Question

ggbio::plotIdeogram() not working on R 3.0.2

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Leonardo Collado Torres ★ 1.0k

@lcolladotor

Last seen 22 days ago

United States

Dear BioC list and Tengfei Yin, I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 that I think is related to changes in R. The error can also be seen in http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf (search 'unnamed' on the pdf). Below is the error from running the example code for plotIdeogram. library(ggbio) library(biovizBase) data(hg19IdeogramCyto, package = "biovizBase") biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE plotIdeogram(hg19IdeogramCyto, "chr1") ## Error in initialize(value, ...) : unnamed argument must extend either the S3 class or the class of the data part; not true of class GGbio traceback() ## 6: stop(gettextf("unnamed argument must extend either the S3 class or the class of the data part; not true of class %s", ## dQuote(Classi)), domain = NA) ## 5: initialize(value, ...) ## 4: initialize(value, ...) ## 3: new("Ideogram", x) ## 2: Ideogram(p) ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") sessionInfo() ## R version 3.0.2 (2013-09-25) ## 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] stats graphics grDevices utils datasets methods base ## other attached packages: ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 ## loaded via a namespace (and not attached): ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 ## [11] dichromat_2.0-0 digest_0.6.3 GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 plyr_1.8 ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 ## [36] stringr_0.6.2 tools_3.0.2 VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 ## [41] zlibbioc_1.8.0 Thank you, Leonardo Leonardo Collado Torres, PhD student Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://www.biostat.jhsph.edu/~lcollado/ Blog: http://lcolladotor.github.io/ [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.5 years ago by Tengfei Yin ▴ 490 • written 10.5 years ago by Leonardo Collado Torres ★ 1.0k

score 0 · Answer 1 · 2013-11-04

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Tengfei Yin ▴ 490

@tengfei-yin-6162

Last seen 9.7 years ago

Hi Leonardo, Thanks for reporting the issue, this is probably not R's problem, should be a bug in ggbio's new class, I will look into this. Tengfei On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres <lcollado@jhsph.edu>wrote: > Dear BioC list and Tengfei Yin, > > I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 > that I think is related to changes in R. The error can also be seen in > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf (search > 'unnamed' on the pdf). > > Below is the error from running the example code for plotIdeogram. > > library(ggbio) > library(biovizBase) > data(hg19IdeogramCyto, package = "biovizBase") > biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE > plotIdeogram(hg19IdeogramCyto, "chr1") > > ## Error in initialize(value, ...) : > unnamed argument must extend either the S3 class or the class of the > data part; not true of class GGbio > > traceback() > > ## 6: stop(gettextf("unnamed argument must extend either the S3 class or > the class of the data part; not true of class %s", > ## dQuote(Classi)), domain = NA) > ## 5: initialize(value, ...) > ## 4: initialize(value, ...) > ## 3: new("Ideogram", x) > ## 2: Ideogram(p) > ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") > > sessionInfo() > > ## R version 3.0.2 (2013-09-25) > ## 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] stats graphics grDevices utils datasets methods base > > > ## other attached packages: > ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 > > ## loaded via a namespace (and not attached): > ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > biomaRt_2.18.0 Biostrings_2.30.0 > ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 > colorspace_1.2-4 DBI_0.2-7 > ## [11] dichromat_2.0-0 digest_0.6.3 > GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 > ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 > IRanges_1.20.4 labeling_0.2 > ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 > parallel_3.0.2 plyr_1.8 > ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 > reshape2_1.2.2 rpart_4.1-3 > ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 > scales_0.2.3 stats4_3.0.2 > ## [36] stringr_0.6.2 tools_3.0.2 > VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 > ## [41] zlibbioc_1.8.0 > > > Thank you, > Leonardo > > Leonardo Collado Torres, PhD student > Department of Biostatistics > Johns Hopkins University > Bloomberg School of Public Health > Website: http://www.biostat.jhsph.edu/~lcollado/ > Blog: http://lcolladotor.github.io/ > -- 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 • link 10.5 years ago Tengfei Yin ▴ 490

