On Sun May 04 20:45:54 2014, SREZIC wrote:
Show quoted text> It seems that the test suite is using the wrong perl. When I try to
> run the test for perl5.19.11, then the following output appears:
>
> Running Build test
> Can't locate Mouse.pm in @INC (@INC contains: /bbbike/cpanbuild/Bio-
> Grid-Run-SGE-0.0383-1L7sHQ/blib/lib /bbbike/cpanbuild/Bio-Grid-Run-
> SGE-0.0383-1L7sHQ/blib/arch /etc/perl /usr/local/lib/perl/5.10.1
> /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5
> /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at
> /bbbike/cpanbuild/Bio-Grid-Run-SGE-0.0383-
> 1L7sHQ/blib/lib/Bio/Grid/Run/SGE/Master.pm line 3.
> BEGIN failed--compilation aborted at /bbbike/cpanbuild/Bio-Grid-Run-
> SGE-0.0383-1L7sHQ/blib/lib/Bio/Grid/Run/SGE/Master.pm line 3.
> ...
>
> The libraries mentioned here belong to perl 5.10.1, which is the
> system perl on this system.
>
> Often this problem can be solved by not using a hardcoded "perl" in
> system() and similar calls, but instead use the variable $^X. See also
> perldoc perlvar.
>
> Regards,
> Slaven
Patches attached.
--- t/Bio-Grid-Run-SGE-Worker.t.orig 2014-05-05 09:31:14.841184421 +0100
+++ t/Bio-Grid-Run-SGE-Worker.t 2014-05-05 09:32:15.499505848 +0100
@@ -56,7 +56,7 @@
for ( my $tid = 1; $tid <= 45; $tid++ ) {
$ENV{SGE_TASK_ID} = $tid;
- system("perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
+ system("$^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
test_atomic( $job_id, $tid - 1, $tid - 1, $seqs );
@@ -80,7 +80,7 @@
for ( my $tid = 1; $tid <= 23; $tid++ ) {
$ENV{SGE_TASK_ID} = $tid;
- system("perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
+ system("$^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
test_atomic( $job_id, $tid - 1, $tid - 1, $seqs );
test_atomic( $job_id, 22 + $tid, 22 + $tid, $seqs ) if ( 22 + $tid < 45 );
}
@@ -104,7 +104,7 @@
for ( my $tid = 1; $tid <= 15; $tid++ ) {
$ENV{SGE_TASK_ID} = $tid;
- system("perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
+ system("$^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null");
test_atomic( $job_id, ( $tid * 3 ) - 3, ( $tid * 3 ) - 3, $seqs );
test_atomic( $job_id, ( $tid * 3 ) - 2, ( $tid * 3 ) - 2, $seqs );
--- perf/test.pl.orig 2014-05-05 09:32:39.171338467 +0100
+++ perf/test.pl 2014-05-05 09:34:05.382425183 +0100
@@ -49,7 +49,7 @@
working_dir => $td,
submit_bin => 't/Bio-Grid-Run-SGE-Master.qsub.pl',
cmd => ['t/Bio-Grid-Run-SGE-Master.script.pl'],
- perl_bin => 'perl',
+ perl_bin => '$^X',
input => [ { format => 'General', sep => '^>', files => ['t/data/test.fa'], } ],
use_stdin => 1,
result_on_stdout => 1,
@@ -61,7 +61,7 @@
for ( my $tid = 1; $tid <= 45; $tid++ ) {
last;
$ENV{SGE_TASK_ID} = $tid;
- system( "perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
+ system( "^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
test_atomic($job_id, $tid-1, $tid-1, $seqs);
@@ -73,7 +73,7 @@
working_dir => $td,
submit_bin => 't/Bio-Grid-Run-SGE-Master.qsub.pl',
cmd => ['t/Bio-Grid-Run-SGE-Master.script.pl'],
- perl_bin => 'perl',
+ perl_bin => '$^X',
input => [ { format => 'General', sep => '^>', files => ['t/data/test.fa'], } ],
use_stdin => 1,
result_on_stdout => 1,
@@ -86,7 +86,7 @@
for ( my $tid = 1; $tid <= 23; $tid++ ) {
last;
$ENV{SGE_TASK_ID} = $tid;
- system( "perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
+ system( "$^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
test_atomic($job_id, $tid-1, $tid - 1, $seqs);
test_atomic($job_id, 22+$tid, 22+$tid , $seqs) if(22+$tid < 45);
}
@@ -100,7 +100,7 @@
working_dir => $td,
submit_bin => 't/Bio-Grid-Run-SGE-Master.qsub.pl',
cmd => ['t/Bio-Grid-Run-SGE-Master.script.pl'],
- perl_bin => 'perl',
+ perl_bin => '$^X',
input => [ { format => 'General', sep => '^>', files => ['t/data/test.fa'], } ],
use_stdin => 1,
result_on_stdout => 1,
@@ -112,7 +112,7 @@
for ( my $tid = 1; $tid <= 15; $tid++ ) {
$ENV{SGE_TASK_ID} = $tid;
- say( "perl t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
+ say( "$^X t/Bio-Grid-Run-SGE-Master.script.pl -w $td/master_config$job_id 2>/dev/null" );
last;
test_atomic($job_id, ($tid*3)-3, ($tid*3)-3, $seqs);
