Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

use option -std=c99 or -std=gnu99 to compile your code #3

Open
Cam-Baker opened this issue Nov 8, 2022 · 4 comments
Open

use option -std=c99 or -std=gnu99 to compile your code #3

Cam-Baker opened this issue Nov 8, 2022 · 4 comments

Comments

@Cam-Baker
Copy link

Hello,

I am trying to install CApy into my conda environment and am running into issues.

Install command:

python setup.py install

Command output:

running install
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
writing capy.egg-info/PKG-INFO
writing dependency_links to capy.egg-info/dependency_links.txt
writing requirements to capy.egg-info/requires.txt
writing top-level names to capy.egg-info/top_level.txt
reading manifest file 'capy.egg-info/SOURCES.txt'
writing manifest file 'capy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building 'fastmmap' extension
gcc -pthread -B /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/include -fPIC -O2 -isystem /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/include -fPIC -I/scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/numpy/core/include -I/scratch/grc_group/.conda/envs/RNA-Mutect-WMN/include/python3.11 -c capy/fastmmap.c -o build/temp.linux-x86_64-cpython-311/capy/fastmmap.o
In file included from /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1948:0,
                 from /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from capy/fastmmap.c:12:
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN/lib/python3.11/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^
capy/fastmmap.c: In function ‘query’:
capy/fastmmap.c:39:4: error: ‘for’ loop initial declarations are only allowed in C99 mode
    for(int64_t i = 0; i < n_offsets; i++) {
    ^
capy/fastmmap.c:39:4: note: use option -std=c99 or -std=gnu99 to compile your code
capy/fastmmap.c:45:7: error: ‘for’ loop initial declarations are only allowed in C99 mode
       for(int64_t j = 0; j < width; j++) *(buf++) = map[width*offsets[i] + j];
       ^
error: command '/usr/bin/gcc' failed with exit code 1

Conda environment:

name: RNA-Mutect-WMN
channels:
  - bcbio
  - bioconda
  - r
  - defaults
  - conda-forge
  - biobuilds
  - biobakery
  - qiime2
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - alsa-lib=1.2.7.2=h166bdaf_0
  - attr=2.5.1=h166bdaf_1
  - brotli=1.0.9=h5eee18b_7
  - brotli-bin=1.0.9=h5eee18b_7
  - brotlipy=0.7.0=py311hd4cff14_1005
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.18.1=h7f98852_0
  - ca-certificates=2022.10.11=h06a4308_0
  - cairo=1.16.0=ha61ee94_1013
  - certifi=2022.9.24=pyhd8ed1ab_0
  - cffi=1.15.1=py311h409f033_2
  - charset-normalizer=2.1.1=pyhd8ed1ab_0
  - colorama=0.4.6=pyhd8ed1ab_0
  - conda=22.9.0=py311h38be061_2
  - conda-package-handling=1.9.0=py311hd4cff14_1
  - contourpy=1.0.6=py311h4dd048b_0
  - cryptography=38.0.3=py311hb3c386c_0
  - curl=7.86.0=h7bff187_1
  - cycler=0.11.0=pyhd3eb1b0_0
  - dbus=1.13.18=hb2f20db_0
  - expat=2.4.9=h6a678d5_0
  - fftw=3.3.10=nompi_hf0379b8_105
  - fmt=9.1.0=h924138e_0
  - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
  - font-ttf-inconsolata=2.001=hcb22688_0
  - font-ttf-source-code-pro=2.030=hd3eb1b0_0
  - font-ttf-ubuntu=0.83=h8b1ccd4_0
  - fontconfig=2.14.1=hc2a2eb6_0
  - fonts-anaconda=1=h8fa9717_0
  - fonts-conda-ecosystem=1=hd3eb1b0_0
  - fonttools=4.25.0=pyhd3eb1b0_0
  - freetype=2.12.1=h4a9f257_0
  - fribidi=1.0.10=h7b6447c_0
  - gatk=3.8=hdfd78af_11
  - gettext=0.21.1=h27087fc_0
  - glib=2.74.1=h6239696_1
  - glib-tools=2.74.1=h6239696_1
  - graphite2=1.3.14=h295c915_1
  - gst-plugins-base=1.20.3=h57caac4_1
  - gstreamer=1.20.3=hd4edc92_1
  - harfbuzz=4.4.1=hf9f4e7c_0
  - htslib=1.16=h6bc39ce_0
  - icu=70.1=h27087fc_0
  - idna=3.4=pyhd8ed1ab_0
  - jack=1.9.21=h2a1e645_0
  - joblib=1.1.0=pyhd3eb1b0_0
  - jpeg=9e=h7f8727e_0
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.4=py311h4dd048b_1
  - krb5=1.19.3=h3790be6_0
  - lame=3.100=h7b6447c_0
  - lcms2=2.12=h3be6417_0
  - ld_impl_linux-64=2.39=hc81fddc_0
  - lerc=4.0.0=h27087fc_0
  - libarchive=3.5.2=h5de8990_0
  - libblas=3.9.0=16_linux64_openblas
  - libbrotlicommon=1.0.9=h5eee18b_7
  - libbrotlidec=1.0.9=h5eee18b_7
  - libbrotlienc=1.0.9=h5eee18b_7
  - libcap=2.66=ha37c62d_0
  - libcblas=3.9.0=16_linux64_openblas
  - libclang=14.0.6=default_hc1a23ef_0
  - libclang13=14.0.6=default_h31cde19_0
  - libcups=2.3.3=h3e49a29_2
  - libcurl=7.86.0=h7bff187_1
  - libdb=6.2.32=h6a678d5_1