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Hi I just fixed this bug in 1.10.1 in release branch, please update one or two days later. Thanks Tengfei On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > Thanks for reporting the issue, this is probably not R's problem, should > be a bug in ggbio's new class, I will look into this. > > Tengfei > > > On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Dear BioC list and Tengfei Yin, >> >> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >> that I think is related to changes in R. The error can also be seen in >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf (search >> 'unnamed' on the pdf). >> >> Below is the error from running the example code for plotIdeogram. >> >> library(ggbio) >> library(biovizBase) >> data(hg19IdeogramCyto, package = "biovizBase") >> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >> plotIdeogram(hg19IdeogramCyto, "chr1") >> >> ## Error in initialize(value, ...) : >> unnamed argument must extend either the S3 class or the class of the >> data part; not true of class GGbio >> >> traceback() >> >> ## 6: stop(gettextf("unnamed argument must extend either the S3 class or >> the class of the data part; not true of class %s", >> ## dQuote(Classi)), domain = NA) >> ## 5: initialize(value, ...) >> ## 4: initialize(value, ...) >> ## 3: new("Ideogram", x) >> ## 2: Ideogram(p) >> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >> >> sessionInfo() >> >> ## R version 3.0.2 (2013-09-25) >> ## 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] stats graphics grDevices utils datasets methods base >> >> >> ## other attached packages: >> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >> >> ## loaded via a namespace (and not attached): >> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >> colorspace_1.2-4 DBI_0.2-7 >> ## [11] dichromat_2.0-0 digest_0.6.3 >> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >> IRanges_1.20.4 labeling_0.2 >> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >> parallel_3.0.2 plyr_1.8 >> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> reshape2_1.2.2 rpart_4.1-3 >> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >> ## [36] stringr_0.6.2 tools_3.0.2 >> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >> ## [41] zlibbioc_1.8.0 >> >> >> Thank you, >> Leonardo >> >> Leonardo Collado Torres, PhD student >> Department of Biostatistics >> Johns Hopkins University >> Bloomberg School of Public Health >> Website: http://www.biostat.jhsph.edu/~lcollado/ >> Blog: http://lcolladotor.github.io/ >> > > > > -- > 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 • link 10.5 years ago Tengfei Yin ▴ 490

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Thank you very much Tengfei! On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi > > I just fixed this bug in 1.10.1 in release branch, please update one or > two days later. > > Thanks > > Tengfei > > > On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi Leonardo, >> >> Thanks for reporting the issue, this is probably not R's problem, should >> be a bug in ggbio's new class, I will look into this. >> >> Tengfei >> >> >> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Dear BioC list and Tengfei Yin, >>> >>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>> that I think is related to changes in R. The error can also be seen in >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf (search >>> 'unnamed' on the pdf). >>> >>> Below is the error from running the example code for plotIdeogram. >>> >>> library(ggbio) >>> library(biovizBase) >>> data(hg19IdeogramCyto, package = "biovizBase") >>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>> plotIdeogram(hg19IdeogramCyto, "chr1") >>> >>> ## Error in initialize(value, ...) : >>> unnamed argument must extend either the S3 class or the class of the >>> data part; not true of class GGbio >>> >>> traceback() >>> >>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class or >>> the class of the data part; not true of class %s", >>> ## dQuote(Classi)), domain = NA) >>> ## 5: initialize(value, ...) >>> ## 4: initialize(value, ...) >>> ## 3: new("Ideogram", x) >>> ## 2: Ideogram(p) >>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>> >>> sessionInfo() >>> >>> ## R version 3.0.2 (2013-09-25) >>> ## 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] stats graphics grDevices utils datasets methods base >>> >>> >>> ## other attached packages: >>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>> >>> ## loaded via a namespace (and not attached): >>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>> colorspace_1.2-4 DBI_0.2-7 >>> ## [11] dichromat_2.0-0 digest_0.6.3 >>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>> IRanges_1.20.4 labeling_0.2 >>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>> parallel_3.0.2 plyr_1.8 >>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> reshape2_1.2.2 rpart_4.1-3 >>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>> ## [36] stringr_0.6.2 tools_3.0.2 >>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>> ## [41] zlibbioc_1.8.0 >>> >>> >>> Thank you, >>> Leonardo >>> >>> Leonardo Collado Torres, PhD student >>> Department of Biostatistics >>> Johns Hopkins University >>> Bloomberg School of Public Health >>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>> Blog: http://lcolladotor.github.io/ >>> >> >> >> >> -- >> 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 • link 10.5 years ago Leonardo Collado Torres ★ 1.0k

