[Debian-med-packaging] Bug#723064: pu: package emboss-explorer/2.2.0-7+deb7u1

[Charles Plessy]

Subject: pu: package emboss-explorer/2.2.0-7+deb7u1
Package: release.debian.org
User: release.debian.org at packages.debian.org
Usertags: pu
Severity: normal
X-Debbugs-CC: debian-med-packaging at lists.alioth.debian.org

Le Sun, Sep 15, 2013 at 11:13:05AM +0200, Paul Gevers a écrit :
> 
> > + -- Charles Plessy <admin at ip-172-31-27-246.ap-northeast-1.compute.internal>  Sun, 15 Sep 2013 05:16:46 +0000
> 
> This does not look good and in my interpretation against Debian policy.
> Your e-mail is not accessible from the world.

Hi Paul, Adam and everybody,

thanks for the information and sorry for having let slipped a wrong email
address in the changelog.

To summarise: emboss-explorer, a graphical frontend to EMBOSS, can not be used
with the EMBOSS version in Wheezy without a patch, that this proposed update
adds:

+--- emboss-explorer/lib/EMBOSS/GUI/XHTML.pm.orig	2012-11-15 09:35:20.390050595 -0700
++++ emboss-explorer/lib/EMBOSS/GUI/XHTML.pm	2012-11-15 09:35:58.083051229 -0700
+@@ -314,7 +314,7 @@
+ 	my $html = <<EOF;
+     <div id='menu'>
+ EOF
+-	if (@{$entries[0]} > 2) {	# entries are groups...
++	if (ref($entries[0][1]) eq "ARRAY") {	# entries are groups...
+ 		my $menu_url = $self->{static} ?
+ 			"alphamenu.html" : "$self->{script_url}/menu?sort=alpha";
+ 		$html .= <<EOF;

Please let me know if you prefer that I upload a repaired version (with my
correct email address) as 2.2.0-7+deb7u1 or 2.2.0-7+deb7u2.

For your reference, here is the debdiff of the package I uploaded, where my
email address needs to be corrected.

diff -u emboss-explorer-2.2.0/debian/changelog emboss-explorer-2.2.0/debian/changelog
--- emboss-explorer-2.2.0/debian/changelog
+++ emboss-explorer-2.2.0/debian/changelog
@@ -1,3 +1,9 @@
+emboss-explorer (2.2.0-7deb7u1) stable; urgency=low
+
+  * Patch to use with EMBOSS 6.4 and higer (Closes: #722982).
+
+ -- Charles Plessy <admin at ip-172-31-27-246.ap-northeast-1.compute.internal>  Sun, 15 Sep 2013 05:16:46 +0000
+
 emboss-explorer (2.2.0-7) unstable; urgency=low
 
   * debian/emboss-explorer.postinst: reloads apache.
diff -u emboss-explorer-2.2.0/debian/patches/00list emboss-explorer-2.2.0/debian/patches/00list
--- emboss-explorer-2.2.0/debian/patches/00list
+++ emboss-explorer-2.2.0/debian/patches/00list
@@ -3,0 +4 @@
+emboss-6.4-group-list.patch
only in patch2:
unchanged:
--- emboss-explorer-2.2.0.orig/debian/patches/emboss-6.4-group-list.patch
+++ emboss-explorer-2.2.0/debian/patches/emboss-6.4-group-list.patch
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## emboss-6.4-group-list.patch
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Description: correct menu when using EMBOSS >= 6.4.
+## DP: Origin: http://sourceforge.net/p/embossgui/bugs/_discuss/thread/b0c058e8/fc9b/attachment/emboss-6.4-group-list.patch
+## DP: Bug: http://sourceforge.net/p/embossgui/bugs/21/
+## DP: Bug-Debian: http://bugs.debian.org/722982
+--- emboss-explorer/lib/EMBOSS/GUI/XHTML.pm.orig	2012-11-15 09:35:20.390050595 -0700
++++ emboss-explorer/lib/EMBOSS/GUI/XHTML.pm	2012-11-15 09:35:58.083051229 -0700
+@@ -314,7 +314,7 @@
+ 	my $html = <<EOF;
+     <div id='menu'>
+ EOF
+-	if (@{$entries[0]} > 2) {	# entries are groups...
++	if (ref($entries[0][1]) eq "ARRAY") {	# entries are groups...
+ 		my $menu_url = $self->{static} ?
+ 			"alphamenu.html" : "$self->{script_url}/menu?sort=alpha";
+ 		$html .= <<EOF;

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan