Hi Martin,
I was able to successfully install Rsamtools with "R CMD INSTALL Rsamtools"
after changing Makevars.common. I was also able to install the ShortRead
package (dependent on Rsamtools) so everything seems to be in order. Thanks
again everyone for all your help and patience.

Best,
Kathryn

On Thu, Sep 22, 2011 at 1:02 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 09/22/2011 09:51 AM, Kathryn Iverson wrote:
>
>> Hi Martin,
>> I don't seem to have
>>
>>    PKG_LIBS += \
>>      $(SHLIB_OPENMP_CFLAGS) \
>>      -L. -lbam -lbcf -ltabix
>>
>>
>> in any of the Makevars files. The copy of Rsamtools I grabbed is from
>> bioconductor here [0]. See below for the contents of Makevars*
>>
>> [0] http://www.bioconductor.org/**packages/devel/bioc/html/**
>> Rsamtools.html<http://www.bioconductor.org/packages/devel/bioc/html/Rsamtools.html>
>>
>
> Hi Kathryn
>
> Several confusions, some on my part. You're using the release version of R,
> so you need the release version of Rsamtools
>
> http://www.bioconductor.org/**packages/release/bioc/html/**Rsamtools.html<http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html>
>
> then in that file there is a Makevars.common, but the change required is
>
> PKG_LIBS += ./libbam.a ./libbcf.a
>
> instead of
>
> PKG_LIBS += -L. -lbam -lbcf
>
> Please let me know if this is on the right track.
>
> Martin
>
>  Thanks,
>> Kathryn
>>
>> [kiverson@axiom src]$ more Makevars.common
>> PKG_OBJECTS = \
>>   io_sam.o utilities.o encode.o \
>>   Biostrings_stubs.o IRanges_stubs.o \
>>   R_init_Rsamtools.o
>> SAMTOOLS_OBJECTS = \
>>   bam.o bam_import.o bam_index.o kstring.o bam_aux.o \
>>   sam_header.o \
>>   bgzf.o razf.o \
>>   knetfile.o \
>>   sam.o bam_pileup.o faidx.o
>> # these flags are for SAMTOOLS; -Dinline="" turns off inlining, which
>> # is leads to undefined symbols for gcc -O0
>> DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64
>> PKG_CFLAGS += $(DFLAGS)
>>
>>
>> [kiverson@axiom src]$ more Makevars.in
>> PKG_LIBS+=@LIBS@
>> include Makevars.common
>> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%)
>>
>> all: $(SHLIB)
>>
>> clean:
>> rm -f $(OBJECTS)
>>
>>
>> [kiverson@axiom src]$ more Makevars.win
>> PKG_LIBS+=$(ZLIB_LIBS) -lws2_32
>> include Makevars.common
>> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%)
>>
>> all: $(SHLIB)
>>
>> clean:
>> rm -f $(OBJECTS)
>>
>>
>> [kiverson@axiom src]$ more Makevars
>> PKG_LIBS+=-lz
>> include Makevars.common
>> OBJECTS = $(PKG_OBJECTS) $(SAMTOOLS_OBJECTS:%=samtools/**%)
>>
>> all: $(SHLIB)
>>
>> clean:
>> rm -f $(OBJECTS)
>> [kiverson@axiom src]$
>>
>>    Martin
>>
>>
>>        Thanks again,
>>        Kathryn
>>
>>        On Thu, Sep 22, 2011 at 11:52 AM, Gordon Brown
>>        <Gordon.Brown@cancer.org.uk
>>        <mailto:Gordon.Brown@cancer.**org.uk <Gordon.Brown@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@umich.edu
>>            <mailto:kiverson@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
>>                    <http://bioconductor.org/**biocLite.R<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
>>                Ś/home/kiverson/R/x86_64-__**
>> redhat-linux-gnu-library/2.13ą
>>                (as Ślibą is unspecified)
>>                trying URL '
>>
>>            http://bioconductor.org/__**packages/2.8/bioc/src/contrib/**
>> __Rsamtools_1.4.3.tar.gz<http://bioconductor.org/__packages/2.8/bioc/src/contrib/__Rsamtools_1.4.3.tar.gz>
>>            <http://bioconductor.org/**packages/2.8/bioc/src/contrib/**
>> Rsamtools_1.4.3.tar.gz<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 ŚRsamtoolsą ...
>>                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 Śsamopeną:
>>                samtools/sam.c:96: warning: ignoring return value of
>>                Śfwriteą, 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 Śbam_index_saveą:
>>                samtools/bam_index.c:258: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:261: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:262: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:270: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:271: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:277: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:278: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:283: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:289: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:290: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:291: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:298: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:299: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:304: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:307: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:312: warning: ignoring return value
>>                of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c: In function Śbam_index_load_coreą:
>>                samtools/bam_index.c:326: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:333: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:346: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:349: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:353: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:357: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:367: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c:371: warning: ignoring return value