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Hi Tengfei, Sadly, I am currently having the same issue with version 1.10.7 from the release branch. Also, http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst /doc/ggbio.pdf compiled on Nov 14th has the same issue as expected (R session at the end shows that it was compiled with version 1.10.7). The devel branch http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/doc/g gbio.pdf from Nov 14th does have a working plotIdeogram(). In our local R-devel version, I cannot load ggbio due to namespace errors. Note that this R-devel version is from Nov 15th, so maybe some changes were introduced to Rsamtools that day that broke things in ggbio. Best, Leonardo ### Session information using version 1.10.7 where the example of plotIdeogram() fails > sessionInfo() R version 3.0.2 (2013-09-25) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 ggplot2_0.9.3.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 stringr_0.6.2 [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 XVector_0.2.0 zlibbioc_1.8.0 #### Session information using local R-devel $ R-devel R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered Consequences" [removed other info] > library(ggbio) Loading required package: ggplot2 No methods found in "Rsamtools" for requests: readGAlignmentsFromBam Error : object 'readGAlignmentsFromBam' is not exported by 'namespace:Rsamtools' Error: package or namespace load failed for 'ggbio' > sessionInfo() R Under development (unstable) (2013-11-15 r64218) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] ggplot2_0.9.3.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 [13] digest_0.6.3 GenomicAlignments_0.99.2 GenomicFeatures_1.15.2 [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 > On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Thank you very much Tengfei! > > > On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi >> >> I just fixed this bug in 1.10.1 in release branch, please update one or >> two days later. >> >> Thanks >> >> Tengfei >> >> >> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >> >>> Hi Leonardo, >>> >>> Thanks for reporting the issue, this is probably not R's problem, should >>> be a bug in ggbio's new class, I will look into this. >>> >>> Tengfei >>> >>> >>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Dear BioC list and Tengfei Yin, >>>> >>>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>>> that I think is related to changes in R. The error can also be seen in >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio /inst/doc/ggbio.pdf (search >>>> 'unnamed' on the pdf). >>>> >>>> Below is the error from running the example code for plotIdeogram. >>>> >>>> library(ggbio) >>>> library(biovizBase) >>>> data(hg19IdeogramCyto, package = "biovizBase") >>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>> >>>> ## Error in initialize(value, ...) : >>>> unnamed argument must extend either the S3 class or the class of the >>>> data part; not true of class GGbio >>>> >>>> traceback() >>>> >>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>> or the class of the data part; not true of class %s", >>>> ## dQuote(Classi)), domain = NA) >>>> ## 5: initialize(value, ...) >>>> ## 4: initialize(value, ...) >>>> ## 3: new("Ideogram", x) >>>> ## 2: Ideogram(p) >>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>> >>>> sessionInfo() >>>> >>>> ## R version 3.0.2 (2013-09-25) >>>> ## 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] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> ## other attached packages: >>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>> >>>> ## loaded via a namespace (and not attached): >>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>>> colorspace_1.2-4 DBI_0.2-7 >>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>> IRanges_1.20.4 labeling_0.2 >>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>> parallel_3.0.2 plyr_1.8 >>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>> reshape2_1.2.2 rpart_4.1-3 >>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>> ## [41] zlibbioc_1.8.0 >>>> >>>> >>>> Thank you, >>>> Leonardo >>>> >>>> Leonardo Collado Torres, PhD student >>>> Department of Biostatistics >>>> Johns Hopkins University >>>> Bloomberg School of Public Health >>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>> Blog: http://lcolladotor.github.io/ >>>> >>> >>> >>> >>> -- >>> 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 • link 10.5 years ago Leonardo Collado Torres ★ 1.0k

