Hello group ,

I am still having problems with installing the GOstats package & its not a
typo error ... I am pasting my workspace image along with the error it
shows:

> source("http://bioconductor.org/biocLite.R")
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
> biocLite("GOstats")
Running biocinstall version 2.4.10 with R version 2.9.0
Your version of R requires version 2.4 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  argument 'lib' is missing: using
'/home/mlscub1/R/i486-pc-linux-gnu-library/2.9'
also installing the dependencies ‘XML’, ‘GSEABase’, ‘Category’

trying URL '
http://bioconductor.org/packages/2.4/extra/src/contrib/XML_2.3-0.tar.gz'
Content type 'application/x-gzip' length 659797 bytes (644 Kb)
opened URL
==================================================
downloaded 644 Kb

trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/GSEABase_1.6.0.tar.gz'
Content type 'application/x-gzip' length 174211 bytes (170 Kb)
opened URL
==================================================
downloaded 170 Kb

trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/Category_2.10.0.tar.gz
'
Content type 'application/x-gzip' length 458431 bytes (447 Kb)
opened URL
==================================================
downloaded 447 Kb

trying URL '
http://bioconductor.org/packages/2.4/bioc/src/contrib/GOstats_2.10.0.tar.gz'
Content type 'application/x-gzip' length 2404620 bytes (2.3 Mb)
opened URL
==================================================
downloaded 2.3 Mb

* Installing *source* package ‘XML’ ...
checking for gcc... gcc
checking for C compiler default output file name... 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 xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/XML’
* Installing *source* package ‘GSEABase’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
  there is no package called 'XML'
ERROR: lazy loading failed for package ‘GSEABase’
* Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/GSEABase’
* Installing *source* package ‘Category’ ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Error in loadNamespace(imp[[1L]], c(lib.loc, .libPaths())) :
  there is no package called 'GSEABase'
ERROR: lazy loading failed for package ‘Category’
* Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/Category’
* Installing *source* package ‘GOstats’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Error : package 'Category' required by 'GOstats' could not be found
ERROR: lazy loading failed for package ‘GOstats’
* Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/GOstats’

The downloaded packages are in
    ‘/tmp/RtmpykjLAI/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'XML' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'GSEABase' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'Category' had non-zero exit status
> library(GOstats)
Error in library(GOstats) : there is no package called 'GOstats'

Any advice will be greatly appreciated ....

Thankfully
A.Ashwin
MLSC
Department of Biotechnology
Manipal University
INDIA

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