Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'], chrootPath='/var/lib/mock/openeuler-22.03_LTS_SP1-x86_64-1686472511.921166/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=True) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False /etc/profile.d/system-info.sh: line 55: ps: command not found Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/python-ORG.asm-1.0.3-1.src.rpm Child return code was: 0 Mock Version: 3.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'], chrootPath='/var/lib/mock/openeuler-22.03_LTS_SP1-x86_64-1686472511.921166/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=True) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False /etc/profile.d/system-info.sh: line 55: ps: command not found Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/python-ORG.asm-1.0.3-1.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'], chrootPath='/var/lib/mock/openeuler-22.03_LTS_SP1-x86_64-1686472511.921166/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=True) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False /etc/profile.d/system-info.sh: line 55: ps: command not found Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.ZjbNI1 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf ORG.asm-1.0.3 + /usr/bin/gzip -dc /builddir/build/SOURCES/ORG.asm-1.0.3.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd ORG.asm-1.0.3 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.7SAxkV + umask 022 + cd /builddir/build/BUILD + cd ORG.asm-1.0.3 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s' ['/builddir/build/BUILD/ORG.asm-1.0.3', '/usr/lib64/python39.zip', '/usr/lib64/python3.9', '/usr/lib64/python3.9/lib-dynload', '/usr/lib64/python3.9/site-packages', '/usr/lib/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/distutils.ext', '/builddir/build/BUILD/ORG.asm-1.0.3/python'] ---------------- setup.py build --executable=/usr/bin/python3 -s ---------------- Installing ORG.asm (1.0.3) in serenity mode You are running the good python Restarting installation within the ORG.asm-1.0.3 virtualenv Install script restarting... ['/builddir/build/BUILD/ORG.asm-1.0.3', '/usr/lib64/python39.zip', '/usr/lib64/python3.9', '/usr/lib64/python3.9/lib-dynload', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/distutils.ext', '/builddir/build/BUILD/ORG.asm-1.0.3/python'] ---------------- setup.py build --executable=/usr/bin/python3 -s ---------------- Installing ORG.asm (1.0.3) in serenity mode You are running the good python ORG.asm will be installed with python : /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/python Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : not installed Installing requirement : Cython Looking in indexes: https://pypi.org/simple, https://pypi.python.org/simple/ WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError(': Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/cython/ Collecting Cython Downloading Cython-0.29.35-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (2.0 MB) Requirement already satisfied: pip in ./ORG.asm-1.0.3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (21.3.1) Collecting Sphinx Downloading sphinx-7.0.1-py3-none-any.whl (3.0 MB) Collecting imagesize>=1.3 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting alabaster<0.8,>=0.7 Downloading alabaster-0.7.13-py3-none-any.whl (13 kB) Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Collecting requests>=2.25.0 Downloading requests-2.31.0-py3-none-any.whl (62 kB) Collecting babel>=2.9 Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB) Collecting docutils<0.21,>=0.18.1 Downloading docutils-0.20.1-py3-none-any.whl (572 kB) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting snowballstemmer>=2.0 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting importlib-metadata>=4.8 Downloading importlib_metadata-6.6.0-py3-none-any.whl (22 kB) Collecting Jinja2>=3.0 Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB) Collecting Pygments>=2.13 Downloading Pygments-2.15.1-py3-none-any.whl (1.1 MB) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Collecting packaging>=21.0 Downloading packaging-23.1-py3-none-any.whl (48 kB) Collecting zipp>=0.5 Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting certifi>=2017.4.17 Downloading certifi-2023.5.7-py3-none-any.whl (156 kB) Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) Collecting urllib3<3,>=1.21.1 Downloading urllib3-2.0.3-py3-none-any.whl (123 kB) Collecting charset-normalizer<4,>=2 Downloading charset_normalizer-3.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (199 kB) Installing collected packages: zipp, urllib3, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, requests, Pygments, packaging, Jinja2, importlib-metadata, imagesize, docutils, babel, alabaster, Sphinx, Cython Successfully installed Cython-0.29.35 Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.15.1 Sphinx-7.0.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.1.0 docutils-0.20.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.6.0 packaging-23.1 requests-2.31.0 snowballstemmer-2.2.0 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 urllib3-2.0.3 zipp-3.15.0 WARNING: You are using pip version 21.3.1; however, version 23.1.2 is available. You should consider upgrading via the '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/python3 -m pip install --upgrade pip' command. Look for package Sphinx : ok version 7.0.1 installed Restarting installation with all dependencies ok Install script restarting... ['/builddir/build/BUILD/ORG.asm-1.0.3', '/usr/lib64/python39.zip', '/usr/lib64/python3.9', '/usr/lib64/python3.9/lib-dynload', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/distutils.ext', '/builddir/build/BUILD/ORG.asm-1.0.3/python'] ---------------- setup.py build --executable=/usr/bin/python3 -s ---------------- Installing ORG.asm (1.0.3) in serenity mode You are running the good python ORG.asm will be installed with python : /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/python Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed You are running the good python Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h'] Cython module : [] Cython module : [] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h'] running build running littlebigman creating build creating build/temp.linux-x86_64-3.9 building 'littlebigman' program creating build/temp.linux-x86_64-3.9/distutils.ext creating build/temp.linux-x86_64-3.9/distutils.ext/src gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -c distutils.ext/src/littlebigman.c -o build/temp.linux-x86_64-3.9/distutils.ext/src/littlebigman.o -msse2 distutils.ext/src/littlebigman.c: In function ‘main’: distutils.ext/src/littlebigman.c:20:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 20 | else | ^~~~ distutils.ext/src/littlebigman.c:23:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 23 | return 0; | ^~~~~~ gcc build/temp.linux-x86_64-3.9/distutils.ext/src/littlebigman.o -o build/temp.linux-x86_64-3.9/littlebigman Your CPU is in mode : -DLITTLE_END running build_py creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/orgasm copying python/orgasm/version.py -> build/lib.linux-x86_64-3.9/orgasm copying python/orgasm/config.py -> build/lib.linux-x86_64-3.9/orgasm copying python/orgasm/tango.py -> build/lib.linux-x86_64-3.9/orgasm copying python/orgasm/__init__.py -> build/lib.linux-x86_64-3.9/orgasm creating build/lib.linux-x86_64-3.9/orgasm/graph copying python/orgasm/graph/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/graph creating build/lib.linux-x86_64-3.9/orgasm/files copying python/orgasm/files/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/files creating build/lib.linux-x86_64-3.9/orgasm/apps copying python/orgasm/apps/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/apps creating build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/index.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/graphstats.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/cutlow.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/restore.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/graph.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/clone.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/substract.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/unfoldrdna.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/unfold.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/list.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/seeds.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/compact.py -> build/lib.linux-x86_64-3.9/orgasm/commands copying python/orgasm/commands/buildgraph.py -> build/lib.linux-x86_64-3.9/orgasm/commands creating build/lib.linux-x86_64-3.9/orgasm/format copying python/orgasm/format/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/format creating build/lib.linux-x86_64-3.9/orgasm/utils copying python/orgasm/utils/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/utils creating build/lib.linux-x86_64-3.9/orgasm/samples copying python/orgasm/samples/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/samples copying python/orgasm/samples/phix.py -> build/lib.linux-x86_64-3.9/orgasm/samples creating build/lib.linux-x86_64-3.9/orgasm/indexer copying python/orgasm/indexer/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/indexer creating build/lib.linux-x86_64-3.9/orgasm/reads copying python/orgasm/reads/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/reads creating build/lib.linux-x86_64-3.9/orgasm/backtranslate copying python/orgasm/backtranslate/fasta.py -> build/lib.linux-x86_64-3.9/orgasm/backtranslate copying python/orgasm/backtranslate/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/backtranslate creating build/lib.linux-x86_64-3.9/orgasm/fiboheap copying python/orgasm/fiboheap/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/fiboheap creating build/lib.linux-x86_64-3.9/orgasm/assembler copying python/orgasm/assembler/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/assembler creating build/lib.linux-x86_64-3.9/orgasm/multialign copying python/orgasm/multialign/__init__.py -> build/lib.linux-x86_64-3.9/orgasm/multialign running build_ext Look for CPU architecture... [('LITTLE_END', None)] running build_files running build_ctools building 'buildcomplement' program creating build/temp.linux-x86_64-3.9/src gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/buildcomplement.c -o build/temp.linux-x86_64-3.9/src/buildcomplement.o -msse2 gcc build/temp.linux-x86_64-3.9/src/buildcomplement.o -o build/temp.linux-x86_64-3.9/buildcomplement building 'buildcode' program gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/buildcode.c -o build/temp.linux-x86_64-3.9/src/buildcode.o -msse2 src/buildcode.c: In function ‘main’: src/buildcode.c:44:39: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 44 | fprintf(stdout," INT64_C(0x%16llX), // %04X --> %8s \n", *((uint64_t*)nuc),code,nuc); | ~~~~~^ ~~~~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %16lX src/buildcode.c:46:39: warning: format ‘%llX’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long unsigned int’} [-Wformat=] 46 | fprintf(stdout," INT64_C(0x%16llX) // %04X --> %8s \n", *((uint64_t*)nuc),code,nuc); | ~~~~~^ ~~~~~~~~~~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %16lX gcc build/temp.linux-x86_64-3.9/src/buildcode.o -o build/temp.linux-x86_64-3.9/buildcode building 'buildexpand8bits' program gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/buildexpand8bits.c -o build/temp.linux-x86_64-3.9/src/buildexpand8bits.o -msse2 src/buildexpand8bits.c: In function ‘main’: src/buildexpand8bits.c:40:1: warning: multi-line comment [-Wcomment] 40 | // *((uint32_t*)nuc) = *((uint32_t*)nuc) >> 24 | \ | ^ gcc build/temp.linux-x86_64-3.9/src/buildexpand8bits.o -o build/temp.linux-x86_64-3.9/buildexpand8bits Building file : codecomp.c --> build/temp.linux-x86_64-3.9/buildcomplement > build/temp.linux-x86_64-3.9/codecomp.c Done. Building file : code16bits.c --> build/temp.linux-x86_64-3.9/buildcode > build/temp.linux-x86_64-3.9/code16bits.c Done. Building file : expand8bits.c --> build/temp.linux-x86_64-3.9/buildexpand8bits > build/temp.linux-x86_64-3.9/expand8bits.c Done. running build_cexe Look for CPU architecture... [('LITTLE_END', None)] creating build/scripts-3.9 orgasmi :-> src/orgasmi.c ok orgasmi :-> src/buffer.c ok orgasmi :-> src/buildindex.c ok orgasmi :-> @code16bits.c changed to build/temp.linux-x86_64-3.9/code16bits.c orgasmi :-> @codecomp.c changed to build/temp.linux-x86_64-3.9/codecomp.c orgasmi :-> src/compsort.c ok orgasmi :-> src/debug.c ok orgasmi :-> src/decode.c ok orgasmi :-> src/encode.c ok orgasmi :-> src/fastq.c ok orgasmi :-> src/indexinput.c ok orgasmi :-> src/indexoutput.c ok orgasmi :-> src/load.c ok orgasmi :-> src/lookfor.c ok orgasmi :-> src/malloc.c ok orgasmi :-> src/fgetln.c ok orgasmi :-> src/sort.c ok building 'orgasmi' program creating build/temp.linux-x86_64-3.9/build creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/orgasmi.c -o build/temp.linux-x86_64-3.9/src/orgasmi.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/buffer.c -o build/temp.linux-x86_64-3.9/src/buffer.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/buildindex.c -o build/temp.linux-x86_64-3.9/src/buildindex.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.9/code16bits.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/code16bits.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c build/temp.linux-x86_64-3.9/codecomp.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/codecomp.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/compsort.c -o build/temp.linux-x86_64-3.9/src/compsort.o -msse2 src/compsort.c: In function ‘sortCompSuffix’: src/compsort.c:305:9: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 305 | if (i > nextprint) | ^ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/debug.c -o build/temp.linux-x86_64-3.9/src/debug.o -msse2 src/debug.c: In function ‘int2bin’: src/debug.c:23:10: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 23 | u = *(unsigned *)&i; | ^~~~~~~~~~~~~~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/decode.c -o build/temp.linux-x86_64-3.9/src/decode.o -msse2 src/decode.c: In function ‘decodeComp’: src/decode.c:96:13: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for (i=0; i0 && forwardLength= readLength) && (reverseLength >= readLength)) { | ^~ src/fastq.c:171:54: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 171 | if ((forwardLength >= readLength) && (reverseLength >= readLength)) { | ^~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/indexinput.c -o build/temp.linux-x86_64-3.9/src/indexinput.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/indexoutput.c -o build/temp.linux-x86_64-3.9/src/indexoutput.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/load.c -o build/temp.linux-x86_64-3.9/src/load.o -msse2 src/load.c: In function ‘indexReverseComplement’: src/load.c:19:13: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 19 | for (i=0;i < reads->readCount; i++) | ^ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/lookfor.c -o build/temp.linux-x86_64-3.9/src/lookfor.o -msse2 src/lookfor.c: In function ‘shiftKey’: src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable] 47 | uint8_t rmask; | ^~~~~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/malloc.c -o build/temp.linux-x86_64-3.9/src/malloc.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/fgetln.c -o build/temp.linux-x86_64-3.9/src/fgetln.o -msse2 gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -c src/sort.c -o build/temp.linux-x86_64-3.9/src/sort.o -msse2 src/sort.c: In function ‘sortSuffix’: src/sort.c:406:9: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 406 | if (i > nextprint) | ^ src/sort.c: In function ‘indexForward’: src/sort.c:435:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 435 | for (i=0; i < buffer->readCount; i++) | ^ src/sort.c: In function ‘indexReverse’: src/sort.c:468:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 468 | for (i=0; i < buffer->readCount; i++) | ^ gcc build/temp.linux-x86_64-3.9/src/orgasmi.o build/temp.linux-x86_64-3.9/src/buffer.o build/temp.linux-x86_64-3.9/src/buildindex.o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/code16bits.o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/codecomp.o build/temp.linux-x86_64-3.9/src/compsort.o build/temp.linux-x86_64-3.9/src/debug.o build/temp.linux-x86_64-3.9/src/decode.o build/temp.linux-x86_64-3.9/src/encode.o build/temp.linux-x86_64-3.9/src/fastq.o build/temp.linux-x86_64-3.9/src/indexinput.o build/temp.linux-x86_64-3.9/src/indexoutput.o build/temp.linux-x86_64-3.9/src/load.o build/temp.linux-x86_64-3.9/src/lookfor.o build/temp.linux-x86_64-3.9/src/malloc.o build/temp.linux-x86_64-3.9/src/fgetln.o build/temp.linux-x86_64-3.9/src/sort.o -o build/scripts-3.9/orgasmi orgasm.graph._fibominintheap :-> python/orgasm/graph/_fibominintheap.pyx ok orgasm.graph._fibominintheap :-> fiboheap/fibo.c ok orgasm.graph._graphmultiedge :-> python/orgasm/graph/_graphmultiedge.pyx ok orgasm.graph._graph :-> python/orgasm/graph/_graph.pyx ok orgasm.graph._fibomaxintheap :-> python/orgasm/graph/_fibomaxintheap.pyx ok orgasm.graph._fibomaxintheap :-> fiboheap/fibo.c ok orgasm.graph._fibointheap :-> python/orgasm/graph/_fibointheap.pyx ok orgasm.graph._fibointheap :-> fiboheap/fibo.c ok orgasm.files.uncompress :-> python/orgasm/files/uncompress.pyx ok orgasm.files.linebuffer :-> python/orgasm/files/linebuffer.pyx ok orgasm.files.universalopener :-> python/orgasm/files/universalopener.pyx ok orgasm.apps.arguments :-> python/orgasm/apps/arguments.pyx ok orgasm.apps.counter :-> python/orgasm/apps/counter.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.format.sam :-> python/orgasm/format/sam.pyx ok orgasm.utils.dna :-> python/orgasm/utils/dna.pyx ok orgasm.utils._progress :-> python/orgasm/utils/_progress.pyx ok orgasm.indexer.fakereads :-> python/orgasm/indexer/fakereads.pyx ok orgasm.indexer._orgasm :-> python/orgasm/indexer/_orgasm.pyx ok orgasm.indexer._orgasm :-> src/buffer.c ok orgasm.indexer._orgasm :-> src/buildindex.c ok orgasm.indexer._orgasm :-> @code16bits.c changed to build/temp.linux-x86_64-3.9/code16bits.c orgasm.indexer._orgasm :-> @codecomp.c changed to build/temp.linux-x86_64-3.9/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.reads._fasta :-> python/orgasm/reads/_fasta.pyx ok orgasm.reads._fastq :-> python/orgasm/reads/_fastq.pyx ok orgasm.reads._sequences :-> python/orgasm/reads/_sequences.pyx ok orgasm.backtranslate._bitvector :-> python/orgasm/backtranslate/_bitvector.pyx ok orgasm.backtranslate._ahocorasick :-> python/orgasm/backtranslate/_ahocorasick.pyx ok orgasm.backtranslate._ahocorasick :-> @expand8bits.c changed to build/temp.linux-x86_64-3.9/expand8bits.c orgasm.fiboheap._fiboheap :-> python/orgasm/fiboheap/_fiboheap.pyx ok orgasm.fiboheap._fiboheap :-> fiboheap/fibo.c ok orgasm.assembler._asmbgraph :-> python/orgasm/assembler/_asmbgraph.pyx ok orgasm.assembler._tango :-> python/orgasm/assembler/_tango.pyx ok orgasm.assembler._assembler :-> python/orgasm/assembler/_assembler.pyx ok orgasm.multialign._multi :-> python/orgasm/multialign/_multi.pyx ok orgasm.multialign._dynamic :-> python/orgasm/multialign/_dynamic.pyx ok orgasm.graph._fibominintheap :-> ['python/orgasm/graph/_fibominintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibominintheap.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibominintheap.c creating build/temp.linux-x86_64-3.9/pyrex creating build/temp.linux-x86_64-3.9/pyrex/orgasm creating build/temp.linux-x86_64-3.9/pyrex/orgasm/graph building 'orgasm.graph._fibominintheap' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph creating build/temp.linux-x86_64-3.9/fiboheap gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibominintheap.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibominintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibominintheap.o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/graph/_fibominintheap.cpython-39-x86_64-linux-gnu.so orgasm.graph._graphmultiedge :-> ['python/orgasm/graph/_graphmultiedge.pyx'] cythoning python/orgasm/graph/_graphmultiedge.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graphmultiedge.c building 'orgasm.graph._graphmultiedge' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graphmultiedge.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graphmultiedge.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graphmultiedge.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/graph/_graphmultiedge.cpython-39-x86_64-linux-gnu.so orgasm.graph._graph :-> ['python/orgasm/graph/_graph.pyx'] cythoning python/orgasm/graph/_graph.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graph.c building 'orgasm.graph._graph' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graph.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_graph.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/graph/_graph.cpython-39-x86_64-linux-gnu.so orgasm.graph._fibomaxintheap :-> ['python/orgasm/graph/_fibomaxintheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibomaxintheap.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibomaxintheap.c building 'orgasm.graph._fibomaxintheap' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibomaxintheap.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibomaxintheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibomaxintheap.o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/graph/_fibomaxintheap.cpython-39-x86_64-linux-gnu.so orgasm.graph._fibointheap :-> ['python/orgasm/graph/_fibointheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/graph/_fibointheap.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibointheap.c building 'orgasm.graph._fibointheap' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibointheap.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibointheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/graph/_fibointheap.o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/graph/_fibointheap.cpython-39-x86_64-linux-gnu.so orgasm.files.uncompress :-> ['python/orgasm/files/uncompress.pyx'] cythoning python/orgasm/files/uncompress.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/files/uncompress.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/files building 'orgasm.files.uncompress' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/files/uncompress.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/uncompress.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/uncompress.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/files/uncompress.cpython-39-x86_64-linux-gnu.so orgasm.files.linebuffer :-> ['python/orgasm/files/linebuffer.pyx'] cythoning python/orgasm/files/linebuffer.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/files/linebuffer.c building 'orgasm.files.linebuffer' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/files/linebuffer.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/linebuffer.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/linebuffer.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/files/linebuffer.cpython-39-x86_64-linux-gnu.so orgasm.files.universalopener :-> ['python/orgasm/files/universalopener.pyx'] cythoning python/orgasm/files/universalopener.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/files/universalopener.c building 'orgasm.files.universalopener' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/files/universalopener.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/universalopener.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/files/universalopener.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/files/universalopener.cpython-39-x86_64-linux-gnu.so orgasm.apps.arguments :-> ['python/orgasm/apps/arguments.pyx'] cythoning python/orgasm/apps/arguments.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/arguments.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/apps building 'orgasm.apps.arguments' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/arguments.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/arguments.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/arguments.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/arguments.cpython-39-x86_64-linux-gnu.so orgasm.apps.counter :-> ['python/orgasm/apps/counter.pyx'] cythoning python/orgasm/apps/counter.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c building 'orgasm.apps.counter' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.o build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c: In function ‘__pyx_pf_6orgasm_4apps_7counter_15ProgressCounter_2__call__’: build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c:2531:47: warning: field width specifier ‘*’ expects argument of type ‘int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=] 2531 | ((void)fprintf(stderr, ((char *)"\r%s [%*d] speed : %*.1f %s/s"), __pyx_v_self->chead, __pyx_v_self->digits, __pyx_v_ipos, __pyx_v_self->digits, __pyx_v_speed, __pyx_v_self->cunit)); | ~^~ ~~~~~~~~~~~~~~~~~~~~ | | | | int long long unsigned int build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c:2531:48: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=] 2531 | ((void)fprintf(stderr, ((char *)"\r%s [%*d] speed : %*.1f %s/s"), __pyx_v_self->chead, __pyx_v_self->digits, __pyx_v_ipos, __pyx_v_self->digits, __pyx_v_speed, __pyx_v_self->cunit)); | ~~^ ~~~~~~~~~~~~ | | | | int long long unsigned int | %*lld build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.c:2531:60: warning: field width specifier ‘*’ expects argument of type ‘int’, but argument 6 has type ‘long long unsigned int’ [-Wformat=] 2531 | ((void)fprintf(stderr, ((char *)"\r%s [%*d] speed : %*.1f %s/s"), __pyx_v_self->chead, __pyx_v_self->digits, __pyx_v_ipos, __pyx_v_self->digits, __pyx_v_speed, __pyx_v_self->cunit)); | ~^~~~ ~~~~~~~~~~~~~~~~~~~~ | | | | int long long unsigned int gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/counter.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/counter.cpython-39-x86_64-linux-gnu.so orgasm.apps.command :-> ['python/orgasm/apps/command.pyx'] cythoning python/orgasm/apps/command.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/command.c building 'orgasm.apps.command' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/command.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/command.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/command.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/command.cpython-39-x86_64-linux-gnu.so orgasm.apps.config :-> ['python/orgasm/apps/config.pyx'] cythoning python/orgasm/apps/config.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/config.c building 'orgasm.apps.config' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/config.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/config.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/config.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/config.cpython-39-x86_64-linux-gnu.so orgasm.apps.logging :-> ['python/orgasm/apps/logging.pyx'] cythoning python/orgasm/apps/logging.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/logging.c building 'orgasm.apps.logging' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/logging.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/logging.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/logging.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/logging.cpython-39-x86_64-linux-gnu.so orgasm.apps.progress :-> ['python/orgasm/apps/progress.pyx'] cythoning python/orgasm/apps/progress.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c building 'orgasm.apps.progress' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.o build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c: In function ‘__pyx_pf_6orgasm_4apps_8progress_11ProgressBar_2__call__’: build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c:2640:59: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=] 2640 | ((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->diese, (__pyx_v_self->wheel[__pyx_v_self->arrow]), (50 - __pyx_v_fraction), __pyx_v_self->spaces, __pyx_v_days, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec)); | ~~^~ ~~~~~~~~~~~~~~~~ | | | | int long long unsigned int build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c:2640:65: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 8 has type ‘long long unsigned int’ [-Wformat=] 2640 | ((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->diese, (__pyx_v_self->wheel[__pyx_v_self->arrow]), (50 - __pyx_v_fraction), __pyx_v_self->spaces, __pyx_v_days, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec)); | ~~^~ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long long unsigned int build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c:2668:59: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=] 2668 | ((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->diese, (__pyx_v_self->wheel[__pyx_v_self->arrow]), (50 - __pyx_v_fraction), __pyx_v_self->spaces, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec)); | ~~^~ ~~~~~~~~~~~~~~~~ | | | | int long long unsigned int build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.c:2668:65: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 8 has type ‘long long unsigned int’ [-Wformat=] 2668 | ((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->diese, (__pyx_v_self->wheel[__pyx_v_self->arrow]), (50 - __pyx_v_fraction), __pyx_v_self->spaces, __pyx_v_hour, __pyx_v_minu, __pyx_v_sec)); | ~~^~ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long long unsigned int gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/apps/progress.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/apps/progress.cpython-39-x86_64-linux-gnu.so orgasm.format.sam :-> ['python/orgasm/format/sam.pyx'] cythoning python/orgasm/format/sam.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/format/sam.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/format building 'orgasm.format.sam' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/format gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/format/sam.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/format/sam.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/format/sam.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/format/sam.cpython-39-x86_64-linux-gnu.so orgasm.utils.dna :-> ['python/orgasm/utils/dna.pyx'] cythoning python/orgasm/utils/dna.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/dna.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/utils building 'orgasm.utils.dna' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/utils gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/dna.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/dna.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/dna.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/utils/dna.cpython-39-x86_64-linux-gnu.so orgasm.utils._progress :-> ['python/orgasm/utils/_progress.pyx'] cythoning python/orgasm/utils/_progress.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/_progress.c building 'orgasm.utils._progress' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/_progress.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/_progress.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/utils/_progress.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/utils/_progress.cpython-39-x86_64-linux-gnu.so orgasm.indexer.fakereads :-> ['python/orgasm/indexer/fakereads.pyx'] cythoning python/orgasm/indexer/fakereads.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer building 'orgasm.indexer.fakereads' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.o build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c: In function ‘__pyx_f_6orgasm_7indexer_9fakereads_9FakeReads_isFake’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c:1845:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1845 | __pyx_t_7 = ((abs(__pyx_v_id) >= __pyx_v_self->_firstid) != 0); | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c:1851:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1851 | __pyx_t_7 = ((abs(__pyx_v_id) < __pyx_v_self->_nextid) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c: In function ‘__pyx_f_6orgasm_7indexer_9fakereads_9FakeReads__getid’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c:2080:53: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2080 | if (unlikely(!((PyBytes_GET_SIZE(__pyx_v_seq) == __pyx_v_self->_readsize) != 0))) { | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.c:941:43: note: in definition of macro ‘unlikely’ 941 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/fakereads.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/indexer/fakereads.cpython-39-x86_64-linux-gnu.so orgasm.indexer._orgasm :-> ['python/orgasm/indexer/_orgasm.pyx', 'src/buffer.c', 'src/buildindex.c', 'build/temp.linux-x86_64-3.9/code16bits.c', 'build/temp.linux-x86_64-3.9/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.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c building 'orgasm.indexer._orgasm' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/code16bits.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/code16bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/codecomp.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/codecomp.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getRead’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:4708:35: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 4708 | if (unlikely(!((__pyx_v_begin < __pyx_v_self->_index->readSize) != 0))) { | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:955:43: note: in definition of macro ‘unlikely’ 955 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:4724:54: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 4724 | if (unlikely(!(((__pyx_v_begin + __pyx_v_length) <= __pyx_v_self->_index->readSize) != 0))) { | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:955:43: note: in definition of macro ‘unlikely’ 955 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:4776:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 4776 | __pyx_t_11 = ((abs(__pyx_v_readid) > __pyx_v_self->_index->readCount) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getReadIds’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:7492:31: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 7492 | if (unlikely(!((__pyx_t_5 == __pyx_v_self->_index->readSize) != 0))) { | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:955:43: note: in definition of macro ‘unlikely’ 955 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getPairedRead’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:7861:29: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 7861 | __pyx_t_7 = ((__pyx_v_iid > __pyx_v_self->_index->readCount) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c: In function ‘__pyx_f_6orgasm_7indexer_7_orgasm_5Index_getIds’: build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:9850:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9850 | __pyx_t_6 = ((__pyx_v_y > __pyx_v_self->_index->readCount) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:662:40: warning: ‘__pyx_v_t’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.c:9685:7: note: ‘__pyx_v_t’ was declared here 9685 | int __pyx_v_t; | ^~~~~~~~~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/buffer.c -o build/temp.linux-x86_64-3.9/src/buffer.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/buildindex.c -o build/temp.linux-x86_64-3.9/src/buildindex.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/compsort.c -o build/temp.linux-x86_64-3.9/src/compsort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/compsort.c: In function ‘sortCompSuffix’: src/compsort.c:305:9: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 305 | if (i > nextprint) | ^ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/debug.c -o build/temp.linux-x86_64-3.9/src/debug.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/debug.c: In function ‘int2bin’: src/debug.c:23:10: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 23 | u = *(unsigned *)&i; | ^~~~~~~~~~~~~~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/decode.c -o build/temp.linux-x86_64-3.9/src/decode.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/decode.c: In function ‘decodeComp’: src/decode.c:96:13: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 96 | for (i=0; i0 && forwardLength= readLength) && (reverseLength >= readLength)) { | ^~ src/fastq.c:171:54: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 171 | if ((forwardLength >= readLength) && (reverseLength >= readLength)) { | ^~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/fgetln.c -o build/temp.linux-x86_64-3.9/src/fgetln.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/indexinput.c -o build/temp.linux-x86_64-3.9/src/indexinput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/indexoutput.c -o build/temp.linux-x86_64-3.9/src/indexoutput.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/load.c -o build/temp.linux-x86_64-3.9/src/load.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/load.c: In function ‘indexReverseComplement’: src/load.c:19:13: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 19 | for (i=0;i < reads->readCount; i++) | ^ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/lookfor.c -o build/temp.linux-x86_64-3.9/src/lookfor.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/lookfor.c: In function ‘shiftKey’: src/lookfor.c:47:10: warning: variable ‘rmask’ set but not used [-Wunused-but-set-variable] 47 | uint8_t rmask; | ^~~~~ gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/malloc.c -o build/temp.linux-x86_64-3.9/src/malloc.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c src/sort.c -o build/temp.linux-x86_64-3.9/src/sort.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts src/sort.c: In function ‘sortSuffix’: src/sort.c:406:9: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 406 | if (i > nextprint) | ^ src/sort.c: In function ‘indexForward’: src/sort.c:435:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 435 | for (i=0; i < buffer->readCount; i++) | ^ src/sort.c: In function ‘indexReverse’: src/sort.c:468:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 468 | for (i=0; i < buffer->readCount; i++) | ^ gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/code16bits.o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/codecomp.o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/indexer/_orgasm.o build/temp.linux-x86_64-3.9/src/buffer.o build/temp.linux-x86_64-3.9/src/buildindex.o build/temp.linux-x86_64-3.9/src/compsort.o build/temp.linux-x86_64-3.9/src/debug.o build/temp.linux-x86_64-3.9/src/decode.o build/temp.linux-x86_64-3.9/src/encode.o build/temp.linux-x86_64-3.9/src/fastq.o build/temp.linux-x86_64-3.9/src/fgetln.o build/temp.linux-x86_64-3.9/src/indexinput.o build/temp.linux-x86_64-3.9/src/indexoutput.o build/temp.linux-x86_64-3.9/src/load.o build/temp.linux-x86_64-3.9/src/lookfor.o build/temp.linux-x86_64-3.9/src/malloc.o build/temp.linux-x86_64-3.9/src/sort.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/indexer/_orgasm.cpython-39-x86_64-linux-gnu.so orgasm.reads._fasta :-> ['python/orgasm/reads/_fasta.pyx'] cythoning python/orgasm/reads/_fasta.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fasta.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/reads /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/ORG.asm-1.0.3/python/orgasm/reads/_fasta.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'orgasm.reads._fasta' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fasta.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fasta.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fasta.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/reads/_fasta.cpython-39-x86_64-linux-gnu.so orgasm.reads._fastq :-> ['python/orgasm/reads/_fastq.pyx'] cythoning python/orgasm/reads/_fastq.