[maker-devel] symbol lookup error: ProcessTable.so: undefined symbol: Perl_Tstack_sp_ptr

Carson Holt carsonhh at gmail.com
Wed Mar 13 07:24:44 MDT 2013 

I'm very glad it's working.  Those kind of errors are the hardest to track
down.

--Carson


On 13-03-12 10:18 PM, "Alex Marshall" <alex.marshall at ed.ac.uk> wrote:

>I have some great news. I uninstalled every one of my local perl
>libraries. Basically by getting rid of my libraries, and then using your
>Build script to install the maker dependencies totally fixed it. It
>worked with the test.fasta file, no errors whatsoever. I am smiling so
>much right now that my face might crack ;) you were right, broken perl.
>I just checked, getting lots of finished in the
>master_datastore_index.log. thank you so much.
>
>Alex
>
>
>
>
>
>On 12/03/2013 19:11, Carson Holt wrote:
>> I do think your perl has a problem.  I've added some changes to each of
>> these modules that should help force perl to generate the correct object
>> method lookup table.
>>
>> Could you test them out (place most under the /lib/Iterator/
>>subdirectory).
>>
>> --Carson
>>
>>
>> On 13-03-12 3:00 PM, "Alex Marshall" <alex.marshall at ed.ac.uk> wrote:
>>
>>> We had maker working happily for ages.
>>>
>>> Then we upgraded from perl version 5.8.8 to 5.10 which stopped maker
>>> working.
>>>
>>> Maker said it couldn't find forks.pm, added that library path, to fix
>>> the error.
>>>
>>> Then that particular error below started happening.
>>>
>>> Alex
>>>
>>>
>>> On 12/03/2013 18:54, Alex Marshall wrote:
>>>> version 5.10 on a hpc cluster
>>>>
>>>> Alex
>>>>
>>>>
>>>>
>>>> On 12/03/2013 18:48, Carson Holt wrote:
>>>>> That means the first time it called fileHandle it didn't die (which
>>>>> should
>>>>> be impossible)
>>>>>
>>>>> Then the second time it called it, it died.  It begs the question,
>>>>>what
>>>>> happened to the first call.
>>>>>
>>>>> This is looking more and more like you have a broken perl.
>>>>>
>>>>> What version of perl are you using?
>>>>>
>>>>> --Carson
>>>>>
>>>>>
>>>>>
>>>>> On 13-03-12 2:28 PM, "Alex Marshall" <alex.marshall at ed.ac.uk> wrote:
>>>>>
>>>>>> I deleted Iterator.pm, I put the new one in the maker/lib folder,
>>>>>>then
>>>>>> reran maker
>>>>>>
>>>>>> vi interator.pm confirms this:
>>>>>>
>>>>>> sub fileHandle {
>>>>>> die "this should die";
>>>>>>
>>>>>> error:
>>>>>> STATUS: Parsing control files...
>>>>>> Opening a new filehandle: Iterator:GFF3
>>>>>> Gettign the existing filehandle: Iterator::GFF3
>>>>>> Checking if it still exists: Iterator::GFF3
>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>> --> rank=NA, hostname=frontend04
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 12/03/2013 18:21, Carson Holt wrote:
>>>>>>> Try this one.
>>>>>>>
>>>>>>> It should fail immediately
>>>>>>>
>>>>>>> Code --> die	"this should die";
>>>>>>>
>>>>>>>
>>>>>>> I'm just making sure it's being called as expected.
>>>>>>>
>>>>>>> --Carson
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 13-03-12 2:18 PM, "Alex Marshall" <alex.marshall at ed.ac.uk>
>>>>>>>wrote:
>>>>>>>
>>>>>>>> I have Iterator.pm and GFF3.pm in the right place:
>>>>>>>>
>>>>>>>> ..../software/maker2/maker-2.27/lib/Iterator.pm
>>>>>>>> ..../software/maker2/maker-2.27/lib/Iterator/GFF3.pm
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 12/03/2013 18:16, Alex Marshall wrote:
>>>>>>>>> I have deleted Iterator.pm, and replaced again (just to be sure).
>>>>>>>>>
>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>> Opening a new filehandle: Iterator:GFF3
>>>>>>>>> Gettign the existing filehandle: Iterator::GFF3
>>>>>>>>> Checking if it still exists: Iterator::GFF3
>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 12/03/2013 18:11, Carson Holt wrote:
>>>>>>>>>> It's missing all the standard error from the Iterator.pm
>>>>>>>>>>message I
>>>>>>>>>> added?
>>>>>>>>>> Could you double check that you replaced that one too.
>>>>>>>>>>
>>>>>>>>>> --Carson
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 13-03-12 2:07 PM, "Alex Marshall" <alex.marshall at ed.ac.uk>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>> Opening a new filehandle: Iterator:GFF3
>>>>>>>>>>> Gettign the existing filehandle: Iterator::GFF3
>>>>>>>>>>> Checking if it still exists: Iterator::GFF3
>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 12/03/2013 18:02, Carson Holt wrote:
>>>>>>>>>>>> Please use these two and send me the full STDERR (replaces
>>>>>>>>>>>>also
>>>>>>>>>>>> Iterator/GFF3.pm).
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Carson
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 13-03-12 1:55 PM, "Alex Marshall" <alex.marshall at ed.ac.uk>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> same again:
>>>>>>>>>>>>>
>>>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On 12/03/2013 17:45, Carson Holt wrote:
>>>>>>>>>>>>>> Try this one.  This is a code snippet -->
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> my $fh = new FileHandle();
>>>>>>>>>>>>>>                 $fh->open("$arg") or die "ERROR: Could not
>>>>>>>>>>>>>> open
>>>>>>>>>>>>>> file:
>>>>>>>>>>>>>> $!\n";
>>>>>>>>>>>>>>                 $self->{fileHandle} = $fh;
>>>>>>>>>>>>>> 		$self->startPos($fh->getpos());
>>>>>>>>>>>>>>                 if (! openhandle($fh)){ #checks to see if
>>>>>>>>>>>>>>file
>>>>>>>>>>>>>> handle
>>>>>>>>>>>>>> is
>>>>>>>>>>>>>> open
>>>>>>>>>>>>>>     confess "ERROR: No open filehandle in Iterator\n";
>>>>>>>>>>>>>>                 }
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> All it does is open the handle, check the reading position
>>>>>>>>>>>>>>and
>>>>>>>>>>>>>> then
>>>>>>>>>>>>>> check
>>>>>>>>>>>>>> to see if the handle is still open.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --Carson
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 13-03-12 1:37 PM, "Alex Marshall"
>>>>>>>>>>>>>><alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [1] If I comment out the error in the GFF3.pm file:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>>>>>> Can't call method "getpos" without a package or object
>>>>>>>>>>>>>>> reference
>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>/exports/work/biology_ieb_mblaxter/software/maker2/maker-2.2
>>>>>>>>>>>>>>>7/
>>>>>>>>>>>>>>> bin
>>>>>>>>>>>>>>> /.
>>>>>>>>>>>>>>> ./l
>>>>>>>>>>>>>>> ib
>>>>>>>>>>>>>>> /I
>>>>>>>>>>>>>>> terator/GFF3.pm
>>>>>>>>>>>>>>> line 42, <CTL> line 121.
>>>>>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> [2] If I add the error comment back to the GFF3.pm, and add
>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>> second
>>>>>>>>>>>>>>> new Iterator.pm:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On 12/03/2013 17:31, Carson Holt wrote:
>>>>>>>>>>>>>>>> There is one other thing it does right before.  It calls
>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>> -->
>>>>>>>>>>>>>>>> $self->fileHandle()->getpos()
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I switched the chaining off so it is just $fh->getpos in
>>>>>>>>>>>>>>>>the
>>>>>>>>>>>>>>>> attached
>>>>>>>>>>>>>>>> module (replace again).
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I don't see why a failure would happen special for you
>>>>>>>>>>>>>>>> there,
>>>>>>>>>>>>>>>> but
>>>>>>>>>>>>>>>> try
>>>>>>>>>>>>>>>> it
>>>>>>>>>>>>>>>> again.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> --Carson
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On 13-03-12 1:24 PM, "Carson Holt" <carsonhh at gmail.com>
>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> This is the new line in Iterator.pm
>>>>>>>>>>>>>>>>> --> $fh->open("$arg") or die "ERROR: Could not open file:
>>>>>>>>>>>>>>>>> $!\n";
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> The extra info would be from $!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> In the place where the error is occurring, all MAKER does
>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>> open a
>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>> handle in Iterator.pm and then check to see if it is open
>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>> Iterator::GFF3 (it does one and then instantly the
>>>>>>>>>>>>>>>>>other).
