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’

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"




On Tue, Mar 26, 2013 at 1:58 AM, Henrik Bengtsson <hb@biostat.ucsf.edu>wrote:

> On Mon, Mar 25, 2013 at 7:16 AM, Russell Williams
> <russell.d.williams@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@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@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@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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