GitLab

I also tried to compile directly the source, but same problem. I ended with a partially functional executable, without some options (i.e.--estimate-length, and probably others), and weird results in some case I don't know if it's due to the partial compilation or to my data.... In addition, I installed the different packages for the compilation, but they seem to be unavailable to the installer ? Thanks in advance !

$ python3 get-orgasm.py Unable to install ORG.asm on your system DEPRECATION: pip install --download has been deprecated and will be removed in the future. Pip now has a download command that should be used instead. Collecting ORG.asm Downloading ORG.asm-0.2.06.tar.gz (251kB) 100% |████████████████████████████████| 256kB 63kB/s Saved /var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06.tar.gz Successfully downloaded ORG.asm ['/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06', '/Applications', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python35.zip', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/plat-darwin', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/lib-dynload', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/distutils.ext', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/python'] ['/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python35.zip', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/plat-darwin', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/lib-dynload', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/distutils.ext', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/python'] Installing ORG.asm (0.2.06) in serenity mode You are running the good python Restarting installation within the /Applications/ORG.asm-0.2.06 virtualenv Install script restarting... ['/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python35.zip', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/plat-darwin', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/lib-dynload', '/Applications/ORG.asm-0.2.06/lib/python3.5/site-packages', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/distutils.ext', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/python'] Installing ORG.asm (0.2.06) in serenity mode You are running the good python ORG.asm will be installed with python : /Applications/ORG.asm-0.2.06/bin/python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : not installed Installing requirement : Cython>=0.24 Collecting Cython>=0.24 Using cached Cython-0.24.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Installing collected packages: Cython Successfully installed Cython-0.24.1 You are using pip version 8.1.1, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Look for package Sphinx (>=1.3) : not installed Installing requirement : Sphinx>=1.3 Collecting Sphinx>=1.3 Using cached Sphinx-1.4.6-py2.py3-none-any.whl Collecting alabaster<0.8,>=0.7 (from Sphinx>=1.3) Using cached alabaster-0.7.9-py2.py3-none-any.whl Collecting Pygments>=2.0 (from Sphinx>=1.3) Using cached Pygments-2.1.3-py2.py3-none-any.whl Collecting Jinja2>=2.3 (from Sphinx>=1.3) Using cached Jinja2-2.8-py2.py3-none-any.whl Collecting imagesize (from Sphinx>=1.3) Using cached imagesize-0.7.1-py2.py3-none-any.whl Collecting docutils>=0.11 (from Sphinx>=1.3) Using cached docutils-0.12-py3-none-any.whl Collecting six>=1.5 (from Sphinx>=1.3) Using cached six-1.10.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from Sphinx>=1.3) Using cached Babel-2.3.4-py2.py3-none-any.whl Collecting snowballstemmer>=1.1 (from Sphinx>=1.3) Using cached snowballstemmer-1.2.1-py2.py3-none-any.whl Collecting MarkupSafe (from Jinja2>=2.3->Sphinx>=1.3) Using cached MarkupSafe-0.23.tar.gz Collecting pytz>=0a (from babel!=2.0,>=1.3->Sphinx>=1.3) Using cached pytz-2016.6.1-py2.py3-none-any.whl Installing collected packages: alabaster, Pygments, MarkupSafe, Jinja2, imagesize, docutils, six, pytz, babel, snowballstemmer, Sphinx Running setup.py install for MarkupSafe ... done Successfully installed Jinja2-2.8 MarkupSafe-0.23 Pygments-2.1.3 Sphinx-1.4.6 alabaster-0.7.9 babel-2.3.4 docutils-0.12 imagesize-0.7.1 pytz-2016.6.1 six-1.10.0 snowballstemmer-1.2.1 You are using pip version 8.1.1, however version 8.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Restarting installation with all dependencies ok Install script restarting... ['/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python35.zip', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/plat-darwin', '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/lib-dynload', '/Applications/ORG.asm-0.2.06/lib/python3.5/site-packages', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/distutils.ext', '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/python'] Installing ORG.asm (0.2.06) in serenity mode You are running the good python ORG.asm will be installed with python : /Applications/ORG.asm-0.2.06/bin/python Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : ok version 0.24.1 installed Look for package Sphinx (>=1.3) : ok version 1.4.6 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 (>=0.24) : ok version 0.24.1 installed Look for package Sphinx (>=1.3) : ok version 1.4.6 installed Required packages for the installation : Look for package pip (>=8.0) : ok version 8.1.1 installed Look for package Cython (>=0.24) : ok version 0.24.1 installed Look for package Sphinx (>=1.3) : ok version 1.4.6 installed Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['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.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['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 : ['src/orgasm.h'] running install running build running littlebigman creating build creating build/temp.macosx-10.6-intel-3.5 building 'littlebigman' program creating build/temp.macosx-10.6-intel-3.5/distutils.ext creating build/temp.macosx-10.6-intel-3.5/distutils.ext/src /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -c distutils.ext/src/littlebigman.c -o build/temp.macosx-10.6-intel-3.5/distutils.ext/src/littlebigman.o -msse2 /usr/bin/clang build/temp.macosx-10.6-intel-3.5/distutils.ext/src/littlebigman.o -o build/temp.macosx-10.6-intel-3.5/littlebigman Your CPU is in mode : -DLITTLE_END running pidname creating build/scripts-3.5 building 'pidname' program /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -c distutils.ext/src/pidname.c -o build/temp.macosx-10.6-intel-3.5/distutils.ext/src/pidname.o -msse2 /usr/bin/clang build/temp.macosx-10.6-intel-3.5/distutils.ext/src/pidname.o -o build/scripts-3.5/pidname running build_py creating build/lib.macosx-10.6-intel-3.5 creating build/lib.macosx-10.6-intel-3.5/orgasm copying python/orgasm/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm copying python/orgasm/config.py -> build/lib.macosx-10.6-intel-3.5/orgasm copying python/orgasm/tango.py -> build/lib.macosx-10.6-intel-3.5/orgasm copying python/orgasm/version.py -> build/lib.macosx-10.6-intel-3.5/orgasm creating build/lib.macosx-10.6-intel-3.5/orgasm/apps copying python/orgasm/apps/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/apps creating build/lib.macosx-10.6-intel-3.5/orgasm/assembler copying python/orgasm/assembler/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/assembler creating build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate copying python/orgasm/backtranslate/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate copying python/orgasm/backtranslate/fasta.py -> build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate creating build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/buildgraph.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/clone.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/compact.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/cutlow.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/fasta.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/graphstats.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/index.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/list.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/path.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/seeds.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/substract.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/unfold.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands copying python/orgasm/commands/unfoldrdna.py -> build/lib.macosx-10.6-intel-3.5/orgasm/commands creating build/lib.macosx-10.6-intel-3.5/orgasm/fiboheap copying python/orgasm/fiboheap/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/fiboheap creating build/lib.macosx-10.6-intel-3.5/orgasm/files copying python/orgasm/files/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/files creating build/lib.macosx-10.6-intel-3.5/orgasm/graph copying python/orgasm/graph/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/graph creating build/lib.macosx-10.6-intel-3.5/orgasm/indexer copying python/orgasm/indexer/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/indexer creating build/lib.macosx-10.6-intel-3.5/orgasm/multialign copying python/orgasm/multialign/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/multialign creating build/lib.macosx-10.6-intel-3.5/orgasm/samples copying python/orgasm/samples/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/samples creating build/lib.macosx-10.6-intel-3.5/orgasm/utils copying python/orgasm/utils/init.py -> build/lib.macosx-10.6-intel-3.5/orgasm/utils running build_ext Look for CPU architecture... [('LITTLE_END', None)] running build_files running build_ctools building 'buildcomplement' program creating build/temp.macosx-10.6-intel-3.5/src /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/buildcomplement.c -o build/temp.macosx-10.6-intel-3.5/src/buildcomplement.o -msse2 /usr/bin/clang build/temp.macosx-10.6-intel-3.5/src/buildcomplement.o -o build/temp.macosx-10.6-intel-3.5/buildcomplement building 'buildcode' program /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/buildcode.c -o build/temp.macosx-10.6-intel-3.5/src/buildcode.o -msse2 /usr/bin/clang build/temp.macosx-10.6-intel-3.5/src/buildcode.o -o build/temp.macosx-10.6-intel-3.5/buildcode building 'buildexpand8bits' program /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.macosx-10.6-intel-3.5/src/buildexpand8bits.o -msse2 /usr/bin/clang build/temp.macosx-10.6-intel-3.5/src/buildexpand8bits.o -o build/temp.macosx-10.6-intel-3.5/buildexpand8bits Building file : codecomp.c --> build/temp.macosx-10.6-intel-3.5/buildcomplement > build/temp.macosx-10.6-intel-3.5/codecomp.c Done.

Building file : code16bits.c --> build/temp.macosx-10.6-intel-3.5/buildcode > build/temp.macosx-10.6-intel-3.5/code16bits.c Done.

Building file : expand8bits.c --> build/temp.macosx-10.6-intel-3.5/buildexpand8bits > build/temp.macosx-10.6-intel-3.5/expand8bits.c Done.

running build_cexe Look for CPU architecture... [('LITTLE_END', None)] orgasmi :-> src/orgasmi.c ok orgasmi :-> src/buffer.c ok orgasmi :-> src/buildindex.c ok orgasmi :-> @code16bits.c changed to build/temp.macosx-10.6-intel-3.5/code16bits.c orgasmi :-> @codecomp.c changed to build/temp.macosx-10.6-intel-3.5/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.macosx-10.6-intel-3.5/build creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/orgasmi.c -o build/temp.macosx-10.6-intel-3.5/src/orgasmi.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/buffer.c -o build/temp.macosx-10.6-intel-3.5/src/buffer.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/buildindex.c -o build/temp.macosx-10.6-intel-3.5/src/buildindex.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c build/temp.macosx-10.6-intel-3.5/code16bits.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/code16bits.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c build/temp.macosx-10.6-intel-3.5/codecomp.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/codecomp.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/compsort.c -o build/temp.macosx-10.6-intel-3.5/src/compsort.o -msse2 src/compsort.c:301:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ 1 warning generated. src/compsort.c:301:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/debug.c -o build/temp.macosx-10.6-intel-3.5/src/debug.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/decode.c -o build/temp.macosx-10.6-intel-3.5/src/decode.o -msse2 src/decode.c:96:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i<lkey;i++) ~^~~~~ src/decode.c:111:6: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] i < lcompact; ~ ^ ~~~~~~~~ 2 warnings generated. src/decode.c:96:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i<lkey;i++) ~^~~~~ src/decode.c:111:6: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] i < lcompact; ~ ^ ~~~~~~~~ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/encode.c -o build/temp.macosx-10.6-intel-3.5/src/encode.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/fastq.c -o build/temp.macosx-10.6-intel-3.5/src/fastq.o -msse2 src/fastq.c:132:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] forwardLength>0 && forwardLength<readLength; ~~~~~~~~~~~~~^~~~~~~~~~~ src/fastq.c:163:25: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] reverseLength < readLength ); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:21: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:54: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ 4 warnings generated. src/fastq.c:132:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] forwardLength>0 && forwardLength<readLength; ~~~~~~~~~~~~~^~~~~~~~~~~ src/fastq.c:163:25: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] reverseLength < readLength ); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:21: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:54: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/indexinput.c -o build/temp.macosx-10.6-intel-3.5/src/indexinput.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/indexoutput.c -o build/temp.macosx-10.6-intel-3.5/src/indexoutput.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/load.c -o build/temp.macosx-10.6-intel-3.5/src/load.o -msse2 src/load.c:19:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0;i < reads->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~ 1 warning generated. src/load.c:19:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0;i < reads->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/lookfor.c -o build/temp.macosx-10.6-intel-3.5/src/lookfor.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/malloc.c -o build/temp.macosx-10.6-intel-3.5/src/malloc.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/fgetln.c -o build/temp.macosx-10.6-intel-3.5/src/fgetln.o -msse2 /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -c src/sort.c -o build/temp.macosx-10.6-intel-3.5/src/sort.o -msse2 src/sort.c:402:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ src/sort.c:430:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ src/sort.c:463:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ 3 warnings generated. src/sort.c:402:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ src/sort.c:430:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ src/sort.c:463:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ 3 warnings generated. /usr/bin/clang build/temp.macosx-10.6-intel-3.5/src/orgasmi.o build/temp.macosx-10.6-intel-3.5/src/buffer.o build/temp.macosx-10.6-intel-3.5/src/buildindex.o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/code16bits.o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/codecomp.o build/temp.macosx-10.6-intel-3.5/src/compsort.o build/temp.macosx-10.6-intel-3.5/src/debug.o build/temp.macosx-10.6-intel-3.5/src/decode.o build/temp.macosx-10.6-intel-3.5/src/encode.o build/temp.macosx-10.6-intel-3.5/src/fastq.o build/temp.macosx-10.6-intel-3.5/src/indexinput.o build/temp.macosx-10.6-intel-3.5/src/indexoutput.o build/temp.macosx-10.6-intel-3.5/src/load.o build/temp.macosx-10.6-intel-3.5/src/lookfor.o build/temp.macosx-10.6-intel-3.5/src/malloc.o build/temp.macosx-10.6-intel-3.5/src/fgetln.o build/temp.macosx-10.6-intel-3.5/src/sort.o -o build/scripts-3.5/orgasmi orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok orgasm.apps.command :-> python/orgasm/apps/command.pyx ok orgasm.apps.config :-> python/orgasm/apps/config.pyx ok orgasm.apps.logging :-> python/orgasm/apps/logging.pyx ok orgasm.apps.progress :-> python/orgasm/apps/progress.pyx ok orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.macosx-10.6-intel-3.5/expand8bits.c orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok orgasm.files.linebuffer :-> python/orgasm/files/linebuffer.pyx ok orgasm.files.uncompress :-> python/orgasm/files/uncompress.pyx ok orgasm.files.universalopener :-> python/orgasm/files/universalopener.pyx ok orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok orgasm.graph._fibointheap :-> fiboheap/fibo.c ok orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.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.macosx-10.6-intel-3.5/code16bits.c orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.macosx-10.6-intel-3.5/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.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok orgasm.apps.arguments :-> ['python/orgasm/apps/arguments.pyx'] cythoning python/orgasm/apps/arguments.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c creating build/temp.macosx-10.6-intel-3.5/pyrex creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps building 'orgasm.apps.arguments' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3853:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3850:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3915:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3965:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:4027:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3094:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_InitDefaults(PyObject func, size_t size, int pyobjects) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3103:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject func, PyObject tuple) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3108:27: warning: unused function '__Pyx_CyFunction_SetDefaultsKwDict' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject func, PyObject dict) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3113:27: warning: unused function '__Pyx_CyFunction_SetAnnotationsDict' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject func, PyObject dict) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3348:42: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3397:37: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3582:36: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 12 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3853:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3850:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3915:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3965:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:4027:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3094:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_InitDefaults(PyObject func, size_t size, int pyobjects) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3103:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject func, PyObject tuple) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3108:27: warning: unused function '__Pyx_CyFunction_SetDefaultsKwDict' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject func, PyObject dict) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3113:27: warning: unused function '__Pyx_CyFunction_SetAnnotationsDict' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject func, PyObject dict) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3348:42: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3397:37: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.c:3582:36: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 12 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/arguments.o -o build/lib.macosx-10.6-intel-3.5/orgasm/apps/arguments.cpython-35m-darwin.so orgasm.apps.command :-> ['python/orgasm/apps/command.pyx'] cythoning python/orgasm/apps/command.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c building 'orgasm.apps.command' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3559:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3556:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3671:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3733:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:1738:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_List_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:1753:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:2110:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:2295:30: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 8 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3559:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3556:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3671:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:3733:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:1738:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_List_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:1753:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:2110:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.c:2295:30: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 8 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/command.o -o build/lib.macosx-10.6-intel-3.5/orgasm/apps/command.cpython-35m-darwin.so orgasm.apps.config :-> ['python/orgasm/apps/config.pyx'] cythoning python/orgasm/apps/config.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c building 'orgasm.apps.config' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4164:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4161:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4276:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4338:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2827:32: warning: unused function '__Pyx_PyBytes_Equals' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject s1, PyObject s2, int equals) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2950:27: warning: unused function '__Pyx_ErrRestoreInState' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState tstate, PyObject type, PyObject value, PyObject tb) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2962:27: warning: unused function '__Pyx_ErrFetchInState' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState tstate, PyObject type, PyObject value, PyObject tb) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3587:40: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3636:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3821:34: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 10 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4164:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4161:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4276:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:4338:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2827:32: warning: unused function '__Pyx_PyBytes_Equals' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject s1, PyObject s2, int equals) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2950:27: warning: unused function '__Pyx_ErrRestoreInState' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState tstate, PyObject type, PyObject value, PyObject tb) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:2962:27: warning: unused function '__Pyx_ErrFetchInState' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState tstate, PyObject type, PyObject value, PyObject tb) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3587:40: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3636:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.c:3821:34: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 10 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/config.o -o build/lib.macosx-10.6-intel-3.5/orgasm/apps/config.cpython-35m-darwin.so orgasm.apps.logging :-> ['python/orgasm/apps/logging.pyx'] cythoning python/orgasm/apps/logging.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c building 'orgasm.apps.logging' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2605:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2602:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2717:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2779:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2100:40: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2149:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2334:34: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2605:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2602:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2717:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2779:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2100:40: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2149:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.c:2334:34: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/logging.o -o build/lib.macosx-10.6-intel-3.5/orgasm/apps/logging.cpython-35m-darwin.so orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx'] cythoning python/orgasm/apps/progress.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c building 'orgasm.apps.progress' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1674:21: warning: passing 'clock_t ' (aka 'unsigned long ') to parameter of type 'const time_t ' (aka 'const long ') converts between pointers to integer types with different sign [-Wpointer-sign] ((void)gmtime_r((&__pyx_v_more), (&__pyx_v_remain))); ^~~~~~~~~~~~~~~ /usr/include/time.h:125:46: note: passing argument to parameter here struct tm gmtime_r(const time_t * __restrict, struct tm * __restrict); ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1761:59: warning: field precision should have type 'int', but argument has type 'unsigned long long' [-Wformat] ((void)fprintf(stderr, ((char )"\r%s %5.1f %% |%.s%c%.s] remain : %d days %02d:%02d:%02d"), __pyx_v_self->chead, (__pyx_v_percent * 100.0), __pyx_v_fraction, __pyx_v_self... ~~^~ ~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1789:59: warning: field precision should have type 'int', but argument has type 'unsigned long long' [-Wformat] ((void)fprintf(stderr, ((char )"\r%s %5.1f %% |%.s%c%.s] remain : %02d:%02d:%02d"), __pyx_v_self->chead, (__pyx_v_percent * 100.), __pyx_v_fraction, __pyx_v_self-... ~~^~ ~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3961:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:4076:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:4138:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3631:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3658:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 8 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1674:21: warning: passing 'clock_t ' (aka 'unsigned long ') to parameter of type 'const time_t ' (aka 'const long ') converts between pointers to integer types with different sign [-Wpointer-sign] ((void)gmtime_r((&__pyx_v_more), (&__pyx_v_remain))); ^~~~~~~~~~~~~~~ /usr/include/time.h:125:46: note: passing argument to parameter here struct tm gmtime_r(const time_t * __restrict, struct tm * __restrict); ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1761:59: warning: field precision should have type 'int', but argument has type 'unsigned long long' [-Wformat] ((void)fprintf(stderr, ((char )"\r%s %5.1f %% |%.s%c%.s] remain : %d days %02d:%02d:%02d"), __pyx_v_self->chead, (__pyx_v_percent * 100.0), __pyx_v_fraction, __pyx_v_self... ~~^~ ~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:1789:59: warning: field precision should have type 'int', but argument has type 'unsigned long long' [-Wformat] ((void)fprintf(stderr, ((char )"\r%s %5.1f %% |%.s%c%.s] remain : %02d:%02d:%02d"), __pyx_v_self->chead, (__pyx_v_percent * 100.), __pyx_v_fraction, __pyx_v_self-... ~~^~ ~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3961:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:4076:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:4138:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3631:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.c:3658:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 8 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/apps/progress.o -o build/lib.macosx-10.6-intel-3.5/orgasm/apps/progress.cpython-35m-darwin.so orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx'] cythoning python/orgasm/assembler/_asmbgraph.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_asmbgraph.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler building 'orgasm.assembler._asmbgraph' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_asmbgraph.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_asmbgraph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_asmbgraph.o -o build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_asmbgraph.cpython-35m-darwin.so orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx'] cythoning python/orgasm/assembler/_assembler.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_assembler.c building 'orgasm.assembler._assembler' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_assembler.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_assembler.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_assembler.o -o build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_assembler.cpython-35m-darwin.so orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx'] cythoning python/orgasm/assembler/_tango.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_tango.c building 'orgasm.assembler._tango' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_tango.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_tango.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/assembler/_tango.o -o build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_tango.cpython-35m-darwin.so orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.macosx-10.6-intel-3.5/expand8bits.c'] cythoning python/orgasm/backtranslate/_ahocorasick.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate building 'orgasm.backtranslate._ahocorasick' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -Isrc -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:5323:34: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_1 = ((__pyx_v_position > __pyx_v_self->_maxpos) != 0); ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:5872:39: warning: array subscript is of type 'char' [-Wchar-subscripts] __pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]); ^~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:6895:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { ~~~~~~~~~ ^ ~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:8998:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_11; __pyx_t_8+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:9192:47: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = (__pyx_t_6 - 1); __pyx_t_8 > __pyx_t_11; __pyx_t_8-=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10482:50: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_12 = (((__pyx_v_wc[__pyx_v_p]) > __pyx_v_wcmax) != 0); ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10597:36: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_19 = ((__pyx_v_wcmax > __pyx_v_wordmax) != 0); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10833:36: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_19 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:11506:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_11; __pyx_t_8+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:12854:36: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_19 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ 10 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:5323:34: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_1 = ((__pyx_v_position > __pyx_v_self->_maxpos) != 0); ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:5872:39: warning: array subscript is of type 'char' [-Wchar-subscripts] __pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]); ^~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:6895:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { ~~~~~~~~~ ^ ~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:8998:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_11; __pyx_t_8+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:9192:47: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = (__pyx_t_6 - 1); __pyx_t_8 > __pyx_t_11; __pyx_t_8-=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10482:50: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_12 = (((__pyx_v_wc[__pyx_v_p]) > __pyx_v_wcmax) != 0); ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10597:36: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_19 = ((__pyx_v_wcmax > __pyx_v_wordmax) != 0); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:10833:36: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_19 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:11506:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_11; __pyx_t_8+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.c:12854:36: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare] __pyx_t_19 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~ 10 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -Isrc -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/expand8bits.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_ahocorasick.o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/expand8bits.o -o build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-darwin.so orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx'] cythoning python/orgasm/backtranslate/_bitvector.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c building 'orgasm.backtranslate._bitvector' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3403:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3400:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3465:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3515:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:2957:36: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:2984:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3169:30: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3403:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3400:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3465:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3515:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:2957:36: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:2984:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.c:3169:30: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/backtranslate/_bitvector.o -o build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/_bitvector.cpython-35m-darwin.so orgasm.fiboheap._fiboheap :-> ['python/orgasm/fiboheap/_fiboheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/fiboheap/_fiboheap.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap/_fiboheap.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap building 'orgasm.fiboheap._fiboheap' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap creating build/temp.macosx-10.6-intel-3.5/fiboheap /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap/_fiboheap.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap/_fiboheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c fiboheap/fibo.c -o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/fiboheap/_fiboheap.o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -o build/lib.macosx-10.6-intel-3.5/orgasm/fiboheap/_fiboheap.cpython-35m-darwin.so orgasm.files.linebuffer :-> ['python/orgasm/files/linebuffer.pyx'] cythoning python/orgasm/files/linebuffer.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files building 'orgasm.files.linebuffer' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3460:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3457:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3522:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3572:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3634:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:2206:34: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:2233:29: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3460:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3457:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3522:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3572:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:3634:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:2206:34: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.c:2233:29: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/linebuffer.o -o build/lib.macosx-10.6-intel-3.5/orgasm/files/linebuffer.cpython-35m-darwin.so orgasm.files.uncompress :-> ['python/orgasm/files/uncompress.pyx'] cythoning python/orgasm/files/uncompress.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c building 'orgasm.files.uncompress' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6171:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6168:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6283:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6345:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:4472:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_List_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:4487:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:5131:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6171:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6168:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6283:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:6345:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:4472:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_List_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:4487:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.c:5131:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/uncompress.o -o build/lib.macosx-10.6-intel-3.5/orgasm/files/uncompress.cpython-35m-darwin.so orgasm.files.universalopener :-> ['python/orgasm/files/universalopener.pyx'] cythoning python/orgasm/files/universalopener.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c building 'orgasm.files.universalopener' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2588:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2585:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2650:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2700:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2762:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2000:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2049:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2234:32: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 8 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2588:28: warning: unused function '__Pyx_PyObject_AsString' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyObject_AsString(PyObject o) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2585:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2650:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2700:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2762:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2000:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2049:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.c:2234:32: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 8 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/files/universalopener.o -o build/lib.macosx-10.6-intel-3.5/orgasm/files/universalopener.cpython-35m-darwin.so orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibointheap.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibointheap.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph building 'orgasm.graph._fibointheap' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibointheap.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibointheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c fiboheap/fibo.c -o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibointheap.o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -o build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibointheap.cpython-35m-darwin.so orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibomaxintheap.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibomaxintheap.c building 'orgasm.graph._fibomaxintheap' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibomaxintheap.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibomaxintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c fiboheap/fibo.c -o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibomaxintheap.o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -o build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibomaxintheap.cpython-35m-darwin.so orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibominintheap.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibominintheap.c building 'orgasm.graph._fibominintheap' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibominintheap.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibominintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c fiboheap/fibo.c -o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_fibominintheap.o build/temp.macosx-10.6-intel-3.5/fiboheap/fibo.o -o build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibominintheap.cpython-35m-darwin.so orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx'] cythoning python/orgasm/graph/_graph.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graph.c building 'orgasm.graph._graph' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -Isrc -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graph.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graph.o -o build/lib.macosx-10.6-intel-3.5/orgasm/graph/_graph.cpython-35m-darwin.so orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx'] cythoning python/orgasm/graph/_graphmultiedge.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graphmultiedge.c building 'orgasm.graph._graphmultiedge' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graphmultiedge.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graphmultiedge.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/graph/_graphmultiedge.o -o build/lib.macosx-10.6-intel-3.5/orgasm/graph/_graphmultiedge.cpython-35m-darwin.so orgasm.indexer._orgasm :-> ['python/orgasm/indexer/_orgasm.pyx', 'src/buffer.c', 'src/buildindex.c', 'build/temp.macosx-10.6-intel-3.5/code16bits.c', 'build/temp.macosx-10.6-intel-3.5/codecomp.c', 'src/compsort.c', 'src/debug.c', '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/sort.c', 'src/fgetln.c'] cythoning python/orgasm/indexer/_orgasm.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer building 'orgasm.indexer._orgasm' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3718:35: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((__pyx_v_begin < __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3734:54: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!