Dear list, I get the following error when trying to update geneplotter to the version packaged with the new Bioconductor 2.9: > update.packages(repos=biocinstallRepos(), ask=F,checkBuilt=T) trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/ geneplotter_1.31.4.tar.gz' Content type 'application/x-gzip' length 1387616 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb * installing *source* package ???geneplotter??? ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... *** tangling vignette sources ... ???byChroms.Rnw??? ???visualize.Rnw??? ** testing if installed package can be loaded Error in namespaceExport(ns, exports) : undefined exports: .__C__file, .__C__connection Error: loading failed Execution halted ERROR: loading failed * removing ???/usr/local/lib/R/site-library/geneplotter??? * restoring previous ???/usr/local/lib/R/site-library/geneplotter??? The downloaded packages are in ???/tmp/RtmpUnjUVh/downloaded_packages??? Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ???geneplotter??? had non-zero exit status -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.0 loaded via a namespace (and not attached): [1] annotate_1.32.0 AnnotationDbi_1.16.0 Biobase_2.14.0 [4] DBI_0.2-5 genefilter_1.36.0 IRanges_1.12.0 [7] mnormt_1.4-3 RSQLite_0.10.0 sn_0.4-17 [10] splines_2.14.0 survival_2.36-10 tcltk_2.14.0 [13] tools_2.14.0 xtable_1.6-0 -- Sent via the guest posting facility at bioconductor.org.

Hello, On Wed, Nov 2, 2011 at 8:57 AM, Ignacio Lopez de Ullibarri [guest] <guest at="" bioconductor.org=""> wrote: > > Dear list, > > I get the following error when trying to update geneplotter to the version packaged with the new Bioconductor 2.9: > >> update.packages(repos=biocinstallRepos(), ask=F,checkBuilt=T) > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contri b/geneplotter_1.31.4.tar.gz' > Content type 'application/x-gzip' length 1387616 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > * installing *source* package ???geneplotter??? ... > ** R > ** data > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > *** tangling vignette sources ... > ? ???byChroms.Rnw??? > ? ???visualize.Rnw??? > ** testing if installed package can be loaded > Error in namespaceExport(ns, exports) : > ?undefined exports: .__C__file, .__C__connection > Error: loading failed > Execution halted > ERROR: loading failed > * removing ???/usr/local/lib/R/site-library/geneplotter??? > * restoring previous ???/usr/local/lib/R/site-library/geneplotter??? > > The downloaded packages are in > ? ? ? ????/tmp/RtmpUnjUVh/downloaded_packages??? > Warning message: > In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, ?: > ?installation of package ???geneplotter??? had non-zero exit status > > > ?-- output of sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8 > ?[5] LC_MONETARY=en_GB.UTF-8 ? ?LC_MESSAGES=en_GB.UTF-8 > ?[7] LC_PAPER=C ? ? ? ? ? ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] BiocInstaller_1.2.0 > > loaded via a namespace (and not attached): > ?[1] annotate_1.32.0 ? ? ?AnnotationDbi_1.16.0 Biobase_2.14.0 > ?[4] DBI_0.2-5 ? ? ? ? ? ?genefilter_1.36.0 ? ?IRanges_1.12.0 > ?[7] mnormt_1.4-3 ? ? ? ? RSQLite_0.10.0 ? ? ? sn_0.4-17 > [10] splines_2.14.0 ? ? ? survival_2.36-10 ? ? tcltk_2.14.0 > [13] tools_2.14.0 ? ? ? ? xtable_1.6-0 > > -- > Sent via the guest posting facility at bioconductor.org. We will have an updated version of geneplotter (1.32.1) available in a couple of hours. Thanks, Dan > > _______________________________________________ > 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 >