[Bioperl-l] Bioperl MAN pages install: where?

Jason Stajich jason at cgt.duhs.duke.edu
Sat Jan 31 10:25:21 EST 2004

Dave -

Generation of manfile is disabled because of problems with the number of
perl modules and the way that ExtUtils::MakeMaker generates the Makefile.
The lines in the makefile are too long for many shells/OSes which causes
the make procedure to fail.

I think the current fix is what Ewan put in looks like this
sub MY::manifypods {
  my $self = shift;
  #print STDERR "In manifypods moment\n";
  if( 1 ) {
    return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
  else {
    return $self->SUPER::manifypods(@_);

If you change that if ( 1 ) {   ---->  if (0) {
you will get manifypods to work.

Now I don't know if this is actually in the INSTALL documentation or not -
if it isn't I apologize we'll need to make sure it is added.

In general we seem to be taxing the conventional Perl route for module
installs because we have so many modules.  We've had some help with the
ExtUtils::MakeMaker developers but there still seems to be situations
where things don't work properly on every OS.  We just had some alpha/OSF1
and alpha/*BSD problems reported this week.  The future solutions might be

1) Add methods to Makefile.PL which can override the problems in
ExtUtils::MakeMaker (and lobby for fixes to get merged back into that

2) Look at other things like Module::Builder instead of
ExtUtils::MakeMaker, this may introduce more bioperl dependancies, but
people already complain about too many so what is one more... ;-)

3) Shrink the size of the packages by somehow splitting parts of the
toolkit off (as we have done for bioperl-run, db, microarray, pedigree).

As you can imagine this is sort of tedious when we'd like to focus [and
can justify volunteer time when not working on stuff we're paid to do] on
the {Bio} issues rather than the perl/system issues so it probably
doesn't get as much attention.

It needs to be resolved though so thanks for bringing it back up.
Squeaky wheel typically gets the grease around here - I keep hoping for
more grease monkeys to show up...  =)


On Sat, 31 Jan 2004, Dave NO SPAM Ardell wrote:

> Hi again!
> I've been confounded trying to reach the documentation by man to the
> bioperl modules. On my system at least, they seem not to be installed
> anywhere.  That is to say, "man MODULE" doesn't work and
> "updatedb;locate MODULE" doesn't reveal anything that is there but
> not in my manpath. Anybody else with this problem? Couldn't find
> anything
> about it on the web, bioperl archives, or documentation.
> I can of course, access the docs through "perldoc MODULE" but without
> manpages
> I can't query the module listing with "apropos" or "man -k."
> After scrutinizing the Makefile.PL and the Makefile, I can't really
> tell what's going
> on. The docs imply standard installation should occur, but on my systems
> (both linux and Mac OS X), since perhaps bioperl 1.2.3, they seem not
> to be.
> I've noticed that the installation output is not like those for
> standard perl
> modules, perhaps among other reasons, because a certain variable
> NOECHO is defined?
> Thanks for your advice-
> Dave
> --+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--
> +--
> David Ardell, Asst. Professor.  			tel   : 46 (0) 18 471 6694
> Linnaeus Centre for Bioinformatics		fax  : 46 (0) 18 471 6698
> Uppsala University Biomedical Center      http://www.lcb.uu.se/~dave
> Husargatan 3, Box 598,
> SE 751 24 Uppsala SWEDEN.
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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