(((__pyx_v_begin + __pyx_v_length) <= __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3786:38: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_11 = ((abs(__pyx_v_readid) > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:6386:31: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((__pyx_t_6 == __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:6743:29: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((__pyx_v_iid > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8355:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_7 = ((__pyx_v_y > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8451:7: warning: variable '__pyx_v_t' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (__pyx_t_7) { ^~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8599:36: note: uninitialized use occurs here __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 447, __pyx_L1_error) ^~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8451:3: note: remove the 'if' if its condition is always true if (__pyx_t_7) { ^~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8194:16: note: initialize the variable '__pyx_v_t' to silence this warning int __pyx_v_t; ^ = 0 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3718:35: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((__pyx_v_begin < __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3734:54: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!(((__pyx_v_begin + __pyx_v_length) <= __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:3786:38: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_11 = ((abs(__pyx_v_readid) > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:6386:31: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((__pyx_t_6 == __pyx_v_self->_index->readSize) != 0))) { ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:480:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:6743:29: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((__pyx_v_iid > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8355:27: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_7 = ((__pyx_v_y > __pyx_v_self->_index->readCount) != 0); ~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8451:7: warning: variable '__pyx_v_t' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (__pyx_t_7) { ^~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8599:36: note: uninitialized use occurs here __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 447, __pyx_L1_error) ^~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8451:3: note: remove the 'if' if its condition is always true if (__pyx_t_7) { ^~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.c:8194:16: note: initialize the variable '__pyx_v_t' to silence this warning int __pyx_v_t; ^ = 0 7 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/buffer.c -o build/temp.macosx-10.6-intel-3.5/src/buffer.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/buildindex.c -o build/temp.macosx-10.6-intel-3.5/src/buildindex.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/code16bits.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/code16bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/codecomp.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/codecomp.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/compsort.c -o build/temp.macosx-10.6-intel-3.5/src/compsort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/compsort.c:301:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ 1 warning generated. src/compsort.c:301:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/debug.c -o build/temp.macosx-10.6-intel-3.5/src/debug.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/decode.c -o build/temp.macosx-10.6-intel-3.5/src/decode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/decode.c:96:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i<lkey;i++) ~^~~~~ src/decode.c:111:6: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] i < lcompact; ~ ^ ~~~~~~~~ 2 warnings generated. src/decode.c:96:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i<lkey;i++) ~^~~~~ src/decode.c:111:6: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] i < lcompact; ~ ^ ~~~~~~~~ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/encode.c -o build/temp.macosx-10.6-intel-3.5/src/encode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/fastq.c -o build/temp.macosx-10.6-intel-3.5/src/fastq.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/fastq.c:132:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] forwardLength>0 && forwardLength<readLength; ~~~~~~~~~~~~~^~~~~~~~~~~ src/fastq.c:163:25: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] reverseLength < readLength ); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:21: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:54: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ 4 warnings generated. src/fastq.c:132:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] forwardLength>0 && forwardLength<readLength; ~~~~~~~~~~~~~^~~~~~~~~~~ src/fastq.c:163:25: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] reverseLength < readLength ); ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:21: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ src/fastq.c:169:54: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if ((forwardLength >= readLength) && (reverseLength >= readLength)) { ~~~~~~~~~~~~~ ^ ~~~~~~~~~~ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/indexinput.c -o build/temp.macosx-10.6-intel-3.5/src/indexinput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/indexoutput.c -o build/temp.macosx-10.6-intel-3.5/src/indexoutput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/load.c -o build/temp.macosx-10.6-intel-3.5/src/load.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/load.c:19:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0;i < reads->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~ 1 warning generated. src/load.c:19:13: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0;i < reads->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/lookfor.c -o build/temp.macosx-10.6-intel-3.5/src/lookfor.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/malloc.c -o build/temp.macosx-10.6-intel-3.5/src/malloc.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/sort.c -o build/temp.macosx-10.6-intel-3.5/src/sort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/sort.c:402:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ src/sort.c:430:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ src/sort.c:463:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ 3 warnings generated. src/sort.c:402:9: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare] if (i > nextprint) ~ ^ ~~~~~~~~~ src/sort.c:430:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ src/sort.c:463:14: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (i=0; i < buffer->readCount; i++) ~ ^ ~~~~~~~~~~~~~~~~~ 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -Ifiboheap -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c src/fgetln.c -o build/temp.macosx-10.6-intel-3.5/src/fgetln.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/_orgasm.o build/temp.macosx-10.6-intel-3.5/src/buffer.o build/temp.macosx-10.6-intel-3.5/src/buildindex.o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/code16bits.o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/codecomp.o build/temp.macosx-10.6-intel-3.5/src/compsort.o build/temp.macosx-10.6-intel-3.5/src/debug.o build/temp.macosx-10.6-intel-3.5/src/decode.o build/temp.macosx-10.6-intel-3.5/src/encode.o build/temp.macosx-10.6-intel-3.5/src/fastq.o build/temp.macosx-10.6-intel-3.5/src/indexinput.o build/temp.macosx-10.6-intel-3.5/src/indexoutput.o build/temp.macosx-10.6-intel-3.5/src/load.o build/temp.macosx-10.6-intel-3.5/src/lookfor.o build/temp.macosx-10.6-intel-3.5/src/malloc.o build/temp.macosx-10.6-intel-3.5/src/sort.o build/temp.macosx-10.6-intel-3.5/src/fgetln.o -o build/lib.macosx-10.6-intel-3.5/orgasm/indexer/_orgasm.cpython-35m-darwin.so orgasm.indexer.fakereads :-> ['python/orgasm/indexer/fakereads.pyx'] cythoning python/orgasm/indexer/fakereads.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c building 'orgasm.indexer.fakereads' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1082:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((abs(__pyx_v_id) >= __pyx_v_self->_firstid) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1088:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((abs(__pyx_v_id) < __pyx_v_self->_nextid) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1309:53: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((PyBytes_GET_SIZE(__pyx_v_seq) == __pyx_v_self->_readsize) != 0))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:472:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:4312:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:4427:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:3917:36: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:3944:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1082:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((abs(__pyx_v_id) >= __pyx_v_self->_firstid) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1088:33: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] __pyx_t_8 = ((abs(__pyx_v_id) < __pyx_v_self->_nextid) != 0); ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:1309:53: warning: comparison of integers of different signs: 'Py_ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare] if (unlikely(!((PyBytes_GET_SIZE(__pyx_v_seq) == __pyx_v_self->_readsize) != 0))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:472:43: note: expanded from macro 'unlikely' #define unlikely(x) __builtin_expect(!!(x), 0) ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:4312:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char* c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:4427:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:3917:36: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.c:3944:31: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/indexer/fakereads.o -o build/lib.macosx-10.6-intel-3.5/orgasm/indexer/fakereads.cpython-35m-darwin.so orgasm.multialign._dynamic :-> ['python/orgasm/multialign/_dynamic.pyx'] cythoning python/orgasm/multialign/_dynamic.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign building 'orgasm.multialign._dynamic' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4725:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char* c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4790:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4840:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4902:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4272:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4457:26: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ 6 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4725:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4790:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4840:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4902:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4272:27: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.c:4457:26: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { ^ 6 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_dynamic.o -o build/lib.macosx-10.6-intel-3.5/orgasm/multialign/_dynamic.cpython-35m-darwin.so orgasm.multialign._multi :-> ['python/orgasm/multialign/_multi.pyx'] cythoning python/orgasm/multialign/_multi.