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