Installation error - Githubissues

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.

tanghaibao / jcvi

Installation error #298