when I install "org.Hs.eg.db" package on Linux, there are some errors, I do not know why. Thanks! -- output of sessionInfo(): Warning in gzfile(file, mode) : cannot open compressed file '/home/comp/kaishi/R/x86_64-unknown- linux-gnu-library/3.0/org.Hs.eg.db/help/paths.rds', probable reason 'No such file or directory' Error in gzfile(file, mode) : cannot open the connection ERROR: installing Rd objects failed for package ??org.Hs.eg.db?? * removing ??/home/comp/kaishi/R/x86_64-unknown-linux-gnu- library/3.0/org.Hs.eg.db?? The downloaded source packages are in ??/tmp/RtmpHRvkWg/downloaded_packages?? Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ??org.Hs.eg.db?? had non-zero exit status 2: installed directory not writable, cannot update packages 'class', 'foreign', 'MASS', 'mgcv', 'nlme', 'nnet', 'spatial' > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BiocInstaller_1.10.2 gcrma_2.32.0 affy_1.38.1 [4] preprocessCore_1.22.0 plyr_1.8 GEOquery_2.26.1 [7] Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 Biostrings_2.28.0 IRanges_1.18.1 RCurl_1.95-4.1 [5] splines_3.0.1 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [9] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.

On Wed, Jul 10, 2013 at 5:02 AM, sk [guest] <guest at="" bioconductor.org=""> wrote: > > when I install "org.Hs.eg.db" package on Linux, there are some errors, I do not know why. Thanks! > > -- output of sessionInfo(): > > Warning in gzfile(file, mode) : > cannot open compressed file '/home/comp/kaishi/R/x86_64-unknown- linux-gnu-library/3.0/org.Hs.eg.db/help/paths.rds', probable reason 'No such file or directory' > Error in gzfile(file, mode) : cannot open the connection > ERROR: installing Rd objects failed for package ??org.Hs.eg.db?? > * removing ??/home/comp/kaishi/R/x86_64-unknown-linux-gnu- library/3.0/org.Hs.eg.db?? > > The downloaded source packages are in > ??/tmp/RtmpHRvkWg/downloaded_packages?? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ??org.Hs.eg.db?? had non-zero exit status > 2: installed directory not writable, cannot update packages 'class', 'foreign', > 'MASS', 'mgcv', 'nlme', 'nnet', 'spatial' > > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BiocInstaller_1.10.2 gcrma_2.32.0 affy_1.38.1 > [4] preprocessCore_1.22.0 plyr_1.8 GEOquery_2.26.1 > [7] Biobase_2.20.1 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 Biostrings_2.28.0 IRanges_1.18.1 RCurl_1.95-4.1 > [5] splines_3.0.1 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 > [9] zlibbioc_1.6.0 > > What command are you using to try and install the package? Also, have you tried starting R with the --vanilla option? Dan > > -- > 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