Hi Tung, I've attached the full build log of the Debian package.
Hope this helps
Andreas.
On Mon, Jun 27, 2016 at 09:55:06AM +0000, Tung Nguyen wrote:
> Dear Andreas,
>
> Could you provide us the gcc version and flags that were used for build?
> Currently we have no idea what might have went wrong. On our system,
> everything works fine.
>
> Cheers
> Tung
>
> On Fri, Jun 24, 2016 at 10:19 PM Andreas Tille <andr...@an3as.eu> wrote:
>
> > 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
> >
--
http://fam-tille.de
iqtree_1.4.2+dfsg-1_amd64.build.gz
Description: application/gzip
