Your message dated Sat, 11 Feb 2017 13:18:42 +0000 with message-id <[email protected]> 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 [email protected] immediately.) -- 854500: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854500 Debian Bug Tracking System Contact [email protected] 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.
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Andreas Tille <[email protected]> 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----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlifBr0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGADg/9GrYwYOsQc0+GR8o+isEBBBdaW8J9hmyk bd0Wy/C/N/p/pCQxfIIJmIPLubzQqlZbZ7GwE9BxKyOSCgHZ6NALyQzrgDxg1KNu VdjRWmg5i/mYJGePFomun8hlTCQSeLNUyqqiTcXBtzLUq/C3iiDTinYvEkE0pQri fTt9k/jJgiJ/Do0dRQIobXc09ssNnEXJFi6K1tOPNVlwCWYbeFGxBFEmTuLlWVEv DLTQOObnJE41/fb7sOJjo8hHnOkfgAHJuqII8CISgmBvkufD1MRKv2+tKcAiA5sZ 5mf3CGoregeNWjBb1cdTb7x421Llhbrpwgcgqbp908a0o44CBvno4AAZXQTCqKVY IkwVWAZwyP6eN344sIkmEupjsGiv9HgSudQsF65KRd5HMEhrcIVY2sm9hevp8w0a QdpC0pEEBkd4A2G3/vhf6LQjQiNgGJPw4ZM+4vkbsRN+1Kvl56ZAJIl83YByfXA8 09+ODLMa7Pd56ajSg3VXtonXBAc6RZlCYUKuSQmDDT09FVvxgriHHdQB4y2uf0Sz 6iRH6M97a5rC/GSrDx7OhQL+zfGloBpXDnT+Razc9ApZJmCxiQ02ILDBJK1N5qTq agEL1j5uB+7GXTE9qUpRl/2IuC2vDus2NbNQVY/1iiCeaUcr0228W04wmoQwN6iz AF7MpSge2aw= =yCNW -----END PGP SIGNATURE-----
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