[Debian-med-packaging] Dialign-t and gcc-4.2

Charles Plessy charles-listes-med-packaging at plessy.org
Mon Dec 17 09:35:05 UTC 2007

Dear Amarendran,

I tried to contact you in November for a compilation bug with gcc-4.2,
but apparently my email failed to reach you. For this reason, I did not
try to contact you for the missing latex sources that made us split
dialign-t in two packages in Debian.

There is a copy of the mail about the compilation problem after my
signature. Apparently, newer version of gcc will be corrected. In the
meantime, we use -Os for the compilation, which gives only a performance
loss of about 10 %.

For the package split, if you provide us the LaTeX sources of the
Dialign documentation, we can re-unify the Debian package. If you are
preparing an upgrade anyway and want to avoid to increase the version
number for a non-programmatic change, it is enough if you communicate us
the sources directly and that we include them in the Debian source

How different will dialign-tx be from dialign-t ? If it is a complete
replacement, then we do not need to do too much extra for the current
package. If it is different enough that you would like to see them both
distributed in Debian together, then it is better to release an updated
source tarball, that we would then use to produce an updated Debian

Have a nice day,

-- Charles Plessy, Debian-Med packaging team, Wakō, Saitama. Japan

Le Tue, Nov 13, 2007 at 10:11:10AM +0900, Charles Plessy a écrit :
> Dear Dr Subramanian,
> I am preparing an installation package for Dialign-t on the Debian
> operating system. Unfortunately, our default compiler is gcc-4.2, and
> Dialign-t does not build on Intel systems with gcc versions higher that
> 4.1.
> I reported the problem in the Debian bug tracking system, as it may be a
> compiler bug rather than a Dialign bug : with the same compiler the
> build goes fine on a powerpc platform.
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=446714
> I am not a C programmer, so I can not diagnose the problem further. But
> if you see a workaround to this problem, it could greatly speed up the
> release of a Debian package for Dialign-t.
> As part of the packaging work, I also prepared a manpage for Dialign-t.
> You can find it and its xml source in our subversion repository:
> http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml?op=file&rev=0&sc=0
> http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/debian/dialign-t.1?op=file&rev=0&sc=0
> Best regards,
> -- 
> Charles Plessy
> Debian-Med packaging team
> http://www.debian.org/devel/debian-med/index.html
> Wako, Saitama, Japan

Le Mon, Dec 17, 2007 at 09:59:26AM +0100, Andreas Tille a écrit :
> Hi Amarendran,
> thanks for your interest in Debian.  I'm forewarding your full mail to
> the Debian-Med packaging list.  It is really nice that you contacted
> Debian with your mail but ftpmaster is probably the wrong place for this
> kind of requests.  If you are interested in biological software I would
> recommend subsrcibing the Debian-Med mailing list at
>     http://lists.debian.org/debian-med/
> This list would be the first choice for the kind of requests you had
> in your mail.
> The actual packaging work of dialign-t was done by Charles Plessy and
> I'm sure he will help you to apply the fixes that are needed (if there
> are any).
> Kind regards and good luck in finishing your PhD ;-))
>         Andreas.
> On Mon, 17 Dec 2007, Amarendran Subramanian wrote:
> >Hi,
> >
> >as you probably might know i am the author of dialign-t.
> >when i monitored some mailing lists i noticed a discussion about problems 
> >integrating dialign-t into debian. however i am not a debian or linux 
> >specialist (damn scientists that try to write linux compatible software 
> >;-)) i could figure out from the discussion that it might be helpful 
> >incorporating some fixes. so if i can be of any assistance please let me 
> >know, it'd be no problem for me to issue a dialign-t 0.2.3 that enables 
> >the software to be properly included into the debian distribution.
> >
> >FYI: a new version of dialign-t (which will be called dialign-tx) will be 
> >issued within the first quarter of 2008 (which finally enables me to 
> >finish my PhD;-)) - so if there is anything i can consider to make it more 
> >compatible with the debian distribution i'd be happy to know.
> >
> >regards amar
> >
> >Amarendran R. Subramanian
> >Universität Tübingen
> >
> >
> -- 
> http://fam-tille.de

Charles Plessy
Wakō, Saitama, Japan

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