Release 1.5.2

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This is a developer release. It integrated new features whilst making a start on the 1.6 goals. Sendu Bala was the Release pumpkin.

Questions and discussion should go on the discussion page, or to the mailing list.


Obtain it

1.5.2 was released on December 6th 2006. It can be obtained using CPAN, CVS, PPM or by downloading the following packages. Md5 checksums are in: SIGNATURES.md5.

New Features


Enumerable thanks are due for the tireless efforts of Christopher Fields (bug fixing, testing, documentation, discussion), Nathan Haigh (Windows&pre-requisite issues, testing) and Mauricio Herrera Cuadra (testing, documentation, support). Feedback and ideas provided by Hilmar Lapp, Jason Stajich, Torsten Seemann and others on the mailing list and elsewhere proved invaluable. None of this would have been possible without the behind-the-scenes work of the open-bio support team. I'd also like to acknowledge Andreas J. Koenig for his help with CPAN matters.

Finally, thank you to everyone who tried out the release candidates, and especially those that took the time to file bug reports or report problems.


  • The core package was updated to 1.5.2_101 on 23/01/07 to address installation issues with future versions of CPAN. An updated ppm for Windows users was not required. Existing users do not need to upgrade.
  • The core package was updated to 1.5.2_102 on 14/02/07 to remove the installation recommendation for XML::SAX::ExpatXS, given bugfixes in XML::SAX 0.15. Existing users do not need to upgrade.


As a developer release, maintainance and support will cease at the time of the next bioperl release.

If you run into problems with 1.5.2, discuss them on the mailing list or file a bug report.

The following are known issues with 1.5.2; most of them are not bugs in the bioperl code and as such will not be fixed by us.

  • v34t25d4 of the fasta package causes failures in t/StandAloneFasta.t: I conclude that this particular version is simply bugged and gives wrong answers (other versions in the 25 series and more recent versions are all fine). It shouldn't be used, so the test failures will at least encourage the user to upgrade to a working version of the program. --Senduran 04:46, 8 November 2006 (EST)
  • v3.1.6 of RepeatMasker causes failures in t/RepeatMasker.t: 3.1.6 contains a trivial bug that prevents one of its options from working (-noint). Sadly, the test script makes use of that option. I'm going to go ahead and ignore this issue; presumably it will be fixed in 3.1.7 (I've reported it to the authors). --Senduran
  • v 4.68 of TCoffee causes a test failure, but other versions (including more recent 4.70) are fine: I conclude this particular version is bugged and shouldn't be used. --Senduran
  • The Lagan port in FreeBSD is compiled using the base system's gcc. In FreeBSD 5 the version of gcc is 3.4.2 and produces a mlagan binary that aborts unexpectedly (t/Lagan.t stops at subtest 5). In FreeBSD 6 the version of gcc is 3.4.6 and produces a mlagan binary that works fine (t/Lagan.t fully passes). I'm working with the Lagan port maintainer to see if we can modify the port to be compiled using a ported version of gcc (3.4.6 or higher). -- Mauricio 23:54, 22 November 2006 (EST)
  • For bioperl packages with no scripts, during 'Build test' you see 'Can't stat scripts: No such file or directory at C:/Perl/site/lib/Module/Build/ line 3683'. This is a harmless warning and can be ignored.
  • Tempfiles not removed with BioDBSeqFeature.t on WinXP, but tests pass. This is relatively harmless but should be checked out; it may have something in common with Issue #2119.
    • My guess is it may have something to do with tied filehandles not closing on DESTROY. Not a blocker but annoying... --Chris Fields 15:40, 10 November 2006 (EST)
ok 50
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Can't remove file C:\Temp\jl4Pw2uUkw/sequence.1088.fasta (Permission denied) at C:/Perl/site/lib/File/ line 914
Can't remove directory C:\Temp\jl4Pw2uUkw (Directory not empty) at C:/Perl/site/lib/File/ line 914
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