[maker-devel] Can install but Cannot Run MAKER

[xpeng at ucsb.edu]

Dear Yandell Lab,

 

I am writing to get a bit of help on making MAKER to work.

 

I downloaded the v3.01.03 maker and followed the instructions on your wiki
page to install, both on my local computer as sudo and on PSC Bridges (with
MPI). 

 

The installation seemed to have completed successfully.

 

However, when I ran "maker -h" I received error messages (attached) that I
don't know what to do about. Could you please advise a solution?

 

Thank you!

 

Nick (Xuefeng Peng)

 

Postdoctoral Scholar

University of California

Santa Barbara, CA

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$ ./maker -h
Possible precedence issue with control flow operator at /usr/share/perl5/Bio/DB/IndexedBase.pm line 845.
syntax error at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 105, near ")

	if"
syntax error at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 106, near "]{strand"
Global symbol "$strand" requires explicit package name (did you forget to declare "my $strand"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 106.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$strand" requires explicit package name (did you forget to declare "my $strand"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 109.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$strand" requires explicit package name (did you forget to declare "my $strand"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 113.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "%g" requires explicit package name (did you forget to declare "my %g"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "$id" requires explicit package name (did you forget to declare "my $id"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "$i" requires explicit package name (did you forget to declare "my $i"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name (did you forget to declare "my @stuff"?) at /home/csp/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Execution of /home/csp/software/maker/bin/../lib/Widget/trnascan.pm aborted due to compilation errors.
Compilation failed in require at /home/csp/software/maker/bin/../lib/GI.pm line 40.
BEGIN failed--compilation aborted at /home/csp/software/maker/bin/../lib/GI.pm line 40.
Compilation failed in require at ./maker line 46.
BEGIN failed--compilation aborted at ./maker line 46.
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$ maker -h
syntax error at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 105, near ")

	if"
syntax error at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 106, near "]{strand"
Global symbol "$strand" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 106.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 107.
Global symbol "$strand" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 109.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 110.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 111.
Global symbol "$strand" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 113.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 114.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 115.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 120.
Global symbol "%g" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "$id" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "$i" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
Global symbol "@stuff" requires explicit package name at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 121.
syntax error at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm line 122, near "}"
/pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/Widget/trnascan.pm has too many errors.
Compilation failed in require at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/GI.pm line 40.
BEGIN failed--compilation aborted at /pylon5/bi5618p/hmahzpxf/software/maker/bin/../lib/GI.pm line 40.
Compilation failed in require at /pylon5/bi5618p/hmahzpxf/software/maker/bin/maker line 46.
BEGIN failed--compilation aborted at /pylon5/bi5618p/hmahzpxf/software/maker/bin/maker line 46.