compiling maker 2.09

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compiling maker 2.09

smg283

Hi,
I am trying to compile maker2.09 on RH 64 bit cluster.  I am getting a warning during perl Build.PL (Warning: ExtUtils::CBuilder not installed or no compiler detected) and an error during ./Build install (Error: no compiler detected to compile 'lib/Parallel/MPIcar.c'.  Aborting). 

I have ExtUtils::CBuilder installed and in PERL5LIB path (although it is not at /usr/lib/…..), mpich2 is installed and working. 

 

Any thoughts on what may be missing during install? 

 

 

$ perl Build.PL

 

WARNING: the following files are missing in your kit:

        bin/maker2zff.pl

Please inform the author.

 

Warning: ExtUtils::CBuilder not installed or no compiler detected

Proceeding with configuration, but compilation may fail during Build

 

Using built-in specs.

Target: x86_64-unknown-linux-gnu

Configured with: ../gcc-4.3.3/configure --prefix=/opt/gcc-4.3.0

Thread model: posix

gcc version 4.3.3 (GCC)

 

Your system appears to be configured for MPICH2. Would

you like to install the MPI version of MAKER? [Y ]

Y

Creating new 'MYMETA.yml' with configuration results

Creating new 'Build' script for 'MAKER' version '2.09'

 

 

The file 'Build' has been created for you to finish installing MAKER.

 

 

==============================================================================

STATUS MAKER 2.09

==============================================================================

PERL Dependencies:      INSTALLED

External Programs:      INSTALLED

MPI SUPPORT:            INSTALLED

MAKER:                  INSTALLED

 

 

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 (no 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 install

 

Building MAKER

Error: no compiler detected to compile 'lib/Parallel/MPIcar.c'.  Aborting

 

 

Thanks in advance,

Scott


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Re: compiling maker 2.09

Carson Hinton Holt
Re: [maker-devel] compiling maker 2.09 Yes.  I’ve seen this before.  It is a weird issue with Module::Build.  The easiest way to resolve this that usually works is to install Bundle::CPAN via the CPAN shell.  You may have to do force install to force a reinstall of perl modules that may already exist, but aren't acting properly.

In terminal:
perl -MCPAN -e shell
force install Bundle::CPAN



If you don’t have root access to the machine and cannot install PERL modules, you can build your own personal library this way.

In terminal:
mkdir ~/my_perl

Start CPAN as follows:
perl -MCPAN -e shell

In cpan:
o conf makepl_arg "DESTDIR=~/my_perl/ INSTALLDIRS=perl INSTALLMAN1DIR=none INSTALLMAN3DIR=none INSTALLARCHLIB=lib/ INSTALLPRIVLIB=lib/ INSTALLBIN=bin/"
o conf commit

Open ~/.bash_profile using a text editor like emacs or vi and add:
export PERL5LIB=$HOME/my_perl:$PERL5LIB

Back in terminal you need to load the changes you just made:
source ~/.bash_profile

Now install Bundle::CPAN as I mentioned before:
perl -MCPAN -e shell
force install Bundle::CPAN

--Carson




On 3/14/11 6:36 PM, "Scott Geib" <smg283@...> wrote:

Hi,
I am trying to compile maker2.09 on RH 64 bit cluster.  I am getting a warning during perl Build.PL (Warning: ExtUtils::CBuilder not installed or no compiler detected) and an error during ./Build install (Error: no compiler detected to compile 'lib/Parallel/MPIcar.c'.  Aborting). 
I have ExtUtils::CBuilder installed and in PERL5LIB path (although it is not at /usr/lib/…..), mpich2 is installed and working. 
 
Any thoughts on what may be missing during install? 
 
 
$ perl Build.PL
 
WARNING: the following files are missing in your kit:
        bin/maker2zff.pl <http://maker2zff.pl>
Please inform the author.
 
Warning: ExtUtils::CBuilder not installed or no compiler detected
Proceeding with configuration, but compilation may fail during Build
 
Using built-in specs.
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.3.3/configure --prefix=/opt/gcc-4.3.0
Thread model: posix
gcc version 4.3.3 (GCC)
 
Your system appears to be configured for MPICH2. Would
you like to install the MPI version of MAKER? [Y ]
Y
Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'MAKER' version '2.09'
 
 
The file 'Build' has been created for you to finish installing MAKER.
 
 
==============================================================================
STATUS MAKER 2.09
==============================================================================
PERL Dependencies:      INSTALLED
External Programs:      INSTALLED
MPI SUPPORT:            INSTALLED
MAKER:                  INSTALLED
 
 
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 (no 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 install
 
Building MAKER
Error: no compiler detected to compile 'lib/Parallel/MPIcar.c'.  Aborting
 
 
Thanks in advance,
Scott


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