Error in setting up the environment
jchariker opened this issue · comments
Hi,
I used the following command:
conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt
And I received this error message:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- python==3.5.1
- docutils==0.12
Current channels:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/ostrokach/linux-64
- https://conda.anaconda.org/ostrokach/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Do you have any advice for solving this?
Thanks for your help!
Hi
many thanks for your feedback!
May I ask you to try the following:
Instead of the initial command include conda-forge as channel and run the command as follows conda create -n paqr_kapac -c bioconda -c ostrokach -c conda-forge --file requirements_py3.txt
Please let us know if this solves the problem.
Best
Ralf
Thank you for your quick response!
Using the following command:
conda create -n paqr_kapac -c bioconda -c ostrokach -c conda-forge --file requirements_py3.txt
I received the following information in the console:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Package xz conflicts for:
pyyaml==3.12 -> python[version='2.7.,3.4.,3.5.,>=3.5,<3.6.0a0,>=3.6,<3.7.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
snakemake==3.13.0 -> pandas -> numpy[version='1.10.,1.12.,1.13.,>=1.11.3,<2.0a0,>=1.14.6,<2.0a0,>=1.9.'] -> mkl_random[version='>=1.0.2,<2.0a0'] -> numpy-base[version='>=1.0.2,<2.0a0'] -> python[version='>=3.5,<3.6.0a0,>=3.6,<3.7.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
docutils==0.12 -> python[version='3.4.,>=3.5,<3.6.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
r-optparse==1.3.2 -> r=3.3.1 -> r-recommended==3.3.1 -> r-survival -> r-matrix[version='>=1.2.12,<1.2.13.0a0'] -> r-lattice[version='>=0.20.35,<0.20.36.0a0'] -> r-base[version='3.1.3.,3.2.0.,3.2.1.,3.3.1.,3.3.2.,3.4.1.'] -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.0.,5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
r-base==3.3.2 -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
numpy==1.11.3 -> numpy-base[version='>=1.0.2,<2.0a0'] -> python[version='>=2.7,<2.8.0a0,>=3.5,<3.6.0a0,>=3.6,<3.7.0a0,>=3.7,<3.8.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
graphviz==2.38.0 -> pango[version='1.40.,>=1.40.14,<1.41.0a0'] -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.0.,5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
Package python conflicts for:
python==3.5.1
Package libxml2 conflicts for:
r-base==3.3.2 -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9
graphviz==2.38.0 -> pango[version='1.40.,>=1.40.14,<1.41.0a0'] -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9
r-optparse==1.3.2 -> r=3.3.1 -> r-recommended==3.3.1 -> r-survival -> r-matrix[version='>=1.2.12,<1.2.13.0a0'] -> r-lattice[version='>=0.20.35,<0.20.36.0a0'] -> r-base[version='3.1.3.,3.2.0.,3.2.1.,3.3.1.,3.3.2.,3.4.1.'] -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.*,>=2.13.0,<3.0a0'] -> libxml2=2.9
Thanks again for helping with this!
Many thanks for the report.
I checked our environment again and, apparently, some of the package versions we use for our environment are not available anymore.
To solve this problem, I will assemble a new environment and come back to you soon.
Ralf
Thank you, Ralf. I appreciate you taking the time to do that!
Julia
Hi Julia
As far as I can tell, one of the packages we use in our environment (r-optparse) has changed to an extent that makes it incompatible with the rest of our environment.
In order to circumvent this problem, I established another requirements file called requirements_py3_UPDATED.txt that should be used instead. Next, the missing package r-optparse must be installed manually. I included a short paragraph for this in the README file. Can you please check again and let us know if this solves your problem?
Best
Ralf
Hi Ralf,
Your instructions were very clear, and I had no errors during installation. Thank you for quickly finding these solutions so that I can move forward with my analysis! I am now working on getting my input files together and editing the config.yaml file where needed.
Julia