GitLab

hzs@lh:~/bin/org-asm-master$ chmod u+x setup.py hzs@lh:~/bin/org-asm-master$ python3 setup.py --serenity install ['/home/hzs/bin/org-asm-master', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/home/hzs/.local/lib/python3.4/site-packages', '/usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages', '/home/hzs/bin/org-asm-master/distutils.ext', '/home/hzs/bin/org-asm-master/python'] Installing ORG.asm (0.2.03) in serenity mode You are running the good python Restarting installation within the ORG.asm-0.2.03 virtualenv Install script restarting... ['/home/hzs/bin/org-asm-master', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/lib/python3.4/site-packages', '/home/hzs/bin/org-asm-master/distutils.ext', '/home/hzs/bin/org-asm-master/python'] Collecting pip Downloading pip-8.1.1-py2.py3-none-any.whl (1.2MB) 100% |████████████████████████████████| 1.2MB 929kB/s Collecting setuptools Downloading setuptools-20.10.1-py2.py3-none-any.whl (509kB) 100% |████████████████████████████████| 512kB 381kB/s Collecting wheel Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB) 100% |████████████████████████████████| 71kB 6.8MB/s Installing collected packages: pip, setuptools, wheel Successfully installed pip-8.1.1 setuptools-20.10.1 wheel-0.29.0 ['/home/hzs/bin/org-asm-master', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/lib/python3.4/site-packages', '/home/hzs/bin/org-asm-master/distutils.ext', '/home/hzs/bin/org-asm-master/python'] Installing ORG.asm (0.2.03) in serenity mode You are running the good python ORG.asm will be installed with python : /home/hzs/bin/org-asm-master/ORG.asm-0.2.03/bin/python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (==0.23.5) : not installed Installing requirement : Cython==0.23.5 Collecting Cython==0.23.5 Downloading Cython-0.23.5-cp34-cp34m-manylinux1_x86_64.whl (6.4MB) 100% |████████████████████████████████| 6.4MB 267kB/s Installing collected packages: Cython Successfully installed Cython-0.23.5 Look for package Sphinx (>=1.3) : not installed Installing requirement : Sphinx>=1.3 Collecting Sphinx>=1.3 Downloading Sphinx-1.4.1-py2.py3-none-any.whl (1.6MB) 100% |████████████████████████████████| 1.6MB 118kB/s Collecting babel!=2.0,>=1.3 (from Sphinx>=1.3) Downloading Babel-2.3.4-py2.py3-none-any.whl (7.1MB) 100% |████████████████████████████████| 7.1MB 244kB/s Collecting six>=1.4 (from Sphinx>=1.3) Downloading six-1.10.0-py2.py3-none-any.whl Collecting Pygments>=2.0 (from Sphinx>=1.3) Downloading Pygments-2.1.3-py2.py3-none-any.whl (755kB) 100% |████████████████████████████████| 757kB 312kB/s Collecting imagesize (from Sphinx>=1.3) Downloading imagesize-0.7.1-py2.py3-none-any.whl Collecting docutils>=0.11 (from Sphinx>=1.3) Downloading docutils-0.12-py3-none-any.whl (508kB) 100% |████████████████████████████████| 512kB 1.8MB/s Collecting Jinja2>=2.3 (from Sphinx>=1.3) Downloading Jinja2-2.8-py2.py3-none-any.whl (263kB) 100% |████████████████████████████████| 266kB 3.8MB/s Collecting alabaster<0.8,>=0.7 (from Sphinx>=1.3) Downloading alabaster-0.7.7-py2.py3-none-any.whl Collecting snowballstemmer>=1.1 (from Sphinx>=1.3) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB) 100% |████████████████████████████████| 71kB 6.5MB/s Collecting pytz>=0a (from babel!=2.0,>=1.3->Sphinx>=1.3) Downloading pytz-2016.4-py2.py3-none-any.whl (480kB) 100% |████████████████████████████████| 481kB 340kB/s Collecting MarkupSafe (from Jinja2>=2.3->Sphinx>=1.3) Downloading MarkupSafe-0.23.tar.gz Building wheels for collected packages: MarkupSafe Running setup.py bdist_wheel for MarkupSafe ... done Stored in directory: /home/hzs/.cache/pip/wheels/a3/fa/dc/0198eed9ad95489b8a4f45d14dd5d2aee3f8984e46862c5748 Successfully built MarkupSafe Installing collected packages: pytz, babel, six, Pygments, imagesize, docutils, MarkupSafe, Jinja2, alabaster, snowballstemmer, Sphinx Successfully installed Jinja2-2.8 MarkupSafe-0.23 Pygments-2.1.3 Sphinx-1.4.1 alabaster-0.7.7 babel-2.3.4 docutils-0.12 imagesize-0.7.1 pytz-2016.4 six-1.10.0 snowballstemmer-1.2.1 Restarting installation with all dependencies ok Install script restarting... ['/home/hzs/bin/org-asm-master', '/usr/lib/python3.4', '/usr/lib/python3.4/plat-x86_64-linux-gnu', '/usr/lib/python3.4/lib-dynload', '/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/lib/python3.4/site-packages', '/home/hzs/bin/org-asm-master/distutils.ext', '/home/hzs/bin/org-asm-master/python'] Installing ORG.asm (0.2.03) in serenity mode You are running the good python ORG.asm will be installed with python : /home/hzs/bin/org-asm-master/ORG.asm-0.2.03/bin/python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (==0.23.5) : ok version 0.23.5 installed Look for package Sphinx (>=1.3) : ok version 1.4.1 installed You are running the good python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (==0.23.5) : ok version 0.23.5 installed Look for package Sphinx (>=1.3) : ok version 1.4.1 installed Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (==0.23.5) : ok version 0.23.5 installed Look for package Sphinx (>=1.3) : ok version 1.4.1 installed Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h'] running install running build running littlebigman creating build creating build/temp.linux-x86_64-3.4 building 'littlebigman' program creating build/temp.linux-x86_64-3.4/distutils.ext creating build/temp.linux-x86_64-3.4/distutils.ext/src x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-3.4/distutils.ext/src/littlebigman.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.4/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-3.4/littlebigman Your CPU is in mode : -DLITTLE_END running build_py creating build/lib.linux-x86_64-3.4 creating build/lib.linux-x86_64-3.4/orgasm copying python/orgasm/init.py -> build/lib.linux-x86_64-3.4/orgasm copying python/orgasm/tango.py -> build/lib.linux-x86_64-3.4/orgasm copying python/orgasm/version.py -> build/lib.linux-x86_64-3.4/orgasm copying python/orgasm/config.py -> build/lib.linux-x86_64-3.4/orgasm creating build/lib.linux-x86_64-3.4/orgasm/assembler copying python/orgasm/assembler/init.py -> build/lib.linux-x86_64-3.4/orgasm/assembler creating build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/clone.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/buildgraph.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/graphstats.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/init.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/list.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/cutlow.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/seeds.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/index.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/path.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/unfoldrdna.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/fasta.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/unfold.py -> build/lib.linux-x86_64-3.4/orgasm/commands copying python/orgasm/commands/compact.py -> build/lib.linux-x86_64-3.4/orgasm/commands creating build/lib.linux-x86_64-3.4/orgasm/backtranslate copying python/orgasm/backtranslate/init.py -> build/lib.linux-x86_64-3.4/orgasm/backtranslate copying python/orgasm/backtranslate/fasta.py -> build/lib.linux-x86_64-3.4/orgasm/backtranslate creating build/lib.linux-x86_64-3.4/orgasm/graph copying python/orgasm/graph/init.py -> build/lib.linux-x86_64-3.4/orgasm/graph creating build/lib.linux-x86_64-3.4/orgasm/apps copying python/orgasm/apps/init.py -> build/lib.linux-x86_64-3.4/orgasm/apps creating build/lib.linux-x86_64-3.4/orgasm/indexer copying python/orgasm/indexer/init.py -> build/lib.linux-x86_64-3.4/orgasm/indexer creating build/lib.linux-x86_64-3.4/orgasm/samples copying python/orgasm/samples/init.py -> build/lib.linux-x86_64-3.4/orgasm/samples creating build/lib.linux-x86_64-3.4/orgasm/fiboheap copying python/orgasm/fiboheap/init.py -> build/lib.linux-x86_64-3.4/orgasm/fiboheap creating build/lib.linux-x86_64-3.4/orgasm/multialign copying python/orgasm/multialign/init.py -> build/lib.linux-x86_64-3.4/orgasm/multialign creating build/lib.linux-x86_64-3.4/orgasm/utils copying python/orgasm/utils/init.py -> build/lib.linux-x86_64-3.4/orgasm/utils running build_ext Look for CPU architecture... [('LITTLE_END', None)] running build_files running build_ctools building 'buildcomplement' program creating build/temp.linux-x86_64-3.4/src x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcomplement.c -o build/temp.linux-x86_64-3.4/src/buildcomplement.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.4/src/buildcomplement.o -o build/temp.linux-x86_64-3.4/buildcomplement building 'buildcode' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildcode.c -o build/temp.linux-x86_64-3.4/src/buildcode.o -msse2 src/buildcode.c: In function ‘main’: src/buildcode.c:44:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", ((uint64_t)nuc),code,nuc); ^ src/buildcode.c:44:4: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ [-Wformat=] src/buildcode.c:46:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", ((uint64_t)nuc),code,nuc); ^ src/buildcode.c:46:4: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ [-Wformat=] x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.4/src/buildcode.o -o build/temp.linux-x86_64-3.4/buildcode building 'buildexpand8bits' program x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.linux-x86_64-3.4/src/buildexpand8bits.o -msse2 src/buildexpand8bits.c: In function ‘main’: src/buildexpand8bits.c:40:1: warning: multi-line comment [-Wcomment] // ((uint32_t)nuc) = ((uint32_t)nuc) >> 24 |
