[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 ‘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/olivier/R/x86_64-pc-linux-gnu-library/3.0/XML’
ERROR: dependency ‘XML’ is not available for package ‘annotate’
* removing ‘/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/annotate’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/olivier/R/x86_64-pc-linux-gnu-library/3.0/genefilter’

The downloaded source packages are in
	‘/tmp/Rtmpylk0c1/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 ‘genefilter’ 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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