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.c building 'orgasm.multialign._multi' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -Isrc -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.c:2654:68: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_9 = ((-__pyx_v_delta) + __pyx_v_shift); __pyx_t_9 < __pyx_t_13; __pyx_t_9+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ 1 warning generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.c:2654:68: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] for (__pyx_t_9 = ((-__pyx_v_delta) + __pyx_v_shift); __pyx_t_9 < __pyx_t_13; __pyx_t_9+=1) { ~~~~~~~~~ ^ ~~~~~~~~~~ 1 warning generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/multialign/_multi.o -o build/lib.macosx-10.6-intel-3.5/orgasm/multialign/_multi.cpython-35m-darwin.so orgasm.utils._progress :-> ['python/orgasm/utils/_progress.pyx'] cythoning python/orgasm/utils/_progress.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c creating build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils building 'orgasm.utils._progress' extension creating build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:1624:21: warning: passing 'clock_t *' (aka 'unsigned long *') to parameter of type 'const time_t ' (aka 'const long ') converts between pointers to integer types with different sign [-Wpointer-sign] ((void)gmtime_r((&__pyx_v_more), (&__pyx_v_remain))); ^~~~~~~~~~~~~~~ /usr/include/time.h:125:46: note: passing argument to parameter here struct tm gmtime_r(const time_t * __restrict, struct tm * __restrict); ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4112:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4227:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4289:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:2513:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:2528:32: warning: unused function '__Pyx_GetItemInt_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:3761:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { ^ 7 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:1624:21: warning: passing 'clock_t *' (aka 'unsigned long *') to parameter of type 'const time_t ' (aka 'const long ') converts between pointers to integer types with different sign [-Wpointer-sign] ((void)gmtime_r((&__pyx_v_more), (&__pyx_v_remain))); ^~~~~~~~~~~~~~~ /usr/include/time.h:125:46: note: passing argument to parameter here struct tm gmtime_r(const time_t * __restrict, struct tm * __restrict); ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4112:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4227:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:4289:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:2513:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:2528:32: warning: unused function '__Pyx_GetItemInt_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Fast(PyObject o, Py_ssize_t i, int is_list, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.c:3761:35: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 7 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/_progress.o -o build/lib.macosx-10.6-intel-3.5/orgasm/utils/_progress.cpython-35m-darwin.so orgasm.utils.dna :-> ['python/orgasm/utils/dna.pyx'] cythoning python/orgasm/utils/dna.pyx to build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c building 'orgasm.utils.dna' extension /usr/bin/clang -fno-strict-aliasing -Wsign-compare -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -arch i386 -arch x86_64 -g -DLITTLE_END -I/Applications/ORG.asm-0.2.06/include -I/Library/Frameworks/Python.framework/Versions/3.5/include/python3.5m -c build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c -o build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.o build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3154:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3219:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3269:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3331:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2307:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2322:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_GetItemInt_Tuple_Fast(PyObject o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2591:32: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2776:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2803:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject x) { ^ 9 warnings generated. build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3154:32: warning: unused function '__Pyx_PyUnicode_FromString' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyUnicode_FromString(const char c_str) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3219:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3269:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject b) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:3331:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2307:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2322:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2591:32: warning: function '__Pyx_PyInt_As_int' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject x) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2776:38: warning: unused function '__Pyx_PyInt_From_long' [-Wunused-function] static CYTHON_INLINE PyObject __Pyx_PyInt_From_long(long value) { ^ build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.c:2803:33: warning: function '__Pyx_PyInt_As_long' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { ^ 9 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/build/temp.macosx-10.6-intel-3.5/pyrex/orgasm/utils/dna.o -o build/lib.macosx-10.6-intel-3.5/orgasm/utils/dna.cpython-35m-darwin.so running build_scripts creating build/raw_scripts Store the raw script python/oa.py -> build/raw_scripts/oa.py copying python/oa.py -> build/raw_scripts copying and adjusting python/oa.py -> build/scripts-3.5 changing mode of build/scripts-3.5/oa from 644 to 755 running build_sphinx creating /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx creating /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/doctrees creating /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html Running Sphinx v1.4.6 WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. loading pickled environment... not yet created building [mo]: targets for 0 po files that are out of date building [html]: targets for 33 source files that are out of date updating environment: 33 added, 0 changed, 0 removed reading sources... [100%] utilities
/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:32: ERROR: Unexpected indentation. /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:59: WARNING: Inline substitution_reference start-string without end-string. /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:60: WARNING: Definition list ends without a blank line; unexpected unindent. /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:105: ERROR: Unexpected indentation. /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/buildgraph.rst:223: WARNING: Duplicate explicit target name: "bwa". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/fillgaps.rst:26: ERROR: Error in "program" directive: no content permitted.

.. program:: oa fillgaps

usage: oa fillgaps [-h] [--minread BUILDGRAPH:MINREAD]
                   [--coverage BUILDGRAPH:COVERAGE]
                   [--minratio BUILDGRAPH:MINRATIO]
                   [--mincov BUILDGRAPH:MINCOV]
                   [--minoverlap BUILDGRAPH:MINOVERLAP]
                   [--smallbranches BUILDGRAPH:SMALLBRANCHES]
                   [--lowcomplexity] [--back ORGASM:BACK] [--snp]
                   [--adapt5 adapt5] [--adapt3 adapt3]
                   [--seeds seeds] [--kup ORGASM:KUP]
                   index [output]

/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/fillgaps.rst:196: WARNING: Duplicate explicit target name: "bwa". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:85: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:160: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://pypi.python.org/pypi/org.asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://git.metabarcoding.org/org-asm/org-asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:41: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:44: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:81: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:619: WARNING: Duplicate explicit target name: "yed". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:12: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:13: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:449: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.intermediate.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:454: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:568: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.path.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:583: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.fasta /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.assembler". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/userapi.rst:2: SEVERE: Duplicate ID: "module-orgasm.tango". looking for now-outdated files... none found pickling environment... done checking consistency... /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done preparing documents... done None:None: WARNING: no matching candidate for image URI 'genome_size.'
None:None: WARNING: no matching candidate for image URI 'algorithms.' None:None: WARNING: no matching candidate for image URI 'algorithms/../extension.'
None:None: WARNING: no matching candidate for image URI 'algorithms/ahocorasick.'
None:None: WARNING: no matching candidate for image URI 'commands/../oa-buildgraph.'
None:None: WARNING: no matching candidate for image URI 'commands/../extension.' None:None: WARNING: no matching candidate for image URI 'commands/../oa-cutlow.'
None:None: WARNING: no matching candidate for image URI 'commands/../oa-fillgaps.'
None:None: WARNING: no matching candidate for image URI 'commands/../extension.' None:None: WARNING: no matching candidate for image URI 'commands/../oa-seeds.'
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting
None:None: WARNING: no matching candidate for image URI 'butterfly.mito.path.'
None:None: WARNING: no matching candidate for image URI './Kmer-histogram.'
