failed to install pysam shown below

[andy123]

Could any one help me why pysam installation failure ?



[root@localhost pysam-0.4.1]# python setup.py build
running build
running build_py
running build_ext
skipping 'pysam/csamtools.c' Cython extension (up-to-date)
building 'csamtools' extension
gcc -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -g -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.6/pysam/csamtools.o
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_fetch’:
pysam/csamtools.c:7771: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:613: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_mate’:
pysam/csamtools.c:8168: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:613: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_count’:
pysam/csamtools.c:8685: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:613: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_pileup’:
pysam/csamtools.c:9146: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:613: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_f_9csamtools_13SNPCallerBase___dump’:
pysam/csamtools.c:25100: error: format not a string literal and no format arguments
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_15IndelCallerBase__call’:
pysam/csamtools.c:27457: warning: assignment discards qualifiers from pointer target type
error: command 'gcc' failed with exit status 1
[root@localhost pysam-0.4.1]#

[asangqi]

may be you should update your Cython extension vesion.

[andy123]

Thanks, but I already got Cython is 0.14.1 installed

[kadoo]

Hello,

I am also getting similar error compiling pysam.
I have:
Mandriva Linux 2010.2 (64 bit)
samtools-0.1.14
cython 0.12.1
zlib 1.2.3
gcc 4.4.3

Executing "python setup.py build" as root throws the following error
-------------------------------
running build
running build_py
warning: build_py: byte-compiling is disabled, skipping.
running build_ext
building 'csamtools' extension
gcc -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wformat -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector --param=ssp-buffer-size=4 -g -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.6/pysam/csamtools.o
pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_fetch':
pysam/csamtools.c:7771: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
samtools/bam.h:615: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_mate':
pysam/csamtools.c:8168: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
samtools/bam.h:615: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_count':
pysam/csamtools.c:8685: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
samtools/bam.h:615: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
pysam/csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_pileup':
pysam/csamtools.c:9146: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
samtools/bam.h:615: note: expected 'bam_fetch_f' but argument is of type 'int (*)(struct bam1_t *, void *)'
pysam/csamtools.c: In function '__pyx_f_9csamtools_13SNPCallerBase___dump':
pysam/csamtools.c:25100: error: format not a string literal and no format arguments
pysam/csamtools.c: In function '__pyx_pf_9csamtools_15IndelCallerBase__call':
pysam/csamtools.c:27457: warning: assignment discards qualifiers from pointer target type
error: command 'gcc' failed with exit status 1
-------------------------------

Thanks