[Debian-med-packaging] Bug#918575: abyss FTBFS on 32bit big endian: test failures
Adrian Bunk
bunk at debian.org
Mon Jan 7 13:59:47 GMT 2019
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-users at bcgsc.ca
============================================================================
make[4]: *** [Makefile:1662: test-suite.log] Error 1
(powerpcspe builds with nocheck)
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