[Debian-med-packaging] Bug#963927: predictprotein:Unusable, fails with: Assigning non-zero to $[ is no longer possible

[Nilesh Patra]

Package: predictprotein
Version: 1.1.09-2
Severity: severe

Dear Maintainer,

predictprotein uses `$[ = 1` which is no longer supported with newer
perl versions.
Way to reproduce:

Get the predictprotein source package, and cd there. Try running
examples with predictprotein:

$ cd examples
$ predictprotein --seqfile p53.fasta --output-dir test
Assigning non-zero to $[ is no longer possible at
/usr/share/librg-utils-perl//copf.pl line 11.
make: *** [/usr/share/predictprotein/MakefilePP.mk:475: query.fasta]
Error 255
make --no-builtin-rules INFILE=query.in -C /tmp/9BCtEP40vL JOBID=query
-j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/
PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17
PROFROOT=/usr/share/profphd/prof/
BIGBLASTDB=/mnt/project/rost_db/data/blast/big
BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80
PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls
PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm
PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat
PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat
PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl
SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt
SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f
/usr/share/predictprotein/MakefilePP.mk all failed: 512 at
/usr/bin/predictprotein line 393.

Thanks

-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 4.19.0-6-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd

Versions of packages predictprotein depends on:
ii  bioperl               1.7.7-1
ii  disulfinder           1.2.11-8
ii  hmmer                 3.3+dfsg2-1
ii  hmmer2                2.3.2+dfsg-6
ii  librg-exception-perl  1.0.3-4
ii  librg-utils-perl      1.0.43-6
ii  make                  4.2.1-1.2
ii  metastudent           2.0.1-8
ii  ncbi-blast+-legacy    2.9.0-4
ii  ncbi-seg              0.0.20000620-5
ii  ncoils                2002-7
ii  norsnet               1.0.17-6
ii  norsp                 1.0.6-4
ii  perl                  5.30.0-10
ii  predictnls            1.0.20-6
ii  profbval              1.0.22-6
ii  profisis              1.0.11-5
ii  profphd               1.0.42-3
ii  proftmb               1.1.12-8+b1
ii  reprof                1.0.1-7

predictprotein recommends no packages.

Versions of packages predictprotein suggests:
pn  pp-cache-mgr            <none>
ii  pp-popularity-contest   1.0.6-4+b1
pn  predictprotein-nonfree  <none>

-- no debconf information