Failed building wheel for ariba #161
Comments
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What happens if you download the release tarball, unpack it and run |
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...have no clue :) Will run this tomorrow and report back. |
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...correction, wed. The cluster is down for maintenance, so won't be able to check before it's up again. |
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OK. I haven't yet managed to get a VM running centos 6.8 up and running, so I'm hoping the setup.py method works... |
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Ok, just tested this. It appears that I'm lacking several of the python modules: package init file 'samtools/init.py' not found (or not a regular file) I will get those in, and then try again to see what happens. Will report back 😄 |
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This is a guess, but that's looking like pysam install issues. Maybe worth trying |
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Thanks for the tip, will try that. |
I am working on a CentOS 6.8 cluster where I don't have root access.
This system uses the modules system to load software:
http://modules.sourceforge.net/
To make things a bit neater and easier on myself, I use virtualenvs to install python stuff. This system has python 2.6 running natively and other pythons are loaded via the module system. Thus, I load python3 before creating a new virtualenv for ariba. Thus my python version is now
(ariba)[karinlag@abel nn9305k]$ python
Python 3.5.0 (default, Oct 9 2015, 14:50:11)
my gcc version is
(ariba)[karinlag@abel nn9305k]$ gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
I ensure that I have all the required modules loaded (bowtie2, mummer, cd-hit) before pip3 installing ariba (not sure that actually makes a difference for install, but better safe than sorry).
I am giving you output until the first error (it keeps running after that, but that also just gives errors, I can get you those if you want too).
(ariba)[karinlag@abel virtenv]$ pip3 install ariba
Collecting ariba
Using cached ariba-2.7.2.tar.gz
Collecting BeautifulSoup4>=4.1.0 (from ariba)
Using cached beautifulsoup4-4.5.3-py3-none-any.whl
Collecting dendropy>=4.2.0 (from ariba)
Collecting pyfastaq>=3.12.0 (from ariba)
Collecting pysam>=0.9.1 (from ariba)
Using cached pysam-0.10.0.tar.gz
Collecting pymummer>=0.10.2 (from ariba)
Requirement already satisfied (use --upgrade to upgrade): setuptools in ./ariba/lib/python3.5/site-packages (from dendropy>=4.2.0->ariba)
Building wheels for collected packages: ariba, pysam
Running setup.py bdist_wheel for ariba
Complete output from command /work/projects/nn9305k/bin/virtenv/ariba/bin/python3.5 -c "import setuptools;file='/tmp/pip-build-63898kee/ariba/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" bdist_wheel -d /tmp/tmpthur2d5opip-wheel-:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/ariba
copying ariba/report.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/common.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/samtools_variants.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/ref_preparer.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/mlst_profile.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/external_progs.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/scaffold_graph.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/aln_to_metadata.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/assembly.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/clusters.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/ref_seq_chooser.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/faidx.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/link.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/pubmlst_ref_preparer.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/megares_data_finder.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/reference_data.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/report_filter.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/summary_cluster.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/sequence_variant.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/summary.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/read_store.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/assembly_compare.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/cdhit.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/refdata_query.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/summary_sample.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/mlst_reporter.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/vfdb_parser.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/sequence_metadata.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/card_record.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/versions.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/cluster.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/assembly_variants.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/flag.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/megares_zip_parser.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/summary_cluster_variant.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/histogram.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/read_filter.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/pubmlst_getter.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/bam_parse.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/ref_genes_getter.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/init.py -> build/lib.linux-x86_64-3.5/ariba
copying ariba/mapping.py -> build/lib.linux-x86_64-3.5/ariba
creating build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/getref.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/pubmlstget.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/pubmlstspecies.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/run.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/aln2meta.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/summary.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/prepareref.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/reportfilter.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/flag.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/refquery.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/test.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/version.py -> build/lib.linux-x86_64-3.5/ariba/tasks
copying ariba/tasks/init.py -> build/lib.linux-x86_64-3.5/ariba/tasks
creating build/lib.linux-x86_64-3.5/ariba/test_run_data
copying ariba/test_run_data/metadata.tsv -> build/lib.linux-x86_64-3.5/ariba/test_run_data
copying ariba/test_run_data/reads_1.fq -> build/lib.linux-x86_64-3.5/ariba/test_run_data
copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> build/lib.linux-x86_64-3.5/ariba/test_run_data
