[BioC] Installing Gostat

[R [guest]]

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/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 ‘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

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