UnsatisfiableError: The following specifications were found to be incompatible with each other
Issue #17
resolved
Hello,
I am trying to install iPHoP using conda, but after running:
conda install -c conda-forge -c bioconda iphop
I get the following error:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
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::__glibc==2.28=0
- feature:|@/linux-64::__glibc==2.28=0
- iphop -> libstdcxx-ng=11.2.0 -> __glibc[version='>=2.17']
- iphop -> tensorflow=2.7.0 -> __cuda
Your installed version is: 2.28
Kind regards,
Alyzza
Comments (28)
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repo owner
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reporter
Hello,
I create a new one every time my installation fails. I did try it with mamba:
(iphop_env) mamba install -c conda-forge -c bioconda iphop __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (1.0.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Looking for: ['iphop'] conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/r/linux-64 No change pkgs/main/noarch No change pkgs/r/noarch No change pkgs/main/linux-64 5.0MB @ 3.3MB/s 1.6s Pinned packages: - python 3.8.* Encountered problems while solving: - package iphop-1.0.0-pyhdfd78af_0 requires perl-bioperl 1.6.924.*, but none of the providers can be installedI do use the same name when I make a new environment, i.e. I remove the environment then create another one with the same name. Could that be a problem?
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repo owner
Well, I was able to reproduce the bug, which is good in a way because it means it’s not a problem on your side, but is also bad because that means the conda distribution is broken …
I’ll need to look into it, and let you know when it’s fixed. Thanks for reporting !
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repo owner
- changed status to open
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repo owner
Ok, we updated the bioconda recipe, and it seems to work better now. Please try again in a new environment with python 3.8, i.e. something like:
$ conda create -n iphop_test python=3.8 $ conda activate iphop_test $ mamba install -c conda-forge -c bioconda iphopAnd let us know if it works now !
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reporter
It worked! Running:
iphop -hand
iphop predict -halso works now. Thank you!
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i’m still getting the message below when trying to install via conda/mamba
iphop-1.0.0-pyhdfd78af_0 requires perl 5.26.*, but none of the providers can be installed
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repo owner
This is weird, I just tried the following
$ conda create -n iphop_env python=3.8 $ conda activate iphop_env $ mamba install -c conda-forge -c bioconda iphopand did not get any error.
Are you trying to install the latest version of iphop, or a specific version ? (The latest I see on my side is pyhdfd78af_2, but it seems like on your side conda is trying to install pyhdfd78af_0) ?
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Yeah its weird. I’m not trying to install a particular version and when i run the code you give above i get:
iphop-1.0.0-pyhdfd78af_0 requires perl-bioperl 1.6.924.*, but none of the providers can be installedSo i dont know why my conda is defaulting to an older version. I also uninstalled and reinstalled conda but still get the same error
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found the fix… something weird was going on in .condarc
i deleted it and then reran the above and all was well
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repo owner
Glad to hear, thanks for the update !
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Hello Simon,
I tried to use conda to install IPHoP in my MacOS (Monterey 12.6.2):
$ conda create -n iphop_env python=3.8 $ conda activate iphop_env $ conda install -c conda-forge -c bioconda iphopBut it would get stuck in “Solving environment“ then failed. So I also tried using mamba:
$ conda create -n iphop_env -c conda-forge python=3.8 mamba $ conda activate iphop_env $ mamba install -c conda-forge -c bioconda iphopThen I got the error message below:
$ mamba install -c conda-forge -c bioconda iphop __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (1.1.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Looking for: ['iphop'] pkgs/main/osx-64 4.8MB @ 2.5MB/s 2.2s bioconda/osx-64 3.8MB @ 1.5MB/s 2.7s pkgs/r/noarch 1.3MB @ 473.1kB/s 0.9s bioconda/noarch 4.1MB @ 1.3MB/s 3.5s pkgs/r/osx-64 820.9kB @ 233.1kB/s 0.8s pkgs/main/noarch 818.5kB @ 225.6kB/s 1.1s conda-forge/noarch 10.7MB @ 2.5MB/s 4.9s conda-forge/osx-64 26.0MB @ 3.0MB/s 10.1s Pinned packages: - python 3.8.* Could not solve for environment specs Encountered problems while solving: - nothing provides libstdcxx-ng 11.2.0.* needed by iphop-1.0.0-pyhdfd78af_0 The environment can't be solved, aborting the operationCould you please help to check this issue? Many thanks.
Best wishes,
Ernie
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repo owner
This is weird, it looks like it’s trying to install the version 1.0.0, while the latest on bioconda is 1.2.0. Can you try to specify a version, e.g. “iphop=1.2.0” ?
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Hi,
I have tried to specify it to iphop=1.2.0 but it still failed to install:
Looking for: ['iphop=1.2.0'] pkgs/main/osx-64 4.8MB @ 2.7MB/s 2.1s pkgs/r/noarch 1.3MB @ 556.7kB/s 0.6s bioconda/osx-64 3.8MB @ 1.6MB/s 2.7s bioconda/noarch 4.1MB @ 1.5MB/s 3.0s pkgs/main/noarch 818.5kB @ 270.3kB/s 0.6s pkgs/r/osx-64 820.9kB @ 253.9kB/s 0.8s conda-forge/noarch 10.7MB @ 1.7MB/s 6.7s conda-forge/osx-64 26.0MB @ 3.2MB/s 9.7s Pinned packages: - python 3.8.* Could not solve for environment specs Encountered problems while solving: - nothing provides libstdcxx-ng 11.2.0.* needed by iphop-1.2.0-pyhdfd78af_0 The environment can't be solved, aborting the operationI also just tried updating all packages in the iphop_env then ran it again, but it still failed for its installation. Thanks.
