biocLite breaks when `svn rev` is "unknown"
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@michael-lawrence-3846
Last seen 2.9 years ago
United States
This is what I get: > biocLite("TxDb.Hsapiens.UCSC.hg19") Error in if (svnRev < 55733) .stop("R-2.14 r55733 or newer required.") : missing value where TRUE/FALSE needed My `svn rev` in Rversion() is "unknown". No idea why. Maybe it's just really old and the computer forgot? Maybe a warning should be issued, and then continue? > sessionInfo() R version 2.14.0 Under development (unstable) (--) Platform: i686-pc-linux-gnu (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.1.28 rtracklayer_1.13.19 RCurl_1.5-0 [4] bitops_1.0-4.1 loaded via a namespace (and not attached): [1] BSgenome_1.21.3 Biostrings_2.21.11 GenomicRanges_1.5.49 [4] IRanges_1.11.27 XML_3.2-0 tools_2.14.0 [7] zlibbioc_0.1.6 Thanks, Michael [[alternative HTML version deleted]]
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@martin-morgan-1513
Last seen 3 months ago
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On 10/22/2011 08:33 AM, Michael Lawrence wrote: > This is what I get: > >> biocLite("TxDb.Hsapiens.UCSC.hg19") > Error in if (svnRev< 55733) .stop("R-2.14 r55733 or newer required.") : > missing value where TRUE/FALSE needed > > My `svn rev` in Rversion() is "unknown". No idea why. Maybe it's just > really old and the computer forgot? Maybe a warning should be issued, and > then continue? Thanks Michael -- this should be fixed in BiocInstaller version 1.1.29; because the error is in your installed package, you'll (currently) need to remove.packages("BiocInstaller") before source("http://bioconductor.org/biocLite.R"); biocLite(character()) or whatever. Martin > >> sessionInfo() > R version 2.14.0 Under development (unstable) (--) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.1.28 rtracklayer_1.13.19 RCurl_1.5-0 > [4] bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.21.3 Biostrings_2.21.11 GenomicRanges_1.5.49 > [4] IRanges_1.11.27 XML_3.2-0 tools_2.14.0 > [7] zlibbioc_0.1.6 > > Thanks, > Michael > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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On Sat, Oct 22, 2011 at 11:03 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 10/22/2011 08:33 AM, Michael Lawrence wrote: > >> This is what I get: >> >> biocLite("TxDb.Hsapiens.UCSC.**hg19") >>> >> Error in if (svnRev< 55733) .stop("R-2.14 r55733 or newer required.") : >> missing value where TRUE/FALSE needed >> >> My `svn rev` in Rversion() is "unknown". No idea why. Maybe it's just >> really old and the computer forgot? Maybe a warning should be issued, and >> then continue? >> > > Thanks Michael -- this should be fixed in BiocInstaller version 1.1.29; > because the error is in your installed package, you'll (currently) need to > remove.packages("**BiocInstaller") before source("http://bioconductor.** > org/biocLite.R <http: bioconductor.org="" bioclite.r="">"); > biocLite(character()) or whatever. > > Maybe the biocLite.R script could check for a newer version of BiocInstaller? > Martin > > >> sessionInfo() >>> >> R version 2.14.0 Under development (unstable) (--) >> Platform: i686-pc-linux-gnu (32-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.1.28 rtracklayer_1.13.19 RCurl_1.5-0 >> [4] bitops_1.0-4.1 >> >> loaded via a namespace (and not attached): >> [1] BSgenome_1.21.3 Biostrings_2.21.11 GenomicRanges_1.5.49 >> [4] IRanges_1.11.27 XML_3.2-0 tools_2.14.0 >> [7] zlibbioc_0.1.6 >> >> Thanks, >> Michael >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > [[alternative HTML version deleted]]
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On 10/22/2011 10:14 PM, Michael Lawrence wrote: > > > On Sat, Oct 22, 2011 at 11:03 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 10/22/2011 08:33 AM, Michael Lawrence wrote: > > This is what I get: > > biocLite("TxDb.Hsapiens.UCSC.__hg19") > > Error in if (svnRev< 55733) .stop("R-2.14 r55733 or newer > required.") : > missing value where TRUE/FALSE needed > > My `svn rev` in Rversion() is "unknown". No idea why. Maybe > it's just > really old and the computer forgot? Maybe a warning should be > issued, and > then continue? > > > Thanks Michael -- this should be fixed in BiocInstaller version > 1.1.29; because the error is in your installed package, you'll > (currently) need to remove.packages("__BiocInstaller") before > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">"); biocLite(character()) or > whatever. > > > Maybe the biocLite.R script could check for a newer version of > BiocInstaller? It does; there are some edge cases and I thought this might be one of them, offering remove.packages to hedge my bets. Martin > > Martin > > > sessionInfo() > > R version 2.14.0 Under development (unstable) (--) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.1.28 rtracklayer_1.13.19 RCurl_1.5-0 > [4] bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.21.3 Biostrings_2.21.11 GenomicRanges_1.5.49 > [4] IRanges_1.11.27 XML_3.2-0 tools_2.14.0 > [7] zlibbioc_0.1.6 > > Thanks, > Michael > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <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 <tel:206%20667-2793> > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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hi, this is what i get, the error seems to point out to something about the X11 font installation in my mac but i'm pretty lost about this, so any hint will be highly appreciated: library(ShortRead) q <- qa(system.file("unitTests", "cases", package="ShortRead"), pattern="solexa.fastq", type="fastq") rptReads <- report(q) Error in grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x$y, : could not find any X11 fonts Check that the Font Path is correct. In addition: Warning messages: 1: In jpeg(file.path(imgDir, jpegFile), ...) : locale not supported by Xlib: some X ops will operate in C locale 2: In jpeg(file.path(imgDir, jpegFile), ...) : X cannot set locale modifiers sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-33 [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] Biobase_2.12.2 grid_2.13.0 hwriter_1.3 thanks!! robert.
