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mhammell-laboratory / ezBAMQC

NGS data alignment file QC Package
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Trouble installing from source for v0.6.4 #5

Open olivertam opened 8 years ago

olivertam commented 8 years ago

I downloaded the source code using the link from Pypi, and tried to install using the instructions in doc/INSTALL. I am using gcc v4.8.1 and python 2.7. make on htslib gave no errors, but make on the root installation directory gave the following errors:

g++ -shared  -lpthread -O9 -fpermissive -o libBAMqc.so src/bamqc/GeneFeatures.o src/bamqc/rRNA.o src/bamqc/IntervalTree.o src/bamqc/InnerDist_prof.o src/bamqc/Results.o src/bamqc/Mappability.o src/bamqc/Coverage_prof.o src/bamqc/parseBAM.o ./src/htslib/libhts.a  -lz -lm
/home/tam/bin/ld: ./src/htslib/libhts.a(hts.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
./src/htslib/libhts.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [libBAMqc.so] Error 1

This appears to ask for a recompile. Is it an error while compiling htslib, or some configuration issue (e.g. multiple gcc in PATH) that is causing confusion?

molikd commented 8 years ago 
[PROD] 08:15:13 dmolik@bsr02.cshl {~/bamqc}(master)[]$  python2.7 setup.py build
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'dependency_links'
  warnings.warn(msg)
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
  warnings.warn(msg)
/usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'
  warnings.warn(msg)
running build
running build_ext
building 'htslib' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/htslib
creating build/temp.linux-x86_64-2.7/src/htslib/cram
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/bgzf.c -o build/temp.linux-x86_64-2.7/src/htslib/bgzf.o -Wno-error=declaration-after-statement
src/htslib/bgzf.c: In function ‘bgzf_index_dump’:
src/htslib/bgzf.c:996:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
         fwrite(ed_swap_8p(&x), 1, sizeof(x), idx);
         ^
src/htslib/bgzf.c:999:41: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
             x = fp->idx->offs[i].caddr; fwrite(ed_swap_8p(&x), 1, sizeof(x), idx);
                                         ^
src/htslib/bgzf.c:1000:41: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
             x = fp->idx->offs[i].uaddr; fwrite(ed_swap_8p(&x), 1, sizeof(x), idx);
                                         ^
src/htslib/bgzf.c:1006:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
         fwrite(&x, 1, sizeof(x), idx);
         ^
src/htslib/bgzf.c:1009:13: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
             fwrite(&fp->idx->offs[i].caddr, 1, sizeof(fp->idx->offs[i].caddr), idx);
             ^
src/htslib/bgzf.c:1010:13: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
             fwrite(&fp->idx->offs[i].uaddr, 1, sizeof(fp->idx->offs[i].uaddr), idx);
             ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/faidx.c -o build/temp.linux-x86_64-2.7/src/htslib/faidx.o -Wno-error=declaration-after-statement
src/htslib/faidx.c: In function ‘download_and_open’:
src/htslib/faidx.c:270:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
         fwrite(buf, 1, l, fp);
         ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/hfile.c -o build/temp.linux-x86_64-2.7/src/htslib/hfile.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/src/htslib/hfile_net.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/hts.c -o build/temp.linux-x86_64-2.7/src/htslib/hts.o -Wno-error=declaration-after-statement
src/htslib/hts.c: In function ‘hts_idx_save’:
src/htslib/hts.c:1152:9: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
         fwrite("BAI\1", 1, 4, fp);
         ^
src/htslib/hts.c: In function ‘test_and_fetch’:
src/htslib/hts.c:1612:59: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result [-Wunused-result]
         while ((l = hread(fp_remote, buf, buf_size)) > 0) fwrite(buf, 1, l, fp);
                                                           ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/kfunc.c -o build/temp.linux-x86_64-2.7/src/htslib/kfunc.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/knetfile.c -o build/temp.linux-x86_64-2.7/src/htslib/knetfile.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/kstring.c -o build/temp.linux-x86_64-2.7/src/htslib/kstring.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/regidx.c -o build/temp.linux-x86_64-2.7/src/htslib/regidx.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/sam.c -o build/temp.linux-x86_64-2.7/src/htslib/sam.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/src/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/tbx.c -o build/temp.linux-x86_64-2.7/src/htslib/tbx.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/vcf.c -o build/temp.linux-x86_64-2.7/src/htslib/vcf.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/src/htslib/vcfutils.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement
src/htslib/cram/cram_encode.c: In function ‘process_one_read’:
src/htslib/cram/cram_encode.c:2463:10: warning: unused variable ‘brg’ [-Wunused-variable]
  SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN");
          ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_index.o -Wno-error=declaration-after-statement
src/htslib/cram/cram_index.c: In function ‘cram_index_build’:
src/htslib/cram/cram_index.c:483:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable]
     off_t cpos, spos, hpos;
                       ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_io.o -Wno-error=declaration-after-statement
src/htslib/cram/cram_io.c: In function ‘cram_uncompress_block’:
src/htslib/cram/cram_io.c:969:15: warning: unused variable ‘usize’ [-Wunused-variable]
  unsigned int usize = b->uncomp_size, usize2;
               ^
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/files.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/files.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/mFILE.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/md5.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/rANS_static.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/rANS_static.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/sam_header.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/vlen.o -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/src/htslib/cram/zfio.o -Wno-error=declaration-after-statement
creating build/lib.linux-x86_64-2.7
gcc -pthread -shared build/temp.linux-x86_64-2.7/src/htslib/bgzf.o build/temp.linux-x86_64-2.7/src/htslib/faidx.o build/temp.linux-x86_64-2.7/src/htslib/hfile.o build/temp.linux-x86_64-2.7/src/htslib/hfile_net.o build/temp.linux-x86_64-2.7/src/htslib/hts.o build/temp.linux-x86_64-2.7/src/htslib/kfunc.o build/temp.linux-x86_64-2.7/src/htslib/knetfile.o build/temp.linux-x86_64-2.7/src/htslib/kstring.o build/temp.linux-x86_64-2.7/src/htslib/regidx.o build/temp.linux-x86_64-2.7/src/htslib/sam.o build/temp.linux-x86_64-2.7/src/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/src/htslib/tbx.o build/temp.linux-x86_64-2.7/src/htslib/vcf.o build/temp.linux-x86_64-2.7/src/htslib/vcfutils.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/src/htslib/cram/cram_stats.o build/temp.linux-x86_64-2.7/src/htslib/cram/files.o build/temp.linux-x86_64-2.7/src/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/src/htslib/cram/md5.o build/temp.linux-x86_64-2.7/src/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/src/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/src/htslib/cram/rANS_static.o build/temp.linux-x86_64-2.7/src/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/src/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/src/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/src/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/src/htslib/cram/zfio.o -L/usr/lib64 -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/htslib.so
building 'libBAMqc' extension
creating build/temp.linux-x86_64-2.7/src/bamqc
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/Coverage_prof.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/Coverage_prof.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/GeneFeatures.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/GeneFeatures.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/InnerDist_prof.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/InnerDist_prof.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/IntervalTree.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/IntervalTree.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/Mappability.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/Mappability.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/parseBAM.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/parseBAM.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/ReadDup_prof.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/ReadDup_prof.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/Results.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/Results.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE= -D_CURSES_LIB=1 -I./src/bamqc -I./src/htslib -I./src/htslib/htslib -I./src/htslib/cram -I/usr/include/python2.7 -c src/bamqc/rRNA.cpp -o build/temp.linux-x86_64-2.7/src/bamqc/rRNA.o -fpermissive -O3 -std=c++11 -Wno-error=declaration-after-statement
g++ -pthread -shared build/temp.linux-x86_64-2.7/src/bamqc/Coverage_prof.o build/temp.linux-x86_64-2.7/src/bamqc/GeneFeatures.o build/temp.linux-x86_64-2.7/src/bamqc/InnerDist_prof.o build/temp.linux-x86_64-2.7/src/bamqc/IntervalTree.o build/temp.linux-x86_64-2.7/src/bamqc/Mappability.o build/temp.linux-x86_64-2.7/src/bamqc/parseBAM.o build/temp.linux-x86_64-2.7/src/bamqc/ReadDup_prof.o build/temp.linux-x86_64-2.7/src/bamqc/Results.o build/temp.linux-x86_64-2.7/src/bamqc/rRNA.o build/lib.linux-x86_64-2.7/htslib.so -L/usr/lib64 -lpython2.7 -o build/lib.linux-x86_64-2.7/libBAMqc.so
running build_scripts
creating build/scripts-2.7
copying and adjusting BAMqc -> build/scripts-2.7
changing mode of build/scripts-2.7/BAMqc from 644 to 755
[PROD] 08:16:01 dmolik@bsr02.cshl {~/bamqc}(master)[1]$  gcc --version
gcc (GCC) 4.9.2 20150212 (Red Hat 4.9.2-6)
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[PROD] 08:16:40 dmolik@bsr02.cshl {~/bamqc}(master)[1]$  python2.7 --version
Python 2.7.10

I am able to build using setup.py's provisions and gcc 4.9.1and python 2.7.10

molikd commented 8 years ago

I was also able to build on the gcc 4.9.1/python 2.7.10 box via pypi:

[PROD] 08:21:40 dmolik@bsr02.cshl {/usr/lib64/python2.7/site-packages}$  sudo pip2.7 install --upgrade BAMqc
Collecting BAMqc
  Downloading BAMQC-0.6.4.tar.gz (402kB)
    100% |████████████████████████████████| 405kB 843kB/s 
Building wheels for collected packages: BAMqc
  Running setup.py bdist_wheel for BAMqc
  Stored in directory: /root/.cache/pip/wheels/a8/25/13/e2fd374238d097dd5ed6c238ae939fd2ba07a7aac996f93084
Successfully built BAMqc
Installing collected packages: BAMqc
  Found existing installation: BAMQC 0.6.0
    Uninstalling BAMQC-0.6.0:
      Successfully uninstalled BAMQC-0.6.0
Successfully installed BAMqc-0.6.4
[PROD] 08:22:31 dmolik@bsr02.cshl {/usr/lib64/python2.7/site-packages}$  ls
backports  BAMQC-0.6.4.dist-info  htslib.so  libBAMqc.so  lxml  lxml-3.5.0-py2.7.egg-info  psutil  psutil-3.2.2-py2.7.egg-info  pynche  README