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

[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.