Thanks for sending the file. Now fixed in devel 1.1.64. Valerie On 03/12/2012 04:04 AM, Lescai, Francesco wrote: > It's small enough. > I'll send you privately: or do you prefer me to post in on the list? > cheers, > Francesco > > > > On 11 Mar 2012, at 20:02, Valerie Obenchain wrote: > >> Hi Francesco, >> >> Looks like you've hit a bug. Is your GRanges too large to attach or >> make available for testing? >> >> Valerie >> >> On 03/11/12 12:29, Lescai, Francesco wrote: >>> but.. I have another different error with a different dataset. >>> >>> k1.ranges = GRanges( >>> seqnames=paste("chr",CEUstats.variants$chromosome,sep=""), >>> IRanges(start=CEUstats.variants$position, >>> width=1) >>> ) >>> >>>> head(k1.ranges) >>> GRanges with 6 ranges and 0 elementMetadata cols: >>> seqnames ranges strand >>> <rle> <iranges> <rle> >>> [1] chr1 [1177919, 1177919] * >>> [2] chr1 [1234763, 1234763] * >>> [3] chr1 [1246257, 1246257] * >>> [4] chr1 [1564953, 1564953] * >>> [5] chr1 [1887112, 1887112] * >>> [6] chr1 [1900107, 1900107] * >>> --- >>> seqlengths: >>> chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 ... chr22 >>> chr3 chr4 chr5 chr6 chr7 chr8 chr9 >>> NA NA NA NA NA NA NA NA NA ... NA >>> NA NA NA NA NA NA NA >>> >>>> k1.locations = locateVariants(k1.ranges, txdb19) >>> Error in DataFrame(queryID = which(intergenic), location = location, >>> txID = NA_integer_, : >>> different row counts implied by arguments >>> >>> sessionInfo is the same as below. >>> thanks very much, >>> >>> Francesco >>> >>> >>> On 11 Mar 2012, at 18:53, Lescai, Francesco wrote: >>> >>> Adopted the suggestion of Steve and went the "hard" way of >>> re-compiling from source the packages in my session. >>> not it seems to work :-)) >>> therefore, no idea where the problem was but at least it is solved! >>> VariantAnnotation is no .63 instead of .61, that might have changed >>> few things together with the other packages. >>> >>> this is my session in case it might be useful for the developers. >>> >>> thanks very much for your help!! >>> Francesco >>> >>> >>> sessionInfo() >>> R Under development (unstable) (2012-01-20 r58146) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C/en_US.UTF-8/C/C/C/C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.4 GenomicFeatures_1.7.30 >>> [3] AnnotationDbi_1.17.27 Biobase_2.15.4 >>> [5] VariantAnnotation_1.1.63 Rsamtools_1.7.40 >>> [7] Biostrings_2.23.6 GenomicRanges_1.7.34 >>> [9] IRanges_1.13.30 BiocGenerics_0.1.14 >>> >>> loaded via a namespace (and not attached): >>> [1] BSgenome_1.23.4 DBI_0.2-5 Matrix_1.0-4 >>> RCurl_1.91-1 RSQLite_0.11.1 >>> [6] XML_3.9-4 biomaRt_2.11.1 bitops_1.0-4.1 >>> ggplot2_0.8.9 grid_2.15.0 >>> [11] lattice_0.20-0 plyr_1.7.1 rtracklayer_1.15.7 >>> snpStats_1.5.5 splines_2.15.0 >>> [16] stats4_2.15.0 survival_2.36-12 tools_2.15.0 >>> zlibbioc_1.1.1 >>> >>> >>> On 11 Mar 2012, at 18:34, Martin Morgan wrote: >>> >>> On 03/11/2012 10:39 AM, Lescai, Francesco wrote: >>> Hi, this is the traceback output. >>> >>> traceback() >>> 12: stop(gettextf("invalid names for slots of class %s: %s", >>> dQuote(Class), >>> paste(snames[is.na(which)], collapse = ", ")), domain = NA) >>> 11: initialize(value, ...) >>> 10: initialize(value, ...) >>> 9: new("RangesMatching", matchMatrix = matchMatrix, DIM = DIM) >>> 8: .local(query, subject, maxgap, minoverlap, type, select, ...) >>> 7: findOverlaps(query, unlistSubject, maxgap = maxgap, type = type, >>> select = "all", ignore.strand = ignore.strand) >>> 6: findOverlaps(query, unlistSubject, maxgap = maxgap, type = type, >>> select = "all", ignore.strand = ignore.strand) >>> 5: .local(query, subject, maxgap, minoverlap, type, select, ...) >>> 4: findOverlaps(queryAdj, cdsByTx, type = "within") >>> 3: findOverlaps(queryAdj, cdsByTx, type = "within") >>> >>> 'cdsByTx' isn't used in this context in VariantAnnotation 1.1.61, >>> which has two lines like >>> >>> cdsCO<- countOverlaps(query, cache[["cdsByTx"]], type="within") >>> txFO<- findOverlaps(query, cache[["tx"]], type="within") >>> >>> that might be the current implementation. This line >>> >>> cdsFO<- findOverlaps(queryAdj, cdsByTx, type="within") >>> >>> _is_ in VariantAnnotation 1.0.5; I think you are getting the wrong >>> version of VariantAnnotation, but this is not consistent with your >>> sessionInfo(). >>> >>> Martin >>> >>> >>> 2: locateVariants(my.ranges, txdb19) >>> 1: locateVariants(my.ranges, txdb19) >>> >>> I tried to install the package, but it seems it still picks up the >>> old version. >>> >>> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.3.7. >>> Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene' >>> Installing package(s) into >>> Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library‚ >>> (as Œlib‚ is unspecified) >>> Warning: unable to access index for repository >>> http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15 >>> trying URL >>> 'http://bioconductor.org/packages/2.10/data/annotation/bin/macosx/ leopard/contrib/2.15/TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2.tgz' >>> <http: bioconductor.org="" packages="" 2.10="" data="" annotation="" bin="" macosx="" leopard="" contrib="" 2.15="" txdb.hsapiens.ucsc.hg19.knowngene_2.6.2.tgz%27=""> >>> Content type 'application/x-gzip' length 16722765 bytes (15.9 Mb) >>> opened URL >>> ================================================== >>> downloaded 15.9 Mb >>> >>> and I checked on the website for the 2.10 release and the Mac >>> version of the packages seems to be still 2.6.2. >>> >>> Is there any other package I can try to install manually? >>> It seems now I cannot access to the developer wiki of BioC. >>> >>> thanks >>> Francesco >>> >>> >>> >>> >>> >>> On 10 Mar 2012, at 19:01, Martin Morgan wrote: >>> >>> On 03/10/2012 10:14 AM, Lescai, Francesco wrote: >>> Thanks Martin, >>> done, but I still get the same error. >>> >>> I can't spot the problem; maybe someone else will chime in. >>> >>> (a) TxDb.Hsapiens... is still out-of-date; maybe it isn't checked by >>> biocLite() >>> >>> (b) the error >>> >>> my.locations = locateVariants(my.ranges, txdb19) >>> Error in initialize(value, ...) : >>> invalid names for slots of class „RangesMatching‰: matchMatrix, DIM >>> >>> definitely looks like an 'old package' issue -- the RangesMatching >>> class was replaced by the 'Hits' class during this release cycle. It >>> might help to call >>> >>> traceback() >>> >>> after the error, and to confirm that you are accessing only >>> functions defined in the loaded packages by starting your R session with >>> >>> R --vanilla >>> >>> Obviously, the sessionInfo() needs to reflect the session the >>> command fails in not, e.g., R gui in one instance and the terminal >>> in the other. >>> >>> Martin >>> >>> >>> My new sessionInfo is >>> >>> sessionInfo() >>> R Under development (unstable) (2012-01-20 r58146) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C/en_US.UTF-8/C/C/C/C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] BiocInstaller_1.3.7 >>> TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 >>> [3] GenomicFeatures_1.7.30 VariantAnnotation_1.1.61 >>> [5] Rsamtools_1.7.38 Biostrings_2.23.6 >>> [7] AnnotationDbi_1.17.27 Biobase_2.15.4 >>> [9] GenomicRanges_1.7.33 IRanges_1.13.28 >>> [11] BiocGenerics_0.1.12 biomaRt_2.11.1 >>> >>> loaded via a namespace (and not attached): >>> [1] BSgenome_1.23.4 DBI_0.2-5 Matrix_1.0-4 >>> RCurl_1.91-1 RSQLite_0.11.1 >>> [6] XML_3.9-4 bitops_1.0-4.1 ggplot2_0.8.9 >>> grid_2.15.0 lattice_0.20-0 >>> [11] plyr_1.7.1 rtracklayer_1.15.7 snpStats_1.5.5 >>> splines_2.15.0 survival_2.36-12 >>> [16] tools_2.15.0 zlibbioc_1.1.1 >>> >>> >>> On 10 Mar 2012, at 17:50, Martin Morgan wrote: >>> >>> On 03/10/2012 09:39 AM, Lescai, Francesco wrote: >>> Hi there, >>> maybe I'm just doing a silly error somewhere, but I get an error >>> when trying to locate the variants from a GRanges object. >>> I have a file with SNP positions, thefore I build up the GRanges >>> this way >>> >>> my.ranges = GRanges( >>> seqnames=paste("chr", my.snp.unique$chromosome, sep=""), >>> IRanges(start= my.snp.unique$position, >>> width=1)) >>> >>> head(my.ranges) >>> GRanges with 6 ranges and 0 elementMetadata values: >>> seqnames ranges strand >>> <rle> <iranges> <rle> >>> [1] chr1 [ 1323144, 1323144] * >>> [2] chr1 [ 3544236, 3544236] * >>> [3] chr1 [ 6252966, 6252966] * >>> [4] chr1 [ 7861154, 7861154] * >>> [5] chr1 [10425118, 10425118] * >>> [6] chr1 [10502308, 10502308] * >>> --- >>> seqlengths: >>> chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 ... chr4 >>> chr5 chr6 chr7 chr8 chr9 chrX chrY >>> NA NA NA NA NA NA NA NA NA ... NA >>> NA NA NA NA NA NA NA >>> >>> library(TxDb.Hsapiens.UCSC.hg19.knownGene) >>> txdb19<- TxDb.Hsapiens.UCSC.hg19.knownGene >>> # >>> my.locations = locateVariants(my.ranges, txdb19) >>> Error in initialize(value, ...) : >>> invalid names for slots of class „RangesMatching‰: matchMatrix, DIM >>> >>> What am I doing wrong? >>> >>> Your devel packages are out of date, so I'd start with >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite(character()) >>> >>> Martin >>> >>> >>> thanks, >>> Francesco >>> >>> >>> sessionInfo() >>> R Under development (unstable) (2012-01-20 r58146) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] C/en_US.UTF-8/C/C/C/C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 GenomicFeatures_1.6.7 >>> [3] VariantAnnotation_1.1.33 Rsamtools_1.7.27 >>> [5] Biostrings_2.23.6 AnnotationDbi_1.17.15 >>> [7] Biobase_2.15.3 GenomicRanges_1.7.16 >>> [9] IRanges_1.13.22 BiocGenerics_0.1.4 >>> [11] biomaRt_2.11.1 >>> >>> loaded via a namespace (and not attached): >>> [1] BSgenome_1.23.2 DBI_0.2-5 Matrix_1.0-3 >>> RCurl_1.9-5 RSQLite_0.11.1 >>> [6] XML_3.8-0 bitops_1.0-4.1 ggplot2_0.8.9 >>> grid_2.15.0 lattice_0.20-0 >>> [11] plyr_1.7.1 rtracklayer_1.15.7 snpStats_1.5.3 >>> splines_2.15.0 survival_2.36-10 >>> [16] tools_2.15.0 zlibbioc_1.1.1 >>> >>> ------------------------------------------------------------------ --------------- >>> Francesco Lescai, PhD, EDBT >>> Senior Research Associate in Genome Analysis >>> University College London >>> Faculty of Population Health Sciences >>> Dept. Genes, Development& Disease >>> ICH - Molecular Medicine Unit, GOSgene team >>> 30 Guilford Street >>> WC1N 1EH London UK >>> >>> email: f.lescai@ucl.ac.uk >>> <mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.le scai@ucl.ac.uk=""><mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk>< mailto:f.lescai@ucl.ac.uk> >>> phone: +44.