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Analysis components from Oxford Nanopore Research
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Installing pomoxis on MacOS Mojave (10.14.2) #28

Closed Ekrates closed 5 years ago

Ekrates commented 5 years ago

I am trying to install Pomoxis on MacOS Mojave. I have been able to solve all the other issues, except something related with gcc. I get error messages: 1 warning and 1 error generated. error: command 'gcc' failed with exit status 1 And at the end of the process I have this line: **make: * [conda] Error 1

The full command line output is attached below.

Any idea how to solve? I have already updated OsX command line tools. Would it be better to try to update gcc or g++ etc?

Any help appreciated.

The full command line output (from the most recent re-installation after updating the command line tools):

CONDA=~/miniconda3/ make conda . /Users/ejvest/miniconda3//etc/profile.d/conda.sh && conda remove -n pomoxis --all

Remove all packages in environment /Users/ejvest/miniconda3/envs/pomoxis:

Package Plan

environment location: /Users/ejvest/miniconda3/envs/pomoxis

The following packages will be REMOVED:

bcftools:        1.7-0                           bioconda   
bzip2:           1.0.6-h1de35cc_1002             conda-forge
ca-certificates: 2018.11.29-ha4d7672_0           conda-forge
certifi:         2018.11.29-py36_1000            conda-forge
curl:            7.63.0-heae2a1f_1000            conda-forge
krb5:            1.16.3-h24a3359_1000            conda-forge
libcurl:         7.63.0-h76de61e_1000            conda-forge
libcxx:          7.0.0-h2d50403_2                conda-forge
libdeflate:      1.0-h470a237_0                  bioconda   
libedit:         3.1.20170329-0                  conda-forge
libffi:          3.2.1-1                         bioconda   
libssh2:         1.8.0-hf30b1f0_1003             conda-forge
llvm-meta:       7.0.0-0                         conda-forge
miniasm:         0.3_r179-ha92aebf_0             bioconda   
minimap2:        2.14-ha92aebf_0                 bioconda   
ncurses:         5.9-10                          conda-forge
openssl:         1.0.2p-h1de35cc_1002            conda-forge
pigz:            2.3.4-0                         conda-forge
pip:             18.1-py36_1000                  conda-forge
porechop:        0.2.3_seqan2.1.1-py36h470a237_3 bioconda   
python:          3.6.6-h4a56312_1003             conda-forge
racon:           1.3.1-he941832_5                bioconda   
readline:        7.0-0                           conda-forge
samtools:        1.8-h46bd0b3_5                  bioconda   
seqkit:          0.8.0-2                         bioconda   
setuptools:      40.6.3-py36_0                   conda-forge
sqlite:          3.26.0-ha441bb4_0                          
tk:              8.6.9-ha441bb4_1000             conda-forge
wheel:           0.32.3-py36_0                   conda-forge
xz:              5.2.4-h1de35cc_1001             conda-forge
zlib:            1.2.11-h1de35cc_1004            conda-forge

Proceed ([y]/n)? y

. /Users/ejvest/miniconda3//etc/profile.d/conda.sh && conda create -y -n pomoxis -c bioconda -c conda-forge porechop \ samtools=1.8 bcftools=1.7 seqkit=0.8.0 \ miniasm=0.3 minimap2=2.14 racon=1.3.1 \ python=3.6 Solving environment: / done

Package Plan

environment location: /Users/ejvest/miniconda3/envs/pomoxis

added / updated specs:

The following NEW packages will be INSTALLED:

bcftools:        1.7-0                           bioconda   
bzip2:           1.0.6-h1de35cc_1002             conda-forge
ca-certificates: 2018.11.29-ha4d7672_0           conda-forge
certifi:         2018.11.29-py36_1000            conda-forge
curl:            7.63.0-heae2a1f_1000            conda-forge
krb5:            1.16.3-h24a3359_1000            conda-forge
libcurl:         7.63.0-h76de61e_1000            conda-forge
libcxx:          7.0.0-h2d50403_2                conda-forge
libdeflate:      1.0-h470a237_0                  bioconda   
libedit:         3.1.20170329-0                  conda-forge
libffi:          3.2.1-1                         bioconda   
libssh2:         1.8.0-hf30b1f0_1003             conda-forge
llvm-meta:       7.0.0-0                         conda-forge
miniasm:         0.3_r179-ha92aebf_0             bioconda   
minimap2:        2.14-ha92aebf_0                 bioconda   
ncurses:         5.9-10                          conda-forge
openssl:         1.0.2p-h1de35cc_1002            conda-forge
pigz:            2.3.4-0                         conda-forge
pip:             18.1-py36_1000                  conda-forge
porechop:        0.2.3_seqan2.1.1-py36h470a237_3 bioconda   
python:          3.6.6-h4a56312_1003             conda-forge
racon:           1.3.1-he941832_5                bioconda   
readline:        7.0-0                           conda-forge
samtools:        1.8-h46bd0b3_5                  bioconda   
seqkit:          0.8.0-2                         bioconda   
setuptools:      40.6.3-py36_0                   conda-forge
sqlite:          3.26.0-ha441bb4_0                          
tk:              8.6.9-ha441bb4_1000             conda-forge
wheel:           0.32.3-py36_0                   conda-forge
xz:              5.2.4-h1de35cc_1001             conda-forge
zlib:            1.2.11-h1de35cc_1004            conda-forge

Preparing transaction: done Verifying transaction: done Executing transaction: done #

To activate this environment, use

#

$ conda activate pomoxis

#

To deactivate an active environment, use

#

$ conda deactivate

grep -v Porechop requirements.txt > conda_reqs.txt . /Users/ejvest/miniconda3//etc/profile.d/conda.sh && conda activate pomoxis && pip install -r conda_reqs.txt Collecting aiozmq (from -r conda_reqs.txt (line 3)) Using cached https://files.pythonhosted.org/packages/c8/5b/4ce8584fcd676664ba43170d9871ae177837fa72f59c08766bc0c589e177/aiozmq-0.7.1-py3-none-any.whl Collecting biopython>=1.63 (from -r conda_reqs.txt (line 4)) Using cached https://files.pythonhosted.org/packages/e3/ef/5325c1c28b11e459fadb8a2a42662d34c1cbabef93fd8c7cfb7b9e60a0ff/biopython-1.73-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting cffi (from -r conda_reqs.txt (line 5)) Using cached https://files.pythonhosted.org/packages/8e/be/40b1bc2c3221acdefeb9dab6773d43cda7543ed0d8c8df8768f05af2d01e/cffi-1.11.5-cp36-cp36m-macosx_10_6_intel.whl Collecting fast5_research (from -r conda_reqs.txt (line 6)) Collecting intervaltree<3 (from -r conda_reqs.txt (line 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cffi->-r conda_reqs.txt (line 5)) Collecting progressbar2 (from fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/0c/78/0ae9129f12098adbcfee0c51a81dfa94cdc1853142aa4d62e63c6a355bd7/progressbar2-3.39.2-py2.py3-none-any.whl Collecting h5py<2.9.0 (from fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/44/81/50a0560aac57a33c2a624d9e160735f39d7a6324e3f6f115425a1bf01dd9/h5py-2.8.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting sortedcontainers (from intervaltree<3->-r conda_reqs.txt (line 7)) Using cached https://files.pythonhosted.org/packages/13/f3/cf85f7c3a2dbd1a515d51e1f1676d971abe41bba6f4ab5443240d9a78e5b/sortedcontainers-2.1.0-py2.py3-none-any.whl Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl Collecting python-dateutil>=2.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl Collecting cycler>=0.10 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Collecting kiwisolver>=1.0.1 (from matplotlib->-r conda_reqs.txt (line 8)) Using cached https://files.pythonhosted.org/packages/fb/96/619db9bf08f652790fa9f3c3884a67dc43da4bdaa185a5aa2117eb4651e1/kiwisolver-1.0.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting pytz>=2011k (from pandas->-r conda_reqs.txt (line 12)) Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl Collecting six (from pybedtools->-r conda_reqs.txt (line 13)) Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting PyYAML>=3.10 (from watchdog->-r conda_reqs.txt (line 16)) Collecting argh>=0.24.1 (from watchdog->-r conda_reqs.txt (line 16)) Using cached https://files.pythonhosted.org/packages/06/1c/e667a7126f0b84aaa1c56844337bf0ac12445d1beb9c8a6199a7314944bf/argh-0.26.2-py2.py3-none-any.whl Collecting pathtools>=0.1.1 (from watchdog->-r conda_reqs.txt (line 16)) Collecting python-utils>=2.3.0 (from progressbar2->fast5_research->-r conda_reqs.txt (line 6)) Using cached https://files.pythonhosted.org/packages/eb/a0/19119d8b7c05be49baf6c593f11c432d571b70d805f2fe94c0585e55e4c8/python_utils-2.3.0-py2.py3-none-any.whl Requirement already satisfied: setuptools in /Users/ejvest/miniconda3/envs/pomoxis/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib->-r conda_reqs.txt (line 8)) (40.6.3) Building wheels for collected packages: pybedtools, scrappie Running setup.py bdist_wheel for pybedtools ... error Complete output from command /Users/ejvest/miniconda3/envs/pomoxis/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/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 /private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-wheel-kfg43nms --python-tag cp36: running bdist_wheel The [wheel] section is deprecated. Use [bdist_wheel] instead. running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/version.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/paths.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/filenames.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/init.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/logger.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/stats.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/settings.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/bedtool.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/parallel.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/helpers.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/genome_registry.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/main.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_contrib.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test1.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/init.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/tfuncs.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_issues.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_len_leak.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test copying pybedtools/test/test_scripts.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/init.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/contrib creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_gchart.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intron_exon_reads.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/init.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/venn_mpl.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/py_ms_example.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/peak_pie.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts copying pybedtools/scripts/intersection_matrix.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/init.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data running egg_info creating pybedtools.egg-info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt writing manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest file 'pybedtools.egg-info/SOURCES.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' copying pybedtools/cbedtools.cpp -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/featurefuncs.cpp -> build/lib.macosx-10.7-x86_64-3.6/pybedtools creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/include copying pybedtools/include/bedFile.cpp -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/include copying pybedtools/include/fileType.cpp -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/include copying pybedtools/include/gzstream.cpp -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/include copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/164.gtf -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.links.html -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/y.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/v.vcf -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/m1.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/b.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/exons.gff -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/d.gff -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/small.fastq -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/test/data copying pybedtools/featurefuncs.pyx -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pyx -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/_Window.pyx -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/cbedtools.pxd -> build/lib.macosx-10.7-x86_64-3.6/pybedtools copying pybedtools/scripts/pybedtools -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts creating build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts/examples copying pybedtools/scripts/examples/pbt_plotting_example.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools/scripts/examples running build_ext building 'pybedtools.cbedtools' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/pybedtools creating build/temp.macosx-10.7-x86_64-3.6/pybedtools/include gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -Ipybedtools/include/ -I/Users/ejvest/miniconda3/envs/pomoxis/include/python3.6m -c pybedtools/cbedtools.cpp -o build/temp.macosx-10.7-x86_64-3.6/pybedtools/cbedtools.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] pybedtools/cbedtools.cpp:654:10: fatal error: 'ios' file not found

include "ios"

       ^~~~~

1 warning and 1 error generated. error: command 'gcc' failed with exit status 1

Failed building wheel for pybedtools Running setup.py clean for pybedtools Complete output from command /Users/ejvest/miniconda3/envs/pomoxis/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/pybedtools/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" clean --all: usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: -c --help [cmd1 cmd2 ...] or: -c --help-commands or: -c cmd --help

error: option --all not recognized

Failed cleaning build dir for pybedtools Running setup.py bdist_wheel for scrappie ... error Complete output from command /Users/ejvest/miniconda3/envs/pomoxis/bin/python -u -c "import setuptools, tokenize;file='/private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/scrappie/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 /private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-wheel-9g3w8sp4 --python-tag cp36: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/scrappy copying scrappy/init.py -> build/lib.macosx-10.7-x86_64-3.6/scrappy running build_ext generating cffi module 'build/temp.macosx-10.7-x86_64-3.6/libscrappy.c' creating build/temp.macosx-10.7-x86_64-3.6 building 'libscrappy' extension creating build/temp.macosx-10.7-x86_64-3.6/build creating build/temp.macosx-10.7-x86_64-3.6/build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/src gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -Isrc -I/Users/ejvest/miniconda3/envs/pomoxis/include/python3.6m -c build/temp.macosx-10.7-x86_64-3.6/libscrappy.c -o build/temp.macosx-10.7-x86_64-3.6/build/temp.macosx-10.7-x86_64-3.6/libscrappy.o -std=c99 -msse3 -O3 In file included from build/temp.macosx-10.7-x86_64-3.6/libscrappy.c:496: In file included from src/util.h:8: src/sse_mathfun.h:343:13: warning: unused function 'sin_ps' [-Wunused-function] static v4sf sin_ps(v4sf x) { // any x ^ src/sse_mathfun.h:460:13: warning: unused function 'cos_ps' [-Wunused-function] static v4sf cos_ps(v4sf x) { // any x ^ src/sse_mathfun.h:579:13: warning: unused function 'sincos_ps' [-Wunused-function] static void sincos_ps(v4sf x, v4sf s, v4sf c) { ^ 3 warnings generated. gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -Isrc -I/Users/ejvest/miniconda3/envs/pomoxis/include/python3.6m -c src/decode.c -o build/temp.macosx-10.7-x86_64-3.6/src/decode.o -std=c99 -msse3 -O3 src/decode.c:25:38: warning: attribute declaration must precede definition [-Wignored-attributes] static inline m128i attribute((gnu_inline, always_inline)) _mm_mullo_epi32(const m128i x, const m128i y) { ^ /Library/Developer/CommandLineTools/usr/lib/clang/10.0.0/include/smmintrin.h:561:1: note: previous definition is here _mm_mullo_epi32 (m128i V1, m128i V2) ^ src/decode.c:25:74: error: redefinition of '_mm_mullo_epi32' static inline m128i attribute((gnu_inline, always_inline__)) _mm_mullo_epi32(const m128i x, const __m128i y) { ^ /Library/Developer/CommandLineTools/usr/lib/clang/10.0.0/include/smmintrin.h:561:1: note: previous definition is here _mm_mullo_epi32 (m128i V1, m128i V2) ^ src/decode.c:82:19: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare] if(seq[i] == n){


  src/decode.c:90:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
          if(seq[i] == n + 1){
             ~~~~~~ ^  ~~~~~
  src/decode.c:500:45: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
          for (size_t kmer = seq[k], i = 0; i < ol; i++) {
                                            ~ ^ ~~
  src/decode.c:1221:28: warning: comparison of integers of different signs: 'unsigned long' and 'int32_t' (aka 'int') [-Wsign-compare]
              if(nfstate - 1 != path[sample_max - 1]){
                 ~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~
  src/decode.c:1228:29: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
              if(path[sample] >= nfstate){
                 ~~~~~~~~~~~~ ^  ~~~~~~~
  src/decode.c:1520:28: warning: comparison of integers of different signs: 'const size_t' (aka 'const unsigned long') and 'int' [-Wsign-compare]
              if(START_STATE == path[blk] || END_STATE == path[blk]){
                 ~~~~~~~~~~~ ^  ~~~~~~~~~
  src/decode.c:1520:54: warning: comparison of integers of different signs: 'const size_t' (aka 'const unsigned long') and 'int' [-Wsign-compare]
              if(START_STATE == path[blk] || END_STATE == path[blk]){
                                             ~~~~~~~~~ ^  ~~~~~~~~~
  8 warnings and 1 error generated.
  error: command 'gcc' failed with exit status 1

  ----------------------------------------
  Failed building wheel for scrappie
  Running setup.py clean for scrappie
Failed to build pybedtools scrappie
Installing collected packages: pyzmq, aiozmq, numpy, biopython, pycparser, cffi, six, python-utils, progressbar2, h5py, fast5-research, sortedcontainers, intervaltree, pyparsing, python-dateutil, cycler, kiwisolver, matplotlib, mappy, msgpack-python, pytz, pandas, pysam, pybedtools, scrappie, PyYAML, argh, pathtools, watchdog
  Running setup.py install for pybedtools ... error
    Complete output from command /Users/ejvest/miniconda3/envs/pomoxis/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/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 /private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-record-mqx5h7tj/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    copying pybedtools/version.py -> build/lib.macosx-10.7-x86_64-3.6/pybedtools
    running egg_info
    writing pybedtools.egg-info/PKG-INFO
    writing dependency_links to pybedtools.egg-info/dependency_links.txt
    writing requirements to pybedtools.egg-info/requires.txt
    writing top-level names to pybedtools.egg-info/top_level.txt
    reading manifest file 'pybedtools.egg-info/SOURCES.txt'
    writing manifest file 'pybedtools.egg-info/SOURCES.txt'
    running build_ext
    building 'pybedtools.cbedtools' extension
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -I/Users/ejvest/miniconda3/envs/pomoxis/include -arch x86_64 -Ipybedtools/include/ -I/Users/ejvest/miniconda3/envs/pomoxis/include/python3.6m -c pybedtools/cbedtools.cpp -o build/temp.macosx-10.7-x86_64-3.6/pybedtools/cbedtools.o
    warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
    pybedtools/cbedtools.cpp:654:10: fatal error: 'ios' file not found
    #include "ios"
             ^~~~~
    1 warning and 1 error generated.
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/Users/ejvest/miniconda3/envs/pomoxis/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/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 /private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-record-mqx5h7tj/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/tl/fjzy_0ld1xv6k34zt836rmdh0000gp/T/pip-install-y_ad1khi/pybedtools/
make: *** [conda] Error 1
>
cjw85 commented 5 years ago

Hi @Ekrates

It looks like the compilation of both scrappie and pybedtools are failing.

Compilation of scrappie on MacOS is known to be finicky (compatibility). scrappie is used only to provide functionality of read simulation, if you are not interested in this you could remove scrappie from the requirements.txt file before running CONDA=~/miniconda3/ make conda.

For pybedtools, you can also remove this package from requirements.txt and use conda install pybedtools to install the package from conda (the Makefile currently handles this requirement through pip/pypi). We will amend this behaviour in the next update.

cjw85 commented 5 years ago

Release v0.2.1 removes the pybedtools requirement entirely.

The scrappie error on MacOS is that which is reported in https://github.com/nanoporetech/scrappie/issues/27