IQtree failed build time test
Hi,
I intended to upgrade the IQtree Debian package. When trying to build
it some of the build time tests failed. The script
sh example.short
is used to test the functionality. Here is the output:
time sh example.short
Executing tests using /build/iqtree-1.4.2+dfsg/obj-x86_64-linux-gnu/iqtree ...
IQ-TREE version 1.4.2 for Linux 64-bit built Jun 24 2016
Copyright (c) 2011-2015 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.
Host: energija (SSE4.1, 7 GB RAM)
Command: /build/iqtree-1.4.2+dfsg/obj-x86_64-linux-gnu/iqtree -s example.phy
Seed: 318091 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Jun 24 20:00:40 2016
Kernel: SSE3
NOTE: Consider using the multicore version because your CPU has 2 cores!
Reading alignment file example.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 44 sequences with 384 columns and 355 patterns (322 informative sites)
Gap/Ambiguity Composition p-value
1 FL-1-103 19.53% failed 0.00%
2 OSH-1-103 19.53% failed 0.00%
3 CEU-1-103 19.53% failed 0.79%
4 TH-1-103 19.53% failed 0.10%
5 CAa1-103 19.53% failed 0.14%
6 CAb1-103 19.53% failed 0.00%
7 SI-1-103 19.53% failed 0.00%
8 LU-1-103 19.53% failed 0.01%
9 SU-1-103 19.53% failed 0.00%
10 RP-56-175 6.25% failed 4.72%
11 A-14-133 6.25% failed 3.08%
12 PR-57-176 6.25% passed 63.84%
13 PY-61-180 6.25% passed 69.25%
14 MGI-58-176 7.03% failed 0.05%
15 SCR-58-177 6.25% passed 94.64%
16 SA-60-179 6.25% passed 66.43%
17 BR-60-179 6.25% passed 27.40%
18 CPL-58-177 6.25% passed 55.10%
19 LTU-59-178 6.25% passed 28.43%
20 TSP-58-177 6.25% passed 51.74%
21 YBN-56-175 6.25% passed 72.08%
22 AN-56-175 6.25% passed 52.14%
23 HI-60-179 6.25% passed 51.36%
24 ANA-56-175 6.25% passed 88.34%
25 ZE-48-166 7.03% failed 0.05%
26 EAT-48-166 7.03% passed 14.40%
27 YSA-46-164 7.03% passed 6.42%
28 TH-52-170 7.03% passed 20.58%
29 LA-68-186 7.03% passed 10.46%
30 GR-854-978 2.34% failed 0.02%
31 MO-29-154 1.56% failed 0.00%
32 OE-36-161 1.56% passed 15.04%
33 EME-43-168 1.56% failed 1.16%
34 LRE-46-171 1.56% failed 0.00%
35 P6-2-107 17.19% passed 44.21%
36 HO-1-106 17.19% passed 14.57%
37 SP-1-106 17.19% failed 2.41%
38 PA-1-105 17.97% failed 0.00%
39 NE-2-109 15.62% passed 53.11%
40 IFE-2-109 15.62% passed 63.82%
41 HS-9-115 16.41% failed 0.03%
42 RVI-7-114 15.62% failed 0.12%
43 IFE-8-115 15.62% passed 39.01%
44 RVI-5-112 15.62% failed 0.04%
**** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... STACK TRACE FOR DEBUGGING:
1 funcAbort()
2 ()
3 allocateParsimonyDataStructures()
4 pllComputeRandomizedStepwiseAdditionParsimonyTree()
5 IQTree::computeInitialTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, LikelihoodKernel)
6 runTreeReconstruction(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, IQTree&, std::vector<ModelInfo, std::allocator<ModelInfo> >&)
7 runPhyloAnalysis(Params&, Checkpoint*)
8 main()
9 __libc_start_main()
10 _start()
*** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
*** For bug report please send to developers:
*** Log file: example.phy.log
*** Alignment files (if possible)
Command terminated by signal 11
0.00user 0.00system 0:00.01elapsed 57%CPU (0avgtext+0avgdata 6888maxresident)k
152inputs+8outputs (1major+318minor)pagefaults 0swaps
IQ-TREE multicore version 1.4.2 for Linux 64-bit built Jun 24 2016
Copyright (c) 2011-2015 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.
