s6juncheng
commented
5 years ago Hi @herrroaa, can you try to install Cython with pip install Cython first. Try to install MMSplice again after intalling Cython.
Closed herrroaa closed 5 years ago
s6juncheng
commented
5 years ago Hi @herrroaa, can you try to install Cython with pip install Cython first. Try to install MMSplice again after intalling Cython.
herrroaa
commented
5 years ago HI @s6juncheng I tried with installing Cython first, but now I am getting different errors
$ pip install mmsplice
Collecting mmsplice
Using cached https://files.pythonhosted.org/packages/75/67/c04e48b46c8d32f948b7d4ccd84ef28f209c64fb6986fe776bc989e47cc9/mmsplice-0.2.7-py2.py3-none-any.whl
Collecting sklearn (from mmsplice)
Collecting click (from mmsplice)
Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl
Collecting cyvcf2==0.9.0 (from mmsplice)
Using cached https://files.pythonhosted.org/packages/3f/21/29c8dc12e91d55e953f230bf9e96af779b224f6d59f4eacc3dcb80753d34/cyvcf2-0.9.0.tar.gz
Collecting pyfaidx (from mmsplice)
Collecting setuptools<=39.1.0 (from mmsplice)
Downloading https://files.pythonhosted.org/packages/8c/10/79282747f9169f21c053c562a0baa21815a8c7879be97abd930dbcf862e8/setuptools-39.1.0-py2.py3-none-any.whl (566kB)
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Collecting concise (from mmsplice)
Collecting tqdm (from mmsplice)
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Collecting gffutils (from mmsplice)
Collecting kipoi>=0.4.1 (from mmsplice)
Using cached https://files.pythonhosted.org/packages/5a/49/7e61be887bcc8b9133d0fa3853ce0bdd35284ce40cb4889a46b1226483dd/kipoi-0.6.13-py3-none-any.whl
Collecting tensorflow (from mmsplice)
Downloading https://files.pythonhosted.org/packages/f6/7b/5ab19bac13810661ff9e2485811553f1dea9a5d611ce846345aed4766bbe/tensorflow-1.13.1-cp36-cp36m-macosx_10_11_x86_64.whl (71.6MB)
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Collecting keras (from mmsplice)
Downloading https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl (312kB)
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Requirement already satisfied: pandas in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from mmsplice) (0.24.2)
Collecting scikit-learn (from sklearn->mmsplice)
Using cached https://files.pythonhosted.org/packages/f2/46/4e68feb391f049b7ef9fe9bad355eecc208b3cfb324c47410580b4854cde/scikit_learn-0.21.2-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
Requirement already satisfied: numpy in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from cyvcf2==0.9.0->mmsplice) (1.16.4)
Requirement already satisfied: six in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from pyfaidx->mmsplice) (1.12.0)
Collecting shapely (from concise->mmsplice)
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Collecting matplotlib (from concise->mmsplice)
Downloading https://files.pythonhosted.org/packages/45/bf/8d8233749b5f8580bdfdb2aeed0d2df177daab44cfebc5c0de827ce1b11e/matplotlib-3.1.0-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 (14.4MB)
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Collecting descartes (from concise->mmsplice)
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Collecting gtfparse>=1.0.7 (from concise->mmsplice)
Collecting hyperopt (from concise->mmsplice)
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Collecting scipy (from concise->mmsplice)
Downloading https://files.pythonhosted.org/packages/81/ae/125c21f09b202c3009ad7d9fb0263fb7d6053813d4b67ccbbe4d65f7f53a/scipy-1.3.0-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 (27.7MB)
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Collecting simplejson (from gffutils->mmsplice)
Collecting argcomplete (from gffutils->mmsplice)
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Collecting argh (from gffutils->mmsplice)
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Collecting enum34 (from kipoi>=0.4.1->mmsplice)
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Collecting jinja2 (from kipoi>=0.4.1->mmsplice)
Downloading https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl (124kB)
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Collecting h5py (from kipoi>=0.4.1->mmsplice)
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Collecting future (from kipoi>=0.4.1->mmsplice)
Collecting urllib3>=1.21.1 (from kipoi>=0.4.1->mmsplice)
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Collecting related>=0.6.0 (from kipoi>=0.4.1->mmsplice)
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Collecting cookiecutter>=1.6.0 (from kipoi>=0.4.1->mmsplice)
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Collecting kipoi-conda>=0.1.6 (from kipoi>=0.4.1->mmsplice)
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Collecting pyyaml (from kipoi>=0.4.1->mmsplice)
Downloading https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz (274kB)
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Collecting colorlog (from kipoi>=0.4.1->mmsplice)
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Collecting deprecation>=2.0.6 (from kipoi>=0.4.1->mmsplice)
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Collecting attrs>=17.4.0 (from kipoi>=0.4.1->mmsplice)
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Collecting tinydb (from kipoi>=0.4.1->mmsplice)
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Collecting kipoi-utils>=0.1.12 (from kipoi>=0.4.1->mmsplice)
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Collecting absl-py>=0.1.6 (from tensorflow->mmsplice)
Downloading https://files.pythonhosted.org/packages/da/3f/9b0355080b81b15ba6a9ffcf1f5ea39e307a2778b2f2dc8694724e8abd5b/absl-py-0.7.1.tar.gz (99kB)
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Collecting grpcio>=1.8.6 (from tensorflow->mmsplice)
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Collecting termcolor>=1.1.0 (from tensorflow->mmsplice)
Requirement already satisfied: wheel>=0.26 in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from tensorflow->mmsplice) (0.33.4)
Collecting tensorflow-estimator<1.14.0rc0,>=1.13.0 (from tensorflow->mmsplice)
Downloading https://files.pythonhosted.org/packages/bb/48/13f49fc3fa0fdf916aa1419013bb8f2ad09674c275b4046d5ee669a46873/tensorflow_estimator-1.13.0-py2.py3-none-any.whl (367kB)
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Collecting keras-applications>=1.0.6 (from tensorflow->mmsplice)
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Collecting gast>=0.2.0 (from tensorflow->mmsplice)
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Collecting tensorboard<1.14.0,>=1.13.0 (from tensorflow->mmsplice)
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Collecting astor>=0.6.0 (from tensorflow->mmsplice)
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Collecting protobuf>=3.6.1 (from tensorflow->mmsplice)
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Requirement already satisfied: python-dateutil>=2.5.0 in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from pandas->mmsplice) (2.8.0)
Requirement already satisfied: pytz>=2011k in /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages (from pandas->mmsplice) (2019.1)
Collecting joblib>=0.11 (from scikit-learn->sklearn->mmsplice)
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Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib->concise->mmsplice)
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Collecting kiwisolver>=1.0.1 (from matplotlib->concise->mmsplice)
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Collecting cycler>=0.10 (from matplotlib->concise->mmsplice)
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Collecting pymongo (from hyperopt->concise->mmsplice)
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Collecting networkx (from hyperopt->concise->mmsplice)
Collecting MarkupSafe>=0.23 (from jinja2->kipoi>=0.4.1->mmsplice)
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Collecting binaryornot>=0.2.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting poyo>=0.1.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting whichcraft>=0.4.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting requests>=2.18.0 (from cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Collecting idna<2.9,>=2.5 (from requests>=2.18.0->cookiecutter>=1.6.0->kipoi>=0.4.1->mmsplice)
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Building wheels for collected packages: cyvcf2, pyyaml, absl-py, gast
Building wheel for cyvcf2 (setup.py) ... error
ERROR: Complete output from command /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-install-6f9_85kl/cyvcf2/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/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-wheel-rvtfqjb5 --python-tag cp36:
ERROR: 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/cyvcf2
copying cyvcf2/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cli.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/__main__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
creating build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_reader.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_hemi.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
running egg_info
writing cyvcf2.egg-info/PKG-INFO
writing dependency_links to cyvcf2.egg-info/dependency_links.txt
writing entry points to cyvcf2.egg-info/entry_points.txt
writing requirements to cyvcf2.egg-info/requires.txt
writing top-level names to cyvcf2.egg-info/top_level.txt
reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
copying cyvcf2/cyvcf2.c -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cyvcf2.pxd -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cyvcf2.pyx -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/helpers.c -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/helpers.h -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/relatedness.h -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/tests/__init__.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/bug.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/decomposed.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/empty.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/issue_44.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/o.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/seg.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr-1.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-format-string.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-haploidX.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-hemi.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-issue-48.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.t.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_hemi.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_reader.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
running build_ext
cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-install-6f9_85kl/cyvcf2/cyvcf2/cyvcf2.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline.
warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared
warning: cyvcf2/cyvcf2.pxd:274:30: Declarations should not be declared inline.
building 'cyvcf2.cyvcf2' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/cyvcf2
creating build/temp.macosx-10.7-x86_64-3.6/htslib
creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c cyvcf2/cyvcf2.c -o build/temp.macosx-10.7-x86_64-3.6/cyvcf2/cyvcf2.o
In file included from cyvcf2/cyvcf2.c:599:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
In file included from cyvcf2/cyvcf2.c:602:
In file included from cyvcf2/helpers.h:1:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:39:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:35:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts_log.h:52:35: warning: this function declaration is not a prototype [-Wstrict-prototypes]
enum htsLogLevel hts_get_log_level();
^
void
In file included from cyvcf2/cyvcf2.c:604:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hfile.h:245:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
if (fp->limit - fp->begin < nbytes){
~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
cyvcf2/cyvcf2.c:7951:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:443:35: note: passing argument to parameter 'h' here
int bcf_hdr_append(bcf_hdr_t *h, const char *line);
^
cyvcf2/cyvcf2.c:7993:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:8509:37: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:315:40: note: passing argument to parameter 'hdr' here
int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
^
cyvcf2/cyvcf2.c:8804:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:443:35: note: passing argument to parameter 'h' here
int bcf_hdr_append(bcf_hdr_t *h, const char *line);
^
cyvcf2/cyvcf2.c:8857:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:9066:34: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:796:102: note: expanded from macro 'bcf_itr_querys'
#define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
^~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:675:97: note: passing argument to parameter 'hdr' here
hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);
^
cyvcf2/cyvcf2.c:10325:134: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 411, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:2918:118: note: passing argument to parameter here
static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
^
cyvcf2/cyvcf2.c:11981:21: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
bcf_hdr_destroy(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:261:37: note: passing argument to parameter 'h' here
void bcf_hdr_destroy(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:12462:15: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:440:9: note: 'bcf_hdr_fmt_text' has been explicitly marked deprecated here
HTS_DEPRECATED("use bcf_hdr_format() instead");
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts_defs.h:65:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
^
cyvcf2/cyvcf2.c:12715:18: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:12824:24: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:799:111: note: expanded from macro 'bcf_index_seqnames'
#define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
^~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:677:92: note: passing argument to parameter 'hdr' here
const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
^
cyvcf2/cyvcf2.c:12824:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:12997:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:22708:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:24755:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:31829:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:31921:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:32133:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:32191:29: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'Py_ssize_t' (aka 'long') [-Wsign-compare]
__pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:34303:13: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_h = __pyx_t_6;
^ ~~~~~~~~~
cyvcf2/cyvcf2.c:37255:16: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:38238:18: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_i->hdr = __pyx_t_4;
^ ~~~~~~~~~
cyvcf2/cyvcf2.c:38759:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:38787:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:38853:54: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:320:47: note: passing argument to parameter 'h' here
int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:39025:36: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:482:37: note: passing argument to parameter 'hdr' here
int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
^
cyvcf2/cyvcf2.c:39063:25: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:39122:76: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2072, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:370:43: note: passing argument to parameter 'h' here
int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
^
cyvcf2/cyvcf2.c:6578:18: warning: unused function '__pyx_f_6cyvcf2_6cyvcf2_xstr' [-Wunused-function]
static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
^
32 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/faidx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/faidx.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/vcfutils.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/vcfutils.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/regidx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/regidx.o
htslib/regidx.c:155:30: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
htslib/regidx.c:155:61: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~~~^ ~~~~~~~~~
htslib/regidx.c:155:89: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~^~~~~~~~
3 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/tbx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/tbx.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/probaln.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/probaln.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/kfunc.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/kfunc.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/errmod.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/errmod.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/realn.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/realn.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/hfile_net.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/hfile_net.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/hts.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/hts.o
In file included from htslib/hts.c:39:
In file included from htslib/cram/cram.h:45:
In file included from htslib/cram/cram_samtools.h:61:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/sam.h:359:5: error: unknown type name 'hts_itr_multi_t'
hts_itr_multi_t *sam_itr_regions(const hts_idx_t *idx, bam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount);
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/sam.h:359:76: error: unknown type name 'hts_reglist_t'
hts_itr_multi_t *sam_itr_regions(const hts_idx_t *idx, bam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount);
^
In file included from htslib/hts.c:39:
In file included from htslib/cram/cram.h:52:
htslib/cram/cram_codecs.h:162:13: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
(blk->byte >= blk->uncomp_size && nbits > 0) ||
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~
htslib/cram/cram_codecs.h:164:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
(blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
htslib/hts.c:1256:34: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if ( kh_key(bidx, k) < idx->n_bins )
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
htslib/hts.c:1283:55: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
htslib/hts.c:1308:51: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
5 warnings and 2 errors generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for cyvcf2
Running setup.py clean for cyvcf2
Building wheel for pyyaml (setup.py) ... done
Stored in directory: /Users/tarekmagdyshehatamohamed/Library/Caches/pip/wheels/ad/56/bc/1522f864feb2a358ea6f1a92b4798d69ac783a28e80567a18b
Building wheel for absl-py (setup.py) ... done
Stored in directory: /Users/tarekmagdyshehatamohamed/Library/Caches/pip/wheels/ee/98/38/46cbcc5a93cfea5492d19c38562691ddb23b940176c14f7b48
Building wheel for gast (setup.py) ... done
Stored in directory: /Users/tarekmagdyshehatamohamed/Library/Caches/pip/wheels/5c/2e/7e/a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd
Successfully built pyyaml absl-py gast
Failed to build cyvcf2
Installing collected packages: scipy, joblib, scikit-learn, sklearn, click, cyvcf2, setuptools, pyfaidx, h5py, keras-applications, pyyaml, keras-preprocessing, keras, shapely, pyparsing, kiwisolver, cycler, matplotlib, descartes, gtfparse, pymongo, future, decorator, networkx, tqdm, hyperopt, concise, simplejson, argcomplete, argh, gffutils, enum34, MarkupSafe, jinja2, urllib3, attrs, related, chardet, binaryornot, poyo, arrow, jinja2-time, whichcraft, idna, requests, cookiecutter, kipoi-utils, kipoi-conda, colorlog, packaging, deprecation, tinydb, kipoi, absl-py, grpcio, termcolor, mock, tensorflow-estimator, gast, markdown, werkzeug, protobuf, tensorboard, astor, tensorflow, mmsplice
Running setup.py install for cyvcf2 ... error
ERROR: Complete output from command /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-install-6f9_85kl/cyvcf2/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/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-record-kk35wz4e/install-record.txt --single-version-externally-managed --compile:
ERROR: running install
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/cyvcf2
copying cyvcf2/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cli.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/__main__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
creating build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_reader.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/__init__.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_hemi.py -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
running egg_info
writing cyvcf2.egg-info/PKG-INFO
writing dependency_links to cyvcf2.egg-info/dependency_links.txt
writing entry points to cyvcf2.egg-info/entry_points.txt
writing requirements to cyvcf2.egg-info/requires.txt
writing top-level names to cyvcf2.egg-info/top_level.txt
reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
copying cyvcf2/cyvcf2.c -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cyvcf2.pxd -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/cyvcf2.pyx -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/helpers.c -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/helpers.h -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/relatedness.h -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2
copying cyvcf2/tests/__init__.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/bug.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/decomposed.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/empty.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/issue_44.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/o.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/seg.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr-1.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-format-string.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-haploidX.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-hemi.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-issue-48.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.t.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_hemi.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
copying cyvcf2/tests/test_reader.pyc -> build/lib.macosx-10.7-x86_64-3.6/cyvcf2/tests
running build_ext
skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date)
building 'cyvcf2.cyvcf2' extension
creating build/temp.macosx-10.7-x86_64-3.6
creating build/temp.macosx-10.7-x86_64-3.6/cyvcf2
creating build/temp.macosx-10.7-x86_64-3.6/htslib
creating build/temp.macosx-10.7-x86_64-3.6/htslib/cram
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c cyvcf2/cyvcf2.c -o build/temp.macosx-10.7-x86_64-3.6/cyvcf2/cyvcf2.o
In file included from cyvcf2/cyvcf2.c:599:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
In file included from cyvcf2/cyvcf2.c:602:
In file included from cyvcf2/helpers.h:1:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:39:
In file included from /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:35:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts_log.h:52:35: warning: this function declaration is not a prototype [-Wstrict-prototypes]
enum htsLogLevel hts_get_log_level();
^
void
In file included from cyvcf2/cyvcf2.c:604:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hfile.h:245:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
if (fp->limit - fp->begin < nbytes){
~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
cyvcf2/cyvcf2.c:7951:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:443:35: note: passing argument to parameter 'h' here
int bcf_hdr_append(bcf_hdr_t *h, const char *line);
^
cyvcf2/cyvcf2.c:7993:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:8509:37: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:315:40: note: passing argument to parameter 'hdr' here
int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
^
cyvcf2/cyvcf2.c:8804:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:443:35: note: passing argument to parameter 'h' here
int bcf_hdr_append(bcf_hdr_t *h, const char *line);
^
cyvcf2/cyvcf2.c:8857:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:9066:34: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:796:102: note: expanded from macro 'bcf_itr_querys'
#define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
^~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:675:97: note: passing argument to parameter 'hdr' here
hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);
^
cyvcf2/cyvcf2.c:10325:134: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 411, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:2918:118: note: passing argument to parameter here
static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
^
cyvcf2/cyvcf2.c:11981:21: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
bcf_hdr_destroy(__pyx_v_self->hdr);
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:261:37: note: passing argument to parameter 'h' here
void bcf_hdr_destroy(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:12462:15: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
__pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:440:9: note: 'bcf_hdr_fmt_text' has been explicitly marked deprecated here
HTS_DEPRECATED("use bcf_hdr_format() instead");
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts_defs.h:65:49: note: expanded from macro 'HTS_DEPRECATED'
#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
^
cyvcf2/cyvcf2.c:12715:18: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:12824:24: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:799:111: note: expanded from macro 'bcf_index_seqnames'
#define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
^~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/hts.h:677:92: note: passing argument to parameter 'hdr' here
const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
^
cyvcf2/cyvcf2.c:12824:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:12997:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:22708:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:24755:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:31829:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:31921:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:32133:33: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:32191:29: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'Py_ssize_t' (aka 'long') [-Wsign-compare]
__pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
~~~~~~~~~ ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:34303:13: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_h = __pyx_t_6;
^ ~~~~~~~~~
cyvcf2/cyvcf2.c:37255:16: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:38238:18: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_i->hdr = __pyx_t_4;
^ ~~~~~~~~~
cyvcf2/cyvcf2.c:38759:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
^~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:38787:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:38853:54: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:320:47: note: passing argument to parameter 'h' here
int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:39025:36: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:482:37: note: passing argument to parameter 'hdr' here
int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
^
cyvcf2/cyvcf2.c:39063:25: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
(void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:479:33: note: passing argument to parameter 'h' here
int bcf_hdr_sync(bcf_hdr_t *h);
^
cyvcf2/cyvcf2.c:39122:76: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2072, __pyx_L1_error)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/vcf.h:370:43: note: passing argument to parameter 'h' here
int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
^
cyvcf2/cyvcf2.c:6578:18: warning: unused function '__pyx_f_6cyvcf2_6cyvcf2_xstr' [-Wunused-function]
static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
^
32 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/faidx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/faidx.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/vcfutils.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/vcfutils.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/regidx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/regidx.o
htslib/regidx.c:155:30: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
htslib/regidx.c:155:61: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~~~^ ~~~~~~~~~
htslib/regidx.c:155:89: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
~~~~~~~~~~~~~^~~~~~~~
3 warnings generated.
