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': 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/window s/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/window s/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@umh.es [[alternative HTML version deleted]]

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 encontr? 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 encontr? 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 encontr? 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/wind ows/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\Configuraci?n 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 encontr? 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/wind ows/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\Configuraci?n 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 encontr? el proceso especificado. > Error: package/namespace load failed for 'oligo' > > Luis M. Valor, PhD > Instituto de Neurociencias > Universidad Miguel Hern?ndez-CSIC > Campus de San Juan > Avenida Ram?n 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

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 Hern?ndez-CSIC > Campus de San Juan > Avenida Ram?n 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 encontr? 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 encontr? 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 encontr? 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\Configuraci?n > 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 encontr? 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\Configuraci?n > 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 encontr? el proceso especificado. > > Error: package/namespace load failed for 'oligo' > > > > Luis M. Valor, PhD > > Instituto de Neurociencias > > Universidad Miguel Hern?ndez-CSIC > > Campus de San Juan > > Avenida Ram?n 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

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. 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@umh.es ________________________________ De: James W. MacDonald [mailto:jmacdon@uw.edu] Enviado el: mar 08/01/2013 17:32 Para: Valor Becerra, Luis Miguel CC: bioconductor@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/wind ows/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 <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/wind ows/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@umh.es > > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

Thanks, Jim. I tried some things but I was unsuccessful. Next I summarize the procedure of my trials: 1) I noticed that my mirror was different from yours (see below) so I changed it accordingly. > 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.cnr.Berkeley.edu <http: cran.cnr.berkeley.edu=""/> " CRANextra "http://www.stats.ox.ac.uk/pub/RWin" MBNI "http://brainarray.mbni.med.umich.edu/bioc" 2) I relaunched a new R session, re-installed 'oligo' and tried again. 3) I re-installed R from the Seattle CRAN (http://cran.fhcrc.org), removed the affxparser folder, re-installed 'oligo' and tried again. 4) I installed R and all the required stuff in another PC computer, just to rule out I'm experiencing some weird compatibility issue in my own computer, without success. Any suggestions? Regards, Luis 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@umh.es [[alternative HTML version deleted]]