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i fail to reproduce on 2.13 as noted below or on 2.14 -- maybe alter locale setting? > q class: FastqQA(10) QA elements (access with qa[["elt"]]): readCounts: data.frame(1 3) baseCalls: data.frame(1 5) readQualityScore: data.frame(1 4) baseQuality: data.frame(94 3) alignQuality: data.frame(1 3) frequentSequences: data.frame(1 4) sequenceDistribution: data.frame(1 4) perCycle: list(2) baseCall: data.frame(47 4) quality: data.frame(47 5) perTile: list(2) readCounts: data.frame(0 4) medianReadQualityScore: data.frame(0 4) adapterContamination: data.frame(1 2) > sessionInfo() R version 2.13.0 Patched (2011-04-14 r55443) Platform: x86_64-apple-darwin10.6.0/x86_64 (64-bit) locale: [1] en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII attached base packages: [1] stats graphics grDevices datasets utils tools methods [8] base other attached packages: [1] ShortRead_1.10.4 Rsamtools_1.5.2 lattice_0.19-33 [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 [7] weaver_1.18.0 codetools_0.2-8 digest_0.5.0 loaded via a namespace (and not attached): [1] Biobase_2.12.2 grid_2.13.0 hwriter_1.3 On Sat, Oct 22, 2011 at 9:28 PM, Robert Castelo <robert.castelo at="" upf.edu=""> wrote: > hi, this is what i get, the error seems to point out to something about the > X11 font installation in my mac but i'm pretty lost about this, so any hint > will be highly appreciated: > > library(ShortRead) > q <- qa(system.file("unitTests", "cases", package="ShortRead"), > pattern="solexa.fastq", type="fastq") > > rptReads <- report(q) > Error in grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x$y, ?: > ?could not find any X11 fonts > Check that the Font Path is correct. > In addition: Warning messages: > 1: In jpeg(file.path(imgDir, jpegFile), ...) : > ?locale not supported by Xlib: some X ops will operate in C locale > 2: In jpeg(file.path(imgDir, jpegFile), ...) : > ?X cannot set locale modifiers > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] ShortRead_1.10.4 ? ?Rsamtools_1.4.3 ? ? lattice_0.19-33 > [4] Biostrings_2.20.4 ? GenomicRanges_1.4.8 IRanges_1.10.6 > > loaded via a namespace (and not attached): > [1] Biobase_2.12.2 grid_2.13.0 ? ?hwriter_1.3 > > > thanks!! > robert. > > _______________________________________________ > 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 >
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thanks Vincent, the verification on your side confirms this is a locale issue and i could sort it out thanks to the following trick kindly sent to me by Martin: Sys.setlocale(locale="C") right before the call to report(). cheers, robert. On 10/23/11 3:55 AM, Vincent Carey wrote: > i fail to reproduce on 2.13 as noted below or on 2.14 -- maybe alter > locale setting? > >> q > class: FastqQA(10) > QA elements (access with qa[["elt"]]): > readCounts: data.frame(1 3) > baseCalls: data.frame(1 5) > readQualityScore: data.frame(1 4) > baseQuality: data.frame(94 3) > alignQuality: data.frame(1 3) > frequentSequences: data.frame(1 4) > sequenceDistribution: data.frame(1 4) > perCycle: list(2) > baseCall: data.frame(47 4) > quality: data.frame(47 5) > perTile: list(2) > readCounts: data.frame(0 4) > medianReadQualityScore: data.frame(0 4) > adapterContamination: data.frame(1 2) >> sessionInfo() > R version 2.13.0 Patched (2011-04-14 r55443) > Platform: x86_64-apple-darwin10.6.0/x86_64 (64-bit) > > locale: > [1] en_US.US-ASCII/en_US.US-ASCII/C/C/en_US.US-ASCII/en_US.US-ASCII > > attached base packages: > [1] stats graphics grDevices datasets utils tools methods > [8] base > > other attached packages: > [1] ShortRead_1.10.4 Rsamtools_1.5.2 lattice_0.19-33 > [4] Biostrings_2.20.3 GenomicRanges_1.4.8 IRanges_1.10.6 > [7] weaver_1.18.0 codetools_0.2-8 digest_0.5.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.12.2 grid_2.13.0 hwriter_1.3 > > > On Sat, Oct 22, 2011 at 9:28 PM, Robert Castelo<robert.castelo at="" upf.edu=""> wrote: >> hi, this is what i get, the error seems to point out to something about the >> X11 font installation in my mac but i'm pretty lost about this, so any hint >> will be highly appreciated: >> >> library(ShortRead) >> q<- qa(system.file("unitTests", "cases", package="ShortRead"), >> pattern="solexa.fastq", type="fastq") >> >> rptReads<- report(q) >> Error in grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x$y, : >> could not find any X11 fonts >> Check that the Font Path is correct. >> In addition: Warning messages: >> 1: In jpeg(file.path(imgDir, jpegFile), ...) : >> locale not supported by Xlib: some X ops will operate in C locale >> 2: In jpeg(file.path(imgDir, jpegFile), ...) : >> X cannot set locale modifiers >> sessionInfo() >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C/UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] ShortRead_1.10.4 Rsamtools_1.4.3 lattice_0.19-33 >> [4] Biostrings_2.20.4 GenomicRanges_1.4.8 IRanges_1.10.6 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.12.2 grid_2.13.0 hwriter_1.3 >> >> >> thanks!! >> robert. >> >> _______________________________________________ >> 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 >>
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