 3.1 > > >> > > to 3.1patched (which is the version I downloaded, but well, > > >> > > anything > > >> > > except for 3.1 would work), compressed it again, and then > > >expanded > > >> > > it > > >> > > at the root location. > > >> > > > > >> > > So it would be something like this: > > >> > > > > >> > > wget > > >> > > > > >> > > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > > >> > > tar -xvf R-*gz > > >> > > mv Library/Frameworks/R.framework/Versions/3.1 > > >> > > Library/Frameworks/R.framework/Versions/3.1patched > > >> > > tar -cvzf Rlib.tgz Library > > >> > > sudo tar fvxz Rlib.tgz -C / > > >> > > > > >> > > Then used RSwitch, and was able to install BioC-devel. > > >> > > > > >> > > I might try out your renv at a different time. It's great > > >> > > to > > >know > > >> > > that it exists =) > > >> > > > > >> > > Cheers, > > >> > > Leo > > >> > > > > >> > > > > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > > >> > > < tengfei.yin at sbgenomics.com > wrote: > > >> > >> Hi Dan, > > >> > >> > > >> > >> It works like a charm, thanks! > > >> > >> > > >> > >> I use your method, then I changed /Library/Framework/ > > >> > >> folder > > >> > >> and > > >> > >> R.Framework > > >> > >> folder ownership to myself so I don't have to sudo it, then > > >> > >> I > > >just > > >> > >> add alias > > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R > > >> > >> first. > > >> > >> This solves > > >> > >> my problem. > > >> > >> > > >> > >> Try to customize variable for R hooks in emacs as > > >> > >> alternative > > >> > >> solution, but > > >> > >> may need more time. > > >> > >> > > >> > >> Thanks again! > > >> > >> > > >> > >> Tengfei > > >> > >> > > >> > >> > > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > > >> > >> < dtenenba at fhcrc.org > wrote: > > >> > >>> > > >> > >>> Hi Tengfei, > > >> > >>> > > >> > >>> ----- Original Message ----- > > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > >> > >>> > Cc: "Bioconductor mailing list" < > > >> > >>> > bioconductor at r-project.org >, > > >> > >>> > lcollado at jhu.edu > > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > > >> > >>> > example > > >> > >>> > is broken > > >> > >>> > > > >> > >>> > > > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all > > >> > >>> > on > > >the > > >> > >>> > R 3.1? > > >> > >>> > > >> > >>> Yes, install two copies of R 3.1 and switch between them. > > >> > >>> > > >> > >>> > And do some sort of switch for bioc? The website you > > >> > >>> > send > > >> > >>> > to > > >me > > >> > >>> > also > > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on > > >R-devel > > >> > >>> > and > > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R > > >> > >>> > only > > >to > > >> > >>> > switch bioc, so that I could debug and maintain released > > >> > >>> > and > > >> > >>> > devel > > >> > >>> > version. > > >> > >>> > > >> > >>> PLEASE don't use R-devel at all. > > >> > >>> > > >> > >>> Just use R-3.1.0. > > >> > >>> > > >> > >>> You can use the Rswitch app but as you point out it won't > > >> > >>> work > > >> > >>> within > > >> > >>> emacs. > > >> > >>> > > >> > >>> This is what I do: > > >> > >>> > > >> > >>> Every time I download a new version of R, I run its > > >> > >>> installer. > > >> > >>> The > > >> > >>> installer always puts it in > > >> > >>> > > >> > >>> /Library/Frameworks/R.framework > > >> > >>> > > >> > >>> So after I install each version of R, I rename the > > >> > >>> R.framework > > >> > >>> directory > > >> > >>> to something like > > >> > >>> R.framework.bioc214_snowleopard > > >> > >>> > > >> > >>> And then I make a symlink from > > >> > >>> R.framework.bioc214_snowleopard > > >to > > >> > >>> R.framework. > > >> > >>> > > >> > >>> I have a little script at https://github.com/dtenenba/renv > > >which > > >> > >>> lets me > > >> > >>> see what the various installed Rs are: > > >> > >>> > > >> > >>> $renv > > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > > >> > >>> > > >> > >>> This tells me that the currently active R is nicknamed > > >> > >>> "releaseMav" (this > > >> > >>> means there is a link from > > >> > >>> /Library/Frameworks/R.framework.releaseMav to > > >> > >>> /Library/Frameworks/R.framework. It shows the versions, > > >> > >>> svn > > >> > >>> revisions, > > >> > >>> dates, and architectures of each version. (darwin10.8.0 is > > >> > >>> Snow > > >> > >>> Leopard; > > >> > >>> darwin13.1.0 is Mavericks). > > >> > >>> > > >> > >>> Note that in my nomenclature devel means BioC devel, not > > >R-devel. > > >> > >>> > > >> > >>> So if I wanted to switch to the "develSL" version I would > > >> > >>> do: > > >> > >>> > > >> > >>> sudo renv develSL > > >> > >>> > > >> > >>> HTH > > >> > >>> Dan > > >> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > > >> > >>> > dtenenba at fhcrc.org > > > >> > >>> > wrote: > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > Hi Tengfei, > > >> > >>> > > > >> > >>> > ----- Original Message ----- > > >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > >> > >>> > > > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > >> > >>> > > Cc: "Bioconductor mailing list" < > > > bioconductor at r-project.org > > >> > >>> > > >, > > >> > >>> > > lcollado at jhu.edu > > >> > >>> > > > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > > >example > > >> > >>> > > is > > >> > >>> > > broken > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I > > >> > >>> > > am > > >still > > >> > >>> > > a > > >> > >>> > > newbie to OSX ... I got R-devel running and I will try > > >> > >>> > > Rswitcher, I > > >> > >>> > > also want to do that switch easily in emacs too. > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) > > >> > >>> > and > > >> > >>> > BioC > > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released > > >> > >>> > version of > > >> > >>> > R. > > >> > >>> > > > >> > >>> > I think the Rswitch app just sets a symbolic link, so > > >> > >>> > you > > >> > >>> > should be > > >> > >>> > able to do that within emacs. Run it and see what it > > >> > >>> > does > > >> > >>> > to > > >> > >>> > /Library/Frameworks/R.framework. > > >> > >>> > > > >> > >>> > Dan > > >> > >>> > > > >> > >>> > > > >> > >>> > > > > >> > >>> > > cheers > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > Tengfei > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > >> > >>> > > > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > > >> > >>> > > dtenenba at fhcrc.org > > >> > >>> > > > > > >> > >>> > > wrote: > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > ----- Original Message ----- > > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > >> > >>> > > > > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > > > >> > >>> > > > Cc: "Bioconductor mailing list" < > > >> > >>> > > > bioconductor at r-project.org >, > > >> > >>> > > > lcollado at jhu.edu > > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > > >> > >>> > > > txdb > > >> > >>> > > > example is > > >> > >>> > > > broken > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > >> > >>> > > > Hi Dan, > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it > > >should > > >> > >>> > > > work? > > >> > >>> > > > > >> > >>> > > Yes. > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > ? Is > > >> > >>> > > > there a way to build from source using biocLite, > > >> > >>> > > > like > > >type > > >> > >>> > > > = > > >> > >>> > > > "source", this is what I got > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > library(BiocInstaller) > > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), > > >?biocLite > > >> > >>> > > > for > > >> > >>> > > > help > > >> > >>> > > > > biocLite("GenomicRanges") > > >> > >>> > > > BioC_mirror: http://bioconductor.org > > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller > > >> > >>> > > > 1.14.1), R > > >> > >>> > > > version > > >> > >>> > > > 3.1.0. > > >> > >>> > > > Installing package(s) 'GenomicRanges' > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > package ?GenomicRanges? is available as a source > > >> > >>> > > > package > > >> > >>> > > > but not > > >> > >>> > > > as > > >> > >>> > > > a > > >> > >>> > > > binary > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > Warning message: > > >> > >>> > > > package ?GenomicRanges? is not available (for R > > >> > >>> > > > version > > >> > >>> > > > 3.1.0) > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > Just wondering is there a solution without > > >> > >>> > > > re-install > > >> > >>> > > > R > > >for > > >> > >>> > > > snow > > >> > >>> > > > leopard. And what's the plan for maverick? > > >> > >>> > > > > > >> > >>> > > > > >> > >>> > > You can do > > >> > >>> > > biocLite("GenomicRanges", type="source") > > >> > >>> > > > > >> > >>> > > but you need to have the appropriate compilers, etc. > > >> > >>> > > > > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. > > >> > >>> > > You > > >can > > >> > >>> > > have > > >> > >>> > > multiple installations of R on your Mac and switch > > >> > >>> > > between > > >> > >>> > > them > > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or > > >another > > >> > >>> > > easy > > >> > >>> > > > >> > >>> > > > >> > >>> > > mechanism. > > >> > >>> > > > > >> > >>> > > We are building packages for Mavericks now, we just > > >> > >>> > > have > > >> > >>> > > to > > >> > >>> > > resolve > > >> > >>> > > a > > >> > >>> > > few build issues and test the resulting packages, we > > >> > >>> > > still > > >> > >>> > > hope to > > >> > >>> > > have them available by the end of the month. But since > > >> > >>> > > you > > >> > >>> > > can > > >> > >>> > > install the Snow Leopard build without needing to > > >> > >>> > > remove > > >your > > >> > >>> > > Mavericks build, you should do that. > > >> > >>> > > > > >> > >>> > > Dan > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > > >> > >>> > > > Thanks > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > Tengfei > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > > >> > >>> > > > dtenenba at fhcrc.org > > >> > >>> > > > > wrote: > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > Hi Tengfei, > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > ----- Original Message ----- > > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > > > >> > >>> > > > > To: lcollado at jhu.edu > > >> > >>> > > > > Cc: bioconductor at r-project.org > > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > > >> > >>> > > > > txdb > > >> > >>> > > > > example > > >> > >>> > > > > is > > >> > >>> > > > > broken > > >> > >>> > > > > > > >> > >>> > > > > btw, based on the error, let me try to debug it. > > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > > >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: > > >> > >>> > > > > > > >> > >>> > > > > > Hi Leonardo, > > >> > >>> > > > > > > > >> > >>> > > > > > Frankly speaking, the vignette is still in > > >> > >>> > > > > > progress, > > >> > >>> > > > > > and > > >> > >>> > > > > > there > > >> > >>> > > > > > are > > >> > >>> > > > > > some > > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying > > >> > >>> > > > > > to > > >find > > >> > >>> > > > > > a > > >> > >>> > > > > > time > > >> > >>> > > > > > to > > >> > >>> > > > > > do that > > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and > > >> > >>> > > > > > Bioc > > >> > >>> > > > > > 2.14 on > > >> > >>> > > > > > my > > >> > >>> > > > > > new MBP > > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build > > >> > >>> > > > > > is > > >not > > >> > >>> > > > > > ready > > >> > >>> > > > > > for > > >> > >>> > > > > > maverick > > >> > >>> > > > > > yet, maybe available by the end of April? > > >> > >>> > > > > > > > >> > >>> > > > > > Thanks for reporting the bug, I will keep you > > >> > >>> > > > > > posted > > >on > > >> > >>> > > > > > this > > >> > >>> > > > > > when > > >> > >>> > > > > > I > > >> > >>> > > > > > successfully get it on my laptop and start > > >> > >>> > > > > > fixing > > >> > >>> > > > > > the > > >> > >>> > > > > > problems. > > >> > >>> > > > > > > > >> > >>> > > > > > >> > >>> > > > You can install the Snow Leopard build of R and > > >> > >>> > > > should > > >have > > >> > >>> > > > no > > >> > >>> > > > problems, binary packages are available for that > > >> > >>> > > > version. > > >> > >>> > > > It will > > >> > >>> > > > run fine on Mavericks. > > >> > >>> > > > > > >> > >>> > > > Dan > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > cheers > > >> > >>> > > > > > > > >> > >>> > > > > > Tengfei > > >> > >>> > > > > > > > >> > >>> > > > > > > > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo > > >> > >>> > > > > > Collado > > >> > >>> > > > > > Torres < > > >> > >>> > > > > > lcollado at jhsph.edu > wrote: > > >> > >>> > > > > > > > >> > >>> > > > > >> Hello Tengfei + bioc list, > > >> > >>> > > > > >> > > >> > >>> > > > > >> From > > >> > >>> > > > > >> > > >> > >>> > > > > >> > > >> > > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbi o/inst/doc/ggbio.pdf > > >> > >>> > > > > >> page 4 (complied on april 11 2014), the > > >> > >>> > > > > >> following > > >> > >>> > > > > >> example > > >> > >>> > > > > >> loads > > >> > >>> > > > > >> to > > >> > >>> > > > > >> an > > >> > >>> > > > > >> error as shown below. I wasn't seeing this > > >> > >>> > > > > >> error > > >> > >>> > > > > >> before > > >> > >>> > > > > >> (aka, > > >> > >>> > > > > >> last > > >> > >>> > > > > >> week). The only guess that comes to mind is the > > >recent > > >> > >>> > > > > >> update > > >> > >>> > > > > >> to > > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't > > >> > >>> > > > > >> seem > > >> > >>> > > > > >> to > > >> > >>> > > > > >> be > > >> > >>> > > > > >> related > > >> > >>> > > > > >> from > > >> > >>> > > > > >> the traceback() output, well... maybe it's > > >> > >>> > > > > >> related > > >to > > >> > >>> > > > > >> the > > >> > >>> > > > > >> ignore.strand = TRUE part as described in the > > >> > >>> > > > > >> error. > > >> > >>> > > > > >> > > >> > >>> > > > > >> I'll create a GitHub issue just for > > >> > >>> > > > > >> completeness. > > >> > >>> > > > > >> > > >> > >>> > > > > >> Thank you, > > >> > >>> > > > > >> Leonardo > > >> > >>> > > > > >> > > >> > >>> > > > > >> > library(ggbio) > > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary > > >> > >>> > > > > >> > > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > >> > >>> > > > > >> ## Removed the output > > >> > >>> > > > > >> > > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") > > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > > >> > >>> > > > > >> > genesymbol["BRCA1"]) > > >> > >>> > > > > >> Aggregating TranscriptDb... > > >> > >>> > > > > >> Parsing transcripts... > > >> > >>> > > > > >> Parsing exons... > > >> > >>> > > > > >> Parsing cds... > > >> > >>> > > > > >> Parsing utrs... > > >> > >>> > > > > >> ------exons... > > >> > >>> > > > > >> ------cdss... > > >> > >>> > > > > >> ------introns... > > >> > >>> > > > > >> ------utr... > > >> > >>> > > > > >> aggregating... > > >> > >>> > > > > >> Done > > >> > >>> > > > > >> Constructing graphics... > > >> > >>> > > > > >> Error in sapply(listData, function(Xi) > > >> > >>> > > > > >> extends(class(Xi), > > >> > >>> > > > > >> elementTypeX)) : > > >> > >>> > > > > >> error in evaluating the argument 'X' in > > >> > >>> > > > > >> selecting > > >> > >>> > > > > >> a > > >> > >>> > > > > >> method > > >> > >>> > > > > >> for > > >> > >>> > > > > >> function 'sapply': Error in > > >> > >>> > > > > >> unlist(range(ranges(x.n, > > >> > >>> > > > > >> ignore.strand > > >> > >>> > > > > >> = > > >> > >>> > > > > >> TRUE))) : > > >> > >>> > > > > >> error in evaluating the argument 'x' in > > >> > >>> > > > > >> selecting > > >> > >>> > > > > >> a > > >> > >>> > > > > >> method > > >> > >>> > > > > >> for > > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : > > >> > >>> > > > > >> unused > > >> > >>> > > > > >> argument > > >> > >>> > > > > >> (ignore.strand = TRUE) > > >> > >>> > > > > >> > > >> > >>> > > > > >> > traceback() > > >> > >>> > > > > >> 15: sapply(listData, function(Xi) > > >> > >>> > > > > >> extends(class(Xi), > > >> > >>> > > > > >> elementTypeX)) > > >> > >>> > > > > >> 14: .updateCompressedList(X, > > >lapply_CompressedList(X, > > >> > >>> > > > > >> FUN, > > >> > >>> > > > > >> ...)) > > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > > >> > >>> > > > > >> if (!is.null( group.name )) { > > >> > >>> > > > > >> if (!group.selfish) { > > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> > >>> > > > > >> TRUE))) > > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > > >> > >>> > > > > >> width(irs) + > > >> > >>> > > > > >> extend.size) > > >> > >>> > > > > >> irs.new <- sort(irs.new) > > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > > >> > >>> > > > > >> values(x)$stepping <- > > >> > >>> > > > > >> .lvs[as.character(values(x)[, > > >> > >>> > > > > >> group.name ])] > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> else { > > >> > >>> > > > > >> values(x)$stepping <- > > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > > >> > >>> > > > > >> group.name ])) > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> } > > >> > >>> > > > > >> else { > > >> > >>> > > > > >> irs <- ranges(x) > > >> > >>> > > > > >> values(x)$stepping <- > > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > > >> > >>> > > > > >> fix = "center", width = width(irs) + > > >> > >>> > > > > >> extend.size))) > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> }) > > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > > >> > >>> > > > > >> if (!is.null( group.name )) { > > >> > >>> > > > > >> if (!group.selfish) { > > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > > >> > >>> > > > > >> TRUE))) > > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > > >> > >>> > > > > >> width(irs) + > > >> > >>> > > > > >> extend.size) > > >> > >>> > > > > >> irs.new <- sort(irs.new) > > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > > >> > >>> > > > > >> values(x)$stepping <- > > >> > >>> > > > > >> .lvs[as.character(values(x)[, > > >> > >>> > > > > >> group.name ])] > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> else { > > >> > >>> > > > > >> values(x)$stepping <- > > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > > >> > >>> > > > > >> group.name ])) > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> } > > >> > >>> > > > > >> else { > > >> > >>> > > > > >> irs <- ranges(x) > > >> > >>> > > > > >> values(x)stepping <- > > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > > >> > >>> > > > > >> fix = "center", width = width(irs) + > > >> > >>> > > > > >> extend.size))) > > >> > >>> > > > > >> x > > >> > >>> > > > > >> } > > >> > >>> > > > > >> }) > > >> > >>> > > > > >> 11: .local(obj, ...) > > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > > >> > >>> > > > > >> group.selfish = > > >> > >>> > > > > >> FALSE, > > >> > >>> > > > > >> fix = "start", extend.size = es) > > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", > > >group.selfish > > >> > >>> > > > > >> = > > >> > >>> > > > > >> FALSE, > > >> > >>> > > > > >> fix = "start", extend.size = es) > > >> > >>> > > > > >> 8: .local(data, ...) > > >> > >>> > > > > >> 7: (function (data, ...) > > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> > >> > >>> > > > > >> object > > >> > >>> > > > > >> of > > >> > >>> > > > > >> class > > >> > >>> > > > > >> "TranscriptDb">, > > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > > >> > >>> > > > > >> "alignment", > > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > > >> > >>> > > > > >> label > > >> > >>> > > > > >> = > > >> > >>> > > > > >> TRUE, > > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> > >>> > > > > >> 6: (function (data, ...) > > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> > >> > >>> > > > > >> object > > >> > >>> > > > > >> of > > >> > >>> > > > > >> class > > >> > >>> > > > > >> "TranscriptDb">, > > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > > >> > >>> > > > > >> "alignment", > > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > > >> > >>> > > > > >> label > > >> > >>> > > > > >> = > > >> > >>> > > > > >> TRUE, > > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) > > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) > > >> > >>> > > > > >> 3: .local(object, ...) > > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > > >> > >>> > > > > >> > > >> > >>> > > > > >> > > >> > >>> > > > > >> > sessionInfo() > > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) > > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > > >> > >>> > > > > >> > > >> > >>> > > > > >> locale: > > >> > >>> > > > > >> [1] > > >> > >>> > > > > >> > > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > >> > >>> > > > > >> > > >> > >>> > > > > >> attached base packages: > > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils > > >> > >>> > > > > >> datasets > > >> > >>> > > > > >> methods base > > >> > >>> > > > > >> > > >> > >>> > > > > >> other attached packages: > > >> > >>> > > > > >> [1] XVector_0.4.0 > > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > > >> > >>> > > > > >> GenomicFeatures_1.16.0 > > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > > >> > >>> > > > > >> GenomicRanges_1.16.2 > > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > > >> > >>> > > > > >> ggbio_1.12.0 > > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > > >> > >>> > > > > >> > > >> > >>> > > > > >> loaded via a namespace (and not attached): > > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > > >> > >>> > > > > >> Biostrings_2.32.0 > > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > > >> > >>> > > > > >> Formula_1.1-1 > > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > > >> > >>> > > > > >> Hmisc_3.14-4 > > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 > > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 > > >> > >>> > > > > >> MASS_7.3-31 > > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 > > >> > >>> > > > > >> Rcpp_0.11.1 > > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > > >> > >>> > > > > >> stringr_0.6.2 > > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 > > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > > >> > >>> > > > > >> zlibbioc_1.10.0 > > >> > >>> > > > > >> > > > >> > >>> > > > > >> > > >> > >>> > > > > > > > >> > >>> > > > > > > > >> > >>> > > > > > > > >> > >>> > > > > > -- > > >> > >>> > > > > > Tengfei Yin, PhD > > >> > >>> > > > > > Seven Bridges Genomics > > >> > >>> > > > > > sbgenomics.com > > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 > > >> > >>> > > > > > Cambridge, MA 02138 > > >> > >>> > > > > > (617) 866-0446 > > >> > >>> > > > > > > > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > > > >> > >>> > > > > -- > > >> > >>> > > > > Tengfei Yin, PhD > > >> > >>> > > > > Seven Bridges Genomics > > >> > >>> > > > > sbgenomics.com > > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 > > >> > >>> > > > > Cambridge, MA 02138 > > >> > >>> > > > > (617) 866-0446 > > >> > >>> > > > > > > >> > >>> > > > > [[alternative HTML version deleted]] > > >> > >>> > > > > > > >> > >>> > > > > _______________________________________________ > > >> > >>> > > > > Bioconductor mailing list > > >> > >>> > > > > Bioconductor at r-project.org > > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> > >>> > > > > Search the archives: > > >> > >>> > > > > > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > >>> > > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > -- > > >> > >>> > > > > > >> > >>> > > > > > >> > >>> > > > Tengfei