[BioC] Rsamtools installation

[Martin Morgan]

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.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!

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'
>
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