[maker-devel] MAKER can't find forks in @INC, but it is there
Seth Munholland
munholl at uwindsor.ca
Tue Feb 21 11:05:48 MST 2017
I wasn't sure what modules were separated (figured it was wroth a shot),
however, I did the force install of forks and I still get the same error.
I tried uninstalling and reinstalling all the forks installations that
showed up and commented out the PERL5LIB export I had in my ~/.bashrc (then
reloaded) to make sure I wasn't getting some kind of conflicting
libraries/modules. and I'm back to:
Can't locate forks.pm in @INC (you may need to install the forks module)
(@INC contains: /Data/Apps/maker/bin/../perl/lib
/Data/Apps/maker/bin/../lib /Data/Apps/maker/bin/../src/inc/perl/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
/Data/Apps/maker/bin/maker line 42.
BEGIN failed--compilation aborted at /Data/Apps/maker/bin/maker line 42.
along with:
$ sudo updatedb
$ 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
Now it's a maker issue, not a forks issue (if I'm reading it correctly), so
I reinstalled Maker (made sure to direct to mpicc and mpi.h properly) and
got:
$ sudo ./Build install
Installing MAKER...
Configuring MAKER with MPI support
Skip
/Data/Apps/maker/src/../perl/config-x86_64-linux-gnu-thread-multi-5.022001
(unchanged)
I don't believe that's an error or even a warning, but I get the same
"can't locate forks" error when I try to run it.
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 Tue, Feb 21, 2017 at 12:19 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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> 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
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>>
>
>
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