[maker-devel] Fwd: possible problems in maker

[Barry Moore]

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



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