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fastq.c /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/ORG.asm-1.0.3/python/orgasm/reads/_fastq.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'orgasm.reads._fastq' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fastq.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fastq.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_fastq.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/reads/_fastq.cpython-39-x86_64-linux-gnu.so orgasm.reads._sequences :-> ['python/orgasm/reads/_sequences.pyx'] cythoning python/orgasm/reads/_sequences.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/ORG.asm-1.0.3/python/orgasm/reads/_sequences.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'orgasm.reads._sequences' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c: In function ‘__pyx_f_6orgasm_5reads_10_sequences_bestQuality.constprop.isra’: build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c:662:40: warning: ‘__pyx_v_maxend’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c:5680:7: note: ‘__pyx_v_maxend’ was declared here 5680 | int __pyx_v_maxend; | ^~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c:662:40: warning: ‘__pyx_v_maxbegin’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c:5679:7: note: ‘__pyx_v_maxbegin’ was declared here 5679 | int __pyx_v_maxbegin; | ^~~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.c:5822:8: warning: ‘__pyx_v_maxscore’ may be used uninitialized in this function [-Wmaybe-uninitialized] 5822 | if (__pyx_t_2) { | ^ gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/reads/_sequences.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/reads/_sequences.cpython-39-x86_64-linux-gnu.so orgasm.backtranslate._bitvector :-> ['python/orgasm/backtranslate/_bitvector.pyx'] cythoning python/orgasm/backtranslate/_bitvector.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_bitvector.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate building 'orgasm.backtranslate._bitvector' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_bitvector.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_bitvector.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_bitvector.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/backtranslate/_bitvector.cpython-39-x86_64-linux-gnu.so orgasm.backtranslate._ahocorasick :-> ['python/orgasm/backtranslate/_ahocorasick.pyx', 'build/temp.linux-x86_64-3.9/expand8bits.c'] cythoning python/orgasm/backtranslate/_ahocorasick.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c building 'orgasm.backtranslate._ahocorasick' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/expand8bits.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/expand8bits.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_setAsTerminal’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:6169:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 6169 | __pyx_t_1 = ((__pyx_v_position > __pyx_v_self->_maxpos) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_simpleMatch’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:6718:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 6718 | __pyx_v_nextstate = (__pyx_v_table[__pyx_v_letter]); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_11AhoCorasick_addCWord’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:7765:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 7765 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_addSequence’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:10068:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 10068 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_13; __pyx_t_6+=1) { | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:10341:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 10341 | for (__pyx_t_6 = (__pyx_t_12 - 1); __pyx_t_6 > __pyx_t_13; __pyx_t_6-=1) { | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:9781:8: warning: variable ‘__pyx_v_letter’ set but not used [-Wunused-but-set-variable] 9781 | char __pyx_v_letter[2]; | ^~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:11768:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 11768 | __pyx_t_12 = (((__pyx_v_wc[__pyx_v_p]) > __pyx_v_wcmax) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:11883:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 11883 | __pyx_t_20 = ((__pyx_v_wcmax > __pyx_v_wordmax) != 0); | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:12109:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 12109 | __pyx_t_20 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_addSequence’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:12955:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 12955 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_12; __pyx_t_6+=1) { | ^ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:14387:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 14387 | __pyx_t_20 = ((__pyx_v_nbreads >= __pyx_v_covmin) != 0); | ^~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_15ProtAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:662:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:10802:7: note: ‘__pyx_v_locmax’ was declared here 10802 | int __pyx_v_locmax; | ^~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c: In function ‘__pyx_f_6orgasm_13backtranslate_12_ahocorasick_14NucAhoCorasick_scanIndex’: build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:662:40: warning: ‘__pyx_v_locmax’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.c:13321:7: note: ‘__pyx_v_locmax’ was declared here 13321 | int __pyx_v_locmax; | ^~~~~~~~~~~~~~ gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/expand8bits.o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/backtranslate/_ahocorasick.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/backtranslate/_ahocorasick.cpython-39-x86_64-linux-gnu.so orgasm.fiboheap._fiboheap :-> ['python/orgasm/fiboheap/_fiboheap.pyx', 'fiboheap/fibo.c'] cythoning python/orgasm/fiboheap/_fiboheap.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap/_fiboheap.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap building 'orgasm.fiboheap._fiboheap' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap/_fiboheap.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap/_fiboheap.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c fiboheap/fibo.c -o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/fiboheap/_fiboheap.o build/temp.linux-x86_64-3.9/fiboheap/fibo.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/fiboheap/_fiboheap.cpython-39-x86_64-linux-gnu.so orgasm.assembler._asmbgraph :-> ['python/orgasm/assembler/_asmbgraph.pyx'] cythoning python/orgasm/assembler/_asmbgraph.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_asmbgraph.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler warning: python/orgasm/assembler/_asmbgraph.pyx:161:4: Overriding cdef method with def method. building 'orgasm.assembler._asmbgraph' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_asmbgraph.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_asmbgraph.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_asmbgraph.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/assembler/_asmbgraph.cpython-39-x86_64-linux-gnu.so orgasm.assembler._tango :-> ['python/orgasm/assembler/_tango.pyx'] cythoning python/orgasm/assembler/_tango.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_tango.c building 'orgasm.assembler._tango' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_tango.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_tango.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_tango.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/assembler/_tango.cpython-39-x86_64-linux-gnu.so orgasm.assembler._assembler :-> ['python/orgasm/assembler/_assembler.pyx'] cythoning python/orgasm/assembler/_assembler.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_assembler.c /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/ORG.asm-1.0.3/python/orgasm/assembler/_assembler.