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Entering edit mode

Hi Leonardo, Thanks for your feedback. It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason I updated the GGbio class and default ggplot() method, I just fixed it in released branch 1.10.8. I will work on the devel branch problem you reported. cheers Tengfei On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < lcollado@jhsph.edu> wrote: > Hi Tengfei, > > Sadly, I am currently having the same issue with version 1.10.7 from the > release branch. Also, > http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/in st/doc/ggbio.pdf compiled > on Nov 14th has the same issue as expected (R session at the end shows that > it was compiled with version 1.10.7). The devel branch > http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/doc /ggbio.pdf from > Nov 14th does have a working plotIdeogram(). > > In our local R-devel version, I cannot load ggbio due to namespace errors. > Note that this R-devel version is from Nov 15th, so maybe some changes were > introduced to Rsamtools that day that broke things in ggbio. > > Best, > Leonardo > > > > ### Session information using version 1.10.7 where the example of > plotIdeogram() fails > > > sessionInfo() > R version 3.0.2 (2013-09-25) > 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 > ggplot2_0.9.3.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 > biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 > [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 > DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 > [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 > gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 > [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 > MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 > [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 > RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 > [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 > scales_0.2.3 stats4_3.0.2 stringr_0.6.2 > [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 > XVector_0.2.0 zlibbioc_1.8.0 > > > #### Session information using local R-devel > > $ R-devel > > R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered > Consequences" > > [removed other info] > > > library(ggbio) > Loading required package: ggplot2 > No methods found in "Rsamtools" for requests: readGAlignmentsFromBam > Error : object 'readGAlignmentsFromBam' is not exported by > 'namespace:Rsamtools' > Error: package or namespace load failed for 'ggbio' > > sessionInfo() > R Under development (unstable) (2013-11-15 r64218) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=en_US.iso885915 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] ggplot2_0.9.3.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 > [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 > [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 > [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 > [13] digest_0.6.3 GenomicAlignments_0.99.2 > GenomicFeatures_1.15.2 > [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 > [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 > [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 > [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 > [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 > [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 > [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 > [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 > [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 > > > > > > On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Thank you very much Tengfei! >> >> >> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>> > wrote: >> >>> Hi >>> >>> I just fixed this bug in 1.10.1 in release branch, please update one or >>> two days later. >>> >>> Thanks >>> >>> Tengfei >>> >>> >>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >>> >>>> Hi Leonardo, >>>> >>>> Thanks for reporting the issue, this is probably not R's problem, >>>> should be a bug in ggbio's new class, I will look into this. >>>> >>>> Tengfei >>>> >>>> >>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>> lcollado@jhsph.edu> wrote: >>>> >>>>> Dear BioC list and Tengfei Yin, >>>>> >>>>> I am encountering an error when using ggbio::plotIdeogram() on R 3.0.2 >>>>> that I think is related to changes in R. The error can also be seen in >>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbi o/inst/doc/ggbio.pdf (search >>>>> 'unnamed' on the pdf). >>>>> >>>>> Below is the error from running the example code for plotIdeogram. >>>>> >>>>> library(ggbio) >>>>> library(biovizBase) >>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>> >>>>> ## Error in initialize(value, ...) : >>>>> unnamed argument must extend either the S3 class or the class of the >>>>> data part; not true of class GGbio >>>>> >>>>> traceback() >>>>> >>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>>> or the class of the data part; not true of class %s", >>>>> ## dQuote(Classi)), domain = NA) >>>>> ## 5: initialize(value, ...) >>>>> ## 4: initialize(value, ...) >>>>> ## 3: new("Ideogram", x) >>>>> ## 2: Ideogram(p) >>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>> >>>>> sessionInfo() >>>>> >>>>> ## R version 3.0.2 (2013-09-25) >>>>> ## 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] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> ## other attached packages: >>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>> >>>>> ## loaded via a namespace (and not attached): >>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4 >>>>> colorspace_1.2-4 DBI_0.2-7 >>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>> IRanges_1.20.4 labeling_0.2 >>>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>>> parallel_3.0.2 plyr_1.8 >>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>>> reshape2_1.2.2 rpart_4.1-3 >>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>> ## [41] zlibbioc_1.8.0 >>>>> >>>>> >>>>> Thank you, >>>>> Leonardo >>>>> >>>>> Leonardo Collado Torres, PhD student >>>>> Department of Biostatistics >>>>> Johns Hopkins University >>>>> Bloomberg School of Public Health >>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>> Blog: http://lcolladotor.github.io/ >>>>> >>>> >>>> >>>> >>>> -- >>>> 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 • link 10.5 years ago Tengfei Yin ▴ 490

