[BioC] Trouble installing "preprocessCore" on 32 bit debian Linux

[Sean Davis]

On Thu, Apr 3, 2008 at 4:52 AM, Sonia Ting <soniagarden at gmail.com> wrote:
> Dear consulter,
>
>  I tried to install Bioconductor on my 32 bit debian linux and faced some
>  problem.
>  Basically I think it happened on the first installation: preprocessCore
>  I do have libgfortran.so.2.0.0 and 3.0.0 under /usr/lib/
>  following message is the error message that came out.
>  Please help me with it!!! Thanks a million.
>
>
>  *********************************************
>  > source("http://bioconductor.org/biocLite.R")
>  Warning messages:
>  1: In safeSource() : Redefining 'biocinstall'
>  2: In safeSource() : Redefining 'biocinstallPkgGroups'
>  3: In safeSource() : Redefining 'biocinstallRepos'
>  >     biocLite("preprocessCore")
>  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 '/usr/local/lib/R/site-library'
>  trying URL '
>  http://bioconductor.org/packages/2.1/bioc/src/contrib/preprocessCore_1.0.0.tar.gz
>  '
>  Content type 'application/x-gzip' length 48446 bytes (47 Kb)
>  opened URL
>  ==================================================
>  downloaded 47 Kb
>
>  * Installing *source* package 'preprocessCore' ...
>  ** libs
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c avg.c -o avg.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c avg_log.c -o avg_log.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c biweight.c -o biweight.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c init_package.c -o init_package.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c lm.c -o lm.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c log_avg.c -o log_avg.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c log_median.c -o log_median.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c matrix_functions.c -o matrix_functions.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c median.c -o median.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c median_log.c -o median_log.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c medianpolish.c -o medianpolish.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c psi_fns.c -o psi_fns.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c qnorm.c -o qnorm.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c R_colSummarize.c -o R_colSummarize.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c rlm_anova.c -o rlm_anova.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c rlm.c -o rlm.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c rlm_se.c -o rlm_se.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c rma_common.c -o rma_common.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
>  gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
>  -O2 -c R_subColSummarize.c -o R_subColSummarize.o
>  gcc -std=gnu99 -shared  -o preprocessCore.so avg.o avg_log.o biweight.o
>  init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o
>  median_log.o medianpolish.o psi_fns.o qnorm.o R_colSummarize.o rlm_anova.o
>  rlm.o rlm_se.o rma_common.o R_rlm_interfaces.o R_subColSummarize.o
>  -L/usr/lib/gcc/i486-linux-gnu/4.3 -lgfortran -lm -lgcc_s -L/usr/lib/R/lib
>  -lRlapack -lblas  -L/usr/lib/R/lib -lR
>  /usr/bin/ld: cannot find -lgfortran

Looks like you do not have gfortran and/or the gfortran devel packages
installed?  I'm not a debian user, but I think it is worth checking
that detail.

Sean

>  collect2: ld returned 1 exit status
>  make: *** [preprocessCore.so] Error 1
>  ERROR: compilation failed for package 'preprocessCore'
>  ** Removing '/usr/local/lib/R/site-library/preprocessCore'
>
>  The downloaded packages are in
>         /tmp/RtmpHAk372/downloaded_packages
>  Warning message:
>  In install.packages(pkgs = pkgs, repos = repos, dependencies =
>  dependencies,  :
>   installation of package 'preprocessCore' had non-zero exit status
>
>         [[alternative HTML version deleted]]
>
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