rbuels

Restarting web server: apache2Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
Global $r object is not available. Set:\n\tPerlOptions +GlobalRequest\nin httpd.conf at /usr/local/lib/site_perl/CXGN/Apache/Request.pm line 118.\nCompilation failed in require at (eval 350) line 1.\nCompilation failed in require at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nCompilation failed in require at /etc/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted\t(in cleanup) Global $r object is not available. Set:\n\tPerlOptions +GlobalRequest\nin httpd.conf at /usr/local/lib/site_perl/CXGN/Apache/Request.pm line 118.\nCompilation failed in require at (eval 350) line 1.\nCompilation failed in require at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 21.\nCompilation failed in require at /etc/apa

rbuels

my $pub_cv =
    $schema->resultset('Cv::Cv')
           ->find_or_create({ name => 'publication' });

my $journal_cvterm = $pub_cv->find_related('cvterms',
					   { name => 'journal' }
					  );

$journal_cvterm ||= $schema->resultset('General::Db')
                           ->find_or_create( { name => 'null' } )

rbuels

Restarting web server: apache2Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
Couldn't load class (SGN) because: Couldn't load class (SGN::Role::Site::DBConnector) because: Can't locate DBIx/Connector/RollbackError.pm in @INC (@INC contains: /home/tecle/cxgn/local-lib/lib/perl5/i486-linux-gnu-thread-multi
 /home/tecle/cxgn/local-lib/lib/perl5/i486-linux-gnu-thread-multi /home/tecle/cxgn/local-lib/lib/perl5 /home/tecle/cxgn/Cview/lib /home/tecle/cxgn/tomato_genome/lib /home/tecle/cxgn/cxgn-corelibs/lib /home/tecle/cxgn/ITAG/lib /home/tecle/cxgn/Phenome/lib /home/tecle/cxgn/sgn/lib /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl . /etc/apache2) at (eval 359) line 3.
	...propagated at /usr/share/perl/5.10/base.pm line 92.
BEGIN failed--compilation aborted at /home/tecle/cxgn/local-lib/lib/perl5/DBIx/Connector/Driver.pm line 92.
Compilation failed in require at /home/tecle/cxgn/local-lib/l

rbuels

my @files = qw(
    ITAG1_genomic_reference.gff3
    ITAG1_genomic.fasta
    ITAG1_genomic_all.gff3
    ITAG1_sgn_data.gff3
    ITAG1_protein_reference.gff3
    ITAG1_proteins.fasta
    ITAG1_protein_functional.gff3
);

rbuels

t/01app.t ...................................... ok
t/02pod.t ...................................... skipped: set TEST_POD to enable this test
t/03podcoverage.t .............................. skipped: set TEST_POD to enable this test
t/Bio/SecreTary/tmpred.t ....................... ok
t/CXGN/Bulk/unigene_converter.t ................ ok
Issuing rollback() for database handle being DESTROY'd without explicit disconnect().
t/CXGN/Cview/Map/SGN/genetic.t ................. ok
ITAG_devel_genomic.conf [main:database] not available
t/CXGN/Cview/MapFactory/sgn.t .................. ok
t/CXGN/Page/Form/forms.t ....................... ok

rbuels

name    = Bio-AGP
version = 0.1
author  = Sheena Scroggins
license = Perl_5
copyright_holder = Sheena Scroggins

[@Bioperl]

rbuels

Note: this isn't my solution, this is simply my findings from many github issues and blog posts coalesced into a single place.

To fix node-oracledb's reference to Oracle Instant Client on El Capitan, you'll need to run this from any repo that has node-oracledb as a dependency. Lines 16 and 17 need to point to the location of your zip files.

First, you'll need Oracle Instant Client on your machine. Once you click the environment that suits your needs, you'll need to grab two packages: basic, and sdk. Here's an example for the OSX client.

In the bash file also included with this gist, lines 16 and 17 need to be tweaked to point to those zip files you just downloaded.

Once that's done, you'll need to run it from your repo that has node-oracledb as a dependency. So, for example, let's say I had a folder structure like so:

• dev