[BioC] Problem installing Rsamtools

Thu Sep 22 19:19:15 CEST 2011

Hi Kathryn,

On 11-09-22 09:41 AM, Martin Morgan wrote:
> On 09/22/2011 09:15 AM, Kathryn Iverson wrote:
>> Hi Gord,
>> Thanks for the information, although I'm not quite sure how to proceed.
>> My understanding is I need to compile a shared library libbam and put
>> it in
>> /usr/local/lib64. Is the source for this library in Rsamtools itself?
>> I've
>> untared Rsamtools and am looking around for some kind of makefile but
>> can't
>> seem to find it. I see something in src/Makvars but there is no target
>> for
>> dylib.
>
>
> As a workaround I *think* you can edit src/Makevars.common to read
>
> PKG_LIBS += \
> $(SHLIB_OPENMP_CFLAGS) \
> -Llibbam.a -Llibbcf.a -Llibtabix.a
>
> instead of
>
> PKG_LIBS += \
> $(SHLIB_OPENMP_CFLAGS) \
> -L. -lbam -lbcf -ltabix

Alternatively, you could just uninstall the samtools that has been
compiled and installed under /usr/local/. Rsamtools contains its own
copy of the samtools source code so having an external installation
of samtools is not needed.

H.

>
> Martin
>
>>
>> Thanks again,
>> Kathryn
>>
>> On Thu, Sep 22, 2011 at 11:52 AM, Gordon Brown
>> <Gordon.Brown at cancer.org.uk>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.
>>>
>>> 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]]
>>>>
>>>
>>>
>>> NOTICE AND DISCLAIMER
>>> This e-mail (including any attachments) is intended fo...{{dropped:29}}
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319