>>>>>>>>>>>>>>>>> The
>>>>>>>>>>>>>>>>> second
>>>>>>>>>>>>>>>>> failure is just the check on the filehandle.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If the open succeeds, but for some reason it can't tell
>>>>>>>>>>>>>>>>>it
>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>> open,
>>>>>>>>>>>>>>>>> then
>>>>>>>>>>>>>>>>> it is something to do with your system.  You can try
>>>>>>>>>>>>>>>>> reinstalling
>>>>>>>>>>>>>>>>> Scalar::Util as that is the module that implements
>>>>>>>>>>>>>>>>> openhandle
>>>>>>>>>>>>>>>>> method
>>>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>>>> is called.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> You can also try just commenting out line 37 of
>>>>>>>>>>>>>>>>> lib/Iterator/GFF3.pm
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> --Carson
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On 13-03-12 1:15 PM, "Alex Marshall"
>>>>>>>>>>>>>>>>> <alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> I am looking at Iterator.pm
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> so it should of thrown more error information?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On 12/03/2013 17:14, Alex Marshall wrote:
>>>>>>>>>>>>>>>>>>> replaced Iterator.pm in maker2/maker-2.27/lib
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> error: same as before
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ...../software/maker2/maker-2.27/lib/Iterator/GFF3.pm
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> in sub new
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> my $fh = $self->fileHandle();
>>>>>>>>>>>>>>>>>>>         if (! openhandle($fh)){ #checks to see if file
>>>>>>>>>>>>>>>>>>> handle
>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>> open
>>>>>>>>>>>>>>>>>>>             die "ERROR: No open filehandle
>>>>>>>>>>>>>>>>>>> Iterator::GFF3\n";
>>>>>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On 12/03/2013 17:06, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>> I get not errors, and don¹t see any issues.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Could you replace the Iterator.pm in the lib directory
>>>>>>>>>>>>>>>>>>>> with
>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>> one.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I
>>>>>>>>>>>>>>>>>>>> added some more output to the STDERR if opening a
>>>>>>>>>>>>>>>>>>>> filehandle
>>>>>>>>>>>>>>>>>>>> fails.
>>>>>>>>>>>>>>>>>>>> At
>>>>>>>>>>>>>>>>>>>> least it should provide more information.  Could you
>>>>>>>>>>>>>>>>>>>> then
>>>>>>>>>>>>>>>>>>>> let me
>>>>>>>>>>>>>>>>>>>> know
>>>>>>>>>>>>>>>>>>>> what
>>>>>>>>>>>>>>>>>>>> it says.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>> Carson
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On 13-03-12 12:35 PM, "Alex Marshall"
>>>>>>>>>>>>>>>>>>>> <alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> please find: maker_opts.ctl and test.fa attached
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 16:31, Alex Marshall wrote:
>>>>>>>>>>>>>>>>>>>>>> will send to you now...
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 16:29, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>> Could you send me the entire captured STDERR, your
>>>>>>>>>>>>>>>>>>>>>>> maker_opts.ctl
>>>>>>>>>>>>>>>>>>>>>>> file and
>>>>>>>>>>>>>>>>>>>>>>> you test.fasta?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>> Carson
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On 13-03-12 12:23 PM, "Alex Marshall"
>>>>>>>>>>>>>>>>>>>>>>> <alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> It is in fasta format not GFF format
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 16:16, Alex Marshall wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> I have been looking through maker_opts.ctl
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> #-----Genome (Required for De-Novo Annotation)
>>>>>>>>>>>>>>>>>>>>>>>>> genome=test.fna #genome sequence (fasta format or
>>>>>>>>>>>>>>>>>>>>>>>>> fasta
>>>>>>>>>>>>>>>>>>>>>>>>> embeded
>>>>>>>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>>>>>>>> GFF3)
>>>>>>>>>>>>>>>>>>>>>>>>> organism_type=eukaryotic #eukaryotic or prokaryotic.
>>>>>>>>>>>>>>>>>>>>>>>>> Default
>>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>>> eukaryotic
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> I added the path to the genome, same error.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 16:11, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> What does you maker_opts.ctl file look like.  What is
>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>> value
>>>>>>>>>>>>>>>>>>>>>>>>>> for
>>>>>>>>>>>>>>>>>>>>>>>>>> genome? If you did not give a genome fasta file and
are
>>>>>>>>>>>>>>>>>>>>>>>>>> using
>>>>>>>>>>>>>>>>>>>>>>>>>> a
>>>>>>>>>>>>>>>>>>>>>>>>>> gff3 as
>>>>>>>>>>>>>>>>>>>>>>>>>> input, is there a FASTA file embedded in it?
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> --Carson
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On 13-03-12 12:06 PM, "Alex Marshall"
>>>>>>>>>>>>>>>>>>>>>>>>>> <alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> [1] hard drive - enough space
>>>>>>>>>>>>>>>>>>>>>>>>>>> [2] ./Build realclean - done
>>>>>>>>>>>>>>>>>>>>>>>>>>> [3] delete the maker_path/perl directory and
>>>>>>>>>>>>>>>>>>>>>>>>>>> maker_path/bin -
>>>>>>>>>>>>>>>>>>>>>>>>>>> done
>>>>>>>>>>>>>>>>>>>>>>>>>>> [4] LD_PRELOAD=/.....path...../openmpi/lib/libmpi.so
-
>>>>>>>>>>>>>>>>>>>>>>>>>>> done
>>>>>>>>>>>>>>>>>>>>>>>>>>> [5] perl Build.PL - done
>>>>>>>>>>>>>>>>>>>>>>>>>>> [6] installation of 2.27 worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> and back to original error:
>>>>>>>>>>>>>>>>>>>>>>>>>>> STATUS: Parsing control files...
>>>>>>>>>>>>>>>>>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>>>>>>>>>>>>>>>>>> --> rank=NA, hostname=frontend04
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 15:26, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> So the odd unrelated errors you are getting suggest
>>>>>>>>>>>>>>>>>>>>>>>>>>>> there
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> something
>>>>>>>>>>>>>>>>>>>>>>>>>>>> else going on that needs to be resolved first.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Check your drive space 'df -h maker_path'.  Make
sure
>>>>>>>>>>>>>>>>>>>>>>>>>>>> you
>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't
>>>>>>>>>>>>>>>>>>>>>>>>>>>> just
>>>>>>>>>>>>>>>>>>>>>>>>>>>> have
>>>>>>>>>>>>>>>>>>>>>>>>>>>> a full hard drive.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Run './Build realclean', and delete the
>> maker_path/perl
>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory and
>>>>>>>>>>>>>>>>>>>>>>>>>>>> maker_path/bin sidreactory completely.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Make sure to execute the export
>>>>>>>>>>>>>>>>>>>>>>>>>>>> LD_PRELOAD=/.....path...../openmpi/lib/libmpi.so
>> comamnd
>>>>>>>>>>>>>>>>>>>>>>>>>>>> before
>>>>>>>>>>>>>>>>>>>>>>>>>>>> ever
>>>>>>>>>>>>>>>>>>>>>>>>>>>> running 'perl Build.PL'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Which version of OPenMPI are you using.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Carson
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 13-03-12 11:21 AM, "Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Marshall"<alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am using openmpi and yes I ran ./Build install
>> step.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Configuring MAKER with MPI support
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "/bin/sh": Argument list too long at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /....path...../lib/perl5/Inline/C.pm line 801.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> A problem was encountered while attempting to
>> compile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> install
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Inline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> C code. The command that failed was:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       /usr/bin/perl Makefile.PL > out.Makefile_PL
>> 2>&1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The build directory was:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>> /....path...../maker2/maker-2.27/src/blib/build/Parallel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /A
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> li
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ati
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MPI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To debug the problem, cd to the build directory,
and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inspect
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> output
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>> /....path...../maker2/maker-2.27/src/lib/Parallel/Applic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> io
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> n/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> M
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PI.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 223.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 15:14, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also the place it is trying to load from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>> /....path...../maker2/maker-2.27/src/blib/lib/auto/Para
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ll
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> el
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /A
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> p
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pli
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /M
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /MPI.so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is not the final install location?  Did you
>> run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> './Build
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> install'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> step?  When that runs everything related to MPI
>> will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> here -->
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>> /....path...../maker2/maker-2.27/perl/lib/auto/Parallel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /A
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> li
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> c
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ati
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MPI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /M
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --Carson
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 13-03-12 11:11 AM, "Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Marshall"<alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> now getting mpi problems:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't load
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>> '/....path...../maker2/maker-2.27/src/blib/lib/auto/Para
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ll
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> el
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> App
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ati
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /M
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PI/MPI.so'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for module Parallel::Application::MPI:
>>>>> libmpich.so.1.0:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cannot
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> open
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> shared object file: No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /usr/lib64/perl5/DynaLoader.pm line 200.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       at /....path...../lib/perl5/Inline.pm line
>> 536.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>> /....path...../maker2/maker-2.27/src/lib/Parallel/Applic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> io
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> n
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /MP
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I.p
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> m
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line 223
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you suggest: export
