[BioC] Problem loading the "affxparser" dependency of the "oligo" package.

[Henrik Bengtsson]

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]]
>
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