Rsamtools installation
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@bruce-hayward-4551
Last seen 9.6 years ago
Hi, I'm trying to install Rsamtools (Rsamtools_1.6.3) on a FreeBSD8.2 amd64 system with R (R-2.14.2) and quite a few other Bioconductor packages successfully running. I'm running the installation as root btw. The error line is (the full installation output is at the end of this post): Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so': /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol "ti_conf_sam" Following previously posted suggestions on Rsamtools installation problems which suggests an underlying zlib.h problem https://stat.ethz.ch/pipermail/bioconductor/2012-February/043348.html http://permalink.gmane.org/gmane.science.biology.informatics.conductor /38853 I have done > R CMD nm Rsamtools/src/Rsamtools.so |grep ti_conf_sam U ti_conf_sam and ~/.R/Makevars to contain the lines CFLAGS += "-v" \ -Dinline="" as well as (separately) adding to Rsamtools/src/Makevars.common the suggestion in the UsingZlibbioc.pdf PKG_CFLAGS+=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\ "${R_HOME}/bin/R" --vanilla --slave) PKG_LIBS+=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_static")'|\ "${R_HOME}/bin/R" --vanilla --slave) None of which has solved the problem. If this is due to R finding an old system zlib.h (ie not the one in /usr/include which has a 2009 datestamp) how do I go about determining that (not being an expert on the inner workings of R)? If it isn't a zlib.h problem .... help! Thanx, Bruce Hayward Installation script output: >R CMD INSTALL Rsamtools processing 'Rsamtools' a directory * installing to library '/usr/local/lib/R/library' * build_help_types= * DBG: 'R CMD INSTALL' now doing do_install() * created lock directory '/usr/local/lib/R/library/00LOCK-Rsamtools' * installing *source* package 'Rsamtools' ... ** libs about to run R CMD SHLIB -o Rsamtools.so Biostrings_stubs.c IRanges_stubs.c R_init_Rsamtools.c as_bam.c bamfile.c bcffile.c encode.c fafile.c io_sam.c pileupbam.c samtools_patch.c tabixfile.c utilities.c vcffile.c zip_compression.c gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bgzf.c -o samtools/bgzf.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/kstring.c -o samtools/kstring.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_aux.c -o samtools/bam_aux.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam.c -o samtools/bam.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_import.c -o samtools/bam_import.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/sam.c -o samtools/sam.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_index.c -o samtools/bam_index.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_pileup.c -o samtools/bam_pileup.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_md.c -o samtools/bam_md.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/razf.c -o samtools/razf.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/faidx.c -o samtools/faidx.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/knetfile.c -o samtools/knetfile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_sort.c -o samtools/bam_sort.o samtools/bam_sort.c:309:1: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static [enabled by default] samtools/bam_sort.c:53:1: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static [enabled by default] gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/sam_header.c -o samtools/sam_header.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bam_reheader.c -o samtools/bam_reheader.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/kprobaln.c -o samtools/kprobaln.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools_patch.c -o samtools_patch.o /usr/local/bin/ar -crus libbam.a gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o samtools/bcftools/prob1.c: In function 'mc_cal_y': samtools/bcftools/prob1.c:340:3: warning: implicit declaration of function 'expl' [-Wimplicit-function-declaration] samtools/bcftools/prob1.c:340:7: warning: incompatible implicit declaration of built-in function 'expl' [enabled by default] gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/index.c -o samtools/bcftools/index.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o /usr/local/bin/ar -crus libbcf.a gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tabix/index.c -o tabix/index.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tabix/bedidx.c -o tabix/bedidx.o /usr/local/bin/ar -crus libtabix.a mkdir -p "/usr/local/lib/R/library/Rsamtools/usretc" cp ../Rsamtools.mk "/usr/local/lib/R/library/Rsamtools/usretc" mkdir -p "/usr/local/lib/R/library/Rsamtools/include/samtools/bcftools" mkdir -p "/usr/local/lib/R/library/Rsamtools/include/tabix" cp samtools/*.h "/usr/local/lib/R/library/Rsamtools/include/samtools/" cp samtools/bcftools/*h "/usr/local/lib/R/library/Rsamtools/include/samtools/bcftools/" cp tabix/*h "/usr/local/lib/R/library/Rsamtools/include/tabix/" mkdir -p "/usr/local/lib/R/library/Rsamtools/usrlib" cp libbam.a libbcf.a libtabix.a "/usr/local/lib/R/library/Rsamtools/usrlib" gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c Biostrings_stubs.c -o Biostrings_stubs.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c IRanges_stubs.c -o IRanges_stubs.