Your message dated Sat, 11 Feb 2017 13:18:42 +0000
with message-id <e1ccxza-000aaj...@fasolo.debian.org>
and subject line Bug#854500: fixed in iqtree 1.5.3+dfsg-2
has caused the Debian Bug report #854500,
regarding iqtree: FTBFS on single-CPU machines (ERROR: You have specified more
threads than CPU cores available)
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.)
--
854500: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854500
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:iqtree
Version: 1.5.3+dfsg-1
Severity: serious
Dear maintainer:
I tried to build this package in stretch with "dpkg-buildpackage -B"
but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/iqtree-1.5.3+dfsg'
dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp"
cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc
-DCMAKE_INSTALL_LOCALSTATEDIR=/var -DIQTREE_FLAGS=omp
-- The C compiler identification is GNU 6.3.0
-- The CXX compiler identification is GNU 6.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
[... snipped ...]
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -23117.037
Optimal log-likelihood: -23117.034
Rate parameters: A-C: 1.000 A-G: 2.440 A-T: 1.000 C-G: 1.000 C-T: 2.440
G-T: 1.000
Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225
Parameters optimization took 1 rounds (0.013 sec)
BEST SCORE FOUND : -23117.034
Total tree length: 2.805
Total number of iterations: 102
CPU time used for tree search: 9.360 sec (0h:0m:9s)
Wall-clock time used for tree search: 9.601 sec (0h:0m:9s)
Total CPU time used: 9.492 sec (0h:0m:9s)
Total wall-clock time used: 9.763 sec (0h:0m:9s)
Analysis results written to:
IQ-TREE report: example.phy.iqtree
Maximum-likelihood tree: example.phy.treefile
Likelihood distances: example.phy.mldist
Screen log file: example.phy.log
Date and Time: Tue Jan 31 06:15:04 2017
9.50user 0.09system 0:09.79elapsed 97%CPU (0avgtext+0avgdata 8292maxresident)k
536inputs+88outputs (0major+719minor)pagefaults 0swaps
IQ-TREE multicore version 1.5.3 for Linux 64-bit built Jan 19 2017
Copyright (c) 2011-2016 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and
Bui Quang Minh.
Host: leaseweb1 (SSE3, 0 GB RAM)
Command: /<<BUILDDIR>>/iqtree-1.5.3+dfsg/build.omp/iqtree-omp -s example.phy
-omp 2 -redo
Seed: 870150 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Tue Jan 31 06:15:04 2017
Kernel: SSE3 - 2 threads(1 CPU cores detected)
ERROR: You have specified more threads than CPU cores available
Command exited with non-zero status 2
0.00user 0.00system 0:00.04elapsed 17%CPU (0avgtext+0avgdata 5124maxresident)k
2528inputs+8outputs (11major+251minor)pagefaults 0swaps
Command exited with non-zero status 2
9.51user 0.11system 0:09.97elapsed 96%CPU (0avgtext+0avgdata 8292maxresident)k
5040inputs+176outputs (16major+2178minor)pagefaults 0swaps
debian/rules:58: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/iqtree-1.5.3+dfsg'
debian/rules:12: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
To reproduce, please try using sbuild on a single CPU virtual machine,
because that was actually what I was doing and the error message speaks
by itself:
ERROR: You have specified more threads than CPU cores available
I think the following changelog entry may be related:
* Enable build of MPI-parallelised executable
I guess you could always disable such change so that the package
builds everywhere again (multi-core is not part of build-essential
definition).
Thanks.
--- End Message ---
--- Begin Message ---
Source: iqtree
Source-Version: 1.5.3+dfsg-2
We believe that the bug you reported is fixed in the latest version of
iqtree, 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 854...@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 iqtree 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: Sat, 11 Feb 2017 12:52:45 +0100
Source: iqtree
Binary: iqtree
Architecture: source amd64
Version: 1.5.3+dfsg-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:
iqtree - efficient phylogenetic software by maximum likelihood
Closes: 854500
Changes:
iqtree (1.5.3+dfsg-2) unstable; urgency=medium
.
[ Roger Shimizu ]
* debian/rules:
- Run dh_auto_test only if CPUs >= 2 (Closes: #854500).
.
[ Andreas Tille ]
* Implement remarks given by upstream
(https://github.com/Cibiv/IQ-TREE/issues/17)
Checksums-Sha1:
568e9c727c1c544a33b8b0580ced886600c8b0a8 2180 iqtree_1.5.3+dfsg-2.dsc
04de99c21d368dec2921dbaba9d66621191a9adc 19016
iqtree_1.5.3+dfsg-2.debian.tar.xz
cb455e8df1d8d769b631637bf87b2a658b0a49fe 34975624
iqtree-dbgsym_1.5.3+dfsg-2_amd64.deb
f271df2071b0bcb98d899e4687adb92ee38393c2 6473
iqtree_1.5.3+dfsg-2_amd64.buildinfo
9ac3fb73f926270957ab2a026d4ea32590b4ef45 2489136 iqtree_1.5.3+dfsg-2_amd64.deb
Checksums-Sha256:
0cddbb6f0ecb89a5891c732999a40a4b6d6aa77bed121a202bf192760ba405e3 2180
iqtree_1.5.3+dfsg-2.dsc
d63ddaef7591f4c08f797983ee3374844ce630aa03aecbff8dce55c5559f212e 19016
iqtree_1.5.3+dfsg-2.debian.tar.xz
1f20effce7597e882c05fa3c7330591e453da96de86c736c3618257d4f3cb24e 34975624
iqtree-dbgsym_1.5.3+dfsg-2_amd64.deb
f8f32028efaa3f48de705e93666fce96808e6ec0f2f827eec35f135e797b6d73 6473
iqtree_1.5.3+dfsg-2_amd64.buildinfo
488efdbce70a6fc24dbdff472355ee4e45a22f20c4e835ee93ec53590642965b 2489136
iqtree_1.5.3+dfsg-2_amd64.deb
Files:
b331ef155418699da2600931645160ed 2180 science optional iqtree_1.5.3+dfsg-2.dsc
88d5070f7c95b524de246641063cc642 19016 science optional
iqtree_1.5.3+dfsg-2.debian.tar.xz
e35f8f8ca2572f69bec7e461b30ffe8b 34975624 debug extra
iqtree-dbgsym_1.5.3+dfsg-2_amd64.deb
481071fcb8d0d7d860ea5ebe243d36a7 6473 science optional
iqtree_1.5.3+dfsg-2_amd64.buildinfo
fc1c4e63f4873e329859ecd7d484f979 2489136 science optional
iqtree_1.5.3+dfsg-2_amd64.deb
-----BEGIN PGP SIGNATURE-----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=yCNW
-----END PGP SIGNATURE-----
--- End Message ---
