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Question: install qvalue
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3.9 years ago by
Guest User12k
Guest User12k wrote:
Hi, I try to install qvalue. > source("http://bioconductor.org/biocLite.R") A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("qvalue") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'qvalue' ??????????????? 1: package ???qvalue??? is not available (for R version 2.15.1) 2: installed directory not writable, cannot update packages 'car', 'chron', 'colorspace', 'effects', 'Hmisc', 'lmtest', 'multcomp', 'mvtnorm', 'rgl', 'sandwich', 'sm', 'strucchange', 'XML', 'zoo', 'cluster', 'KernSmooth', 'lattice', 'Matrix', 'mgcv', 'nnet', 'rpart', 'survival' Thank you in advance for great help! Best, liyue -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 3.9 years ago by Martin Morgan ♦♦ 20k • written 3.9 years ago by Guest User12k
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gravatar for Dan Tenenbaum
3.9 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
Hi, You might try changing Bioconductor mirrors with the chooseBioCmirror() command. For users in China the mirror in Anhui usually works. Dan ----- Original Message ----- > From: "liyue [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, yueli7 at 126.com > Cc: "qvalue Maintainer" <jstorey at="" u.washington.edu=""> > Sent: Thursday, January 2, 2014 6:22:14 AM > Subject: [BioC] install qvalue > > > Hi, > > I try to install qvalue. > > > source("http://bioconductor.org/biocLite.R") > A new version of Bioconductor is available after installing the most > recent version of R; see http://bioconductor.org/install > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > > biocLite("qvalue") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version > 2.15. > Installing package(s) 'qvalue' > ??????????????? > 1: package ???qvalue??? is not available (for R version 2.15.1) > 2: installed directory not writable, cannot update packages 'car', > 'chron', > 'colorspace', 'effects', 'Hmisc', 'lmtest', 'multcomp', 'mvtnorm', > 'rgl', > 'sandwich', 'sm', 'strucchange', 'XML', 'zoo', 'cluster', > 'KernSmooth', > 'lattice', 'Matrix', 'mgcv', 'nnet', 'rpart', 'survival' > > Thank you in advance for great help! > > Best, > > liyue > > -- output of sessionInfo(): > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C > [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 > [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 COMMENTlink written 3.9 years ago by Dan Tenenbaum ♦♦ 8.2k
Actually, it turns out that the mirror in Anhui does not contain a mirror of BioC 2.11. If it is feasible, you might consider upgrading to the release version of R (3.0.2) and Bioconductor (2.13). Then you would be able to use that mirror. Dan ----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > To: "liyue [guest]" <guest at="" bioconductor.org=""> > Cc: "qvalue Maintainer" <jstorey at="" u.washington.edu="">, bioconductor at r-project.org > Sent: Thursday, January 2, 2014 8:15:38 AM > Subject: Re: [BioC] install qvalue > > Hi, > > You might try changing Bioconductor mirrors with the > chooseBioCmirror() command. > For users in China the mirror in Anhui usually works. > > Dan > > > ----- Original Message ----- > > From: "liyue [guest]" <guest at="" bioconductor.org=""> > > To: bioconductor at r-project.org, yueli7 at 126.com > > Cc: "qvalue Maintainer" <jstorey at="" u.washington.edu=""> > > Sent: Thursday, January 2, 2014 6:22:14 AM > > Subject: [BioC] install qvalue > > > > > > Hi, > > > > I try to install qvalue. > > > > > source("http://bioconductor.org/biocLite.R") > > A new version of Bioconductor is available after installing the > > most > > recent version of R; see http://bioconductor.org/install > > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > > > biocLite("qvalue") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version > > 2.15. > > Installing package(s) 'qvalue' > > ??????????????? > > 1: package ???qvalue??? is not available (for R version 2.15.1) > > 2: installed directory not writable, cannot update packages 'car', > > 'chron', > > 'colorspace', 'effects', 'Hmisc', 'lmtest', 'multcomp', > > 'mvtnorm', > > 'rgl', > > 'sandwich', 'sm', 'strucchange', 'XML', 'zoo', 'cluster', > > 'KernSmooth', > > 'lattice', 'Matrix', 'mgcv', 'nnet', 'rpart', 'survival' > > > > Thank you in advance for great help! > > > > Best, > > > > liyue > > > > -- output of sessionInfo(): > > > > > sessionInfo() > > R version 2.15.1 (2012-06-22) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 > > [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > [1] tools_2.15.1 > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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 3.9 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Martin Morgan
3.9 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
On 01/02/2014 06:22 AM, liyue [guest] wrote: > > Hi, > > I try to install qvalue. > >> source("http://bioconductor.org/biocLite.R") > A new version of Bioconductor is available after installing the most > recent version of R; see http://bioconductor.org/install > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help >> biocLite("qvalue") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'qvalue' > ??????????????? > 1: package ???qvalue??? is not available (for R version 2.15.1) As Dan mentions it's probably a good idea to update to the latest R (version 3.0.1) It would help to understand why you are unable to install qvalue, in particular whether the following files are accessible from your location http://bioconductor.org/packages/2.11/bioc/src/contrib/PACKAGES.gz http://bioconductor.org/packages/2.11/bioc/src/contrib/qvalue_1.32.0.t ar.gz and whether the problem still occurs, or only occurred transiently? Martin > 2: installed directory not writable, cannot update packages 'car', 'chron', > 'colorspace', 'effects', 'Hmisc', 'lmtest', 'multcomp', 'mvtnorm', 'rgl', > 'sandwich', 'sm', 'strucchange', 'XML', 'zoo', 'cluster', 'KernSmooth', > 'lattice', 'Matrix', 'mgcv', 'nnet', 'rpart', 'survival' > > Thank you in advance for great help! > > Best, > > liyue > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C > [3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=zh_CN.UTF-8 > [5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 3.9 years ago by Martin Morgan ♦♦ 20k
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