None:None: WARNING: no matching candidate for image URI './graph.' None:None: WARNING: no matching candidate for image URI 'command-flowgram.' writing output... [100%] utilities
/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ### /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.## generating indices... genindex py-modindex highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... search copying static files... WARNING: html_static_path entry '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 48 warnings. creating /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/epub Running Sphinx v1.4.6 WARNING: while setting up extension sphinx.ext.autodoc: directive 'automodule' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoclass' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoexception' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autodata' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autofunction' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'automethod' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoattribute' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoinstanceattribute' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.todo: directive 'todo' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.todo: directive 'todolist' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'graphviz' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'graph' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'digraph' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.inheritance_diagram: directive 'inheritance-diagram' is already registered, it will be overridden WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.pngmath: role 'math' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.pngmath: role 'eq' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.pngmath: directive 'math' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testsetup' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testcleanup' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'doctest' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testcode' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testoutput' is already registered, it will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden WARNING: while setting up extension numfig: role 'page' is already registered, it will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden WARNING: while setting up extension numfig: role 'num' is already registered, it will be overridden loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [epub]: targets for 33 source files that are out of date updating environment: 0 added, 3 changed, 0 removed reading sources... [100%] mitochondrion
/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:85: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:160: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://pypi.python.org/pypi/org.asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://git.metabarcoding.org/org-asm/org-asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:41: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:44: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:81: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:619: WARNING: Duplicate explicit target name: "yed". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:12: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:13: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:449: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.intermediate.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:454: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:568: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.path.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:583: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.fasta looking for now-outdated files... none found pickling environment... done checking consistency... /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done preparing documents... done None:None: WARNING: no matching candidate for image URI 'genome_size.'
None:None: WARNING: no matching candidate for image URI 'algorithms.' None:None: WARNING: no matching candidate for image URI 'algorithms/../extension.'
None:None: WARNING: no matching candidate for image URI 'algorithms/ahocorasick.'
None:None: WARNING: no matching candidate for image URI 'commands/../oa-buildgraph.'
None:None: WARNING: no matching candidate for image URI 'commands/../extension.' None:None: WARNING: no matching candidate for image URI 'commands/../oa-cutlow.'
None:None: WARNING: no matching candidate for image URI 'commands/../oa-fillgaps.'
None:None: WARNING: no matching candidate for image URI 'commands/../extension.' None:None: WARNING: no matching candidate for image URI 'commands/../oa-seeds.'
WARNING: LaTeX command 'latex' cannot be run (needed for math display), check the pngmath_latex setting
None:None: WARNING: no matching candidate for image URI 'butterfly.mito.path.'
None:None: WARNING: no matching candidate for image URI './Kmer-histogram.'
None:None: WARNING: no matching candidate for image URI './graph.' None:None: WARNING: no matching candidate for image URI 'command-flowgram.' writing output... [100%] utilities
/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ### /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.## generating indices... genindex py-modindex highlighting module code... [100%] orgasm.assembler._assembler
writing additional pages... copying static files... WARNING: html_static_path entry '/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/_static' does not exist done copying extra files... done writing mimetype file... writing META-INF/container.xml file... writing content.opf file... writing toc.ncx file... writing OrganelleAssembler.epub file... build succeeded, 71 warnings. creating /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/man Running Sphinx v1.4.6 WARNING: while setting up extension sphinx.ext.autodoc: directive 'automodule' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoclass' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoexception' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autodata' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autofunction' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'automethod' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoattribute' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.autodoc: directive 'autoinstanceattribute' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todolist' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.todo']: node class 'todo_node' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.todo: directive 'todo' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.todo: directive 'todolist' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.graphviz']: node class 'graphviz' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'graphviz' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'graph' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.graphviz: directive 'digraph' is already registered, it will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.inheritance_diagram']: node class 'inheritance_diagram' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.inheritance_diagram: directive 'inheritance-diagram' is already registered, it will be overridden WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead. WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'displaymath' is already registered, its visitors will be overridden WARNING: while setting up extension ['?', 'sphinx.ext.pngmath']: node class 'eqref' is already registered, its visitors will be overridden WARNING: while setting up extension sphinx.ext.pngmath: role 'math' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.pngmath: role 'eq' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.pngmath: directive 'math' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testsetup' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testcleanup' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'doctest' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testcode' is already registered, it will be overridden WARNING: while setting up extension sphinx.ext.doctest: directive 'testoutput' is already registered, it will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'page_ref' is already registered, its visitors will be overridden WARNING: while setting up extension numfig: role 'page' is already registered, it will be overridden WARNING: while setting up extension ['?', 'numfig']: node class 'num_ref' is already registered, its visitors will be overridden WARNING: while setting up extension numfig: role 'num' is already registered, it will be overridden loading pickled environment... done building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: 0 added, 3 changed, 0 removed reading sources... [100%] mitochondrion
/private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:85: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/fastq.rst:160: WARNING: image file not readable: Probabilitymetrics.png /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://pypi.python.org/pypi/org.asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:10: ERROR: Unknown target name: "https://git.metabarcoding.org/org-asm/org-asm". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:41: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:44: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/install.rst:81: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/get_orgasm/get-orgasm.py /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:619: WARNING: Duplicate explicit target name: "yed". /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:12: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:13: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R1.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:149: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/papi_R2.fastq.gz /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:449: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.intermediate.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:454: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:568: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.path.gml /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/mitochondrion.rst:583: WARNING: download file not readable: /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/samples/butterfly.mito.fasta looking for now-outdated files... none found pickling environment... done checking consistency... /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/chroroplast.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/graphstats.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/iupac.rst:: WARNING: document isn't included in any toctree /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/userapi.rst:: WARNING: document isn't included in any toctree done writing... organelleassembler.1 { install oa preparing commands/index assembling commands/seeds commands/buildgraph finishing commands/fillgaps commands/cutlow unfolding commands/unfold commands/unfoldrdna commands/path commands/fasta utilities commands/list commands/compact fasta fastq embl mitochondrion algorithms algorithms/seedselection algorithms/graphextension algorithms/graphcleanning algorithms/gapfilling algorithms/graphunfolding } /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --length ### /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/doc/sphinx/source/commands/index.rst:211: WARNING: unknown option: --estimate-length #.##