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'orgasm.assembler._assembler' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -Ifiboheap -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_assembler.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_assembler.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/assembler/_assembler.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/assembler/_assembler.cpython-39-x86_64-linux-gnu.so orgasm.multialign._multi :-> ['python/orgasm/multialign/_multi.pyx'] cythoning python/orgasm/multialign/_multi.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.c creating build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign building 'orgasm.multialign._multi' extension creating build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -Isrc -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.o -msse2 -Wno-unused-function -Wmissing-braces -Wchar-subscripts build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.c: In function ‘__pyx_f_6orgasm_10multialign_6_multi_cmpHash’: build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.c:3347:68: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3347 | for (__pyx_t_6 = ((-__pyx_v_delta) + __pyx_v_shift); __pyx_t_6 < __pyx_t_16; __pyx_t_6+=1) { | ^ gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_multi.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/multialign/_multi.cpython-39-x86_64-linux-gnu.so orgasm.multialign._dynamic :-> ['python/orgasm/multialign/_dynamic.pyx'] cythoning python/orgasm/multialign/_dynamic.pyx to build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_dynamic.c building 'orgasm.multialign._dynamic' extension gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -D_GNU_SOURCE -fPIC -fwrapv -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -D_GNU_SOURCE -fPIC -fwrapv -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -DLITTLE_END -I/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/include -I/usr/include/python3.9 -c build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_dynamic.c -o build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_dynamic.o gcc -shared -g -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-x86_64-3.9/build/temp.linux-x86_64-3.9/pyrex/orgasm/multialign/_dynamic.o -L/usr/lib64 -o build/lib.linux-x86_64-3.9/orgasm/multialign/_dynamic.cpython-39-x86_64-linux-gnu.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-3.9 changing mode of build/scripts-3.9/oa from 644 to 755 + sleep 1 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.bSPlfP + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 ++ dirname /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 + cd ORG.asm-1.0.3 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/generic-hardened-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/generic-hardened-ld' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 ['/builddir/build/BUILD/ORG.asm-1.0.3', '/usr/lib64/python39.zip', '/usr/lib64/python3.9', '/usr/lib64/python3.9/lib-dynload', '/usr/lib64/python3.9/site-packages', '/usr/lib/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/distutils.ext', '/builddir/build/BUILD/ORG.asm-1.0.3/python'] ---------------- setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 ---------------- Installing ORG.asm (1.0.3) in serenity mode You are running the good python Restarting installation within the ORG.asm-1.0.3 virtualenv Install script restarting... ['/builddir/build/BUILD/ORG.asm-1.0.3', '/usr/lib64/python39.zip', '/usr/lib64/python3.9', '/usr/lib64/python3.9/lib-dynload', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib/python3.9/site-packages', '/builddir/build/BUILD/ORG.asm-1.0.3/distutils.ext', '/builddir/build/BUILD/ORG.asm-1.0.3/python'] ---------------- setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64 ---------------- Installing ORG.asm (1.0.3) in serenity mode You are running the good python ORG.asm will be installed with python : /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/python Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed You are running the good python Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed Required packages for the installation : Look for package pip : ok version 21.3.1 installed Look for package Cython : ok version 0.29.35 installed Look for package Sphinx : ok version 7.0.1 installed Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/buffer.c', 'src/buildindex.c', '@code16bits.c', '@codecomp.c', 'src/compsort.c', 'src/debug.c', 'src/debug.h', 'src/decode.c', 'src/encode.c', 'src/fastq.c', 'src/indexinput.c', 'src/indexoutput.c', 'src/load.c', 'src/lookfor.c', 'src/malloc.c', 'src/orgasm.h', 'src/sort.c', 'src/fgetln.c', 'fiboheap/fibo.h'] Cython module : [] Cython module : [] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h'] Cython module : ['fiboheap/fibo.h', 'src/orgasm.h', '@expand8bits.c'] Cython module : ['fiboheap/fibo.c', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/_sse.h', 'src/orgasm.h', 'fiboheap/fibo.h'] Cython module : ['src/orgasm.h'] running install running install_lib creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3 creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3 creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64 creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9 creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm copying build/lib.linux-x86_64-3.9/orgasm/version.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm copying build/lib.linux-x86_64-3.9/orgasm/config.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm copying build/lib.linux-x86_64-3.9/orgasm/tango.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/_graph.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/_graphmultiedge.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/_fibomaxintheap.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/_fibointheap.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/_fibominintheap.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph copying build/lib.linux-x86_64-3.9/orgasm/graph/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files copying build/lib.linux-x86_64-3.9/orgasm/files/universalopener.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files copying build/lib.linux-x86_64-3.9/orgasm/files/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files copying build/lib.linux-x86_64-3.9/orgasm/files/linebuffer.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files copying build/lib.linux-x86_64-3.9/orgasm/files/uncompress.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/counter.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/command.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/progress.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/logging.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/arguments.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps copying build/lib.linux-x86_64-3.9/orgasm/apps/config.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/index.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/graphstats.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/cutlow.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/restore.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/graph.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/clone.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/substract.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/unfoldrdna.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/unfold.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/list.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/seeds.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/compact.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands copying build/lib.linux-x86_64-3.9/orgasm/commands/buildgraph.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/format copying build/lib.linux-x86_64-3.9/orgasm/format/sam.