Closed siva5 closed 3 years ago
Hi Haibao,
I am trying to install the jcvi package using python3.7 -m pip install jcvi. I got the following error -
ERROR: Command errored out with exit status 1: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"'; file='"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-_6yevuza/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/siva/.local/include/python3.7m/jcvi Check the logs for full command output.
All the packages including the wheel packages are up to date, but there is an error while building the wheel for jcvi.
@siva5
Need to install Python development headers. See also: https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory
Thanks!! That did the trick..
Hi Haibao,
I am trying to install the jcvi package using python3.7 -m pip install jcvi. I got the following error -
Defaulting to user installation because normal site-packages is not writeable Collecting jcvi Using cached jcvi-1.0.9.tar.gz (832 kB) Requirement already satisfied: biopython in /usr/local/lib/python3.7/dist-packages (from jcvi) (1.77) Requirement already satisfied: boto3 in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (1.14.61) Requirement already satisfied: coveralls in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (2.1.2) Requirement already satisfied: cython in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (0.29.21) Requirement already satisfied: deap in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (1.3.1) Requirement already satisfied: ete3 in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (3.1.2) Requirement already satisfied: gffutils in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (0.10.1) Requirement already satisfied: goatools in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (1.0.6) Requirement already satisfied: jinja2 in /usr/lib/python3/dist-packages (from jcvi) (2.8) Requirement already satisfied: matplotlib in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (3.3.2) Requirement already satisfied: networkx in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (2.5) Requirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from jcvi) (1.19.1) Requirement already satisfied: graphviz in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (0.14.1) Requirement already satisfied: PyPDF2 in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (1.26.0) Requirement already satisfied: pytest in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (6.0.2) Requirement already satisfied: pytest-cov in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (2.10.1) Requirement already satisfied: pytest-benchmark in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (3.2.3) Requirement already satisfied: PyYAML in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (5.3.1) Requirement already satisfied: scipy in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (1.5.2) Requirement already satisfied: seaborn in /home/siva/.local/lib/python3.7/site-packages (from jcvi) (0.11.0) Requirement already satisfied: botocore<1.18.0,>=1.17.61 in /home/siva/.local/lib/python3.7/site-packages (from boto3->jcvi) (1.17.61) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/siva/.local/lib/python3.7/site-packages (from boto3->jcvi) (0.10.0) Requirement already satisfied: s3transfer<0.4.0,>=0.3.0 in /home/siva/.local/lib/python3.7/site-packages (from boto3->jcvi) (0.3.3) Requirement already satisfied: docopt>=0.6.1 in /home/siva/.local/lib/python3.7/site-packages (from coveralls->jcvi) (0.6.2) Requirement already satisfied: requests>=1.0.0 in /usr/lib/python3/dist-packages (from coveralls->jcvi) (2.9.1) Requirement already satisfied: coverage<6.0,>=4.1 in /home/siva/.local/lib/python3.7/site-packages (from coveralls->jcvi) (5.3) Requirement already satisfied: argh>=0.26.2 in /home/siva/.local/lib/python3.7/site-packages (from gffutils->jcvi) (0.26.2) Requirement already satisfied: six>=1.12.0 in /home/siva/.local/lib/python3.7/site-packages (from gffutils->jcvi) (1.15.0) Requirement already satisfied: argcomplete>=1.9.4 in /home/siva/.local/lib/python3.7/site-packages (from gffutils->jcvi) (1.12.0) Requirement already satisfied: pyfaidx>=0.5.5.2 in /home/siva/.local/lib/python3.7/site-packages (from gffutils->jcvi) (0.5.9.1) Requirement already satisfied: simplejson in /home/siva/.local/lib/python3.7/site-packages (from gffutils->jcvi) (3.17.2) Requirement already satisfied: xlrd in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (1.2.0) Requirement already satisfied: statsmodels in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (0.12.0) Requirement already satisfied: pydot in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (1.4.1) Requirement already satisfied: pandas in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (1.1.2) Requirement already satisfied: wget in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (3.2) Requirement already satisfied: xlsxwriter in /usr/lib/python3/dist-packages (from goatools->jcvi) (0.7.3) Requirement already satisfied: nose in /home/siva/.local/lib/python3.7/site-packages (from goatools->jcvi) (1.3.7) Requirement already satisfied: certifi>=2020.06.20 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (2020.6.20) Requirement already satisfied: pillow>=6.2.0 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (7.2.0) Requirement already satisfied: cycler>=0.10 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (2.8.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (1.2.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/siva/.local/lib/python3.7/site-packages (from matplotlib->jcvi) (2.4.7) Requirement already satisfied: decorator>=4.3.0 in /home/siva/.local/lib/python3.7/site-packages (from networkx->jcvi) (4.4.2) Requirement already satisfied: iniconfig in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (1.0.1) Requirement already satisfied: packaging in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (20.4) Requirement already satisfied: pluggy<1.0,>=0.12 in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (0.13.1) Requirement already satisfied: py>=1.8.2 in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (1.9.0) Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (1.7.0) Requirement already satisfied: attrs>=17.4.0 in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (20.2.0) Requirement already satisfied: more-itertools>=4.0.0 in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (8.5.0) Requirement already satisfied: toml in /home/siva/.local/lib/python3.7/site-packages (from pytest->jcvi) (0.10.1) Requirement already satisfied: py-cpuinfo in /home/siva/.local/lib/python3.7/site-packages (from pytest-benchmark->jcvi) (7.0.0) Requirement already satisfied: docutils<0.16,>=0.10 in /home/siva/.local/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.61->boto3->jcvi) (0.15.2) Requirement already satisfied: urllib3<1.26,>=1.20; python_version != "3.4" in /home/siva/.local/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.61->boto3->jcvi) (1.25.10) Requirement already satisfied: setuptools>=0.7 in /usr/local/lib/python3.7/dist-packages (from pyfaidx>=0.5.5.2->gffutils->jcvi) (50.3.0) Requirement already satisfied: patsy>=0.5 in /home/siva/.local/lib/python3.7/site-packages (from statsmodels->goatools->jcvi) (0.5.1) Requirement already satisfied: pytz>=2017.2 in /home/siva/.local/lib/python3.7/site-packages (from pandas->goatools->jcvi) (2020.1) Requirement already satisfied: zipp>=0.5 in /home/siva/.local/lib/python3.7/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest->jcvi) (3.1.0) Building wheels for collected packages: jcvi Building wheel for jcvi (setup.py) ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"'; file='"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-1uk9u7fm cwd: /tmp/pip-install-nslbjzgz/jcvi/ Complete output (244 lines): /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:452: UserWarning: Normalizing 'v1.0.9' to '1.0.9' warnings.warn(tmpl.format(**locals())) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/jcvi copying jcvi/init.py -> build/lib.linux-x86_64-3.7/jcvi copying jcvi/_version.py -> build/lib.linux-x86_64-3.7/jcvi creating build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/natsort.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/aws.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/init.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/ez_setup.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/main.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/webcolors.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/iter.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/taxonomy.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/range.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/db.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/orderedcollections.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/progressbar.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/counter.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/brewer2mpl.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/table.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/grouper.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/cbook.py -> build/lib.linux-x86_64-3.7/jcvi/utils creating build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/karyotype.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/init.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/main.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/align.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/synteny.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/logo.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/mummerplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/wheel.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/grabseeds.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/tree.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/glyph.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/dotplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/assembly.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/graph.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/base.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/heatmap.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/blastplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/landscape.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/chromosome.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/table.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/histogram.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/coverage.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/whisker.py -> build/lib.linux-x86_64-3.7/jcvi/graphics creating build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/pasa.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/train.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/depth.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/init.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/main.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/stats.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/automaton.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/evm.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/ahrd.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/qc.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/maker.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/reformat.py -> build/lib.linux-x86_64-3.7/jcvi/annotation creating build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/deconvolute.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/init.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/main.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/phase.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/tassel.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/str.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/impute.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/delly.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/snp.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/cnv.py -> build/lib.linux-x86_64-3.7/jcvi/variation creating build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/console.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/lastz.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/init.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/main.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/align.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/bwa.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/gbsubmit.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/blastplus.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/ks.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/vecscreen.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/cdhit.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/grid.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/gmap.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/restriction.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/fetch.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/uniprot.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/r.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/base.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/biomart.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/softlink.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/mask.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/bowtie.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/cap3.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/script.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/phylo.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/uclust.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/tesseract.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/emboss.py -> build/lib.linux-x86_64-3.7/jcvi/apps creating build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/maxsum.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/init.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/main.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/lpsolve.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/supermap.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/graph.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/ec.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/tsp.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/ml.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/lis.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/matrix.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/formula.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms creating build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/soap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/gaps.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/trinity.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/init.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/main.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/geneticmap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/patch.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/unitig.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/allmaps.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/hic.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/ca.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/postprocess.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/automaton.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/sim.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/amos.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/base.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/allpaths.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/bambus.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/meraculous.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/coverage.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/sspace.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/goldenpath.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/pbjelly.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/preprocess.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/opticalmap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/kmer.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/syntenypath.py -> build/lib.linux-x86_64-3.7/jcvi/assembly creating build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sam.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/init.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/main.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/bed.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/posmap.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/cdt.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/chain.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/excel.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/html.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/gff.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/agp.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/pyblast.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sbt.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/base.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/ace.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/genbank.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/pdf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/vcf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fpc.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/coords.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/maf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/contig.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fasta.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fastq.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/obo.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/psl.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/btab.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/blast.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sizes.py -> build/lib.linux-x86_64-3.7/jcvi/formats creating build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/ies.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/alfalfa.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/init.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/main.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/heterosis.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/str.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/tgbs.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/allmaps.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/misc.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/bites.