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bcgsc / NanoSim

Nanopore sequence read simulator
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Fix dependencies install in Python 3.6 #103

Closed jkomyno closed 3 years ago

jkomyno commented 3 years ago

This PR fixes dependencies install in Python 3.6. The error log I got when installing the dependencies from the previous requirements.txt is shown below:

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## Error log ```bash Collecting HTSeq==0.9.1 Downloading HTSeq-0.9.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Collecting numpy==1.13.3 Downloading numpy-1.13.3-cp36-cp36m-manylinux1_x86_64.whl (17.0 MB) Collecting pybedtools==0.7.10 Downloading pybedtools-0.7.10.tar.gz (12.6 MB) Collecting pysam==0.13 Downloading pysam-0.13-cp36-cp36m-manylinux1_x86_64.whl (9.3 MB) Collecting scipy==1.0.0 Downloading scipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (50.0 MB) Collecting six==1.10.0 Downloading six-1.10.0-py2.py3-none-any.whl (10 kB) Collecting scikit-learn==0.20.0 Downloading scikit_learn-0.20.0-cp36-cp36m-manylinux1_x86_64.whl (5.3 MB) Building wheels for collected packages: pybedtools Building wheel for pybedtools (setup.py): started Building wheel for pybedtools (setup.py): finished with status 'error' ERROR: Command errored out with exit status 1: command: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-maurcii8/pybedtools/setup.py'"'"'; __file__='"'"'/tmp/pip-install-maurcii8/pybedtools/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-j1e3r28i cwd: /tmp/pip-install-maurcii8/pybedtools/ Complete output (127 lines): running bdist_wheel The [wheel] section is deprecated. Use [bdist_wheel] instead. running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/__main__.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/helpers.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/stats.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/parallel.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/logger.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/version.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/settings.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/filenames.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools creating build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_scripts.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test1.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test creating build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/classifier.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib creating build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/annotate.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/peak_pie.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts creating build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/featurefuncs.cxx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/cbedtools.cxx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/_Window.c -> build/lib.linux-x86_64-3.6/pybedtools running build_ext building 'pybedtools.cbedtools' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/src creating build/temp.linux-x86_64-3.6/pybedtools gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -Isrc/ -I/usr/local/include/python3.6m -c src/fileType.cpp -o build/temp.linux-x86_64-3.6/src/fileType.o gcc: error trying to exec 'cc1plus': execvp: No such file or directory error: command 'gcc' failed with exit status 1 ---------------------------------------- ERROR: Failed building wheel for pybedtools Running setup.py clean for pybedtools Failed to build pybedtools Installing collected packages: pysam, numpy, HTSeq, six, pybedtools, scipy, scikit-learn Running setup.py install for pybedtools: started Running setup.py install for pybedtools: finished with status 'error' ERROR: Command errored out with exit status 1: command: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-maurcii8/pybedtools/setup.py'"'"'; __file__='"'"'/tmp/pip-install-maurcii8/pybedtools/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-xvyelhk2/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6m/pybedtools cwd: /tmp/pip-install-maurcii8/pybedtools/ Complete output (152 lines): running install running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/__main__.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/helpers.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/stats.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/parallel.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/logger.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/version.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/settings.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/filenames.py -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools creating build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_scripts.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/test1.py -> build/lib.linux-x86_64-3.6/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test creating build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/classifier.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib creating build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/annotate.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intron_exon_reads.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_mpl.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_gchart.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intersection_matrix.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/py_ms_example.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/peak_pie.py -> build/lib.linux-x86_64-3.6/pybedtools/scripts creating build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-3.6/pybedtools running build_ext Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-maurcii8/pybedtools/setup.py", line 385, in **setuptools_kwargs) File "/usr/local/lib/python3.6/site-packages/setuptools/__init__.py", line 153, in setup return distutils.core.setup(**attrs) File "/usr/local/lib/python3.6/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/local/lib/python3.6/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/usr/local/lib/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/local/lib/python3.6/site-packages/setuptools/command/install.py", line 61, in run return orig.install.run(self) File "/usr/local/lib/python3.6/distutils/command/install.py", line 545, in run self.run_command('build') File "/usr/local/lib/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/local/lib/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/local/lib/python3.6/distutils/command/build.py", line 135, in run self.run_command(cmd_name) File "/usr/local/lib/python3.6/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/usr/local/lib/python3.6/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/local/lib/python3.6/distutils/command/build_ext.py", line 339, in run self.build_extensions() File "/tmp/pip-install-maurcii8/pybedtools/setup.py", line 269, in build_extensions self.check_cython_extensions(self.extensions) File "/tmp/pip-install-maurcii8/pybedtools/setup.py", line 266, in check_cython_extensions """ % src) Exception: Cython-generated file 'pybedtools/cbedtools.cxx' not found. Cython is required to compile pybedtools from a development branch. Please install Cython or download a source release of pybedtools. ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/local/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-maurcii8/pybedtools/setup.py'"'"'; __file__='"'"'/tmp/pip-install-maurcii8/pybedtools/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-xvyelhk2/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.6m/pybedtools Check the logs for full command output. The command '/bin/sh -c pip install -r ./NanoSim/requirements.txt' returned a non-zero code: ```

The easiest fix is deleting the explicit pybedtools dependency from requirements.txt, leaving the other dependencies untouched.

Test

You can test this PR by using Docker. Create a new file called 'Dockerfile' with the following content:

FROM python:3.6-slim-buster

# install native dependencies
RUN apt-get update
RUN apt-get install -y --no-install-recommends \
  make \
  gcc \
  python3-dev \
  gfortran \
  libopenblas-dev \
  liblapack-dev \
  zlib1g-dev

# copy NanoSim source
COPY NanoSim ./NanoSim

# install Python dependencies
RUN pip install -r ./NanoSim/requirements.txt

Assuming you have cloned NanoSim's repository in the current directory, run the following command:

docker build -t nanosim/fix-python-3.6 .

The process should terminate successfully.

jkomyno commented 3 years ago

Moreover, the joblib should be explicitly referenced in the requirements.txt file. After NanoSim@3.0.0 got released, joblib isn't bound to sklearn.externals anymore. Which version should we bind in the requirements.txt file?

cheny19 commented 3 years ago

Hi @jkomyno,

Thanks for contributing! We decided to add joblib to the requirements.txt and removed the version number of all packages to solve the problem. So we won't merge this branch now.

We really appreciate your contribution, and please do not hesitate to provide more suggestions or feature requests.

Thanks, Chen