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Question: Error to install a package for Affymetrix data‏
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gravatar for chm chag
4.9 years ago by
chm chag30
chm chag30 wrote:
Dear Sir, The instalation of the 'oligo' package does not work and I have these error messages: > source("http://bioconductor.org/biocLite.R") > biocLite("oligo") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'oligo' Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 essai de l'URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows /contrib/2.15/oligo_1.22.0.zip' Content type 'application/zip' length 5765066 bytes (5.5 Mb) URL ouverte downloaded 5.5 Mb package ‘oligo’ successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Documents and Settings\Administrateur\Local Settings\Temp\Rtmp4CqL4q\downloaded_packages Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 And when I compile the command: > library(oligo) I have this: Error in inDL(x, as.logical(local), as.logical(now), ...) : impossible de charger l'objet partagé 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': LoadLibrary failure: La procédure spécifiée est introuvable. Erreur : le chargement du package / espace de noms a échoué pour ‘oligo’ And even by compiling this commands for instaling "hugene21sttranscriptcluster.db" package I have this error message: > source("http://bioconductor.org/biocLite.R") > biocLite("hugene21sttranscriptcluster.db", type="source") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'hugene21sttranscriptcluster.db' Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 Message d'avis : package ‘hugene21sttranscriptcluster.db’ is not available (for R version 2.15.3) cordially; Madiha Chagdal SITN Master-2 : Statistics, Computer and Digital Techniques Claude Bernard Lyon-1 University [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.9 years ago by James W. MacDonald46k • written 4.9 years ago by chm chag30
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gravatar for James W. MacDonald
4.9 years ago by
United States
James W. MacDonald46k wrote:
You need to first upgrade to the current version of R and re-install Bioconductor. Best, Jim On 6/21/2013 9:23 AM, chm chag wrote: > Dear Sir, > > The instalation of the 'oligo' package does not work and I have these error messages: > >> source("http://bioconductor.org/biocLite.R") >> biocLite("oligo") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version > 2.15. > Installing package(s) 'oligo' > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > essai de l'URL 'http://bioconductor.org/packages/2.11/bioc/bin/windo ws/contrib/2.15/oligo_1.22.0.zip' > Content type 'application/zip' length 5765066 bytes (5.5 Mb) > URL ouverte > downloaded 5.5 Mb > package ?oligo? successfully unpacked and MD5 sums checked > The downloaded binary packages are in > C:\Documents and Settings\Administrateur\Local Settings\Temp\Rtmp4CqL4q\downloaded_packages > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > > > And when I compile the command:> library(oligo) I have this: > > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > impossible de charger l'objet partag? 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': > LoadLibrary failure: La proc?dure sp?cifi?e est introuvable. > Erreur : le chargement du package / espace de noms a ?chou? pour ?oligo? > > And even by compiling this commands for instaling "hugene21sttranscriptcluster.db" package I have this error message: >> source("http://bioconductor.org/biocLite.R") >> biocLite("hugene21sttranscriptcluster.db", type="source") > > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'hugene21sttranscriptcluster.db' > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > Message d'avis : > package ?hugene21sttranscriptcluster.db? is not available (for R version 2.15.3) > > cordially; > > > Madiha Chagdal > SITN Master-2 : Statistics, Computer and Digital Techniques > Claude Bernard Lyon-1 University > > > [[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
ADD COMMENTlink written 4.9 years ago by James W. MacDonald46k
Dear Sir; I reinstalled the latest version of R (R-3.0.1) as bioconductor but it still does not work: By installing the oligo package I always have this error message (Warning: unable to move temporary installation "C: \ Program Files \ R \ R-3.0.1 \ library \ file5bc5cca72b1 \ trace 'to' C: \ Program Files \ R \ R-3.0.1 \ library \ trace ') and when running the command: library (oligo) I have this error message, in addition to this dialog window (see picture attached). thank you for your help. Cordially; Madiha Chagdal; > Date: Mon, 24 Jun 2013 09:59:32 -0400 > From: jmacdon at uw.edu > To: chagdal-madiha at hotmail.com > CC: bioconductor at r-project.org > Subject: Re: [BioC] Error to install a package for Affymetrix data? > > You need to first upgrade to the current version of R and re-install > Bioconductor. > > Best, > > Jim > > > > On 6/21/2013 9:23 AM, chm chag wrote: > > Dear Sir, > > > > The instalation of the 'oligo' package does not work and I have these error messages: > > > >> source("http://bioconductor.org/biocLite.R") > >> biocLite("oligo") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version > > 2.15. > > Installing package(s) 'oligo' > > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > > essai de l'URL 'http://bioconductor.org/packages/2.11/bioc/bin/win dows/contrib/2.15/oligo_1.22.0.zip' > > Content type 'application/zip' length 5765066 bytes (5.5 Mb) > > URL ouverte > > downloaded 5.5 Mb > > package ?oligo? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > > C:\Documents and Settings\Administrateur\Local Settings\Temp\Rtmp4CqL4q\downloaded_packages > > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > > > > > > And when I compile the command:> library(oligo) I have this: > > > > > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > > impossible de charger l'objet partag? 