[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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