Yin, PhD > > >> > >>> > > > Seven Bridges Genomics > > >> > >>> > > > sbgenomics.com > > >> > >>> > > > 625 Mt. Auburn St. Suite #208 > > >> > >>> > > > Cambridge, MA 02138 > > >> > >>> > > > (617) 866- 0446 > > >> > >>> > > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > -- > > >> > >>> > > > > >> > >>> > > > > >> > >>> > > Tengfei Yin, PhD > > >> > >>> > > Seven Bridges Genomics > > >> > >>> > > sbgenomics.com > > >> > >>> > > 625 Mt. Auburn St. Suite #208 > > >> > >>> > > Cambridge, MA 02138 > > >> > >>> > > (617) 866- 0446 > > >> > >>> > > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > > > >> > >>> > -- > > >> > >>> > > > >> > >>> > > > >> > >>> > Tengfei Yin, PhD > > >> > >>> > Seven Bridges Genomics > > >> > >>> > sbgenomics.com > > >> > >>> > 625 Mt. Auburn St. Suite #208 > > >> > >>> > Cambridge, MA 02138 > > >> > >>> > (617) 866- 0446 > > >> > >>> > > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> -- > > >> > >> Tengfei Yin, PhD > > >> > >> Seven Bridges Genomics > > >> > >> sbgenomics.com > > >> > >> 625 Mt. Auburn St. Suite #208 > > >> > >> Cambridge, MA 02138 > > >> > >> (617) 866-0446 > > >> > > > >> > > > > > > > > > > > > > > -- > > > > > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866- 0446 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor ADD REPLY 0 Entering edit mode I just noticed that ggbio is building now http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html and I'm happy to report that the problem I mentioned is resolved with ggbio 1.12.3. Thank you Tengfei and Dan! For reference, here is the working session information. > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 [5] Biobase_2.24.0 GenomicRanges_1.16.2 [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 [9] ggbio_1.12.3 ggplot2_0.9.3.1 [11] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 [25] labeling_0.2 lattice_0.20-29 latticeExtra_0.6-26 [28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1 [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 [34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0 [37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4 [40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 [43] stringr_0.6.2 survival_2.37-7 tools_3.1.0 [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > > > ----- Original Message ----- >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> Cc: lcollado at jhu.edu, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> >> Sent: Saturday, April 26, 2014 7:33:41 PM >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken >> >> >> >> ----- Original Message ----- >> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> > To: lcollado at jhu.edu >> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing >> > list" <bioconductor at="" r-project.org=""> >> > Sent: Saturday, April 26, 2014 1:58:01 PM >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >> > broken >> > >> > >> > right, it's failing to build and I am trying to figure out why now, >> > because it passes check/build and works on my laptop, but it >> > doesn't >> > pass bioc build for both release and devel, let me dig into it >> > tonight. >> > >> >> Seems like this could be fixed if you just add >> >> library(ggbio) >> >> to your vignette before the ggbio() function is called on line 557 of >> vignettes/realvignettes/ggbio.Rnw. >> > > Sorry, I spoke too soon; that just changes the error message you receive. > Dan > > >> Dan >> >> >> > >> > thanks for your patience >> > >> > >> > Tengfei >> > >> > >> > >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < >> > lcollado at jhsph.edu > wrote: >> > >> > >> > >> > Oh ok. Thanks for the info >> > >> > >> > >> > >> > >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < >> > dtenenba at fhcrc.org >> > > wrote: >> > >> > >> > >> > >> > >> > Leonardo Collado Torres < lcollado at jhsph.edu > wrote: >> > >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC >> > >release? >> > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html >> > >still >> > >points to 1.12.0 >> > > >> > >> > It's failing to build: >> > >> > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> > >> > >> > >> > Dan >> > >> > > >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < >> > >dtenenba at fhcrc.org >> > >> >> > >wrote: >> > > >> > >> >> > >> >> > >> ----- Original Message ----- >> > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu > >> > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor >> > >> > mailing >> > >list" < >> > >> bioconductor at r-project.org > >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >> > >> > is >> > >broken >> > >> > >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. See >> > >> > below >> > >> > again >.< >> > >> > >> > >> > On the email topic, is it possible to be subscribed with 2 >> > >> > emails >> > >> > accounts to the BioC mailing list but only get emails with >> > >> > one? >> > >> > I >> > >> > believe that I have to choose to either get the daily digest >> > >> > or >> > >> > get >> > >a >> > >> > single for every message sent. If not, I'll probably just drop >> > >> > my >> > >> > @ jhsph.edu subscription and re-subscribe with the new @ >> > >> > jhu.edu >> > >> > mail >> > >I >> > >> > got (our university is pushing these mails). >> > >> > >> > >> >> > >> I don't know; you could try it. Another option would be to >> > >> configure >> > >your >> > >> mail client with a filter to drop the undesired bioc emails. >> > >> >> > >> Dan >> > >> >> > >> >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres >> > >> > < lcollado at jhu.edu > wrote: >> > >> > > Hi Dan, >> > >> > > >> > >> > > I got RSwitch to work with a second installation of R 3.1. >> > >> > > Basically, >> > >> > > I downloaded the leopard tarball, expanded it, renamed the >> > >> > > folder >> > >> > > 3.1 >> > >> > > to 3.1patched (which is the version I downloaded, but well, >> > >> > > anything >> > >> > > except for 3.1 would work), compressed it again, and then >> > >expanded >> > >> > > it >> > >> > > at the root location. >> > >> > > >> > >> > > So it would be something like this: >> > >> > > >> > >> > > wget >> > >> > > >> > >> >> > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1 -branch-snowleopard-sa-x86_64.tar.gz >> > >> > > tar -xvf R-*gz >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1 >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched >> > >> > > tar -cvzf Rlib.tgz Library >> > >> > > sudo tar fvxz Rlib.tgz -C / >> > >> > > >> > >> > > Then used RSwitch, and was able to install BioC-devel. >> > >> > > >> > >> > > I might try out your renv at a different time. It's great >> > >> > > to >> > >know >> > >> > > that it exists =) >> > >> > > >> > >> > > Cheers, >> > >> > > Leo >> > >> > > >> > >> > > >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin >> > >> > > < tengfei.yin at sbgenomics.com > wrote: >> > >> > >> Hi Dan, >> > >> > >> >> > >> > >> It works like a charm, thanks! >> > >> > >> >> > >> > >> I use your method, then I changed /Library/Framework/ >> > >> > >> folder >> > >> > >> and >> > >> > >> R.Framework >> > >> > >> folder ownership to myself so I don't have to sudo it, then >> > >> > >> I >> > >just >> > >> > >> add alias >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R >> > >> > >> first. >> > >> > >> This solves >> > >> > >> my problem. >> > >> > >> >> > >> > >> Try to customize variable for R hooks in emacs as >> > >> > >> alternative >> > >> > >> solution, but >> > >> > >> may need more time. >> > >> > >> >> > >> > >> Thanks again! >> > >> > >> >> > >> > >> Tengfei >> > >> > >> >> > >> > >> >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum >> > >> > >> < dtenenba at fhcrc.org > wrote: >> > >> > >>> >> > >> > >>> Hi Tengfei, >> > >> > >>> >> > >> > >>> ----- Original Message ----- >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> > >> > >>> > Cc: "Bioconductor mailing list" < >> > >> > >>> > bioconductor at r-project.org >, >> > >> > >>> > lcollado at jhu.edu >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> > >> > >>> > example >> > >> > >>> > is broken >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all >> > >> > >>> > on >> > >the >> > >> > >>> > R 3.1? >> > >> > >>> >> > >> > >>> Yes, install two copies of R 3.1 and switch between them. >> > >> > >>> >> > >> > >>> > And do some sort of switch for bioc? The website you >> > >> > >>> > send >> > >> > >>> > to >> > >me >> > >> > >>> > also >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on >> > >R-devel >> > >> > >>> > and >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R >> > >> > >>> > only >> > >to >> > >> > >>> > switch bioc, so that I could debug and maintain released >> > >> > >>> > and >> > >> > >>> > devel >> > >> > >>> > version. >> > >> > >>> >> > >> > >>> PLEASE don't use R-devel at all. >> > >> > >>> >> > >> > >>> Just use R-3.1.0. >> > >> > >>> >> > >> > >>> You can use the Rswitch app but as you point out it won't >> > >> > >>> work >> > >> > >>> within >> > >> > >>> emacs. >> > >> > >>> >> > >> > >>> This is what I do: >> > >> > >>> >> > >> > >>> Every time I download a new version of R, I run its >> > >> > >>> installer. >> > >> > >>> The >> > >> > >>> installer always puts it in >> > >> > >>> >> > >> > >>> /Library/Frameworks/R.framework >> > >> > >>> >> > >> > >>> So after I install each version of R, I rename the >> > >> > >>> R.framework >> > >> > >>> directory >> > >> > >>> to something like >> > >> > >>> R.framework.bioc214_snowleopard >> > >> > >>> >> > >> > >>> And then I make a symlink from >> > >> > >>> R.framework.bioc214_snowleopard >> > >to >> > >> > >>> R.framework. >> > >> > >>> >> > >> > >>> I have a little script at https://github.com/dtenenba/renv >> > >which >> > >> > >>> lets me >> > >> > >>> see what the various installed Rs are: >> > >> > >>> >> > >> > >>> renv >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> > >> > >>> >> > >> > >>> This tells me that the currently active R is nicknamed >> > >> > >>> "releaseMav" (this >> > >> > >>> means there is a link from >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions, >> > >> > >>> svn >> > >> > >>> revisions, >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 is >> > >> > >>> Snow >> > >> > >>> Leopard; >> > >> > >>> darwin13.1.0 is Mavericks). >> > >> > >>> >> > >> > >>> Note that in my nomenclature devel means BioC devel, not >> > >R-devel. >> > >> > >>> >> > >> > >>> So if I wanted to switch to the "develSL" version I would >> > >> > >>> do: >> > >> > >>> >> > >> > >>> sudo renv develSL >> > >> > >>> >> > >> > >>> HTH >> > >> > >>> Dan >> > >> > >>> >> > >> > >>> >> > >> > >>> >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < >> > >> > >>> > dtenenba at fhcrc.org > >> > >> > >>> > wrote: >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > Hi Tengfei, >> > >> > >>> > >> > >> > >>> > ----- Original Message ----- >> > >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >> > >>> > >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> > >> > >>> > > Cc: "Bioconductor mailing list" < >> > > bioconductor at r-project.org >> > >> > >>> > > >, >> > >> > >>> > > lcollado at jhu.edu >> > >> > >>> > >> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM >> > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> > >example >> > >> > >>> > > is >> > >> > >>> > > broken >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > >> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I >> > >> > >>> > > am >> > >still >> > >> > >>> > > a >> > >> > >>> > > newbie to OSX ... I got R-devel running and I will try >> > >> > >>> > > Rswitcher, I >> > >> > >>> > > also want to do that switch easily in emacs too. >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > >> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) >> > >> > >>> > and >> > >> > >>> > BioC >> > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released >> > >> > >>> > version of >> > >> > >>> > R. >> > >> > >>> > >> > >> > >>> > I think the Rswitch app just sets a symbolic link, so >> > >> > >>> > you >> > >> > >>> > should be >> > >> > >>> > able to do that within emacs. Run it and see what it >> > >> > >>> > does >> > >> > >>> > to >> > >> > >>> > /Library/Frameworks/R.framework. >> > >> > >>> > >> > >> > >>> > Dan >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > > >> > >> > >>> > > cheers >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > Tengfei >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < >> > >> > >>> > > dtenenba at fhcrc.org >> > >> > >>> > > > >> > >> > >>> > > wrote: >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > ----- Original Message ----- >> > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >> > >>> > > >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> > >> > >>> > > > Cc: "Bioconductor mailing list" < >> > >> > >>> > > > bioconductor at r-project.org >, >> > >> > >>> > > > lcollado at jhu.edu >> > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM >> > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with >> > >> > >>> > > > txdb >> > >> > >>> > > > example is >> > >> > >>> > > > broken >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > > Hi Dan, >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it >> > >should >> > >> > >>> > > > work? >> > >> > >>> > > >> > >> > >>> > > Yes. >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > ? Is >> > >> > >>> > > > there a way to build from source using biocLite, >> > >> > >>> > > > like >> > >type >> > >> > >>> > > > = >> > >> > >>> > > > "source", this is what I got >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > > library(BiocInstaller) >> > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), >> > >?biocLite >> > >> > >>> > > > for >> > >> > >>> > > > help >> > >> > >>> > > > > biocLite("GenomicRanges") >> > >> > >>> > > > BioC_mirror: http://bioconductor.org >> > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller >> > >> > >>> > > > 1.14.1), R >> > >> > >>> > > > version >> > >> > >>> > > > 3.1.0. >> > >> > >>> > > > Installing package(s) 'GenomicRanges' >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > package ?GenomicRanges? is available as a source >> > >> > >>> > > > package >> > >> > >>> > > > but not >> > >> > >>> > > > as >> > >> > >>> > > > a >> > >> > >>> > > > binary >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > Warning message: >> > >> > >>> > > > package ?GenomicRanges? is not available (for R >> > >> > >>> > > > version >> > >> > >>> > > > 3.1.0) >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > Just wondering is there a solution without >> > >> > >>> > > > re-install >> > >> > >>> > > > R >> > >for >> > >> > >>> > > > snow >> > >> > >>> > > > leopard. And what's the plan for maverick? >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > You can do >> > >> > >>> > > biocLite("GenomicRanges", type="source") >> > >> > >>> > > >> > >> > >>> > > but you need to have the appropriate compilers, etc. >> > >> > >>> > > >> > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. >> > >> > >>> > > You >> > >can >> > >> > >>> > > have >> > >> > >>> > > multiple installations of R on your Mac and switch >> > >> > >>> > > between >> > >> > >>> > > them >> > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or >> > >another >> > >> > >>> > > easy >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > > mechanism. >> > >> > >>> > > >> > >> > >>> > > We are building packages for Mavericks now, we just >> > >> > >>> > > have >> > >> > >>> > > to >> > >> > >>> > > resolve >> > >> > >>> > > a >> > >> > >>> > > few build issues and test the resulting packages, we >> > >> > >>> > > still >> > >> > >>> > > hope to >> > >> > >>> > > have them available by the end of the month. But since >> > >> > >>> > > you >> > >> > >>> > > can >> > >> > >>> > > install the Snow Leopard build without needing to >> > >> > >>> > > remove >> > >your >> > >> > >>> > > Mavericks build, you should do that. >> > >> > >>> > > >> > >> > >>> > > Dan >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > > >> > >> > >>> > > > Thanks >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > Tengfei >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < >> > >> > >>> > > > dtenenba at fhcrc.org >> > >> > >>> > > > > wrote: >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > Hi Tengfei, >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > ----- Original Message ----- >> > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> > >> > >>> > > > > To: lcollado at jhu.edu >> > >> > >>> > > > > Cc: bioconductor at r-project.org >> > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM >> > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with >> > >> > >>> > > > > txdb >> > >> > >>> > > > > example >> > >> > >>> > > > > is >> > >> > >>> > > > > broken >> > >> > >>> > > > > >> > >> > >>> > > > > btw, based on the error, let me try to debug it. >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin >> > >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: >> > >> > >>> > > > > >> > >> > >>> > > > > > Hi Leonardo, >> > >> > >>> > > > > > >> > >> > >>> > > > > > Frankly speaking, the vignette is still in >> > >> > >>> > > > > > progress, >> > >> > >>> > > > > > and >> > >> > >>> > > > > > there >> > >> > >>> > > > > > are >> > >> > >>> > > > > > some >> > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying >> > >> > >>> > > > > > to >> > >find >> > >> > >>> > > > > > a >> > >> > >>> > > > > > time >> > >> > >>> > > > > > to >> > >> > >>> > > > > > do that >> > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and >> > >> > >>> > > > > > Bioc >> > >> > >>> > > > > > 2.14 on >> > >> > >>> > > > > > my >> > >> > >>> > > > > > new MBP >> > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build >> > >> > >>> > > > > > is >> > >not >> > >> > >>> > > > > > ready >> > >> > >>> > > > > > for >> > >> > >>> > > > > > maverick >> > >> > >>> > > > > > yet, maybe available by the end of April? >> > >> > >>> > > > > > >> > >> > >>> > > > > > Thanks for reporting the bug, I will keep you >> > >> > >>> > > > > > posted >> > >on >> > >> > >>> > > > > > this >> > >> > >>> > > > > > when >> > >> > >>> > > > > > I >> > >> > >>> > > > > > successfully get it on my laptop and start >> > >> > >>> > > > > > fixing >> > >> > >>> > > > > > the >> > >> > >>> > > > > > problems. >> > >> > >>> > > > > > >> > >> > >>> > > > >> > >> > >>> > > > You can install the Snow Leopard build of R and >> > >> > >>> > > > should >> > >have >> > >> > >>> > > > no >> > >> > >>> > > > problems, binary packages are available for that >> > >> > >>> > > > version. >> > >> > >>> > > > It will >> > >> > >>> > > > run fine on Mavericks. >> > >> > >>> > > > >> > >> > >>> > > > Dan >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > > > cheers >> > >> > >>> > > > > > >> > >> > >>> > > > > > Tengfei >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo >> > >> > >>> > > > > > Collado >> > >> > >>> > > > > > Torres < >> > >> > >>> > > > > > lcollado at jhsph.edu > wrote: >> > >> > >>> > > > > > >> > >> > >>> > > > > >> Hello Tengfei + bioc list, >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> From >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> >> > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggb io/inst/doc/ggbio.pdf >> > >> > >>> > > > > >> page 4 (complied on april 11 2014), the >> > >> > >>> > > > > >> following >> > >> > >>> > > > > >> example >> > >> > >>> > > > > >> loads >> > >> > >>> > > > > >> to >> > >> > >>> > > > > >> an >> > >> > >>> > > > > >> error as shown below. I wasn't seeing this >> > >> > >>> > > > > >> error >> > >> > >>> > > > > >> before >> > >> > >>> > > > > >> (aka, >> > >> > >>> > > > > >> last >> > >> > >>> > > > > >> week). The only guess that comes to mind is the >> > >recent >> > >> > >>> > > > > >> update >> > >> > >>> > > > > >> to >> > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't >> > >> > >>> > > > > >> seem >> > >> > >>> > > > > >> to >> > >> > >>> > > > > >> be >> > >> > >>> > > > > >> related >> > >> > >>> > > > > >> from >> > >> > >>> > > > > >> the traceback() output, well... maybe it's >> > >> > >>> > > > > >> related >> > >to >> > >> > >>> > > > > >> the >> > >> > >>> > > > > >> ignore.strand = TRUE part as described in the >> > >> > >>> > > > > >> error. >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> I'll create a GitHub issue just for >> > >> > >>> > > > > >> completeness. >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> Thank you, >> > >> > >>> > > > > >> Leonardo >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> > library(ggbio) >> > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> > >> > >>> > > > > >> ## Removed the output >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") >> > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = >> > >> > >>> > > > > >> > genesymbol["BRCA1"]) >> > >> > >>> > > > > >> Aggregating TranscriptDb... >> > >> > >>> > > > > >> Parsing transcripts... >> > >> > >>> > > > > >> Parsing exons... >> > >> > >>> > > > > >> Parsing cds... >> > >> > >>> > > > > >> Parsing utrs... >> > >> > >>> > > > > >> ------exons... >> > >> > >>> > > > > >> ------cdss... >> > >> > >>> > > > > >> ------introns... >> > >> > >>> > > > > >> ------utr... >> > >> > >>> > > > > >> aggregating... >> > >> > >>> > > > > >> Done >> > >> > >>> > > > > >> Constructing graphics... >> > >> > >>> > > > > >> Error in sapply(listData, function(Xi) >> > >> > >>> > > > > >> extends(class(Xi), >> > >> > >>> > > > > >> elementTypeX)) : >> > >> > >>> > > > > >> error in evaluating the argument 'X' in >> > >> > >>> > > > > >> selecting >> > >> > >>> > > > > >> a >> > >> > >>> > > > > >> method >> > >> > >>> > > > > >> for >> > >> > >>> > > > > >> function 'sapply': Error in >> > >> > >>> > > > > >> unlist(range(ranges(x.n, >> > >> > >>> > > > > >> ignore.strand >> > >> > >>> > > > > >> = >> > >> > >>> > > > > >> TRUE))) : >> > >> > >>> > > > > >> error in evaluating the argument 'x' in >> > >> > >>> > > > > >> selecting >> > >> > >>> > > > > >> a >> > >> > >>> > > > > >> method >> > >> > >>> > > > > >> for >> > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : >> > >> > >>> > > > > >> unused >> > >> > >>> > > > > >> argument >> > >> > >>> > > > > >> (ignore.strand = TRUE) >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> > traceback() >> > >> > >>> > > > > >> 15: sapply(listData, function(Xi) >> > >> > >>> > > > > >> extends(class(Xi), >> > >> > >>> > > > > >> elementTypeX)) >> > >> > >>> > > > > >> 14: .updateCompressedList(X, >> > >lapply_CompressedList(X, >> > >> > >>> > > > > >> FUN, >> > >> > >>> > > > > >> ...)) >> > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { >> > >> > >>> > > > > >> if (!is.null( group.name )) { >> > >> > >>> > > > > >> if (!group.selfish) { >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> > >> > >>> > > > > >> TRUE))) >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> > >> > >>> > > > > >> width(irs) + >> > >> > >>> > > > > >> extend.size) >> > >> > >>> > > > > >> irs.new <- sort(irs.new) >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, >> > >> > >>> > > > > >> group.name ])] >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> else { >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> > >> > >>> > > > > >> group.name ])) >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> else { >> > >> > >>> > > > > >> irs <- ranges(x) >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> > >> > >>> > > > > >> fix = "center", width = width(irs) + >> > >> > >>> > > > > >> extend.size))) >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> }) >> > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { >> > >> > >>> > > > > >> if (!is.null( group.name )) { >> > >> > >>> > > > > >> if (!group.selfish) { >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> > >> > >>> > > > > >> TRUE))) >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> > >> > >>> > > > > >> width(irs) + >> > >> > >>> > > > > >> extend.size) >> > >> > >>> > > > > >> irs.new <- sort(irs.new) >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, >> > >> > >>> > > > > >> group.name ])] >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> else { >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> > >> > >>> > > > > >> group.name ])) >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> else { >> > >> > >>> > > > > >> irs <- ranges(x) >> > >> > >>> > > > > >> values(x)$stepping <- >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> > >> > >>> > > > > >> fix = "center", width = width(irs) + >> > >> > >>> > > > > >> extend.size))) >> > >> > >>> > > > > >> x >> > >> > >>> > > > > >> } >> > >> > >>> > > > > >> }) >> > >> > >>> > > > > >> 11: .local(obj, ...) >> > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", >> > >> > >>> > > > > >> group.selfish = >> > >> > >>> > > > > >> FALSE, >> > >> > >>> > > > > >> fix = "start", extend.size = es) >> > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", >> > >group.selfish >> > >> > >>> > > > > >> = >> > >> > >>> > > > > >> FALSE, >> > >> > >>> > > > > >> fix = "start", extend.size = es) >> > >> > >>> > > > > >> 8: .local(data, ...) >> > >> > >>> > > > > >> 7: (function (data, ...) >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4>> > >> > >>> > > > > >> object >> > >> > >>> > > > > >> of >> > >> > >>> > > > > >> class >> > >> > >>> > > > > >> "TranscriptDb">, >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> > >> > >>> > > > > >> "alignment", >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", >> > >> > >>> > > > > >> label >> > >> > >>> > > > > >> = >> > >> > >>> > > > > >> TRUE, >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> > >> > >>> > > > > >> 6: (function (data, ...) >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4>> > >> > >>> > > > > >> object >> > >> > >>> > > > > >> of >> > >> > >>> > > > > >> class >> > >> > >>> > > > > >> "TranscriptDb">, >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> > >> > >>> > > > > >> "alignment", >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", >> > >> > >>> > > > > >> label >> > >> > >>> > > > > >> = >> > >> > >>> > > > > >> TRUE, >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) >> > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) >> > >> > >>> > > > > >> 3: .local(object, ...) >> > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> > sessionInfo() >> > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) >> > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> locale: >> > >> > >>> > > > > >> [1] >> > >> > >>> > > > > >> >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> attached base packages: >> > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils >> > >> > >>> > > > > >> datasets >> > >> > >>> > > > > >> methods base >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> other attached packages: >> > >> > >>> > > > > >> [1] XVector_0.4.0 >> > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> > >> > >>> > > > > >> GenomicFeatures_1.16.0 >> > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> > >> > >>> > > > > >> GenomicRanges_1.16.2 >> > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> > >> > >>> > > > > >> ggbio_1.12.0 >> > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> loaded via a namespace (and not attached): >> > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 >> > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 >> > >> > >>> > > > > >> Biostrings_2.32.0 >> > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 >> > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 >> > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 >> > >> > >>> > > > > >> Formula_1.1-1 >> > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 >> > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 >> > >> > >>> > > > > >> Hmisc_3.14-4 >> > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 >> > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 >> > >> > >>> > > > > >> MASS_7.3-31 >> > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 >> > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 >> > >> > >>> > > > > >> Rcpp_0.11.1 >> > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 >> > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 >> > >> > >>> > > > > >> stringr_0.6.2 >> > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 >> > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 >> > >> > >>> > > > > >> zlibbioc_1.10.0 >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > > -- >> > >> > >>> > > > > > Tengfei Yin, PhD >> > >> > >>> > > > > > Seven Bridges Genomics >> > >> > >>> > > > > > sbgenomics.com >> > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 >> > >> > >>> > > > > > Cambridge, MA 02138 >> > >> > >>> > > > > > (617) 866-0446 >> > >> > >>> > > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > -- >> > >> > >>> > > > > Tengfei Yin, PhD >> > >> > >>> > > > > Seven Bridges Genomics >> > >> > >>> > > > > sbgenomics.com >> > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 >> > >> > >>> > > > > Cambridge, MA 02138 >> > >> > >>> > > > > (617) 866-0446 >> > >> > >>> > > > > >> > >> > >>> > > > > [[alternative HTML version deleted]] >> > >> > >>> > > > > >> > >> > >>> > > > > _______________________________________________ >> > >> > >>> > > > > Bioconductor mailing list >> > >> > >>> > > > > Bioconductor at r-project.org >> > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >> > >>> > > > > Search the archives: >> > >> > >>> > > > > >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >>> > > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > -- >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > Tengfei Yin, PhD >> > >> > >>> > > > Seven Bridges Genomics >> > >> > >>> > > > sbgenomics.com >> > >> > >>> > > > 625 Mt. Auburn St. Suite #208 >> > >> > >>> > > > Cambridge, MA 02138 >> > >> > >>> > > > (617) 866- 0446 >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > -- >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > Tengfei Yin, PhD >> > >> > >>> > > Seven Bridges Genomics >> > >> > >>> > > sbgenomics.com >> > >> > >>> > > 625 Mt. Auburn St. Suite #208 >> > >> > >>> > > Cambridge, MA 02138 >> > >> > >>> > > (617) 866- 0446 >> > >> > >>> > > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > -- >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > Tengfei Yin, PhD >> > >> > >>> > Seven Bridges Genomics >> > >> > >>> > sbgenomics.com >> > >> > >>> > 625 Mt. Auburn St. Suite #208 >> > >> > >>> > Cambridge, MA 02138 >> > >> > >>> > (617) 866- 0446 >> > >> > >>> > >> > >> > >> >> > >> > >> >> > >> > >> >> > >> > >> >> > >> > >> -- >> > >> > >> Tengfei Yin, PhD >> > >> > >> Seven Bridges Genomics >> > >> > >> sbgenomics.com >> > >> > >> 625 Mt. Auburn St. Suite #208 >> > >> > >> Cambridge, MA 02138 >> > >> > >> (617) 866-0446 >> > >> > >> > >> >> > >> > >> > >> > >> > >> > >> > -- >> > >> > >> > Tengfei Yin, PhD >> > Seven Bridges Genomics >> > sbgenomics.com >> > 625 Mt. Auburn St. Suite #208 >> > Cambridge, MA 02138 >> > (617) 866- 0446 >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
it's good it's building, but it's very weird that it works, because I simply removed eval = TRUE for that chunk which is default. I came across some really weird *bug* in knitr which I try to reproduce with a minimal example, if you look closely, I put three blank code chunk at the front to avoid the figures orders being messed up somehow and I don't know why. I guess until I have a minimal example, I cannot really report it to yihui to fix it. On Tue, Apr 29, 2014 at 7:03 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > I just noticed that ggbio is building now > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > and I'm happy to report that the problem I mentioned is resolved with > ggbio 1.12.3. Thank you Tengfei and Dan! > > > For reference, here is the working session information. > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 > [5] Biobase_2.24.0 GenomicRanges_1.16.2 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 > [9] ggbio_1.12.3 ggplot2_0.9.3.1 > [11] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 > [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 > [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 > [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 > [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 > [25] labeling_0.2 lattice_0.20-29 latticeExtra_0.6-26 > [28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1 > [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > [34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0 > [37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4 > [40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 > [43] stringr_0.6.2 survival_2.37-7 tools_3.1.0 > [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 > > On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > wrote: > > > > > > ----- Original Message ----- > >> From: "Dan Tenenbaum" <dtenenba@fhcrc.org> > >> To: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> Cc: lcollado@jhu.edu, "Bioconductor mailing list" < > bioconductor@r-project.org> > >> Sent: Saturday, April 26, 2014 7:33:41 PM > >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken > >> > >> > >> > >> ----- Original Message ----- > >> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> > To: lcollado@jhu.edu > >> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing > >> > list" <bioconductor@r-project.org> > >> > Sent: Saturday, April 26, 2014 1:58:01 PM > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > >> > broken > >> > > >> > > >> > right, it's failing to build and I am trying to figure out why now, > >> > because it passes check/build and works on my laptop, but it > >> > doesn't > >> > pass bioc build for both release and devel, let me dig into it > >> > tonight. > >> > > >> > >> Seems like this could be fixed if you just add > >> > >> library(ggbio) > >> > >> to your vignette before the ggbio() function is called on line 557 of > >> vignettes/realvignettes/ggbio.Rnw. > >> > > > > Sorry, I spoke too soon; that just changes the error message you receive. > > Dan > > > > > >> Dan > >> > >> > >> > > >> > thanks for your patience > >> > > >> > > >> > Tengfei > >> > > >> > > >> > > >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < > >> > lcollado@jhsph.edu > wrote: > >> > > >> > > >> > > >> > Oh ok. Thanks for the info > >> > > >> > > >> > > >> > > >> > > >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < > >> > dtenenba@fhcrc.org > >> > > wrote: > >> > > >> > > >> > > >> > > >> > > >> > Leonardo Collado Torres < lcollado@jhsph.edu > wrote: > >> > > >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC > >> > >release? > >> > > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html > >> > >still > >> > >points to 1.12.0 > >> > > > >> > > >> > It's failing to build: > >> > > >> > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > >> > > >> > > >> > > >> > Dan > >> > > >> > > > >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < > >> > >dtenenba@fhcrc.org > >> > >> > >> > >wrote: > >> > > > >> > >> > >> > >> > >> > >> ----- Original Message ----- > >> > >> > From: "Leonardo Collado Torres" < lcollado@jhsph.edu > > >> > >> > To: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >> > Cc: "Dan Tenenbaum" < dtenenba@fhcrc.org >, "Bioconductor > >> > >> > mailing > >> > >list" < > >> > >> bioconductor@r-project.org > > >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM > >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >> > >> > is > >> > >broken > >> > >> > > >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. See > >> > >> > below > >> > >> > again >.< > >> > >> > > >> > >> > On the email topic, is it possible to be subscribed with 2 > >> > >> > emails > >> > >> > accounts to the BioC mailing list but only get emails with > >> > >> > one? > >> > >> > I > >> > >> > believe that I have to choose to either get the daily digest > >> > >> > or > >> > >> > get > >> > >a > >> > >> > single for every message sent. If not, I'll probably just drop > >> > >> > my > >> > >> > @ jhsph.edu subscription and re-subscribe with the new @ > >> > >> > jhu.edu > >> > >> > mail > >> > >I > >> > >> > got (our university is pushing these mails). > >> > >> > > >> > >> > >> > >> I don't know; you could try it. Another option would be to > >> > >> configure > >> > >your > >> > >> mail client with a filter to drop the undesired bioc emails. > >> > >> > >> > >> Dan > >> > >> > >> > >> > >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > >> > >> > < lcollado@jhu.edu > wrote: > >> > >> > > Hi Dan, > >> > >> > > > >> > >> > > I got RSwitch to work with a second installation of R 3.1. > >> > >> > > Basically, > >> > >> > > I downloaded the leopard tarball, expanded it, renamed the > >> > >> > > folder > >> > >> > > 3.1 > >> > >> > > to 3.1patched (which is the version I downloaded, but well, > >> > >> > > anything > >> > >> > > except for 3.1 would work), compressed it again, and then > >> > >expanded > >> > >> > > it > >> > >> > > at the root location. > >> > >> > > > >> > >> > > So it would be something like this: > >> > >> > > > >> > >> > > wget > >> > >> > > > >> > >> > >> > > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > >> > >> > > tar -xvf R-*gz > >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1 > >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched > >> > >> > > tar -cvzf Rlib.tgz Library > >> > >> > > sudo tar fvxz Rlib.tgz -C / > >> > >> > > > >> > >> > > Then used RSwitch, and was able to install BioC-devel. > >> > >> > > > >> > >> > > I might try out your renv at a different time. It's great > >> > >> > > to > >> > >know > >> > >> > > that it exists =) > >> > >> > > > >> > >> > > Cheers, > >> > >> > > Leo > >> > >> > > > >> > >> > > > >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > >> > >> > > < tengfei.yin@sbgenomics.com > wrote: > >> > >> > >> Hi Dan, > >> > >> > >> > >> > >> > >> It works like a charm, thanks! > >> > >> > >> > >> > >> > >> I use your method, then I changed /Library/Framework/ > >> > >> > >> folder > >> > >> > >> and > >> > >> > >> R.Framework > >> > >> > >> folder ownership to myself so I don't have to sudo it, then > >> > >> > >> I > >> > >just > >> > >> > >> add alias > >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R > >> > >> > >> first. > >> > >> > >> This solves > >> > >> > >> my problem. > >> > >> > >> > >> > >> > >> Try to customize variable for R hooks in emacs as > >> > >> > >> alternative > >> > >> > >> solution, but > >> > >> > >> may need more time. > >> > >> > >> > >> > >> > >> Thanks again! > >> > >> > >> > >> > >> > >> Tengfei > >> > >> > >> > >> > >> > >> > >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > >> > >> > >> < dtenenba@fhcrc.org > wrote: > >> > >> > >>> > >> > >> > >>> Hi Tengfei, > >> > >> > >>> > >> > >> > >>> ----- Original Message ----- > >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> > >> > >>> > Cc: "Bioconductor mailing list" < > >> > >> > >>> > bioconductor@r-project.org >, > >> > >> > >>> > lcollado@jhu.edu > >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >> > >>> > example > >> > >> > >>> > is broken > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all > >> > >> > >>> > on > >> > >the > >> > >> > >>> > R 3.1? > >> > >> > >>> > >> > >> > >>> Yes, install two copies of R 3.1 and switch between them. > >> > >> > >>> > >> > >> > >>> > And do some sort of switch for bioc? The website you > >> > >> > >>> > send > >> > >> > >>> > to > >> > >me > >> > >> > >>> > also > >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on > >> > >R-devel > >> > >> > >>> > and > >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R > >> > >> > >>> > only > >> > >to > >> > >> > >>> > switch bioc, so that I could debug and maintain released > >> > >> > >>> > and > >> > >> > >>> > devel > >> > >> > >>> > version. > >> > >> > >>> > >> > >> > >>> PLEASE don't use R-devel at all. > >> > >> > >>> > >> > >> > >>> Just use R-3.1.0. > >> > >> > >>> > >> > >> > >>> You can use the Rswitch app but as you point out it won't > >> > >> > >>> work > >> > >> > >>> within > >> > >> > >>> emacs. > >> > >> > >>> > >> > >> > >>> This is what I do: > >> > >> > >>> > >> > >> > >>> Every time I download a new version of R, I run its > >> > >> > >>> installer. > >> > >> > >>> The > >> > >> > >>> installer always puts it in > >> > >> > >>> > >> > >> > >>> /Library/Frameworks/R.framework > >> > >> > >>> > >> > >> > >>> So after I install each version of R, I rename the > >> > >> > >>> R.framework > >> > >> > >>> directory > >> > >> > >>> to something like > >> > >> > >>> R.framework.bioc214_snowleopard > >> > >> > >>> > >> > >> > >>> And then I make a symlink from > >> > >> > >>> R.framework.bioc214_snowleopard > >> > >to > >> > >> > >>> R.framework. > >> > >> > >>> > >> > >> > >>> I have a little script at https://github.com/dtenenba/renv > >> > >which > >> > >> > >>> lets me > >> > >> > >>> see what the various installed Rs are: > >> > >> > >>> > >> > >> > >>> $renv > >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> > >> > >>> > >> > >> > >>> This tells me that the currently active R is nicknamed > >> > >> > >>> "releaseMav" (this > >> > >> > >>> means there is a link from > >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to > >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions, > >> > >> > >>> svn > >> > >> > >>> revisions, > >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 is > >> > >> > >>> Snow > >> > >> > >>> Leopard; > >> > >> > >>> darwin13.1.0 is Mavericks). > >> > >> > >>> > >> > >> > >>> Note that in my nomenclature devel means BioC devel, not > >> > >R-devel. > >> > >> > >>> > >> > >> > >>> So if I wanted to switch to the "develSL" version I would > >> > >> > >>> do: > >> > >> > >>> > >> > >> > >>> sudo renv develSL > >> > >> > >>> > >> > >> > >>> HTH > >> > >> > >>> Dan > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >> > >> > >>> > dtenenba@fhcrc.org > > >> > >> > >>> > wrote: > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > Hi Tengfei, > >> > >> > >>> > > >> > >> > >>> > ----- Original Message ----- > >> > >> > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >> > >>> > > >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> > >> > >>> > > Cc: "Bioconductor mailing list" < > >> > > bioconductor@r-project.org > >> > >> > >>> > > >, > >> > >> > >>> > > lcollado@jhu.edu > >> > >> > >>> > > >> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >> > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> > >example > >> > >> > >>> > > is > >> > >> > >>> > > broken > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I > >> > >> > >>> > > am > >> > >still > >> > >> > >>> > > a > >> > >> > >>> > > newbie to OSX ... I got R-devel running and I will try > >> > >> > >>> > > Rswitcher, I > >> > >> > >>> > > also want to do that switch easily in emacs too. > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) > >> > >> > >>> > and > >> > >> > >>> > BioC > >> > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released > >> > >> > >>> > version of > >> > >> > >>> > R. > >> > >> > >>> > > >> > >> > >>> > I think the Rswitch app just sets a symbolic link, so > >> > >> > >>> > you > >> > >> > >>> > should be > >> > >> > >>> > able to do that within emacs. Run it and see what it > >> > >> > >>> > does > >> > >> > >>> > to > >> > >> > >>> > /Library/Frameworks/R.framework. > >> > >> > >>> > > >> > >> > >>> > Dan > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > > >> > >> > >>> > > cheers > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > Tengfei > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >> > >> > >>> > > dtenenba@fhcrc.org > >> > >> > >>> > > > > >> > >> > >>> > > wrote: > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > ----- Original Message ----- > >> > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >> > >>> > > > >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> > >> > >>> > > > Cc: "Bioconductor mailing list" < > >> > >> > >>> > > > bioconductor@r-project.org >, > >> > >> > >>> > > > lcollado@jhu.edu > >> > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >> > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > >> > >> > >>> > > > txdb > >> > >> > >>> > > > example is > >> > >> > >>> > > > broken > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > >> > >> > >>> > > > Hi Dan, > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it > >> > >should > >> > >> > >>> > > > work? > >> > >> > >>> > > > >> > >> > >>> > > Yes. > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > ? Is > >> > >> > >>> > > > there a way to build from source using biocLite, > >> > >> > >>> > > > like > >> > >type > >> > >> > >>> > > > = > >> > >> > >>> > > > "source", this is what I got > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > library(BiocInstaller) > >> > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), > >> > >?biocLite > >> > >> > >>> > > > for > >> > >> > >>> > > > help > >> > >> > >>> > > > > biocLite("GenomicRanges") > >> > >> > >>> > > > BioC_mirror: http://bioconductor.org > >> > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller > >> > >> > >>> > > > 1.14.1), R > >> > >> > >>> > > > version > >> > >> > >>> > > > 3.1.0. > >> > >> > >>> > > > Installing package(s) 'GenomicRanges' > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > package âGenomicRangesâ is available as a source > >> > >> > >>> > > > package > >> > >> > >>> > > > but not > >> > >> > >>> > > > as > >> > >> > >>> > > > a > >> > >> > >>> > > > binary > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > Warning message: > >> > >> > >>> > > > package âGenomicRangesâ is not available (for R > >> > >> > >>> > > > version > >> > >> > >>> > > > 3.1.0) > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > Just wondering is there a solution without > >> > >> > >>> > > > re-install > >> > >> > >>> > > > R > >> > >for > >> > >> > >>> > > > snow > >> > >> > >>> > > > leopard. And what's the plan for maverick? > >> > >> > >>> > > > > >> > >> > >>> > > > >> > >> > >>> > > You can do > >> > >> > >>> > > biocLite("GenomicRanges", type="source") > >> > >> > >>> > > > >> > >> > >>> > > but you need to have the appropriate compilers, etc. > >> > >> > >>> > > > >> > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. > >> > >> > >>> > > You > >> > >can > >> > >> > >>> > > have > >> > >> > >>> > > multiple installations of R on your Mac and switch > >> > >> > >>> > > between > >> > >> > >>> > > them > >> > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or > >> > >another > >> > >> > >>> > > easy > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > mechanism. > >> > >> > >>> > > > >> > >> > >>> > > We are building packages for Mavericks now, we just > >> > >> > >>> > > have > >> > >> > >>> > > to > >> > >> > >>> > > resolve > >> > >> > >>> > > a > >> > >> > >>> > > few build issues and test the resulting packages, we > >> > >> > >>> > > still > >> > >> > >>> > > hope to > >> > >> > >>> > > have them available by the end of the