Hi,
you are running an old R version,
the actual one is R-2.9 and therfore new  Bioc release 
have to be updated.

Cheers 

Anna

 Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.




________________________________
Da: Ashwin Kumar <ashwin.havoc@gmail.com>
A: bioconductor <bioconductor@stat.math.ethz.ch>
Inviato: Martedì 12 maggio 2009, 9:01:09
Oggetto: [BioC] Packages not getting installed

Hello group,
                    I am working on microarray data analysis using
bioconductor, I was able to install some basic packages such as limma , GO,
KEGG, etc but some of the other packages such as annotate ,GOstats ,gTools
are not getting installed below is the workspace of my installation set up
....

> source("http://bioconductor.org/biocLite.R")
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
> biocLite("annotate")
Running biocinstall version 2.1.11 with R version 2.6.2
Your version of R requires version 2.1 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/2.6'
also installing the dependencies ‘RSQLite’, ‘Biobase’, ‘AnnotationDbi’

trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.7-1.tar.gz'
Content type 'application/x-gzip' length 1015918 bytes (992 Kb)
opened URL
==================================================
downloaded 992 Kb

trying URL '
http://bioconductor.org/packages/2.1/bioc/src/contrib/Biobase_1.16.3.tar.gz'
Content type 'application/x-gzip' length 1879209 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb

trying URL '
http://bioconductor.org/packages/2.1/bioc/src/contrib/AnnotationDbi_1.0.6.tar.gz
'
Content type 'application/x-gzip' length 228996 bytes (223 Kb)
opened URL
==================================================
downloaded 223 Kb

trying URL '
http://bioconductor.org/packages/2.1/bioc/src/contrib/annotate_1.16.1.tar.gz
'
Content type 'application/x-gzip' length 1526767 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

* Installing *source* package 'RSQLite' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name...
configure: error: C compiler cannot create executables
See `config.log' for more details.
ERROR: configuration failed for package 'RSQLite'
** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/RSQLite'
* Installing *source* package 'Biobase' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
-O2 -c anyMissing.c -o anyMissing.o
In file included from /usr/share/R/include/Rdefines.h:26,
                 from anyMissing.c:11:
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
directory
In file included from /usr/share/R/include/Rinternals.h:28,
                 from /usr/share/R/include/Rdefines.h:29,
                 from anyMissing.c:11:
/usr/share/R/include/R_ext/Arith.h:35:19: error: math.h: No such file or
directory
In file included from /usr/share/R/include/Rdefines.h:29,
                 from anyMissing.c:11:
/usr/share/R/include/Rinternals.h:36:34: error: stdio.h: No such file or
directory
In file included from /usr/share/R/include/Rdefines.h:29,
                 from anyMissing.c:11:
/usr/share/R/include/Rinternals.h:757: error: expected declaration
specifiers or ‘...’ before ‘FILE’
/usr/share/R/include/Rinternals.h:760: error: expected declaration
specifiers or ‘...’ before ‘FILE’
anyMissing.c: In function ‘anyMissing’:
anyMissing.c:33: warning: implicit declaration of function ‘isnan’
make: *** [anyMissing.o] Error 1
ERROR: compilation failed for package 'Biobase'
** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/Biobase'
* Installing *source* package 'AnnotationDbi' ...
** R
** inst
** preparing package for lazy loading
Error: package 'Biobase' required by 'AnnotationDbi' could not be found
Execution halted
ERROR: lazy loading failed for package 'AnnotationDbi'
** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/AnnotationDbi'
* Installing *source* package 'annotate' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Warning in library(pkg, character.only = TRUE, logical.return = TRUE,
lib.loc = lib.loc) :
  there is no package called 'Biobase'
Error: package 'Biobase' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'annotate'
** Removing '/home/mlscub1/R/i486-pc-linux-gnu-library/2.6/annotate'

The downloaded packages are in
    /tmp/RtmpaoFwjZ/downloaded_packages
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'RSQLite' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'Biobase' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'AnnotationDbi' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'annotate' had non-zero exit status
> library(annotate)
Error in library(annotate) : there is no package called 'annotate'

If anyone could explain the problem or suggest a suitable solution will be
very helpfull....

A.Ashwin
Departement of Biotechnology
Manipal Life Science Center
Manipal University
INDIA

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