[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Chris Fields cjfields at illinois.edu
Wed Jan 21 03:23:00 UTC 2009

Okay, so here's what happens.

A -x file test is run on the passed exe (in this case, 'gunzip').  If  
it fails to find it, then the PATH directories are iterated through,  
attempting to find the exe using -x each time.  However, the last  
instance doesn't test -l.  I added that in and it quieted the warnings  
for me.


On Jan 20, 2009, at 1:56 PM, Martin MOKREJŠ wrote:

> Mark Johnson wrote:
>>>> t/Root/Utilities.............................1/50
>>>> --------------------- WARNING ---------------------
>>>> MSG: find_exe: Multiple paths to 'gunzip' found. Using first.
>>>> ---------------------------------------------------
>>>> $ whereis gunzip
>>>> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip
>>>> /usr/bin/X11/gunzip
>>>> $ :-((
>>>> In my case all the other gzunzips are soflinks to /bin/gunzip.
>>> File this as a bug.  The check should make sure the others are not  
>>> soft
>>> links.  Won't be fixed in time for 1.6, though, but I remember  
>>> this popping
>>> up sporadically elsewhere.
> Filed as http://bugzilla.open-bio.org/show_bug.cgi?id=2737
>> I got that warning too, and chased it a bit...turns out that locally
>> we have some directories in PATH more than once.  Maybe that's  
>> worth a
>> warning, maybe not, but if so, it should be a bit more specific.
> I do not have duplicated entries in $PATH.
> Martin
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