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/tbx.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/tbx.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/probaln.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/probaln.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/kfunc.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/kfunc.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/errmod.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/errmod.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/realn.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/realn.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/hfile_net.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/hfile_net.o
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include -arch x86_64 -Ihtslib -Icyvcf2 -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/lib/python3.6/site-packages/numpy/core/include -I/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/python3.6m -c htslib/hts.c -o build/temp.macosx-10.7-x86_64-3.6/htslib/hts.o
In file included from htslib/hts.c:39:
In file included from htslib/cram/cram.h:45:
In file included from htslib/cram/cram_samtools.h:61:
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/sam.h:359:5: error: unknown type name 'hts_itr_multi_t'
hts_itr_multi_t *sam_itr_regions(const hts_idx_t *idx, bam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount);
^
/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/include/htslib/sam.h:359:76: error: unknown type name 'hts_reglist_t'
hts_itr_multi_t *sam_itr_regions(const hts_idx_t *idx, bam_hdr_t *hdr, hts_reglist_t *reglist, unsigned int regcount);
^
In file included from htslib/hts.c:39:
In file included from htslib/cram/cram.h:52:
htslib/cram/cram_codecs.h:162:13: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
(blk->byte >= blk->uncomp_size && nbits > 0) ||
~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~
htslib/cram/cram_codecs.h:164:53: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
(blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
htslib/hts.c:1256:34: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if ( kh_key(bidx, k) < idx->n_bins )
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
htslib/hts.c:1283:55: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
htslib/hts.c:1308:51: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
5 warnings and 2 errors generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command "/Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo2/bin/python -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-install-6f9_85kl/cyvcf2/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/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-record-kk35wz4e/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/pm/y6_x4m551tx4l6b0kwnbh_ch0000gp/T/pip-install-6f9_85kl/cyvcf2/
(bioinfo2)
Which version of python you are using? You can try to install cyvcf2 with bioconda: https://anaconda.org/bioconda/cyvcf2
MuhammedHasan
commented
5 years ago Hi @herrroaa, we have dropped the requirement of cyvcf2. Now it is an optional dependency. However, the current version is not updated in PYPI. So you may install mmsplice from github and install cyvcf2 from bioconda.
herrroaa
commented
5 years ago Hi @MuhammedHasan
I installed mmsplice and cycf2 from github and bioconda, respectively. I then tried to run notebook/example.ipynb, but it is still asking for cycf2
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-4-de7beed805ef> in <module>()
----> 1 next(dl)
~/.local/lib/python3.6/site-packages/mmsplice-0.2.8-py3.6.egg/mmsplice/vcf_dataloader.py in __next__(self)
397
398 def __next__(self):
--> 399 ss, var = next(self.ssGenerator)
400 seq = ss.get_seq(self.fasta).upper()
401 mut_seq = ss.get_mut_seq(self.fasta, var).upper()
~/.local/lib/python3.6/site-packages/mmsplice-0.2.8-py3.6.egg/mmsplice/vcf_dataloader.py in spliceSiteGenerator(vcf_file, exonTree, variant_filter)
371 @staticmethod
372 def spliceSiteGenerator(vcf_file, exonTree, variant_filter=True):
--> 373 from cyvcf2 import VCF
374 variants = VCF(vcf_file)
375 for var in variants:
ModuleNotFoundError: No module named 'cyvcf2'Hi @herrroaa. Are you sure did you install cycvf2 in the right environment? Please create a conda environment, install cyvcf2 from bioconda and try to import cyvcf2.If works, then install mmsplice from github and run the notebook.
herrroaa
commented
5 years ago Hi @MuhammedHasan I create a new environment to get it to work, Thanks. Did you train the model using intronic SNPs as well? I have a list of intronic SNPs that I would like to analyze using mmsplice.
