[Debian-med-packaging] Bug#1078860: unifrac-tools: FTBFS against HDF5 1.14

[Gilles Filippini]

Source: unifrac-tools
Version: 1.4-3
Severity: important

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Hi,

The unifrac-tools package fails to build from source in a test rebuild against
hdf5 1.14 currently in experimental. The failure occurs during the
post-build tests.

Here is the related exerpt from the log:

   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/unifrac-tools-tWlv7l/unifrac-tools-1.4'
export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/build/unifrac-tools-tWlv7l/unifrac-tools-1.4/debian/tmp/usr/bin ; \
cd ci ; \
./crawford_test.sh
HDF5-DIAG: Error detected in HDF5 (1.14.4-3) thread 1:
  #000: ../../../src/H5D.c line 403 in H5Dopen2(): unable to synchronously open dataset
    major: Dataset
    minor: Can't open object
  #001: ../../../src/H5D.c line 359 in H5D__open_api_common(): can't set object access arguments
    major: Dataset
    minor: Can't set value
  #002: ../../../src/H5VLint.c line 2602 in H5VL_setup_acc_args(): invalid location identifier
    major: Invalid arguments to routine
    minor: Inappropriate type
  #003: ../../../src/H5VLint.c line 1733 in H5VL_vol_object(): invalid identifier
    major: Invalid arguments to routine
    minor: Inappropriate type
terminate called after throwing an instance of 'H5::FileIException'
./crawford_test.sh: line 12: 61153 Aborted                 ssu -i crawford.biom -t crawford.tre -o test.dm -m unweighted
make[1]: *** [debian/rules:21: override_dh_auto_test] Error 134


Full build log attached.

Best,
_g.


- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-21-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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