[BioC] Problems with 'affxparser' package
James W. MacDonald
jmacdon at uw.edu
Tue Jan 8 18:31:17 CET 2013
Hi Luis,
On 1/8/2013 12:01 PM, Valor Becerra, Luis Miguel wrote:
> Thanks for your quick response.
> It seems I haven't explained the issue properly. I verified that the
> file is where it is supposed to be located and I tried the
> re-installation without success. Working in an earlier version of R
> (2.14.0), the package works nicely and this is why I reasoned it was a
> matter of package update. Hopefully this new piece of information may
> help.
I doubt it is the package - I have it installed in the same version of R
on Windows and it works. So I still think it is a corrupt dll. What
repository are you using? I don't know if biocLite() uses a European
repo or not. I have
> library(BiocInstaller)
> biocinstallRepos()
BioCsoft
"http://bioconductor.org/packages/2.11/bioc"
BioCann
"http://bioconductor.org/packages/2.11/data/annotation"
BioCexp
"http://bioconductor.org/packages/2.11/data/experiment"
BioCextra
"http://bioconductor.org/packages/2.11/extra"
CRAN
"http://cran.fhcrc.org"
CRANextra
"http://www.stats.ox.ac.uk/pub/RWin"
MBNI
"http://brainarray.mbni.med.umich.edu/bioc"
So I am getting things from Seattle. Are you using a different repo? If
so you might try re-installing from Seattle.
BTW, here is my sessionInfo:
> sessionInfo()
R version 2.15.2 (2012-10-26)
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] oligo_1.22.0 Biobase_2.18.0 oligoClasses_1.20.0
[4] BiocGenerics_0.4.0 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] affxparser_1.30.0 affyio_1.26.0 Biostrings_2.26.2
[4] bit_1.1-9 codetools_0.2-8 DBI_0.2-5
[7] ff_2.2-10 foreach_1.4.0 GenomicRanges_1.10.5
[10] IRanges_1.16.4 iterators_1.0.6 parallel_2.15.2
[13] preprocessCore_1.20.0 splines_2.15.2 stats4_2.15.2
[16] tools_2.15.2 zlibbioc_1.4.0
Best,
Jim
> Best regards,
> Luis M. Valor, PhD
> Instituto de Neurociencias
> Universidad Miguel Hernández-CSIC
> Campus de San Juan
> Avenida Ramón y Cajal, s/n
> 03550 San Juan (Alicante) - Spain
> Telf Lab: +34 965 919 265
> Telf Office: +34 965 919 531
> E-mail: lmv at umh.es <mailto:lmv at umh.es>
>
> ------------------------------------------------------------------------
> *De:* James W. MacDonald [mailto:jmacdon at uw.edu]
> *Enviado el:* mar 08/01/2013 17:32
> *Para:* Valor Becerra, Luis Miguel
> *CC:* bioconductor at r-project.org
> *Asunto:* Re: [BioC] Problems with 'affxparser' package
>
> Hi Luis,
>
> On 1/8/2013 8:16 AM, Valor Becerra, Luis Miguel wrote:
> > Hi all,
> >
> > I'm Luis M. Valor from Alicante, Spain. After updating R to version
> 2.15.2 and subsequently Bioconductor to the latest version 2.11 I have
> experienced problems with both 'oligo' and 'pdInfoBuilder' packages:
> thye both produce messages referring to a file not found in the
> 'affxparser' associated package. It seems that this package is not
> updated for Windows since my lab mate, who is using Mac, is not
> experiencing such problems. I copy my session for a closer inspection
> in which I highlight the error messages.
> >
> > Thank you in advance
> >
> > R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> > Copyright (C) 2012 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> > Platform: i386-w64-mingw32/i386 (32-bit)
> >> library(oligo)
> > Loading required package: BiocGenerics
> > Attaching package: 'BiocGenerics'
> > The following object(s) are masked from 'package:stats':
> > xtabs
> > The following object(s) are masked from 'package:base':
> > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
> > get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
> > pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
> > rownames, sapply, setdiff, table, tapply, union, unique
> > Loading required package: oligoClasses
> > Loading package bit 1.1-9
> > package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
> > creators: bit bitwhich
> > coercion: as.logical as.integer as.bit as.bitwhich which
> > operator: !& | xor != ==
> > querying: print length any all min max range sum summary
> > bit access: length<- [ [<- [[ [[<-
> > for more help type ?bit
> > Loading package ff2.2-10
> > - getOption("fftempdir")=="C:/DOCUME~1/lmv/CONFIG~1/Temp/RtmpUZCMo2"
> > - getOption("ffextension")=="ff"
> > - getOption("ffdrop")==TRUE
> > - getOption("fffinonexit")==TRUE
> > - getOption("ffpagesize")==65536
> > - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if
> your system stalls on large writes
> > - getOption("ffbatchbytes")==16095641.6 -- consider a different
> value for tuning your system
> > - getOption("ffmaxbytes")==804782080 -- consider a different value
> for tuning your system
> > Welcome to oligoClasses version 1.20.0
> > Loading required package: Biobase
> > Welcome to Bioconductor
> > Vignettes contain introductory material; view with
> > 'browseVignettes()'. To cite Bioconductor, see
> > 'citation("Biobase")', and for packages 'citation("pkgname")'.
> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
> > unable to load shared object 'C:/Archivos de
> programa/R/R-2.15.2/library/affxparser/libs/i386/affxparser.dll':
>
> You are either missing or have a corrupt dll for affxparser. The easiest
> thing to do first is to re-install and see if that helps.
>
> Best,
>
> Jim
>
>
> > LoadLibrary failure: No se encontró el proceso especificado.
> > Error: package/namespace load failed for 'oligo'
> >> library(pdInfoBuilder)
> > Loading required package: RSQLite
> > Loading required package: DBI
> > Loading required package: affxparser
> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
> > unable to load shared object 'C:/Archivos de
> programa/R/R-2.15.2/library/affxparser/libs/i386/affxparser.dll':
> > LoadLibrary failure: No se encontró el proceso especificado.
> > Error: package 'affxparser' could not be loaded
> >> library(affxparser)
> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
> > unable to load shared object 'C:/Archivos de
> programa/R/R-2.15.2/library/affxparser/libs/i386/affxparser.dll':
> > LoadLibrary failure: No se encontró el proceso especificado.
> > Error: package/namespace load failed for 'affxparser'
> >> library(limma)
> >> library(affy)
> > Attaching package: 'affy'
> > The following object(s) are masked from 'package:oligoClasses':
> > list.celfiles
> >> sessionInfo()
> > R version 2.15.2 (2012-10-26)
> > Platform: i386-w64-mingw32/i386 (32-bit)
> > locale:
> > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> > [5] LC_TIME=Spanish_Spain.1252
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> > other attached packages:
> > [1] affy_1.36.0 limma_3.14.3 RSQLite_0.11.2
> DBI_0.2-5 Biobase_2.18.0 oligoClasses_1.20.0
> > [7] BiocGenerics_0.4.0
> > loaded via a namespace (and not attached):
> > [1] affyio_1.26.0 BiocInstaller_1.8.3
> Biostrings_2.26.2 bit_1.1-9 codetools_0.2-8
> > [6] ff_2.2-10 foreach_1.4.0
> GenomicRanges_1.10.5 IRanges_1.16.4 iterators_1.0.6
> > [11] parallel_2.15.2 preprocessCore_1.20.0
> stats4_2.15.2 zlibbioc_1.4.0
> >> biocLite("affxparser")
> > BioC_mirror: http://bioconductor.org <http://bioconductor.org/>
> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> > Installing package(s) 'affxparser'
> > probando la URL
> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/affxparser_1.30.0.zip'
> <http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/affxparser_1.30.0.zip%27>
> > Content type 'application/zip' length 1916002 bytes (1.8 Mb)
> > URL abierta
> > downloaded 1.8 Mb
> > package 'affxparser' successfully unpacked and MD5 sums checked
> > The downloaded binary packages are in
> > C:\Documents and Settings\lmv\Configuración
> local\Temp\RtmpUZCMo2\downloaded_packages
> >> library(oligo)
> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
> > unable to load shared object 'C:/Archivos de
> programa/R/R-2.15.2/library/affxparser/libs/i386/affxparser.dll':
> > LoadLibrary failure: No se encontró el proceso especificado.
> > Error: package/namespace load failed for 'oligo'
> >> biocLite("affxparser")
> > BioC_mirror: http://bioconductor.org <http://bioconductor.org/>
> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> > Installing package(s) 'affxparser'
> > probando la URL
> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/affxparser_1.30.0.zip'
> <http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/affxparser_1.30.0.zip%27>
> > Content type 'application/zip' length 1916002 bytes (1.8 Mb)
> > URL abierta
> > downloaded 1.8 Mb
> > package 'affxparser' successfully unpacked and MD5 sums checked
> > The downloaded binary packages are in
> > C:\Documents and Settings\lmv\Configuración
> local\Temp\RtmpUZCMo2\downloaded_packages
> >> library(oligo)
> > Error in inDL(x, as.logical(local), as.logical(now), ...) :
> > unable to load shared object 'C:/Archivos de
> programa/R/R-2.15.2/library/affxparser/libs/i386/affxparser.dll':
> > LoadLibrary failure: No se encontró el proceso especificado.
> > Error: package/namespace load failed for 'oligo'
> >
> > Luis M. Valor, PhD
> > Instituto de Neurociencias
> > Universidad Miguel Hernández-CSIC
> > Campus de San Juan
> > Avenida Ramón y Cajal, s/n
> > 03550 San Juan (Alicante) - Spain
> > Telf Lab: +34 965 919 265
> > Telf Office: +34 965 919 531
> > E-mail: lmv at umh.es
> >
> >
> > [[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
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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