[BioC] Packages not getting installed

Tue May 12 15:41:56 CEST 2009

Hi Ashwin,

Looks to me like you are missing (at the very least) the C header files. 
You or your sysadmin need to install glibc-headers and maybe 
glibc-devel. Not sure exactly what all you need, as I have never used a 
Linux distro that didn't have these by default (unless you count Mac OSX).

Best,

Jim

Ashwin Kumar wrote:
> 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
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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734-615-7826