(0)207.905.2274 >>> [ext: 2274] >>> ------------------------------------------------------------------ -------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> <mailto:bioconductor@r-project.org><mailto:bioconductor@r-project. org=""><mailto:bioconductor@r-project.org><mailto:bioconductor@r-project. org=""><mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> >>> ------------------------------------------------------------------ --------------- >>> Francesco Lescai, PhD, EDBT >>> Senior Research Associate in Genome Analysis >>> University College London >>> Faculty of Population Health Sciences >>> Dept. Genes, Development& Disease >>> ICH - Molecular Medicine Unit, GOSgene team >>> 30 Guilford Street >>> WC1N 1EH London UK >>> >>> email: f.lescai@ucl.ac.uk >>> <mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.le scai@ucl.ac.uk=""><mailto:f.lescai@ucl.ac.uk> >>> phone: +44.(0)207.905.2274 >>> [ext: 2274] >>> ------------------------------------------------------------------ -------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> <mailto:bioconductor@r-project.org><mailto:bioconductor@r-project. org=""><mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> >>> ------------------------------------------------------------------ --------------- >>> Francesco Lescai, PhD, EDBT >>> Senior Research Associate in Genome Analysis >>> University College London >>> Faculty of Population Health Sciences >>> Dept. Genes, Development& Disease >>> ICH - Molecular Medicine Unit, GOSgene team >>> 30 Guilford Street >>> WC1N 1EH London UK >>> >>> email: f.lescai@ucl.ac.uk >>> <mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.le scai@ucl.ac.uk=""> >>> phone: +44.(0)207.905.2274 >>> [ext: 2274] >>> ------------------------------------------------------------------ -------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> <mailto:bioconductor@r-project.org><mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >>> >>> ------------------------------------------------------------------ --------------- >>> Francesco Lescai, PhD, EDBT >>> Senior Research Associate in Genome Analysis >>> University College London >>> Faculty of Population Health Sciences >>> Dept. Genes, Development& Disease >>> ICH - Molecular Medicine Unit, GOSgene team >>> 30 Guilford Street >>> WC1N 1EH London UK >>> >>> email: f.lescai@ucl.ac.uk >>> <mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk> >>> phone: +44.(0)207.905.2274 >>> [ext: 2274] >>> ------------------------------------------------------------------ -------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> ------------------------------------------------------------------ --------------- >>> Francesco Lescai, PhD, EDBT >>> Senior Research Associate in Genome Analysis >>> University College London >>> Faculty of Population Health Sciences >>> Dept. Genes, Development& Disease >>> ICH - Molecular Medicine Unit, GOSgene team >>> 30 Guilford Street >>> WC1N 1EH London UK >>> >>> email: f.lescai@ucl.ac.uk >>> <mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk> >>> phone: +44.(0)207.905.2274 >>> [ext: 2274] >>> ------------------------------------------------------------------ -------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > -------------------------------------------------------------------- ------------- > *Francesco Lescai, PhD, EDBT* > Senior Research Associate in Genome Analysis > University College London > Faculty of Population Health Sciences > Dept. Genes, Development & Disease > ICH - Molecular Medicine Unit, GOSgene team > 30 Guilford Street > WC1N 1EH London UK > > email: f.lescai@ucl.ac.uk <mailto:f.lescai@ucl.ac.uk> > phone: +44.(0)207.905.2274 > [ext: 2274] > -------------------------------------------------------------------- ------------ > [[alternative HTML version deleted]]