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/napus.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/pistachio.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/synfind.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/age.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/pineapple.py -> build/lib.linux-x86_64-3.7/jcvi/projects creating build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/init.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/catalog.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/main.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/synteny.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/phylogeny.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/fractionation.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/quota.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/synfind.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/blastfilter.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/pad.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/reconstruct.py -> build/lib.linux-x86_64-3.7/jcvi/compara creating build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/init.py -> build/lib.linux-x86_64-3.7/jcvi/utils/data running egg_info writing jcvi.egg-info/PKG-INFO writing dependency_links to jcvi.egg-info/dependency_links.txt writing requirements to jcvi.egg-info/requires.txt writing top-level names to jcvi.egg-info/top_level.txt reading manifest file 'jcvi.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'jcvi.egg-info/SOURCES.txt' copying jcvi/assembly/chic.pyx -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/formats/cblast.pyx -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/utils/data/Airswing.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/Collegia.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/HookedUp.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/Humor-Sans.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/TREDs.meta.csv -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/adapters.fasta -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/blosum80.mat -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/colorbrewer_all_schemes.json -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/colorchecker.txt -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/hg38.band.txt -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/hg38.chrom.sizes -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/instance.json -> build/lib.linux-x86_64-3.7/jcvi/utils/data UPDATING build/lib.linux-x86_64-3.7/jcvi/_version.py set build/lib.linux-x86_64-3.7/jcvi/_version.py to 'v1.0.9' running build_ext cythoning jcvi/assembly/chic.pyx to jcvi/assembly/chic.c /home/siva/.local/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-nslbjzgz/jcvi/jcvi/assembly/chic.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning jcvi/formats/cblast.pyx to jcvi/formats/cblast.c building 'jcvi.assembly.chic' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/jcvi creating build/temp.linux-x86_64-3.7/jcvi/assembly x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c jcvi/assembly/chic.c -o build/temp.linux-x86_64-3.7/jcvi/assembly/chic.o -O3 jcvi/assembly/chic.c:4:20: fatal error: Python.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
ERROR: Failed building wheel for jcvi Running setup.py clean for jcvi Failed to build jcvi Installing collected packages: jcvi Running setup.py install for jcvi ... error ERROR: Command errored out with exit status 1: command: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"'; file='"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-_6yevuza/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/siva/.local/include/python3.7m/jcvi cwd: /tmp/pip-install-nslbjzgz/jcvi/ Complete output (242 lines): /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:452: UserWarning: Normalizing 'v1.0.9' to '1.0.9' warnings.warn(tmpl.format(**locals())) running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/jcvi copying jcvi/init.py -> build/lib.linux-x86_64-3.7/jcvi copying jcvi/_version.py -> build/lib.linux-x86_64-3.7/jcvi creating build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/natsort.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/aws.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/init.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/ez_setup.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/main.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/webcolors.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/iter.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/taxonomy.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/range.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/db.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/orderedcollections.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/progressbar.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/counter.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/brewer2mpl.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/table.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/grouper.py -> build/lib.linux-x86_64-3.7/jcvi/utils copying jcvi/utils/cbook.py -> build/lib.linux-x86_64-3.7/jcvi/utils creating build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/karyotype.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/init.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/main.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/align.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/synteny.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/logo.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/mummerplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/wheel.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/grabseeds.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/tree.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/glyph.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/dotplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/assembly.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/graph.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/base.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/heatmap.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/blastplot.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/landscape.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/chromosome.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/table.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/histogram.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/coverage.py -> build/lib.linux-x86_64-3.7/jcvi/graphics copying jcvi/graphics/whisker.py -> build/lib.linux-x86_64-3.7/jcvi/graphics creating build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/pasa.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/train.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/depth.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/init.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/main.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/stats.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/automaton.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/evm.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/ahrd.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/qc.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/maker.py -> build/lib.linux-x86_64-3.7/jcvi/annotation copying jcvi/annotation/reformat.py -> build/lib.linux-x86_64-3.7/jcvi/annotation creating build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/deconvolute.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/init.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/main.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/phase.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/tassel.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/str.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/impute.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/delly.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/snp.py -> build/lib.linux-x86_64-3.7/jcvi/variation copying jcvi/variation/cnv.py -> build/lib.linux-x86_64-3.7/jcvi/variation creating build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/console.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/lastz.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/init.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/main.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/align.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/bwa.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/gbsubmit.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/blastplus.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/ks.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/vecscreen.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/cdhit.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/grid.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/gmap.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/restriction.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/fetch.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/uniprot.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/r.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/base.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/biomart.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/softlink.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/mask.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/bowtie.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/cap3.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/script.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/phylo.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/uclust.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/tesseract.py -> build/lib.linux-x86_64-3.7/jcvi/apps copying jcvi/apps/emboss.py -> build/lib.linux-x86_64-3.7/jcvi/apps creating build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/maxsum.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/init.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/main.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/lpsolve.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/supermap.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/graph.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/ec.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/tsp.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/ml.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/lis.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/matrix.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms copying jcvi/algorithms/formula.py -> build/lib.linux-x86_64-3.7/jcvi/algorithms creating build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/soap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/gaps.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/trinity.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/init.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/main.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/geneticmap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/patch.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/unitig.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/allmaps.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/hic.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/ca.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/postprocess.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/automaton.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/sim.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/amos.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/base.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/allpaths.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/bambus.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/meraculous.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/coverage.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/sspace.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/goldenpath.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/pbjelly.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/preprocess.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/opticalmap.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/kmer.py -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/assembly/syntenypath.py -> build/lib.linux-x86_64-3.7/jcvi/assembly creating build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sam.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/init.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/main.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/bed.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/posmap.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/cdt.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/chain.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/excel.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/html.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/gff.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/agp.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/pyblast.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sbt.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/base.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/ace.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/genbank.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/pdf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/vcf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fpc.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/coords.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/maf.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/contig.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fasta.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/fastq.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/obo.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/psl.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/btab.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/blast.py -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/formats/sizes.py -> build/lib.linux-x86_64-3.7/jcvi/formats creating build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/ies.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/alfalfa.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/init.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/main.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/heterosis.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/str.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/tgbs.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/allmaps.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/misc.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/bites.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/napus.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/pistachio.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/synfind.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/age.py -> build/lib.linux-x86_64-3.7/jcvi/projects copying jcvi/projects/pineapple.py -> build/lib.linux-x86_64-3.7/jcvi/projects creating build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/init.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/catalog.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/main.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/synteny.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/phylogeny.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/fractionation.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/quota.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/synfind.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/blastfilter.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/pad.py -> build/lib.linux-x86_64-3.7/jcvi/compara copying jcvi/compara/reconstruct.py -> build/lib.linux-x86_64-3.7/jcvi/compara creating build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/init.py -> build/lib.linux-x86_64-3.7/jcvi/utils/data running egg_info writing jcvi.egg-info/PKG-INFO writing dependency_links to jcvi.egg-info/dependency_links.txt writing requirements to jcvi.egg-info/requires.txt writing top-level names to jcvi.egg-info/top_level.txt reading manifest file 'jcvi.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'jcvi.egg-info/SOURCES.txt' copying jcvi/assembly/chic.pyx -> build/lib.linux-x86_64-3.7/jcvi/assembly copying jcvi/formats/cblast.pyx -> build/lib.linux-x86_64-3.7/jcvi/formats copying jcvi/utils/data/Airswing.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/Collegia.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/HookedUp.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/Humor-Sans.ttf -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/TREDs.meta.csv -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/adapters.fasta -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/blosum80.mat -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/chrY.hg38.unique_ccn.gc -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/colorbrewer_all_schemes.json -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/colorchecker.txt -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/hg38.band.txt -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/hg38.chrom.sizes -> build/lib.linux-x86_64-3.7/jcvi/utils/data copying jcvi/utils/data/instance.json -> build/lib.linux-x86_64-3.7/jcvi/utils/data UPDATING build/lib.linux-x86_64-3.7/jcvi/_version.py set build/lib.linux-x86_64-3.7/jcvi/_version.py to 'v1.0.9' running build_ext skipping 'jcvi/assembly/chic.c' Cython extension (up-to-date) skipping 'jcvi/formats/cblast.c' Cython extension (up-to-date) building 'jcvi.assembly.chic' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/jcvi creating build/temp.linux-x86_64-3.7/jcvi/assembly x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/lib/python3.7/dist-packages/numpy/core/include -I/usr/include/python3.7m -c jcvi/assembly/chic.c -o build/temp.linux-x86_64-3.7/jcvi/assembly/chic.o -O3 jcvi/assembly/chic.c:4:20: fatal error: Python.h: No such file or directory compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
ERROR: Command errored out with exit status 1: /usr/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"'; file='"'"'/tmp/pip-install-nslbjzgz/jcvi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-_6yevuza/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/siva/.local/include/python3.7m/jcvi Check the logs for full command output.
All the packages including the wheel packages are up to date, but there is an error while building the wheel for jcvi.