Bug 243679 - math/R version 3.6.2 builds and packages with ports-mgmt/synth on 12.1-RELEASE AMD64 but fails to install
Summary: math/R version 3.6.2 builds and packages with ports-mgmt/synth on 12.1-RELEAS...
Status: Closed Overcome By Events
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: amd64 Any
: --- Affects Only Me
Assignee: Joseph Mingrone
Depends on:
Reported: 2020-01-28 20:36 UTC by dal36
Modified: 2020-12-15 21:47 UTC (History)
1 user (show)

See Also:


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Description dal36 2020-01-28 20:36:23 UTC
I've attempted to build and install math/R on my system using Synth. OpenMP is enabled in the port options. Based on the build logs for this package, the build and packaging processes were successful. However, the installation of
the resulting package did not occur. The following output was produced after Synth had completed the building process:
        # synth install math/R

        Stand by, recursively scanning 1 port serially.

        Scanning existing packages.

        R-3.6.2.txz failed dependency check.

        Packages validated, rebuilding local repository.

        Local repository successfully rebuilt

        Updating Synth repository catalogue...

        Fetching meta.txz: 100%    260 B   0.3kB/s    00:01

        Fetching packagesite.txz: 100%  209 KiB 214.3kB/s    00:01

        Processing entries: 100%

        Synth repository update completed. 848 packages processed.

        All repositories are up to date.

        pkg: No packages available to install matching 'R-3.6.2' have been found in the repositories

        Unfortunately, the system upgraded failed.

The following line was present near the end of the build logs for this port:

actual-package-depends: dependency on /usr/lib/libomp.so not registered (normal if it belongs to base)

My understanding is that openmp was added to the base system in 12.1. To me, this issue appears to be similar to the situation described at the two links below, where, as I understand, Synth is expecting to find a port that makes
this file available, but doesn't succeed since it's in base instead.
Comment 1 dal36 2020-02-01 12:56:24 UTC
I should perhaps have noted that in the (apparently similar) cases at the links above, the suggestion was that the way in which the port dealt with this dependency was what was leading to the observed behaviour.
Comment 2 Joseph Mingrone freebsd_committer 2020-12-10 20:46:09 UTC

R maintainer here.  This report was never assigned to me, so I missed it.  After digging a little now, I'm guessing the issue is now resolved, since openmp doesn't appear in LIB_DEPENDS.  Is this correct and the bug can be closed?
Comment 3 dal36 2020-12-15 21:39:57 UTC
Yes, it seems to be installing correctly now - thanks.
Comment 4 Joseph Mingrone freebsd_committer 2020-12-15 21:47:27 UTC
Thanks for reporting back.