[Debian-med-packaging] FFT-NS-i test data unreproducible with mafft 7.113 on a Debian system.

[Kazutaka Katoh]

Dear Dr Plessy,

Thank you for reporting that problem.  My mistake!  I think it has been fixed in v7.123.
http://mafft.cbrc.jp/alignment/software/source.html

Also, I've added a link to 
http://packages.debian.org/mafft 
from 
http://mafft.cbrc.jp/alignment/software/linux.html


Thanks again,
----------------------------------
Kazutaka Katoh

katoh at ifrec.osaka-u.ac.jp
IFReC, Osaka University
Suita 565-0871, Japan

kazutaka.katoh at aist.go.jp
RNA team, CBRC, AIST
Tokyo 135-0064, Japan

twitter.com/katoh16
----------------------------------

On 2013/10/14, at 10:38, Charles Plessy <plessy at debian.org> wrote:

> Dear Dr Katoh,
> 
> I was preparing to update MAFFT to version 7.113 in Debian
> (packages.debian.org/mafft), but stopped when I realised that, in contrary with
> version 7.058, I can not reproduce the reference alignment from the test
> directory.  I attached the differences produced by the following command.
> 
>    mafft --thread 0 --maxiterate 100 sample | diff sample.fftnsi - > sample.fftnsi.diff
> 
> I also attached the script that we use as regression test in Debian, inspired
> by the test commands in MAFFT's readme file.
> 
> Just in case you need more details on how I compiled MAFFT, I also attached the
> full build log.  The key line is probably the following.
> 
>    /usr/bin/make -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" CPPFLAGS="-D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security" LDFLAGS="-Wl,-z,relro"
> 
> Have a nice day,
> 
> -- 
> Charles Plessy
> Debian Med packaging team
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
> <sample.fftnsi.diff><with-example-data.txt><mafft_7.113-1_amd64.build>