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

[Henrik Bengtsson]

On Mon, Mar 25, 2013 at 7:16 AM, Russell Williams
<russell.d.williams at gmail.com> wrote:
> Okay, I tried just reinstalling affxparser in a fresh R session from the
> terminal. The response is the same:
>
> Error in inDL(x, as.logical(local), as.logical(now), ...)
> unable to load shared object "C:/Program
> Files/R/R-2.15.3/libs/i386/affxparser.dll":
> LoadLibrary failure: The specified procedure could not be found.
> Error: package/namespace load failed for "affxparser"

Hmm... the pathname in that error message indicates that something is
really wrong.  It is also *not* the same path that you had in your
previous message.  What does:

system.file(package="tools")

output?  Exactly how do you install affxparser?  Have to tried to
uninstall affxparser first (and verified that it's really gone)?

/Henrik

>
> Again, installing and loading other packages, including other BioConductor
> packages, works fine. I accept there might be a problem with my local
> configuration, but what kind of local problem would cause all installs of
> only this one package to fail?
>
>
> On Sun, Mar 24, 2013 at 3:04 PM, Henrik Bengtsson <hb at biostat.ucsf.edu>
> wrote:
>>
>> 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
>
>