Question: fail to load BSgenome.Hsapiens.UCSC.hg19
0
gravatar for Yue Li
5.5 years ago by
Yue Li370
USA
Yue Li370 wrote:
Dear List, I am experiencing the following problem after I updated some of the packages today and wonder if there's a quick fix for it. Thanks in advance! Yue ################################################################ R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(BSgenome.Hsapiens.UCSC.hg19) Loading required package: BSgenome Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: S4Vectors Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Attaching package: ?GenomicRanges? The following objects are masked from ?package:GenomeInfoDb?: dropSeqlevels, genome, genome<-, isCircular, isCircular<-, keepSeqlevels, keepStandardChromosomes, renameSeqlevels, restoreSeqlevels, seqinfo, Seqinfo, seqinfo<-, seqlengths, seqlengths<-, seqlevels, seqlevels<-, seqlevels0, seqlevelsInUse, seqnames, seqnames<-, seqnameStyle, seqnameStyle<-, sortSeqlevels Loading required package: Biostrings Loading required package: XVector There were 44 warnings (use warnings() to see them) Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details: call: seqlengths(seqinfo(x)) error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?seqinfo? for signature ?"FastaNamedSequences"? Error: package or namespace load failed for ?BSgenome.Hsapiens.UCSC.hg19? > sessionInfo() R version 3.1.0 Patched (2014-04-15 r65398) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome_1.33.2 Biostrings_2.33.6 XVector_0.5.6 [4] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3 IRanges_1.99.13 [7] S4Vectors_0.0.6 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] bitops_1.0-6 Rsamtools_1.17.9 stats4_3.1.0 zlibbioc_1.11.1
• 1.5k views
ADD COMMENTlink modified 5.5 years ago by Hervé Pagès ♦♦ 14k • written 5.5 years ago by Yue Li370
Answer: fail to load BSgenome.Hsapiens.UCSC.hg19
0
gravatar for Hervé Pagès
5.5 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Yue, Please ask Bioc-devel questions on the Bioc-devel mailing list. While working on re-syncing some packages with the latest changes in GenomicRanges/GenomeInfoDb a couple of days ago I inadvertently decreased Rsamtools version from 1.17.9 to 1.17.8 instead of bumping it. So my changes to Rsamtools did not propagate to the public repositories. Yesterday I realized my mistake and bumped Rsamtools version to 1.17.10. However this won't propagate to the public repos until tomorrow. In the meantime you can grab and install the latest Rsamtools from svn: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools R CMD INSTALL Rsamtools Let me know if you still run into problems after this. Sorry for the inconvenience, H. On 05/06/2014 12:33 PM, Yue Li wrote: > Dear List, > > I am experiencing the following problem after I updated some of the packages today and wonder if there's a quick fix for it. > > Thanks in advance! > Yue > > > ################################################################ > > R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > >> library(BSgenome.Hsapiens.UCSC.hg19) > Loading required package: BSgenome > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, > do.call, duplicated, eval, evalq, Filter, Find, get, intersect, > is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, > rownames, sapply, setdiff, sort, table, tapply, union, unique, > unlist > > Loading required package: S4Vectors > Loading required package: IRanges > Loading required package: GenomeInfoDb > Loading required package: GenomicRanges > > Attaching package: ?GenomicRanges? > > The following objects are masked from ?package:GenomeInfoDb?: > > dropSeqlevels, genome, genome<-, isCircular, isCircular<-, > keepSeqlevels, keepStandardChromosomes, renameSeqlevels, > restoreSeqlevels, seqinfo, Seqinfo, seqinfo<-, seqlengths, > seqlengths<-, seqlevels, seqlevels<-, seqlevels0, seqlevelsInUse, > seqnames, seqnames<-, seqnameStyle, seqnameStyle<-, sortSeqlevels > > Loading required package: Biostrings > Loading required package: XVector > There were 44 warnings (use warnings() to see them) > Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details: > call: seqlengths(seqinfo(x)) > error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?seqinfo? for signature ?"FastaNamedSequences"? > > Error: package or namespace load failed for ?BSgenome.Hsapiens.UCSC.hg19? >> sessionInfo() > R version 3.1.0 Patched (2014-04-15 r65398) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome_1.33.2 Biostrings_2.33.6 XVector_0.5.6 > [4] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3 IRanges_1.99.13 > [7] S4Vectors_0.0.6 BiocGenerics_0.11.2 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 Rsamtools_1.17.9 stats4_3.1.0 zlibbioc_1.11.1 > _______________________________________________ > 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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 5.5 years ago by Hervé Pagès ♦♦ 14k
