[BioC] Problems with 'affxparser' package

Tue Jan 8 17:32:23 CET 2013

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
> 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'
> 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
> 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'
> 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
>
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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