Bugs

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Bug submission

NOTE BioPerl will switch all active bugs to GitHub Issues. We will have access to the Redmine instance mentioned below, but this will be effectively read-only. We no longer support access to the original Bugzilla instance.

BioPerl has switched (as of mid-March, 2011) to using a Redmine-based tracking system. We still have access to our older Bugzilla-based system, but addition of new bugs has been disabled.

Don't make me bug you!

Please submit bugs or enhancement requests to our BioPerl Redmine tracking system. We really do want you to submit bugs, even though it means more things for us to do! It means there is something we didn't think of or test in the particular module and we won't know about this unless you tell us. The Redmine system requires you register to avoid spam and to allow us to contact you again when the bug is fixed or to clarify the problem and solutions.

It is important that you record the version of BioPerl you are running (if you don't know, see the FAQ the question is addressed there). You can also include the version of Perl you are using and the Operating System you are running.

Simon Tatham has a great resource on how to effectively report bugs.

Submitting Bugs

When submitting new bugs on Redmine, enter a brief description and other general information. You can use markup to add links, syntax highlighting, and so on; see the Redmine user manual for more.

Do not paste data or scripts into the description field! This is particularly important; if we can't reproduce the error due to arbitrary (and hard-to-fix) issues from the automated text-wrapping in that field, we can't fix the bug, therefore we'll have to rule the bug report as invalid. We'll send along a reminder via Redmine if this occurs to fix the issue.

After the report is generated, you can create attachments for any relevant data, code, or patches for the bug using the 'Create a New Attachment' link on the bug report page.

Submitting Patches

We gladly welcome patches. Patches for bioperl code should be created as described in the SubmitPatch HOWTO. Try to ensure the patch is derived against the latest code checked out from Git, particularly if the patch is large.

Briefly, you can generate the patch using the following command:

diff -u old new

For best results, follow this example:

cd $YOUR_WORKING_DIST_DIRECTORY/Bio/Frobnicator
git pull
git diff GrokFrobnicator.pm > my-patch.dif

To submit the patch on Redmine, attach a file on the initial bug report or in subsequent comments, then fill out the form that appears. This is the most convenient method for the devs, but you can put the patch in a comment or even post it to the mailing list.

Submitting New Modules and Code Snippets

We also accept new code, either as full-fledged modules or as snippets of code (snippets work better as a patch). New code must include documentation, example code (typically listed in a SYNOPSIS section), and tests with decent test coverage following our testing standards in our Writing_BioPerl_Tests HOWTO). Because we are moving to a more modular scheme for future Bioperl installations we highly suggest individual submission of modules to CPAN, primarily to help lower the barrier to submitting bug fixes.

Etiquette

Good bug reports are ones which provide a small amount of code and the necessary test files to reproduce your bug. By doing this work up front you insure the developer spends most of his or her time actually working on the problem. Pasting your entire 600 line program into the comment buffer is probably not going to get an enthusiastic response. In addition, isolating the problem down to a small amount of your code will help ensure that the bug is not on your end before we dive in and start working on it.

Open Bugs

This list details the open Bugs on Redmine for BioPerl.

BioPerl: Issues

Bug #3459 (New): Bio::DB::Taxonomy::flatfile.pm - temporary files at /var/tmp/DBD*
Bug #3457 (New): Bio::Tools::Primer3 - Exception raised with Primer3 2.3.X
Feature #3452 (New): Bio::SeqIO Interproscan XML parsing issue
Bug #3431 (New): Bio::DB::EntrezGene no longer returning gene names via get_Stream_by_id
Bug #3429 (New): Bio::Biblio example doesn't work
Feature #3428 (New): Reducing the time complexity of Bio/TreeIO/NewickParser.pm
Bug #3426 (New): Documentation auto-generated from github repository is out-of-date
Bug #3425 (New): Bio::Assembly::IO can not correctly parse all ace contig ids
Feature #3420 (New): Bio::DB::Taxonomy look under a root node for get_taxon
Bug #3417 (New): Bio::SeqIO unable to parse "PIR" format sequence with no description line
Bug #3416 (New): get_lca() test mixing local and remote databases not working
Bug #3414 (New): Bio::DB::GenBank/GenPept get_Seq/Stream_by_id no longer retrieves LOCUS IDs
Bug #3413 (New): Failed to add annotation in Bio::TreeIO for the phyloXML format
Bug #3406 (New): incorrect documentation of bioperl-run TCoffee module
Bug #3397 (In Progress): Making Bio::DB::Fasta Storable and thread safe
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