gistfile1.txt

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/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted at /etc/apache2/sites-enabled/sgn line 18.\n
 failed!

gistfile2.txt

Restarting web server: apache2Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
IPC::System::Simple required for Fatalised/autodying system() at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14.\nCompilation failed in require at /etc/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted\t(in cleanup) IPC::System::Simple required for Fatalised/autodying system() at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14\nBEGIN failed--compilation aborted at /home/naama/cxgn/sgn/lib/SGN/Apache2/Startup.pm line 14.\nCompilation failed in require at /etc/apache2/sites-enabled/sgn line 18.\nBEGIN failed--compilation aborted at /etc/apache2/sites-enabled/sgn line 18.\n
 failed!

gistfile3.txt

Syntax error on line 14 of /etc/apache2/sites-enabled/sgn:
DBI connect('dbname=cxgn;host=db.sgn.cornell.edu','web_usr',...) failed: fe_sendauth: no password supplied at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/DB/Connection.pm line 384\nCompilation failed in require at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.\nBEGIN failed--compilation aborted at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.\nCompilation failed in require at (eval 4515) 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) DBI connect('dbname=cxgn;host=db.sgn.cornell.edu','web_usr',...) failed: fe_sendauth: no password supplied at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/DB/Connection.pm line 384\nCompilation failed in require at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.\nBEGIN failed--compilation aborted at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.\nCompilation failed in require at (eval 4515) 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 at /etc/apache2/sites-enabled/sgn line 18.\n
 failed!

gistfile4.txt

naama@virtual:~/cxgn$ cd ~/cxgn; CXGN_DB_CONNECTION_TRACE_CONNECTIONS=1 perl -Isgn/lib -MCXGN::Search::CannedForms -e 42; cat /tmp/cxgn_db_connections.log
CXGN::VHost is deprecated, please remove this use.

For most modules, all database connections, paths, etc that are now
being read from CXGN::VHost should be passed in via mandatory
arguments to new(), or similar.
 at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Scrap.pm line 24
WARNING: CXGN::DB::Connection needs to be explicitly configured with host, user, etc.  Falling back to values from CXGN::Config at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Publication.pm line 31
WARNING: dbschema argument to CXGN::DB::Connection is ignored.  Set the dbsearchpath configuration variable instead at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Publication.pm line 31
DBI connect('dbname=cxgn;host=db.sgn.cornell.edu','web_usr',...) failed: fe_sendauth: no password supplied at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/DB/Connection.pm line 384
Compilation failed in require at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.
BEGIN failed--compilation aborted at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Search/CannedForms.pm line 14.
Compilation failed in require.
BEGIN failed--compilation aborted.
cat: /tmp/cxgn_db_connections.log: No such file or directory

gistfile5.txt

WARNING: CXGN::DB::Connection needs to be explicitly configured with host, user, etc.  Falling back to SGN::Config since we seem to be running under the SGN site at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/DB/DBICFactory.pm line 54
[Wed Dec 02 13:23:40 2009] [error] Anonymous function called in forbidden list context; faulting at /home/naama/cxgn/cxgn-corelibs/lib/CXGN/Config.pm line 127\n

sgn

# enable extended apache server status, which is sometimes useful for debugging
ExtendedStatus On

<VirtualHost *:80>

    ServerName sgn.localhost.localdomain

    PerlWarn On
    PerlTaintCheck On

    LogLevel info

    <Perl>
       use lib '/home/naama/cxgn/sgn/lib';
       use lib '/home/naama/cxgn/cxgn-corelibs/lib';
       use local::lib '/home/naama/cxgn/local-lib';

       use SGN::Apache2::Startup vhost => 1;

       $SIG{__DIE__}  = \&CXGN::Apache::Error::cxgn_die_handler;
       $SIG{__WARN__} = \&CXGN::Apache::Error::cxgn_warn_handler;
    </Perl>

</VirtualHost>