[BioC] Problem installing genefilter (Ubuntu 12.04; Bioconductor v2.12)
Olivier [guest]
guest at bioconductor.org
Wed Jul 31 17:54:50 CEST 2013
I'm having problems installing genefilter. Grateful if you could help. Thanks.
> biocLite('genefilter')
... (ommitted lines for clarity)
* 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/olivier/R/x86_64-pc-linux-gnu-library/3.0/XMLâ
ERROR: dependency âXMLâ is not available for package âannotateâ
* removing â/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/annotateâ
ERROR: dependency âannotateâ is not available for package âgenefilterâ
* removing â/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/genefilterâ
The downloaded source packages are in
â/tmp/Rtmpylk0c1/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 âgenefilterâ had non-zero exit status
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] tools parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.10.3 ALL_1.4.14 Biobase_2.20.1 BiocGenerics_0.6.0
[5] limma_3.16.7
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