https://bioinformaticsonline.com/snippets/view/37998/installing-platypus-on-ubuntu? https://bioinformaticsonline.com/snippets/view/37998/installing-platypus-on-ubuntu Thu, 25 Oct 2018 07:07:02 -0500 https://bioinformaticsonline.com/snippets/view/37998/installing-platypus-on-ubuntu (py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git Cloning into 'Platypus'... remote: Enumerating objects: 1394, done. remote: Total 1394 (delta 0), reused 0 (delta 0), pack-reused 1394 Receiving objects: 100% (1394/1394), 54.69 MiB | 1.11 MiB/s, done. Resolving deltas: 100% (729/729), done. (py27) ➜ Tools git:(master) ✗ cd Platypus (py27) ➜ Platypus git:(master) ls Dockerfile extensions LICENSE Makefile misc README.md release sanityChecks.py scripts src test ➜ Platypus git:(master) sudo apt-get install python3-dev Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libpython3-dev libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib python3.6 python3.6-dev python3.6-minimal Suggested packages: python3.6-venv python3.6-doc binfmt-support The following NEW packages will be installed: libpython3-dev libpython3.6-dev python3-dev python3.6-dev The following packages will be upgraded: libpython3.6 libpython3.6-minimal libpython3.6-stdlib python3.6 python3.6-minimal 5 upgraded, 4 newly installed, 0 to remove and 138 not upgraded. Need to get 50,8 MB of archives. After this operation, 76,7 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6 amd64 3.6.6-1~18.04 [1.420 kB] Get:2 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6 amd64 3.6.6-1~18.04 [190 kB] Get:3 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-stdlib amd64 3.6.6-1~18.04 [1.713 kB] Get:4 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6-minimal amd64 3.6.6-1~18.04 [1.617 kB] Get:5 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-minimal amd64 3.6.6-1~18.04 [532 kB] Get:6 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-dev amd64 3.6.6-1~18.04 [44,8 MB] Get:7 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3-dev amd64 3.6.5-3ubuntu1 [7.300 B] Get:8 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6-dev amd64 3.6.6-1~18.04 [508 kB] Get:9 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-dev amd64 3.6.5-3ubuntu1 [1.292 B] Fetched 50,8 MB in 8s (6.724 kB/s) (Reading database ... 501922 files and directories currently installed.) Preparing to unpack .../0-libpython3.6_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../1-python3.6_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../2-libpython3.6-stdlib_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-stdlib:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../3-python3.6-minimal_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6-minimal (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../4-libpython3.6-minimal_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-minimal:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Selecting previously unselected package libpython3.6-dev:amd64. Preparing to unpack .../5-libpython3.6-dev_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-dev:amd64 (3.6.6-1~18.04) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../6-libpython3-dev_3.6.5-3ubuntu1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.6.5-3ubuntu1) ... Selecting previously unselected package python3.6-dev. Preparing to unpack .../7-python3.6-dev_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6-dev (3.6.6-1~18.04) ... Selecting previously unselected package python3-dev. Preparing to unpack .../8-python3-dev_3.6.5-3ubuntu1_amd64.deb ... Unpacking python3-dev (3.6.5-3ubuntu1) ... Processing triggers for mime-support (3.60ubuntu1) ... Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ... Setting up libpython3.6-minimal:amd64 (3.6.6-1~18.04) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for man-db (2.8.3-2) ... Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ... Setting up libpython3.6-stdlib:amd64 (3.6.6-1~18.04) ... Setting up python3.6-minimal (3.6.6-1~18.04) ... Setting up libpython3.6:amd64 (3.6.6-1~18.04) ... Setting up python3.6 (3.6.6-1~18.04) ... Setting up libpython3.6-dev:amd64 (3.6.6-1~18.04) ... Setting up python3.6-dev (3.6.6-1~18.04) ... Setting up libpython3-dev:amd64 (3.6.5-3ubuntu1) ... Setting up python3-dev (3.6.5-3ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... ➜ htslib-1.9 git:(master) ✗ make install zsh: correct 'install' to 'INSTALL' [nyae]? n echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig mkdir: cannot create directory ‘/usr/local/include/htslib’: Permission denied mkdir: cannot create directory ‘/usr/local/share/man/man5’: Permission denied Makefile:447: recipe for target 'installdirs' failed make: *** [installdirs] Error 1 ➜ htslib-1.9 git:(master) ✗ sudo make install [sudo] password for urbe: mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -I. -fpic -c -o hts_os.pico hts_os.c gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.9 ln -sf libhts.so.1.9 /usr/local/lib/libhts.so ln -sf libhts.so.1.9 /usr/local/lib/libhts.so.2 sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9#g' htslib.pc.tmp > /usr/local/lib/pkgconfig/htslib.pc chmod 644 /usr/local/lib/pkgconfig/htslib.pc install -p bgzip htsfile tabix /usr/local/bin if test -n ""; then install -p ; fi install -p -m 644 htslib/*.h /usr/local/include/htslib install -p -m 644 libhts.a /usr/local/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /usr/local/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5 (py27) ➜ Platypus git:(master) pip install Cython Collecting Cython Downloading https://files.pythonhosted.org/packages/85/29/ccdbce68ba5fb97fd11c08e3cc79576f13e6e300d32a7953cd4c878c0996/Cython-0.29-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB) 100% |████████████████████████████████| 2.0MB 401kB/s Installing collected packages: Cython Successfully installed Cython-0.29 You are using pip version 9.0.3, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. (py27) ➜ Platypus git:(master) make (py27) ➜ Platypus git:(master) ✗ make echo 'Building Platypus' Building Platypus cd src; python setup.py build running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_ext skipping 'cython/htslibWrapper.c' Cython extension (up-to-date) building 'htslibWrapper' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/htslibWrapper.c -o build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function creating build/lib.linux-x86_64-2.7 gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -L./lib -L/home/urbe/anaconda3/envs/py27/lib -lhts -lpython2.7 -o build/lib.linux-x86_64-2.7/htslibWrapper.so cythoning cython/arrays.pyx to cython/arrays.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/arrays.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cython/arrays.pyx:1:0: __getslice__, __setslice__, and __delslice__ are not supported by Python 3, use __getitem__, __setitem__, and __delitem__ instead warning: cython/arrays.pyx:1:0: __getslice__, __setslice__, and __delslice__ are not supported by Python 3, use __getitem__, __setitem__, and __delitem__ instead building 'arrays' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/arrays.c -o build/temp.linux-x86_64-2.7/cython/arrays.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/arrays.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/arrays.so cythoning cython/fastafile.pyx to cython/fastafile.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/fastafile.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'fastafile' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/fastafile.c -o build/temp.linux-x86_64-2.7/cython/fastafile.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/fastafile.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/fastafile.so cythoning cython/variant.pyx to cython/variant.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variant.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'variant' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variant.c -o build/temp.linux-x86_64-2.7/cython/variant.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variant.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variant.so cythoning cython/cerrormodel.pyx to cython/cerrormodel.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cerrormodel.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cerrormodel' extension creating build/temp.linux-x86_64-2.7/c gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cerrormodel.c -o build/temp.linux-x86_64-2.7/cython/cerrormodel.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/tandem.c -o build/temp.linux-x86_64-2.7/c/tandem.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function c/tandem.c:267:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int main() ^~~~ c/tandem.c:108:35: warning: ‘MIN_PARTIAL_MATCH’ is static but used in inline function ‘foundmatch’ which is not static if (size < displacement + min(MIN_PARTIAL_MATCH, displacement)) ^~~~~~~~~~~~~~~~~ gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cerrormodel.o build/temp.linux-x86_64-2.7/c/tandem.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cerrormodel.so cythoning cython/calign.pyx to cython/calign.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/calign.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'calign' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/calign.c -o build/temp.linux-x86_64-2.7/cython/calign.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/align.c -o build/temp.linux-x86_64-2.7/c/align.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/calign.o build/temp.linux-x86_64-2.7/c/align.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/calign.so cythoning cython/chaplotype.pyx to cython/chaplotype.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/chaplotype.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'chaplotype' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/chaplotype.c -o build/temp.linux-x86_64-2.7/cython/chaplotype.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/align.c -o build/temp.linux-x86_64-2.7/c/align.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/chaplotype.o build/temp.linux-x86_64-2.7/c/align.