Bug: installation in conda env fails to find zlib.h & zconf.h

[darked89]

Describe the bug

installation of macs3 inside of the conda environment fails because of "missing" zlib.h and then zconf.h

MACS3/fermi-lite/bseq.c:1:10: fatal error: zlib.h: No such file or directory
    1 | #include <zlib.h>

and:

/some/path/.conda/envs/macs3/include/python3.8/zlib.h:34:10: fatal error: zconf.h: No such file or directory
   34 | #include "zconf.h"

(this one after creating the first soft link, see below)

The above errors did occur during running:

 python setup.py install --prefix /some/path/soft

In a directory created after unpacking

https://files.pythonhosted.org/packages/f9/72/d1a7578f0888b1e07823d33d564c316e5af1be79466e120028b41a37b0ce/MACS3-3.0.0a7.tar.gz

This is due to:

-I/some/path/.conda/envs/macs3/include/python3.8

To semi-resolve it I did:

cd /some/path/.conda/envs/macs3/include/python3.8/
ln -s ../zlib.h .
ln -s ../zconf.h .

but I think it should be fixed upstream, so /some/path/.conda/envs/macs3/include/ is included.

Hope it helps

Darek Kedra

PS I am on Centos 7 inside of the conda env with the following packages:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
blas                      2.3                    openblas    conda-forge
ca-certificates           2020.10.14                    0    anaconda
certifi                   2020.6.20                py38_0    anaconda
cykhash                   2.0.0            py38hfa26641_1    conda-forge
cython                    0.29.28          py38hfa26641_2    conda-forge
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
gcc                       11.2.0               h702ea55_9    conda-forge
gcc_impl_linux-64         11.2.0              h82a94d6_15    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libblas                   3.9.0                3_openblas    conda-forge
libcblas                  3.9.0                3_openblas    conda-forge
libedit                   3.1.20191231         h14c3975_1    anaconda
libffi                    3.3                  he6710b0_2    anaconda
libgcc-devel_linux-64     11.2.0              h0952999_15    conda-forge
libgcc-ng                 11.2.0              h1d223b6_15    conda-forge
libgfortran-ng            7.5.0               h14aa051_20    conda-forge
libgfortran4              7.5.0               h14aa051_20    conda-forge
libgomp                   11.2.0              h1d223b6_15    conda-forge
liblapack                 3.9.0                3_openblas    conda-forge
liblapacke                3.9.0                3_openblas    conda-forge
libopenblas               0.3.12          pthreads_hb3c22a3_1    conda-forge
libsanitizer              11.2.0              he4da1e4_15    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_15    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               13.0.1               he0ac6c6_1    conda-forge
ncurses                   6.2                  he6710b0_1    anaconda
numpy                     1.19.1           py38h30dfecb_0    anaconda
numpy-base                1.19.1           py38h75fe3a5_0    anaconda
openssl                   1.1.1h               h7b6447c_0    anaconda
pip                       20.2.4                   py38_0    anaconda
python                    3.8.5                h7579374_1    anaconda
python-devtools           0.8.0              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
readline                  8.0                  h7b6447c_0    anaconda
setuptools                50.3.0           py38hb0f4dca_1    anaconda
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.33.0               h62c20be_0    anaconda
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tk                        8.6.10               hbc83047_0    anaconda
wheel                     0.35.1                     py_0    anaconda
xz                        5.2.5                h7b6447c_0    anaconda
zlib                      1.2.11            h36c2ea0_1013    conda-forge