[Debian-med-packaging] Bug#854500: iqtree: FTBFS on single-CPU machines (ERROR: You have specified more threads than CPU cores available)

[Santiago Vila]

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.