[BioC] Rsamtools installation

Bruce Hayward medbha at leeds.ac.uk
Thu Mar 29 13:22:34 CEST 2012


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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