^ src/buildexpand8bits.c:47:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," 0x%08XUL, // %04X\n", ((uint32_t)nuc),code); ^ src/buildexpand8bits.c:49:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] fprintf(stdout," 0x%08XUL // %04X\n", ((uint32_t)nuc),code); ^ x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.4/src/buildexpand8bits.o -o build/temp.linux-x86_64-3.4/buildexpand8bits Building file : codecomp.c --> build/temp.linux-x86_64-3.4/buildcomplement > build/temp.linux-x86_64-3.4/codecomp.c Done.

Building file : code16bits.c --> build/temp.linux-x86_64-3.4/buildcode > build/temp.linux-x86_64-3.4/code16bits.c Done.

Building file : expand8bits.c --> build/temp.linux-x86_64-3.4/buildexpand8bits > build/temp.linux-x86_64-3.4/expand8bits.c Done.

running build_cexe Look for CPU architecture... [('LITTLE_END', None)] creating build/scripts-3.4 orgasmi :-> src/orgasmi.c ok orgasmi :-> src/buffer.c ok orgasmi :-> src/buildindex.c ok orgasmi :-> @code16bits.c changed to build/temp.linux-x86_64-3.4/code16bits.c orgasmi :-> @codecomp.c changed to build/temp.linux-x86_64-3.4/codecomp.c orgasmi :-> src/compsort.c ok orgasmi :-> src/debug.c ok orgasmi :-> src/decode.c ok orgasmi :-> src/encode.c ok orgasmi :-> src/fastq.c ok orgasmi :-> src/indexinput.c ok orgasmi :-> src/indexoutput.c ok orgasmi :-> src/load.c ok orgasmi :-> src/lookfor.c ok orgasmi :-> src/malloc.c ok orgasmi :-> src/fgetln.c ok orgasmi :-> src/sort.c ok building 'orgasmi' program creating build/temp.linux-x86_64-3.4/build creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/orgasmi.c -o build/temp.linux-x86_64-3.4/src/orgasmi.o -msse2 src/orgasmi.c:27:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void PrintHelp() ^ src/orgasmi.c:62:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void ExitUsage(stat) ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buffer.c -o build/temp.linux-x86_64-3.4/src/buffer.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/buildindex.c -o build/temp.linux-x86_64-3.4/src/buildindex.o -msse2 src/buildindex.c: In function ‘buildIndex’: src/buildindex.c:44:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ofx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.4/code16bits.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/code16bits.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.4/codecomp.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/codecomp.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/compsort.c -o build/temp.linux-x86_64-3.4/src/compsort.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/debug.c -o build/temp.linux-x86_64-3.4/src/debug.o -msse2 src/debug.c: In function ‘int2bin’: src/debug.c:23:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] u = *(unsigned *)&i; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/decode.c -o build/temp.linux-x86_64-3.4/src/decode.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/encode.c -o build/temp.linux-x86_64-3.4/src/encode.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fastq.c -o build/temp.linux-x86_64-3.4/src/fastq.o -msse2 src/fastq.c: In function ‘readFastq’: src/fastq.c:40:2: warning: implicit declaration of function ‘fgetln’ [-Wimplicit-function-declaration] buffer = fgetln(in,&lseq); ^ src/fastq.c:40:9: warning: assignment makes pointer from integer without a cast buffer = fgetln(in,&lseq); ^ src/fastq.c:43:10: warning: assignment makes pointer from integer without a cast buffer = fgetln(in,&lseq); ^ src/fastq.c:57:9: warning: assignment makes pointer from integer without a cast buffer = fgetln(in,&lseq); ^ src/fastq.c:58:9: warning: assignment makes pointer from integer without a cast buffer = fgetln(in,&lseq); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexinput.c -o build/temp.linux-x86_64-3.4/src/indexinput.o -msse2 src/indexinput.c: In function ‘loadGeneralData’: src/indexinput.c:54:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,1,sizeof(buffer_t),input); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/indexoutput.c -o build/temp.linux-x86_64-3.4/src/indexoutput.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/load.c -o build/temp.linux-x86_64-3.4/src/load.o -msse2 src/load.c: In function ‘loadIndexedReads’: src/load.c:34:2: warning: implicit declaration of function ‘asprintf’ [-Wimplicit-function-declaration] asprintf(&indexFileName,"%s.ogx",indexname); ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/lookfor.c -o build/temp.linux-x86_64-3.4/src/lookfor.o -msse2 src/lookfor.c: In function ‘shiftKey’: src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable] uint8_t rmask; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/malloc.c -o build/temp.linux-x86_64-3.4/src/malloc.