[BioC] package \"affyPLM\" install errors on linux

Thu Jul 11 05:05:59 CEST 2013

when I install package "affyPLM" on Linux ,there are some errors I can't deal with, please help me 

 -- output of sessionInfo(): 

[kaishi at csr60 ~]$ R --vanilla

R version 3.0.1 (2013-05-16) -- "Good Sport"
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Platform: x86_64-unknown-linux-gnu (64-bit)

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> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.12 (BiocInstaller 1.10.2), ?biocLite for help

> biocLite("affyPLM")
\BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.2), R version 3.0.1.
Installing package(s) 'affyPLM'
trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/affyPLM_1.36.0.tar.gz'
Content type 'application/x-gzip' length 6135144 bytes (5.9 Mb)
opened URL
==================================================
downloaded 5.9 Mb

* installing *source* package Ã¢affyPLMÃ¢ ...
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c LESN.c -o LESN.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c common_types.c -o common_types.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c rma_common.c -o rma_common.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c scaling.c -o scaling.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c threestep.c -o threestep.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/preprocessCore/include"   -fpic  -g -O2  -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -lgfortran -lm -L/usr/local/lib64/R/lib -lRlapack -L/usr/local/lib64/R/lib -lRblas -lz
installing to /home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/affyPLM/libs
** R
Warning in dir.create(outCodeDir) :
  cannot create dir '/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/affyPLM/R', reason 'Disk quota exceeded'
Error in .install_package_code_files(".", instdir) : 
  cannot open directory '/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/affyPLM/R'
ERROR: unable to collate and parse R files for package Ã¢affyPLMÃ¢
* removing Ã¢/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/affyPLMÃ¢

The downloaded source packages are in
        Ã¢/tmp/RtmpgTxnpB/downloaded_packagesÃ¢
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package Ã¢affyPLMÃ¢ had non-zero exit status
2: installed directory not writable, cannot update packages 'class', 'foreign',
  'MASS', 'mgcv', 'nlme', 'nnet', 'spatial' 

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