build succeeded, 55 warnings. running install_lib creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm copying build/lib.macosx-10.6-intel-3.5/orgasm/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/pycache/tango.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/pycache/version.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/pycache creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/arguments.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/command.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/config.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/logging.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps copying build/lib.macosx-10.6-intel-3.5/orgasm/apps/progress.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/apps creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler copying build/lib.macosx-10.6-intel-3.5/orgasm/assembler/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/assembler/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_asmbgraph.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler copying build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_assembler.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler copying build/lib.macosx-10.6-intel-3.5/orgasm/assembler/_tango.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/assembler creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/pycache/fasta.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/_ahocorasick.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/_bitvector.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate copying build/lib.macosx-10.6-intel-3.5/orgasm/backtranslate/fasta.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/backtranslate creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/buildgraph.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/clone.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/compact.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/cutlow.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/fasta.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/graphstats.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/index.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/list.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/path.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/seeds.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/substract.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/unfold.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/commands/unfoldrdna.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands copying build/lib.macosx-10.6-intel-3.5/orgasm/config.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/fiboheap copying build/lib.macosx-10.6-intel-3.5/orgasm/fiboheap/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/fiboheap copying build/lib.macosx-10.6-intel-3.5/orgasm/fiboheap/_fiboheap.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/fiboheap creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files copying build/lib.macosx-10.6-intel-3.5/orgasm/files/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files copying build/lib.macosx-10.6-intel-3.5/orgasm/files/linebuffer.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files copying build/lib.macosx-10.6-intel-3.5/orgasm/files/uncompress.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files copying build/lib.macosx-10.6-intel-3.5/orgasm/files/universalopener.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibointheap.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibomaxintheap.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/_fibominintheap.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/_graph.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph copying build/lib.macosx-10.6-intel-3.5/orgasm/graph/_graphmultiedge.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/graph creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer copying build/lib.macosx-10.6-intel-3.5/orgasm/indexer/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/indexer/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/indexer/_orgasm.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer copying build/lib.macosx-10.6-intel-3.5/orgasm/indexer/fakereads.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/indexer creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign copying build/lib.macosx-10.6-intel-3.5/orgasm/multialign/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/multialign/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/multialign/_dynamic.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign copying build/lib.macosx-10.6-intel-3.5/orgasm/multialign/_multi.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/multialign creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/samples copying build/lib.macosx-10.6-intel-3.5/orgasm/samples/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/samples creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/samples/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/samples/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/samples/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/tango.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils copying build/lib.macosx-10.6-intel-3.5/orgasm/utils/init.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils creating /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/utils/pycache/init.cpython-35.pyc -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils/pycache copying build/lib.macosx-10.6-intel-3.5/orgasm/utils/_progress.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils copying build/lib.macosx-10.6-intel-3.5/orgasm/utils/dna.cpython-35m-darwin.so -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/utils copying build/lib.macosx-10.6-intel-3.5/orgasm/version.py -> /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/buildgraph.py to buildgraph.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/clone.py to clone.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/compact.py to compact.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/cutlow.py to cutlow.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/fasta.py to fasta.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/graphstats.py to graphstats.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/index.py to index.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/list.py to list.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/path.py to path.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/seeds.py to seeds.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/substract.py to substract.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/unfold.py to unfold.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/commands/unfoldrdna.py to unfoldrdna.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/config.py to config.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/fiboheap/init.py to init.cpython-35.pyc byte-compiling /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/orgasm/files/init.py to init.cpython-35.pyc running install_scripts copying build/scripts-3.5/oa -> /Applications/ORG.asm-0.2.06/bin copying build/scripts-3.5/orgasmi -> /Applications/ORG.asm-0.2.06/bin copying build/scripts-3.5/pidname -> /Applications/ORG.asm-0.2.06/bin changing mode of /Applications/ORG.asm-0.2.06/bin/oa to 755 changing mode of /Applications/ORG.asm-0.2.06/bin/orgasmi to 755 changing mode of /Applications/ORG.asm-0.2.06/bin/pidname to 755 creating /Applications/ORG.asm-0.2.06/export creating /Applications/ORG.asm-0.2.06/export/bin exporting file /Applications/ORG.asm-0.2.06/bin/oa -> /Applications/ORG.asm-0.2.06/export/bin/oa exporting file /Applications/ORG.asm-0.2.06/bin/orgasmi -> /Applications/ORG.asm-0.2.06/export/bin/orgasmi exporting file /Applications/ORG.asm-0.2.06/bin/pidname -> /Applications/ORG.asm-0.2.06/export/bin/pidname running install_egg_info Writing /Applications/ORG.asm-0.2.06/lib/python3.5/site-packages/ORG.asm-0.2.06-py3.5.egg-info running install_sphinx creating /Applications/ORG.asm-0.2.06/export/share creating /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/.buildinfo -> /Applications/ORG.asm-0.2.06/export/share/html creating /Applications/ORG.asm-0.2.06/export/share/html/_modules copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_modules/index.html -> /Applications/ORG.asm-0.2.06/export/share/html/_modules creating /Applications/ORG.asm-0.2.06/export/share/html/_modules/orgasm copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_modules/orgasm/tango.html -> /Applications/ORG.asm-0.2.06/export/share/html/_modules/orgasm creating /Applications/ORG.asm-0.2.06/export/share/html/_sources creating /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms/gapfilling.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms/graphcleanning.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms/graphextension.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms/graphunfolding.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms/seedselection.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/algorithms.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/assembling.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/chroroplast.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources creating /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/buildgraph.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/compact.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/cutlow.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/fasta.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/fillgaps.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/graphstats.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/index.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/list.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/path.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/seeds.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/unfold.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/commands/unfoldrdna.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/embl.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/fasta.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/fastq.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/finishing.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/index.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/install.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/iupac.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/mitochondrion.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/oa.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/preparing.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/unfolding.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/userapi.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_sources/utilities.txt -> /Applications/ORG.asm-0.2.06/export/share/html/_sources creating /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/ajax-loader.gif -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/basic.css -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/comment-bright.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/comment-close.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/comment.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/doctools.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/down-pressed.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/down.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/file.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/jquery-1.11.1.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/jquery.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/minus.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/nature.css -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/plus.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/pygments.css -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/searchtools.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/underscore-1.3.1.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/underscore.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/up-pressed.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/up.png -> /Applications/ORG.asm-0.2.06/export/share/html/_static copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/_static/websupport.js -> /Applications/ORG.asm-0.2.06/export/share/html/_static creating /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms/gapfilling.html -> /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms/graphcleanning.html -> /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms/graphextension.html -> /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms/graphunfolding.html -> /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms/seedselection.html -> /Applications/ORG.asm-0.2.06/export/share/html/algorithms copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/algorithms.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/assembling.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/chroroplast.html -> /Applications/ORG.asm-0.2.06/export/share/html creating /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/buildgraph.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/compact.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/cutlow.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/fasta.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/fillgaps.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/graphstats.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/index.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/list.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/path.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/seeds.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/unfold.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/commands/unfoldrdna.html -> /Applications/ORG.asm-0.2.06/export/share/html/commands copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/embl.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/fasta.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/fastq.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/finishing.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/genindex.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/index.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/install.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/iupac.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/mitochondrion.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/oa.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/objects.inv -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/preparing.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/py-modindex.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/search.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/searchindex.js -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/unfolding.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/userapi.html -> /Applications/ORG.asm-0.2.06/export/share/html copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/html/utilities.html -> /Applications/ORG.asm-0.2.06/export/share/html creating /Applications/ORG.asm-0.2.06/export/share/man creating /Applications/ORG.asm-0.2.06/export/share/man/man1 copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/man/organelleassembler.1 -> /Applications/ORG.asm-0.2.06/export/share/man/man1 copying /private/var/folders/_l/38kbt7dd0s7fnxxgyjk0cwyw0000gp/T/tmpe6lvac83/ORG.asm-0.2.06/build/sphinx/epub/OrganelleAssembler.epub -> /Applications/ORG.asm-0.2.06/export/share