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cancerit / cgpCaVEManPostProcessing

Flagging add on to CaVEMan
http://cancerit.github.io/cgpCaVEManPostProcessing/
GNU Affero General Public License v3.0
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make throws many warnings #11

Closed keiranmraine closed 8 years ago

keiranmraine commented 8 years ago

CavemanPostProcessor.pm doesn't have use warnings; (ideally FATAL=>all) so when run under make install we see many warnings of:

Use of uninitialized value $xt in string eq at /tmp/downloads/cgpCaVEManPostProcessing/blib/lib/Sanger/CGP/CavemanPostProcessor.pm line 506.

This line should be modified to:

return if ($keepSW == 0 && defined $xt && $xt eq 'M');

Additionally to ensure that these do not slip through the prerelease.sh can be modified to behave like make by changing this line to:

prove --nocolor -w -I ./lib | sed 's/^/  /' # indent output of prove