[BioC] Installing Gostat
R [guest]
guest at bioconductor.org
Wed Oct 16 13:06:08 CEST 2013
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 âGSEABaseâ, âgenefilterâ, âXMLâ, âCategoryâ, âannotateâ
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GSEABase_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/genefilter_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/Category_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/annotate_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/GOstats_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 âXMLâ ...
** package âXMLâ 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 âXMLâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/XMLâ
ERROR: dependency âXMLâ is not available for package âannotateâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/annotateâ
ERROR: dependencies âannotateâ, âXMLâ are not available for package âGSEABaseâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/GSEABaseâ
ERROR: dependency âannotateâ is not available for package âgenefilterâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/genefilterâ
ERROR: dependencies âGSEABaseâ, âgenefilterâ, âannotateâ are not available for package âCategoryâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/Categoryâ
ERROR: dependencies âCategoryâ, âannotateâ are not available for package âGOstatsâ
* removing â/home/robinm/R/x86_64-pc-linux-gnu-library/3.0/GOstatsâ
The downloaded source packages are in
â/tmp/Rtmppuncin/downloaded_packagesâ
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âXMLâ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âannotateâ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âGSEABaseâ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âgenefilterâ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âCategoryâ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package âGOstatsâ 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
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