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c R_init_Rsamtools.c -o R_init_Rsamtools.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c as_bam.c -o as_bam.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c bamfile.c -o bamfile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c bcffile.c -o bcffile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c encode.c -o encode.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c fafile.c -o fafile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c io_sam.c -o io_sam.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c pileupbam.c -o pileupbam.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c tabixfile.c -o tabixfile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c utilities.c -o utilities.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c vcffile.c -o vcffile.o gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I"/usr/local/lib/R/library/Biostrings/include" -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c zip_compression.c -o zip_compression.o zip_compression.c: In function '_zip_error': zip_compression.c:31:5: warning: implicit declaration of function 'close' [-Wimplicit-function-declaration] zip_compression.c: In function 'bgzip': zip_compression.c:50:5: warning: implicit declaration of function 'read' [-Wimplicit-function-declaration] gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -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 /usr/local/lib/R/library/Rsamtools/usrlib/libbam.a /usr/local/lib/R/library/Rsamtools/usrlib/libbcf.a /usr/local/lib/R/library/Rsamtools/usrlib/libtabix.a -lz -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/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 '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so': /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol "ti_conf_sam" Error: loading failed Execution halted ERROR: loading failed * removing '/usr/local/lib/R/library/Rsamtools'
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@martin-morgan-1513
Last seen 6 weeks ago
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On 03/29/2012 04:22 AM, Bruce Hayward wrote: > Hi, > I'm trying to install Rsamtools (Rsamtools_1.6.3) on a FreeBSD8.2 amd64 > system with R (R-2.14.2) and quite a few other Bioconductor packages > successfully running. > I'm running the installation as root btw. > The error line is (the full installation output is at the end of this > post): > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so': > /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol > "ti_conf_sam" > > Following previously posted suggestions on Rsamtools installation > problems which suggests an underlying zlib.h problem > https://stat.ethz.ch/pipermail/bioconductor/2012-February/043348.html > http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/38853 > > > I have done > > R CMD nm Rsamtools/src/Rsamtools.so |grep ti_conf_sam > U ti_conf_sam > > and > ~/.R/Makevars > > to contain the lines > > CFLAGS += "-v" \ > -Dinline="" > > as well as (separately) adding to Rsamtools/src/Makevars.common the > suggestion in the UsingZlibbioc.pdf > PKG_CFLAGS+=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\ > "${R_HOME}/bin/R" --vanilla --slave) > PKG_LIBS+=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_static")'|\ > "${R_HOME}/bin/R" --vanilla --slave) > > None of which has solved the problem. > If this is due to R finding an old system zlib.h (ie not the one in > /usr/include which has a 2009 datestamp) how do I go about determining > that (not being an expert on the inner workings of R)? > If it isn't a zlib.h problem .... help! Hi Bruce -- I don't think it's zlib.h, so revert all those changes (FWIW, the 'devel' version of Rsamtools addresses the problem in the post you cite). ti_conf_sam should be defined in libtabix.a R CMD nm Rsamtools/src/libtabix.a |grep ti_conf_sam 0000000000000060 D ti_conf_sam and Rsamtools.so should be built to find it in the final line of the compilation output below gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -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 /usr/local/lib/R/library/Rsamtools/usrlib/libbam.a /usr/local/lib/R/library/Rsamtools/usrlib/libbcf.a /usr/local/lib/R/library/Rsamtools/usrlib/libtabix.a -lz -L/usr/local/lib/R/lib -lR I wonder if there is a libtabix.a already under /usr/local/lib find /usr/local/lib -name libtabix.a and if it does not have ti_conf_sam (test via nm and grep)? Also, I do not have immediate access to gcc 4.6, which appears to be the version you're using? > > Thanx, > Bruce Hayward > > > Installation script output: > > >R CMD INSTALL Rsamtools > processing 'Rsamtools' > a directory > * installing to library '/usr/local/lib/R/library' > * build_help_types= > * DBG: 'R CMD INSTALL' now doing do_install() > * created lock directory '/usr/local/lib/R/library/00LOCK-Rsamtools' > * installing *source* package 'Rsamtools' ... > ** libs > about to run R CMD SHLIB -o Rsamtools.so Biostrings_stubs.c > IRanges_stubs.c R_init_Rsamtools.c as_bam.c bamfile.c bcffile.c encode.c > fafile.c io_sam.c pileupbam.c samtools_patch.c tabixfile.c utilities.c > vcffile.c zip_compression.c > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bgzf.c -o samtools/bgzf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/kstring.c -o samtools/kstring.