Thanks T
s6juncheng
commented
5 years ago Glad it worked, MMSplice can be applied to score intronic SNPs.
herrroaa
commented
5 years ago I tried mmsplice with my files, but I got this error message (Interval chromosome name no match", UserWarning).
I rechecked my vcf, gtf, and fa files, and all of them have the same chromosome notation (without chr).
I attached my notebook file.
Do I need ti change anything when it comes to the gtfIntervalTree = '../tests/data/test.pkl' # pickle exon interval Tree
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/mmsplice-0.2.8-py3.6.egg/mmsplice/interval_tree.py:50: UserWarning: Interval chromosome name no match
warnings.warn("Interval chromosome name no match", UserWarning)
---------------------------------------------------------------------------
StopIteration Traceback (most recent call last)
<ipython-input-4-de7beed805ef> in <module>()
----> 1 next(dl)
~/.local/lib/python3.6/site-packages/mmsplice-0.2.8-py3.6.egg/mmsplice/vcf_dataloader.py in __next__(self)
397
398 def __next__(self):
--> 399 ss, var = next(self.ssGenerator)
400 seq = ss.get_seq(self.fasta).upper()
401 mut_seq = ss.get_mut_seq(self.fasta, var).upper()
StopIteration: I also got these warning message, however I think it is not a problem.
Using TensorFlow backend.
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/scikit_learn-0.21.2-py3.6-macosx-10.7-x86_64.egg/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
warnings.warn(msg, category=DeprecationWarning)
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/scikit_learn-0.21.2-py3.6-macosx-10.7-x86_64.egg/sklearn/base.py:306: UserWarning: Trying to unpickle estimator HuberRegressor from version 0.19.2 when using version 0.21.2. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/scikit_learn-0.21.2-py3.6-macosx-10.7-x86_64.egg/sklearn/base.py:306: UserWarning: Trying to unpickle estimator StandardScaler from version 0.19.2 when using version 0.21.2. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/scikit_learn-0.21.2-py3.6-macosx-10.7-x86_64.egg/sklearn/base.py:306: UserWarning: Trying to unpickle estimator LogisticRegression from version 0.19.2 when using version 0.21.2. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/Users/tarekmagdyshehatamohamed/.local/lib/python3.6/site-packages/scikit_learn-0.21.2-py3.6-macosx-10.7-x86_64.egg/sklearn/base.py:306: UserWarning: Trying to unpickle estimator Pipeline from version 0.19.2 when using version 0.21.2. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
[```[](url)](url
[notebook_error.pdf](https://github.com/gagneurlab/MMSplice/files/3266832/notebook_error.pdf)
)You need to regenerate interval-tree with your new GTF file. So delete old interval-tree or use a new name for new interval-tree.
herrroaa
commented
5 years ago Where can I find the interval-tree file? Do I need to use an external tool to generate pickle interval-tree file for my GTF file?
Thanks T
MuhammedHasan
commented
5 years ago You provide location of interval_tree while creating dataloader:
dl = SplicingVCFDataloader(gtf_path, fasta_path, vcf_path, out_file=interval_tree_path)When you run MMSplice next time, you do not need to provide gtf file path but interval tree file path:
dl = SplicingVCFDataloader(interval_tree_path, fasta_path, vcf_path)Or you can run generate interval_tree explicitly with GenerateExonIntervalTree function which creates and save interval_tree:
GenerateExonIntervalTree(gtf_file, out_file=interval_tree_path)
dl = SplicingVCFDataloader(interval_tree_path, fasta_path, vcf_path)Thanks for your feedback. If you are not able to use MMSplice smoothly, then our api is not intuitive. So we start planning to improve MMSplice api #11 and ship it with pre-build interval_tree for Grch38 and Grch37 #12. So most of the user who run MMSplice for standard annotation will not be to generate interval tree.
MuhammedHasan
commented
5 years ago Dear @herroaa,
Please see the new version of mmsplice which don't requires intervel tree generation and come with prebuild exon list for grch37, grch38.
You can also try it online with colab. Please see the document.
We are ready to help you if you need further help.
Description
I got an error while installing mmsplice.
What I Did