[Debian-med-packaging] Need Perl help for gff2aplot

[Alex Mestiashvili]

On 1/29/19 4:19 PM, Andreas Tille wrote:
> Hi,
> 
> I added an autopkg test (seems right in time ;-) ) to gff2aplot[1].  I
> think / hope I was able to fix some issues in the code.  The autopkgtest
> also works with the locally installed package and than runing the test
> script[3] (which basically fixes some scripts provided upstream and runs
> these).  If you uncomment line 9 in the run-unit-test script[3] to make
> sure the temporary dir remains you get some log files.  The file
> 
>    wublast/taf6.mmhs.genomic.blastn.aplot_conf.log
> 
> (and others but 'set -e' forces the script to stop) says:
> 
>    Can't use an undefined value as an ARRAY reference at /usr/bin/gff2aplot line 1737, <THIS> line 12.
> 
> This is refering to line 1736 in the original source[4] and
> unfortunately my Perl knowledge is too poor to make some sensible
> replacement for this.
> 
> I'd also love some critical view on my patch[2] if some volunteer is
> kind enough to spent some time cycles on this issue.
> 
> Kind regards
> 
>       Andreas.
> 
> 
> [1] https://salsa.debian.org/med-team/gff2aplot
> [2] https://salsa.debian.org/med-team/gff2aplot/blob/master/debian/patches/perl_5.28.patch
> [3] https://salsa.debian.org/med-team/gff2aplot/blob/master/debian/tests/run-unit-test
> [4] https://salsa.debian.org/med-team/gff2aplot/blob/master/src/gff2aplot.pl
> 

Hi Andreas,

Please have a look on the last commits.
I've tried to implement a better check and added a patch fixing a few
issues detected by perlcritic.
Your patch looks sane to me.
One can see what is happening there by dumping all the vars with
Data::Dumper to a file.

The autopkgtest fails anyway at the end, but I didn't have time to look
on that so far.

Best regards,
Alex