  - libdeflate=1.13=h166bdaf_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libevent=2.1.10=h9b69904_4
  - libffi=3.4.2=h7f98852_5
  - libflac=1.4.2=h27087fc_0
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=12.2.0=h65d4601_19
  - libgfortran-ng=11.2.0=h00389a5_1
  - libgfortran5=11.2.0=h1234567_1
  - libglib=2.74.1=h606061b_1
  - libgomp=12.2.0=h65d4601_19
  - libiconv=1.17=h166bdaf_0
  - liblapack=3.9.0=16_linux64_openblas
  - libllvm14=14.0.6=he0ac6c6_0
  - libmamba=1.0.0=hb5f4133_2
  - libmambapy=1.0.0=py311h72e054f_2
  - libnghttp2=1.47.0=hdcd2b5c_1
  - libnsl=2.0.0=h7f98852_0
  - libogg=1.3.5=h27cfd23_1
  - libopenblas=0.3.21=h043d6bf_0
  - libopus=1.3.1=h7b6447c_0
  - libpng=1.6.37=hbc83047_0
  - libpq=14.5=hd77ab85_1
  - libsndfile=1.1.0=h27087fc_0
  - libsolv=0.7.22=h6239696_0
  - libsqlite=3.39.4=h753d276_0
  - libssh2=1.10.0=h8f2d780_0
  - libstdcxx-ng=12.2.0=h46fd767_19
  - libtiff=4.4.0=h0e0dad5_3
  - libtool=2.4.6=h295c915_1008
  - libudev1=252=h166bdaf_0
  - libuuid=2.32.1=h7f98852_1000
  - libvorbis=1.3.7=h7b6447c_0
  - libwebp-base=1.2.4=h5eee18b_0
  - libxcb=1.13=h1bed415_1
  - libxkbcommon=1.0.3=he3ba5ed_0
  - libxml2=2.9.14=h22db469_4
  - libzlib=1.2.13=h166bdaf_4
  - lz4-c=1.9.3=h9c3ff4c_1
  - lzo=2.10=h516909a_1000
  - mamba=1.0.0=py311h51e3938_2
  - matplotlib=3.6.2=py311h38be061_0
  - matplotlib-base=3.6.2=py311he728205_0
  - mpg123=1.30.2=h27087fc_1
  - munkres=1.0.7=py_1
  - mysql-common=8.0.31=haf5c9bc_0
  - mysql-libs=8.0.31=h28c427c_0
  - ncurses=6.3=h27087fc_1
  - nspr=4.33=h295c915_0
  - nss=3.78=h2350873_0
  - numpy=1.23.4=py311h7d28db0_1
  - openjdk=8.0.152=h7b6447c_3
  - openjpeg=2.5.0=h7d73246_1
  - openssl=1.1.1s=h7f8727e_0
  - packaging=21.3=pyhd3eb1b0_0
  - pandas=1.5.1=py311h8b32b4d_1
  - pango=1.50.7=h05da053_0
  - pcre=8.45=h295c915_0
  - pcre2=10.40=hc3806b6_0
  - pillow=9.2.0=py311h9461556_3
  - pip=22.3.1=pyhd8ed1ab_0
  - pixman=0.40.0=h7f8727e_1
  - ply=3.11=py_1
  - pulseaudio=14.0=habe0971_10
  - pybind11-abi=4=hd8ed1ab_3
  - pycosat=0.6.4=py311hd4cff14_1
  - pycparser=2.21=pyhd8ed1ab_0
  - pyopenssl=22.1.0=pyhd8ed1ab_0
  - pyparsing=3.0.4=pyhd3eb1b0_0
  - pyqt=5.15.7=py311h3408d8f_2
  - pyqt5-sip=12.11.0=py311ha362b79_2
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.0=h582c2e5_0_cpython
  - python-dateutil=2.8.2=pyhd3eb1b0_0
  - python_abi=3.11=2_cp311
  - pytz=2021.3=pyhd3eb1b0_0
  - qt-main=5.15.6=hc525480_0
  - r=3.2.2=0
  - r-base=3.2.2=1
  - r-bitops=1.0_6=r3.2.2_1a
  - r-boot=1.3_17=r3.2.2_0a
  - r-catools=1.17.1=r3.2.2_0
  - r-class=7.3_14=r3.2.2_0a
  - r-cluster=2.0.3=r3.2.2_0a
  - r-codetools=0.2_14=r3.2.2_0a
  - r-colorspace=1.2_6=r3.2.2_0a
  - r-dichromat=2.0_0=r3.2.2_2a
  - r-digest=0.6.9=r3.2.2_0
  - r-foreign=0.8_66=r3.2.2_0a
  - r-gdata=2.17.0=r3.2.2_0a
  - r-ggplot2=2.1.0=r3.2.2_0
  - r-gplots=2.17.0=r3.2.2_0a
  - r-gsalib=2.1=r3.2.2_0
  - r-gtable=0.1.2=r3.2.2_2a
  - r-gtools=3.5.0=r3.2.2_0a
  - r-kernsmooth=2.23_15=r3.2.2_0a
  - r-labeling=0.3=r3.2.2_1a
  - r-lattice=0.20_33=r3.2.2_0a
  - r-magrittr=1.5=r3.2.2_0
  - r-mass=7.3_45=r3.2.2_0a
  - r-matrix=1.2_2=r3.2.2_0a
  - r-mgcv=1.8_9=r3.2.2_0a
  - r-munsell=0.4.2=r3.2.2_1a
  - r-nlme=3.1_122=r3.2.2_0a
  - r-nnet=7.3_11=r3.2.2_0a
  - r-plyr=1.8.3=r3.2.2_0a
  - r-rcolorbrewer=1.1_2=r3.2.2_2a
  - r-rcpp=0.12.2=r3.2.2_0a
  - r-recommended=3.2.2=r3.2.2_0
  - r-reshape=0.8.5=r3.2.2_1a
  - r-reshape2=1.4.1=r3.2.2_1a
  - r-rpart=4.1_10=r3.2.2_0a
  - r-scales=0.3.0=r3.2.2_0a
  - r-spatial=7.3_11=r3.2.2_0a
  - r-stringi=1.0_1=r3.2.2_0a
  - r-stringr=1.0.0=r3.2.2_0a
  - r-survival=2.38_3=r3.2.2_0a
  - readline=8.1.2=h0f457ee_0
  - reproc=14.2.3=h7f98852_0
  - reproc-cpp=14.2.3=h9c3ff4c_0
  - requests=2.28.1=pyhd8ed1ab_1
  - ruamel_yaml=0.15.80=py311hd4cff14_1008
  - samtools=1.16.1=h6899075_1
  - scikit-learn=1.1.3=py311h3b52e38_1
  - scipy=1.9.3=py311h69910c8_1
  - setuptools=65.5.1=pyhd8ed1ab_0
  - sip=6.7.4=py311ha362b79_0
  - six=1.16.0=pyhd3eb1b0_1
  - sqlite=3.39.3=h5082296_0
  - threadpoolctl=2.2.0=pyh0d69192_0
  - tk=8.6.12=h27826a3_0
  - toml=0.10.2=pyhd3eb1b0_0
  - toolz=0.12.0=pyhd8ed1ab_0
  - tornado=6.2=py311hd4cff14_1
  - tqdm=4.64.1=pyhd8ed1ab_0
  - tzdata=2022f=h191b570_0
  - urllib3=1.26.11=pyhd8ed1ab_0
  - wheel=0.38.2=pyhd8ed1ab_0
  - xcb-util=0.4.0=h516909a_0
  - xcb-util-image=0.4.0=h166bdaf_0
  - xcb-util-keysyms=0.4.0=h516909a_0
  - xcb-util-renderutil=0.3.9=h166bdaf_0
  - xcb-util-wm=0.4.1=h516909a_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxext=1.3.4=h7f98852_1
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h27cfd23_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yaml-cpp=0.7.0=h27087fc_2
  - zlib=1.2.13=h166bdaf_4
  - zstd=1.5.2=h6239696_4
prefix: /scratch/grc_group/.conda/envs/RNA-Mutect-WMN

