Problem loading the "affxparser" dependency of the "oligo" package.
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@russell-williams-5844
Last seen 8.2 years ago
On Windows XP, after updating to R 2.15.3 and updating all libraries, I was no longer able to load the "oligo" package from BioConductor because of a problem loading the "affxparser" dependency. Other packages, including BioC ones, install and load fine. To recreate: source("http://bioconductor.org/biocLite.R") #install the BioC installer biocLite("oligo") #download and install the oligo package library("oligo") #attempt to load Gets the following error: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': LoadLibrary failure: The specified procedure could not be found. The file it mentions, "C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll", is right where it's supposed to be. sessionInfo() returns: R version 2.15.3 (2013-03-01) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.3 [4] bit_1.1-10 codetools_0.2-8 ff_2.2-11 [7] foreach_1.4.0 GenomicRanges_1.10.7 IRanges_1.16.6 [10] iterators_1.0.6 parallel_2.15.3 stats4_2.15.3 [13] tools_2.15.3 zlibbioc_1.4.0 .libPaths() returns: [1] "C:/Program Files/R/R-2.15.3/library" [2] "C:/Program Files/RStudio/R/library" Is the file corrupt, or is there another solution I haven't found? [[alternative HTML version deleted]]
oligo oligo • 834 views
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@henrik-bengtsson-4333
Last seen 8 weeks ago
United States
FYI, I cannot reproduce this on Windows 7 using: R version 2.15.3 Patched (2013-03-03 r62136) (a) Platform: i386-w64-mingw32/i386 (32-bit) (b) Platform: x86_64-w64-mingw32/x64 (64-bit) with all packages up-to-date. Since it appears to be 'affxparser', I recommend that you troubleshoot to get: library("affxparser") to work in a fresh R session and in plain R (not Rstudio if that's what you're using). Then 'oligo' will probably load as well. My $.02 /Henrik > sessionInfo() R version 2.15.3 Patched (2013-03-03 r62136) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0 [4] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.31.3 affyio_1.26.0 BiocInstaller_1.8.3 [4] Biostrings_2.26.3 bit_1.1-10 codetools_0.2-8 [7] DBI_0.2-5 ff_2.2-11 foreach_1.4.0 [10] GenomicRanges_1.10.7 IRanges_1.16.6 iterators_1.0.6 [13] parallel_2.15.3 preprocessCore_1.20.0 splines_2.15.3 [16] stats4_2.15.3 tools_2.15.3 zlibbioc_1.4.0 On Fri, Mar 22, 2013 at 7:54 AM, Russell Williams <russell.d.williams at="" gmail.com=""> wrote: > On Windows XP, after updating to R 2.15.3 and updating all libraries, I was > no longer able to load the "oligo" package from BioConductor because of a > problem loading the "affxparser" dependency. Other packages, including BioC > ones, install and load fine. > > To recreate: > > source("http://bioconductor.org/biocLite.R") #install the BioC installer > biocLite("oligo") #download and install the oligo package > library("oligo") #attempt to load > > Gets the following error: > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared object 'C:/Program > Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': > LoadLibrary failure: The specified procedure could not be found. > > The file it mentions, "C:/Program > Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll", is right > where it's supposed to be. > > sessionInfo() returns: > > R version 2.15.3 (2013-03-01) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biobase_2.18.0 oligoClasses_1.20.0 BiocGenerics_0.4.0 > > > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.3 > [4] bit_1.1-10 codetools_0.2-8 ff_2.2-11 > [7] foreach_1.4.0 GenomicRanges_1.10.7 IRanges_1.16.6 > [10] iterators_1.0.6 parallel_2.15.3 stats4_2.15.3 > [13] tools_2.15.3 zlibbioc_1.4.0 > > .libPaths() returns: > > [1] "C:/Program Files/R/R-2.15.3/library" > [2] "C:/Program Files/RStudio/R/library" > > Is the file corrupt, or is there another solution I haven't found? > > [[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
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