Hi Herv?, Thanks a lot! I actually went the brute force way by restoring my whole library via time machine backup. I will try my luck again tomorrow. Best, Yue On May 6, 2014, at 3:47 PM, Hervé Pagès <hpages at="" fhcrc.org=""> wrote: > Hi Yue, > > Please ask Bioc-devel questions on the Bioc-devel mailing list. > > While working on re-syncing some packages with the latest changes in > GenomicRanges/GenomeInfoDb a couple of days ago I inadvertently > decreased Rsamtools version from 1.17.9 to 1.17.8 instead of bumping > it. So my changes to Rsamtools did not propagate to the public > repositories. > > Yesterday I realized my mistake and bumped Rsamtools version to 1.17.10. > However this won't propagate to the public repos until tomorrow. > > In the meantime you can grab and install the latest Rsamtools from > svn: > > svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools > R CMD INSTALL Rsamtools > > Let me know if you still run into problems after this. > > Sorry for the inconvenience, > H. > > On 05/06/2014 12:33 PM, Yue Li wrote: >> Dear List, >> >> I am experiencing the following problem after I updated some of the packages today and wonder if there's a quick fix for it. >> >> Thanks in advance! >> Yue >> >> >> ################################################################ >> >> R version 3.1.0 Patched (2014-04-15 r65398) -- "Spring Dance" >> Copyright (C) 2014 The R Foundation for Statistical Computing >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> >>> library(BSgenome.Hsapiens.UCSC.hg19) >> Loading required package: BSgenome >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, >> do.call, duplicated, eval, evalq, Filter, Find, get, intersect, >> is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, >> pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, >> rownames, sapply, setdiff, sort, table, tapply, union, unique, >> unlist >> >> Loading required package: S4Vectors >> Loading required package: IRanges >> Loading required package: GenomeInfoDb >> Loading required package: GenomicRanges >> >> Attaching package: ?GenomicRanges? >> >> The following objects are masked from ?package:GenomeInfoDb?: >> >> dropSeqlevels, genome, genome<-, isCircular, isCircular<-, >> keepSeqlevels, keepStandardChromosomes, renameSeqlevels, >> restoreSeqlevels, seqinfo, Seqinfo, seqinfo<-, seqlengths, >> seqlengths<-, seqlevels, seqlevels<-, seqlevels0, seqlevelsInUse, >> seqnames, seqnames<-, seqnameStyle, seqnameStyle<-, sortSeqlevels >> >> Loading required package: Biostrings >> Loading required package: XVector >> There were 44 warnings (use warnings() to see them) >> Error : .onLoad failed in loadNamespace() for 'BSgenome.Hsapiens.UCSC.hg19', details: >> call: seqlengths(seqinfo(x)) >> error: error in evaluating the argument 'x' in selecting a method for function 'seqlengths': Error in (function (classes, fdef, mtable) : >> unable to find an inherited method for function ?seqinfo? for signature ?"FastaNamedSequences"? >> >> Error: package or namespace load failed for ?BSgenome.Hsapiens.UCSC.hg19? >>> sessionInfo() >> R version 3.1.0 Patched (2014-04-15 r65398) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] BSgenome_1.33.2 Biostrings_2.33.6 XVector_0.5.6 >> [4] GenomicRanges_1.17.12 GenomeInfoDb_1.1.3 IRanges_1.99.13 >> [7] S4Vectors_0.0.6 BiocGenerics_0.11.2 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-6 Rsamtools_1.17.9 stats4_3.1.0 zlibbioc_1.11.1 >> _______________________________________________ >> 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 >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
ADD REPLYlink written 5.5 years ago by Yue Li370
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 253 users visited in the last hour