[R-pkg-team] Bug#1069509: r-cran-metamix: FTBFS on armhf: tests fail

[Andreas Tille]

Hi Lucas,

thanks a lot for all your work on rebuilding the archive on different
architectures.  That's really appreciated.

In this specific case I wonder whether your build host has simply
trouble initialising MPI given I find strings like

  MPI_ERRORS_ARE_FATAL

Kind regards
   Andreas.

Am Sat, Apr 20, 2024 at 03:14:31PM +0200 schrieb Lucas Nussbaum:
> Source: r-cran-metamix
> Version: 0.3-2
> Severity: serious
> Justification: FTBFS
> Tags: trixie sid ftbfs
> User: lucas at debian.org
> Usertags: ftbfs-20240420 ftbfs-trixie ftbfs-t64-armhf
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build
> on armhf.
> 
> 
> Relevant part (hopefully):
> > make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
> > make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
> > installing to /<<PKGBUILDDIR>>/debian/r-cran-metamix/usr/lib/R/site-library/00LOCK-r-cran-metamix-0.3/00new/metaMix/libs
> > ** R
> > ** data
> > *** moving datasets to lazyload DB
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > --------------------------------------------------------------------------
> > Sorry!  You were supposed to get help about:
> >     pmix_init:startup:internal-failure
> > But I couldn't open the help file:
> >     /usr/share/pmix/help-pmix-runtime.txt: No such file or directory.  Sorry!
> > --------------------------------------------------------------------------
> > [ip-10-84-234-19:2164897] PMIX ERROR: NOT-FOUND in file ../../../../../../../../opal/mca/pmix/pmix3x/pmix/src/server/pmix_server.c at line 237
> > [ip-10-84-234-19:2164891] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 716
> > [ip-10-84-234-19:2164891] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on the local node in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 172
> > --------------------------------------------------------------------------
> > It looks like orte_init failed for some reason; your parallel process is
> > likely to abort.  There are many reasons that a parallel process can
> > fail during orte_init; some of which are due to configuration or
> > environment problems.  This failure appears to be an internal failure;
> > here's some additional information (which may only be relevant to an
> > Open MPI developer):
> > 
> >   orte_ess_init failed
> >   --> Returned value Unable to start a daemon on the local node (-127) instead of ORTE_SUCCESS
> > --------------------------------------------------------------------------
> > --------------------------------------------------------------------------
> > It looks like MPI_INIT failed for some reason; your parallel process is
> > likely to abort.  There are many reasons that a parallel process can
> > fail during MPI_INIT; some of which are due to configuration or environment
> > problems.  This failure appears to be an internal failure; here's some
> > additional information (which may only be relevant to an Open MPI
> > developer):
> > 
> >   ompi_mpi_init: ompi_rte_init failed
> >   --> Returned "Unable to start a daemon on the local node" (-127) instead of "Success" (0)
> > --------------------------------------------------------------------------
> > *** An error occurred in MPI_Init
> > *** on a NULL communicator
> > *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> > ***    and potentially your MPI job)
> > [ip-10-84-234-19:2164891] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
> > ERROR: lazy loading failed for package ‘metaMix’
> > * removing ‘/<<PKGBUILDDIR>>/debian/r-cran-metamix/usr/lib/R/site-library/metaMix’
> > dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-metamix/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 21 Mar 2020 14:53:15 +0100'" returned exit code 1
> > make: *** [debian/rules:4: binary] Error 25
> 
> 
> The full build log is available from:
> http://qa-logs.debian.net/2024/04/20/r-cran-metamix_0.3-2_unstable-armhf.log
> 
> All bugs filed during this archive rebuild are listed at:
> https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240420;users=lucas@debian.org
> or:
> https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240420&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> If you reassign this bug to another package, please mark it as 'affects'-ing
> this package. See https://www.debian.org/Bugs/server-control#affects
> 
> If you fail to reproduce this, please provide a build log and diff it with mine
> so that we can identify if something relevant changed in the meantime.
> 
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