[maker-devel] MAKER can't find forks in @INC, but it is there
Seth Munholland
munholl at uwindsor.ca
Tue Feb 21 10:17:22 MST 2017
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> wrote:
> 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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
> /home/seth/.cpan/build/forks-0.36-0/blib/lib/forks.pm
> /home/seth/.cpan/build/forks-0.36-0/lib/forks.pm
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/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 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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 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 line 83.
> BEGIN failed--compilation aborted at 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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> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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