[med-svn] r5124 - in trunk/packages/embassy-domalign/trunk/debian: . manpages patches

Charles Plessy plessy at alioth.debian.org
Wed Aug 11 11:31:16 UTC 2010 

Author: plessy
Date: 2010-08-11 11:31:15 +0000 (Wed, 11 Aug 2010)
New Revision: 5124

Added:
   trunk/packages/embassy-domalign/trunk/debian/patches/
   trunk/packages/embassy-domalign/trunk/debian/patches/enable-esystemlibs.patch
Modified:
   trunk/packages/embassy-domalign/trunk/debian/changelog
   trunk/packages/embassy-domalign/trunk/debian/control
   trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages
   trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e
   trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e
   trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e
   trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e
   trunk/packages/embassy-domalign/trunk/debian/rules
Log:
Uploaded with a patch.

  * New upstream release in which the version number was unchanged.
  * Build-Depends on emboss 6.3.1 (debian/control, debian/rules,
    closes: #591116).
  * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed.
  * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules).
  * Incremented Standards-Version to reflect conformance with Policy 3.9.1
    (debian/control, no changes needed).
  * Patched src/Makefile.am to use Debian's libexpat, using CDBS
    (debian/patches/enable-esystemlibs.patch, debian/rules, debian/control).
  * Refreshed the manpages.


Modified: trunk/packages/embassy-domalign/trunk/debian/changelog
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/changelog	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/changelog	2010-08-11 11:31:15 UTC (rev 5124)
@@ -1,3 +1,17 @@
+embassy-domalign (0.1.0+20100721-1) unstable; urgency=low
+
+   * New upstream release in which the version number was unchanged.
+   * Build-Depends on emboss 6.3.1 (debian/control, debian/rules,
+     closes: #591116).
+   * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed.
+   * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules).
+   * Incremented Standards-Version to reflect conformance with Policy 3.9.1
+     (debian/control, no changes needed).
+   * Patched src/Makefile.am to use Debian's libexpat, using CDBS
+     (debian/patches/enable-esystemlibs.patch, debian/rules, debian/control).
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 11 Aug 2010 19:45:22 +0900
+
 embassy-domalign (0.1.0+20100115-1) unstable; urgency=low
 
   * New upstream release in which the version number was unchanged.

Modified: trunk/packages/embassy-domalign/trunk/debian/control
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/control	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/control	2010-08-11 11:31:15 UTC (rev 5124)
@@ -1,13 +1,24 @@
 Source: embassy-domalign
 Section: science
 Priority: optional
-Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib (>= 6.2), libx11-dev, libgd2-xpm-dev
+Build-Depends:
+	cdbs,
+	debhelper (>= 7),
+	libajax6-dev (>= 6.3),
+	libnucleus6-dev (>= 6.3),
+	emboss-lib (>= 6.3),
+	libx11-dev,
+	libgd2-xpm-dev,
+	libmysqlclient-dev,
+	libpq-dev,
+	automake
+# automake is necessary as long as src/Makefile.am is patched.
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domalign/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domalign/trunk/
-Standards-Version: 3.8.4
+Standards-Version: 3.9.1
 Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN
 
 Package: embassy-domalign

Modified: trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/embassy-domalign.manpages	2010-08-11 11:31:15 UTC (rev 5124)
@@ -1,4 +1,4 @@
 debian/manpages/allversusall.1e
 debian/manpages/domainalign.1e
+debian/manpages/domainrep.1e
 debian/manpages/seqalign.1e
-debian/manpages/domainrep.1e

Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/manpages/allversusall.1e	2010-08-11 11:31:15 UTC (rev 5124)
@@ -2,12 +2,12 @@
 .\"     Title: ALLVERSUSALL
 .\"    Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 .\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\"      Date: 06/26/2010
+.\"      Date: 08/11/2010
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 0.1.0+20100115
+.\"    Source: DOMALIGN 0.1.0+20100721
 .\"  Language: English
 .\"
-.TH "ALLVERSUSALL" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
+.TH "ALLVERSUSALL" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------

Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainalign.1e	2010-08-11 11:31:15 UTC (rev 5124)
@@ -2,12 +2,12 @@
 .\"     Title: DOMAINALIGN
 .\"    Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 .\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\"      Date: 06/26/2010
+.\"      Date: 08/11/2010
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 0.1.0+20100115
+.\"    Source: DOMALIGN 0.1.0+20100721
 .\"  Language: English
 .\"
-.TH "DOMAINALIGN" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
+.TH "DOMAINALIGN" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------

Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/manpages/domainrep.1e	2010-08-11 11:31:15 UTC (rev 5124)
@@ -2,12 +2,12 @@
 .\"     Title: DOMAINREP
 .\"    Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 .\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\"      Date: 06/26/2010
+.\"      Date: 08/11/2010
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 0.1.0+20100115
+.\"    Source: DOMALIGN 0.1.0+20100721
 .\"  Language: English
 .\"
-.TH "DOMAINREP" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
+.TH "DOMAINREP" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------

Modified: trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/manpages/seqalign.1e	2010-08-11 11:31:15 UTC (rev 5124)
@@ -2,12 +2,12 @@
 .\"     Title: SEQALIGN
 .\"    Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 .\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\"      Date: 06/26/2010
+.\"      Date: 08/11/2010
 .\"    Manual: EMBOSS Manual for Debian
-.\"    Source: EMBOSS 0.1.0+20100115
+.\"    Source: DOMALIGN 0.1.0+20100721
 .\"  Language: English
 .\"
-.TH "SEQALIGN" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
+.TH "SEQALIGN" "1e" "08/11/2010" "DOMALIGN 0.1.0+20100721" "EMBOSS Manual for Debian"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------

Added: trunk/packages/embassy-domalign/trunk/debian/patches/enable-esystemlibs.patch
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/patches/enable-esystemlibs.patch	                        (rev 0)
+++ trunk/packages/embassy-domalign/trunk/debian/patches/enable-esystemlibs.patch	2010-08-11 11:31:15 UTC (rev 5124)
@@ -0,0 +1,15 @@
+Description: To use Debian's libexpat.
+ Upstream provides a configure flag for using the system's zlib and expat
+ libraries, but src/Makefile.am was not updated accordingly (in contrary to
+ other EMBASSY packages, like DOMAINATRIX).
+Forwarded: https://sourceforge.net/tracker/?func=detail&aid=3042988&group_id=93650&atid=605033
+Author: Charles Plessy <plessy at debian.org>
+--- src/Makefile.am.old	2010-08-11 19:18:21.000000000 +0900
++++ src/Makefile.am	2010-08-11 19:19:38.000000000 +0900
+@@ -62,5 +62,5 @@
+ 	../../../plplot/libeplplot.la $(XLIB)
+ else
+ LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \
+-        -lajax -leexpat -lepcre -lezlib -leplplot $(XLIB)
++        -lajax -lepcre $(NLADD) -leplplot $(XLIB)
+ endif

Modified: trunk/packages/embassy-domalign/trunk/debian/rules
===================================================================
--- trunk/packages/embassy-domalign/trunk/debian/rules	2010-08-11 11:28:42 UTC (rev 5123)
+++ trunk/packages/embassy-domalign/trunk/debian/rules	2010-08-11 11:31:15 UTC (rev 5124)
@@ -2,5 +2,9 @@
 
 include /usr/share/cdbs/1/rules/debhelper.mk
 include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
 
-CFLAGS += -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/nucleus
+DEB_CONFIGURE_EXTRA_FLAGS = --enable-systemlibs
+
+CFLAGS += -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus
+LDFLAGS += -Wl,--as-needed

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