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LD_PRELOAD=/.....path...../openmpi/lib/libmpi.so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I do that, and run again, same error.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 14:43, Alex Marshall wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ok I will upgrade to 2.27 now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 14:42, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The original error is caused by an issue in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Proc::ProcessTable
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> systems.  I no longer use that module in maker
>> for
>>>>>>> that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reason.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> After
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> first error, you may have to delete the
>> mpi_blastdb
>>>>>>> and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> any
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> extension .db in the maker.output directory
>> before
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> retrying.  I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recommend using 2.27.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Carson
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 13-03-12 10:40 AM, "Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Marshall"<alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I managed to fix that error.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am using version 2.25-beta.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ERROR: No open filehandle Iterator::GFF3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 12/03/2013 14:27, Carson Holt wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could you try the 2.27 version of MAKER? You
>> are
>>>>>>> using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2.10
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Carson
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On 13-03-11 12:15 PM, "Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Marshall"<alex.marshall at ed.ac.uk>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi to the maker-devel,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am getting an error everytime I run the
>> maker
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> symbol lookup error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> /path/to/software/lib64/perl5/site_perl/5.8.8/x86_64-li
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> n
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ux-
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> thr
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ead
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -m
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ul
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ti/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> au
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to/Proc/ProcessTable/ProcessTable.so:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> undefined symbol: Perl_Tstack_sp_ptr
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Your help would be very appreciated.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best wishes,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh University
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable
>>>>> body,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number
SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> maker-devel mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> maker-devel at box290.bluehost.com
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> yan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> del
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> l-l
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ab
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .o
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> rg
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable
>> body,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable
body,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body,
>>>>>>>>>>>>>>>>>>>>>>>>>>> registered
>>>>>>>>>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body,
>>>>>>>>>>>>>>>>>>>>>>>> registered
>>>>>>>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body,
>>>>>>>>>>>>>>>>>>>>> registered in
>>>>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> -- 
>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body, 
>>>>>>>>>>>>>>>>>> registered
>>>>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>>>> -- 
>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The University of Edinburgh is a charitable body, 
>>>>>>>>>>>>>>>registered 
>>>>>>>>>>>>>>> in
>>>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>>>> -- 
>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>>>> -----------------------------
>>>>>>>>>>>>>
>>>>>>>>>>>>> The University of Edinburgh is a charitable body, registered 
>>>>>>>>>>>>>in
>>>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>>>>> -- 
>>>>>>>>>>> -----------------------------
>>>>>>>>>>> Alex Marshall,
>>>>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>>>>> Ashworth Laboratories,
>>>>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>>>>> The King's Buildings,
>>>>>>>>>>> The University of Edinburgh,
>>>>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>>>>> -----------------------------
>>>>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>>>>> +44(0)131 650 7403
>>>>>>>>>>> -----------------------------
>>>>>>>>>>>
>>>>>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>>>>>> Scotland, with registration number SC005336.
>>>>>>>> -- 
>>>>>>>> -----------------------------
>>>>>>>> Alex Marshall,
>>>>>>>> Room 3.54, Blaxter Lab,
>>>>>>>> Ashworth Laboratories,
>>>>>>>> Institute of Evolutionary Biology,
>>>>>>>> The King's Buildings,
>>>>>>>> The University of Edinburgh,
>>>>>>>> Edinburgh, EH9 3JT
>>>>>>>> -----------------------------
>>>>>>>> alex.marshall at ed.ac.uk
>>>>>>>> +44(0)131 650 7403
>>>>>>>> -----------------------------
>>>>>>>>
>>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>>> Scotland, with registration number SC005336.
>>>>>> -- 
>>>>>> -----------------------------
>>>>>> Alex Marshall,
>>>>>> Room 3.54, Blaxter Lab,
>>>>>> Ashworth Laboratories,
>>>>>> Institute of Evolutionary Biology,
>>>>>> The King's Buildings,
>>>>>> The University of Edinburgh,
>>>>>> Edinburgh, EH9 3JT
>>>>>> -----------------------------
>>>>>> alex.marshall at ed.ac.uk
>>>>>> +44(0)131 650 7403
>>>>>> -----------------------------
>>>>>>
>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>> Scotland, with registration number SC005336.
>>>
>>> -- 
>>> -----------------------------
>>> Alex Marshall,
>>> Room 3.54, Blaxter Lab,
>>> Ashworth Laboratories,
>>> Institute of Evolutionary Biology,
>>> The King's Buildings,
>>> The University of Edinburgh,
>>> Edinburgh, EH9 3JT
>>> -----------------------------
>>> alex.marshall at ed.ac.uk
>>> +44(0)131 650 7403
>>> ----------------------------- 
>>>
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>
>
>-- 
>-----------------------------
>Alex Marshall,
>Room 3.54, Blaxter Lab,
>Ashworth Laboratories,
>Institute of Evolutionary Biology,
>The King's Buildings,
>The University of Edinburgh,
>Edinburgh, EH9 3JT
>-----------------------------
>alex.marshall at ed.ac.uk
>+44(0)131 650 7403
>----------------------------- 
>
>The University of Edinburgh is a charitable body, registered in
>Scotland, with registration number SC005336.

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