command 'gcc' failed with exit status 1 for installation of ngcgh

Question

I am getting gcc failed error while installing ngch : https://github.com/seandavi/ngCGH it gives same error while easy_install as well and I am using windows.

Running pysam-0.7.4\setup.py -q bdist_egg --dist-dir c:\users\sam\appdata\lo
cal\temp\easy_install-ilqggk\pysam-0.7.4\egg-dist-tmp-rolwff
In file included from pysam\csamtools.c:241:
samtools/razf.h:38:18: error: zlib.h: No such file or directory
In file included from pysam\csamtools.c:241:
samtools/razf.h:91: error: expected specifier-qualifier-list before 'z_stream'
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_10fetch':
pysam\csamtools.c:9814: warning: passing argument 7 of 'bam_fetch' from incompatible  
pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_11mate':
pysam\csamtools.c:10254: warning: passing argument 7 of 'bam_fetch' from incompa
tible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_12count':
pysam\csamtools.c:10730: warning: passing argument 7 of 'bam_fetch' from incompa
tible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_13pileup':
pysam\csamtools.c:11148: warning: passing argument 7 of 'bam_fetch' from incompa
tible pointer type
pysam\csamtools.c: In function '__pyx_f_9csamtools___advance_snpcalls':
pysam\csamtools.c:17424: warning: implicit declaration of function 'bam_prob_rea
ln'
pysam\csamtools.c:17452: warning: implicit declaration of function 'bam_cap_mapQ
'
pysam\csamtools.c: In function '__pyx_pf_9csamtools_20IteratorColumnRegion_1__ne
xt__':
pysam\csamtools.c:18907: warning: passing argument 1 of '__pyx_f_9csamtools_make
PileupProxy' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__n
ext__':
pysam\csamtools.c:19134: warning: passing argument 1 of '__pyx_f_9csamtools_make
PileupProxy' from incompatible pointer type
pysam\csamtools.c: In function '__Pyx_InitGlobals':
pysam\csamtools.c:38587: warning: this decimal constant is unsigned only in ISO
C90
error: Setup script exited with error: command 'gcc' failed with exit status 1

can anyone let me know how can I get over this error?

Answer 1

It's most likely pysam that fails to compile due to missing zlib-dev. Try installing it before ie in Ubuntu I did: sudo apt-get install zlib1g-dev

for fedora you can try:
yum install zlib-devel

I don't know about windows though...