How to avoid superceding?

[ijstokes]

I was trying to install a Conda package during a demo. I was surprised to see that the Conda package plan decided to use a Conda package I created end of 2015 and that is available in my channel. I understand why matching packages from explicitly listed channels might have preference, even if it results in a downgrade. But is there a way to say "don't do that?" I imagine if I had a "newer" version in an explicitly listed channel then I might expect different behavior than an older version, but maybe not.

And in the case of Conda (unsurprisingly) there are clearly dangers to having your own conda package in a channel. It isn't a dependency of the listed genepattern package, so this is just the "automatically update conda and conda-env" behavior that is then pulling in my custom Conda build. Which then totally breaks my Anaconda distribution (conda is now gone from my installation -- I will have to hand-patch it back in, I think)

$ conda install -c ijstokes -c conda-forge genepattern
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata .............
Solving package specifications: ..........

Package plan for installation in environment /Users/ijstokes/anaconda:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    conda-env-2.5.1            |           py27_0          26 KB
    conda-3.18.4               |           py27_0         176 KB  ijstokes
    widgetsnbextension-1.2.3   |           py27_1         1.1 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.3 MB

The following NEW packages will be INSTALLED:

    genepattern:        0.5.0-py27_0 ijstokes   
    widgetsnbextension: 1.2.3-py27_1 conda-forge

The following packages will be UPDATED:

    conda-env:          2.5.0-py27_0             --> 2.5.1-py27_0          

The following packages will be SUPERCEDED by a higher-priority channel:

    conda:              4.1.3-py27_0             --> 3.18.4-py27_0 ijstokes

Proceed ([y]/n)? y

Pruning fetched packages from the cache ...
Fetching packages ...
conda-env-2.5. 100% |##############################| Time: 0:00:00 804.36 kB/s
conda-3.18.4-p 100% |##############################| Time: 0:00:00 863.08 kB/s
widgetsnbexten 100% |##############################| Time: 0:00:00   2.02 MB/s
Extracting packages ...
[      COMPLETE      ]|#################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|#################################################| 100%
Linking packages ...
An unexpected error has occurred, please consider sending the           |  25%
following traceback to the conda GitHub issue tracker at:

    https://github.com/conda/conda/issues

Include the output of the command 'conda info' in your report.


Traceback (most recent call last):
  File "/Users/ijstokes/anaconda/bin/conda", line 6, in <module>
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 120, in main
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 130, in args_func
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 69, in execute
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 407, in install
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/plan.py", line 591, in execute_actions
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 136, in execute_instructions
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 79, in LINK_CMD
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/install.py", line 1089, in link
  File "/Users/ijstokes/anaconda/lib/python2.7/site-packages/conda/install.py", line 208, in _link
  File "/Users/ijstokes/anaconda/lib/python2.7/shutil.py", line 130, in copy2
    copyfile(src, dst)
  File "/Users/ijstokes/anaconda/lib/python2.7/shutil.py", line 82, in copyfile
    with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: u'/Users/ijstokes/anaconda/pkgs/conda-3.18.4-py27_0/bin/activate'

[mcg1969]

Yeah, I'd say it's pretty bad to have conda in your own channel.

That said, since conda 3.3.0, it has been possible to disable automatic updates to conda by adding self_update: false to your .condarc. We've recently deprecated that name to auto_update_conda, and made it settable with conda config (i.e., without having to hand-edit `.condarc').

[mcg1969]

And if you want to disable channel priority altogether, you can do channel_priority: false, and you will get the latest version of a package no matter what channel it comes from. (Ties are still broken by channel priority in that case).

[mcg1969]

If we're going to leave conda auto-updates in the code, I think we should probably make sure it doesn't downgrade. What do you think, @kalefranz?

[ijstokes]

@mcg1969 thanks for your feedback. The immediate answer is for me to set channel_priority and auto_update to false.

I realize that complexity is a bad thing, so probably the behavior of channel_priority is fine how it is, but just for consideration I feel like if I explicitly list channels and explicitly list packages then I'd like the explicitly listed packages to come from the channels I've given. I realize that the knock-on effect is tricky, though, around dependencies: I can't honestly tell you what behavior I'd expect or consider "preferable"

Is there a command line flag for channel_priority? (I didn't see one).

[mcg1969]

conda config --set channel_priority false will work...

Do check out my PR #2900 and see what you think.

[kalefranz]

@ijstokes The condarc flag is either self_update or auto_update_conda. Officially, from 4.0.9 on, it's auto_update_conda.

[kalefranz]

If we're going to leave conda auto-updates in the code, I think we should probably make sure it doesn't downgrade

I don't think conda should get a special hack. I think if we get finer-grained channel priority right, we won't need it. I think...

[kalefranz]

I feel like if I explicitly list channels and explicitly list packages then I'd like the explicitly listed packages to come from the channels I've given

Yes, we will have finer-grained control over this. And we'll think through thoroughly what user expectations are, and try to make conda "do what I expect it to do" as much as possible. May still take a couple iterations to get right.

[jolespin]

Will #2900 be a solution to this problem? #5732

[github-actions]

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