Package: src:bali-phy
Version: 3.4+dfsg-1
Severity: important
Hi!
I've been doing a full rebuild of the Debian archive, building all
source packages targeting armel and armhf using arm64 hardware. We are
planning in future to move all of our 32-bit armel/armhf builds to
using arm64 machines, so this rebuild is to identify packages that
might have problems with this configuration.
I've tried to build bali-phy for armhf on top of arm64, and it's
failing a test at the end of the build:
...
dh_auto_test -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 ninja
test
[1/4] Generating git-version.h with a custom command.
[1/2] Running all tests.
1/30 bali-phy version OK 0.04 s
2/30 bali-phy help OK 0.04 s
3/30 bali-phy 5d test OK 3.61 s
4/30 bali-phy 5d +A 50 OK 17.14 s
5/30 bali-phy 5d -A 200 FAIL 7.87 s (exit status 1)
6/30 model_P --help OK 0.04 s
7/30 statreport --help OK 0.03 s
8/30 stats-select --help OK 0.04 s
9/30 alignment-gild --help OK 0.01 s
10/30 alignment-consensus --help OK 0.01 s
11/30 alignment-max --help OK 0.01 s
12/30 alignment-chop-internal --help OK 0.03 s
13/30 alignment-indices --help OK 0.01 s
14/30 alignment-info --help OK 0.01 s
15/30 alignment-cat --help OK 0.01 s
16/30 alignment-translate --help OK 0.02 s
17/30 alignment-find --help OK 0.02 s
18/30 trees-consensus --help OK 0.02 s
19/30 tree-mean-lengths --help OK 0.01 s
20/30 mctree-mean-lengths --help OK 0.01 s
21/30 trees-to-SRQ --help OK 0.01 s
22/30 pickout --help OK 0.01 s
23/30 cut-range --help OK 0.01 s
24/30 trees-distances --help OK 0.01 s
25/30 alignment-thin --help OK 0.01 s
26/30 alignments-diff --help OK 0.01 s
27/30 tree-tool --help OK 0.01 s
28/30 alignment-distances --help OK 0.01 s
29/30 subsample --help OK 0.02 s
30/30 bali-phy testsuite OK 272.10 s
Ok: 29
Expected Fail: 0
Fail: 1
Unexpected Pass: 0
Skipped: 0
Timeout: 0
The output from the failed tests:
5/30 bali-phy 5d -A 200 FAIL 7.87 s (exit status 1)
--- command ---
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta
--iter=200
--package-path=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/builtins:/<<PKGBUILDDIR>>
-Inone
--- stdout ---
T:topology ~ uniform on tree topologies
T:lengths ~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]
Partition P1:
file =
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta
alphabet = DNA
subst = tn93 (S1)
indel = none
scale ~ gamma[0.5,2] (Scale1)
Substitution model S1 priors:
tn93:kappaPur ~ log_normal[log[2],0.25]
tn93:kappaPyr ~ log_normal[log[2],0.25]
tn93:pi ~ dirichlet_on[letters[@a],1]
Beginning pre-burnin: 3 iterations.
Start #1 prior = 2.85078 likelihood = -1171.56 |T| = 0.468531 |A| =
110 Scale1*|T| = 0.80032
Tree (S)ize #1 prior = 2.21294 likelihood = -1097.14 |T| = 0.448637
|A| = 110 Scale1*|T| = 1.30021
Tree (S)ize #2 prior = -13.3031 likelihood = -1001.31 |T| = 0.572728
|A| = 110 Scale1*|T| = 16.6362
Tree (S)ize #3 prior = -12.5843 likelihood = -999.563 |T| = 0.738133
|A| = 110 Scale1*|T| = 18.3298
(S)+Branch (L)engths #1 prior = -8.39757 likelihood = -984.367 |T| =
1.63073 |A| = 110 Scale1*|T| = 6.22256
(S)+Branch (L)engths #2 prior = -15.5928 likelihood = -943.676 |T| =
3.95652 |A| = 110 Scale1*|T| = 13.9505
(S)+Branch (L)engths #3 prior = -6.1693 likelihood = -933.719 |T| =
1.54154 |A| = 110 Scale1*|T| = 6.65305
(S)+(L)+(P)arameters #1 prior = -6.85447 likelihood = -820.042 |T| =
0.83291 |A| = 110 Scale1*|T| = 7.19549
(S)+(L)+(P)arameters #2 prior = -13.9795 likelihood = -804.932 |T| =
2.52913 |A| = 110 Scale1*|T| = 14.9393
(S)+(L)+(P)arameters #3 prior = -14.8455 likelihood = -804.004 |T| =
1.78642 |A| = 110 Scale1*|T| = 11.4421
(S)+(L)+(P)+NNI #1 prior = -14.7193 likelihood = -800.519 |T| = 1.80833
|A| = 110 Scale1*|T| = 11.1644
(S)+(L)+(P)+NNI #2 prior = -14.8403 likelihood = -794.947 |T| = 1.29684
|A| = 110 Scale1*|T| = 8.27748
(S)+(L)+(P)+NNI #3 prior = -18.6064 likelihood = -794.606 |T| = 1.68838
