[maker-devel] MAKER can't find forks in @INC, but it is there

Fri Feb 17 13:39:33 MST 2017

Do a force reinstall of forks via CPAN. The error is coming from forks.pm line 83, so the problem is the forks installation itself.

Thanks,
Carson

> On Feb 17, 2017, at 1:11 PM, Seth Munholland <munholl at uwindsor.ca> wrote:
> 
> Hi Everyone,
> 
> After sorting my MPICH/OpenMPI issue I have come across another: When I try to run MAKER on the demo data via
> 
> $ mpiexec -machinefile /Data/machinefile -n 4 /Data/Apps/maker/bin/maker /Data/Apps/maker/data/maker_exe.ctl /Data/Apps/maker/data/maker_opts.ctl /Data/Apps/maker/data/maker_bopts.ctl
> 
> (-n 4 because I have 4 nodes in my MPI cluster and I wanted to get it working before opening up, if I change the -n value then the error repeats once for each process I attempt to run via MPICH) I got the following:
> 
> Can't locate forks.pm <http://forks.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks.pm <http://forks.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks.pm <http://forks.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks.pm <http://forks.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> 
> However I also see
> $ locate forks.pm <http://forks.pm/>
> /home/seth/.cpan/build/forks-0.36-0/blib/lib/forks.pm <http://forks.pm/>
> /home/seth/.cpan/build/forks-0.36-0/lib/forks.pm <http://forks.pm/>
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/forks.pm <http://forks.pm/>
> 
> Since /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 is in INC I initially thought this was a Perl error.  I hit up perlmonks and found that there is an issue between forks and Storable, where Storable now has a verion number of X.Y_Z but forks is only looking for X.Y (no _Z).  I followed these instructions https://rt.cpan.org/Public/Bug/Display.html?id=102730 <https://rt.cpan.org/Public/Bug/Display.html?id=102730> and tried again.  Now I get:
> 
> $ mpiexec -machinefile /Data/machinefile -n 4 /Data/Apps/maker/bin/maker /Data/Apps/maker/data/maker_exe.ctl /Data/Apps/maker/data/maker_opts.ctl /Data/Apps/maker/data/maker_bopts.ctl
> Can't locate forks/signals.pm <http://signals.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks/signals.pm <http://signals.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks/signals.pm <http://signals.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> Can't locate forks/signals.pm <http://signals.pm/> in @INC (you may need to install the forks::signals module) (@INC contains: /Data/Apps/maker/bin/../perl/lib /Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/lib /Data/Apps/CEGMA_v2.5/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at forks.pm <http://forks.pm/> line 83.
> BEGIN failed--compilation aborted at forks.pm <http://forks.pm/> line 84.
> Compilation failed in require at /Data/Apps/maker/bin/maker line 42.
> BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
> Undefined subroutine &threads::_END called at (eval 2) line 1.
> END failed--call queue aborted at /Data/Apps/maker/bin/maker line 42.
> 
> Clearly MAKER has an issue with forks, but it is installed, it is up to date (I double checked via cpan and apt-get to be sure), and it is in a directory that is in @INC.  Should I pursue this as a MAKER error or as a Perl error?
> 
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755 <>_______________________________________________
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> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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