pod.pl - check the POD documentation syntax in modules and scripts
pod.pl [-d|--dir path ] [-v|--verbose] -b|--blankline [-?|-h|--help]
Checks Plain Old Documentation (POD) with highest possible stringency in every bioperl module and script in CVS modules 'core' and 'run'.
Amounts to same as running
podchecker -warnings -warnings
on every file.
The results are written into file '/tmp/bioperl_pod_check' and displayed after the run. The output is filtered not to show confirmations of correct syntax. The result file is not removed.
The aim is to have as few warnings, and no errors, as possible. Links to web URLs give a warning but that seems to be spurious, so they are filtered out. Currently there are a few cases of "multiple occurrence of link target" in several modules which are harmless.
podchecker, Pod::Checker
Overides the default directories to check by one directory 'path' and all its subdirectories.
Checks POD command paragraphs (lines starting with '=' character) for preceding nonblank lines. These lines are printed out with '++'.
Also, if verbose is turned on, it will report on lines whitespace characters which prevent paragrafs to be recognised by older POD parsers (marked with '+'). Modern perlpod parsers (5.6.0 and later, I suppose) allow for whitespace lines surrounding command lines, but since bioperl still supports older versions, these lines should be cleaned to contain only '\n' and no space or tab characters.
See: perlpodspec
Show the progress through files during the POD checking.
This help text.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email heikki-at-bioperl-dot-org
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.