Description
Hi, I was trying to install the latest MultiQC version with conda install -c bioconda multiqc=1.9
in a new conda environment (no other packages installed yet), but got the following error:
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__cuda==10.1=0
- feature:|@/linux-64::__cuda==10.1=0
Your installed version is: 10.1
My operating system is Ubuntu 18.04.5 LTS and this is the output of the command nvidia-smi | grep Version
, if helpful:
| NVIDIA-SMI 435.21 Driver Version: 435.21 CUDA Version: 10.1 |
Any idea on how to fix this problem?
BTW, apparently the same kind of error has been reported for another software (pytorch-metric-learning). The bug was fixed by the software developer by editing the meta.yaml
file needed to build the conda package (see KevinMusgrave/pytorch-metric-learning#55 ). Could this perhaps help to identify and solve the issue in MultiQC?
Many thanks!
Activity
silvia-s commentedon Sep 4, 2020
I forgot to mention that if I don't specify the MultiQC version I need, conda installs version 0.9 without problems. Could you perhaps check the differences between the
meta.yaml
files of versions 0.9 and 1.9, to see whether there's any dependency breaking the installation?Cheers,
Silvia
tadas-subonis commentedon Sep 6, 2020
This seems to be broken on Win in general
Works:
Fails:
with
ewels commentedon Sep 7, 2020
Hi all,
I wonder if this could be due to a larger bioconda issue with Python 3.8 that was fixed very recently - see bioconda/bioconda-recipes#24215
Would you mind having another go and seeing if you still hit the same problem please?
Note that you should not put
-c bioconda
in the installation command (the docs used to list this but I have since removed it). Instead, make sure that your conda channel priority is set up correctly (see the bioconda docs) and then just doconda install multiqc
. This is because theconda-forge
channel should have top priority.Thanks!
Phil
silvia-s commentedon Sep 7, 2020
Hi Phil,
I've tried specifying
python=3.7
as suggested by @tadas-subonis, but still got the same CUDA incompatibility error - it seems to be independent on the Python 3 version (on Ubuntu, at least!). If I try withpython=2.7
I don't get the error, but can only install MultiQC version 0.9 (i.e. pretty old).I've also looked for MultiQC in the
conda-forge
channel, but it doesn't seem to be included in their list of packages (see output ofconda search multiqc -c conda-forge
and https://conda-forge.org/feedstocks/ ).Could you perhaps find any particular difference between the
meta.yaml
files of versions 0.9 and 1.9, as I mentioned in my second post of this thread?Cheers,
Silvia
mbargull commentedon Sep 7, 2020
multiqc
is available via thebioconda
channel, which itself uses theconda-forge
channel for non-bio related packages.You have to use both channels when using packages from Bioconda, i.e., use
conda create -c conda-forge -c bioconda ...
or add them to your
conda
configuration viaconda config --prepend channels bioconda --prepend channels conda-forge
(you can check your configuration entries via
conda config --show-sources
).Unfortunately,
conda
often does not give helpful error messages for conflicting/missing packages. There is a newer alternative implementation of theconda
package manager, calledmamba
, that usually gives more helpful messages here. If you don't include theconda-forge
channel,mamba install ...
tells you that thelzstring
package cannot be found -- that one is provided byconda-forge
.Cheers, Marcel
silvia-s commentedon Sep 7, 2020
Thanks a lot @mbargull, your solution worked and I could finally install version 1.9! Will definitely look at
mamba
, thank you :)@ewels: it might be a good idea to update the
README.md
file of the MultiQC repository by changing the installation command (currentlyconda install -c bioconda multiqc
) withconda install -c conda-forge -c bioconda multiqc
, for any users (like me) who don't haveconda-forge
among the channels listed in their.condarc
file.Best,
Silvia
ewels commentedon Sep 10, 2020
Great, thanks for the more detailed help @mbargull!
@silvia-s - I used to do this but have stopped, as it caused problems when my docs got out of date. Instead, the MultiQC docs link to the bioconda documentation, which should always be accurate.
Phil