[BioC] RE : rsamtools installation
Wolfgang RAFFELSBERGER
wraff at igbmc.fr
Mon Nov 14 13:39:03 CET 2011
Dear List,
I have trouble too installing Rsamtools and RSQlite with R-2.14.0 on a RedHat system (installation of previous R & BioC versions had no problems on the same system).
In the case of RSQlite I'll try if there is a way of updating/grading our C compiler, but for Rsamtools I don't know what might be the problem (the file 'Rsamtools.so' actually exists in the folder 'Rsamtools').
Initially I ran into the problems using biocLite(), here I'lm reporting the specific messages when looking directly at Rsamtools and RSQlite.
Any hits are appreciated,
Wolfgang
> source("http://www.bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
>
> biocLite("Rsamtools")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'Rsamtools'
trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Rsamtools_1.6.1.tar.gz'
Content type 'application/x-gzip' length 2088996 bytes (2.0 Mb)
opened URL
==================================================
downloaded 2.0 Mb
* installing *source* package 'Rsamtools' ...
** libs
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c encode.c -o encode.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c fafile.c -o fafile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c io_sam.c -o io_sam.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c utilities.c -o utilities.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_index.c -o samtools/bam_index.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/razf.c -o samtools/razf.o
samtools/razf.c:58:2: warning: #warning "zlib < 1.2.2.1; RAZF writing is disabled."
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/knetfile.c -o samtools/knetfile.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bam_reheader.c -o samtools/bam_reheader.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/biolo/R_star/R-2.14.0/lib64/R/include -I/usr/local/include -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/Biostrings/include" -I"/linux/biolo/R_star/R-2.14.0/lib64/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usretc"
cp ../Rsamtools.mk "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usretc"
mkdir -p "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/include/samtools/bcftools"
mkdir -p "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/include/tabix"
cp samtools/*.h "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/include/tabix/"
mkdir -p "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usrlib"
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o vcffile.o zip_compression.o -fopenmp /linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usrlib/libbam.a /linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usrlib/libbcf.a /linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/usrlib/libtabix.a -lz -L/linux/biolo/R_star/R-2.14.0/lib64/R/lib -lR
installing to /linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Rsamtools-Overview.Rnw'
'Rsamtools-UsingCLibraries.Rnw'
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/libs/Rsamtools.so':
/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: razf_write
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/linux/biolo/R_star/R-2.14.0/lib64/R/library/Rsamtools'
The downloaded packages are in
'/tmp/RtmpN7ZA1O/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'Rsamtools' had non-zero exit status
>
>
> ## following a recent related post on the list I tried what was suggested but this had no effect ...
>
> rm(biocLite)
Warning message:
In rm(biocLite) : object 'biocLite' not found
> rm(biocinstallRepos)
Warning message:
In rm(biocinstallRepos) : object 'biocinstallRepos' not found
>
>
>
> biocLite("RSQLite")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'RSQLite'
trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.10.0.tar.gz'
Content type 'application/x-gzip' length 1495533 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb
* installing *source* package 'RSQLite' ...
** package 'RSQLite' successfully unpacked and MD5 sums checked
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.
configure: WARNING: Cache variable ac_cv_prog_ac_ct_CC contains a newline.
ERROR: configuration failed for package 'RSQLite'
* removing '/linux/biolo/R_star/R-2.14.0/lib64/R/library/RSQLite'
The downloaded packages are in
'/tmp/RtmpU91PTB/downloaded_packages'
Updating HTML index of packages in '.Library'
Making packages.html ... done
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'RSQLite' had non-zero exit status
>
>
> ## For completeness
>
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.14.0
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3201
wolfgang.raffelsberger (at) igbmc.fr
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Xavier de Pedro [xavier.depedro at vhir.org]
Date d'envoi : lundi 14 novembre 2011 09:37
? : Martin Morgan
Cc : kthom110 at uncc.edu; bioconductor at r-project.org
Objet : Re: [BioC] rsamtools installation
Hi
I was having a similar issue after upgrading to 2.14 and their
corresponding biocoonductor packages.
And manually installing again bitops (and a few othes with a similar
issue for me), e.g.:
biocLite("bitops")
did the trick. For some reason, the older version didn'thave the
namespace that the new version of packages expects (for what I've noticed)
Cheers
Xavi
On 11/11/11 20:00, Martin Morgan wrote:
> On 11/11/2011 09:55 AM, kevin [guest] wrote:
>>
>> hi,
>>
>> having difficulties installing Rsamtools, through biocLite:
>>
>> Warning: replacing previous import ?EUR?.__C__file?EUR(tm) when loading
>> ?EUR?Biostrings?EUR(tm)
>> Warning: replacing previous import ?EUR?.__C__connection?EUR(tm) when
>> loading ?EUR?Biostrings?EUR(tm)
>> Error : classes "file", "connection" are not exported by
>> 'namespace:Biostrings'
>> ERROR: lazy loading failed for package ?EUR?Rsamtools?EUR(tm)
>> * removing
>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>> * restoring previous
>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>>
>> The downloaded packages are in
>> ?EUR?/tmp/Rtmp6N3TVN/downloaded_packages?EUR(tm)
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>> installation of package 'Rsamtools' had non-zero exit status
>>
>> and via R CMD INSTALL Rsamtools/
>>
>> Error : package 'bitops' does not have a name space
>> ERROR: lazy loading failed for package ?EUR?Rsamtools?EUR(tm)
>> * removing
>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools?EUR(tm)
>> * restoring previous
>> ?EUR?/home/kthom110/R/x86_64-pc-linux-gnu-library/2.12/Rsamtools
>>
>>
>> any help will be appreciated,
>> kevin
>>
>> -- output of sessionInfo():
>>
>> R version 2.12.1 (2010-12-16)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Biostrings_2.22.0 IRanges_1.12.1
>
> Somehow you have managed to install Biostrings and IRanges for version
> 2.14 into your version 2.12 library; biocLite is trying to install the
> version of Rsamtools for 2.12 (presumably; there isn't enough info at
> the top).
>
> Your command line
>
> > and via R CMD INSTALL Rsamtools/
> >
> > Error : package 'bitops' does not have a name space
>
> implies that the R at the command line is version 2.14, i.e., you have
> multiple different versions of R installed on your system.
>
> I'd suggest starting again (with current R 2-14) and sticking with
> biocLite.
>
> Martin
>
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.12.1
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
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