>>                of Śfreadą,
>>                declared with attribute warn_unused_result
>>                samtools/bam_index.c: In function Śdownload_from_remoteą:
>>                samtools/bam_index.c:437: warning: ignoring return value
>>                of Śfwriteą,
>>                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 Śsave_zindexą:
>>                samtools/razf.c:96: warning: ignoring return value of
>>                Śwriteą, declared
>>
>>            with
>>
>>                attribute warn_unused_result
>>                samtools/razf.c:99: warning: ignoring return value of
>>                Śwriteą, declared
>>
>>            with
>>
>>                attribute warn_unused_result
>>                samtools/razf.c:106: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c:107: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c: In function Ś_razf_writeą:
>>                samtools/razf.c:201: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c: In function Śrazf_flushą:
>>                samtools/razf.c:221: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c:234: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c: In function Śrazf_end_flushą:
>>                samtools/razf.c:258: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c: In function Śrazf_closeą:
>>                samtools/razf.c:807: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c:808: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c:811: warning: ignoring return value of
>>                Śwriteą, declared
>>                with attribute warn_unused_result
>>                samtools/razf.c:813: warning: ignoring return value of
>>                Śwriteą, 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 Śdownload_and_openą:
>>                samtools/faidx.c:252: warning: ignoring return value of
>>                Śfwriteą,
>>
>>            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 Śkftp_send_cmdą:
>>                samtools/knetfile.c:236: warning: ignoring return value
>>                of Śwriteą,
>>
>>            declared
>>
>>                with attribute warn_unused_result
>>                samtools/knetfile.c: In function Śkhttp_connect_fileą:
>>                samtools/knetfile.c:415: warning: ignoring return value
>>                of Śwriteą,
>>
>>            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 Śbam_reheaderą:
>>                samtools/bam_reheader.c:25: warning: ignoring return
>>                value of Śfwriteą,
>>                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 Śvcf_hdr_writeą:
>>                samtools/bcftools/vcf.c:128: warning: ignoring return
>>                value of Śfwriteą,
>>                declared with attribute warn_unused_result
>>                samtools/bcftools/vcf.c: In function Śvcf_writeą:
>>                samtools/bcftools/vcf.c:144: warning: ignoring return
>>                value of Śfwriteą,
>>                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
>>                Śdownload_from_remoteą:
>>                samtools/bcftools/index.c:195: warning: ignoring return
>>                value of
>>
>>            Śfwriteą,
>>
>>                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 ŚRsamtoolsą
>>                * removing
>>
>>            Ś/home/kiverson/R/x86_64-__**redhat-linux-gnu-library/2.13/**
>> __Rsamtoolsą
>>
>>
>>                The downloaded packages are in
>>                Ś/tmp/Rtmpc9YtaR/downloaded___**packagesą
>>                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@umich.edu <mailto:kiverson@umich.edu>
>>                www.kathryniverson.com <http://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@r-project.org <mailto:Bioconductor@r-**project.org<Bioconductor@r-project.org>
>> >
>>
>>        https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https://stat.ethz.ch/mailman/__listinfo/bioconductor>
>>        <https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> >
>>        Search the archives:
>>        http://news.gmane.org/gmane.__**science.biology.informatics.__**
>> conductor<http://news.gmane.org/gmane.__science.biology.informatics.__conductor>
>>        <http://news.gmane.org/gmane.**science.biology.informatics.**
>> conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>> >
>>
>>
>>
>>    --
>>    Computational Biology
>>    Fred Hutchinson Cancer Research Center
>>    1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>>    Location: M1-B861
>>    Telephone: 206 667-2793 <tel:206%20667-2793>
>>
>>
>>
>>
>> --
>> Kathryn Iverson, MS Bioinformatics
>> kiverson@umich.edu <mailto:kiverson@umich.edu>
>> www.kathryniverson.com <http://www.kathryniverson.**com/<http://www.kathryniverson.com/>
>> >
>>
>> University of Michigan | Department of Microbiology and Immunology
>> University of Michigan | Center for Computational Medicine and Biology
>>
>>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>



-- 
Kathryn Iverson, MS Bioinformatics
kiverson@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]]

