looks like you need some more disk space

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'

On Thu, Jul 11, 2013 at 5:05 AM, sk [guest] <guest@bioconductor.org> wrote:

>
> when I install package "affyPLM" on Linux ,there are some errors I can't
> deal with, please help me
>
>
>
>  -- output of sessionInfo():
>
> [kaishi@csr60 ~]$ R --vanilla
>
> R version 3.0.1 (2013-05-16) -- "Good Sport"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > 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 âaffyPLMâ ...
> ** 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 âaffyPLMâ
> * removing
> â/home/comp/kaishi/R/x86_64-unknown-linux-gnu-library/3.0/affyPLMâ
>
> The downloaded source packages are in
>         â/tmp/RtmpgTxnpB/downloaded_packagesâ
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>   installation of package âaffyPLMâ had non-zero exit status
> 2: installed directory not writable, cannot update packages 'class',
> 'foreign',
>   'MASS', 'mgcv', 'nlme', 'nnet', 'spatial'
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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