copying ariba/test_run_data/reads_2.fq -> build/lib.linux-x86_64-3.5/ariba/test_run_data
copying ariba/test_run_data/ref_seqs.fa -> build/lib.linux-x86_64-3.5/ariba/test_run_data
running build_ext
building 'minimap_ariba' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/third_party
creating build/temp.linux-x86_64-3.5/third_party/minimap-0.2
creating build/temp.linux-x86_64-3.5/ariba
creating build/temp.linux-x86_64-3.5/ariba/ext
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/bseq.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/bseq.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/index.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/index.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/kthread.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/kthread.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/map.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/map.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/misc.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/misc.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/sdust.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sdust.o
third_party/minimap-0.2/sdust.c(20): warning #2959: function prototype is missing the argument types
KDQ_INIT(int)
^
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/minimap-0.2/sketch.c -o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sketch.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/minimap-0.2 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/minimap_ariba.o
icpc -shared -L/cluster/software/VERSIONS/intel-2016.0/compiler/lib/intel64 -L/cluster/software/VERSIONS/libffi-3.0.13/lib -L/usr/lib/x86_64-linux-gnu -ipo -O2 -xAVX -mavx -O2 -xAVX -mavx -O2 -xAVX -mavx build/temp.linux-x86_64-3.5/third_party/minimap-0.2/bseq.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/index.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/kthread.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/map.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/misc.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sdust.o build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sketch.o build/temp.linux-x86_64-3.5/ariba/ext/minimap_ariba.o -L/cluster/software/VERSIONS/python3-3.5.0/lib -lpython3.5m -o build/lib.linux-x86_64-3.5/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -lz
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/bseq.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/index.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/kthread.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/map.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/misc.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sdust.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/minimap-0.2/sketch.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/ariba/ext/minimap_ariba.o; was the source file compiled with -ipo
building 'fermilite_ariba' extension
creating build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/bfc.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bfc.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/bseq.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bseq.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/bubble.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bubble.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/htab.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/htab.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/ksw.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/ksw.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/kthread.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/kthread.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/mag.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mag.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/misc.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/misc.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/mrope.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mrope.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/rld0.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rld0.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/rle.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rle.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/rope.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rope.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c third_party/fermi-lite-0.1/unitig.c -o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/unitig.o
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -Ithird_party/fermi-lite-0.1 -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/fml-asm_ariba.o
icpc -shared -L/cluster/software/VERSIONS/intel-2016.0/compiler/lib/intel64 -L/cluster/software/VERSIONS/libffi-3.0.13/lib -L/usr/lib/x86_64-linux-gnu -ipo -O2 -xAVX -mavx -O2 -xAVX -mavx -O2 -xAVX -mavx build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bfc.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bseq.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bubble.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/htab.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/ksw.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/kthread.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mag.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/misc.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mrope.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rld0.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rle.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rope.o build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/unitig.o build/temp.linux-x86_64-3.5/ariba/ext/fml-asm_ariba.o -L/cluster/software/VERSIONS/python3-3.5.0/lib -lpython3.5m -o build/lib.linux-x86_64-3.5/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -lz
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bfc.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bseq.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/bubble.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/htab.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/ksw.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/kthread.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mag.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/misc.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/mrope.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rld0.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rle.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/rope.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/third_party/fermi-lite-0.1/unitig.o; was the source file compiled with -ipo
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/ariba/ext/fml-asm_ariba.o; was the source file compiled with -ipo
building 'vcfcall_ariba' extension