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_aux.c -o samtools/bam_aux.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam.c -o samtools/bam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_import.c -o samtools/bam_import.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/sam.c -o samtools/sam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_index.c -o samtools/bam_index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_pileup.c -o samtools/bam_pileup.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_lpileup.c -o samtools/bam_lpileup.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_md.c -o samtools/bam_md.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/razf.c -o samtools/razf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/faidx.c -o samtools/faidx.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/knetfile.c -o samtools/knetfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_sort.c -o samtools/bam_sort.o > samtools/bam_sort.c:309:1: warning: 'bam1_lt' is static but used in > inline function '__ks_insertsort_sort' which is not static [enabled by > default] > samtools/bam_sort.c:53:1: warning: 'heap_lt' is static but used in > inline function '__ks_insertsort_heap' which is not static [enabled by > default] > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/sam_header.c -o samtools/sam_header.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bam_reheader.c -o samtools/bam_reheader.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/kprobaln.c -o samtools/kprobaln.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools_patch.c -o samtools_patch.o > /usr/local/bin/ar -crus libbam.a > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o > samtools/bcftools/prob1.c: In function 'mc_cal_y': > samtools/bcftools/prob1.c:340:3: warning: implicit declaration of > function 'expl' [-Wimplicit-function-declaration] > samtools/bcftools/prob1.c:340:7: warning: incompatible implicit > declaration of built-in function 'expl' [enabled by default] > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/index.c -o samtools/bcftools/index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/fet.c -o samtools/bcftools/fet.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o > /usr/local/bin/ar -crus libbcf.a > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > tabix/index.c -o tabix/index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > tabix/bedidx.c -o tabix/bedidx.o > /usr/local/bin/ar -crus libtabix.a > mkdir -p "/usr/local/lib/R/library/Rsamtools/usretc" > cp ../Rsamtools.mk "/usr/local/lib/R/library/Rsamtools/usretc" > mkdir -p "/usr/local/lib/R/library/Rsamtools/include/samtools/bcftools" > mkdir -p "/usr/local/lib/R/library/Rsamtools/include/tabix" > cp samtools/*.h "/usr/local/lib/R/library/Rsamtools/include/samtools/" > cp samtools/bcftools/*h > "/usr/local/lib/R/library/Rsamtools/include/samtools/bcftools/" > cp tabix/*h "/usr/local/lib/R/library/Rsamtools/include/tabix/" > mkdir -p "/usr/local/lib/R/library/Rsamtools/usrlib" > cp libbam.a libbcf.a libtabix.a "/usr/local/lib/R/library/Rsamtools/usrlib" > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > Biostrings_stubs.c -o Biostrings_stubs.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > IRanges_stubs.c -o IRanges_stubs.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > R_init_Rsamtools.c -o R_init_Rsamtools.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > as_bam.c -o as_bam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > bamfile.c -o bamfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > bcffile.c -o bcffile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > encode.c -o encode.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > fafile.c -o fafile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > io_sam.c -o io_sam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > pileupbam.c -o pileupbam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > tabixfile.c -o tabixfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > utilities.c -o utilities.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > vcffile.c -o vcffile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/Biostrings/include" > -I"/usr/local/lib/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 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -c > zip_compression.c -o zip_compression.o > zip_compression.c: In function '_zip_error': > zip_compression.c:31:5: warning: implicit declaration of function > 'close' [-Wimplicit-function-declaration] > zip_compression.c: In function 'bgzip': > zip_compression.c:50:5: warning: implicit declaration of function 'read' > [-Wimplicit-function-declaration] > gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib > -Wl,-rpath=/usr/local/lib/gcc46 -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 > /usr/local/lib/R/library/Rsamtools/usrlib/libbam.a > /usr/local/lib/R/library/Rsamtools/usrlib/libbcf.a > /usr/local/lib/R/library/Rsamtools/usrlib/libtabix.a -lz > -L/usr/local/lib/R/lib -lR > installing to /usr/local/lib/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 > '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so': > /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol > "ti_conf_sam" > Error: loading failed > Execution halted > ERROR: loading failed > * removing '/usr/local/lib/R/library/Rsamtools' > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > 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Hi Martin, On 03/29/12 17:21, Martin Morgan wrote: > On 03/29/2012 04:22 AM, Bruce Hayward wrote: >> Hi, >> I'm trying to install Rsamtools (Rsamtools_1.6.3) on a FreeBSD8.2 amd64 >> system with R (R-2.14.2) and quite a few other Bioconductor packages >> successfully running. >> I'm running the installation as root btw. >> The error line is (the full installation output is at the end of this >> post): >> >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared object >> '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so': >> /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol >> "ti_conf_sam" >> >> If it isn't a zlib.h problem .... help! > > Hi Bruce -- I don't think it's zlib.h, so revert all those changes > (FWIW, the 'devel' version of Rsamtools addresses the problem in the > post you cite). I have deleted everything and started again from Rsamtools_1.6.3.tar.gz > > ti_conf_sam should be defined in libtabix.a > > R CMD nm Rsamtools/src/libtabix.a |grep ti_conf_sam > 0000000000000060 D ti_conf_sam While Rsamtools/src/libtabix.a exists it does not contain a reference to ti_conf_sam (using the above command) or, apparently, a reference to anything else: >more Rsamtools/src/libtabix.a !<arch> > > and Rsamtools.so should be built to find it in the final line of the > compilation output below > > gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib > -Wl,-rpath=/usr/local/lib/gcc46 -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 > /usr/local/lib/R/library/Rsamtools/usrlib/libbam.a > /usr/local/lib/R/library/Rsamtools/usrlib/libbcf.a > /usr/local/lib/R/library/Rsamtools/usrlib/libtabix.a -lz > -L/usr/local/lib/R/lib -lR > > I wonder if there is a libtabix.a already under /usr/local/lib > > find /usr/local/lib -name libtabix.a There is no other libtabix anywhere in /usr. > > > Also, I do not have immediate access to gcc 4.6, which appears to be > the version you're using? The FreeBSD ports have gcc47 and gcc48 available (as well as older flavours). Bruce > > >
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@vincent-j-carey-jr-4
Last seen 15 days ago
United States
Can I suggest producing a sessionInfo() after biocLite("Rsamtools") fails? On Thu, Mar 29, 2012 at 7:22 AM, Bruce Hayward <medbha@leeds.ac.uk> wrote: > Hi, > I'm trying to install Rsamtools (Rsamtools_1.6.3) on a FreeBSD8.2 amd64 > system with R (R-2.14.2) and quite a few other Bioconductor packages > successfully running. > I'm running the installation as root btw. > The error line is (the full installation output is at the end of this > post): > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object '/usr/local/lib/R/library/** > Rsamtools/libs/Rsamtools.so': > /usr/local/lib/R/library/**Rsamtools/libs/Rsamtools.so: Undefined symbol > "ti_conf_sam" > > Following previously posted suggestions on Rsamtools installation problems > which suggests an underlying zlib.h problem > https://stat.ethz.ch/**pipermail/bioconductor/2012-**February/043348 .html<https: stat.ethz.ch="" pipermail="" bioconductor="" 2012-february="" 043348="" .html=""> > http://permalink.gmane.org/**gmane.science.biology.** > informatics.conductor/38853<http: permalink.gmane.org="" gmane.science="" .biology.informatics.conductor="" 38853=""> > > I have done > > R CMD nm Rsamtools/src/Rsamtools.so |grep ti_conf_sam > U ti_conf_sam > > and > ~/.R/Makevars > > to contain the lines > > CFLAGS += "-v" \ > -Dinline="" > > as well as (separately) adding to Rsamtools/src/Makevars.common the > suggestion in the UsingZlibbioc.pdf > PKG_CFLAGS+=$(shell echo 'zlibbioc::pkgconfig("PKG_**CFLAGS")'|\ > "${R_HOME}/bin/R" --vanilla --slave) > PKG_LIBS+=$(shell echo 'zlibbioc::pkgconfig("PKG_**LIBS_static")'|\ > "${R_HOME}/bin/R" --vanilla --slave) > > None of which has solved the problem. > If this is due to R finding an old system zlib.h (ie not the one in > /usr/include which has a 2009 datestamp) how do I go about determining that > (not being an expert on the inner workings of R)? > If it isn't a zlib.h problem .... help! > > Thanx, > Bruce Hayward > > > Installation script output: > > >R CMD INSTALL Rsamtools > processing 'Rsamtools' > a directory > * installing to library '/usr/local/lib/R/library' > * build_help_types= > * DBG: 'R CMD INSTALL' now doing do_install() > * created lock directory '/usr/local/lib/R/library/**00LOCK- Rsamtools' > * installing *source* package 'Rsamtools' ... > ** libs > about to run R CMD SHLIB -o Rsamtools.so Biostrings_stubs.c > IRanges_stubs.c R_init_Rsamtools.c as_bam.c bamfile.c bcffile.c encode.c > fafile.c io_sam.c pileupbam.c samtools_patch.c tabixfile.c utilities.c > vcffile.c zip_compression.c > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bgzf.c -o samtools/bgzf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/kstring.c -o samtools/kstring.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_aux.c -o samtools/bam_aux.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam.c -o samtools/bam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_import.c -o samtools/bam_import.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/sam.c -o samtools/sam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_index.c -o samtools/bam_index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_pileup.c -o samtools/bam_pileup.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_lpileup.c -o samtools/bam_lpileup.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_md.c -o samtools/bam_md.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/razf.c -o samtools/razf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/faidx.c -o samtools/faidx.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/knetfile.c -o samtools/knetfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_sort.c -o samtools/bam_sort.o > samtools/bam_sort.c:309:1: warning: 'bam1_lt' is static but used in inline > function '__ks_insertsort_sort' which is not static [enabled by default] > samtools/bam_sort.c:53:1: warning: 'heap_lt' is static but used in inline > function '__ks_insertsort_heap' which is not static [enabled by default] > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/sam_header.c -o samtools/sam_header.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bam_reheader.c -o samtools/bam_reheader.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/kprobaln.c -o samtools/kprobaln.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools_patch.c -o samtools_patch.o > /usr/local/bin/ar -crus libbam.a > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o > samtools/bcftools/prob1.c: In function 'mc_cal_y': > samtools/bcftools/prob1.c:340:**3: warning: implicit declaration of > function 'expl' [-Wimplicit-function-**declaration] > samtools/bcftools/prob1.c:340:**7: warning: incompatible implicit > declaration of built-in function 'expl' [enabled by default] > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/index.c -o samtools/bcftools/index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/fet.c -o samtools/bcftools/fet.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o > /usr/local/bin/ar -crus libbcf.a > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > tabix/index.c -o tabix/index.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > tabix/bedidx.c -o tabix/bedidx.o > /usr/local/bin/ar -crus libtabix.a > mkdir -p "/usr/local/lib/R/library/**Rsamtools/usretc" > cp ../Rsamtools.mk "/usr/local/lib/R/library/**Rsamtools/usretc" > mkdir -p "/usr/local/lib/R/library/**Rsamtools/include/samtools/** > bcftools" > mkdir -p "/usr/local/lib/R/library/**Rsamtools/include/tabix" > cp samtools/*.h "/usr/local/lib/R/library/**Rsamtools/include/samtools/" > cp samtools/bcftools/*h "/usr/local/lib/R/library/** > Rsamtools/include/samtools/**bcftools/" > cp tabix/*h "/usr/local/lib/R/library/**Rsamtools/include/tabix/" > mkdir -p "/usr/local/lib/R/library/**Rsamtools/usrlib" > cp libbam.a libbcf.a libtabix.a "/usr/local/lib/R/library/** > Rsamtools/usrlib" > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > Biostrings_stubs.c -o Biostrings_stubs.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > IRanges_stubs.c -o IRanges_stubs.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > R_init_Rsamtools.c -o R_init_Rsamtools.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > as_bam.c -o as_bam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > bamfile.c -o bamfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > bcffile.c -o bcffile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > encode.c -o encode.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > fafile.c -o fafile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > io_sam.c -o io_sam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > pileupbam.c -o pileupbam.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > tabixfile.c -o tabixfile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > utilities.c -o utilities.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > vcffile.c -o vcffile.o > gcc46 -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include > -I"/usr/local/lib/R/library/**Biostrings/include" > -I"/usr/local/lib/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 > -O2 -pipe -Wl,-rpath=/usr/local/lib/**gcc46 -fno-strict-aliasing -c > zip_compression.c -o zip_compression.o > zip_compression.c: In function '_zip_error': > zip_compression.c:31:5: warning: implicit declaration of function 'close' > [-Wimplicit-function-**declaration] > zip_compression.c: In function 'bgzip': > zip_compression.c:50:5: warning: implicit declaration of function 'read' > [-Wimplicit-function-**declaration] > gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib -Wl,-rpath=/usr/local/lib/ > **gcc46 -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 /usr/local/lib/R/library/**Rsamtools/usrlib/libbam.a > /usr/local/lib/R/library/**Rsamtools/usrlib/libbcf.a > /usr/local/lib/R/library/**Rsamtools/usrlib/libtabix.a -lz > -L/usr/local/lib/R/lib -lR > installing to /usr/local/lib/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 '/usr/local/lib/R/library/** > Rsamtools/libs/Rsamtools.so': > /usr/local/lib/R/library/**Rsamtools/libs/Rsamtools.so: Undefined symbol > "ti_conf_sam" > Error: loading failed > Execution halted > ERROR: loading failed > * removing '/usr/local/lib/R/library/**Rsamtools' > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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