[maker-devel] possible problems in maker

Carson Holt carsonhh at gmail.com
Wed Jun 15 08:50:54 MDT 2016 

Yes. I agree. The issue is your copy of some perl modules. You will need to install those via CPAN. Perhaps using the force option.

—Carson



> On Jun 13, 2016, at 11:36 PM, Barry Moore <bmoore at genetics.utah.edu> wrote:
> 
> Hi Alexander,
> 
> I’ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.
> 
> It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:
> 
> sudo cpan forks
> sudo cpan Time::HiRes
> 
> Regards,
> 
> Barry
> 
>> Begin forwarded message:
>> 
>> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>
>> Subject: possible problems in maker
>> Date: June 13, 2016 at 10:33:25 PM MDT
>> To: "barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>>
>> Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>>
>> 
>> Dear All
>> 
>> Please excuse me if you are not the right people to address, but there is no clear support stated in your page. 
>> 
>> I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel). 
>> My perl is 5.10 and my set up libraries are:
>> 
>> Here is my dialog:
>> 
>> ./Build distclean
>> Cleaning up build files
>> Cleaning up configuration files
>> Not in MANIFEST: bin/AED_cdf_generator.pl
>> Not in MANIFEST: bin/quality_filter.pl
>> MANIFEST appears to be out of sync with the distribution
>> 
>> ? 
>> 
>> Next:
>> 
>> The file 'Build' has been created for you to finish installing MAKER.
>> 
>> 
>> ==============================================================================
>> STATUS MAKER 3
>> ==============================================================================
>> PERL Dependencies:
>> VERIFIED
>> External Programs:
>> VERIFIED
>> External C Libraries:
>> VERIFIED
>> MPI SUPPORT:
>> ENABLED
>> MWAS Web Interface:
>> DISABLED
>> MAKER PACKAGE:
>> CONFIGURATION OK
>> 
>> 
>> Important Commands:
>> ./Build installdeps
>> #installs missing PERL dependencies
>> ./Build installexes
>> #installs all missing external programs
>> ./Build install
>> #installs MAKER
>> ./Build status
>> #Shows this status menu
>> 
>> Other Commands:
>> ./Build repeatmasker
>> #installs RepeatMasker (asks for RepBase)
>> ./Build blast
>> #installs BLAST (NCBI BLAST+)
>> ./Build exonerate
>> #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
>> ./Build snap
>> #installs SNAP
>> ./Build augustus
>> #installs Augustus
>> ./Build apollo
>> #installs Apollo
>> ./Build gbrowse
>> #installs GBrowse (must be root)
>> ./Build jbrowse
>> #installs JBrowse (MAKER copy, not web accecible)
>> ./Build webapollo
>> #installs WebApollo (use maker2wap to create DBs)
>> ./Build mpich2
>> #installs MPICH2 (but manual install recommended)
>> 
>> My PERL libraries are: 
>> 
>> ….
>> Characteristics of this binary (from libperl): 
>>   Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>>                         PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>>                         USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>>                         USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>>   Built under linux
>>   Compiled at Nov 22 2013 18:29:21
>>   %ENV:
>>     PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
>> ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
>>   @INC:
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /usr/local/lib64/perl5
>>     /usr/local/share/perl5
>>     /usr/lib64/perl5/vendor_perl
>>     /usr/share/perl5/vendor_perl
>>     /usr/lib64/perl5
>>     /usr/share/perl5
>> 
>> 
>>  The  ./Build install pass without errors. 
>> 
>> However when I try to start the maker exacutable I got the following error:
>> 
>> ./maker
>> Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
>> Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
>> BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
>> Compilation failed in require at ./maker line 42.
>> BEGIN failed--compilation aborted at ./maker line 42.
>> Undefined subroutine &threads::_END called at (eval 6) line 1.
>> END failed--call queue aborted at ./maker line 42.
>> 
>> Is there any other mising module which I have to install in order to make this software work. Thank you in advance
>> 
>> Alexander Tzanov
>> 
>> 
>> 
>> Take a picture. Write a caption. Win a prize.  <>Where’s Danny the Dolphin today? <http://www.csi.cuny.edu/wheresdanny/>
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