[Bioperl-l] tempfiles/tempdirs

[Lincoln Stein]

My suggestion would be to replace the Root tempfile method with a call
to IO::File->new_tempfile, thereby preserving the published API.  The
IO::File call is well-tested and works on all platforms.

Lincoln

Jason Stajich writes:
 > I've been looking through the code to see where we use the Root::IO
 > methods, tempfile and tempdir - not a whole lot.  I am concerned because
 > we seem to be leaving some clutter after running tests and File::Temp
 > files are not necessarily removed when the filehandle closes.  This can be
 > a problem for people running CGI's or many many analyses within a single
 > perl session.
 > 
 > It seems to me that the IO::File way of doing tempfiles
 > 
 > my $fh = IO::File->new_tempfile
 > 
 > might be more sane.  This is r/w capable handle so after writing to it -
 > we can rewind th fh and access what has been written.  This is essentially
 > the behavior needed by some of the parsers.
 > 
 > We do need unique tempfile names to be output for executing programs and
 > IO::File provides the methods tmpnam() to achieve this.  I would like to
 > be able to rely on IO::File being installed (which it appears to be even
 > on perl 5.004_04).  you do have to test that tmpnam returns something
 > valid by doing
 > do { $name = tmpnam() } until sysopen(TMP, $name, .... );
 > while File::Temp assures that your temporary name is valid.
 > 
 > Does anyone have opinions here?  I like the filehandle method better. And
 > I think we can be creative in our tempname generation in the modules that
 > need it.
 > 
 > -jason
 > 
 > -- 
 > Jason Stajich
 > Duke University
 > jason@cgt.mc.duke.edu
 > 
 > 
 > 
 > 
 > 
 > 
 > 
 > 
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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