month. But since > >> > >> > >>> > > you > >> > >> > >>> > > can > >> > >> > >>> > > install the Snow Leopard build without needing to > >> > >> > >>> > > remove > >> > >your > >> > >> > >>> > > Mavericks build, you should do that. > >> > >> > >>> > > > >> > >> > >>> > > Dan > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > > >> > >> > >>> > > > Thanks > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > Tengfei > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >> > >> > >>> > > > dtenenba@fhcrc.org > >> > >> > >>> > > > > wrote: > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > Hi Tengfei, > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > ----- Original Message ----- > >> > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> > >> > >>> > > > > To: lcollado@jhu.edu > >> > >> > >>> > > > > Cc: bioconductor@r-project.org > >> > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >> > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > >> > >> > >>> > > > > txdb > >> > >> > >>> > > > > example > >> > >> > >>> > > > > is > >> > >> > >>> > > > > broken > >> > >> > >>> > > > > > >> > >> > >>> > > > > btw, based on the error, let me try to debug it. > >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >> > >> > >>> > > > > < tengfei.yin@sbgenomics.com >wrote: > >> > >> > >>> > > > > > >> > >> > >>> > > > > > Hi Leonardo, > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > Frankly speaking, the vignette is still in > >> > >> > >>> > > > > > progress, > >> > >> > >>> > > > > > and > >> > >> > >>> > > > > > there > >> > >> > >>> > > > > > are > >> > >> > >>> > > > > > some > >> > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying > >> > >> > >>> > > > > > to > >> > >find > >> > >> > >>> > > > > > a > >> > >> > >>> > > > > > time > >> > >> > >>> > > > > > to > >> > >> > >>> > > > > > do that > >> > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and > >> > >> > >>> > > > > > Bioc > >> > >> > >>> > > > > > 2.14 on > >> > >> > >>> > > > > > my > >> > >> > >>> > > > > > new MBP > >> > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build > >> > >> > >>> > > > > > is > >> > >not > >> > >> > >>> > > > > > ready > >> > >> > >>> > > > > > for > >> > >> > >>> > > > > > maverick > >> > >> > >>> > > > > > yet, maybe available by the end of April? > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > Thanks for reporting the bug, I will keep you > >> > >> > >>> > > > > > posted > >> > >on > >> > >> > >>> > > > > > this > >> > >> > >>> > > > > > when > >> > >> > >>> > > > > > I > >> > >> > >>> > > > > > successfully get it on my laptop and start > >> > >> > >>> > > > > > fixing > >> > >> > >>> > > > > > the > >> > >> > >>> > > > > > problems. > >> > >> > >>> > > > > > > >> > >> > >>> > > > > >> > >> > >>> > > > You can install the Snow Leopard build of R and > >> > >> > >>> > > > should > >> > >have > >> > >> > >>> > > > no > >> > >> > >>> > > > problems, binary packages are available for that > >> > >> > >>> > > > version. > >> > >> > >>> > > > It will > >> > >> > >>> > > > run fine on Mavericks. > >> > >> > >>> > > > > >> > >> > >>> > > > Dan > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > > cheers > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > Tengfei > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo > >> > >> > >>> > > > > > Collado > >> > >> > >>> > > > > > Torres < > >> > >> > >>> > > > > > lcollado@jhsph.edu > wrote: > >> > >> > >>> > > > > > > >> > >> > >>> > > > > >> Hello Tengfei + bioc list, > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> From > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > >> > >> > >> > > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > >> > >> > >>> > > > > >> page 4 (complied on april 11 2014), the > >> > >> > >>> > > > > >> following > >> > >> > >>> > > > > >> example > >> > >> > >>> > > > > >> loads > >> > >> > >>> > > > > >> to > >> > >> > >>> > > > > >> an > >> > >> > >>> > > > > >> error as shown below. I wasn't seeing this > >> > >> > >>> > > > > >> error > >> > >> > >>> > > > > >> before > >> > >> > >>> > > > > >> (aka, > >> > >> > >>> > > > > >> last > >> > >> > >>> > > > > >> week). The only guess that comes to mind is the > >> > >recent > >> > >> > >>> > > > > >> update > >> > >> > >>> > > > > >> to > >> > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't > >> > >> > >>> > > > > >> seem > >> > >> > >>> > > > > >> to > >> > >> > >>> > > > > >> be > >> > >> > >>> > > > > >> related > >> > >> > >>> > > > > >> from > >> > >> > >>> > > > > >> the traceback() output, well... maybe it's > >> > >> > >>> > > > > >> related > >> > >to > >> > >> > >>> > > > > >> the > >> > >> > >>> > > > > >> ignore.strand = TRUE part as described in the > >> > >> > >>> > > > > >> error. > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> I'll create a GitHub issue just for > >> > >> > >>> > > > > >> completeness. > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> Thank you, > >> > >> > >>> > > > > >> Leonardo > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > library(ggbio) > >> > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> > >> > >>> > > > > >> ## Removed the output > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") > >> > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > >> > >> > >>> > > > > >> > genesymbol["BRCA1"]) > >> > >> > >>> > > > > >> Aggregating TranscriptDb... > >> > >> > >>> > > > > >> Parsing transcripts... > >> > >> > >>> > > > > >> Parsing exons... > >> > >> > >>> > > > > >> Parsing cds... > >> > >> > >>> > > > > >> Parsing utrs... > >> > >> > >>> > > > > >> ------exons... > >> > >> > >>> > > > > >> ------cdss... > >> > >> > >>> > > > > >> ------introns... > >> > >> > >>> > > > > >> ------utr... > >> > >> > >>> > > > > >> aggregating... > >> > >> > >>> > > > > >> Done > >> > >> > >>> > > > > >> Constructing graphics... > >> > >> > >>> > > > > >> Error in sapply(listData, function(Xi) > >> > >> > >>> > > > > >> extends(class(Xi), > >> > >> > >>> > > > > >> elementTypeX)) : > >> > >> > >>> > > > > >> error in evaluating the argument 'X' in > >> > >> > >>> > > > > >> selecting > >> > >> > >>> > > > > >> a > >> > >> > >>> > > > > >> method > >> > >> > >>> > > > > >> for > >> > >> > >>> > > > > >> function 'sapply': Error in > >> > >> > >>> > > > > >> unlist(range(ranges(x.n, > >> > >> > >>> > > > > >> ignore.strand > >> > >> > >>> > > > > >> = > >> > >> > >>> > > > > >> TRUE))) : > >> > >> > >>> > > > > >> error in evaluating the argument 'x' in > >> > >> > >>> > > > > >> selecting > >> > >> > >>> > > > > >> a > >> > >> > >>> > > > > >> method > >> > >> > >>> > > > > >> for > >> > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : > >> > >> > >>> > > > > >> unused > >> > >> > >>> > > > > >> argument > >> > >> > >>> > > > > >> (ignore.strand = TRUE) > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > traceback() > >> > >> > >>> > > > > >> 15: sapply(listData, function(Xi) > >> > >> > >>> > > > > >> extends(class(Xi), > >> > >> > >>> > > > > >> elementTypeX)) > >> > >> > >>> > > > > >> 14: .updateCompressedList(X, > >> > >lapply_CompressedList(X, > >> > >> > >>> > > > > >> FUN, > >> > >> > >>> > > > > >> ...)) > >> > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > >> > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >> > >>> > > > > >> if (!group.selfish) { > >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >> > >>> > > > > >> TRUE))) > >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >> > >>> > > > > >> width(irs) + > >> > >> > >>> > > > > >> extend.size) > >> > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >> > >>> > > > > >> values(x)$stepping <- > >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >> > >>> > > > > >> group.name ])] > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> else { > >> > >> > >>> > > > > >> values(x)$stepping <- > >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >> > >>> > > > > >> group.name ])) > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> else { > >> > >> > >>> > > > > >> irs <- ranges(x) > >> > >> > >>> > > > > >> values(x)$stepping <- > >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >> > >>> > > > > >> extend.size))) > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> }) > >> > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > >> > >> > >>> > > > > >> if (!is.null( group.name )) { > >> > >> > >>> > > > > >> if (!group.selfish) { > >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> > >> > >>> > > > > >> TRUE))) > >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> > >> > >>> > > > > >> width(irs) + > >> > >> > >>> > > > > >> extend.size) > >> > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> > >> > >>> > > > > >> values(x)$stepping <- > >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> > >> > >>> > > > > >> group.name ])] > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> else { > >> > >> > >>> > > > > >> values(x)$stepping <- > >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> > >> > >>> > > > > >> group.name ])) > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> else { > >> > >> > >>> > > > > >> irs <- ranges(x) > >> > >> > >>> > > > > >> values(x)stepping <- > >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> > >> > >>> > > > > >> extend.size))) > >> > >> > >>> > > > > >> x > >> > >> > >>> > > > > >> } > >> > >> > >>> > > > > >> }) > >> > >> > >>> > > > > >> 11: .local(obj, ...) > >> > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > >> > >> > >>> > > > > >> group.selfish = > >> > >> > >>> > > > > >> FALSE, > >> > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", > >> > >group.selfish > >> > >> > >>> > > > > >> = > >> > >> > >>> > > > > >> FALSE, > >> > >> > >>> > > > > >> fix = "start", extend.size = es) > >> > >> > >>> > > > > >> 8: .local(data, ...) > >> > >> > >>> > > > > >> 7: (function (data, ...) > >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> > >> > >>> > > > > >> object > >> > >> > >>> > > > > >> of > >> > >> > >>> > > > > >> class > >> > >> > >>> > > > > >> "TranscriptDb">, > >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >> > >>> > > > > >> "alignment", > >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > >> > >> > >>> > > > > >> label > >> > >> > >>> > > > > >> = > >> > >> > >>> > > > > >> TRUE, > >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >> > >>> > > > > >> 6: (function (data, ...) > >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> > >> > >>> > > > > >> object > >> > >> > >>> > > > > >> of > >> > >> > >>> > > > > >> class > >> > >> > >>> > > > > >> "TranscriptDb">, > >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> > >> > >>> > > > > >> "alignment", > >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > >> > >> > >>> > > > > >> label > >> > >> > >>> > > > > >> = > >> > >> > >>> > > > > >> TRUE, > >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) > >> > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) > >> > >> > >>> > > > > >> 3: .local(object, ...) > >> > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> > sessionInfo() > >> > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) > >> > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> locale: > >> > >> > >>> > > > > >> [1] > >> > >> > >>> > > > > >> > >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> attached base packages: > >> > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils > >> > >> > >>> > > > > >> datasets > >> > >> > >>> > > > > >> methods base > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> other attached packages: > >> > >> > >>> > > > > >> [1] XVector_0.4.0 > >> > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> > >> > >>> > > > > >> GenomicFeatures_1.16.0 > >> > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> > >> > >>> > > > > >> GenomicRanges_1.16.2 > >> > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> > >> > >>> > > > > >> ggbio_1.12.0 > >> > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > >> loaded via a namespace (and not attached): > >> > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> > >> > >>> > > > > >> Biostrings_2.32.0 > >> > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >> > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > >> > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > >> > >> > >>> > > > > >> Formula_1.1-1 > >> > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> > >> > >>> > > > > >> Hmisc_3.14-4 > >> > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 > >> > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 > >> > >> > >>> > > > > >> MASS_7.3-31 > >> > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > >> > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 > >> > >> > >>> > > > > >> Rcpp_0.11.1 > >> > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >> > >> > >>> > > > > >> stringr_0.6.2 > >> > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 > >> > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> > >> > >>> > > > > >> zlibbioc_1.10.0 > >> > >> > >>> > > > > >> > > >> > >> > >>> > > > > >> > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > -- > >> > >> > >>> > > > > > Tengfei Yin, PhD > >> > >> > >>> > > > > > Seven Bridges Genomics > >> > >> > >>> > > > > > sbgenomics.com > >> > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 > >> > >> > >>> > > > > > Cambridge, MA 02138 > >> > >> > >>> > > > > > (617) 866-0446 > >> > >> > >>> > > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > > >> > >> > >>> > > > > -- > >> > >> > >>> > > > > Tengfei Yin, PhD > >> > >> > >>> > > > > Seven Bridges Genomics > >> > >> > >>> > > > > sbgenomics.com > >> > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 > >> > >> > >>> > > > > Cambridge, MA 02138 > >> > >> > >>> > > > > (617) 866-0446 > >> > >> > >>> > > > > > >> > >> > >>> > > > > [[alternative HTML version deleted]] > >> > >> > >>> > > > > > >> > >> > >>> > > > > _______________________________________________ > >> > >> > >>> > > > > Bioconductor mailing list > >> > >> > >>> > > > > Bioconductor@r-project.org > >> > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> > >>> > > > > Search the archives: > >> > >> > >>> > > > > > >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > >>> > > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > -- > >> > >> > >>> > > > > >> > >> > >>> > > > > >> > >> > >>> > > > Tengfei Yin, PhD > >> > >> > >>> > > > Seven Bridges Genomics > >> > >> > >>> > > > sbgenomics.com > >> > >> > >>> > > > 625 Mt. Auburn St. Suite #208 > >> > >> > >>> > > > Cambridge, MA 02138 > >> > >> > >>> > > > (617) 866- 0446 > >> > >> > >>> > > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > -- > >> > >> > >>> > > > >> > >> > >>> > > > >> > >> > >>> > > Tengfei Yin, PhD > >> > >> > >>> > > Seven Bridges Genomics > >> > >> > >>> > > sbgenomics.com > >> > >> > >>> > > 625 Mt. Auburn St. Suite #208 > >> > >> > >>> > > Cambridge, MA 02138 > >> > >> > >>> > > (617) 866- 0446 > >> > >> > >>> > > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > -- > >> > >> > >>> > > >> > >> > >>> > > >> > >> > >>> > Tengfei Yin, PhD > >> > >> > >>> > Seven Bridges Genomics > >> > >> > >>> > sbgenomics.com > >> > >> > >>> > 625 Mt. Auburn St. Suite #208 > >> > >> > >>> > Cambridge, MA 02138 > >> > >> > >>> > (617) 866- 0446 > >> > >> > >>> > > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> -- > >> > >> > >> Tengfei Yin, PhD > >> > >> > >> Seven Bridges Genomics > >> > >> > >> sbgenomics.com > >> > >> > >> 625 Mt. Auburn St. Suite #208 > >> > >> > >> Cambridge, MA 02138 > >> > >> > >> (617) 866-0446 > >> > >> > > >> > >> > >> > > >> > > >> > > >> > > >> > > >> > > >> > -- > >> > > >> > > >> > Tengfei Yin, PhD > >> > Seven Bridges Genomics > >> > sbgenomics.com > >> > 625 Mt. Auburn St. Suite #208 > >> > Cambridge, MA 02138 > >> > (617) 866- 0446 > >> > > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]] ADD REPLY 0 Entering edit mode Hi Tengfei, Interesting, I don't really know what's the issue with the bug you found. Looking into ggbio 1.12.3 I noticed a couple of things with autoplot(txdb). Basically, I found three cases. Case 1: function works well, just a message that looks like a warning (it's a message) is printed out. Nothing biggie. Case 2: Labels when using tx_name(gene_id) don't work (although they work in case 1) but they do work individually. Case 3: Function fails because there is nothing in that region. The code is shown below where you only have to specify the region of interest according to the case. Previously, I would use something like this (shown below) to catch case 3. p.transcripts <- tryCatch(autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)"), warning = function(w) { FALSE }) Now that it results in an error, I can detect these cases using: p.transcripts <- tryCatch(autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)"), error = function(e) { FALSE }) However, I thought that this would be a good time to report this. Regarding case 2, in my use case I'm thinking of switching to "tx_name" instead of using "tx_name(gene_id)". But well, it's also worth reporting. ## Case 1 & 2 show the following 'message' that looks like a warning though "gap" is not matching to following arbitrary model terms"cds CDS Cds exon EXON Exon utr UTR Utr" ## Case 3 error Error in data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, : arguments imply differing number of rows: 0, 1 > traceback() 13: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA) 12: data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, type = "exon") 11: .local(obj, ...) 10: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = truncate.fun, ratio = ratio, columns = columns) 9: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = truncate.fun, ratio = ratio, columns = columns) 8: .local(data, ...) 7: (function (data, ...) standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="" "transcriptdb"="">, truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, which = <s4 object="" of="" class="" "granges"="">, list()) 6: (function (data, ...) standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="" "transcriptdb"="">, truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, which = <s4 object="" of="" class="" "granges"="">, list()) 5: do.call(geom_alignment, args.res) 4: do.call(geom_alignment, args.res) 3: .local(object, ...) 2: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") 1: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") Here's the code. ## Load required libs library(ggbio) library(GenomicRanges) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene ### Set up region ## Case 1: Labels don't work for tx_name(gene_id) case # wh <- GRanges("chr21", ranges=IRanges(start=47411800, end=47412600)) ## Case 2: Labels work, although what looks like a warning is still shown # wh <- GRanges("chr17", ranges=IRanges(start=47115000, end=47130000)) ## Case 3: Error wh <- GRanges("chr21", ranges=IRanges(start=36759003, end=36800825)) p1 <- autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") p2 <- autoplot(txdb, which = wh, names.expr = "tx_name") p3 <- autoplot(txdb, which = wh, names.expr = "gene_id") chr <- as.character(seqnames(wh)) ## load the ideogram info hg19IdeogramCyto <- NULL load(system.file("data", "hg19IdeogramCyto.rda", package = "biovizBase", mustWork = TRUE)) p.ideogram <- plotIdeogram(hg19IdeogramCyto, chr) ## Combine info into a tracks plot p.final <- tracks(p.ideogram, tx_name\n(gene_id) = p1, tx_name = p2, gene_id = p3, heights = c(2, 3, 3, 3), xlim = wh, title = "test") + ylab("") + theme_tracks_sunset() p.final > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 [5] Biobase_2.24.0 GenomicRanges_1.16.2 [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 [9] ggbio_1.12.3 ggplot2_0.9.3.1 [11] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 [25] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-32 [28] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 [31] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 [34] reshape2_1.4 Rsamtools_1.16.0 RSQLite_0.11.4 [37] rtracklayer_1.24.0 scales_0.2.4 sendmailR_1.1-2 [40] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 [43] survival_2.37-7 tools_3.1.0 VariantAnnotation_1.10.0 [46] XML_3.98-1.1 zlibbioc_1.10.0 Cheers, Leo On Tue, Apr 29, 2014 at 9:03 PM, Tengfei Yin <tengfei.yin at="" sbgenomics.com=""> wrote: > it's good it's building, but it's very weird that it works, because I simply > removed eval = TRUE for that chunk which is default. I came across some > really weird *bug* in knitr which I try to reproduce with a minimal example, > if you look closely, I put three blank code chunk at the front to avoid the > figures orders being messed up somehow and I don't know why. I guess until I > have a minimal example, I cannot really report it to yihui to fix it. > > > On Tue, Apr 29, 2014 at 7:03 PM, Leonardo Collado Torres > <lcollado at="" jhsph.edu=""> wrote: >> >> I just noticed that ggbio is building now >> >> http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> and I'm happy to report that the problem I mentioned is resolved with >> ggbio 1.12.3. Thank you Tengfei and Dan! >> >> >> For reference, here is the working session information. >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] XVector_0.4.0 >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 >> [5] Biobase_2.24.0 GenomicRanges_1.16.2 >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 >> [9] ggbio_1.12.3 ggplot2_0.9.3.1 >> [11] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 >> [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 >> [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 >> [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 >> [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >> [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 >> [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 >> [25] labeling_0.2 lattice_0.20-29 latticeExtra_0.6-26 >> [28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1 >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> [34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0 >> [37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4 >> [40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 >> [43] stringr_0.6.2 survival_2.37-7 tools_3.1.0 >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >> >> On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >> > >> > >> > ----- Original Message ----- >> >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> >> To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> >> Cc: lcollado at jhu.edu, "Bioconductor mailing list" >> >> <bioconductor at="" r-project.org=""> >> >> Sent: Saturday, April 26, 2014 7:33:41 PM >> >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken >> >> >> >> >> >> >> >> ----- Original Message ----- >> >> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> >> > To: lcollado at jhu.edu >> >> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing >> >> > list" <bioconductor at="" r-project.org=""> >> >> > Sent: Saturday, April 26, 2014 1:58:01 PM >> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >> >> > broken >> >> > >> >> > >> >> > right, it's failing to build and I am trying to figure out why now, >> >> > because it passes check/build and works on my laptop, but it >> >> > doesn't >> >> > pass bioc build for both release and devel, let me dig into it >> >> > tonight. >> >> > >> >> >> >> Seems like this could be fixed if you just add >> >> >> >> library(ggbio) >> >> >> >> to your vignette before the ggbio() function is called on line 557 of >> >> vignettes/realvignettes/ggbio.Rnw. >> >> >> > >> > Sorry, I spoke too soon; that just changes the error message you >> > receive. >> > Dan >> > >> > >> >> Dan >> >> >> >> >> >> > >> >> > thanks for your patience >> >> > >> >> > >> >> > Tengfei >> >> > >> >> > >> >> > >> >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < >> >> > lcollado at jhsph.edu > wrote: >> >> > >> >> > >> >> > >> >> > Oh ok. Thanks for the info >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < >> >> > dtenenba at fhcrc.org >> >> > > wrote: >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > Leonardo Collado Torres < lcollado at jhsph.edu > wrote: >> >> > >> >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC >> >> > >release? >> >> > > >> >> > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html >> >> > >still >> >> > >points to 1.12.0 >> >> > > >> >> > >> >> > It's failing to build: >> >> > >> >> > >> >> > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> >> > >> >> > >> >> > >> >> > Dan >> >> > >> >> > > >> >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < >> >> > >dtenenba at fhcrc.org >> >> > >> >> >> > >wrote: >> >> > > >> >> > >> >> >> > >> >> >> > >> ----- Original Message ----- >> >> > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu > >> >> > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor >> >> > >> > mailing >> >> > >list" < >> >> > >> bioconductor at r-project.org > >> >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM >> >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >> >> > >> > is >> >> > >broken >> >> > >> > >> >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. See >> >> > >> > below >> >> > >> > again >.