[Bioperl-l] verbose turned on by PrimarySeq->new()

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Fri Nov 28 07:49:46 EST 2008


Could this be the same reason LargeLocatableSeq was printing out these
same warnings?
I just hacked it silent in its DESTROY method a few days ago. Maybe
that can be revoked now?

I can not see any reasons why module code itself should increase
verbosity level, so go and fix it.



2008/11/28 Dave Messina <David.Messina at sbc.su.se>:
> Hey everyone,
> In trying to figure out why the SeqIO::largefasta tests were being verbose
> about tempfile cleanup, I discovered that the PrimarySeq constructor turns
> on verbose, which gets inherited by LargePrimarySeq, which in turn cause
> RootIO to overshare about the temp files. (see PrimarySeq.pm line 164).
> The verbose flag was put in when Mira Han added -nowarnonempty. Turning
> verbose off doesn't seem to cause any tests to fail, so it looks like it
> might have been turned on for initial debugging purposes and never removed.
> Mira (or anyone else in the know), could you comment on this?
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Heikki Lehvaslaiho - heikki lehvaslaiho gmail com

More information about the Bioperl-l mailing list