ResolvePackageNotFound while running conda env create -f environment.yml

[MarijaCausevska]

When I run conda env create -f environment.yml

I get the following output

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - freetype==2.10.2=he06d7ca_0
  - mkl==2018.0.3=1
  - libcurl=7.61
  - htslib=1.9
  - libffi==3.3=he6710b0_1
  - libstdcxx-ng==9.1.0=hdf63c60_0
  - hmmlearn==0.2.1=py27h3010b51_1000
  - samtools==1.7=1
  - perl==5.26.2=h14c3975_0
  - tk==8.6.8=hbc83047_0
  - zlib==1.2.11=h7b6447c_3
  - libedit==3.1.20181209=hc058e9b_0
  - jpeg==9d=h516909a_0
  - python==2.7.18=h15b4118_1
  - curl=7.61
  - intel-openmp==2020.1=217
  - krb5=1.16
  - libwebp-base==1.1.0=h516909a_3
  - _libgcc_mutex==0.1=main
  - make==4.2.1=h1bed415_1
  - pillow==5.3.0=py27h00a061d_1000
  - reportlab==3.5.42=py27heca39a3_0
  - scikit-learn==0.19.2=py27h4989274_0
  - bzip2==1.0.8=h7b6447c_0
  - blas==1.0=mkl
  - scipy==1.1.0=py27hd20e5f9_0
  - setuptools==44.0.0=py27_0
  - bwa==0.7.17=hed695b0_7
  - trf==4.09=2
  - lz4-c==1.9.2=he1b5a44_1
  - xz==5.2.5=h7b6447c_0
  - libssh2=1.8
  - numpy==1.12.1=py27h9378851_1
  - swig==3.0.12=h38cdd7d_3
  - biopython==1.66=np112py27_0
  - readline==8.0=h7b6447c_0
  - certifi==2019.11.28=py27_0
  - libgcc-ng==9.1.0=hdf63c60_0
  - openssl=1.0
  - peakutils==1.1.0=py27_0
  - wheel==0.33.6=py27_0
  - zstd==1.4.4=h6597ccf_3
  - sqlite==3.31.1=h62c20be_1
  - ca-certificates==2020.1.1=0
  - ncurses==6.2=he6710b0_1
  - libgcc==7.2.0=h69d50b8_2
  - libpng==1.6.37=hed695b0_1
  - libgfortran-ng==7.3.0=hdf63c60_0
  - libtiff==4.1.0=hc7e4089_6
  - python_abi==2.7=1_cp27mu
  - pip==19.3.1=py27_0
  - pcre==8.43=he6710b0_0
  - msgpack-python==1.0.0=py27h9e3301b_1

Output for conda info

     active environment : None
            shell level : 0
       user config file : /Users/admin/.condarc
 populated config files : /Users/admin/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=arm64
                          __osx=13.2.1=0
                          __unix=0=0
       base environment : /Users/admin/miniconda3  (writable)
      conda av data dir : /Users/admin/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-arm64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/admin/miniconda3/pkgs
                          /Users/admin/.conda/pkgs
       envs directories : /Users/admin/miniconda3/envs
                          /Users/admin/.conda/envs
               platform : osx-arm64
             user-agent : conda/23.3.1 requests/2.29.0 CPython/3.10.10 Darwin/22.3.0 OSX/13.2.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False

OS Info

ProductName:		macOS
ProductVersion:		13.2.1
BuildVersion:		22D68

I am running the code on M1 Mac arm64 chipset.

[arafian]

Did you ever figure this out?

[liuqianhn]

environment2.yml.txt
Use the yml file above should solve the problem.

[NabilAsyraf98]

I ran 'make' after creating a conda env using environment2.yml.text and got this error,

[liuqianhn]

@NabilAsyraf98 This is the mismatch issue of compiler. Could you please share the result of the commands below in your system

~/anaconda3/envs/repeathmmenv/compiler_compat/ld --version
ld --version
gcc --version

[NabilAsyraf98]

Happy to share

[NabilAsyraf98]

Hi, I managed to install RepeatHMM after removing conda compiler_compat folder and exporting my own ld and GCC . But now I have another error when running repeatHMM.py:

Appreicate your help

[liuqianhn]

Hi @NabilAsyraf98 Thank you for sharing your solution. To solve the issue libcrypto, you can create a soft link to the repeatmm environment by using 'ln -s <conda_environment_directory>/lib/libcrypto.so. ~/anaconda3/envs/repeathmmenv/lib/libcrypto.so.1.0.0' .
Please check the lib files you have for <conda_environment_directory>where you have samtools successful installation or what you have in repeathmmenv environment.

ls -l ~/anaconda3/envs/repeathmmenv/lib/libcrypto.so*
ls -l <conda_environment_directory>/lib/libcrypto.so*

[NabilAsyraf98]

Thanks! worked nicely