[BioC] Problem installing Rsamtools
Gordon Brown
Gordon.Brown at cancer.org.uk
Thu Sep 22 17:52:53 CEST 2011
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.
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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