Installing GOstats gives the following error, any ideas what it could be? > biocLite("GOstats") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'GOstats' also installing the dependencies ???GSEABase???, ???genefilter???, ???XML???, ???Category???, ???annotate??? trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GSE ABase_1.24.0.tar.gz' Content type 'application/x-gzip' length 233828 bytes (228 Kb) opened URL ================================================== downloaded 228 Kb trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/gen efilter_1.44.0.tar.gz' Content type 'application/x-gzip' length 1145312 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb trying URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.1.tar.gz' Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/Cat egory_2.28.0.tar.gz' Content type 'application/x-gzip' length 598049 bytes (584 Kb) opened URL ================================================== downloaded 584 Kb trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/ann otate_1.40.0.tar.gz' Content type 'application/x-gzip' length 1834767 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GOs tats_2.28.0.tar.gz' Content type 'application/x-gzip' length 2828202 bytes (2.7 Mb) opened URL ================================================== downloaded 2.7 Mb * installing *source* package ???XML??? ... ** package ???XML??? successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... rm: cannot remove `a.out.dSYM': Is a directory a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ???XML??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/XML??? ERROR: dependency ???XML??? is not available for package ???annotate??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/annotate??? ERROR: dependencies ???annotate???, ???XML??? are not available for package ???GSEABase??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/GSEABase??? ERROR: dependency ???annotate??? is not available for package ???genefilter??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/genefilter??? ERROR: dependencies ???GSEABase???, ???genefilter???, ???annotate??? are not available for package ???Category??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/Category??? ERROR: dependencies ???Category???, ???annotate??? are not available for package ???GOstats??? * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/GOstats??? The downloaded source packages are in ???/tmp/Rtmppuncin/downloaded_packages??? Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???XML??? had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???annotate??? had non-zero exit status 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???GSEABase??? had non-zero exit status 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???genefilter??? had non-zero exit status 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???Category??? had non-zero exit status 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ???GOstats??? had non-zero exit status 7: installed directory not writable, cannot update packages 'lattice', 'spatial' -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.0 edgeR_3.4.0 limma_3.18.0 loaded via a namespace (and not attached): [1] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.

On Wednesday, October 16, 2013 7:06:08 AM, R [guest] wrote: > > Installing GOstats gives the following error, any ideas what it could be? > > > >> biocLite("GOstats") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. > Installing package(s) 'GOstats' > also installing the dependencies ???GSEABase???, ???genefilter???, ???XML???, ???Category???, ???annotate??? > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/G SEABase_1.24.0.tar.gz' > Content type 'application/x-gzip' length 233828 bytes (228 Kb) > opened URL > ================================================== > downloaded 228 Kb > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/g enefilter_1.44.0.tar.gz' > Content type 'application/x-gzip' length 1145312 bytes (1.1 Mb) > opened URL > ================================================== > downloaded 1.1 Mb > > trying URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.1.tar.gz' > Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/C ategory_2.28.0.tar.gz' > Content type 'application/x-gzip' length 598049 bytes (584 Kb) > opened URL > ================================================== > downloaded 584 Kb > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/a nnotate_1.40.0.tar.gz' > Content type 'application/x-gzip' length 1834767 bytes (1.7 Mb) > opened URL > ================================================== > downloaded 1.7 Mb > > trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/G Ostats_2.28.0.tar.gz' > Content type 'application/x-gzip' length 2828202 bytes (2.7 Mb) > opened URL > ================================================== > downloaded 2.7 Mb > > * installing *source* package ???XML??? ... > ** package ???XML??? successfully unpacked and MD5 sums checked > checking for gcc... gcc > checking for C compiler default output file name... > rm: cannot remove `a.out.dSYM': Is a directory > a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > checking for sed... /bin/sed > checking for pkg-config... /usr/bin/pkg-config > checking for xml2-config... no > Cannot find xml2-config ^^^^^^^^^^^ That line is your hint. A quick google search will bring up tons of similar questions, and the answer, which is that you need to install the libxml2 and libxml2-dev packages. How you do that is dependent on your distro, but assuming a Debian variant, you would do something like sudo apt-get install libxml2 libxml2-dev Or maybe you just ask your sysadmin to install it for you, depending on your situation. Best, Jim > ERROR: configuration failed for package ???XML??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/XML??? > ERROR: dependency ???XML??? is not available for package ???annotate??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/annotate??? > ERROR: dependencies ???annotate???, ???XML??? are not available for package ???GSEABase??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/GSEABase??? > ERROR: dependency ???annotate??? is not available for package ???genefilter??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/genefilter??? > ERROR: dependencies ???GSEABase???, ???genefilter???, ???annotate??? are not available for package ???Category??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/Category??? > ERROR: dependencies ???Category???, ???annotate??? are not available for package ???GOstats??? > * removing ???/home/robinm/R/x86_64-pc-linux-gnu- library/3.0/GOstats??? > > The downloaded source packages are in > ???/tmp/Rtmppuncin/downloaded_packages??? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???XML??? had non-zero exit status > 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???annotate??? had non-zero exit status > 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???GSEABase??? had non-zero exit status > 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???genefilter??? had non-zero exit status > 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???Category??? had non-zero exit status > 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???GOstats??? had non-zero exit status > 7: installed directory not writable, cannot update packages 'lattice', 'spatial' > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.12.0 edgeR_3.4.0 limma_3.18.0 > > loaded via a namespace (and not attached): > [1] tools_3.0.2 > > -- > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099