Re: [SRU] perlprimer
Le Sat, Apr 30, 2011 at 01:21:25AM +0900, Charles Plessy a écrit :
> Le Fri, Apr 29, 2011 at 04:59:03PM +0100, Adam D. Barratt a écrit :
> > On Sun, 2011-03-20 at 18:46 +0900, Charles Plessy wrote:
> > >
> > > http://git.debian.org/?p=debian-med/perlprimer.git;a=commitdiff;h=upstream/1.1.20;hp=upstream/1.1.19
> >
> > Which sections of the diff are relevant for the API update? I'm
> > guessing it's the URL change, the "# Find genes and gene_ids" section
> > and the "if (/did not match any records in the database/si) {" block?
>
> I think so as well.
Dear Adam,
I have thought about the upstream changes and looked at the diff again. There
are only corrections, no new functionality added. The package in 1.1.20 Wheezy
had no negative feedback, and I tested it myself multiple times.
Would it be possible to simply take 1.1.20 from Wheezy and include it in the
next update of Squeeze ? That would make everything simpler. It is
architecture independant. It was built against Sid on February 27th; you can
find its build logs here:
http://anonscm.debian.org/gitweb/?p=debian-med/perlprimer.git;a=blob;f=amd64.log;hb=e7738a5c5e67f172bcd77038a08c43c2ffe1633c
Rebuilding it on Squeeze would bring practially no change, as I tested:
debdiff /var/cache/apt/archives/perlprimer_1.1.20-1_all.deb perlprimer_1.1.20-1_all.deb
File lists identical (after any substitutions)
Control files: lines which differ (wdiff format)
------------------------------------------------
Installed-Size: [-548-] {+540+}
Backporting the API correction from 1.1.20 to 1.1.19 would be very similar to
“forward-port” the calculation error in melting temperature from 1.1.19 to
1.1.20 :
1.1.19: my $corrected_tm=(($deltaH * 1000) / ($deltaS + (1.987 * log($oligo_conc_mols)))) - 273.15;
1.1.20: my $corrected_tm=(($deltaH * 1000) / ($deltaS + (1.987 * log($oligo_conc_mols/4)))) - 273.15;
Since we know that the equation in 1.1.19 is wrong, using 1.1.20 for a Stable
update would be – from the biologist point of view – quite appropriate.
Have a nice day,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
Reply to: