[pkg-bioc] svn commit r369 r369 - in /trunk/tools-ng: CRAN2DEB.pm list.d/buildDeps.list pkgbioc.pm r_pkg_ordering.pl

[smoe-guest at users.alioth.debian.org]

Author: smoe-guest
Date: Thu Dec 13 11:24:20 2007
New Revision: 369

URL: http://svn.debian.org/wsvn/pkg-bioc/?sc=1&rev=369
Log:
Nicification of screen logs, regexp patterns are also inspected for the reading of descriptions. Have not tested yet, sorry, submitting prematurely to test on another platform.

Modified:
    trunk/tools-ng/CRAN2DEB.pm
    trunk/tools-ng/list.d/buildDeps.list
    trunk/tools-ng/pkgbioc.pm
    trunk/tools-ng/r_pkg_ordering.pl

Modified: trunk/tools-ng/CRAN2DEB.pm
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools-ng/CRAN2DEB.pm?rev=369&op=diff
==============================================================================
--- trunk/tools-ng/CRAN2DEB.pm (original)
+++ trunk/tools-ng/CRAN2DEB.pm Thu Dec 13 11:24:20 2007
@@ -236,7 +236,14 @@ sub writeConfig($$$) {
       . "Maintainer: $maintainer\n"
       . "Standards-Version: 3.7.0\n"
       . "Build-Depends$indep: r-base-dev (>= 2.6.0), debhelper (>> 4.0.0), cdbs"
-      . "$bdps\n" . "\n"
+      . "$bdps\n";
+
+    $Text::Wrap::columns = 720;    # No wrapping of the URL
+    if ( exists( $pkg->{URL} ) ) { # URL from DESCRIPTION:
+        print FILE "Homepage: " . $pkg->{URL} . "\n";
+    }
+
+    print FILE "\n"
       . "Package: "
       . $pkg->{DebNamePackage} . "\n"
       . "Architecture: "
@@ -288,11 +295,6 @@ sub writeConfig($$$) {
     print FILE wrap( " ", " ", "Date: ", $pkg->{Date}, "\n" )
       if exists( $pkg->{Date} );
 
-    $Text::Wrap::columns = 720;    # No wrapping of the URL
-    if ( exists( $pkg->{URL} ) ) { # URL from DESCRIPTION:
-        print FILE " .\n";
-        print FILE " Homepage: " . $pkg->{URL} . "\n";
-    }
     if ( exists( $pkg->{Tag} ) ) {
         if ( defined( $pkg->{Tag} ) ) {
             print FILE "Tag: " . $pkg->{Tag} . "\n" if $main::tagsincontrol;

Modified: trunk/tools-ng/list.d/buildDeps.list
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools-ng/list.d/buildDeps.list?rev=369&op=diff
==============================================================================
--- trunk/tools-ng/list.d/buildDeps.list (original)
+++ trunk/tools-ng/list.d/buildDeps.list Thu Dec 13 11:24:20 2007
@@ -27,6 +27,7 @@ LDheatmap: genetics
 
 MBA: libboost-graph-dev, libboost-dev
 MBESS: class, gsl
+msm: mvtnorm
 multinomrob: mvtnorm
 
 ncdf: netcdfg-dev

Modified: trunk/tools-ng/pkgbioc.pm
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools-ng/pkgbioc.pm?rev=369&op=diff
==============================================================================
--- trunk/tools-ng/pkgbioc.pm (original)
+++ trunk/tools-ng/pkgbioc.pm Thu Dec 13 11:24:20 2007
@@ -295,12 +295,23 @@ sub populate_source($$$$$) {
     my ( $repo, $directory, $sources, $repoof, $global ) = @_;
     my $ori = cwd();
     print "populate source $repo\n" if $main::verbose;
-    chdir( "../" . $directory . "/$sources" );
+    chdir( "../" . $directory . "/".$sources );
     my @ary = glob("*.tar.gz");
     print "Found " . ( $#ary + 1 ) . " patterns in the repository $repo.\n"
       if $main::verbose;
     foreach my $cur (@ary) {
         next unless defined($cur);
+
+	if (defined($main::pattern) and "" != $main::pattern) {
+		if ($cur =~ /$main::pattern/i) {
+			print STDERR "Accepting $cur.\n" if $verbose;
+		}
+		else {
+			print STDERR "Omitting source $cur (since not /$main::pattern/i)\n" if $main::verbose;
+			next;
+		}
+	}
+
         my ( $head_pkg, $version_pkg, $tail_pkg ) = decomposition($cur);
         push( @{ $global->{srcavailable}->{ lc($head_pkg) } }, $repo );
         if ( !exists $repoof->{ lc($head_pkg) } ) {
@@ -311,7 +322,7 @@ sub populate_source($$$$$) {
                     "problem during mirroing, empty archive"
                 );
                 print $directory
-                  . "/sources/"
+                  . "/".$sources."/"
                   . $cur
                   . " is empty, problem during the mirroring??\n"
                   if $main::verbose;
@@ -345,6 +356,15 @@ sub populate_description($$$$$$) {
     foreach my $cur (@ary) {
         next unless defined($cur);
         my $bfile = basename($cur);
+	if (defined($main::pattern) and "" != $pattern) {
+		if ($cur =~ /$main::pattern/i) {
+			print STDERR "Accepting $cur.\n" if $verbose;
+		}
+		else {
+			print STDERR "Omitting description $cur (since not /$main::pattern/i)\n" if $main::verbose;
+			next;
+		}
+	}
         my ( $head_pkg, $version_pkg, $tail_pkg ) = decomposition($bfile);
         if ( $repoof->{ lc($head_pkg) } !~ /$repo/ ) {
 

Modified: trunk/tools-ng/r_pkg_ordering.pl
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/tools-ng/r_pkg_ordering.pl?rev=369&op=diff
==============================================================================
--- trunk/tools-ng/r_pkg_ordering.pl (original)
+++ trunk/tools-ng/r_pkg_ordering.pl Thu Dec 13 11:24:20 2007
@@ -734,12 +734,13 @@ foreach my $package (@nodes) {
             }
             else {
                 print
-                  "\tPackage '$package' ($debname): last version is already "
-                  . "in our local mirror, skipping\n";
+                  "\tPackage '$package' ($debname): latest version already "
+                  . "in local mirror, ";
                 if ($rebuildmirror) {
-                    print "\tbut rebuilding anyway as you are asking\n";
+                    print "\tbut rebuilding anyway as requested.\n";
                 }
                 else {
+		    print "skipped\n";
                     next;
                 }
             }
@@ -747,13 +748,14 @@ foreach my $package (@nodes) {
 
     }
     elsif ( -s $debfile ) {
-        print "\t$package is already built, $debfile exist, skipping package\n"
+        print "\t$package is already built, $debfile exists";
           if $verbose;
         if ($rebuildlocal) {
-            print "\tbut rebuilding anyway as you are asking\n";
+            print ", but rebuilding anyway as requested.\n";
             unlink $debfile if ( !$dryrun );
         }
         else {
+	    print ", skipped.\n"
             next;
         }
     }