Your message dated Tue, 08 Jan 2019 16:04:01 +0000 with message-id <e1ggtrf-000btu...@fasolo.debian.org> and subject line Bug#918575: fixed in abyss 2.1.5-2 has caused the Debian Bug report #918575, regarding abyss FTBFS on 32bit big endian: test failures to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 918575: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=918575 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: abyss Version: 2.1.1-1 Severity: serious Tags: ftbfs https://buildd.debian.org/status/package.php?p=abyss ... FAIL: common_kmer ================= Running main() from gtest_main.cc [==========] Running 1 test from 1 test case. [----------] Global test environment set-up. [----------] 1 test from Kmer [ RUN ] Kmer.canonicalize Common/KmerTest.cpp:18: Failure Value of: kmer Actual: AGGC Expected: canonical Which is: ATGC Common/KmerTest.cpp:30: Failure Value of: kmer Actual: TTCGG Expected: oddLengthCanonical Which is: CGAGC [ FAILED ] Kmer.canonicalize (0 ms) [----------] 1 test from Kmer (1 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test case ran. (1 ms total) [ PASSED ] 0 tests. [ FAILED ] 1 test, listed below: [ FAILED ] Kmer.canonicalize 1 FAILED TEST FAIL common_kmer (exit status: 1) FAIL: BloomFilter ================= Running main() from gtest_main.cc [==========] Running 8 tests from 2 test cases. [----------] Global test environment set-up. [----------] 6 tests from BloomFilter [ RUN ] BloomFilter.base Konnector/BloomFilter.cc:30: Failure Value of: x[b] Actual: false Expected: true Konnector/BloomFilter.cc:31: Failure Value of: x[Bloom::hash(b) % x.size()] Actual: false Expected: true Konnector/BloomFilter.cc:34: Failure Value of: x[c] Actual: false Expected: true Konnector/BloomFilter.cc:35: Failure Value of: x[Bloom::hash(c) % x.size()] Actual: false Expected: true [ FAILED ] BloomFilter.base (0 ms) [ RUN ] BloomFilter.serialization Konnector/BloomFilter.cc:55: Failure Value of: origBloom[b] Actual: false Expected: true Konnector/BloomFilter.cc:56: Failure Value of: origBloom[c] Actual: false Expected: true Konnector/BloomFilter.cc:73: Failure Value of: copyBloom[b] Actual: false Expected: true Konnector/BloomFilter.cc:74: Failure Value of: copyBloom[c] Actual: false Expected: true [ FAILED ] BloomFilter.serialization (1 ms) [ RUN ] BloomFilter.union_ Konnector/BloomFilter.cc:92: Failure Value of: bloom2[b] Actual: false Expected: true Konnector/BloomFilter.cc:109: Failure Value of: unionBloom[b] Actual: false Expected: true [ FAILED ] BloomFilter.union_ (0 ms) [ RUN ] BloomFilter.intersect Konnector/BloomFilter.cc:132: Failure Value of: bloom2[b] Actual: false Expected: true [ FAILED ] BloomFilter.intersect (0 ms) [ RUN ] BloomFilter.windowSerialization [ OK ] BloomFilter.windowSerialization (0 ms) [ RUN ] BloomFilter.windowUnion [ OK ] BloomFilter.windowUnion (0 ms) [----------] 6 tests from BloomFilter (1 ms total) [----------] 2 tests from CascadingBloomFilter [ RUN ] CascadingBloomFilter.base Konnector/BloomFilter.cc:178: Failure Value of: 2U Actual: 2 Expected: x.popcount() Which is: 1 Konnector/BloomFilter.cc:179: Failure Value of: x[b] Actual: false Expected: true Konnector/BloomFilter.cc:180: Failure Value of: x[Bloom::hash(b) % x.size()] Actual: false Expected: true Konnector/BloomFilter.cc:182: Failure Value of: 3U Actual: 3 Expected: x.popcount() Which is: 1 Konnector/BloomFilter.cc:183: Failure Value of: x[c] Actual: false Expected: true [ FAILED ] CascadingBloomFilter.base (1 ms) [ RUN ] CascadingBloomFilter.window [ OK ] CascadingBloomFilter.window (0 ms) [----------] 2 tests from CascadingBloomFilter (1 ms total) [----------] Global test environment tear-down [==========] 8 tests from 2 test cases ran. (2 ms total) [ PASSED ] 3 tests. [ FAILED ] 5 tests, listed below: [ FAILED ] BloomFilter.base [ FAILED ] BloomFilter.serialization [ FAILED ] BloomFilter.union_ [ FAILED ] BloomFilter.intersect [ FAILED ] CascadingBloomFilter.base 5 FAILED TESTS FAIL BloomFilter (exit status: 1) FAIL: Konnector_DBGBloomAlgorithms ================================== Running main() from gtest_main.cc [==========] Running 8 tests from 2 test cases. [----------] Global test environment set-up. [----------] 4 tests from GetStartKmerPosTest [ RUN ] GetStartKmerPosTest.FullReadMatch [ OK ] GetStartKmerPosTest.FullReadMatch (0 ms) [ RUN ] GetStartKmerPosTest.FullReadMismatch [ OK ] GetStartKmerPosTest.FullReadMismatch (1 ms) [ RUN ] GetStartKmerPosTest.NumMatchesThreshold Konnector/DBGBloomAlgorithmsTest.cpp:85: Failure Value of: getStartKmerPos(testRead, k, FORWARD, g, numMatchesThreshold) Actual: 3 Expected: 5U Which is: 5 [ FAILED ] GetStartKmerPosTest.NumMatchesThreshold (1 ms) [ RUN ] GetStartKmerPosTest.EqualLengthMatchRegions Konnector/DBGBloomAlgorithmsTest.cpp:126: Failure Value of: getStartKmerPos(testRead, k, FORWARD, g, numMatchesThreshold) Actual: 1 Expected: 4U Which is: 4 [ FAILED ] GetStartKmerPosTest.EqualLengthMatchRegions (0 ms) [----------] 4 tests from GetStartKmerPosTest (2 ms total) [----------] 4 tests from CorrectSingleBaseErrorTest [ RUN ] CorrectSingleBaseErrorTest.SingleError Konnector/DBGBloomAlgorithmsTest.cpp:166: Failure Value of: success Actual: false Expected: true [ FAILED ] CorrectSingleBaseErrorTest.SingleError (1 ms) [ RUN ] CorrectSingleBaseErrorTest.ReverseComplement Konnector/DBGBloomAlgorithmsTest.cpp:181: Failure Value of: success Actual: false Expected: true [ FAILED ] CorrectSingleBaseErrorTest.ReverseComplement (1 ms) [ RUN ] CorrectSingleBaseErrorTest.NoError [ OK ] CorrectSingleBaseErrorTest.NoError (1 ms) [ RUN ] CorrectSingleBaseErrorTest.SkipFalsePositive Konnector/DBGBloomAlgorithmsTest.cpp:208: Failure Value of: success Actual: false Expected: true [ FAILED ] CorrectSingleBaseErrorTest.SkipFalsePositive (1 ms) [----------] 4 tests from CorrectSingleBaseErrorTest (4 ms total) [----------] Global test environment tear-down [==========] 8 tests from 2 test cases ran. (7 ms total) [ PASSED ] 3 tests. [ FAILED ] 5 tests, listed below: [ FAILED ] GetStartKmerPosTest.NumMatchesThreshold [ FAILED ] GetStartKmerPosTest.EqualLengthMatchRegions [ FAILED ] CorrectSingleBaseErrorTest.SingleError [ FAILED ] CorrectSingleBaseErrorTest.ReverseComplement [ FAILED ] CorrectSingleBaseErrorTest.SkipFalsePositive 