< >> >> > >> > >> >> > >> > On the email topic, is it possible to be subscribed with 2 >> >> > >> > emails >> >> > >> > accounts to the BioC mailing list but only get emails with >> >> > >> > one? >> >> > >> > I >> >> > >> > believe that I have to choose to either get the daily digest >> >> > >> > or >> >> > >> > get >> >> > >a >> >> > >> > single for every message sent. If not, I'll probably just drop >> >> > >> > my >> >> > >> > @ jhsph.edu subscription and re-subscribe with the new @ >> >> > >> > jhu.edu >> >> > >> > mail >> >> > >I >> >> > >> > got (our university is pushing these mails). >> >> > >> > >> >> > >> >> >> > >> I don't know; you could try it. Another option would be to >> >> > >> configure >> >> > >your >> >> > >> mail client with a filter to drop the undesired bioc emails. >> >> > >> >> >> > >> Dan >> >> > >> >> >> > >> >> >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres >> >> > >> > < lcollado at jhu.edu > wrote: >> >> > >> > > Hi Dan, >> >> > >> > > >> >> > >> > > I got RSwitch to work with a second installation of R 3.1. >> >> > >> > > Basically, >> >> > >> > > I downloaded the leopard tarball, expanded it, renamed the >> >> > >> > > folder >> >> > >> > > 3.1 >> >> > >> > > to 3.1patched (which is the version I downloaded, but well, >> >> > >> > > anything >> >> > >> > > except for 3.1 would work), compressed it again, and then >> >> > >expanded >> >> > >> > > it >> >> > >> > > at the root location. >> >> > >> > > >> >> > >> > > So it would be something like this: >> >> > >> > > >> >> > >> > > wget >> >> > >> > > >> >> > >> >> >> > > >> >> > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1 -branch-snowleopard-sa-x86_64.tar.gz >> >> > >> > > tar -xvf R-*gz >> >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1 >> >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched >> >> > >> > > tar -cvzf Rlib.tgz Library >> >> > >> > > sudo tar fvxz Rlib.tgz -C / >> >> > >> > > >> >> > >> > > Then used RSwitch, and was able to install BioC-devel. >> >> > >> > > >> >> > >> > > I might try out your renv at a different time. It's great >> >> > >> > > to >> >> > >know >> >> > >> > > that it exists =) >> >> > >> > > >> >> > >> > > Cheers, >> >> > >> > > Leo >> >> > >> > > >> >> > >> > > >> >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin >> >> > >> > > < tengfei.yin at sbgenomics.com > wrote: >> >> > >> > >> Hi Dan, >> >> > >> > >> >> >> > >> > >> It works like a charm, thanks! >> >> > >> > >> >> >> > >> > >> I use your method, then I changed /Library/Framework/ >> >> > >> > >> folder >> >> > >> > >> and >> >> > >> > >> R.Framework >> >> > >> > >> folder ownership to myself so I don't have to sudo it, then >> >> > >> > >> I >> >> > >just >> >> > >> > >> add alias >> >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R >> >> > >> > >> first. >> >> > >> > >> This solves >> >> > >> > >> my problem. >> >> > >> > >> >> >> > >> > >> Try to customize variable for R hooks in emacs as >> >> > >> > >> alternative >> >> > >> > >> solution, but >> >> > >> > >> may need more time. >> >> > >> > >> >> >> > >> > >> Thanks again! >> >> > >> > >> >> >> > >> > >> Tengfei >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum >> >> > >> > >> < dtenenba at fhcrc.org > wrote: >> >> > >> > >>> >> >> > >> > >>> Hi Tengfei, >> >> > >> > >>> >> >> > >> > >>> ----- Original Message ----- >> >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> >> > >> > >>> > Cc: "Bioconductor mailing list" < >> >> > >> > >>> > bioconductor at r-project.org >, >> >> > >> > >>> > lcollado at jhu.edu >> >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >> >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >> > >> > >>> > example >> >> > >> > >>> > is broken >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all >> >> > >> > >>> > on >> >> > >the >> >> > >> > >>> > R 3.1? >> >> > >> > >>> >> >> > >> > >>> Yes, install two copies of R 3.1 and switch between them. >> >> > >> > >>> >> >> > >> > >>> > And do some sort of switch for bioc? The website you >> >> > >> > >>> > send >> >> > >> > >>> > to >> >> > >me >> >> > >> > >>> > also >> >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on >> >> > >R-devel >> >> > >> > >>> > and >> >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R >> >> > >> > >>> > only >> >> > >to >> >> > >> > >>> > switch bioc, so that I could debug and maintain released >> >> > >> > >>> > and >> >> > >> > >>> > devel >> >> > >> > >>> > version. >> >> > >> > >>> >> >> > >> > >>> PLEASE don't use R-devel at all. >> >> > >> > >>> >> >> > >> > >>> Just use R-3.1.0. >> >> > >> > >>> >> >> > >> > >>> You can use the Rswitch app but as you point out it won't >> >> > >> > >>> work >> >> > >> > >>> within >> >> > >> > >>> emacs. >> >> > >> > >>> >> >> > >> > >>> This is what I do: >> >> > >> > >>> >> >> > >> > >>> Every time I download a new version of R, I run its >> >> > >> > >>> installer. >> >> > >> > >>> The >> >> > >> > >>> installer always puts it in >> >> > >> > >>> >> >> > >> > >>> /Library/Frameworks/R.framework >> >> > >> > >>> >> >> > >> > >>> So after I install each version of R, I rename the >> >> > >> > >>> R.framework >> >> > >> > >>> directory >> >> > >> > >>> to something like >> >> > >> > >>> R.framework.bioc214_snowleopard >> >> > >> > >>> >> >> > >> > >>> And then I make a symlink from >> >> > >> > >>> R.framework.bioc214_snowleopard >> >> > >to >> >> > >> > >>> R.framework. >> >> > >> > >>> >> >> > >> > >>> I have a little script at https://github.com/dtenenba/renv >> >> > >which >> >> > >> > >>> lets me >> >> > >> > >>> see what the various installed Rs are: >> >> > >> > >>> >> >> > >> > >>> renv >> >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >> >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> > >> > >>> >> >> > >> > >>> This tells me that the currently active R is nicknamed >> >> > >> > >>> "releaseMav" (this >> >> > >> > >>> means there is a link from >> >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to >> >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions, >> >> > >> > >>> svn >> >> > >> > >>> revisions, >> >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 is >> >> > >> > >>> Snow >> >> > >> > >>> Leopard; >> >> > >> > >>> darwin13.1.0 is Mavericks). >> >> > >> > >>> >> >> > >> > >>> Note that in my nomenclature devel means BioC devel, not >> >> > >R-devel. >> >> > >> > >>> >> >> > >> > >>> So if I wanted to switch to the "develSL" version I would >> >> > >> > >>> do: >> >> > >> > >>> >> >> > >> > >>> sudo renv develSL >> >> > >> > >>> >> >> > >> > >>> HTH >> >> > >> > >>> Dan >> >> > >> > >>> >> >> > >> > >>> >> >> > >> > >>> >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < >> >> > >> > >>> > dtenenba at fhcrc.org > >> >> > >> > >>> > wrote: >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > Hi Tengfei, >> >> > >> > >>> > >> >> > >> > >>> > ----- Original Message ----- >> >> > >> > >>> > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> > >> > >>> > >> >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> >> > >> > >>> > > Cc: "Bioconductor mailing list" < >> >> > > bioconductor at r-project.org >> >> > >> > >>> > > >, >> >> > >> > >>> > > lcollado at jhu.edu >> >> > >> > >>> > >> >> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM >> >> > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >> > >example >> >> > >> > >>> > > is >> >> > >> > >>> > > broken >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > >> >> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I >> >> > >> > >>> > > am >> >> > >still >> >> > >> > >>> > > a >> >> > >> > >>> > > newbie to OSX ... I got R-devel running and I will try >> >> > >> > >>> > > Rswitcher, I >> >> > >> > >>> > > also want to do that switch easily in emacs too. >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > >> >> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) >> >> > >> > >>> > and >> >> > >> > >>> > BioC >> >> > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released >> >> > >> > >>> > version of >> >> > >> > >>> > R. >> >> > >> > >>> > >> >> > >> > >>> > I think the Rswitch app just sets a symbolic link, so >> >> > >> > >>> > you >> >> > >> > >>> > should be >> >> > >> > >>> > able to do that within emacs. Run it and see what it >> >> > >> > >>> > does >> >> > >> > >>> > to >> >> > >> > >>> > /Library/Frameworks/R.framework. >> >> > >> > >>> > >> >> > >> > >>> > Dan >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > > >> >> > >> > >>> > > cheers >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > Tengfei >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < >> >> > >> > >>> > > dtenenba at fhcrc.org >> >> > >> > >>> > > > >> >> > >> > >>> > > wrote: >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > ----- Original Message ----- >> >> > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> > >> > >>> > > >> >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> >> > >> > >>> > > > Cc: "Bioconductor mailing list" < >> >> > >> > >>> > > > bioconductor at r-project.org >, >> >> > >> > >>> > > > lcollado at jhu.edu >> >> > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM >> >> > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with >> >> > >> > >>> > > > txdb >> >> > >> > >>> > > > example is >> >> > >> > >>> > > > broken >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > > Hi Dan, >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it >> >> > >should >> >> > >> > >>> > > > work? >> >> > >> > >>> > > >> >> > >> > >>> > > Yes. >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > ? Is >> >> > >> > >>> > > > there a way to build from source using biocLite, >> >> > >> > >>> > > > like >> >> > >type >> >> > >> > >>> > > > = >> >> > >> > >>> > > > "source", this is what I got >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > > library(BiocInstaller) >> >> > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), >> >> > >?biocLite >> >> > >> > >>> > > > for >> >> > >> > >>> > > > help >> >> > >> > >>> > > > > biocLite("GenomicRanges") >> >> > >> > >>> > > > BioC_mirror: http://bioconductor.org >> >> > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller >> >> > >> > >>> > > > 1.14.1), R >> >> > >> > >>> > > > version >> >> > >> > >>> > > > 3.1.0. >> >> > >> > >>> > > > Installing package(s) 'GenomicRanges' >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > package ?GenomicRanges? is available as a source >> >> > >> > >>> > > > package >> >> > >> > >>> > > > but not >> >> > >> > >>> > > > as >> >> > >> > >>> > > > a >> >> > >> > >>> > > > binary >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Warning message: >> >> > >> > >>> > > > package ?GenomicRanges? is not available (for R >> >> > >> > >>> > > > version >> >> > >> > >>> > > > 3.1.0) >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Just wondering is there a solution without >> >> > >> > >>> > > > re-install >> >> > >> > >>> > > > R >> >> > >for >> >> > >> > >>> > > > snow >> >> > >> > >>> > > > leopard. And what's the plan for maverick? >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > You can do >> >> > >> > >>> > > biocLite("GenomicRanges", type="source") >> >> > >> > >>> > > >> >> > >> > >>> > > but you need to have the appropriate compilers, etc. >> >> > >> > >>> > > >> >> > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. >> >> > >> > >>> > > You >> >> > >can >> >> > >> > >>> > > have >> >> > >> > >>> > > multiple installations of R on your Mac and switch >> >> > >> > >>> > > between >> >> > >> > >>> > > them >> >> > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or >> >> > >another >> >> > >> > >>> > > easy >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > > mechanism. >> >> > >> > >>> > > >> >> > >> > >>> > > We are building packages for Mavericks now, we just >> >> > >> > >>> > > have >> >> > >> > >>> > > to >> >> > >> > >>> > > resolve >> >> > >> > >>> > > a >> >> > >> > >>> > > few build issues and test the resulting packages, we >> >> > >> > >>> > > still >> >> > >> > >>> > > hope to >> >> > >> > >>> > > have them available by the end of the month. But since >> >> > >> > >>> > > you >> >> > >> > >>> > > can >> >> > >> > >>> > > install the Snow Leopard build without needing to >> >> > >> > >>> > > remove >> >> > >your >> >> > >> > >>> > > Mavericks build, you should do that. >> >> > >> > >>> > > >> >> > >> > >>> > > Dan >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Thanks >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Tengfei >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < >> >> > >> > >>> > > > dtenenba at fhcrc.org >> >> > >> > >>> > > > > wrote: >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Hi Tengfei, >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > ----- Original Message ----- >> >> > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> > >> > >>> > > > > To: lcollado at jhu.edu >> >> > >> > >>> > > > > Cc: bioconductor at r-project.org >> >> > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM >> >> > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with >> >> > >> > >>> > > > > txdb >> >> > >> > >>> > > > > example >> >> > >> > >>> > > > > is >> >> > >> > >>> > > > > broken >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > btw, based on the error, let me try to debug it. >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin >> >> > >> > >>> > > > > < tengfei.yin at sbgenomics.com >wrote: >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > > Hi Leonardo, >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > Frankly speaking, the vignette is still in >> >> > >> > >>> > > > > > progress, >> >> > >> > >>> > > > > > and >> >> > >> > >>> > > > > > there >> >> > >> > >>> > > > > > are >> >> > >> > >>> > > > > > some >> >> > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying >> >> > >> > >>> > > > > > to >> >> > >find >> >> > >> > >>> > > > > > a >> >> > >> > >>> > > > > > time >> >> > >> > >>> > > > > > to >> >> > >> > >>> > > > > > do that >> >> > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and >> >> > >> > >>> > > > > > Bioc >> >> > >> > >>> > > > > > 2.14 on >> >> > >> > >>> > > > > > my >> >> > >> > >>> > > > > > new MBP >> >> > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build >> >> > >> > >>> > > > > > is >> >> > >not >> >> > >> > >>> > > > > > ready >> >> > >> > >>> > > > > > for >> >> > >> > >>> > > > > > maverick >> >> > >> > >>> > > > > > yet, maybe available by the end of April? >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > Thanks for reporting the bug, I will keep you >> >> > >> > >>> > > > > > posted >> >> > >on >> >> > >> > >>> > > > > > this >> >> > >> > >>> > > > > > when >> >> > >> > >>> > > > > > I >> >> > >> > >>> > > > > > successfully get it on my laptop and start >> >> > >> > >>> > > > > > fixing >> >> > >> > >>> > > > > > the >> >> > >> > >>> > > > > > problems. >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > You can install the Snow Leopard build of R and >> >> > >> > >>> > > > should >> >> > >have >> >> > >> > >>> > > > no >> >> > >> > >>> > > > problems, binary packages are available for that >> >> > >> > >>> > > > version. >> >> > >> > >>> > > > It will >> >> > >> > >>> > > > run fine on Mavericks. >> >> > >> > >>> > > > >> >> > >> > >>> > > > Dan >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > > > cheers >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > Tengfei >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo >> >> > >> > >>> > > > > > Collado >> >> > >> > >>> > > > > > Torres < >> >> > >> > >>> > > > > > lcollado at jhsph.edu > wrote: >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > >> Hello Tengfei + bioc list, >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> From >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> >> >> > >> >> >> > > >> >> > > http://www.bioconductor.org/packages/release/bioc/vignettes/ ggbio/inst/doc/ggbio.pdf >> >> > >> > >>> > > > > >> page 4 (complied on april 11 2014), the >> >> > >> > >>> > > > > >> following >> >> > >> > >>> > > > > >> example >> >> > >> > >>> > > > > >> loads >> >> > >> > >>> > > > > >> to >> >> > >> > >>> > > > > >> an >> >> > >> > >>> > > > > >> error as shown below. I wasn't seeing this >> >> > >> > >>> > > > > >> error >> >> > >> > >>> > > > > >> before >> >> > >> > >>> > > > > >> (aka, >> >> > >> > >>> > > > > >> last >> >> > >> > >>> > > > > >> week). The only guess that comes to mind is the >> >> > >recent >> >> > >> > >>> > > > > >> update >> >> > >> > >>> > > > > >> to >> >> > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't >> >> > >> > >>> > > > > >> seem >> >> > >> > >>> > > > > >> to >> >> > >> > >>> > > > > >> be >> >> > >> > >>> > > > > >> related >> >> > >> > >>> > > > > >> from >> >> > >> > >>> > > > > >> the traceback() output, well... maybe it's >> >> > >> > >>> > > > > >> related >> >> > >to >> >> > >> > >>> > > > > >> the >> >> > >> > >>> > > > > >> ignore.strand = TRUE part as described in the >> >> > >> > >>> > > > > >> error. >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> I'll create a GitHub issue just for >> >> > >> > >>> > > > > >> completeness. >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> Thank you, >> >> > >> > >>> > > > > >> Leonardo >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> > library(ggbio) >> >> > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> >> > >> > >>> > > > > >> ## Removed the output >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> >> > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") >> >> > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = >> >> > >> > >>> > > > > >> > genesymbol["BRCA1"]) >> >> > >> > >>> > > > > >> Aggregating TranscriptDb... >> >> > >> > >>> > > > > >> Parsing transcripts... >> >> > >> > >>> > > > > >> Parsing exons... >> >> > >> > >>> > > > > >> Parsing cds... >> >> > >> > >>> > > > > >> Parsing utrs... >> >> > >> > >>> > > > > >> ------exons... >> >> > >> > >>> > > > > >> ------cdss... >> >> > >> > >>> > > > > >> ------introns... >> >> > >> > >>> > > > > >> ------utr... >> >> > >> > >>> > > > > >> aggregating... >> >> > >> > >>> > > > > >> Done >> >> > >> > >>> > > > > >> Constructing graphics... >> >> > >> > >>> > > > > >> Error in sapply(listData, function(Xi) >> >> > >> > >>> > > > > >> extends(class(Xi), >> >> > >> > >>> > > > > >> elementTypeX)) : >> >> > >> > >>> > > > > >> error in evaluating the argument 'X' in >> >> > >> > >>> > > > > >> selecting >> >> > >> > >>> > > > > >> a >> >> > >> > >>> > > > > >> method >> >> > >> > >>> > > > > >> for >> >> > >> > >>> > > > > >> function 'sapply': Error in >> >> > >> > >>> > > > > >> unlist(range(ranges(x.n, >> >> > >> > >>> > > > > >> ignore.strand >> >> > >> > >>> > > > > >> = >> >> > >> > >>> > > > > >> TRUE))) : >> >> > >> > >>> > > > > >> error in evaluating the argument 'x' in >> >> > >> > >>> > > > > >> selecting >> >> > >> > >>> > > > > >> a >> >> > >> > >>> > > > > >> method >> >> > >> > >>> > > > > >> for >> >> > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : >> >> > >> > >>> > > > > >> unused >> >> > >> > >>> > > > > >> argument >> >> > >> > >>> > > > > >> (ignore.strand = TRUE) >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> > traceback() >> >> > >> > >>> > > > > >> 15: sapply(listData, function(Xi) >> >> > >> > >>> > > > > >> extends(class(Xi), >> >> > >> > >>> > > > > >> elementTypeX)) >> >> > >> > >>> > > > > >> 14: .updateCompressedList(X, >> >> > >lapply_CompressedList(X, >> >> > >> > >>> > > > > >> FUN, >> >> > >> > >>> > > > > >> ...)) >> >> > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { >> >> > >> > >>> > > > > >> if (!is.null( group.name )) { >> >> > >> > >>> > > > > >> if (!group.selfish) { >> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> >> > >> > >>> > > > > >> TRUE))) >> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> >> > >> > >>> > > > > >> width(irs) + >> >> > >> > >>> > > > > >> extend.size) >> >> > >> > >>> > > > > >> irs.new <- sort(irs.new) >> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, >> >> > >> > >>> > > > > >> group.name ])] >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> else { >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> >> > >> > >>> > > > > >> group.name ])) >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> else { >> >> > >> > >>> > > > > >> irs <- ranges(x) >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> >> > >> > >>> > > > > >> fix = "center", width = width(irs) + >> >> > >> > >>> > > > > >> extend.size))) >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> }) >> >> > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { >> >> > >> > >>> > > > > >> if (!is.null( group.name )) { >> >> > >> > >>> > > > > >> if (!group.selfish) { >> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) >> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = >> >> > >> > >>> > > > > >> TRUE))) >> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = >> >> > >> > >>> > > > > >> width(irs) + >> >> > >> > >>> > > > > >> extend.size) >> >> > >> > >>> > > > > >> irs.new <- sort(irs.new) >> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, >> >> > >> > >>> > > > > >> group.name ])] >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> else { >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, >> >> > >> > >>> > > > > >> group.name ])) >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> else { >> >> > >> > >>> > > > > >> irs <- ranges(x) >> >> > >> > >>> > > > > >> values(x)$stepping <- >> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, >> >> > >> > >>> > > > > >> fix = "center", width = width(irs) + >> >> > >> > >>> > > > > >> extend.size))) >> >> > >> > >>> > > > > >> x >> >> > >> > >>> > > > > >> } >> >> > >> > >>> > > > > >> }) >> >> > >> > >>> > > > > >> 11: .local(obj, ...) >> >> > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", >> >> > >> > >>> > > > > >> group.selfish = >> >> > >> > >>> > > > > >> FALSE, >> >> > >> > >>> > > > > >> fix = "start", extend.size = es) >> >> > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", >> >> > >group.selfish >> >> > >> > >>> > > > > >> = >> >> > >> > >>> > > > > >> FALSE, >> >> > >> > >>> > > > > >> fix = "start", extend.size = es) >> >> > >> > >>> > > > > >> 8: .local(data, ...) >> >> > >> > >>> > > > > >> 7: (function (data, ...) >> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4>> >> > >> > >>> > > > > >> object >> >> > >> > >>> > > > > >> of >> >> > >> > >>> > > > > >> class >> >> > >> > >>> > > > > >> "TranscriptDb">, >> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> >> > >> > >>> > > > > >> "alignment", >> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", >> >> > >> > >>> > > > > >> label >> >> > >> > >>> > > > > >> = >> >> > >> > >>> > > > > >> TRUE, >> >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> >> > >> > >>> > > > > >> 6: (function (data, ...) >> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4>> >> > >> > >>> > > > > >> object >> >> > >> > >>> > > > > >> of >> >> > >> > >>> > > > > >> class >> >> > >> > >>> > > > > >> "TranscriptDb">, >> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = >> >> > >> > >>> > > > > >> "alignment", >> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", >> >> > >> > >>> > > > > >> label >> >> > >> > >>> > > > > >> = >> >> > >> > >>> > > > > >> TRUE, >> >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) >> >> > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) >> >> > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) >> >> > >> > >>> > > > > >> 3: .local(object, ...) >> >> > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> > sessionInfo() >> >> > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) >> >> > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> locale: >> >> > >> > >>> > > > > >> [1] >> >> > >> > >>> > > > > >> >> >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> attached base packages: >> >> > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils >> >> > >> > >>> > > > > >> datasets >> >> > >> > >>> > > > > >> methods base >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> other attached packages: >> >> > >> > >>> > > > > >> [1] XVector_0.4.0 >> >> > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> >> > >> > >>> > > > > >> GenomicFeatures_1.16.0 >> >> > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 >> >> > >> > >>> > > > > >> GenomicRanges_1.16.2 >> >> > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 >> >> > >> > >>> > > > > >> ggbio_1.12.0 >> >> > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > >> loaded via a namespace (and not attached): >> >> > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 >> >> > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 >> >> > >> > >>> > > > > >> Biostrings_2.32.0 >> >> > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 >> >> > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 >> >> > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 >> >> > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 >> >> > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 >> >> > >> > >>> > > > > >> Formula_1.1-1 >> >> > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 >> >> > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 >> >> > >> > >>> > > > > >> Hmisc_3.14-4 >> >> > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 >> >> > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 >> >> > >> > >>> > > > > >> MASS_7.3-31 >> >> > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 >> >> > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 >> >> > >> > >>> > > > > >> Rcpp_0.11.1 >> >> > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 >> >> > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 >> >> > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 >> >> > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 >> >> > >> > >>> > > > > >> stringr_0.6.2 >> >> > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 >> >> > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 >> >> > >> > >>> > > > > >> zlibbioc_1.10.0 >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > -- >> >> > >> > >>> > > > > > Tengfei Yin, PhD >> >> > >> > >>> > > > > > Seven Bridges Genomics >> >> > >> > >>> > > > > > sbgenomics.com >> >> > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 >> >> > >> > >>> > > > > > Cambridge, MA 02138 >> >> > >> > >>> > > > > > (617) 866-0446 >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > -- >> >> > >> > >>> > > > > Tengfei Yin, PhD >> >> > >> > >>> > > > > Seven Bridges Genomics >> >> > >> > >>> > > > > sbgenomics.com >> >> > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 >> >> > >> > >>> > > > > Cambridge, MA 02138 >> >> > >> > >>> > > > > (617) 866-0446 >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > [[alternative HTML version deleted]] >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > _______________________________________________ >> >> > >> > >>> > > > > Bioconductor mailing list >> >> > >> > >>> > > > > Bioconductor at r-project.org >> >> > >> > >>> > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > >> > >>> > > > > Search the archives: >> >> > >> > >>> > > > > >> >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> > >>> > > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > -- >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Tengfei Yin, PhD >> >> > >> > >>> > > > Seven Bridges Genomics >> >> > >> > >>> > > > sbgenomics.com >> >> > >> > >>> > > > 625 Mt. Auburn St. Suite #208 >> >> > >> > >>> > > > Cambridge, MA 02138 >> >> > >> > >>> > > > (617) 866- 0446 >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > -- >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > Tengfei Yin, PhD >> >> > >> > >>> > > Seven Bridges Genomics >> >> > >> > >>> > > sbgenomics.com >> >> > >> > >>> > > 625 Mt. Auburn St. Suite #208 >> >> > >> > >>> > > Cambridge, MA 02138 >> >> > >> > >>> > > (617) 866- 0446 >> >> > >> > >>> > > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > -- >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > Tengfei Yin, PhD >> >> > >> > >>> > Seven Bridges Genomics >> >> > >> > >>> > sbgenomics.com >> >> > >> > >>> > 625 Mt. Auburn St. Suite #208 >> >> > >> > >>> > Cambridge, MA 02138 >> >> > >> > >>> > (617) 866- 0446 >> >> > >> > >>> > >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> >> >> > >> > >> -- >> >> > >> > >> Tengfei Yin, PhD >> >> > >> > >> Seven Bridges Genomics >> >> > >> > >> sbgenomics.com >> >> > >> > >> 625 Mt. Auburn St. Suite #208 >> >> > >> > >> Cambridge, MA 02138 >> >> > >> > >> (617) 866-0446 >> >> > >> > >> >> > >> >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > >> >> > >> >> > Tengfei Yin, PhD >> >> > Seven Bridges Genomics >> >> > sbgenomics.com >> >> > 625 Mt. Auburn St. Suite #208 >> >> > Cambridge, MA 02138 >> >> > (617) 866- 0446 >> >> > >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Tengfei Yin, PhD > Seven Bridges Genomics > sbgenomics.com > 625 Mt. Auburn St. Suite #208 > Cambridge, MA 02138 > (617) 866-0446
Hi Leo, Thanks for reporting the bugs, yes, this is a perfect time to report, if you read a new updated vignette (still keep updating it ...) in 1.12.3 http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf You will notice section 'add gene model' changed, it support OrganismDb now, so the name.expr support more items now, if you are using Homo.sapiens, you could label "gene symbols" too, I did lots of change for autoplot,Organism and autoplot,Txdb function, this will probably introduce some bugs you reported. I will work on fixing those bugs you reported and keep you posted. cheers Tengfei On Tue, Apr 29, 2014 at 10:05 PM, Leonardo Collado Torres <lcollado@jhu.edu>wrote: > Hi Tengfei, > > Interesting, I don't really know what's the issue with the bug you found. > > > > Looking into ggbio 1.12.3 I noticed a couple of things with autoplot(txdb). > > Basically, I found three cases. > > Case 1: function works well, just a message that looks like a warning > (it's a message) is printed out. Nothing biggie. > Case 2: Labels when using tx_name(gene_id) don't work (although they > work in case 1) but they do work individually. > Case 3: Function fails because there is nothing in that region. > > The code is shown below where you only have to specify the region of > interest according to the case. > > > > Previously, I would use something like this (shown below) to catch case 3. > > p.transcripts <- tryCatch(autoplot(txdb, which = wh, > names.expr = "tx_name(gene_id)"), warning = function(w) { > FALSE > }) > > Now that it results in an error, I can detect these cases using: > > p.transcripts <- tryCatch(autoplot(txdb, which = wh, > names.expr = "tx_name(gene_id)"), error = function(e) { > FALSE > }) > > > However, I thought that this would be a good time to report this. > > > Regarding case 2, in my use case I'm thinking of switching to > "tx_name" instead of using "tx_name(gene_id)". But well, it's also > worth reporting. > > > > ## Case 1 & 2 show the following 'message' that looks like a warning though > > "gap" is not matching to following arbitrary model terms"cds CDS Cds > exon EXON Exon utr UTR Utr" > > ## Case 3 error > > Error in data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, : > arguments imply differing number of rows: 0, 1 > > traceback() > 13: stop(gettextf("arguments imply differing number of rows: %s", > paste(unique(nrows), collapse = ", ")), domain = NA) > 12: data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, > type = "exon") > 11: .local(obj, ...) > 10: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = > truncate.fun, > ratio = ratio, columns = columns) > 9: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = > truncate.fun, > ratio = ratio, columns = columns) > 8: .local(data, ...) > 7: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 6: (function (data, ...) > standardGeneric("geom_alignment"))(data = <s4 object="" of="" class=""> "TranscriptDb">, > truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", > stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, > which = <s4 object="" of="" class="" "granges"="">, list()) > 5: do.call(geom_alignment, args.res) > 4: do.call(geom_alignment, args.res) > 3: .local(object, ...) > 2: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") > 1: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") > > > > Here's the code. > > > > ## Load required libs > library(ggbio) > library(GenomicRanges) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > ### Set up region > > ## Case 1: Labels don't work for tx_name(gene_id) case > # wh <- GRanges("chr21", ranges=IRanges(start=47411800, end=47412600)) > ## Case 2: Labels work, although what looks like a warning is still shown > # wh <- GRanges("chr17", ranges=IRanges(start=47115000, end=47130000)) > ## Case 3: Error > wh <- GRanges("chr21", ranges=IRanges(start=36759003, end=36800825)) > > p1 <- autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") > p2 <- autoplot(txdb, which = wh, names.expr = "tx_name") > p3 <- autoplot(txdb, which = wh, names.expr = "gene_id") > > chr <- as.character(seqnames(wh)) > > > ## load the ideogram info > hg19IdeogramCyto <- NULL > load(system.file("data", "hg19IdeogramCyto.rda", package = > "biovizBase", mustWork = TRUE)) > p.ideogram <- plotIdeogram(hg19IdeogramCyto, chr) > > ## Combine info into a tracks plot > p.final <- tracks(p.ideogram, tx_name\n(gene_id) = p1, tx_name = > p2, gene_id = p3, heights = c(2, 3, 3, 3), xlim = wh, title = > "test") + ylab("") + theme_tracks_sunset() > p.final > > > > > > > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] XVector_0.4.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 > [5] Biobase_2.24.0 GenomicRanges_1.16.2 > [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 > [9] ggbio_1.12.3 ggplot2_0.9.3.1 > [11] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 > [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 > [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 > [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 > [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 > [25] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-32 > [28] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 > [31] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 > [34] reshape2_1.4 Rsamtools_1.16.0 RSQLite_0.11.4 > [37] rtracklayer_1.24.0 scales_0.2.4 sendmailR_1.1-2 > [40] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 > [43] survival_2.37-7 tools_3.1.0 > VariantAnnotation_1.10.0 > [46] XML_3.98-1.1 zlibbioc_1.10.0 > > > > > Cheers, > Leo > > On Tue, Apr 29, 2014 at 9:03 PM, Tengfei Yin <tengfei.yin@sbgenomics.com> > wrote: > > it's good it's building, but it's very weird that it works, because I > simply > > removed eval = TRUE for that chunk which is default. I came across some > > really weird *bug* in knitr which I try to reproduce with a minimal > example, > > if you look closely, I put three blank code chunk at the front to avoid > the > > figures orders being messed up somehow and I don't know why. I guess > until I > > have a minimal example, I cannot really report it to yihui to fix it. > > > > > > On Tue, Apr 29, 2014 at 7:03 PM, Leonardo Collado Torres > > <lcollado@jhsph.edu> wrote: > >> > >> I just noticed that ggbio is building now > >> > >> > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > >> and I'm happy to report that the problem I mentioned is resolved with > >> ggbio 1.12.3. Thank you Tengfei and Dan! > >> > >> > >> For reference, here is the working session information. > >> > >> > sessionInfo() > >> R version 3.1.0 (2014-04-10) > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> > >> locale: > >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> > >> attached base packages: > >> [1] parallel stats graphics grDevices utils datasets > >> methods base > >> > >> other attached packages: > >> [1] XVector_0.4.0 > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 > >> [5] Biobase_2.24.0 GenomicRanges_1.16.2 > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 > >> [9] ggbio_1.12.3 ggplot2_0.9.3.1 > >> [11] BiocGenerics_0.10.0 > >> > >> loaded via a namespace (and not attached): > >> [1] BatchJobs_1.2 BBmisc_1.6 > BiocParallel_0.6.0 > >> [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 > >> [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 > >> [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 > >> [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 > >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 > >> [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 > >> [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 > >> [25] labeling_0.2 lattice_0.20-29 > latticeExtra_0.6-26 > >> [28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1 > >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 > >> [34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0 > >> [37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4 > >> [40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 > >> [43] stringr_0.6.2 survival_2.37-7 tools_3.1.0 > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 > >> > >> On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba@fhcrc.org> > >> wrote: > >> > > >> > > >> > ----- Original Message ----- > >> >> From: "Dan Tenenbaum" <dtenenba@fhcrc.org> > >> >> To: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> >> Cc: lcollado@jhu.edu, "Bioconductor mailing list" > >> >> <bioconductor@r-project.org> > >> >> Sent: Saturday, April 26, 2014 7:33:41 PM > >> >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > broken > >> >> > >> >> > >> >> > >> >> ----- Original Message ----- > >> >> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com> > >> >> > To: lcollado@jhu.edu > >> >> > Cc: "Dan Tenenbaum" <dtenenba@fhcrc.org>, "Bioconductor mailing > >> >> > list" <bioconductor@r-project.org> > >> >> > Sent: Saturday, April 26, 2014 1:58:01 PM > >> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is > >> >> > broken > >> >> > > >> >> > > >> >> > right, it's failing to build and I am trying to figure out why now, > >> >> > because it passes check/build and works on my laptop, but it > >> >> > doesn't > >> >> > pass bioc build for both release and devel, let me dig into it > >> >> > tonight. > >> >> > > >> >> > >> >> Seems like this could be fixed if you just add > >> >> > >> >> library(ggbio) > >> >> > >> >> to your vignette before the ggbio() function is called on line 557 of > >> >> vignettes/realvignettes/ggbio.Rnw. > >> >> > >> > > >> > Sorry, I spoke too soon; that just changes the error message you > >> > receive. > >> > Dan > >> > > >> > > >> >> Dan > >> >> > >> >> > >> >> > > >> >> > thanks for your patience > >> >> > > >> >> > > >> >> > Tengfei > >> >> > > >> >> > > >> >> > > >> >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < > >> >> > lcollado@jhsph.edu > wrote: > >> >> > > >> >> > > >> >> > > >> >> > Oh ok. Thanks for the info > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < > >> >> > dtenenba@fhcrc.org > >> >> > > wrote: > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > Leonardo Collado Torres < lcollado@jhsph.edu > wrote: > >> >> > > >> >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC > >> >> > >release? > >> >> > > > >> >> > > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html > >> >> > >still > >> >> > >points to 1.12.0 > >> >> > > > >> >> > > >> >> > It's failing to build: > >> >> > > >> >> > > >> >> > > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html > >> >> > > >> >> > > >> >> > > >> >> > Dan > >> >> > > >> >> > > > >> >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < > >> >> > >dtenenba@fhcrc.org > >> >> > >> > >> >> > >wrote: > >> >> > > > >> >> > >> > >> >> > >> > >> >> > >> ----- Original Message ----- > >> >> > >> > From: "Leonardo Collado Torres" < lcollado@jhsph.edu > > >> >> > >> > To: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> >> > >> > Cc: "Dan Tenenbaum" < dtenenba@fhcrc.org >, "Bioconductor > >> >> > >> > mailing > >> >> > >list" < > >> >> > >> bioconductor@r-project.org > > >> >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM > >> >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example > >> >> > >> > is > >> >> > >broken > >> >> > >> > > >> >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. > See > >> >> > >> > below > >> >> > >> > again >.< > >> >> > >> > > >> >> > >> > On the email topic, is it possible to be subscribed with 2 > >> >> > >> > emails > >> >> > >> > accounts to the BioC mailing list but only get emails with > >> >> > >> > one? > >> >> > >> > I > >> >> > >> > believe that I have to choose to either get the daily digest > >> >> > >> > or > >> >> > >> > get > >> >> > >a > >> >> > >> > single for every message sent. If not, I'll probably just drop > >> >> > >> > my > >> >> > >> > @ jhsph.edu subscription and re-subscribe with the new @ > >> >> > >> > jhu.edu > >> >> > >> > mail > >> >> > >I > >> >> > >> > got (our university is pushing these mails). > >> >> > >> > > >> >> > >> > >> >> > >> I don't know; you could try it. Another option would be to > >> >> > >> configure > >> >> > >your > >> >> > >> mail client with a filter to drop the undesired bioc emails. > >> >> > >> > >> >> > >> Dan > >> >> > >> > >> >> > >> > >> >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres > >> >> > >> > < lcollado@jhu.edu > wrote: > >> >> > >> > > Hi Dan, > >> >> > >> > > > >> >> > >> > > I got RSwitch to work with a second installation of R 3.1. > >> >> > >> > > Basically, > >> >> > >> > > I downloaded the leopard tarball, expanded it, renamed the > >> >> > >> > > folder > >> >> > >> > > 3.1 > >> >> > >> > > to 3.1patched (which is the version I downloaded, but well, > >> >> > >> > > anything > >> >> > >> > > except for 3.1 would work), compressed it again, and then > >> >> > >expanded > >> >> > >> > > it > >> >> > >> > > at the root location. > >> >> > >> > > > >> >> > >> > > So it would be something like this: > >> >> > >> > > > >> >> > >> > > wget > >> >> > >> > > > >> >> > >> > >> >> > > > >> >> > > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch- snowleopard-sa-x86_64.tar.gz > >> >> > >> > > tar -xvf R-*gz > >> >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1 > >> >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched > >> >> > >> > > tar -cvzf Rlib.tgz Library > >> >> > >> > > sudo tar fvxz Rlib.tgz -C / > >> >> > >> > > > >> >> > >> > > Then used RSwitch, and was able to install BioC- devel. > >> >> > >> > > > >> >> > >> > > I might try out your renv at a different time. It's great > >> >> > >> > > to > >> >> > >know > >> >> > >> > > that it exists =) > >> >> > >> > > > >> >> > >> > > Cheers, > >> >> > >> > > Leo > >> >> > >> > > > >> >> > >> > > > >> >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin > >> >> > >> > > < tengfei.yin@sbgenomics.com > wrote: > >> >> > >> > >> Hi Dan, > >> >> > >> > >> > >> >> > >> > >> It works like a charm, thanks! > >> >> > >> > >> > >> >> > >> > >> I use your method, then I changed /Library/Framework/ > >> >> > >> > >> folder > >> >> > >> > >> and > >> >> > >> > >> R.Framework > >> >> > >> > >> folder ownership to myself so I don't have to sudo it, then > >> >> > >> > >> I > >> >> > >just > >> >> > >> > >> add alias > >> >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R > >> >> > >> > >> first. > >> >> > >> > >> This solves > >> >> > >> > >> my problem. > >> >> > >> > >> > >> >> > >> > >> Try to customize variable for R hooks in emacs as > >> >> > >> > >> alternative > >> >> > >> > >> solution, but > >> >> > >> > >> may need more time. > >> >> > >> > >> > >> >> > >> > >> Thanks again! > >> >> > >> > >> > >> >> > >> > >> Tengfei > >> >> > >> > >> > >> >> > >> > >> > >> >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum > >> >> > >> > >> < dtenenba@fhcrc.org > wrote: > >> >> > >> > >>> > >> >> > >> > >>> Hi Tengfei, > >> >> > >> > >>> > >> >> > >> > >>> ----- Original Message ----- > >> >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> >> > >> > >>> > Cc: "Bioconductor mailing list" < > >> >> > >> > >>> > bioconductor@r-project.org >, > >> >> > >> > >>> > lcollado@jhu.edu > >> >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM > >> >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> >> > >> > >>> > example > >> >> > >> > >>> > is broken > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all > >> >> > >> > >>> > on > >> >> > >the > >> >> > >> > >>> > R 3.1? > >> >> > >> > >>> > >> >> > >> > >>> Yes, install two copies of R 3.1 and switch between them. > >> >> > >> > >>> > >> >> > >> > >>> > And do some sort of switch for bioc? The website you > >> >> > >> > >>> > send > >> >> > >> > >>> > to > >> >> > >me > >> >> > >> > >>> > also > >> >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on > >> >> > >R-devel > >> >> > >> > >>> > and > >> >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R > >> >> > >> > >>> > only > >> >> > >to > >> >> > >> > >>> > switch bioc, so that I could debug and maintain released > >> >> > >> > >>> > and > >> >> > >> > >>> > devel > >> >> > >> > >>> > version. > >> >> > >> > >>> > >> >> > >> > >>> PLEASE don't use R-devel at all. > >> >> > >> > >>> > >> >> > >> > >>> Just use R-3.1.0. > >> >> > >> > >>> > >> >> > >> > >>> You can use the Rswitch app but as you point out it won't > >> >> > >> > >>> work > >> >> > >> > >>> within > >> >> > >> > >>> emacs. > >> >> > >> > >>> > >> >> > >> > >>> This is what I do: > >> >> > >> > >>> > >> >> > >> > >>> Every time I download a new version