|A| = 110 Scale1*|T| = 6.26695
(S)+(L)+(P)+NNI #4 prior = -17.5519 likelihood = -796.853 |T| = 1.68336
|A| = 110 Scale1*|T| = 5.20335
SPR #1 prior = -17.4975 likelihood = -795.163 |T| = 1.47967 |A| = 110
Scale1*|T| = 4.62688
(S)+(L)+(P)+NNI #1 prior = -14.4695 likelihood = -797.104 |T| = 1.03049
|A| = 110 Scale1*|T| = 4.62992
(S)+(L)+(P)+NNI #2 prior = -17.9617 likelihood = -791.809 |T| = 2.04283
|A| = 110 Scale1*|T| = 8.75168
(S)+(L)+(P)+NNI #3 prior = -17.1506 likelihood = -788.311 |T| = 0.917332
|A| = 110 Scale1*|T| = 8.90935
Finished pre-burnin in 0.26 seconds.
BAli-Phy does NOT detect how many iterations is sufficient:
You need to monitor convergence and kill it when done.
Maximum number of iterations set to 200.
Beginning MCMC computations.
- Future screen output sent to '5d-1/C1.out'
- Future debugging output sent to '5d-1/C1.err'
- Sampled trees logged to '5d-1/C1.trees'
- Sampled alignments logged to '5d-1/C1.P<partition>.fastas'
- Run info written to '5d-1/C1.run.json'
- Sampled numerical parameters logged to '5d-1/C1.log'
You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the
BEAST program Tracer (graphical).
See the manual at http://www.bali-phy.org/README.xhtml for further information.
--- stderr ---
Home directory '/sbuild-nonexistent' does not exist!
Partition #1: 126 columns -> 110 unique patterns.
Created directory '5d-1/' for output files.
bali-phy: Error! move = sampler
submove = tree
move = tree
submove = topology
move = topology
submove = SPR
move = SPR
submove = SPR_all
[single] move = SPR_all
bool sample_SPR_search_one(Parameters&, MCMC::MoveStats&, const tree_edge&,
const spr_range&, bool)int choose_MH(int, const std::vector<T>&) [with F =
log_double_t]:
No option chosen! (current = 0)
*log(Pr[0]) = nan
log(Pr[1]) = nan
log(Pr[2]) = nan
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN16choose_exceptionI12log_double_tEC2EiRKSt6vectorIS0_SaIS0_EE+0xccb)
[0xc09a3c]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_Z9choose_MHI12log_double_tEiiRKSt6vectorIT_SaIS2_EE+0xa0d)
[0xc3ecce]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeRKSt3mapIS4_bSt4lessIS4_ESaISt4pairIS5_bEEEb+0x513)
[0xc7ceb4]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeb+0x3d)
[0xc7dc86]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_Z14sample_SPR_allR9owned_ptrI5ModelERN4MCMC9MoveStatsE+0x7b)
[0xc7e78c]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC10SingleMove7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x39)
[0xc01c76]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x43)
[0xc01d80]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x43)
[0xc01d80]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x43)
[0xc01d80]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x43)
[0xc01d80]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC7Sampler2goER9owned_ptrI5ModelEiiRSo+0x2ab)
[0xc03818]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(_Z11do_samplingRKN5boost15program_options13variables_mapER9owned_ptrI5ModelElRSoRKSt6vectorISt8functionIFvRKS5_lEESaISE_EE+0xa2f)
[0xcbfe68]
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/bali-phy(main+0x1b31) [0xb99f5a]
/lib/arm-linux-gnueabihf/libc.so.6(__libc_start_main+0x97) [0xf6cef4e4]
-------
In fact, checking I can see that the buildd arm-arm-01 (also an arm64
host configured to build armhf) fails in the same way. See
https://buildd.debian.org/status/fetch.php?pkg=bali-phy&arch=armhf&ver=3.4%2Bdfsg-1&stamp=1544787942&raw=0
for the build log. Oddly, I'm not seeing any similar problems
building/testing for armel on top of arm64...
-- System Information:
Debian Release: 9.6
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable-debug'), (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-8-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8),
LANGUAGE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