Host: energija (SSE4.1, 7 GB RAM)
Command: /build/iqtree-1.4.2+dfsg/debian/tmp-omp/usr/bin/iqtree-omp -s example.phy -omp 2
Seed: 339079 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Jun 24 20:00:40 2016
Kernel: SSE3 - 2 threads (2 CPU cores detected)
Reading alignment file example.phy ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 44 sequences with 384 columns and 355 patterns (322 informative sites)
Gap/Ambiguity Composition p-value
1 FL-1-103 19.53% failed 0.00%
2 OSH-1-103 19.53% failed 0.00%
3 CEU-1-103 19.53% failed 0.79%
4 TH-1-103 19.53% failed 0.10%
5 CAa1-103 19.53% failed 0.14%
6 CAb1-103 19.53% failed 0.00%
7 SI-1-103 19.53% failed 0.00%
8 LU-1-103 19.53% failed 0.01%
9 SU-1-103 19.53% failed 0.00%
10 RP-56-175 6.25% failed 4.72%
11 A-14-133 6.25% failed 3.08%
12 PR-57-176 6.25% passed 63.84%
13 PY-61-180 6.25% passed 69.25%
14 MGI-58-176 7.03% failed 0.05%
15 SCR-58-177 6.25% passed 94.64%
16 SA-60-179 6.25% passed 66.43%
17 BR-60-179 6.25% passed 27.40%
18 CPL-58-177 6.25% passed 55.10%
19 LTU-59-178 6.25% passed 28.43%
20 TSP-58-177 6.25% passed 51.74%
21 YBN-56-175 6.25% passed 72.08%
22 AN-56-175 6.25% passed 52.14%
23 HI-60-179 6.25% passed 51.36%
24 ANA-56-175 6.25% passed 88.34%
25 ZE-48-166 7.03% failed 0.05%
26 EAT-48-166 7.03% passed 14.40%
27 YSA-46-164 7.03% passed 6.42%
28 TH-52-170 7.03% passed 20.58%
29 LA-68-186 7.03% passed 10.46%
30 GR-854-978 2.34% failed 0.02%
31 MO-29-154 1.56% failed 0.00%
32 OE-36-161 1.56% passed 15.04%
33 EME-43-168 1.56% failed 1.16%
34 LRE-46-171 1.56% failed 0.00%
35 P6-2-107 17.19% passed 44.21%
36 HO-1-106 17.19% passed 14.57%
37 SP-1-106 17.19% failed 2.41%
38 PA-1-105 17.97% failed 0.00%
39 NE-2-109 15.62% passed 53.11%
40 IFE-2-109 15.62% passed 63.82%
41 HS-9-115 16.41% failed 0.03%
42 RVI-7-114 15.62% failed 0.12%
43 IFE-8-115 15.62% passed 39.01%
44 RVI-5-112 15.62% failed 0.04%
**** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... STACK TRACE FOR DEBUGGING:
1 funcAbort()
2 ()
3 allocateParsimonyDataStructures()
4 pllComputeRandomizedStepwiseAdditionParsimonyTree()
5 IQTree::computeInitialTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, LikelihoodKernel)
6 runTreeReconstruction(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, IQTree&, std::vector<ModelInfo, std::allocator<ModelInfo> >&)
7 runPhyloAnalysis(Params&, Checkpoint*)
8 main()
9 __libc_start_main()
10 _start()
*** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
*** For bug report please send to developers:
*** Log file: example.phy.log
*** Alignment files (if possible)
Command terminated by signal 11
0.00user 0.00system 0:00.01elapsed 36%CPU (0avgtext+0avgdata 6984maxresident)k
192inputs+8outputs (1major+329minor)pagefaults 0swaps
Command exited with non-zero status 139
0.00user 0.00system 0:00.05elapsed 20%CPU (0avgtext+0avgdata 6984maxresident)k
416inputs+64outputs (4major+1868minor)pagefaults 0swaps
debian/rules:46: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 139
make[1]: Leaving directory '/build/iqtree-1.4.2+dfsg'
debian/rules:11: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
I: copying local configuration
E: Failed autobuilding of package
W: no hooks of type C found -- ignoring
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
%
28 TH-52-170 7.03% passed 20.58%
29 LA-68-186 7.03% passed 10.46%
30 GR-854-978 2.34% failed 0.02%
31 MO-29-154 1.56% failed 0.00%
32 OE-36-161 1.56% passed 15.04%
33 EME-43-168 1.56% failed 1.16%
34 LRE-46-171 1.56% failed 0.00%
35 P6-2-107 17.19% passed 44.21%
36 HO-1-106 17.19% passed 14.57%
37 SP-1-106 17.19% failed 2.41%
38 PA-1-105 17.97% failed 0.00%
39 NE-2-109 15.62% passed 53.11%
40 IFE-2-109 15.62% passed 63.82%
41 HS-9-115 16.41% failed 0.03%
42 RVI-7-114 15.62% failed 0.12%
43 IFE-8-115 15.62% passed 39.01%
44 RVI-5-112 15.62% failed 0.04%
**** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... STACK TRACE FOR DEBUGGING:
1 funcAbort()
2 ()
3 allocateParsimonyDataStructures()
4 pllComputeRandomizedStepwiseAdditionParsimonyTree()
5 IQTree::computeInitialTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, LikelihoodKernel)
6 runTreeReconstruction(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, IQTree&, std::vector<ModelInfo, std::allocator<ModelInfo> >&)
7 runPhyloAnalysis(Params&, Checkpoint*)
8 main()
9 __libc_start_main()
10 _start()
*** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
*** For bug report please send to developers:
*** Log file: example.phy.log
*** Alignment files (if possible)
Command terminated by signal 11
0.00user 0.00system 0:00.01elapsed 36%CPU (0avgtext+0avgdata 6984maxresident)k
192inputs+8outputs (1major+329minor)pagefaults 0swaps
Command exited with non-zero status 139
0.00user 0.00system 0:00.05elapsed 20%CPU (0avgtext+0avgdata 6984maxresident)k
416inputs+64outputs (4major+1868minor)pagefaults 0swaps
debian/rules:46: recipe for target 'override_dh_auto_test' failed
Do you have any idea what might be wrong here?
Kind regards
Andreas.
--
http://fam-tille.de
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