[BioC] Problem installing Rsamtools
Martin Morgan
mtmorgan at fhcrc.org
Thu Sep 22 18:41:15 CEST 2011
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
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}}
>
>
>
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