Unable to create a conda environment

[filipsPL]

Hi. I have problems with creating the required conda environment:

conda env create -f rnaposers.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound: 
  - pcre==8.43=h0a44026_0
  - llvm-openmp==4.0.1=hcfea43d_1
  - mkl_fft==1.0.15=py37h5e564d8_0
  - libiconv==1.15=hdd342a3_7
  - zlib==1.2.11=h1de35cc_3
  - xz==5.2.5=h1de35cc_0
  - tk==8.6.9=x11tk0_2000
  - numpy-base==1.18.1=py37h6575580_1
  - libedit==3.1.20181209=hb402a30_0
  - zstd==1.3.7=h5bba6e5_0
  - sqlite==3.31.1=h5c1f38d_1
  - libpng==1.6.37=ha441bb4_0
  - qt==5.9.7=h468cd18_1
  - expat==2.2.6=h0a44026_0
  - dbus==1.13.12=h90a0687_0
  - mengine==1=h1de35cc_1
  - h5py==2.10.0=py37h3134771_0
  - libopenblas==0.3.6=hdc02c5d_2
  - readline==8.0=h1de35cc_0
  - jpeg==9b=he5867d9_2
  - sip==4.19.8=py37h0a44026_0
  - apbs==1.5=h1de35cc_3
  - libcxxabi==4.0.1=hcfea43d_1
  - mkl==2019.4=233
  - pandas==1.0.3=py37h6c726b0_0
  - python==3.7.7=hc70fcce_0_cpython
  - mkl_random==1.1.0=py37ha771720_0
  - libtiff==4.1.0=hcb84e12_0
  - libcxx==4.0.1=hcfea43d_1
  - bzip2==1.0.8=h1de35cc_0
  - gettext==0.19.8.1=h15daf44_3
  - hdf5==1.10.4=hfa1e0ec_0
  - cairo==1.14.12=hc4e6be7_4
  - libgfortran==3.0.1=2000
  - pillow==7.0.0=py37h4655f20_0
  - pymol==2.3.5=py37h95b93ae_0
  - glib==2.63.1=hd977a24_0
  - mpeg_encode==1=h1de35cc_1
  - openssl==1.1.1g=h1de35cc_0
  - libffi==3.2.1=h0a44026_6
  - pixman==0.38.0=h1de35cc_0
  - numpy==1.18.1=py37h7241aed_0
  - mkl-service==2.3.0=py37hfbe908c_0
  - mtz2ccp4_px==1.0=hdc02c5d_3
  - cffi==1.14.0=py37hb5b8e2f_0
  - libxml2==2.9.9=hf6e021a_1
  - intel-openmp==2019.4=233
  - scipy==1.4.1=py37h9fa6033_0
  - ncurses==6.2=h0a44026_0
  - scikit-learn==0.22.1=py37h27c97d8_0
  - fontconfig==2.13.0=h5d5b041_1
  - pyqt==5.9.2=py37h655552a_2
  - icu==58.2=h4b95b61_1
  - freetype==2.9.1=hb4e5f40_0
  - cryptography==2.8=py37ha12b0ac_0

I think the reason can be that the specific builds are no longer available. Maybe removing specific builds/versions could help? Could you provide the yml file without specific builds? Rr verify the env build procedure to ensure that the it can be created?

[filipsPL]

Ok, I prepared the conda env file myself. After removing the build version and few packages which are no longer available (and some which are not necessary, such as mkl) the rnaposers.yml looks like that:

name: rnaposers
channels:
  - openbabel
  - anaconda
  - schrodinger
  - defaults
dependencies:
  - apbs=1.5
  - asn1crypto=1.3.0
  - blas=1.0
  - bzip2=1.0.8
  - ca-certificates=2020.1.1
  - cairo=1.14.12
  - certifi=2020.4.5.1
  - cffi=1.14.0
  - chardet=3.0.4
  - cryptography=2.8
  - dbus=1.13.12
  - expat=2.2.6
  - fontconfig=2.13.0
  - freemol=1.158
  - freetype=2.9.1
  - gettext=0.19.8.1
  - glew=2.0.0
  - glib=2.63.1
  - h5py=2.10.0
  - hdf5=1.10.4
  - icu=58.2
  - idna=2.9
  - intel-openmp=2019.4
  - joblib=0.14.1
  - jpeg=9b
  - libedit=3.1.20181209
  - libffi=3.2.1
  - libiconv=1.15
  - libopenblas=0.3.6
  - libpng=1.6.37
  - libtiff=4.1.0
  - libxml2=2.9.9
  - mengine=1
  - mpeg_encode=1
  - mtz2ccp4_px=1.0
  - ncurses=6.2
  - numpy=1.18.1
  - numpy-base=1.18.1
  - olefile=0.46
  - openbabel=2.4.1
  - openssl=1.1.1g
  - pandas=1.0.3
  - pcre=8.43
  - pdb2pqr=2.1.1
  - pillow=7.0.0
  - pip=20.0.2
  - pixman=0.38.0
  - pmw=2.0.1
  - pycparser=2.20
  - pymol=2.3.5
  - pymol-psico=3.4.1
  - pyopenssl=19.1.0
  - pyqt=5.9.2
  - pysocks=1.7.1
  - python=3.7.7
  - python-dateutil=2.8.1
  - pytz=2019.3
  - qt=5.9.7
  - readline=8.0
  - requests=2.23.0
  - rigimol=1.3
  - scikit-learn=0.22.1
  - scipy=1.4.1
  - setuptools=46.1.3
  - sip=4.19.8
  - six=1.14.0
  - sqlite=3.31.1
  - urllib3=1.25.8
  - wheel=0.34.2
  - xz=5.2.5
  - zlib=1.2.11
  - zstd=1.3.7

I guess one could remove few other packages which are not required and this reduce the size of the environment.

Moreover, to run the software, few other packages should be installed, eg:

apt-get update && apt-get install --no-install-recommends -y make libgl1 libfontconfig1 libxrender1 build-essential

[atfrank]

@filipsPL thanks for posting this issue. I wasn't able to reproduce the error you were getting when trying to create the environment. What kind of computer were you working on?

[filipsPL]

This is the Linux machine with a fresh install of Debian Stable (Debian 11.2). So nothing is installed but the basic system. This should not have influence on the installation process as everything should be provided by the conda.

Anyway, the method described in my previous post enabled me to install and run the software on that system.