[BioC] Problem loading the "affxparser" dependency of the "oligo" package.
Henrik Bengtsson
hb at biostat.ucsf.edu
Tue Mar 26 21:49:34 CET 2013
On Tue, Mar 26, 2013 at 10:20 AM, Russell Williams
<russell.d.williams at gmail.com> wrote:
> Hmm, since that was from a terminal and I had to retype it by hand, I might
> have accidentally left out part of the path name. If that caused confusion,
> I apologize.
>
> Here are the answers to your questions:
>
> All of this was done in a fresh R session.
>
>> system.file(package="tools")
> [1] "C:/PROGRA~1/R/R-215~1.3/library/tools"
>
>>remove.packages("affxparser")
> Removing package(s) from ‘C:/Program Files/R/R-2.15.3/library’
> (as ‘lib’ is unspecified)
>
> Checked the file system that the folder is gone.
> Then ran:
>
>> library("affxparser")
> Error in library("affxparser") : there is no package called ‘affxparser’
>
> So it's gone.
>
> Then, as before:
>>source("http://bioconductor.org/biocLite.R")
>>biocLite("affxparser")
>
> ...
> package ‘affxparser’ successfully unpacked and MD5 sums checked
>
> Here I checked the file system and the folder is there: "C:\Program
> Files\R\R-2.15.3\library\affxparser".
> Then:
>> system.file(package = "affxparser")
> [1] "C:/Program Files/R/R-2.15.3/library/affxparser"
>> library("affxparser")
> 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.
>
> Error: package/namespace load failed for ‘affxparser’
Ok.
>
> As an example of a working package:
>> library("ggplot2")
> Find out what's changed in ggplot2 with
> news(Version == "0.9.3.1", package = "ggplot2")
>> system.file(package = "ggplot2")
> [1] "C:/Program Files/R/R-2.15.3/library/ggplot2"
ggplot2 is not a good comparison, because it contains no
native/compiled code (cf. "NeedsCompilation: no" on
http://cran.r-project.org/web/packages/ggplot2/) and native code
("DLL") is what's the issue here. Either way, I'm sure you use other
BioC packages (e.g. affyPLM, affy, ...) that include native code and
it sounds like those work.
So, here my follow up comments/suggestions:
1. It may be that affxparser does not work with Windows XP (possible
specific to Windows XP 32-bit; note, it works on Windows *7* 32-bit).
If you can find someone else with the same Windows system as you, that
person could confirm/falsify this. FYI, I used to run Windows XP
32-bit a few years ago and at that time affxparser works like a charm
on that system.
2. You antivirus software may incorrectly flag/lock 'affxparser.dll'.
Disable it temporarily to see if that solves the problem.
3. It may be that there is something wrong with the Bioconductor
binary of affxparser. You could try to rebuild affxparser yourself
from source, i.e. biocLite("affxparser", type="source"). That would
require that you install and setup 'Rtools'
[http://cran.r-project.org/bin/windows/Rtools/] on your system - worth
it and not too hard, but if the first time it may take some time.
Hope this helps
Henrik
>
>
>
>
> On Tue, Mar 26, 2013 at 1:58 AM, Henrik Bengtsson <hb at biostat.ucsf.edu>
> wrote:
>>
>> 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]]
>> >> >
>> >> > _______________________________________________
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>> >
>> >
>
>
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