[Debian-med-packaging] Bug#1008252: salmon: FTBFS in unstable and testing

[Graham Inggs]

Source: salmon
Version: 1.6.0+ds1-1
Severity: serious
Tags: ftbfs

Hi Maintainer

Since sometime around the end of January, salmon started to FTBFS in
unstable and testing [1].  I've copied what I hope is the relevant
part of the log below.

Regards
Graham


[1] https://tests.reproducible-builds.org/debian/rb-pkg/salmon.html


test 1
    Start 1: unit_tests

1: Test command: /usr/bin/cmake
"-DTOPLEVEL_DIR=/build/1st/salmon-1.6.0+ds1" "-P"
"/build/1st/salmon-1.6.0+ds1/cmake/UnitTests.cmake"
1: Test timeout computed to be: 10000000
1: -- For unit tests, will set working directory to
/build/1st/salmon-1.6.0+ds1/tests
1: ===============================================================================
1: All tests passed (2008800 assertions in 4 test cases)
1:
1/2 Test #1: unit_tests .......................   Passed    0.37 sec
test 2
    Start 2: salmon_read_test_quasi

2: Test command: /usr/bin/cmake
"-DTOPLEVEL_DIR=/build/1st/salmon-1.6.0+ds1" "-P"
"/build/1st/salmon-1.6.0+ds1/cmake/TestSalmonQuasi.cmake"
2: Test timeout computed to be: 10000000
2: sample_data/
2: sample_data/reads_2.fastq
2: sample_data/sample_alignments.bam
2: sample_data/transcripts.fasta
2: sample_data/reads_1.fastq
2: index ["sample_salmon_quasi_index"] did not previously exist  . . .
creating it
2: [2022-03-23 05:24:43.592] [jLog] [warning] The salmon index is
being built without any decoy sequences.  It is recommended that decoy
sequence (either computed auxiliary decoy sequence or the genome of
the organism) be provided during indexing. Further details can be
found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
2: [2022-03-23 05:24:43.592] [jLog] [info] building index
2: out : sample_salmon_quasi_index
2: [2022-03-23 05:24:43.592] [puff::index::jointLog] [info] Running fixFasta
2:
2: [Step 1 of 4] : counting k-mers
2:
2: [2022-03-23 05:24:43.596] [puff::index::jointLog] [info] Replaced 0
non-ATCG nucleotides
2: [2022-03-23 05:24:43.596] [puff::index::jointLog] [info] Clipped
poly-A tails from 0 transcripts
2: wrote 15 cleaned references
2: CMake Error at
/build/1st/salmon-1.6.0+ds1/cmake/TestSalmonQuasi.cmake:17 (message):
2:   Error running
2:
2:
2/2 Test #2: salmon_read_test_quasi ...........***Failed    0.07 sec
sample_data/
sample_data/reads_2.fastq
sample_data/sample_alignments.bam
sample_data/transcripts.fasta
sample_data/reads_1.fastq
index ["sample_salmon_quasi_index"] did not previously exist  . . . creating it
[2022-03-23 05:24:43.592] [jLog] [warning] The salmon index is being
built without any decoy sequences.  It is recommended that decoy
sequence (either computed auxiliary decoy sequence or the genome of
the organism) be provided during indexing. Further details can be
found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2022-03-23 05:24:43.592] [jLog] [info] building index
out : sample_salmon_quasi_index
[2022-03-23 05:24:43.592] [puff::index::jointLog] [info] Running fixFasta

[Step 1 of 4] : counting k-mers

[2022-03-23 05:24:43.596] [puff::index::jointLog] [info] Replaced 0
non-ATCG nucleotides
[2022-03-23 05:24:43.596] [puff::index::jointLog] [info] Clipped
poly-A tails from 0 transcripts
wrote 15 cleaned references
CMake Error at /build/1st/salmon-1.6.0+ds1/cmake/TestSalmonQuasi.cmake:17
(message):
  Error running




50% tests passed, 1 tests failed out of 2

Total Test time (real) =   0.44 sec

The following tests FAILED:
 2 - salmon_read_test_quasi (Failed)
Errors while running CTest
make[2]: *** [Makefile:94: test] Error 8