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greenelab / deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine
https://greenelab.github.io/deep-review/
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Build error: ResolvePackageNotFound wkhtmltopdf 0.12.3* #625

Closed agitter closed 6 years ago

agitter commented 6 years ago

The Travis CI build failed for #623 because wkhtmltopdf could not be installed. The same thing happened when I tested a different manubot-rootstock derived repository.

The following works for me locally:

conda install -c bioconda wkhtmltopdf=0.12.3

The build log:

$ conda env create --quiet --file build/environment.yml
WARNING: The remote server could not find the noarch directory for the
requested channel with url: https://conda.anaconda.org/bioconda
It is possible you have given conda an invalid channel. Please double-check
your conda configuration using `conda config --show`.
If the requested url is in fact a valid conda channel, please request that the
channel administrator create `noarch/repodata.json` and associated
`noarch/repodata.json.bz2` files, even if `noarch/repodata.json` is empty.
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json
WARNING: The remote server could not find the noarch directory for the
requested channel with url: https://conda.anaconda.org/conda-forge
It is possible you have given conda an invalid channel. Please double-check
your conda configuration using `conda config --show`.
If the requested url is in fact a valid conda channel, please request that the
channel administrator create `noarch/repodata.json` and associated
`noarch/repodata.json.bz2` files, even if `noarch/repodata.json` is empty.
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json
WARNING: The remote server could not find the noarch directory for the
requested channel with url: https://conda.anaconda.org/anaconda
It is possible you have given conda an invalid channel. Please double-check
your conda configuration using `conda config --show`.
If the requested url is in fact a valid conda channel, please request that the
channel administrator create `noarch/repodata.json` and associated
`noarch/repodata.json.bz2` files, even if `noarch/repodata.json` is empty.
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json
ResolvePackageNotFound: 
  - wkhtmltopdf 0.12.3*
The command "conda env create --quiet --file build/environment.yml" failed and exited with 1 during .
agitter commented 6 years ago

Closing this issue. The build process works again without any modifications on our part.