[BioC] Problem installing Rsamtools
Martin Morgan
mtmorgan at fhcrc.org
Thu Sep 22 18:04:09 CEST 2011
On 09/22/2011 08:52 AM, Gordon Brown wrote:
> Hi, Kathryn,
>
> Your copy of libbam (libbam.a) is a static library, not a shared library
> (and you can't, in general, link to a static library when trying to make a
> shared library). If you compile the shared version of libbam ("make dylib"
> in the samtools package will create "libbam.so.1"), and put it in
> /usr/local/lib64, Rsamtools should find that instead and use it.
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so
> Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o
> bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L.
-lbam
> -lbcf -lz -L/usr/lib64/R/lib -lR
> /usr/bin/ld: /usr/local/lib64/libbam.a(bgzf.o): relocation R_X86_64_32
The idea here was to pick up the libbam and libbcf built in the
Rsamtools package, rather than a system installation. I'll work on the
configure script to make this happen more reliably. Martin
>
> Hope this helps.
>
> Cheers,
>
> - Gord
>
>
> On 2011/09/22 16:36, "Kathryn Iverson"<kiverson at umich.edu> wrote:
>
>> Hi everyone,
>> I'm trying to install Rsamtools and I'm getting a compilation error. Please
>> see the transcript below for the error (at the very bottom) and the
>> sessionInfo() output. Thank you in advance.
>>
>>
>>> source("http://bioconductor.org/biocLite.R")
>> BioC_mirror = http://bioconductor.org
>> Change using chooseBioCmirror().
>>> biocLite("Rsamtools")
>> Using R version 2.13.1, biocinstall version 2.8.4.
>> Installing Bioconductor version 2.8 packages:
>> [1] "Rsamtools"
>> Please wait...
>>
>> Installing package(s) into
>> Œ/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13¹
>> (as Œlib¹ is unspecified)
>> trying URL '
>> http://bioconductor.org/packages/2.8/bioc/src/contrib/Rsamtools_1.4.3.tar.gz
>> '
>> Content type 'application/x-gzip' length 2074383 bytes (2.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 2.0 Mb
>>
>> * installing *source* package ŒRsamtools¹ ...
>> checking for gcc... gcc
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc accepts -g... yes
>> checking for gcc option to accept ISO C89... none needed
>> checking for gzeof in -lz... yes
>> checking for bzero... yes
>> checking for memset... yes
>> checking for pow... no
>> checking for sqrt... no
>> checking for strcasecmp... yes
>> checking for strdup... yes
>> checking for strstr... yes
>> checking for strtol... yes
>> checking how to run the C preprocessor... gcc -E
>> checking for grep that handles long lines and -e... /bin/grep
>> checking for egrep... /bin/grep -E
>> checking for ANSI C header files... yes
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking zlib.h usability... yes
>> checking zlib.h presence... yes
>> checking for zlib.h... yes
>> checking fcntl.h usability... yes
>> checking fcntl.h presence... yes
>> checking for fcntl.h... yes
>> checking malloc.h usability... yes
>> checking malloc.h presence... yes
>> checking for malloc.h... yes
>> checking stddef.h usability... yes
>> checking stddef.h presence... yes
>> checking for stddef.h... yes
>> checking for ptrdiff_t... yes
>> checking for an ANSI C-conforming const... yes
>> checking for inline... inline
>> checking for _LARGEFILE_SOURCE value needed for large files... no
>> checking for stdlib.h... (cached) yes
>> checking for GNU libc compatible malloc... yes
>> checking for working memcmp... yes
>> checking for stdlib.h... (cached) yes
>> checking for GNU libc compatible realloc... yes
>> checking for stdbool.h that conforms to C99... yes
>> checking for _Bool... yes
>> checking for off_t... yes
>> checking for size_t... yes
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> config.status: creating src/Rsamtools.mk
>> ** libs
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c Biostrings_stubs.c -o Biostrings_stubs.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c IRanges_stubs.c -o IRanges_stubs.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c R_init_Rsamtools.c -o R_init_Rsamtools.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c as_bam.c -o as_bam.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c bamfile.c -o bamfile.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c bcffile.c -o bcffile.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c encode.c -o encode.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c fafile.c -o fafile.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c io_sam.c -o io_sam.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools_patch.c -o samtools_patch.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c utilities.c -o utilities.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bgzf.c -o samtools/bgzf.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/kstring.c -o samtools/kstring.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_aux.c -o samtools/bam_aux.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam.c -o samtools/bam.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_import.c -o samtools/bam_import.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/sam.c -o samtools/sam.o
>> samtools/sam.c: In function Œsamopen¹:
>> samtools/sam.c:96: warning: ignoring return value of Œfwrite¹, declared with
>> attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_index.c -o samtools/bam_index.o
>> samtools/bam_index.c: In function Œbam_index_save¹:
>> samtools/bam_index.c:258: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:261: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:262: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:270: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:271: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:277: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:278: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:283: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:289: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:290: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:291: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:298: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:299: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:304: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:307: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:312: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c: In function Œbam_index_load_core¹:
