Latest package version check returns lower version

[apeltzer]

e.g. when using jdk 8.0.152 to fix issues with fastqc finally:

Running pipeline tests  [#########################-----------]   70%  00:00:00  'check_readme'         
ERROR: Found test failures in 'check_conda_env_yaml', halting lint run.


INFO: ===========
 LINTING RESULTS
=================
  97 tests passed   0 tests had warnings   1 tests failed

ERROR: Test Failures:
  http://nf-co.re/errors#8: Could not find Conda dependency using the Anaconda API: defaults::openjdk=8.0.152

ERROR: Sorry, some tests failed - exiting with a non-zero error code...

[sven1103]

Hm, the issue is not the linting code, but that there is no such thing as a default channel. It is more a repo of default packages provided by Anaconda, if I understood it correctly https://repo.anaconda.com/pkgs/. Can somebody confirm, that these are the packages living in the anaconda channel, queryable via the anaconda API?

[sven1103]

Or better: it seems that defaults just referrers to a dedicated collection of channels. So I guess you have to pinpoint the JDK you want in the anaconda cloud :(

[apeltzer]

Hm, I thought I tried just setting this to

- openjdk=8.0.152

but it raised the error. When trying again, this seems to work:

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'
    
Running pipeline tests  [##################------------------]   50%  00:00:01  Running pipeline tests  [#####################--------------Running pipeline tests  [####################################]  100%  None                              ck_readme'         

INFO: ===========
 LINTING RESULTS
=================
 101 tests passed   1 tests had warnings   0 tests failed

WARNING: Test Warnings:
  http://nf-co.re/errors#8: Conda package is not latest available: openjdk=8.0.152, 8.0.144 available

[apeltzer]

(Though I think its weird that it complains about the conda package is not latest available when 8.0.152 > 8.0.144 actually ;-))

[sven1103]

Actually, I think now you found a bug ;) I will reopen the issue. The bug lives in this

tools/nf_core/lint.py

Line 552 in 315d995

if last_ver is not None and last_ver != depver:

.

And it happens when the following condition is met:

• conda package found in at least one channel (successful API query against Anaconda cloud)
• version is numeric, but is not part of the versions available on Anaconda cloud

In your case, your given version number was "higher", but not present in the conda API query result, this is why you got the weird error.

@ewels I am thinking about just collecting all available package versions from the JSON result object, and checking explicitly for the version availability.