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In setup.sh, add check to suppress running biodb-to-json.pl if system is on MacOS High Sierra #945

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deepakunni3 commented Dec 1, 2017

This PR is to address the issue observed in GMOD/Apollo#1820

While running setup.sh, the biodb-to-json.pl step keeps running indefinitely while it generates large temp files to the point of filling all available disk space.

The behavior is observed only on MacOS High Sierra.

This PR modifies setup.sh to check if the system is on MacOS High Sierra and skip running biodb-to-json.pl if it is.

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nathandunn commented Dec 1, 2017

I'll test through this shortly. In the interim, could you raise / find an issue here and add that as well to the echoed comments. You can copy me on so that it subscribes me automatically.

https://github.com/bioperl/bioperl-live/issues

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nathandunn commented Dec 1, 2017

That is almost instant. Wow. Yes, good to go once we have a reference for the bioperl issue. The reason for this is for someone to say "hey, its fixed now". I can create it instead if you prefer.

@nathandunn nathandunn merged commit 410d370 into GMOD:master Dec 2, 2017

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nathandunn added a commit to nathandunn/Apollo that referenced this pull request Dec 2, 2017

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deepakunni3 commented Dec 2, 2017

Did not create an issue on the BioPerl issues page because this issue might be occurring within Perl scripts packaged with JBrowse, one of which is biodb-to-json.pl.
If we find that its upstream to JBrowse then we can create an issue and reference it here.

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rbuels commented Jan 23, 2018

@deepakunni3 could you add a line about this in the release-notes.txt?

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rbuels commented Jan 23, 2018

Just update this pull request with the release-notes addition and I'll merge it

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nathandunn commented Jan 23, 2018

Actually @rbuels , the "Gathering System Information" takes forever. I think its just the system_profiler call. Is it necessary for the non-legacy build?

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deepakunni3 commented Jan 23, 2018

@nathandunn Its not "Gathering System Information".

I do agree that the sytem_profiler call does take its time on MacOS, but its not the main cause of this issue.

I debugged through the entire setup.sh script to pin point the exact place where it was getting stuck. And that is at running biodb-to-json.pl step. If I comment that out for Volvox and Yeast, everything works fine.

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nathandunn commented Jan 24, 2018

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rbuels commented Jan 24, 2018

@deepakunni3 could you add a line about this in the release-notes.txt and update this branch with it? Or just add it to master and mention "#945" in the commit message so that it's linked here?

deepakunni3 added a commit to deepakunni3/jbrowse that referenced this pull request Jan 24, 2018

rbuels added a commit that referenced this pull request Jan 24, 2018

Merge pull request #959 from deepakunni3/patch-1
Update release notes for PR #945

rbuels added a commit that referenced this pull request Jan 24, 2018

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rbuels commented Jan 24, 2018

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nathandunn commented Jan 24, 2018

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cjfields commented Jun 21, 2018

@rbuels The issue is on systems with versions of berkeley-db compiled on older Mac OS X releases (along with any Perl libraries like DB_File compiled against it) which are upgraded to High Sierra (and APFS). The issue in the Apple forum:

https://discussions.apple.com/thread/8125401

I have seen this with both the system perl and perlbrew installations; the only workarounds I found:

  1. Install a separate version of berkeley-db from brew or fink, then reinstall DB_File. This seemed the fastest route; I'm not sure whether the system version is updated, but a clean version can be installed via fink or brew
  2. Run a clean installation of perl with a recompiled version of berkeley-db.
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