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Entering edit mode

Thank you for the speedy fix Tengfei! As for the devel branch problem, I think that in Rsamtools 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 that is no longer the case since this function is now in GenomicAlignments::readGAlignments Cheers, Leo On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > Thanks for your feedback. > > It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason > I updated the GGbio class and default ggplot() method, I just fixed it in > released branch 1.10.8. I will work on the devel branch problem you > reported. > > cheers > > Tengfei > > > On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Hi Tengfei, >> >> Sadly, I am currently having the same issue with version 1.10.7 from the >> release branch. Also, >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/i nst/doc/ggbio.pdf compiled >> on Nov 14th has the same issue as expected (R session at the end shows that >> it was compiled with version 1.10.7). The devel branch >> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/do c/ggbio.pdf from >> Nov 14th does have a working plotIdeogram(). >> >> In our local R-devel version, I cannot load ggbio due to namespace >> errors. Note that this R-devel version is from Nov 15th, so maybe some >> changes were introduced to Rsamtools that day that broke things in ggbio. >> >> Best, >> Leonardo >> >> >> >> ### Session information using version 1.10.7 where the example of >> plotIdeogram() fails >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> 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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >> ggplot2_0.9.3.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >> XVector_0.2.0 zlibbioc_1.8.0 >> >> >> #### Session information using local R-devel >> >> $ R-devel >> >> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >> Consequences" >> >> [removed other info] >> >> > library(ggbio) >> Loading required package: ggplot2 >> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >> Error : object 'readGAlignmentsFromBam' is not exported by >> 'namespace:Rsamtools' >> Error: package or namespace load failed for 'ggbio' >> > sessionInfo() >> R Under development (unstable) (2013-11-15 r64218) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] ggplot2_0.9.3.1 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 >> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> [13] digest_0.6.3 GenomicAlignments_0.99.2 >> GenomicFeatures_1.15.2 >> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >> > >> >> >> >> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Thank you very much Tengfei! >>> >>> >>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>> tengfei.yin@sbgenomics.com> wrote: >>> >>>> Hi >>>> >>>> I just fixed this bug in 1.10.1 in release branch, please update one or >>>> two days later. >>>> >>>> Thanks >>>> >>>> Tengfei >>>> >>>> >>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>>>> > wrote: >>>> >>>>> Hi Leonardo, >>>>> >>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>> should be a bug in ggbio's new class, I will look into this. >>>>> >>>>> Tengfei >>>>> >>>>> >>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>> lcollado@jhsph.edu> wrote: >>>>> >>>>>> Dear BioC list and Tengfei Yin, >>>>>> >>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>> in >>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggb io/inst/doc/ggbio.pdf (search >>>>>> 'unnamed' on the pdf). >>>>>> >>>>>> Below is the error from running the example code for plotIdeogram. >>>>>> >>>>>> library(ggbio) >>>>>> library(biovizBase) >>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>> >>>>>> ## Error in initialize(value, ...) : >>>>>> unnamed argument must extend either the S3 class or the class of >>>>>> the data part; not true of class GGbio >>>>>> >>>>>> traceback() >>>>>> >>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 class >>>>>> or the class of the data part; not true of class %s", >>>>>> ## dQuote(Classi)), domain = NA) >>>>>> ## 5: initialize(value, ...) >>>>>> ## 4: initialize(value, ...) >>>>>> ## 3: new("Ideogram", x) >>>>>> ## 2: Ideogram(p) >>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>> >>>>>> sessionInfo() >>>>>> >>>>>> ## R version 3.0.2 (2013-09-25) >>>>>> ## 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] stats graphics grDevices utils datasets methods >>>>>> base >>>>>> >>>>>> ## other attached packages: >>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>> >>>>>> ## loaded via a namespace (and not attached): >>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>>> IRanges_1.20.4 labeling_0.2 >>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 munsell_0.4.2 >>>>>> parallel_3.0.2 plyr_1.8 >>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>> ## [41] zlibbioc_1.8.0 >>>>>> >>>>>> >>>>>> Thank you, >>>>>> Leonardo >>>>>> >>>>>> Leonardo Collado Torres, PhD student >>>>>> Department of Biostatistics >>>>>> Johns Hopkins University >>>>>> Bloomberg School of Public Health >>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>> Blog: http://lcolladotor.github.io/ >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 • link 10.5 years ago Leonardo Collado Torres ★ 1.0k

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Entering edit mode

Hi Leonardo, I think some of the package on your R-devel are our of date, would you please run source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") or biocLite() to update packages You will probably get a new error message, because of affyPLM in devel branch, then update ggbio-devel one day later will fix that. Thanks Tengfei On Wed, Nov 20, 2013 at 2:03 PM, Leonardo Collado Torres <lcollado@jhsph.edu> wrote: > Thank you for the speedy fix Tengfei! > > As for the devel branch problem, I think that in Rsamtools > 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 > that is no longer the case since this function is now > in GenomicAlignments::readGAlignments > > Cheers, > Leo > > > On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > >> Hi Leonardo, >> >> Thanks for your feedback. >> >> It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the reason >> I updated the GGbio class and default ggplot() method, I just fixed it in >> released branch 1.10.8. I will work on the devel branch problem you >> reported. >> >> cheers >> >> Tengfei >> >> >> On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < >> lcollado@jhsph.edu> wrote: >> >>> Hi Tengfei, >>> >>> Sadly, I am currently having the same issue with version 1.10.7 from the >>> release branch. Also, >>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/ inst/doc/ggbio.pdf compiled >>> on Nov 14th has the same issue as expected (R session at the end shows that >>> it was compiled with version 1.10.7). The devel branch >>> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/d oc/ggbio.pdf from >>> Nov 14th does have a working plotIdeogram(). >>> >>> In our local R-devel version, I cannot load ggbio due to namespace >>> errors. Note that this R-devel version is from Nov 15th, so maybe some >>> changes were introduced to Rsamtools that day that broke things in ggbio. >>> >>> Best, >>> Leonardo >>> >>> >>> >>> ### Session information using version 1.10.7 where the example of >>> plotIdeogram() fails >>> >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> 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] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >>> ggplot2_0.9.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >>> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >>> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >>> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >>> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >>> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >>> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >>> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >>> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >>> XVector_0.2.0 zlibbioc_1.8.0 >>> >>> >>> #### Session information using local R-devel >>> >>> $ R-devel >>> >>> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >>> Consequences" >>> >>> [removed other info] >>> >>> > library(ggbio) >>> Loading required package: ggplot2 >>> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >>> Error : object 'readGAlignmentsFromBam' is not exported by >>> 'namespace:Rsamtools' >>> Error: package or namespace load failed for 'ggbio' >>> > sessionInfo() >>> R Under development (unstable) (2013-11-15 r64218) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices datasets utils methods base >>> >>> other attached packages: >>> [1] ggplot2_0.9.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 BiocGenerics_0.9.0 >>> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >>> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >>> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >>> [13] digest_0.6.3 GenomicAlignments_0.99.2 >>> GenomicFeatures_1.15.2 >>> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >>> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >>> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >>> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >>> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >>> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >>> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >>> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >>> > >>> >>> >>> >>> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Thank you very much Tengfei! >>>> >>>> >>>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>>> tengfei.yin@sbgenomics.com> wrote: >>>> >>>>> Hi >>>>> >>>>> I just fixed this bug in 1.10.1 in release branch, please update one >>>>> or two days later. >>>>> >>>>> Thanks >>>>> >>>>> Tengfei >>>>> >>>>> >>>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin < >>>>> tengfei.yin@sbgenomics.com> wrote: >>>>> >>>>>> Hi Leonardo, >>>>>> >>>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>>> should be a bug in ggbio's new class, I will look into this. >>>>>> >>>>>> Tengfei >>>>>> >>>>>> >>>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>>> lcollado@jhsph.edu> wrote: >>>>>> >>>>>>> Dear BioC list and Tengfei Yin, >>>>>>> >>>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>>> in >>>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/gg bio/inst/doc/ggbio.pdf (search >>>>>>> 'unnamed' on the pdf). >>>>>>> >>>>>>> Below is the error from running the example code for plotIdeogram. >>>>>>> >>>>>>> library(ggbio) >>>>>>> library(biovizBase) >>>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>> >>>>>>> ## Error in initialize(value, ...) : >>>>>>> unnamed argument must extend either the S3 class or the class of >>>>>>> the data part; not true of class GGbio >>>>>>> >>>>>>> traceback() >>>>>>> >>>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 >>>>>>> class or the class of the data part; not true of class %s", >>>>>>> ## dQuote(Classi)), domain = NA) >>>>>>> ## 5: initialize(value, ...) >>>>>>> ## 4: initialize(value, ...) >>>>>>> ## 3: new("Ideogram", x) >>>>>>> ## 2: Ideogram(p) >>>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>> >>>>>>> sessionInfo() >>>>>>> >>>>>>> ## R version 3.0.2 (2013-09-25) >>>>>>> ## 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] stats graphics grDevices utils datasets methods >>>>>>> base >>>>>>> >>>>>>> ## other attached packages: >>>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>>> >>>>>>> ## loaded via a namespace (and not attached): >>>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>>>>> IRanges_1.20.4 labeling_0.2 >>>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 >>>>>>> munsell_0.4.2 parallel_3.0.2 plyr_1.8 >>>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>>> ## [41] zlibbioc_1.8.0 >>>>>>> >>>>>>> >>>>>>> Thank you, >>>>>>> Leonardo >>>>>>> >>>>>>> Leonardo Collado Torres, PhD student >>>>>>> Department of Biostatistics >>>>>>> Johns Hopkins University >>>>>>> Bloomberg School of Public Health >>>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>>> Blog: http://lcolladotor.github.io/ >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 • link 10.5 years ago Tengfei Yin ▴ 490