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/fgetln.c -o build/temp.linux-x86_64-3.4/src/fgetln.o -msse2 x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -c src/sort.c -o build/temp.linux-x86_64-3.4/src/sort.o -msse2 x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.4/src/orgasmi.o build/temp.linux-x86_64-3.4/src/buffer.o build/temp.linux-x86_64-3.4/src/buildindex.o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/code16bits.o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/codecomp.o build/temp.linux-x86_64-3.4/src/compsort.o build/temp.linux-x86_64-3.4/src/debug.o build/temp.linux-x86_64-3.4/src/decode.o build/temp.linux-x86_64-3.4/src/encode.o build/temp.linux-x86_64-3.4/src/fastq.o build/temp.linux-x86_64-3.4/src/indexinput.o build/temp.linux-x86_64-3.4/src/indexoutput.o build/temp.linux-x86_64-3.4/src/load.o build/temp.linux-x86_64-3.4/src/lookfor.o build/temp.linux-x86_64-3.4/src/malloc.o build/temp.linux-x86_64-3.4/src/fgetln.o build/temp.linux-x86_64-3.4/src/sort.o -o build/scripts-3.4/orgasmi orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.linux-x86_64-3.4/expand8bits.c orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok orgasm.graph._fibointheap :-> fiboheap/fibo.c ok orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.pyx ok orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok orgasm.apps.progress :-> python/orgasm/apps/progress.pyx ok orgasm.apps.config :-> python/orgasm/apps/config.pyx ok orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok orgasm.apps.logging :-> python/orgasm/apps/logging.pyx ok orgasm.apps.command :-> python/orgasm/apps/command.pyx ok orgasm.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok orgasm.indexer._orgasm :-> python/orgasm/indexer/_orgasm.pyx ok orgasm.indexer._orgasm :-> src/buffer.c ok orgasm.indexer._orgasm :-> src/buildindex.c ok orgasm.indexer._orgasm :-> @code16bits.c changed to build/temp.linux-x86_64-3.4/code16bits.c orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.linux-x86_64-3.4/codecomp.c orgasm.indexer._orgasm :-> src/compsort.c ok orgasm.indexer._orgasm :-> src/debug.c ok orgasm.indexer._orgasm :-> src/decode.c ok orgasm.indexer._orgasm :-> src/encode.c ok orgasm.indexer._orgasm :-> src/fastq.c ok orgasm.indexer._orgasm :-> src/indexinput.c ok orgasm.indexer._orgasm :-> src/indexoutput.c ok orgasm.indexer._orgasm :-> src/load.c ok orgasm.indexer._orgasm :-> src/lookfor.c ok orgasm.indexer._orgasm :-> src/malloc.c ok orgasm.indexer._orgasm :-> src/sort.c ok orgasm.indexer._orgasm :-> src/fgetln.c ok orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx'] cythoning python/orgasm/assembler/_assembler.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_assembler.c creating build/temp.linux-x86_64-3.4/pyrex creating build/temp.linux-x86_64-3.4/pyrex/orgasm creating build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler building 'orgasm.assembler._assembler' extension creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_assembler.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_assembler.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_assembler.o -o build/lib.linux-x86_64-3.4/orgasm/assembler/_assembler.cpython-34m.so orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx'] cythoning python/orgasm/assembler/_tango.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_tango.c building 'orgasm.assembler._tango' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_tango.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_tango.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_tango.o -o build/lib.linux-x86_64-3.4/orgasm/assembler/_tango.cpython-34m.so orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx'] cythoning python/orgasm/assembler/_asmbgraph.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_asmbgraph.c building 'orgasm.assembler._asmbgraph' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_asmbgraph.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_asmbgraph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/assembler/_asmbgraph.o -o build/lib.linux-x86_64-3.4/orgasm/assembler/_asmbgraph.cpython-34m.so orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.linux-x86_64-3.4/expand8bits.c'] cythoning python/orgasm/backtranslate/_ahocorasick.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c creating build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate building 'orgasm.backtranslate._ahocorasick' extension creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_simpleMatch’: build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:5801:5: warning: array subscript has type ‘char’ [-Wchar-subscripts] __pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]); ^ build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_addSequence’: build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:8712:8: warning: variable ‘__pyx_v_letter’ set but not used [-Wunused-but-set-variable] char __pyx_v_letter[2]; ^ build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:137:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^ build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:11801:7: note: ‘__pyx_v_locmax’ was declared here int __pyx_v_locmax; ^ build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:137:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define PyInt_FromLong PyLong_FromLong ^ build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.c:9521:7: note: ‘__pyx_v_locmax’ was declared here int __pyx_v_locmax; ^ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/expand8bits.