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/format copying build/lib.linux-x86_64-3.9/orgasm/format/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/format creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/utils copying build/lib.linux-x86_64-3.9/orgasm/utils/dna.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/utils copying build/lib.linux-x86_64-3.9/orgasm/utils/_progress.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/utils copying build/lib.linux-x86_64-3.9/orgasm/utils/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/utils creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/samples copying build/lib.linux-x86_64-3.9/orgasm/samples/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/samples copying build/lib.linux-x86_64-3.9/orgasm/samples/phix.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/samples creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/indexer copying build/lib.linux-x86_64-3.9/orgasm/indexer/_orgasm.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/indexer copying build/lib.linux-x86_64-3.9/orgasm/indexer/fakereads.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/indexer copying build/lib.linux-x86_64-3.9/orgasm/indexer/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/indexer creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads copying build/lib.linux-x86_64-3.9/orgasm/reads/_fasta.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads copying build/lib.linux-x86_64-3.9/orgasm/reads/_sequences.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads copying build/lib.linux-x86_64-3.9/orgasm/reads/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads copying build/lib.linux-x86_64-3.9/orgasm/reads/_fastq.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads copying build/lib.linux-x86_64-3.9/orgasm/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate copying build/lib.linux-x86_64-3.9/orgasm/backtranslate/fasta.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate copying build/lib.linux-x86_64-3.9/orgasm/backtranslate/_bitvector.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate copying build/lib.linux-x86_64-3.9/orgasm/backtranslate/_ahocorasick.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate copying build/lib.linux-x86_64-3.9/orgasm/backtranslate/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/fiboheap copying build/lib.linux-x86_64-3.9/orgasm/fiboheap/_fiboheap.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/fiboheap copying build/lib.linux-x86_64-3.9/orgasm/fiboheap/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/fiboheap creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler copying build/lib.linux-x86_64-3.9/orgasm/assembler/_tango.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler copying build/lib.linux-x86_64-3.9/orgasm/assembler/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler copying build/lib.linux-x86_64-3.9/orgasm/assembler/_assembler.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler copying build/lib.linux-x86_64-3.9/orgasm/assembler/_asmbgraph.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/multialign copying build/lib.linux-x86_64-3.9/orgasm/multialign/_multi.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/multialign copying build/lib.linux-x86_64-3.9/orgasm/multialign/__init__.py -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/multialign copying build/lib.linux-x86_64-3.9/orgasm/multialign/_dynamic.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/multialign byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/version.py to version.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/config.py to config.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/tango.py to tango.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/graph/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/files/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/apps/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/index.py to index.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/graphstats.py to graphstats.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/cutlow.py to cutlow.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/restore.py to restore.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/graph.py to graph.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/clone.py to clone.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/substract.py to substract.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/unfoldrdna.py to unfoldrdna.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/unfold.py to unfold.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/list.py to list.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/seeds.py to seeds.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/compact.py to compact.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/commands/buildgraph.py to buildgraph.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/format/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/utils/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/samples/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/samples/phix.py to phix.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/indexer/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/reads/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate/fasta.py to fasta.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/backtranslate/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/fiboheap/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/assembler/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/orgasm/multialign/__init__.py to __init__.cpython-39.pyc writing byte-compilation script '/tmp/tmp1vw9ekkx.py' /builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/python /tmp/tmp1vw9ekkx.py removing /tmp/tmp1vw9ekkx.py running install_scripts creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin copying build/scripts-3.9/oa -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin copying build/scripts-3.9/orgasmi -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin changing mode of /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/oa to 755 changing mode of /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/orgasmi to 755 creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/export creating /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/export/bin exporting file /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/oa -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/export/bin/oa exporting file /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/bin/orgasmi -> /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/export/bin/orgasmi running install_egg_info running egg_info creating python/ORG.asm.egg-info writing python/ORG.asm.egg-info/PKG-INFO writing dependency_links to python/ORG.asm.egg-info/dependency_links.txt writing top-level names to python/ORG.asm.egg-info/top_level.txt writing manifest file 'python/ORG.asm.egg-info/SOURCES.txt' Look for CPU architecture... None reading manifest file 'python/ORG.asm.egg-info/SOURCES.txt' writing manifest file 'python/ORG.asm.egg-info/SOURCES.txt' Copying python/ORG.asm.egg-info to /builddir/build/BUILDROOT/python-ORG.asm-1.0.3-1.x86_64/builddir/build/BUILD/ORG.asm-1.0.3/ORG.asm-1.0.3/lib64/python3.9/site-packages/ORG.asm-1.0.3-py3.9.egg-info running install_sphinx error: invalid command 'build_sphinx' error: Bad exit status from /var/tmp/rpm-tmp.bSPlfP (%install) Bad exit status from /var/tmp/rpm-tmp.bSPlfP (%install) RPM build errors: Child return code was: 1 EXCEPTION: [Error('Command failed: \n # bash --login -c /usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec\n', 1)] Traceback (most recent call last): File "/usr/lib/python3.9/site-packages/mockbuild/trace_decorator.py", line 93, in trace result = func(*args, **kw) File "/usr/lib/python3.9/site-packages/mockbuild/util.py", line 598, in do_with_status raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode) mockbuild.exception.Error: Command failed: # bash --login -c /usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-org-asm.spec