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': > > LoadLibrary failure: La proc?dure sp?cifi?e est introuvable. > > Erreur : le chargement du package / espace de noms a ?chou? pour ?oligo? > > > > And even by compiling this commands for instaling "hugene21sttranscriptcluster.db" package I have this error message: > >> source("http://bioconductor.org/biocLite.R") > >> biocLite("hugene21sttranscriptcluster.db", type="source") > > > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > > Installing package(s) 'hugene21sttranscriptcluster.db' > > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 > > Message d'avis : > > package ?hugene21sttranscriptcluster.db? is not available (for R version 2.15.3) > > > > cordially; > > > > > > Madiha Chagdal > > SITN Master-2 : Statistics, Computer and Digital Techniques > > Claude Bernard Lyon-1 University > > > > > > [[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 >
ADD REPLYlink written 4.9 years ago by chm chag30
On Mon, Jun 24, 2013 at 8:47 AM, chm chag <chagdal-madiha at="" hotmail.com=""> wrote: > Dear Sir; > > I reinstalled the latest version of R (R-3.0.1) as bioconductor but it still does not work: By installing the oligo package I always have this error message (Warning: unable to move temporary installation "C: \ Program Files \ R \ R-3.0.1 \ library \ file5bc5cca72b1 \ trace 'to' C: \ Program Files \ R \ R-3.0.1 \ library \ trace ') This sounds like a permissions problem. Are you able to run R as an administrator? That is, can you right-click on the R icon and choose "Run as administrator"? If you can do that, try reinstalling oligo as an administrator. > and when running the command: library (oligo) I have this error message, in addition to this dialog window (see picture attached). Most attachments are stripped off before reaching the list, so we did not see your picture, maybe you can just paste the error text into an email. Thanks, Dan > > thank you for your help. > > > > Cordially; > Madiha Chagdal; > > > > > >> Date: Mon, 24 Jun 2013 09:59:32 -0400 >> From: jmacdon at uw.edu >> To: chagdal-madiha at hotmail.com >> CC: bioconductor at r-project.org >> Subject: Re: [BioC] Error to install a package for Affymetrix data >> >> You need to first upgrade to the current version of R and re- install >> Bioconductor. >> >> Best, >> >> Jim >> >> >> >> On 6/21/2013 9:23 AM, chm chag wrote: >> > Dear Sir, >> > >> > The instalation of the 'oligo' package does not work and I have these error messages: >> > >> >> source("http://bioconductor.org/biocLite.R") >> >> biocLite("oligo") >> > BioC_mirror: http://bioconductor.org >> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version >> > 2.15. >> > Installing package(s) 'oligo' >> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 >> > essai de l'URL 'http://bioconductor.org/packages/2.11/bioc/bin/wi ndows/contrib/2.15/oligo_1.22.0.zip' >> > Content type 'application/zip' length 5765066 bytes (5.5 Mb) >> > URL ouverte >> > downloaded 5.5 Mb >> > package ?oligo? successfully unpacked and MD5 sums checked >> > The downloaded binary packages are in >> > C:\Documents and Settings\Administrateur\Local Settings\Temp\Rtmp4CqL4q\downloaded_packages >> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 >> > >> > >> > And when I compile the command:> library(oligo) I have this: >> > >> > >> > Error in inDL(x, as.logical(local), as.logical(now), ...) : >> > impossible de charger l'objet partag? 'C:/Program Files/R/R-2.15.3/library/affxparser/libs/i386/affxparser.dll': >> > LoadLibrary failure: La proc?dure sp?cifi?e est introuvable. >> > Erreur : le chargement du package / espace de noms a ?chou? pour ?oligo? >> > >> > And even by compiling this commands for instaling "hugene21sttranscriptcluster.db" package I have this error message: >> >> source("http://bioconductor.org/biocLite.R") >> >> biocLite("hugene21sttranscriptcluster.db", type="source") >> > >> > BioC_mirror: http://bioconductor.org >> > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. >> > Installing package(s) 'hugene21sttranscriptcluster.db' >> > Avis : unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 >> > Message d'avis : >> > package ?hugene21sttranscriptcluster.db? is not available (for R version 2.15.3) >> > >> > cordially; >> > >> > >> > Madiha Chagdal >> > SITN Master-2 : Statistics, Computer and Digital Techniques >> > Claude Bernard Lyon-1 University >> > >> > >> > [[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 >> > > > _______________________________________________ > 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
ADD REPLYlink written 4.9 years ago by Dan Tenenbaum ♦♦ 8.2k
Hi, On Mon, Jun 24, 2013 at 8:47 AM, chm chag <chagdal-madiha at="" hotmail.com=""> wrote: > Dear Sir; > > I reinstalled the latest version of R (R-3.0.1) as bioconductor but it still does not work: By installing the oligo package I always have this error message (Warning: unable to move temporary installation "C: \ Program Files \ R \ R-3.0.1 \ library \ file5bc5cca72b1 \ trace 'to' C: \ Program Files \ R \ R-3.0.1 \ library \ trace ') > and when running the command: library (oligo) I have this error message, in addition to this dialog window (see picture attached). Your attachment didn't come through on the mailinglist. Also: is it possible you have some permissions problems here and you need to be logged in as an administrator (or the windows equivalent) to do this? Though, if you installed R w/o a problem, then I guess that couldn't be it -- I guess you installed R with the same user account you are using now? Are you installing oligo using "biocLite"? -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
ADD REPLYlink written 4.9 years ago by Steve Lianoglou12k
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