Best,

Cameron
@julianhess
Copy link
Collaborator

Hi Cameron,

Can you try modifying the ext_modules section of setup.py:

CApy/setup.py

Lines 34 to 38 in 27db25c

ext_modules = [Extension(
'fastmmap',
sources = ['capy/fastmmap.c'],
include_dirs = [np.get_include()]
)]

To instead be

ext_modules = [Extension(
  'fastmmap',
  sources = ['capy/fastmmap.c'],
  include_dirs = [np.get_include()],
  extra_compile_args = ["-std=c99"],
)]

Thanks,
—Julian

@Cam-Baker
Copy link
Author

Hi Julian,

Thanks for the quick response. That lifted up the initial roadblock and now I'm tussling with additional dependencies related to cython and cmake.

I will update if I run into any issues or when it is fully resolved.

Best,

Cameron

@julianhess
Copy link
Collaborator

Please let me know what other roadblocks you encounter, and we can make a PR to amend setup.py accordingly! (I have already drafted one to include the c99 flag.)

@Cam-Baker
Copy link
Author

Cam-Baker commented Nov 8, 2022 •
edited
Loading

Hi Julian,

Another stumbling block you may have a better view into.

I've added cython and cmake to the conda environment.

It appears that there are some issues related to arrow. See logs below

running install
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
writing capy.egg-info/PKG-INFO
writing dependency_links to capy.egg-info/dependency_links.txt
writing requirements to capy.egg-info/requires.txt
writing top-level names to capy.egg-info/top_level.txt
reading manifest file 'capy.egg-info/SOURCES.txt'
writing manifest file 'capy.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-cpython-311/fastmmap.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/mut.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/plots.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/k9.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/txt.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/firecloud.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/__init__.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/liftover.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/num.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/df.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/context.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/seq.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/fwb.py -> build/bdist.linux-x86_64/egg/capy
copying build/lib.linux-x86_64-cpython-311/capy/java.py -> build/bdist.linux-x86_64/egg/capy
byte-compiling build/bdist.linux-x86_64/egg/capy/mut.py to mut.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/plots.py to plots.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/k9.py to k9.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/txt.py to txt.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/firecloud.py to firecloud.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/liftover.py to liftover.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/num.py to num.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/df.py to df.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/context.py to context.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/seq.py to seq.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/fwb.py to fwb.cpython-311.pyc
byte-compiling build/bdist.linux-x86_64/egg/capy/java.py to java.cpython-311.pyc
creating stub loader for fastmmap.cpython-311-x86_64-linux-gnu.so
byte-compiling build/bdist.linux-x86_64/egg/fastmmap.py to fastmmap.cpython-311.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying capy.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying capy.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying capy.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying capy.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying capy.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
__pycache__.fastmmap.cpython-311: module references __file__
creating 'dist/capy-0.1-py3.11-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing capy-0.1-py3.11-linux-x86_64.egg
removing '/gpfs/fs2/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/capy-0.1-py3.11-linux-x86_64.egg' (and everything under it)
creating /gpfs/fs2/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/capy-0.1-py3.11-linux-x86_64.egg
Extracting capy-0.1-py3.11-linux-x86_64.egg to /gpfs/fs2/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages
capy 0.1 is already the active version in easy-install.pth

Installed /gpfs/fs2/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/capy-0.1-py3.11-linux-x86_64.egg
Processing dependencies for capy==0.1
Searching for pyarrow>=0.17.0
Reading https://pypi.org/simple/pyarrow/
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/pkg_resources/__init__.py:123: PkgResourcesDeprecationWarning:  is an invalid version and will not be supported in a future release
  warnings.warn(
Downloading https://files.pythonhosted.org/packages/bd/3d/9594c09e1e2fe2e5ed7ef5c22e4347fee2ea243bccd960442e2c97731fd2/pyarrow-10.0.0.tar.gz#sha256=b153b05765393557716e3729cf988442b3ae4f5567364ded40d58c07feed27c2
Best match: pyarrow 10.0.0
Processing pyarrow-10.0.0.tar.gz
Writing /scratch/cbaker27/tmp/easy_install-2ujw1gk_/pyarrow-10.0.0/setup.cfg
Running pyarrow-10.0.0/setup.py -q bdist_egg --dist-dir /scratch/cbaker27/tmp/easy_install-2ujw1gk_/pyarrow-10.0.0/egg-dist-tmp-zqcmx9kw
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
  warnings.warn(
listing git files failed - pretending there aren't any
warning: no files found matching '../LICENSE.txt'
warning: no files found matching '../NOTICE.txt'
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '#*' found anywhere in distribution
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
no previously-included directories found matching '.asv'
/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:63 (find_package):
  By not providing "FindArrow.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "Arrow", but
  CMake did not find one.

  Could not find a package configuration file provided by "Arrow" with any of
  the following names:

    ArrowConfig.cmake
    arrow-config.cmake

  Add the installation prefix of "Arrow" to CMAKE_PREFIX_PATH or set
  "Arrow_DIR" to a directory containing one of the above files.  If "Arrow"
  provides a separate development package or SDK, be sure it has been
  installed.


-- Configuring incomplete, errors occurred!
See also "/gpfs/fs2/scratch/cbaker27/tmp/easy_install-2ujw1gk_/pyarrow-10.0.0/build/cpp/CMakeFiles/CMakeOutput.log".
-- Running CMake for PyArrow C++
error: Setup script exited with error: command '/scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB/bin/cmake' failed with exit code 1

Additional information into how I'm building the environment. Building CApy as a dependency for https://github.com/yizhak-lab-ccg/RNA_MUTECt_WMN

conda create --prefix /scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB -c conda-forge mamba
conda activate /scratch/grc_group/.conda/envs/RNA-Mutect-WMN-TMB
mamba install cython pandas numpy scikit-learn matplotlib gatk samtools cmake arrow

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@julianhess @Cam-Baker