+1 maintenance report

[Vladimir Petko]

I was on the +1 maintenance shift on the week of July 8th, 2024
and worked from the bottom of the excuses page. The exception to this
rule was Clojure packages.

Thanks to mwhudson for fixing the issue in mescc-tools!!!

pymatgen:
The package fails to build with Python 3.12[1]. It makes
python3-mp-api and python3-emmet-core uninstallable. I have
cherry-picked the upstream commit and applied it to the package. The
package is in the NEW queue. Submitted the patch to Debian[2].

bamtools:
The package contained a buffer overflow in the bam writer[3] and an
infinite loop when reading the filter script[4]. I have added the
patches and submitted them upstream[5][6] and to Debian[7]. Package
migrated.

tools-namespace-clojure:
The package was missing the required dependencies
libjava-classpath-clojure, libtools-reader-clojure, and the
corresponding classpath entries in the jar manifest[9]. The issue was
fixed in Debian, and the package synced.

aevol:
Reviewed existing MR[8] and proposed minor changes to make the fix
easier to understand.

mescc-tools:
The package fails to build due to the illegal instruction in the
ppc64el test[10].  The same issue occurs with the 1.4.0-1 version of
the package. mwhudson investigated the problem: the test assumed r0 to
be 0 at the start of the test program -  the program compared r0 with
1, jumped to the 'overrr' label otherwise, and when r0 was not 0, it
did not go back to 'bakkk' label and crashed. mwhudson uploaded a fix
for the package.

xilinx-runtime:
The package was missing headers for fixed-width integer types required
since GCC 13. Applied upstream patch with minor modifications, package
migrated[11].

woval-wabbit:
The package fails the build time tests[12]. The package is out of
date: 8.6.1 vs 9.9.0 upstream, tests pass for 9.9.0.

gitaly:
The package was uploaded to Oracular by accident. There is an existing
removal bug[13].  I have subscribed ubuntu-archive.

facet-analyser:
The package only exists in -proposed (211 days) and has conflicting
dependencies. python3-paraview and libinsighttoolkit5-dev.
libinsighttoolkit5-dev depends on libvtk9-dev which conflicts with
python3-paraview. I have filed a removal bug[14].

jupiter-ydoc:
The package only exists in -proposed (238 days) and has unsatisfiable
dependencies. I have filed a removal bug[15].

r-cran-withr:
I have filed update-excuses bugs for the migration[16][17][18][19][20][21].

tools-nrepl-clojure:
The build hangs indefinitely.  tools-nrepl-clojure 0.21 use
Thread.stop() that throws UnsupportedException in Java 21. The package
now properly runs build time tests, and this exposed the failure. The
new upstream release does not have the problem[22].

[1] https://bugs.launchpad.net/ubuntu/+source/pymatgen/+bug/2067725
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1069219
[3]https://bugs.launchpad.net/ubuntu/+source/bamtools/+bug/2072463
[4] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=987023
[5] https://github.com/pezmaster31/bamtools/issues/235
[6] https://github.com/pezmaster31/bamtools/pull/238
[7] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075990
[8] https://code.launchpad.net/~pushkarnk/ubuntu/+source/aevol/+git/aevol/+merge/468397
[9] https://bugs.launchpad.net/ubuntu/+source/tools-namespace-clojure/+bug/2072709
[10] https://bugs.launchpad.net/ubuntu/+source/mescc-tools/+bug/2072472
[11] https://launchpad.net/bugs/2072795
[12] https://bugs.launchpad.net/ubuntu/+source/vowpal-wabbit/+bug/2072729
[13] https://bugs.launchpad.net/ubuntu/+source/gitaly/+bug/2069200
[14] https://bugs.launchpad.net/debian/+source/facet-analyser/+bug/2072724
[15] https://bugs.launchpad.net/ubuntu/+source/jupyter-ydoc/+bug/2072723
[16] https://bugs.launchpad.net/ubuntu/+source/r-cran-withr/+bug/2072806
[17] https://bugs.launchpad.net/ubuntu/+source/r-cran-withr/+bug/2072807
[18] https://bugs.launchpad.net/ubuntu/+source/r-cran-withr/+bug/2072808
[19] https://bugs.launchpad.net/ubuntu/+source/r-cran-performance/+bug/2072809
[20] https://bugs.launchpad.net/ubuntu/+source/r-cran-withr/+bug/2072810
[21] https://bugs.launchpad.net/ubuntu/+source/r-cran-testthat/+bug/2072812
[22] https://bugs.launchpad.net/bugs/2072898