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

[Cam-Baker]

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]

Hi Cameron,

Can you try modifying the ext_modules section of setup.py: https://github.com/getzlab/CApy/blob/27db25c428130876e0f9222c2457fbafc5ded530/setup.py#L34-L38

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]

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]

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]

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