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_ahocorasick.o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/expand8bits.o -o build/lib.linux-x86_64-3.4/orgasm/backtranslate/_ahocorasick.cpython-34m.so orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx'] cythoning python/orgasm/backtranslate/_bitvector.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_bitvector.c building 'orgasm.backtranslate._bitvector' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_bitvector.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_bitvector.o x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/backtranslate/_bitvector.o -o build/lib.linux-x86_64-3.4/orgasm/backtranslate/_bitvector.cpython-34m.so orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibomaxintheap.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibomaxintheap.c creating build/temp.linux-x86_64-3.4/pyrex/orgasm/graph building 'orgasm.graph._fibomaxintheap' extension creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph creating build/temp.linux-x86_64-3.4/fiboheap x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibomaxintheap.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibomaxintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibomaxintheap.o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -o build/lib.linux-x86_64-3.4/orgasm/graph/_fibomaxintheap.cpython-34m.so orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx'] cythoning python/orgasm/graph/_graph.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graph.c building 'orgasm.graph._graph' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -Isrc -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graph.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graph.o -o build/lib.linux-x86_64-3.4/orgasm/graph/_graph.cpython-34m.so orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibointheap.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibointheap.c building 'orgasm.graph._fibointheap' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibointheap.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibointheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibointheap.o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -o build/lib.linux-x86_64-3.4/orgasm/graph/_fibointheap.cpython-34m.so orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx'] cythoning python/orgasm/graph/_graphmultiedge.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graphmultiedge.c building 'orgasm.graph._graphmultiedge' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graphmultiedge.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graphmultiedge.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_graphmultiedge.o -o build/lib.linux-x86_64-3.4/orgasm/graph/_graphmultiedge.cpython-34m.so orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibominintheap.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibominintheap.c building 'orgasm.graph._fibominintheap' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibominintheap.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibominintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -Ifiboheap -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/graph/_fibominintheap.o build/temp.linux-x86_64-3.4/fiboheap/fibo.o -o build/lib.linux-x86_64-3.4/orgasm/graph/_fibominintheap.cpython-34m.so orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx'] cythoning python/orgasm/apps/progress.pyx to build/temp.linux-x86_64-3.4/pyrex/orgasm/apps/progress.c creating build/temp.linux-x86_64-3.4/pyrex/orgasm/apps building 'orgasm.apps.progress' extension creating build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/apps x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DLITTLE_END -I/home/hzs/bin/org-asm-master/ORG.asm-0.2.03/include -I/usr/include/python3.4m -c build/temp.linux-x86_64-3.4/pyrex/orgasm/apps/progress.c -o build/temp.linux-x86_64-3.4/build/temp.linux-x86_64-3.4/pyrex/orgasm/apps/progress.o build/temp.linux-x86_64-3.4/pyrex/orgasm/apps/progress.c: In function ‘pyx_pf_6orgasm_4apps_8progress_11ProgressBar_2__call’: build/temp.linux-x86_64-3.4/pyrex/orgasm/apps/progress.c:1814:9: error: format not a string literal and no format arguments [-Werror=format-security] ((void)fprintf(stderr, __pyx_k__6)); ^ cc1: some warnings being treated as errors error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

get-orgasm.py also doesn't work for me. Debian system.