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Installing Platypus on Ubuntu !
By Jit 2012 days ago
(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) ...
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Processing triggers for mime-support (3.60ubuntu1) ...
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Setting up libpython3.6-minimal:amd64 (3.6.6-1~18.04) ...
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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) ...
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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