5 FAILED TESTS FAIL Konnector_DBGBloomAlgorithms (exit status: 1) FAIL: Konnector_konnector ========================= Running main() from gtest_main.cc [==========] Running 3 tests from 2 test cases. [----------] Global test environment set-up. [----------] 2 tests from maskNew [ RUN ] maskNew.read1 ACGTACGTa [ OK ] maskNew.read1 (0 ms) [ RUN ] maskNew.mask [ OK ] maskNew.mask (0 ms) [----------] 2 tests from maskNew (0 ms total) [----------] 1 test from ConnectPairsTest [ RUN ] ConnectPairsTest.MergeOverlappingPair Konnector/konnectorTest.cpp:72: Failure Value of: result.pathResult Actual: 6 Expected: FOUND_PATH Which is: 0 Konnector/konnectorTest.cpp:73: Failure Value of: result.mergedSeqs.size() Actual: 0 Expected: 1u Which is: 1 [ FAILED ] ConnectPairsTest.MergeOverlappingPair (0 ms) [----------] 1 test from ConnectPairsTest (0 ms total) [----------] Global test environment tear-down [==========] 3 tests from 2 test cases ran. (1 ms total) [ PASSED ] 2 tests. [ FAILED ] 1 test, listed below: [ FAILED ] ConnectPairsTest.MergeOverlappingPair 1 FAILED TEST FAIL Konnector_konnector (exit status: 1) FAIL: PairedDBG_LoadAlgorithm ============================= Running main() from gtest_main.cc [==========] Running 1 test from 1 test case. [----------] Global test environment set-up. [----------] 1 test from LoadAlgorithmTest [ RUN ] LoadAlgorithmTest.base PairedDBG/LoadAlgorithmTest.cpp:48: Failure Value of: expectedKmerPairs.find(kmerPair) != expectedKmerPairs.end() Actual: false Expected: true [ FAILED ] LoadAlgorithmTest.base (1242 ms) [----------] 1 test from LoadAlgorithmTest (1243 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test case ran. (1243 ms total) [ PASSED ] 0 tests. [ FAILED ] 1 test, listed below: [ FAILED ] LoadAlgorithmTest.base 1 FAILED TEST FAIL PairedDBG_LoadAlgorithm (exit status: 1) FAIL: PairedDBG_KmerPair ======================== Running main() from gtest_main.cc [==========] Running 5 tests from 1 test case. [----------] Global test environment set-up. [----------] 5 tests from KmerPair [ RUN ] KmerPair.constructors [ OK ] KmerPair.constructors (0 ms) [ RUN ] KmerPair.str [ OK ] KmerPair.str (0 ms) [ RUN ] KmerPair.reverseComplement PairedDBG/KmerPairTest.cc:52: Failure Value of: reverseComplement(k) Actual: ACCAATTG-ACCAATTG Expected: rck Which is: ACGTACGT-CCAAGGTT PairedDBG/KmerPairTest.cc:54: Failure Value of: k Actual: ACGAGAAA-ACGAGAAA Expected: rck Which is: ACGTACGT-CCAAGGTT [ FAILED ] KmerPair.reverseComplement (1 ms) [ RUN ] KmerPair.isPalindrome PairedDBG/KmerPairTest.cc:64: Failure Value of: reverseComplement(kp) Actual: ACGCTGTG-ACGCTGTG Expected: kp Which is: AACCTTGG-CCAAGGTT PairedDBG/KmerPairTest.cc:65: Failure Value of: kp.isPalindrome() Actual: false Expected: true PairedDBG/KmerPairTest.cc:69: Failure Value of: k.isPalindrome() Actual: false Expected: true PairedDBG/KmerPairTest.cc:71: Failure Value of: k.isPalindrome() Actual: false Expected: true [ FAILED ] KmerPair.isPalindrome (0 ms) [ RUN ] KmerPair.isPalindrome_edge PairedDBG/KmerPairTest.cc:86: Failure Value of: kp.isPalindrome(SENSE) Actual: false Expected: true [ FAILED ] KmerPair.isPalindrome_edge (0 ms) [----------] 5 tests from KmerPair (1 ms total) [----------] Global test environment tear-down [==========] 5 tests from 1 test case ran. (1 ms total) [ PASSED ] 2 tests. [ FAILED ] 3 tests, listed below: [ FAILED ] KmerPair.reverseComplement [ FAILED ] KmerPair.isPalindrome [ FAILED ] KmerPair.isPalindrome_edge 3 FAILED TESTS FAIL PairedDBG_KmerPair (exit status: 1) ============================================================================ Testsuite summary for ABySS 2.1.5 ============================================================================ # TOTAL: 32 # PASS: 26 # SKIP: 0 # XFAIL: 0 # FAIL: 6 # XPASS: 0 # ERROR: 0 ============================================================================ See Unittest/test-suite.log Please report to abyss-us...@bcgsc.ca ============================================================================ make[4]: *** [Makefile:1662: test-suite.log] Error 1 (powerpcspe builds with nocheck)
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--- Begin Message ---Source: abyss Source-Version: 2.1.5-2 We believe that the bug you reported is fixed in the latest version of abyss, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 918...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated abyss package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Tue, 08 Jan 2019 15:53:09 +0100 Source: abyss Binary: abyss Architecture: source Version: 2.1.5-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 918575 Changes: abyss (2.1.5-2) unstable; urgency=medium . * Restrict set of architectures to those where package is known to build (or never was successfully build) Closes: #918575 * Standards-Version: 4.3.0 Checksums-Sha1: 0323fdd3e3022fc76c17b70c6b512bed2a7cdc3d 2301 abyss_2.1.5-2.dsc 23f52bec34dfe5bfbc79ceb017defa7690194867 756936 abyss_2.1.5-2.debian.tar.xz Checksums-Sha256: e86dd29b546c544eb8e80add3e8469dbd0cb4329486d2df2e9a84c1fe57a6384 2301 abyss_2.1.5-2.dsc e558fc49dc1ab57b3d89be0b4c5161b6e344a66f5924ec511356d5914fa46300 756936 abyss_2.1.5-2.debian.tar.xz Files: a03ae547b8ed8beaaf014a07cf292550 2301 science optional abyss_2.1.5-2.dsc 038ddd2534cecbfd87126d919e53424d 756936 science optional abyss_2.1.5-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlw0u4ERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH3Aw//bol1xxtG2Ty/Twfg+ouFvOIunMjLBAX3 1wbF21kdp84+nIXh+Rx+kavub9amJ7Jfyg/VtvARlerym0k9pcJ4LPjJG83E12tv Ce0agYEoQCy7MFTK8kYTRJOLCzh/UI5Zt6b/F3t+FPyvniqc+1IcLCnkow52znGd xJujz1Gmk1EX2+72E342mukqtBu4xXDe/dJItvwfZ+VqEOIdWDa6PsnqCDCQ+/SL x7O7biolkEGfFw9dKFF6iRJQbFf613wr68kvkI0Y2+Wm2qHozkkFUE/qPGZg5QHw CdkLDapHClMz4kPLBcUwrS3uAuerIH585ny4a1Frw6IE0mCoazH7dNaiZbhTnfXk 3rKipgpB0B2ZMiUZG77JKDTFCNQGOjWZfCJVJNh+1XTqcG3hNm0npksPVV+rifHZ edmU5qSvzAbQaMLK9UC+wJP1N6eXL3Fhozd9ii54ecZ/Lo6uORjKVpCaYcBpnUQ/ pkVBJV1Zpxmoeu8rLe3mzlgPtlDF940WN80XkaYwsyZdCSWlY5RzYrIsTcKjiwZc nDu14/8WOXnQsr2GTjjb/gc42Hohh7kOewH7+plmUWVg2IHeEE7vZvcoGwaeRXvj i0cqEI+Yu6oDAypW0n5fyLe9q7Kg8zXqAMLzJC2jwj6BZBc1R53FPXPjJS0GAcB7 HgcOul0RxZQ= =lIVq -----END PGP SIGNATURE-----
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