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Entering edit mode

Hi Tengfei, After updating the packages on our R-devel I was able to load ggbio as you stated. Thanks, Leo On Wed, Nov 20, 2013 at 4:13 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: > Hi Leonardo, > > I think some of the package on your R-devel are our of date, would you > please run > > source("http://bioconductor.org/biocLite.R") > biocLite("BiocUpgrade") > > or biocLite() to update packages > > You will probably get a new error message, because of affyPLM in devel > branch, then update ggbio-devel one day later will fix that. > > Thanks > > Tengfei > > > On Wed, Nov 20, 2013 at 2:03 PM, Leonardo Collado Torres < > lcollado@jhsph.edu> wrote: > >> Thank you for the speedy fix Tengfei! >> >> As for the devel branch problem, I think that in Rsamtools >> 1.14.1 readGAlignmentsFromBam was exported but in version Rsamtools_1.15.7 >> that is no longer the case since this function is now >> in GenomicAlignments::readGAlignments >> >> Cheers, >> Leo >> >> >> On Wed, Nov 20, 2013 at 1:43 PM, Tengfei Yin <tengfei.yin@sbgenomics.com>wrote: >> >>> Hi Leonardo, >>> >>> Thanks for your feedback. >>> >>> It was fixed in 1.10.1, but it's introduced back in 1.10.7 for the >>> reason I updated the GGbio class and default ggplot() method, I just fixed >>> it in released branch 1.10.8. I will work on the devel branch problem you >>> reported. >>> >>> cheers >>> >>> Tengfei >>> >>> >>> On Wed, Nov 20, 2013 at 12:54 PM, Leonardo Collado Torres < >>> lcollado@jhsph.edu> wrote: >>> >>>> Hi Tengfei, >>>> >>>> Sadly, I am currently having the same issue with version 1.10.7 from >>>> the release branch. Also, >>>> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio /inst/doc/ggbio.pdf compiled >>>> on Nov 14th has the same issue as expected (R session at the end shows that >>>> it was compiled with version 1.10.7). The devel branch >>>> http://bioconductor.org/packages/devel/bioc/vignettes/ggbio/inst/ doc/ggbio.pdf from >>>> Nov 14th does have a working plotIdeogram(). >>>> >>>> In our local R-devel version, I cannot load ggbio due to namespace >>>> errors. Note that this R-devel version is from Nov 15th, so maybe some >>>> changes were introduced to Rsamtools that day that broke things in ggbio. >>>> >>>> Best, >>>> Leonardo >>>> >>>> >>>> >>>> ### Session information using version 1.10.7 where the example of >>>> plotIdeogram() fails >>>> >>>> > sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> 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] stats graphics grDevices utils datasets methods base >>>> >>>> >>>> other attached packages: >>>> [1] BiocInstaller_1.12.0 biovizBase_1.10.3 ggbio_1.10.7 >>>> ggplot2_0.9.3.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 >>>> biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 >>>> [7] BSgenome_1.30.0 cluster_1.14.4 colorspace_1.2-4 >>>> DBI_0.2-7 dichromat_2.0-0 digest_0.6.3 >>>> [13] GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>> gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.12-2 >>>> [19] IRanges_1.20.5 labeling_0.2 lattice_0.20-24 >>>> MASS_7.3-29 munsell_0.4.2 parallel_3.0.2 >>>> >>>> [25] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 >>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>> [31] Rsamtools_1.14.1 RSQLite_0.11.4 rtracklayer_1.22.0 >>>> scales_0.2.3 stats4_3.0.2 stringr_0.6.2 >>>> [37] tools_3.0.2 VariantAnnotation_1.8.5 XML_3.95-0.2 >>>> XVector_0.2.0 zlibbioc_1.8.0 >>>> >>>> >>>> #### Session information using local R-devel >>>> >>>> $ R-devel >>>> >>>> R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered >>>> Consequences" >>>> >>>> [removed other info] >>>> >>>> > library(ggbio) >>>> Loading required package: ggplot2 >>>> No methods found in "Rsamtools" for requests: readGAlignmentsFromBam >>>> Error : object 'readGAlignmentsFromBam' is not exported by >>>> 'namespace:Rsamtools' >>>> Error: package or namespace load failed for 'ggbio' >>>> > sessionInfo() >>>> R Under development (unstable) (2013-11-15 r64218) >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 >>>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 >>>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices datasets utils methods base >>>> >>>> other attached packages: >>>> [1] ggplot2_0.9.3.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] AnnotationDbi_1.25.3 Biobase_2.23.3 >>>> BiocGenerics_0.9.0 >>>> [4] biomaRt_2.19.1 Biostrings_2.31.2 biovizBase_1.9.4 >>>> [7] bitops_1.0-6 BSgenome_1.31.6 cluster_1.14.4 >>>> [10] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >>>> [13] digest_0.6.3 GenomicAlignments_0.99.2 >>>> GenomicFeatures_1.15.2 >>>> [16] GenomicRanges_1.15.9 grid_3.1.0 gridExtra_0.9.1 >>>> [19] gtable_0.1.2 Hmisc_3.12-2 IRanges_1.21.9 >>>> [22] labeling_0.2 lattice_0.20-24 MASS_7.3-29 >>>> [25] munsell_0.4.2 parallel_3.1.0 plyr_1.8 >>>> [28] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-4.1 >>>> [31] reshape2_1.2.2 rpart_4.1-3 Rsamtools_1.15.7 >>>> [34] RSQLite_0.11.4 rtracklayer_1.23.3 scales_0.2.3 >>>> [37] stats4_3.1.0 stringr_0.6.2 tools_3.1.0 >>>> [40] XML_3.98-1.1 XVector_0.3.1 zlibbioc_1.9.0 >>>> > >>>> >>>> >>>> >>>> On Mon, Nov 11, 2013 at 4:30 PM, Leonardo Collado Torres < >>>> lcollado@jhsph.edu> wrote: >>>> >>>>> Thank you very much Tengfei! >>>>> >>>>> >>>>> On Mon, Nov 11, 2013 at 4:20 PM, Tengfei Yin < >>>>> tengfei.yin@sbgenomics.com> wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> I just fixed this bug in 1.10.1 in release branch, please update one >>>>>> or two days later. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Tengfei >>>>>> >>>>>> >>>>>> On Mon, Nov 4, 2013 at 4:54 PM, Tengfei Yin < >>>>>> tengfei.yin@sbgenomics.com> wrote: >>>>>> >>>>>>> Hi Leonardo, >>>>>>> >>>>>>> Thanks for reporting the issue, this is probably not R's problem, >>>>>>> should be a bug in ggbio's new class, I will look into this. >>>>>>> >>>>>>> Tengfei >>>>>>> >>>>>>> >>>>>>> On Mon, Nov 4, 2013 at 4:49 PM, Leonardo Collado Torres < >>>>>>> lcollado@jhsph.edu> wrote: >>>>>>> >>>>>>>> Dear BioC list and Tengfei Yin, >>>>>>>> >>>>>>>> I am encountering an error when using ggbio::plotIdeogram() on R >>>>>>>> 3.0.2 that I think is related to changes in R. The error can also be seen >>>>>>>> in >>>>>>>> http://www.bioconductor.org/packages/release/bioc/vignettes/g gbio/inst/doc/ggbio.pdf (search >>>>>>>> 'unnamed' on the pdf). >>>>>>>> >>>>>>>> Below is the error from running the example code for plotIdeogram. >>>>>>>> >>>>>>>> library(ggbio) >>>>>>>> library(biovizBase) >>>>>>>> data(hg19IdeogramCyto, package = "biovizBase") >>>>>>>> biovizBase::isIdeogram(hg19IdeogramCyto) ## return TRUE >>>>>>>> plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>>> >>>>>>>> ## Error in initialize(value, ...) : >>>>>>>> unnamed argument must extend either the S3 class or the class of >>>>>>>> the data part; not true of class GGbio >>>>>>>> >>>>>>>> traceback() >>>>>>>> >>>>>>>> ## 6: stop(gettextf("unnamed argument must extend either the S3 >>>>>>>> class or the class of the data part; not true of class %s", >>>>>>>> ## dQuote(Classi)), domain = NA) >>>>>>>> ## 5: initialize(value, ...) >>>>>>>> ## 4: initialize(value, ...) >>>>>>>> ## 3: new("Ideogram", x) >>>>>>>> ## 2: Ideogram(p) >>>>>>>> ## 1: plotIdeogram(hg19IdeogramCyto, "chr1") >>>>>>>> >>>>>>>> sessionInfo() >>>>>>>> >>>>>>>> ## R version 3.0.2 (2013-09-25) >>>>>>>> ## 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] stats graphics grDevices utils datasets methods >>>>>>>> base >>>>>>>> >>>>>>>> ## other attached packages: >>>>>>>> ## [1] biovizBase_1.10.0 ggbio_1.10.0 ggplot2_0.9.3.1 >>>>>>>> >>>>>>>> ## loaded via a namespace (and not attached): >>>>>>>> ## [1] AnnotationDbi_1.24.0 Biobase_2.22.0 >>>>>>>> BiocGenerics_0.8.0 biomaRt_2.18.0 Biostrings_2.30.0 >>>>>>>> ## [6] bitops_1.0-6 BSgenome_1.30.0 >>>>>>>> cluster_1.14.4 colorspace_1.2-4 DBI_0.2-7 >>>>>>>> ## [11] dichromat_2.0-0 digest_0.6.3 >>>>>>>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 grid_3.0.2 >>>>>>>> ## [16] gridExtra_0.9.1 gtable_0.1.2 >>>>>>>> Hmisc_3.12-2 IRanges_1.20.4 labeling_0.2 >>>>>>>> ## [21] lattice_0.20-24 MASS_7.3-29 >>>>>>>> munsell_0.4.2 parallel_3.0.2 plyr_1.8 >>>>>>>> ## [26] proto_0.3-10 RColorBrewer_1.0-5 >>>>>>>> RCurl_1.95-4.1 reshape2_1.2.2 rpart_4.1-3 >>>>>>>> ## [31] Rsamtools_1.14.1 RSQLite_0.11.4 >>>>>>>> rtracklayer_1.22.0 scales_0.2.3 stats4_3.0.2 >>>>>>>> ## [36] stringr_0.6.2 tools_3.0.2 >>>>>>>> VariantAnnotation_1.8.2 XML_3.95-0.2 XVector_0.2.0 >>>>>>>> ## [41] zlibbioc_1.8.0 >>>>>>>> >>>>>>>> >>>>>>>> Thank you, >>>>>>>> Leonardo >>>>>>>> >>>>>>>> Leonardo Collado Torres, PhD student >>>>>>>> Department of Biostatistics >>>>>>>> Johns Hopkins University >>>>>>>> Bloomberg School of Public Health >>>>>>>> Website: http://www.biostat.jhsph.edu/~lcollado/ >>>>>>>> Blog: http://lcolladotor.github.io/ >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 • link 10.5 years ago Leonardo Collado Torres ★ 1.0k