of R, I run its > >> >> > >> > >>> installer. > >> >> > >> > >>> The > >> >> > >> > >>> installer always puts it in > >> >> > >> > >>> > >> >> > >> > >>> /Library/Frameworks/R.framework > >> >> > >> > >>> > >> >> > >> > >>> So after I install each version of R, I rename the > >> >> > >> > >>> R.framework > >> >> > >> > >>> directory > >> >> > >> > >>> to something like > >> >> > >> > >>> R.framework.bioc214_snowleopard > >> >> > >> > >>> > >> >> > >> > >>> And then I make a symlink from > >> >> > >> > >>> R.framework.bioc214_snowleopard > >> >> > >to > >> >> > >> > >>> R.framework. > >> >> > >> > >>> > >> >> > >> > >>> I have a little script at > https://github.com/dtenenba/renv > >> >> > >which > >> >> > >> > >>> lets me > >> >> > >> > >>> see what the various installed Rs are: > >> >> > >> > >>> > >> >> > >> > >>> $renv > >> >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 > >> >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 > >> >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 > >> >> > >> > >>> > >> >> > >> > >>> This tells me that the currently active R is nicknamed > >> >> > >> > >>> "releaseMav" (this > >> >> > >> > >>> means there is a link from > >> >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to > >> >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions, > >> >> > >> > >>> svn > >> >> > >> > >>> revisions, > >> >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 is > >> >> > >> > >>> Snow > >> >> > >> > >>> Leopard; > >> >> > >> > >>> darwin13.1.0 is Mavericks). > >> >> > >> > >>> > >> >> > >> > >>> Note that in my nomenclature devel means BioC devel, not > >> >> > >R-devel. > >> >> > >> > >>> > >> >> > >> > >>> So if I wanted to switch to the "develSL" version I would > >> >> > >> > >>> do: > >> >> > >> > >>> > >> >> > >> > >>> sudo renv develSL > >> >> > >> > >>> > >> >> > >> > >>> HTH > >> >> > >> > >>> Dan > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum < > >> >> > >> > >>> > dtenenba@fhcrc.org > > >> >> > >> > >>> > wrote: > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > Hi Tengfei, > >> >> > >> > >>> > > >> >> > >> > >>> > ----- Original Message ----- > >> >> > >> > >>> > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> >> > >> > >>> > > >> >> > >> > >>> > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> >> > >> > >>> > > Cc: "Bioconductor mailing list" < > >> >> > > bioconductor@r-project.org > >> >> > >> > >>> > > >, > >> >> > >> > >>> > > lcollado@jhu.edu > >> >> > >> > >>> > > >> >> > >> > >>> > > Sent: Wednesday, April 23, 2014 10:46:02 AM > >> >> > >> > >>> > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb > >> >> > >example > >> >> > >> > >>> > > is > >> >> > >> > >>> > > broken > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > Thanks a lot Dan! it's clear to me now, sorry that I > >> >> > >> > >>> > > am > >> >> > >still > >> >> > >> > >>> > > a > >> >> > >> > >>> > > newbie to OSX ... I got R-devel running and I will try > >> >> > >> > >>> > > Rswitcher, I > >> >> > >> > >>> > > also want to do that switch easily in emacs too. > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > You don't want to use R-devel. Both BioC release (2.14) > >> >> > >> > >>> > and > >> >> > >> > >>> > BioC > >> >> > >> > >>> > devel (3.0) are meant to work with R-3.1.0, the released > >> >> > >> > >>> > version of > >> >> > >> > >>> > R. > >> >> > >> > >>> > > >> >> > >> > >>> > I think the Rswitch app just sets a symbolic link, so > >> >> > >> > >>> > you > >> >> > >> > >>> > should be > >> >> > >> > >>> > able to do that within emacs. Run it and see what it > >> >> > >> > >>> > does > >> >> > >> > >>> > to > >> >> > >> > >>> > /Library/Frameworks/R.framework. > >> >> > >> > >>> > > >> >> > >> > >>> > Dan > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > > >> >> > >> > >>> > > cheers > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > Tengfei > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < > >> >> > >> > >>> > > dtenenba@fhcrc.org > >> >> > >> > >>> > > > > >> >> > >> > >>> > > wrote: > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > ----- Original Message ----- > >> >> > >> > >>> > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > To: "Dan Tenenbaum" < dtenenba@fhcrc.org > > >> >> > >> > >>> > > > Cc: "Bioconductor mailing list" < > >> >> > >> > >>> > > > bioconductor@r-project.org >, > >> >> > >> > >>> > > > lcollado@jhu.edu > >> >> > >> > >>> > > > Sent: Wednesday, April 23, 2014 9:24:42 AM > >> >> > >> > >>> > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > >> >> > >> > >>> > > > txdb > >> >> > >> > >>> > > > example is > >> >> > >> > >>> > > > broken > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > Hi Dan, > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > So you mean I install R 3.1 for snow leopard and it > >> >> > >should > >> >> > >> > >>> > > > work? > >> >> > >> > >>> > > > >> >> > >> > >>> > > Yes. > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > ? Is > >> >> > >> > >>> > > > there a way to build from source using biocLite, > >> >> > >> > >>> > > > like > >> >> > >type > >> >> > >> > >>> > > > = > >> >> > >> > >>> > > > "source", this is what I got > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > library(BiocInstaller) > >> >> > >> > >>> > > > Bioconductor version 2.14 (BiocInstaller 1.14.1), > >> >> > >?biocLite > >> >> > >> > >>> > > > for > >> >> > >> > >>> > > > help > >> >> > >> > >>> > > > > biocLite("GenomicRanges") > >> >> > >> > >>> > > > BioC_mirror: http://bioconductor.org > >> >> > >> > >>> > > > Using Bioconductor version 2.14 (BiocInstaller > >> >> > >> > >>> > > > 1.14.1), R > >> >> > >> > >>> > > > version > >> >> > >> > >>> > > > 3.1.0. > >> >> > >> > >>> > > > Installing package(s) 'GenomicRanges' > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > package âGenomicRangesâ is available as a source > >> >> > >> > >>> > > > package > >> >> > >> > >>> > > > but not > >> >> > >> > >>> > > > as > >> >> > >> > >>> > > > a > >> >> > >> > >>> > > > binary > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Warning message: > >> >> > >> > >>> > > > package âGenomicRangesâ is not available (for R > >> >> > >> > >>> > > > version > >> >> > >> > >>> > > > 3.1.0) > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Just wondering is there a solution without > >> >> > >> > >>> > > > re-install > >> >> > >> > >>> > > > R > >> >> > >for > >> >> > >> > >>> > > > snow > >> >> > >> > >>> > > > leopard. And what's the plan for maverick? > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > You can do > >> >> > >> > >>> > > biocLite("GenomicRanges", type="source") > >> >> > >> > >>> > > > >> >> > >> > >>> > > but you need to have the appropriate compilers, etc. > >> >> > >> > >>> > > > >> >> > >> > >>> > > I *STRONGLY* recommend using the Snow Leopard build. > >> >> > >> > >>> > > You > >> >> > >can > >> >> > >> > >>> > > have > >> >> > >> > >>> > > multiple installations of R on your Mac and switch > >> >> > >> > >>> > > between > >> >> > >> > >>> > > them > >> >> > >> > >>> > > using Rswitch ( http://r.research.att.com/#other ) or > >> >> > >another > >> >> > >> > >>> > > easy > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > mechanism. > >> >> > >> > >>> > > > >> >> > >> > >>> > > We are building packages for Mavericks now, we just > >> >> > >> > >>> > > have > >> >> > >> > >>> > > to > >> >> > >> > >>> > > resolve > >> >> > >> > >>> > > a > >> >> > >> > >>> > > few build issues and test the resulting packages, we > >> >> > >> > >>> > > still > >> >> > >> > >>> > > hope to > >> >> > >> > >>> > > have them available by the end of the month. But since > >> >> > >> > >>> > > you > >> >> > >> > >>> > > can > >> >> > >> > >>> > > install the Snow Leopard build without needing to > >> >> > >> > >>> > > remove > >> >> > >your > >> >> > >> > >>> > > Mavericks build, you should do that. > >> >> > >> > >>> > > > >> >> > >> > >>> > > Dan > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Thanks > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Tengfei > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < > >> >> > >> > >>> > > > dtenenba@fhcrc.org > >> >> > >> > >>> > > > > wrote: > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Hi Tengfei, > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > ----- Original Message ----- > >> >> > >> > >>> > > > > From: "Tengfei Yin" < tengfei.yin@sbgenomics.com> > >> >> > >> > >>> > > > > To: lcollado@jhu.edu > >> >> > >> > >>> > > > > Cc: bioconductor@r-project.org > >> >> > >> > >>> > > > > Sent: Wednesday, April 23, 2014 7:52:11 AM > >> >> > >> > >>> > > > > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with > >> >> > >> > >>> > > > > txdb > >> >> > >> > >>> > > > > example > >> >> > >> > >>> > > > > is > >> >> > >> > >>> > > > > broken > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > btw, based on the error, let me try to debug it. > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin > >> >> > >> > >>> > > > > < tengfei.yin@sbgenomics.com >wrote: > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > Hi Leonardo, > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > Frankly speaking, the vignette is still in > >> >> > >> > >>> > > > > > progress, > >> >> > >> > >>> > > > > > and > >> >> > >> > >>> > > > > > there > >> >> > >> > >>> > > > > > are > >> >> > >> > >>> > > > > > some > >> >> > >> > >>> > > > > > known bugs in ggbio I need to fix (still trying > >> >> > >> > >>> > > > > > to > >> >> > >find > >> >> > >> > >>> > > > > > a > >> >> > >> > >>> > > > > > time > >> >> > >> > >>> > > > > > to > >> >> > >> > >>> > > > > > do that > >> >> > >> > >>> > > > > > ... ), I am recently trying to install R 3.1 and > >> >> > >> > >>> > > > > > Bioc > >> >> > >> > >>> > > > > > 2.14 on > >> >> > >> > >>> > > > > > my > >> >> > >> > >>> > > > > > new MBP > >> >> > >> > >>> > > > > > with OSX 10.9, but fails, probably binary build > >> >> > >> > >>> > > > > > is > >> >> > >not > >> >> > >> > >>> > > > > > ready > >> >> > >> > >>> > > > > > for > >> >> > >> > >>> > > > > > maverick > >> >> > >> > >>> > > > > > yet, maybe available by the end of April? > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > Thanks for reporting the bug, I will keep you > >> >> > >> > >>> > > > > > posted > >> >> > >on > >> >> > >> > >>> > > > > > this > >> >> > >> > >>> > > > > > when > >> >> > >> > >>> > > > > > I > >> >> > >> > >>> > > > > > successfully get it on my laptop and start > >> >> > >> > >>> > > > > > fixing > >> >> > >> > >>> > > > > > the > >> >> > >> > >>> > > > > > problems. > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > You can install the Snow Leopard build of R and > >> >> > >> > >>> > > > should > >> >> > >have > >> >> > >> > >>> > > > no > >> >> > >> > >>> > > > problems, binary packages are available for that > >> >> > >> > >>> > > > version. > >> >> > >> > >>> > > > It will > >> >> > >> > >>> > > > run fine on Mavericks. > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Dan > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > > cheers > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > Tengfei > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo > >> >> > >> > >>> > > > > > Collado > >> >> > >> > >>> > > > > > Torres < > >> >> > >> > >>> > > > > > lcollado@jhsph.edu > wrote: > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > >> Hello Tengfei + bioc list, > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> From > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > >> >> > >> > >> >> > > > >> >> > > > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > >> >> > >> > >>> > > > > >> page 4 (complied on april 11 2014), the > >> >> > >> > >>> > > > > >> following > >> >> > >> > >>> > > > > >> example > >> >> > >> > >>> > > > > >> loads > >> >> > >> > >>> > > > > >> to > >> >> > >> > >>> > > > > >> an > >> >> > >> > >>> > > > > >> error as shown below. I wasn't seeing this > >> >> > >> > >>> > > > > >> error > >> >> > >> > >>> > > > > >> before > >> >> > >> > >>> > > > > >> (aka, > >> >> > >> > >>> > > > > >> last > >> >> > >> > >>> > > > > >> week). The only guess that comes to mind is the > >> >> > >recent > >> >> > >> > >>> > > > > >> update > >> >> > >> > >>> > > > > >> to > >> >> > >> > >>> > > > > >> GenomicRanges (1.16.2) although that doesn't > >> >> > >> > >>> > > > > >> seem > >> >> > >> > >>> > > > > >> to > >> >> > >> > >>> > > > > >> be > >> >> > >> > >>> > > > > >> related > >> >> > >> > >>> > > > > >> from > >> >> > >> > >>> > > > > >> the traceback() output, well... maybe it's > >> >> > >> > >>> > > > > >> related > >> >> > >to > >> >> > >> > >>> > > > > >> the > >> >> > >> > >>> > > > > >> ignore.strand = TRUE part as described in the > >> >> > >> > >>> > > > > >> error. > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> I'll create a GitHub issue just for > >> >> > >> > >>> > > > > >> completeness. > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> Thank you, > >> >> > >> > >>> > > > > >> Leonardo > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > library(ggbio) > >> >> > >> > >>> > > > > >> ## Removed the output, nothing out of ordinary > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > >> >> > >> > >>> > > > > >> ## Removed the output > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > >> >> > >> > >>> > > > > >> > data(genesymbol, package = "biovizBase") > >> >> > >> > >>> > > > > >> > p.txdb <- autoplot(txdb, which = > >> >> > >> > >>> > > > > >> > genesymbol["BRCA1"]) > >> >> > >> > >>> > > > > >> Aggregating TranscriptDb... > >> >> > >> > >>> > > > > >> Parsing transcripts... > >> >> > >> > >>> > > > > >> Parsing exons... > >> >> > >> > >>> > > > > >> Parsing cds... > >> >> > >> > >>> > > > > >> Parsing utrs... > >> >> > >> > >>> > > > > >> ------exons... > >> >> > >> > >>> > > > > >> ------cdss... > >> >> > >> > >>> > > > > >> ------introns... > >> >> > >> > >>> > > > > >> ------utr... > >> >> > >> > >>> > > > > >> aggregating... > >> >> > >> > >>> > > > > >> Done > >> >> > >> > >>> > > > > >> Constructing graphics... > >> >> > >> > >>> > > > > >> Error in sapply(listData, function(Xi) > >> >> > >> > >>> > > > > >> extends(class(Xi), > >> >> > >> > >>> > > > > >> elementTypeX)) : > >> >> > >> > >>> > > > > >> error in evaluating the argument 'X' in > >> >> > >> > >>> > > > > >> selecting > >> >> > >> > >>> > > > > >> a > >> >> > >> > >>> > > > > >> method > >> >> > >> > >>> > > > > >> for > >> >> > >> > >>> > > > > >> function 'sapply': Error in > >> >> > >> > >>> > > > > >> unlist(range(ranges(x.n, > >> >> > >> > >>> > > > > >> ignore.strand > >> >> > >> > >>> > > > > >> = > >> >> > >> > >>> > > > > >> TRUE))) : > >> >> > >> > >>> > > > > >> error in evaluating the argument 'x' in > >> >> > >> > >>> > > > > >> selecting > >> >> > >> > >>> > > > > >> a > >> >> > >> > >>> > > > > >> method > >> >> > >> > >>> > > > > >> for > >> >> > >> > >>> > > > > >> function 'unlist': Error in .local(x, ...) : > >> >> > >> > >>> > > > > >> unused > >> >> > >> > >>> > > > > >> argument > >> >> > >> > >>> > > > > >> (ignore.strand = TRUE) > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > traceback() > >> >> > >> > >>> > > > > >> 15: sapply(listData, function(Xi) > >> >> > >> > >>> > > > > >> extends(class(Xi), > >> >> > >> > >>> > > > > >> elementTypeX)) > >> >> > >> > >>> > > > > >> 14: .updateCompressedList(X, > >> >> > >lapply_CompressedList(X, > >> >> > >> > >>> > > > > >> FUN, > >> >> > >> > >>> > > > > >> ...)) > >> >> > >> > >>> > > > > >> 13: endoapply(obj.lst, function(x) { > >> >> > >> > >>> > > > > >> if (!is.null( group.name )) { > >> >> > >> > >>> > > > > >> if (!group.selfish) { > >> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> >> > >> > >>> > > > > >> TRUE))) > >> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> >> > >> > >>> > > > > >> width(irs) + > >> >> > >> > >>> > > > > >> extend.size) > >> >> > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> >> > >> > >>> > > > > >> values(x)$stepping <- > >> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> >> > >> > >>> > > > > >> group.name ])] > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> else { > >> >> > >> > >>> > > > > >> values(x)$stepping <- > >> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> >> > >> > >>> > > > > >> group.name ])) > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> else { > >> >> > >> > >>> > > > > >> irs <- ranges(x) > >> >> > >> > >>> > > > > >> values(x)$stepping <- > >> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> >> > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> >> > >> > >>> > > > > >> extend.size))) > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> }) > >> >> > >> > >>> > > > > >> 12: endoapply(obj.lst, function(x) { > >> >> > >> > >>> > > > > >> if (!is.null( group.name )) { > >> >> > >> > >>> > > > > >> if (!group.selfish) { > >> >> > >> > >>> > > > > >> x.n <- split(x, values(x)[, group.name ]) > >> >> > >> > >>> > > > > >> irs <- unlist(range(ranges(x.n, ignore.strand = > >> >> > >> > >>> > > > > >> TRUE))) > >> >> > >> > >>> > > > > >> irs.new <- resize(irs, fix = fix, width = > >> >> > >> > >>> > > > > >> width(irs) + > >> >> > >> > >>> > > > > >> extend.size) > >> >> > >> > >>> > > > > >> irs.new <- sort(irs.new) > >> >> > >> > >>> > > > > >> .lvs <- disjointBins(irs.new) > >> >> > >> > >>> > > > > >> values(x)$stepping <- > >> >> > >> > >>> > > > > >> .lvs[as.character(values(x)[, > >> >> > >> > >>> > > > > >> group.name ])] > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> else { > >> >> > >> > >>> > > > > >> values(x)$stepping <- > >> >> > >> > >>> > > > > >> as.numeric(as.factor(values(x)[, > >> >> > >> > >>> > > > > >> group.name ])) > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> else { > >> >> > >> > >>> > > > > >> irs <- ranges(x) > >> >> > >> > >>> > > > > >> values(x)stepping <- > >> >> > >> > >>> > > > > >> as.numeric(disjointBins(resize(irs, > >> >> > >> > >>> > > > > >> fix = "center", width = width(irs) + > >> >> > >> > >>> > > > > >> extend.size))) > >> >> > >> > >>> > > > > >> x > >> >> > >> > >>> > > > > >> } > >> >> > >> > >>> > > > > >> }) > >> >> > >> > >>> > > > > >> 11: .local(obj, ...) > >> >> > >> > >>> > > > > >> 10: addStepping(gr, group.name = "tx_id", > >> >> > >> > >>> > > > > >> group.selfish = > >> >> > >> > >>> > > > > >> FALSE, > >> >> > >> > >>> > > > > >> fix = "start", extend.size = es) > >> >> > >> > >>> > > > > >> 9: addStepping(gr, group.name = "tx_id", > >> >> > >group.selfish > >> >> > >> > >>> > > > > >> = > >> >> > >> > >>> > > > > >> FALSE, > >> >> > >> > >>> > > > > >> fix = "start", extend.size = es) > >> >> > >> > >>> > > > > >> 8: .local(data, ...) > >> >> > >> > >>> > > > > >> 7: (function (data, ...) > >> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> >> > >> > >>> > > > > >> object > >> >> > >> > >>> > > > > >> of > >> >> > >> > >>> > > > > >> class > >> >> > >> > >>> > > > > >> "TranscriptDb">, > >> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> >> > >> > >>> > > > > >> "alignment", > >> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > >> >> > >> > >>> > > > > >> label > >> >> > >> > >>> > > > > >> = > >> >> > >> > >>> > > > > >> TRUE, > >> >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> >> > >> > >>> > > > > >> 6: (function (data, ...) > >> >> > >> > >>> > > > > >> standardGeneric("geom_alignment"))(data = <s4> >> >> > >> > >>> > > > > >> object > >> >> > >> > >>> > > > > >> of > >> >> > >> > >>> > > > > >> class > >> >> > >> > >>> > > > > >> "TranscriptDb">, > >> >> > >> > >>> > > > > >> truncate.gaps = FALSE, ratio = 0.0025, geom = > >> >> > >> > >>> > > > > >> "alignment", > >> >> > >> > >>> > > > > >> stat = "identity", names.expr = "tx_name", > >> >> > >> > >>> > > > > >> label > >> >> > >> > >>> > > > > >> = > >> >> > >> > >>> > > > > >> TRUE, > >> >> > >> > >>> > > > > >> which = <s4 object="" of="" class="" "granges"="">, list()) > >> >> > >> > >>> > > > > >> 5: do.call(geom_alignment, args.res) > >> >> > >> > >>> > > > > >> 4: do.call(geom_alignment, args.res) > >> >> > >> > >>> > > > > >> 3: .local(object, ...) > >> >> > >> > >>> > > > > >> 2: autoplot(txdb, which = genesymbol["BRCA1"]) > >> >> > >> > >>> > > > > >> 1: autoplot(txdb, which = genesymbol["BRCA1"]) > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> > sessionInfo() > >> >> > >> > >>> > > > > >> R version 3.1.0 (2014-04-10) > >> >> > >> > >>> > > > > >> Platform: x86_64-apple-darwin10.8.0 (64-bit) > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> locale: > >> >> > >> > >>> > > > > >> [1] > >> >> > >> > >>> > > > > >> > >> >> > >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> attached base packages: > >> >> > >> > >>> > > > > >> [1] parallel stats graphics grDevices utils > >> >> > >> > >>> > > > > >> datasets > >> >> > >> > >>> > > > > >> methods base > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> other attached packages: > >> >> > >> > >>> > > > > >> [1] XVector_0.4.0 > >> >> > >> > >>> > > > > >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 > >> >> > >> > >>> > > > > >> GenomicFeatures_1.16.0 > >> >> > >> > >>> > > > > >> [4] AnnotationDbi_1.26.0 Biobase_2.24.0 > >> >> > >> > >>> > > > > >> GenomicRanges_1.16.2 > >> >> > >> > >>> > > > > >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3 > >> >> > >> > >>> > > > > >> ggbio_1.12.0 > >> >> > >> > >>> > > > > >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0 > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > >> loaded via a namespace (and not attached): > >> >> > >> > >>> > > > > >> [1] BatchJobs_1.2 BBmisc_1.5 > >> >> > >> > >>> > > > > >> BiocParallel_0.6.0 biomaRt_2.20.0 > >> >> > >> > >>> > > > > >> Biostrings_2.32.0 > >> >> > >> > >>> > > > > >> [6] biovizBase_1.12.0 bitops_1.0-6 brew_1.0-6 > >> >> > >> > >>> > > > > >> BSgenome_1.32.0 cluster_1.15.2 > >> >> > >> > >>> > > > > >> [11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 > >> >> > >> > >>> > > > > >> dichromat_2.0-0 digest_0.6.4 > >> >> > >> > >>> > > > > >> [16] fail_1.2 foreach_1.4.2 > >> >> > >> > >>> > > > > >> Formula_1.1-1 > >> >> > >> > >>> > > > > >> GenomicAlignments_1.0.0 grid_3.1.0 > >> >> > >> > >>> > > > > >> [21] gridExtra_0.9.1 gtable_0.1.2 > >> >> > >> > >>> > > > > >> Hmisc_3.14-4 > >> >> > >> > >>> > > > > >> iterators_1.0.7 labeling_0.2 > >> >> > >> > >>> > > > > >> [26] lattice_0.20-29 latticeExtra_0.6-26 > >> >> > >> > >>> > > > > >> MASS_7.3-31 > >> >> > >> > >>> > > > > >> munsell_0.4.2 plyr_1.8.1 > >> >> > >> > >>> > > > > >> [31] proto_0.3-10 RColorBrewer_1.0-5 > >> >> > >> > >>> > > > > >> Rcpp_0.11.1 > >> >> > >> > >>> > > > > >> RCurl_1.95-4.1 reshape2_1.2.2 > >> >> > >> > >>> > > > > >> [36] Rsamtools_1.16.0 RSQLite_0.11.4 > >> >> > >> > >>> > > > > >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2 > >> >> > >> > >>> > > > > >> [41] splines_3.1.0 stats4_3.1.0 > >> >> > >> > >>> > > > > >> stringr_0.6.2 > >> >> > >> > >>> > > > > >> survival_2.37-7 tools_3.1.0 > >> >> > >> > >>> > > > > >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 > >> >> > >> > >>> > > > > >> zlibbioc_1.10.0 > >> >> > >> > >>> > > > > >> > > >> >> > >> > >>> > > > > >> > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > -- > >> >> > >> > >>> > > > > > Tengfei Yin, PhD > >> >> > >> > >>> > > > > > Seven Bridges Genomics > >> >> > >> > >>> > > > > > sbgenomics.com > >> >> > >> > >>> > > > > > 625 Mt. Auburn St. Suite #208 > >> >> > >> > >>> > > > > > Cambridge, MA 02138 > >> >> > >> > >>> > > > > > (617) 866-0446 > >> >> > >> > >>> > > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > -- > >> >> > >> > >>> > > > > Tengfei Yin, PhD > >> >> > >> > >>> > > > > Seven Bridges Genomics > >> >> > >> > >>> > > > > sbgenomics.com > >> >> > >> > >>> > > > > 625 Mt. Auburn St. Suite #208 > >> >> > >> > >>> > > > > Cambridge, MA 02138 > >> >> > >> > >>> > > > > (617) 866-0446 > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > [[alternative HTML version deleted]] > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > _______________________________________________ > >> >> > >> > >>> > > > > Bioconductor mailing list > >> >> > >> > >>> > > > > Bioconductor@r-project.org > >> >> > >> > >>> > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> > >> > >>> > > > > Search the archives: > >> >> > >> > >>> > > > > > >> >> > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > >> > >>> > > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > -- > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > Tengfei Yin, PhD > >> >> > >> > >>> > > > Seven Bridges Genomics > >> >> > >> > >>> > > > sbgenomics.com > >> >> > >> > >>> > > > 625 Mt. Auburn St. Suite #208 > >> >> > >> > >>> > > > Cambridge, MA 02138 > >> >> > >> > >>> > > > (617) 866- 0446 > >> >> > >> > >>> > > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > -- > >> >> > >> > >>> > > > >> >> > >> > >>> > > > >> >> > >> > >>> > > Tengfei Yin, PhD > >> >> > >> > >>> > > Seven Bridges Genomics > >> >> > >> > >>> > > sbgenomics.com > >> >> > >> > >>> > > 625 Mt. Auburn St. Suite #208 > >> >> > >> > >>> > > Cambridge, MA 02138 > >> >> > >> > >>> > > (617) 866- 0446 > >> >> > >> > >>> > > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > -- > >> >> > >> > >>> > > >> >> > >> > >>> > > >> >> > >> > >>> > Tengfei Yin, PhD > >> >> > >> > >>> > Seven Bridges Genomics > >> >> > >> > >>> > sbgenomics.com > >> >> > >> > >>> > 625 Mt. Auburn St. Suite #208 > >> >> > >> > >>> > Cambridge, MA 02138 > >> >> > >> > >>> > (617) 866- 0446 > >> >> > >> > >>> > > >> >> > >> > >> > >> >> > >> > >> > >> >> > >> > >> > >> >> > >> > >> > >> >> > >> > >> -- > >> >> > >> > >> Tengfei Yin, PhD > >> >> > >> > >> Seven Bridges Genomics > >> >> > >> > >> sbgenomics.com > >> >> > >> > >> 625 Mt. Auburn St. Suite #208 > >> >> > >> > >> Cambridge, MA 02138 > >> >> > >> > >> (617) 866-0446 > >> >> > >> > > >> >> > >> > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > > >> >> > > >> >> > Tengfei Yin, PhD > >> >> > Seven Bridges Genomics > >> >> > sbgenomics.com > >> >> > 625 Mt. Auburn St. Suite #208 > >> >> > Cambridge, MA 02138 > >> >> > (617) 866- 0446 > >> >> > > >> >> > >> >> _______________________________________________ > >> >> Bioconductor mailing list > >> >> Bioconductor@r-project.org > >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> >> Search the archives: > >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > > -- > > Tengfei Yin, PhD > > Seven Bridges Genomics > > sbgenomics.com > > 625 Mt. Auburn St. Suite #208 > > Cambridge, MA 02138 > > (617) 866-0446 > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]] ADD COMMENT 0 Entering edit mode Hi Tengfei, No problem and thank you for fixing these issues =) I did notice the new vignette ^_^ and how gene symbols are supported now. I'm thinking of just sticking to tx_name for the txdb objects just because I already have the gene symbol in another part of the track plot. That's why I realized that I don't really need the gene_id, but well, I still found that case where tx_name(gene_id) didn't work together. The only real bug is the one when no annotation is found. Cheers, Leo On Tue, Apr 29, 2014 at 10:36 PM, Tengfei Yin <tengfei.yin at="" sbgenomics.com=""> wrote: > Hi Leo, > > Thanks for reporting the bugs, yes, this is a perfect time to report, if you > read a new updated vignette (still keep updating it ...) in 1.12.3 > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf > You will notice section 'add gene model' changed, it support OrganismDb now, > so the name.expr support more items now, if you are using Homo.sapiens, you > could label "gene symbols" too, I did lots of change for autoplot,Organism > and autoplot,Txdb function, this will probably introduce some bugs you > reported. > > I will work on fixing those bugs you reported and keep you posted. > > cheers > > Tengfei > > > On Tue, Apr 29, 2014 at 10:05 PM, Leonardo Collado Torres <lcollado at="" jhu.edu=""> > wrote: >> >> Hi Tengfei, >> >> Interesting, I don't really know what's the issue with the bug you found. >> >> >> >> Looking into ggbio 1.12.3 I noticed a couple of things with >> autoplot(txdb). >> >> Basically, I found three cases. >> >> Case 1: function works well, just a message that looks like a warning >> (it's a message) is printed out. Nothing biggie. >> Case 2: Labels when using tx_name(gene_id) don't work (although they >> work in case 1) but they do work individually. >> Case 3: Function fails because there is nothing in that region. >> >> The code is shown below where you only have to specify the region of >> interest according to the case. >> >> >> >> Previously, I would use something like this (shown below) to catch case 3. >> >> p.transcripts <- tryCatch(autoplot(txdb, which = wh, >> names.expr = "tx_name(gene_id)"), warning = function(w) { >> FALSE >> }) >> >> Now that it results in an error, I can detect these cases using: >> >> p.transcripts <- tryCatch(autoplot(txdb, which = wh, >> names.expr = "tx_name(gene_id)"), error = function(e) { >> FALSE >> }) >> >> >> However, I thought that this would be a good time to report this. >> >> >> Regarding case 2, in my use case I'm thinking of switching to >> "tx_name" instead of using "tx_name(gene_id)". But well, it's also >> worth reporting. >> >> >> >> ## Case 1 & 2 show the following 'message' that looks like a warning >> though >> >> "gap" is not matching to following arbitrary model terms"cds CDS Cds >> exon EXON Exon utr UTR Utr" >> >> ## Case 3 error >> >> Error in data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, >> : >> arguments imply differing number of rows: 0, 1 >> > traceback() >> 13: stop(gettextf("arguments imply differing number of rows: %s", >> paste(unique(nrows), collapse = ", ")), domain = NA) >> 12: data.frame(tx_id = .nms, tx_name = .tx.nms, gene_id = .gid.nms, >> type = "exon") >> 11: .local(obj, ...) >> 10: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = >> truncate.fun, >> ratio = ratio, columns = columns) >> 9: crunch(data, which, truncate.gaps = truncate.gaps, truncate.fun = >> truncate.fun, >> ratio = ratio, columns = columns) >> 8: .local(data, ...) >> 7: (function (data, ...) >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">> "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, >> which = <s4 object="" of="" class="" "granges"="">, list()) >> 6: (function (data, ...) >> standardGeneric("geom_alignment"))(data = <s4 object="" of="" class="">> "TranscriptDb">, >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment", >> stat = "identity", names.expr = "tx_name(gene_id)", label = TRUE, >> which = <s4 object="" of="" class="" "granges"="">, list()) >> 5: do.call(geom_alignment, args.res) >> 4: do.call(geom_alignment, args.res) >> 3: .local(object, ...) >> 2: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >> 1: autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >> >> >> >> Here's the code. >> >> >> >> ## Load required libs >> library(ggbio) >> library(GenomicRanges) >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >> >> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >> >> ### Set up region >> >> ## Case 1: Labels don't work for tx_name(gene_id) case >> # wh <- GRanges("chr21", ranges=IRanges(start=47411800, end=47412600)) >> ## Case 2: Labels work, although what looks like a warning is still shown >> # wh <- GRanges("chr17", ranges=IRanges(start=47115000, end=47130000)) >> ## Case 3: Error >> wh <- GRanges("chr21", ranges=IRanges(start=36759003, end=36800825)) >> >> p1 <- autoplot(txdb, which = wh, names.expr = "tx_name(gene_id)") >> p2 <- autoplot(txdb, which = wh, names.expr = "tx_name") >> p3 <- autoplot(txdb, which = wh, names.expr = "gene_id") >> >> chr <- as.character(seqnames(wh)) >> >> >> ## load the ideogram info >> hg19IdeogramCyto <- NULL >> load(system.file("data", "hg19IdeogramCyto.rda", package = >> "biovizBase", mustWork = TRUE)) >> p.ideogram <- plotIdeogram(hg19IdeogramCyto, chr) >> >> ## Combine info into a tracks plot >> p.final <- tracks(p.ideogram, tx_name\n(gene_id) = p1, tx_name = >> p2, gene_id = p3, heights = c(2, 3, 3, 3), xlim = wh, title = >> "test") + ylab("") + theme_tracks_sunset() >> p.final >> >> >> >> >> >> >> >> >> > sessionInfo() >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] XVector_0.4.0 >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 >> [5] Biobase_2.24.0 GenomicRanges_1.16.2 >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 >> [9] ggbio_1.12.3 ggplot2_0.9.3.1 >> [11] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 >> [4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1 >> [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 >> [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 >> [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >> [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 >> [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 >> [25] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-32 >> [28] munsell_0.4.2 plyr_1.8.1 proto_0.3-10 >> [31] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 >> [34] reshape2_1.4 Rsamtools_1.16.0 RSQLite_0.11.4 >> [37] rtracklayer_1.24.0 scales_0.2.4 sendmailR_1.1-2 >> [40] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 >> [43] survival_2.37-7 tools_3.1.0 >> VariantAnnotation_1.10.0 >> [46] XML_3.98-1.1 zlibbioc_1.10.0 >> >> >> >> >> Cheers, >> Leo >> >> On Tue, Apr 29, 2014 at 9:03 PM, Tengfei Yin <tengfei.yin at="" sbgenomics.com=""> >> wrote: >> > it's good it's building, but it's very weird that it works, because I >> > simply >> > removed eval = TRUE for that chunk which is default. I came across some >> > really weird *bug* in knitr which I try to reproduce with a minimal >> > example, >> > if you look closely, I put three blank code chunk at the front to avoid >> > the >> > figures orders being messed up somehow and I don't know why. I guess >> > until I >> > have a minimal example, I cannot really report it to yihui to fix it. >> > >> > >> > On Tue, Apr 29, 2014 at 7:03 PM, Leonardo Collado Torres >> > <lcollado at="" jhsph.edu=""> wrote: >> >> >> >> I just noticed that ggbio is building now >> >> >> >> >> >> http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> >> and I'm happy to report that the problem I mentioned is resolved with >> >> ggbio 1.12.3. Thank you Tengfei and Dan! >> >> >> >> >> >> For reference, here is the working session information. >> >> >> >> > sessionInfo() >> >> R version 3.1.0 (2014-04-10) >> >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> >> >> locale: >> >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> >> >> attached base packages: >> >> [1] parallel stats graphics grDevices utils datasets >> >> methods base >> >> >> >> other attached packages: >> >> [1] XVector_0.4.0 >> >> TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 >> >> [3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0 >> >> [5] Biobase_2.24.0 GenomicRanges_1.16.2 >> >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.4 >> >> [9] ggbio_1.12.3 ggplot2_0.9.3.1 >> >> [11] BiocGenerics_0.10.0 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] BatchJobs_1.2 BBmisc_1.6 >> >> BiocParallel_0.6.0 >> >> [4] biomaRt_2.20.0 Biostrings_2.32.0 >> >> biovizBase_1.12.1 >> >> [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 >> >> [10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 >> >> [13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4 >> >> [16] fail_1.2 foreach_1.4.2 Formula_1.1-1 >> >> [19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1 >> >> [22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7 >> >> [25] labeling_0.2 lattice_0.20-29 >> >> latticeExtra_0.6-26 >> >> [28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1 >> >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 >> >> [34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0 >> >> [37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4 >> >> [40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 >> >> [43] stringr_0.6.2 survival_2.37-7 tools_3.1.0 >> >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1 zlibbioc_1.10.0 >> >> >> >> On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> >> wrote: >> >> > >> >> > >> >> > ----- Original Message ----- >> >> >> From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> >> >> >> To: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> >> >> Cc: lcollado at jhu.edu, "Bioconductor mailing list" >> >> >> <bioconductor at="" r-project.org=""> >> >> >> Sent: Saturday, April 26, 2014 7:33:41 PM >> >> >> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >> >> >> broken >> >> >> >> >> >> >> >> >> >> >> >> ----- Original Message ----- >> >> >> > From: "Tengfei Yin" <tengfei.yin at="" sbgenomics.com=""> >> >> >> > To: lcollado at jhu.edu >> >> >> > Cc: "Dan Tenenbaum" <dtenenba at="" fhcrc.org="">, "Bioconductor mailing >> >> >> > list" <bioconductor at="" r-project.org=""> >> >> >> > Sent: Saturday, April 26, 2014 1:58:01 PM >> >> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is >> >> >> > broken >> >> >> > >> >> >> > >> >> >> > right, it's failing to build and I am trying to figure out why >> >> >> > now, >> >> >> > because it passes check/build and works on my laptop, but it >> >> >> > doesn't >> >> >> > pass bioc build for both release and devel, let me dig into it >> >> >> > tonight. >> >> >> > >> >> >> >> >> >> Seems like this could be fixed if you just add >> >> >> >> >> >> library(ggbio) >> >> >> >> >> >> to your vignette before the ggbio() function is called on line 557 >> >> >> of >> >> >> vignettes/realvignettes/ggbio.Rnw. >> >> >> >> >> > >> >> > Sorry, I spoke too soon; that just changes the error message you >> >> > receive. >> >> > Dan >> >> > >> >> > >> >> >> Dan >> >> >> >> >> >> >> >> >> > >> >> >> > thanks for your patience >> >> >> > >> >> >> > >> >> >> > Tengfei >> >> >> > >> >> >> > >> >> >> > >> >> >> > On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres < >> >> >> > lcollado at jhsph.edu > wrote: >> >> >> > >> >> >> > >> >> >> > >> >> >> > Oh ok. Thanks for the info >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < >> >> >> > dtenenba at fhcrc.org >> >> >> > > wrote: >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > Leonardo Collado Torres < lcollado at jhsph.edu > wrote: >> >> >> > >> >> >> > >Is there any reason why ggbio 1.12.2 hasn't made it to BioC >> >> >> > >release? >> >> >> > > >> >> >> > > >> >> >> > > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html >> >> >> > >still >> >> >> > >points to 1.12.0 >> >> >> > > >> >> >> > >> >> >> > It's failing to build: >> >> >> > >> >> >> > >> >> >> > >> >> >> > http://www.bioconductor.org/checkResults/release/bioc- LATEST/ggbio/zin2-buildsrc.html >> >> >> > >> >> >> > >> >> >> > >> >> >> > Dan >> >> >> > >> >> >> > > >> >> >> > >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < >> >> >> > >dtenenba at fhcrc.org >> >> >> > >> >> >> >> > >wrote: >> >> >> > > >> >> >> > >> >> >> >> > >> >> >> >> > >> ----- Original Message ----- >> >> >> > >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu > >> >> >> > >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> >> > >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor >> >> >> > >> > mailing >> >> >> > >list" < >> >> >> > >> bioconductor at r-project.org > >> >> >> > >> > Sent: Wednesday, April 23, 2014 3:38:11 PM >> >> >> > >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example >> >> >> > >> > is >> >> >> > >broken >> >> >> > >> > >> >> >> > >> > Dang it, forgot again to send with my @ jhsph.edu account. >> >> >> > >> > See >> >> >> > >> > below >> >> >> > >> > again >.< >> >> >> > >> > >> >> >> > >> > On the email topic, is it possible to be subscribed with 2 >> >> >> > >> > emails >> >> >> > >> > accounts to the BioC mailing list but only get emails with >> >> >> > >> > one? >> >> >> > >> > I >> >> >> > >> > believe that I have to choose to either get the daily digest >> >> >> > >> > or >> >> >> > >> > get >> >> >> > >a >> >> >> > >> > single for every message sent. If not, I'll probably just >> >> >> > >> > drop >> >> >> > >> > my >> >> >> > >> > @ jhsph.edu subscription and re-subscribe with the new @ >> >> >> > >> > jhu.edu >> >> >> > >> > mail >> >> >> > >I >> >> >> > >> > got (our university is pushing these mails). >> >> >> > >> > >> >> >> > >> >> >> >> > >> I don't know; you could try it. Another option would be to >> >> >> > >> configure >> >> >> > >your >> >> >> > >> mail client with a filter to drop the undesired bioc emails. >> >> >> > >> >> >> >> > >> Dan >> >> >> > >> >> >> >> > >> >> >> >> > >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres >> >> >> > >> > < lcollado at jhu.edu > wrote: >> >> >> > >> > > Hi Dan, >> >> >> > >> > > >> >> >> > >> > > I got RSwitch to work with a second installation of R 3.1. >> >> >> > >> > > Basically, >> >> >> > >> > > I downloaded the leopard tarball, expanded it, renamed the >> >> >> > >> > > folder >> >> >> > >> > > 3.1 >> >> >> > >> > > to 3.1patched (which is the version I downloaded, but well, >> >> >> > >> > > anything >> >> >> > >> > > except for 3.1 would work), compressed it again, and then >> >> >> > >expanded >> >> >> > >> > > it >> >> >> > >> > > at the root location. >> >> >> > >> > > >> >> >> > >> > > So it would be something like this: >> >> >> > >> > > >> >> >> > >> > > wget >> >> >> > >> > > >> >> >> > >> >> >> >> > > >> >> >> > > >> >> >> > > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1 -branch-snowleopard-sa-x86_64.tar.gz >> >> >> > >> > > tar -xvf R-*gz >> >> >> > >> > > mv Library/Frameworks/R.framework/Versions/3.1 >> >> >> > >> > > Library/Frameworks/R.framework/Versions/3.1patched >> >> >> > >> > > tar -cvzf Rlib.tgz Library >> >> >> > >> > > sudo tar fvxz Rlib.tgz -C / >> >> >> > >> > > >> >> >> > >> > > Then used RSwitch, and was able to install BioC- devel. >> >> >> > >> > > >> >> >> > >> > > I might try out your renv at a different time. It's great >> >> >> > >> > > to >> >> >> > >know >> >> >> > >> > > that it exists =) >> >> >> > >> > > >> >> >> > >> > > Cheers, >> >> >> > >> > > Leo >> >> >> > >> > > >> >> >> > >> > > >> >> >> > >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin >> >> >> > >> > > < tengfei.yin at sbgenomics.com > wrote: >> >> >> > >> > >> Hi Dan, >> >> >> > >> > >> >> >> >> > >> > >> It works like a charm, thanks! >> >> >> > >> > >> >> >> >> > >> > >> I use your method, then I changed /Library/Framework/ >> >> >> > >> > >> folder >> >> >> > >> > >> and >> >> >> > >> > >> R.Framework >> >> >> > >> > >> folder ownership to myself so I don't have to sudo it, >> >> >> > >> > >> then >> >> >> > >> > >> I >> >> >> > >just >> >> >> > >> > >> add alias >> >> >> > >> > >> to "emacs2" and "emacs3" to run your renv to switch the R >> >> >> > >> > >> first. >> >> >> > >> > >> This solves >> >> >> > >> > >> my problem. >> >> >> > >> > >> >> >> >> > >> > >> Try to customize variable for R hooks in emacs as >> >> >> > >> > >> alternative >> >> >> > >> > >> solution, but >> >> >> > >> > >> may need more time. >> >> >> > >> > >> >> >> >> > >> > >> Thanks again! >> >> >> > >> > >> >> >> >> > >> > >> Tengfei >> >> >> > >> > >> >> >> >> > >> > >> >> >> >> > >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum >> >> >> > >> > >> < dtenenba at fhcrc.org > wrote: >> >> >> > >> > >>> >> >> >> > >> > >>> Hi Tengfei, >> >> >> > >> > >>> >> >> >> > >> > >>> ----- Original Message ----- >> >> >> > >> > >>> > From: "Tengfei Yin" < tengfei.yin at sbgenomics.com > >> >> >> > >> > >>> > To: "Dan Tenenbaum" < dtenenba at fhcrc.org > >> >> >> > >> > >>> > Cc: "Bioconductor mailing list" < >> >> >> > >> > >>> > bioconductor at r-project.org >, >> >> >> > >> > >>> > lcollado at jhu.edu >> >> >> > >> > >>> > Sent: Wednesday, April 23, 2014 11:01:18 AM >> >> >> > >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb >> >> >> > >> > >>> > example >> >> >> > >> > >>> > is broken >> >> >> > >> > >>> > >> >> >> > >> > >>> > >> >> >> > >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all >> >> >> > >> > >>> > on >> >> >> > >the >> >> >> > >> > >>> > R 3.1? >> >> >> > >> > >>> >> >> >> > >> > >>> Yes, install two copies of R 3.1 and switch between them. >> >> >> > >> > >>> >> >> >> > >> > >>> > And do some sort of switch for bioc? The website you >> >> >> > >> > >>> > send >> >> >> > >> > >>> > to >> >> >> > >me >> >> >> > >> > >>> > also >> >> >> > >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on >> >> >> > >R-devel >> >> >> > >> > >>> > and >> >> >> > >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R >> >> >> > >> > >>> > only >> >> >> > >to >> >> >> > >> > >>> > switch bioc, so that I could debug and maintain >> >> >> > >> > >>> > released >> >> >> > >> > >>> > and >> >> >> > >> > >>> > devel >> >> >> > >> > >>> > version. >> >> >> > >> > >>> >> >> >> > >> > >>> PLEASE don't use R-devel at all. >> >> >> > >> > >>> >> >> >> > >> > >>> Just use R-3.1.0. >> >> >> > >> > >>> >> >> >> > >> > >>> You can use the Rswitch app but as you point out it won't >> >> >> > >> > >>> work >> >> >> > >> > >>> within >> >> >> > >> > >>> emacs. >> >> >> > >> > >>> >> >> >> > >> > >>> This is what I do: >> >> >> > >> > >>> >> >> >> > >> > >>> Every time I download a new version of R, I run its >> >> >> > >> > >>> installer. >> >> >> > >> > >>> The >> >> >> > >> > >>> installer always puts it in >> >> >> > >> > >>> >> >> >> > >> > >>> /Library/Frameworks/R.framework >> >> >> > >> > >>> >> >> >> > >> > >>> So after I install each version of R, I rename the >> >> >> > >> > >>> R.framework >> >> >> > >> > >>> directory >> >> >> > >> > >>> to something like >> >> >> > >> > >>> R.framework.bioc214_snowleopard >> >> >> > >> > >>> >> >> >> > >> > >>> And then I make a symlink from >> >> >> > >> > >>> R.framework.bioc214_snowleopard >> >> >> > >to >> >> >> > >> > >>> R.framework. >> >> >> > >> > >>> >> >> >> > >> > >>> I have a little script at >> >> >> > >> > >>> https://github.com/dtenenba/renv >> >> >> > >which >> >> >> > >> > >>> lets me >> >> >> > >> > >>> see what the various installed Rs are: >> >> >> > >> > >>> >> >> >> > >> > >>> renv >> >> >> > >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0 >> >> >> > >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> >> > >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> >> > >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0 >> >> >> > >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0 >> >> >> > >> > >>> >> >> >> > >> > >>> This tells me that the currently active R is nicknamed >> >> >> > >> > >>> "releaseMav" (this >> >> >> > >> > >>> means there is a link from >> >> >> > >> > >>> /Library/Frameworks/R.framework.releaseMav to >> >> >> > >> > >>> /Library/Frameworks/R.framework. It shows the versions, >> >> >> > >> > >>> svn >> >> >> > >> > >>> revisions, >> >> >> > >> > >>> dates, and architectures of each version. (darwin10.8.0 >> >> >> > >> > >>> is >> >> >> > >> > >>> Snow >> >> >> > >> > >>> Leopard; >> >> >> > >> > >>> darwin13.1.0 is Mavericks). >> >> >> > >> > >>> >> >> >> > >> > >>> Note that in my nomenclature devel means BioC devel, not >> >> >> > >R-devel. >> >> >> > >> > >>> >> >> >> > >> > >>> So if I wanted to switch to the "develSL" version I would >> >>