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

Tue Feb 21 10:19:30 MST 2017

forks::signals is part of forks. It’s not a separate package. If it’s missing, there is a problem with the forks installation. So you need to do a force install of forks to force the reinstall.

Example —>         cpan[1]> force install forks

—Carson

> On Feb 21, 2017, at 10:17 AM, Seth Munholland <munholl at uwindsor.ca> wrote:
> 
> I tried this and still get the same error.  Then I tried forcing a reinstall of forks/signals and got:
> 
> cpan[1]> install forks::signals
> Warning: Cannot install forks::signals, don't know what it is.
> Try the command
> 
>     i /forks::signals/
> 
> to find objects with matching identifiers.
> 
> but scrolling through the install scroll of the forks reinstall I do see it got installed properly.
> 
> 
> 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 <>
> On Fri, Feb 17, 2017 at 3:39 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> Do a force reinstall of forks via CPAN. The error is coming from forks.pm <http://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 <mailto: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 <>_______________________________________________
>> maker-devel mailing list
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> 
> 

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