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