>> samtools/bam_index.c:326: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:333: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:346: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:349: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:353: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:357: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:367: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c:371: warning: ignoring return value of Œfread¹,
>> declared with attribute warn_unused_result
>> samtools/bam_index.c: In function Œdownload_from_remote¹:
>> samtools/bam_index.c:437: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_pileup.c -o samtools/bam_pileup.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_md.c -o samtools/bam_md.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/glf.c -o samtools/glf.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/razf.c -o samtools/razf.o
>> samtools/razf.c: In function Œsave_zindex¹:
>> samtools/razf.c:96: warning: ignoring return value of Œwrite¹, declared with
>> attribute warn_unused_result
>> samtools/razf.c:99: warning: ignoring return value of Œwrite¹, declared with
>> attribute warn_unused_result
>> samtools/razf.c:106: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c:107: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c: In function Œ_razf_write¹:
>> samtools/razf.c:201: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c: In function Œrazf_flush¹:
>> samtools/razf.c:221: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c:234: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c: In function Œrazf_end_flush¹:
>> samtools/razf.c:258: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c: In function Œrazf_close¹:
>> samtools/razf.c:807: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c:808: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c:811: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/razf.c:813: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/faidx.c -o samtools/faidx.o
>> samtools/faidx.c: In function Œdownload_and_open¹:
>> samtools/faidx.c:252: warning: ignoring return value of Œfwrite¹, declared
>> with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/knetfile.c -o samtools/knetfile.o
>> samtools/knetfile.c: In function Œkftp_send_cmd¹:
>> samtools/knetfile.c:236: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> samtools/knetfile.c: In function Œkhttp_connect_file¹:
>> samtools/knetfile.c:415: warning: ignoring return value of Œwrite¹, declared
>> with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_sort.c -o samtools/bam_sort.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/sam_header.c -o samtools/sam_header.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bam_reheader.c -o samtools/bam_reheader.o
>> samtools/bam_reheader.c: In function Œbam_reheader¹:
>> samtools/bam_reheader.c:25: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/kprobaln.c -o samtools/kprobaln.o
>> ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o
>> samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o
>> samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o
>> samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o
>> samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o
>> samtools/kprobaln.o samtools_patch.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
>> samtools/bcftools/vcf.c: In function Œvcf_hdr_write¹:
>> samtools/bcftools/vcf.c:128: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> samtools/bcftools/vcf.c: In function Œvcf_write¹:
>> samtools/bcftools/vcf.c:144: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/index.c -o samtools/bcftools/index.o
>> samtools/bcftools/index.c: In function Œdownload_from_remote¹:
>> samtools/bcftools/index.c:195: warning: ignoring return value of Œfwrite¹,
>> declared with attribute warn_unused_result
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
>> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Biostrings/include"
>> -I"/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/IRanges/include"
>> -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf
>> -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools
>> -I./samtools/bcftools -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
>> ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o
>> samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o
>> samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o
>> samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
>> mkdir -p
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usretc
>> cp Rsamtools.mk
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usretc
>> mkdir -p
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/include/samtoo
>> ls/bcftools
>> cp samtools/*.h
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/include/samtoo
>> ls/
>> cp samtools/bcftools/*h
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/include/samtoo
>> ls/bcftools/
>> mkdir -p
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usrlib
>> cp libbam.a libbcf.a
>> /home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools/usrlib
>> gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so
>> Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o
>> bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam
>> -lbcf -lz -L/usr/lib64/R/lib -lR
>> /usr/bin/ld: /usr/local/lib64/libbam.a(bgzf.o): relocation R_X86_64_32
>> against `a local symbol' can not be used when making a shared object;
>> recompile with -fPIC
>> /usr/local/lib64/libbam.a: could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> make: *** [Rsamtools.so] Error 1
>> ERROR: compilation failed for package ŒRsamtools¹
>> * removing Œ/home/kiverson/R/x86_64-redhat-linux-gnu-library/2.13/Rsamtools¹
>>
>> The downloaded packages are in
>> Œ/tmp/Rtmpc9YtaR/downloaded_packages¹
>> Warning message:
>> In install.packages(pkgs = pkgs, repos = repos, ...) :
>> installation of package 'Rsamtools' had non-zero exit status
>>
>>
>>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.13.1
>>
>>
>>
>> Thank you very much for your help,
>> Kathryn
>>
>> --
>> Kathryn Iverson, MS Bioinformatics
>> kiverson at umich.edu
>> www.kathryniverson.com
>> University of Michigan | Department of Microbiology and Immunology
>> University of Michigan | Center for Computational Medicine and Biology
>>
>> [[alternative HTML version deleted]]
>>
>
>
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