Help to get Perl scripts of clonalorigin working needed

[Andreas Tille <andreas@an3as.eu>]

Hi,

I intend to package ClonalOrigin and the packaging is ready in Debian
Med Git[1] in principle.  The installer installs some Perl scripts
besides the main executable.  Upstream of ClonalOrigin is in CC of this
mail to clarify the role of these scripts but I think they should be
working in any case.  I get the following output when simply calling the
scripts:

$ blocksplit
Use of uninitialized value $fname in string at /usr/bin/blocksplit line 6.
Use of uninitialized value $fname in concatenation (.) or string at /usr/bin/blocksplit line 6.
Unable to open input XMFA file 

$ computeMedians -h
Unable to parse XML of -h, error Couldn't open -h:
No such file or directory at /usr/bin/computeMedians line 43.

lensum is 0
Use of uninitialized value within @tsort in hash element at /usr/bin/computeMedians line 79.
Use of uninitialized value $ttally in numeric lt (<) at /usr/bin/computeMedians line 79.
Use of uninitialized value within @tsort in concatenation (.) or string at /usr/bin/computeMedians line 83.
Median theta: 
Use of uninitialized value within @dsort in hash element at /usr/bin/computeMedians line 86.
Use of uninitialized value $dtally in numeric lt (<) at /usr/bin/computeMedians line 86.
Use of uninitialized value within @dsort in concatenation (.) or string at /usr/bin/computeMedians line 90.
Median delta: 
Use of uninitialized value within @rsort in hash element at /usr/bin/computeMedians line 93.
Use of uninitialized value $rtally in numeric lt (<) at /usr/bin/computeMedians line 93.
Use of uninitialized value within @rsort in concatenation (.) or string at /usr/bin/computeMedians line 97.
Median rho: 


$ makeMauveWargFile
Found -1 xml block files
Use of uninitialized value $base in substitution (s///) at /usr/bin/makeMauveWargFile line 15.
Use of uninitialized value $base in concatenation (.) or string at /usr/bin/makeMauveWargFile line 17.


I'm not sure whether this output is the "intended behavior" (= no proper
error processing) or whether this is an issue with a higher Perl version.
 
Any hint from a kind Perl educated soul would be really appreciated.
 
Kind regards
 
     Andreas.
 
[1] https://anonscm.debian.org/git/debian-med/clonalorigin.git

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