It appears that at line 7739 in /usr/share/profphd/prof/scr/lib/lib-prof.pl:
$tmpend[$cth]=$tmplen[$cth] if (! defined $tmpend[$cth]);
The command that is being run is:
prof query.hsspPsiFil both fileRdb=query.profRdb numresMin=17 nresPerLineAli=60 riSubSec=4 riSubAcc=3 riSubSym=.
Both $tmpend[$cth] and $tmpend[$cth] are undefined at this point on the first iteration of the function. On the cluster node (using perl 5.14), the assignment works; however, on debian-unstable (using perl 5.20), prof fails with "Modification of non-creatable array value attempted, subscript -1 at /usr/share/profphd/prof/scr/lib/lib-prof.pl line 7739.”, although at this point on both servers the value of $cth is 0.
On 17 Jul 2016, at 19:51, merlettaia <merlettaia@gmail.com> wrote:Thank you for any answer.Can you remember what exact error was produced? And what erratic behaviour did you noticed?Hi Timothy,I'm an intern in Debian Med Team, and I'm working on autopkgtest testsuites for various packages. I found your email in profphd upstream's ChangeLog.
"
profphd (1.0.42) unstable; urgency=low
* Make prof work with Debian Jessie by requiring perlbrew package
and have it install independent perl v5.10 instance. $[ has been
moved from perl core >=5.16.0 into arybase, and does not produce
the same side effects as in previous perl versions, therefore
breaking prof when run using perl v5.20 in Jessie.
-- Timothy Karl (Aerialis) <karl@rostlab.org> Thu, 23 Jul 2015 16:44:30 +0200
"I've read arybase description here http://search.cpan.org/dist/perl-5.17.1/ext/arybase/arybase. , and for me it is unclear what specific side effect makes reprof break in latest versions of perl (and how exactly this breaks reprof?).pm#HISTORY
Unfortunately, I don't speak Perl fluently now and can't afford myself full source code investigation - my internship ends in August, and I wish to write tests for as many other packages as possible before it ends (and I've already spent 1 month while working on RostLab's packages). Also, I couldn't make perl 10.1 work in autopkgtest testsuite for now, even with perlbrew installed, so I'll try to make patch to update package to use latest Perl version if it is possible.
That's why any information would be helpful.--Regards,Tanya.
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