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/chaplotype.so skipping 'pysam/ctabix.c' Cython extension (up-to-date) building 'ctabix' extension creating build/temp.linux-x86_64-2.7/pysam creating build/temp.linux-x86_64-2.7/tabix gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-x86_64-2.7/pysam/ctabix.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_9Tabixfile_7contigs___get__’: pysam/ctabix.c:3304:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_13TabixIterator_4__next__’: pysam/ctabix.c:3858:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__’: pysam/ctabix.c:4239:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__’: pysam/ctabix.c:5249:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-x86_64-2.7/pysam/tabix_util.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/knetfile.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/knetfile.c.pysam.c:51:0: tabix/knetfile.c.pysam.c: In function ‘kftp_send_cmd’: tabix/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ tabix/knetfile.c.pysam.c:241:2: note: in expansion of macro ‘netwrite’ netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ tabix/knetfile.c.pysam.c: In function ‘khttp_connect_file’: tabix/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ tabix/knetfile.c.pysam.c:420:2: note: in expansion of macro ‘netwrite’ netwrite(fp->fd, buf, l); ^~~~~~~~ tabix/knetfile.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/index.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/index.c.pysam.c:9:0: tabix/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline int bam_is_big_endian() ^~~~~~~~~~~~~~~~~ In file included from tabix/index.c.pysam.c:6:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:453:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^~~~~~~~~~ tabix/index.c.pysam.c:36:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT’ KHASH_MAP_INIT_INT(i, ti_binlist_t) ^~~~~~~~~~~~~~~~~~ tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^~~~~~~~~~ tabix/index.c.pysam.c:37:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’ KHASH_MAP_INIT_STR(s, int) ^~~~~~~~~~~~~~~~~~ cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bgzip.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static int bgzip_main_usage() ^~~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: In function ‘main’: tabix/bgzip.c.pysam.c:200:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(f_dst, buffer, c); ^~~~~~~~~~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: In function ‘write_open’: tabix/bgzip.c.pysam.c:59:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%c", &c); ^~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/kstring.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bgzf.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/bgzf.c.pysam.c:40:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:468:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^~~~~~~~~~ tabix/bgzf.c.pysam.c:46:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT64’ KHASH_MAP_INIT_INT64(cache, cache_t) ^~~~~~~~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static BGZF *bgzf_read_init() ^~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c: In function ‘bgzf_close’: tabix/bgzf.c.pysam.c:632:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int count, block_length = deflate_block(fp, 0); ^~~~~ tabix/bgzf.c.pysam.c: In function ‘bgzf_check_EOF’: tabix/bgzf.c.pysam.c:683:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/bedidx.c.pysam.c:21:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^~~~~~~~~~ tabix/bedidx.c.pysam.c:22:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’ KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^~~~~~~~~~~~~~~~~~ cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/pysam/ctabix.o build/temp.linux-x86_64-2.7/pysam/tabix_util.o build/temp.linux-x86_64-2.7/tabix/knetfile.c.pysam.o build/temp.linux-x86_64-2.7/tabix/index.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzip.c.pysam.o build/temp.linux-x86_64-2.7/tabix/kstring.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzf.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o -L/home/urbe/anaconda3/envs/py27/lib -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/ctabix.so skipping 'pysam/TabProxies.c' Cython extension (up-to-date) building 'TabProxies' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/TabProxies.c -o build/temp.linux-x86_64-2.7/pysam/TabProxies.o -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/pysam/TabProxies.o -L/home/urbe/anaconda3/envs/py27/lib -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/TabProxies.so cythoning cython/cwindow.pyx to cython/cwindow.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cwindow.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cwindow' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cwindow.c -o build/temp.linux-x86_64-2.7/cython/cwindow.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cwindow.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cwindow.so cythoning cython/assembler.pyx to cython/assembler.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/assembler.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'assembler' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/assembler.c -o build/temp.linux-x86_64-2.7/cython/assembler.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/assembler.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/assembler.so cythoning cython/cgenotype.pyx to cython/cgenotype.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cgenotype.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cgenotype' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cgenotype.c -o build/temp.linux-x86_64-2.7/cython/cgenotype.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cgenotype.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cgenotype.so cythoning cython/platypusutils.pyx to cython/platypusutils.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/platypusutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'platypusutils' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/platypusutils.c -o build/temp.linux-x86_64-2.7/cython/platypusutils.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/platypusutils.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/platypusutils.so cythoning cython/vcfutils.pyx to cython/vcfutils.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/vcfutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'vcfutils' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/vcfutils.c -o build/temp.linux-x86_64-2.7/cython/vcfutils.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/vcfutils.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/vcfutils.so cythoning cython/cpopulation.pyx to cython/cpopulation.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cpopulation.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cpopulation' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cpopulation.c -o build/temp.linux-x86_64-2.7/cython/cpopulation.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cpopulation.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cpopulation.so cythoning cython/variantFilter.pyx to cython/variantFilter.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variantFilter.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'variantFilter' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variantFilter.c -o build/temp.linux-x86_64-2.7/cython/variantFilter.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variantFilter.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variantFilter.so cythoning cython/variantcaller.pyx to cython/variantcaller.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variantcaller.pyx tree = Parsing.p_module(s, pxd, full_module_name) warning: cython/variantcaller.pyx:529:9: Unreachable code building 'variantcaller' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variantcaller.c -o build/temp.linux-x86_64-2.7/cython/variantcaller.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variantcaller.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variantcaller.so mkdir -p bin cp src/build/*/*.so bin/ cp src/build/*/python/*.py bin/ (py27) ➜ 3-unzip conda install platypus-variant Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/py27 added / updated specs: - platypus-variant The following packages will be downloaded: package | build ---------------------------|----------------- htslib-1.9 | h57f8fdf_0 1.2 MB bioconda libssh2-1.8.0 | h5b517e9_2 240 KB conda-forge platypus-variant-0.8.1.1 | py27hdbffeaa_3 10.1 MB bioconda curl-7.61.0 | h93b3f91_2 859 KB conda-forge ------------------------------------------------------------ Total: 12.4 MB The following NEW packages will be INSTALLED: bzip2: 1.0.6-h470a237_2 conda-forge curl: 7.61.0-h93b3f91_2 conda-forge htslib: 1.9-h57f8fdf_0 bioconda krb5: 1.14.6-0 conda-forge libdeflate: 1.0-h470a237_0 bioconda libssh2: 1.8.0-h5b517e9_2 conda-forge platypus-variant: 0.8.1.1-py27hdbffeaa_3 bioconda The following packages will be UPDATED: ca-certificates: 2018.4.16-0 conda-forge --> 2018.10.15-ha4d7672_0 conda-forge certifi: 2018.4.16-py27_0 conda-forge --> 2018.10.15-py27_1000 conda-forge openssl: 1.0.2o-0 conda-forge --> 1.0.2p-h470a237_1 conda-forge Proceed ([y]/n)? y Downloading and Extracting Packages htslib-1.9 | 1.2 MB | ############################################################################################################################################################################################### | 100% libssh2-1.8.0 | 240 KB | ############################################################################################################################################################################################### | 100% platypus-variant-0.8 | 10.1 MB | ############################################################################################################################################################################################### | 100% curl-7.61.0 | 859 KB | ############################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Jit