icc -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -O2 -xAVX -mavx -fPIC -I/cluster/software/VERSIONS/python3-3.5.0/include/python3.5m -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-3.5/ariba/ext/vcfcall_ariba.o
icpc -shared -L/cluster/software/VERSIONS/intel-2016.0/compiler/lib/intel64 -L/cluster/software/VERSIONS/libffi-3.0.13/lib -L/usr/lib/x86_64-linux-gnu -ipo -O2 -xAVX -mavx -O2 -xAVX -mavx -O2 -xAVX -mavx build/temp.linux-x86_64-3.5/ariba/ext/vcfcall_ariba.o -L/cluster/software/VERSIONS/python3-3.5.0/lib -lpython3.5m -o build/lib.linux-x86_64-3.5/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so
ipo: warning #11003: no IR in object file build/temp.linux-x86_64-3.5/ariba/ext/vcfcall_ariba.o; was the source file compiled with -ipo
running build_scripts
creating build/scripts-3.5
copying and adjusting scripts/ariba -> build/scripts-3.5
changing mode of build/scripts-3.5/ariba from 664 to 775
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/wheel
copying build/lib.linux-x86_64-3.5/fermilite_ariba.cpython-35m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/report.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/common.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/samtools_variants.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/ref_preparer.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/mlst_profile.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/external_progs.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/scaffold_graph.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/aln_to_metadata.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/assembly.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/clusters.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/ref_seq_chooser.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/faidx.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/link.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/pubmlst_ref_preparer.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/megares_data_finder.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/reference_data.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/report_filter.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/summary_cluster.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/sequence_variant.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/summary.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/read_store.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/assembly_compare.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/cdhit.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/refdata_query.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/summary_sample.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/mlst_reporter.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/vfdb_parser.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/sequence_metadata.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/card_record.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/versions.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/cluster.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/assembly_variants.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/flag.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/megares_zip_parser.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/summary_cluster_variant.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/histogram.py -> build/bdist.linux-x86_64/wheel/ariba
creating build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/test_run_data/metadata.tsv -> build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/test_run_data/reads_1.fq -> build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/test_run_data/reads_2.fq -> build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/test_run_data/ref_seqs.fa -> build/bdist.linux-x86_64/wheel/ariba/test_run_data
copying build/lib.linux-x86_64-3.5/ariba/read_filter.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/pubmlst_getter.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/bam_parse.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/ref_genes_getter.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/init.py -> build/bdist.linux-x86_64/wheel/ariba
copying build/lib.linux-x86_64-3.5/ariba/mapping.py -> build/bdist.linux-x86_64/wheel/ariba
creating build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/getref.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/pubmlstget.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/pubmlstspecies.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/run.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/aln2meta.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/summary.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/prepareref.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/reportfilter.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/flag.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/refquery.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/test.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/version.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/ariba/tasks/init.py -> build/bdist.linux-x86_64/wheel/ariba/tasks
copying build/lib.linux-x86_64-3.5/vcfcall_ariba.cpython-35m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
copying build/lib.linux-x86_64-3.5/minimap_ariba.cpython-35m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
running install_egg_info
running egg_info
writing requirements to ariba.egg-info/requires.txt
writing ariba.egg-info/PKG-INFO
writing top-level names to ariba.egg-info/top_level.txt
writing dependency_links to ariba.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'ariba.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'ariba.egg-info/SOURCES.txt'
Copying ariba.egg-info to build/bdist.linux-x86_64/wheel/ariba-2.7.2-py3.5.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/ariba-2.7.2.data
creating build/bdist.linux-x86_64/wheel/ariba-2.7.2.data/scripts
copying build/scripts-3.5/ariba -> build/bdist.linux-x86_64/wheel/ariba-2.7.2.data/scripts
changing mode of build/bdist.linux-x86_64/wheel/ariba-2.7.2.data/scripts/ariba to 775
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-build-63898kee/ariba/setup.py", line 80, in
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
File "/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/cluster/software/VERSIONS/python3-3.5.0/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/wheel/bdist_wheel.py", line 213, in run
archive_basename = self.get_archive_basename()
File "/work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/wheel/bdist_wheel.py", line 161, in get_archive_basename
impl_tag, abi_tag, plat_tag = self.get_tag()
File "/work/projects/nn9305k/bin/virtenv/ariba/lib/python3.5/site-packages/wheel/bdist_wheel.py", line 155, in get_tag
assert tag == supported_tags[0]
AssertionError
Failed building wheel for ariba
The text was updated successfully, but these errors were encountered: