[Debian-med-packaging] Bug#853835: seaview: Wrong results in connection with multi-processing phyml

[Andreas Tille]

Package: seaview
Severity: grave
Justification: renders package unusable

Hi,

when using phyml on multiprocessor machines it might happen that a
greater number of bootstraps than specified by seaview is done by phyml.
Phyml "decides" itself how many bootstrap steps it takes depending from
the amount of processors can be used.  I have described the issue in
Debian bug #853738[1] and fixed the bug in a way which allows the user
to call seaview like:

   PHYMLCPUS=8 seaview *.fna

when intending to do for instance 1000 bootstrap steps.  This works
since 1000%8=0.  However, for other numbers of CPUs for instance when
calling

   PHYMLCPUS=16 seaview *.fna

phyml would do

   (1000 / 16 + 1) * 16 = 1008

bootstrap processes.  From phyml perspective this does not matter but
the effect in seaview is that if 1000 bootstraps are considered 100%
some values might end up beeing 101% which is nonsense.

So seaview need to parse the phyml output for changed numbers of
bootstraps to adjust the base of the calculations that are based on the
effective number of bootstraps.

Kind regards

      Andreas.


-- System Information:
Debian Release: 8.7
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages seaview depends on:
ii  libc6              2.19-18+deb8u7
pn  libfltk-images1.3  <none>
pn  libfltk1.3         <none>
ii  libgcc1            1:4.9.2-10
ii  libstdc++6         4.9.2-10
ii  libx11-6           2:1.6.2-3
ii  zlib1g             1:1.2.8.dfsg-2+b1

Versions of packages seaview recommends:
pn  clustalo  <none>
pn  muscle    <none>
pn  phyml     <none>

seaview suggests no packages.