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Conda hangs when solving package specifications #5536
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More info . . . I tried again and was able build the above previously-hanging environment in about 2.5 mins. So to make things harder it may be non-deterministic. However as part of this additional troubleshooting I removed the This may be causing the problem because there was recently a big push to migrate from the If I downgrade to (ping @bgruening & @johanneskoester) |
Ok, @kalefranz @msarahan with many duplicated R packages between the r channel and conda-forge, the solver seems to run into problems (see above). Is this something you are already working on? |
In the meantime, if you want to remove the
or at this point even just
|
Thanks! We look forward to the solution! Can you keep us posted here? |
Yes we can use this ticket as the hub for all the related issues.
… On Jun 21, 2017, at 10:14 AM, Johannes Köster ***@***.***> wrote:
Thanks! We look forward to the solution! Can you keep us posted here?
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Hi all! New conda user here. I'm trying to install a second python environment with Here is my .condarc `channels:
Here is the output of conda info `Current conda install:
` |
@eredekop can you try to set the default channels without the Myself fought also with 'hang' issues (but having a quite long list of dependencies, too long to post here, incl. a 'pip' section) .. here's some learnings and notes:
later, since I downgraded the initial install to Miniconda 4.2.12 (latest 4.2.x binaries that I found in the repos, for linux x64):
ref: command used todo the update (generated by our ansible role): |
@kalefranz, any updates on this? I am occasionally seeing users complaining about hangs. Is this already resolved, and is there a minimum conda version we can point to? |
@lhoss I tried setting default channels as in #5536, but it did not change anything. I only needed to add extra lines at the end of .condarc, correct? The file now looks like this:
Without quick solution, I actually ended up translating my python2 scripts into python3 with 2to3 command. However, it would still be good to know the solution to the hang problem with creating new environments. |
did you check the final channels with
|
@kalefranz we see this more and more often. Any information we can collect to help resolving this? |
@kalefranz you can reproduce the error with
|
Another example here:
stopped it after a weekend without progress. When some of the channels are removed it works:
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And a new one in bioconda/bioconda-recipes#6365 :( |
Another, super-simple example to replicate: |
It would be ideal if Update: A colleague showed me how to use the option -nodefaults to modify the default channels without having to modify
This ignores the |
For anyone else still following this, you may want to also include the
EDIT by @mbargull: If you opt to change default_channels:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/free (note the order; |
For some cases this was improved with
might also do the trick. EDIT: If you opt to change default_channels:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/free (note the order; |
Also, always recommend putting pkgs/main at higher priority than pkgs/free. I might correct that in your post later. Don’t want misinformation like that propagating. :)
…Sent from my iPhone
On May 6, 2018, at 8:44 PM, Marcel Bargull ***@***.***> wrote:
For some cases this was improved with conda >=4.4, but there are still other cases where the pkgs/r+conda-forge combo causes seemingly endless solving phases.
Apart from thedefault_channels modification workaround, a simple
conda config --add pinned_packages 'r-base >=3.4'
might also do the trick.
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@kalefranz, I just copied the edit I made to my post earlier to @daler's (hope you don't mind @daler!) |
@kalefranz are you still working on a fix? |
I am still facing the same issue. It hangs forever. conda info :
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The work around that worked for me was deleting the ~/.condarc then specifying what channel to use, like this |
xref: gh-7700 |
same thing for me. what can be done? |
I was wondering if anyone has found any stopgaps or quick and dirty fixes to get this working temporarily? EDIT:
or
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You can try conda 4.6.0's pre-release:
It has several optimizations that might help. |
* #190, #95, #94, #93, #191 * Rewrote Python script for Python 3 compatibility * Renamed README to README.rst * Bumped version to 1.1.0 * Returns error code from .pl file, and reason * Update to gnuplot 5.2.7 * Address linting errors * Add Python 3 to dependencies, fix formatting * Argument ordering * Downgrade to python 3.7.6 * Add strict channel priority * Conda Solving Env Fix conda/conda#5536 * Add travis wait for 30 minutes for planemo * Remove travis wait, re-order channels * Use python 3.7.3 * Revert .travis.yml, remove Python 3 as dep * bump bioperl to work on travis * Add python 3.7.6 to requirements Co-authored-by: Matt <matthew.gopez@canada.ca> Co-authored-by: Darian <46600008+DarianHole@users.noreply.github.com> Co-authored-by: Darian Hole <darian.hole@canada.ca>
Years later and this is still happening. The question should really be, why the hell is this a problem (still)? Installing a package is among the most basic operations in python, which comes at the beginning of every script. R has a single command to do it that does not have these issues (not that it has none). Conda install, pip install, and easy_install fail like this with vague, useless error messages - thus the length of this and many other threads. |
This still happens a year later, too. Workaround is to use mamba to do the resolution. Is mamba working around the bug, or somehow handling my channels "differently"? Don't know. |
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Hi, here is another data point related to #5219, #4077, #4467 where the solver hangs on particular combos of dependencies. Pinging @mcg1969 since you're mentioned in those other issues.
After trying different combinations trying to pin down the culprit, the best I could figure out is that it seems to be a critical mass of R packages across bioconda and conda-forge that cause the issue. Here's an example:
From that last one, the output from
conda env create -n tmp --file env.yml -vv
is here. And myconda info
is:The text was updated successfully, but these errors were encountered: