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VariantAnnotation development branch issue

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Hamid Bolouri ▴ 90

@hamid-bolouri-4258

Last seen 4.8 years ago

United States

hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration: > fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", + mustWork=TRUE) > tbx <- TabixFile(fl) Error in eval(expr, envir, enclos) : no slot of name "generator" for this object of class "refObjectGenerator" > > traceback() 7: eval(expr, envir, enclos) 6: eval(expr, p) 5: eval.parent(substitute(x at generator$name)) 4: g$new 3: g$new 2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize, ...) 1: TabixFile(fl) > > sessionInfo() R Under development (unstable) (2012-11-01 r61067) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.11.1 [3] org.Hs.eg.db_2.8.0 RSQLite_0.11.2 [5] DBI_0.2-5 AnnotationDbi_1.21.4 [7] Biobase_2.19.0 VariantAnnotation_1.5.7 [9] Rsamtools_1.11.5 Biostrings_2.27.6 [11] GenomicRanges_1.11.8 IRanges_1.17.10 [13] BiocGenerics_0.5.1 loaded via a namespace (and not attached): [1] biomaRt_2.15.0 bitops_1.0-4.1 BSgenome_1.27.1 RCurl_1.95-3 rtracklayer_1.19.2 [6] stats4_2.16.0 tools_2.16.0 XML_3.95-0.1 zlibbioc_1.5.0 Any thoughts? Thanks! Hamid -- http://labs.fhcrc.org/bolouri

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ADD COMMENT • link updated 12.2 years ago by Steve Lianoglou ★ 13k • written 12.2 years ago by Hamid Bolouri ▴ 90

score 0 · Answer 1 · 2012-11-05

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Hi, On Mon, Nov 5, 2012 at 9:42 PM, Hamid Bolouri <hbolouri at="" fhcrc.org=""> wrote: > hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration: > >> fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", > + mustWork=TRUE) >> tbx <- TabixFile(fl) > Error in eval(expr, envir, enclos) : > no slot of name "generator" for this object of class "refObjectGenerator" >> >> traceback() > 7: eval(expr, envir, enclos) > 6: eval(expr, p) > 5: eval.parent(substitute(x at generator$name)) > 4: g$new > 3: g$new > 2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize, > ...) > 1: TabixFile(fl) >> >> sessionInfo() > R Under development (unstable) (2012-11-01 r61067) > Platform: x86_64-w64-mingw32/x64 (64-bit) Could it be related to this issue? https://stat.ethz.ch/pipermail/r-devel/2012-October/065109.html Perhaps the machine that has this working is using a version of R-devel from svn that's pre r61035? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 12.2 years ago Steve Lianoglou ★ 13k

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On 11/05/2012 07:00 PM, Steve Lianoglou wrote: > Hi, > > On Mon, Nov 5, 2012 at 9:42 PM, Hamid Bolouri <hbolouri at="" fhcrc.org=""> wrote: >> hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration: >> >>> fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", >> + mustWork=TRUE) >>> tbx <- TabixFile(fl) >> Error in eval(expr, envir, enclos) : >> no slot of name "generator" for this object of class "refObjectGenerator" >>> >>> traceback() >> 7: eval(expr, envir, enclos) >> 6: eval(expr, p) >> 5: eval.parent(substitute(x at generator$name)) >> 4: g$new >> 3: g$new >> 2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize, >> ...) >> 1: TabixFile(fl) >>> >>> sessionInfo() >> R Under development (unstable) (2012-11-01 r61067) >> Platform: x86_64-w64-mingw32/x64 (64-bit) > > Could it be related to this issue? > > https://stat.ethz.ch/pipermail/r-devel/2012-October/065109.html > > Perhaps the machine that has this working is using a version of > R-devel from svn that's pre r61035? Re-installing Rsamtools (and other packages with reference classes) seems to do the trick, in a new session source("http://bioconductor.org/biocLite.R') biocLite('Rsamtools') and then library(Rsamtools) example(TabixFile) Martin > > -steve > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD REPLY • link 12.2 years ago Martin Morgan 25k

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Thanks very much for the quick diagnosis & fix Martin. Will do. Hamid ----- Original Message ----- From: "Martin Morgan" <mtmorgan@fhcrc.org> To: "Steve Lianoglou" <mailinglist.honeypot at="" gmail.com=""> Cc: "Hamid Bolouri" <hbolouri at="" fhcrc.org="">, bioconductor at r-project.org Sent: Monday, November 5, 2012 8:30:13 PM Subject: Re: [BioC] VariantAnnotation development branch issue On 11/05/2012 07:00 PM, Steve Lianoglou wrote: > Hi, > > On Mon, Nov 5, 2012 at 9:42 PM, Hamid Bolouri <hbolouri at="" fhcrc.org=""> wrote: >> hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration: >> >>> fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools", >> + mustWork=TRUE) >>> tbx <- TabixFile(fl) >> Error in eval(expr, envir, enclos) : >> no slot of name "generator" for this object of class "refObjectGenerator" >>> >>> traceback() >> 7: eval(expr, envir, enclos) >> 6: eval(expr, p) >> 5: eval.parent(substitute(x at generator$name)) >> 4: g$new >> 3: g$new >> 2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize, >> ...) >> 1: TabixFile(fl) >>> >>> sessionInfo() >> R Under development (unstable) (2012-11-01 r61067) >> Platform: x86_64-w64-mingw32/x64 (64-bit) > > Could it be related to this issue? > > https://stat.ethz.ch/pipermail/r-devel/2012-October/065109.html > > Perhaps the machine that has this working is using a version of > R-devel from svn that's pre r61035? Re-installing Rsamtools (and other packages with reference classes) seems to do the trick, in a new session source("http://bioconductor.org/biocLite.R') biocLite('Rsamtools') and then library(Rsamtools) example(TabixFile) Martin > > -steve > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 -- http://labs.fhcrc.org/bolouri

ADD REPLY • link 12.2 years ago Hamid Bolouri ▴ 90