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repo owner
I just tried it on my linux and the same command work. It may be either something weird with your .condarc (this was apparently an issue for other users above), or it’s something specific to Mac OS. If it’s the latter though, I’ll not be able to troubleshoot before I get my hands on a Mac, so not until January, sorry !
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repo owner
Hi, and thanks for your patience !
We were able to test this on another OS X, and indeed there is a dependency that can not be solved in this system (libstdcxx is only available for linux in conda-forge). So that means that, unfortunately, the conda installation will not be possible with a Mac. We’re now adjusting the package so that iphop does not appear in the list of available packages from Mac OS X. If you want to run on this machine, your best bet is most likely to try to run iphop through the Docker container (https://hub.docker.com/r/simroux/iphop). Sorry about this, and hopefully there will be a way for you to either run on linux or run through the container !
Best,
Simon
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Hi Simon,
Thanks so much for your help. I have also tried to install it on my linux-based VM using the same command work, then it showed an error message like below:
(iphop) $ mamba install -c conda-forge -c bioconda iphop __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (1.1.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Looking for: ['iphop'] conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/linux-64 No change pkgs/main/noarch No change pkgs/r/noarch No change pkgs/r/linux-64 No change Pinned packages: - python 3.8.* Could not solve for environment specs Encountered problems while solving: - package iphop-1.0.0-pyhdfd78af_0 requires perl-bioperl 1.6.924.*, but none of the providers can be installed The environment can't be solved, aborting the operationThen, I tried to specify iphop=1.2.0 and ran it again:
(iphop) $ mamba install -c conda-forge -c bioconda iphop=1.2.0 __ __ __ __ / \ / \ / \ / \ / \/ \/ \/ \ ███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ \____ / / \_/ \_/ \_/ \ o \__, / _/ \_____/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝ mamba (1.1.0) supported by @QuantStack GitHub: https://github.com/mamba-org/mamba Twitter: https://twitter.com/QuantStack █████████████████████████████████████████████████████████████ Looking for: ['iphop=1.2.0'] conda-forge/linux-64 Using cache conda-forge/noarch Using cache bioconda/linux-64 Using cache bioconda/noarch Using cache pkgs/main/linux-64 No change pkgs/main/noarch No change pkgs/r/linux-64 No change pkgs/r/noarch No change Pinned packages: - python 3.8.* Could not solve for environment specs Encountered problems while solving: - package iphop-1.2.0-pyhdfd78af_0 requires blast 2.12.0.*, but none of the providers can be installed The environment can't be solved, aborting the operationShould I need to pre-install blast=2.12.0? I tried it first and then ran iphop=1.2.0 installation again but it still failed:
Could not solve for environment specs Encountered problems while solving: - package perl-carp-1.50-pl5321hd8ed1ab_0 requires perl >=5.32.1,<6.0a0 *_perl5, but none of the providers can be installed The environment can't be solved, aborting the operationDo you have any ideas? Many thanks.
Best
Ernie
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repo owner
Ugh, sorry.. The best explanation I have is that the VM is a linux 32-bit while bioconda (and a number of the packages that iphop depends on) requires a linux 64-bit ?
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Well, my VM is ubuntu linux 64-bit.
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repo owner
Ok, so not that. I’m really confused about this message then “blast 2.12.0.*, but none of the providers can be installed”, since blast 2.12 is clearly available from bioconda (https://anaconda.org/bioconda/blast/files). Same for perl which is in conda-forge (https://anaconda.org/conda-forge/perl/files). I’ve never seen that, not sure what’s happening.
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repo owner
For reference, I just ran
$ mamba create -n iphop_test -c conda-forge -c anaconda -c bioconda iphopOn a Ubuntu machine, and this successfully installed iphop 1.2.0. I’m not sure why the VM behaves differently, but the fact that it defaults to iphop-1.0.0 is not a good sign (it seems to be doing something similar as when it was on OS X, basically)
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Hi Simon,
After some efforts were made, I have moved the run to our HPC site and it can work as expected now.
Thank you for your help!
Best
Ernie
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repo owner
Awesome ! Sorry I made the mistake with the “noarch” setting which makes conda (wrongly) believe that iPHoP will work on a Mac, but I’m glad if you found a workaround and got it to run somewhere :-)
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repo owner
- changed status to resolved
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Hi there - FYI I was getting similar errors (tensorflow-related) and what ended up working was a
mamba create -n iphop -c conda-forge -c bioconda iphop=1.2.0 -c anacondadirectly. Hope this helps if someone has a similar problem in the future. -
repo owner
Thanks for sharing ! Does this only work with iphop=1.2.0 or does this also work for iphop=1.3.2 ?
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Actually on my side it did work for both versions :)
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repo owner
Great, thanks !
- Log in to comment
Hi,
This is weird, I have never seen this issue. Are you trying to install the package in an existing conda environment ? If so, did you try to create a new one, and then install iPHoP there ? (I would also recommend using mamba rather than conda, as mamba essentially creates conda environments but in a much faster way)