[med-svn] [emboss] 01/01: I started off just trying to fix the JEmboss icon, which at least in Ubuntu refers to a non-existent icon image. But then I ended up making a bunch of other modifications. I don't know why this source is tagged as DFSG, as it contains a whole load of binary JAR files and failed to actually recompile JEmboss at all. I have partially fixed this, and also made the build fail in a timely manner if building the JAR fails. TIM
Timothy Booth
tbooth-guest at moszumanska.debian.org
Fri Apr 10 12:55:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
tbooth-guest pushed a commit to branch master
in repository emboss.
commit 83a0b12eef0e3e9f8a7367308a3a4fd3bf4f18af
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Fri Apr 10 13:49:52 2015 +0100
I started off just trying to fix the JEmboss icon, which at least in
Ubuntu refers to a non-existent icon image.
But then I ended up making a bunch of other modifications.
I don't know why this source is tagged as DFSG, as it contains a whole
load of binary JAR files and failed to actually recompile JEmboss at all.
I have partially fixed this, and also made the build fail in a timely
manner if building the JAR fails.
TIM
---
debian/changelog | 15 ++++++++++++
debian/control | 11 +++++----
debian/jemboss.desktop | 4 ++--
debian/jemboss.install | 1 +
debian/jemboss.links | 1 +
debian/jemboss_icon.png | Bin 0 -> 12275 bytes
debian/patches/no_makejar.patch | 46 +++++++++++++++++++++++++++++++++++++
debian/patches/path_max.patch | 4 ++--
debian/patches/series | 1 +
debian/rules | 49 ++++++++++++++++++++++++++--------------
debian/source/include-binaries | 1 +
11 files changed, 108 insertions(+), 25 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f44c33d..e6cabb5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,18 @@
+emboss (6.6.0+dfsg-2biolinux1) trusty; urgency=medium
+
+ * Current package builds jemboss from source but then installs
+ the pre-built jemboss.jar from the tarball - not good!!
+ Add ant dep and ensure that jemboss.jar really builds
+ * Include image for icon and edit .desktop file
+ * Add /usr/bin/jemboss
+ * Clean ./jemboss/runJemboss.sh which is created on build
+ * Clean various other files that blocked debuild -S (but note
+ we are still using some convenience copies of JARs)
+ * Remove makeJar.csh, and thus remove jemboss dep on csh
+ * Remove activation.jar which does not seem to be used at all
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Wed, 08 Apr 2015 19:06:09 +0100
+
emboss (6.6.0+dfsg-2) UNRELEASED; urgency=medium
* Make sure we will not delete documentation files from new upstream
diff --git a/debian/control b/debian/control
index 7f92a2c..e5cf27a 100644
--- a/debian/control
+++ b/debian/control
@@ -6,6 +6,7 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
+# javahelper,
libx11-dev,
x11proto-core-dev,
libgdchart-gd2-xpm-dev,
@@ -20,8 +21,9 @@ Build-Depends: debhelper (>= 9),
autotools-dev,
tcsh | csh | c-shell,
dh-autoreconf,
-# Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031
- default-jdk
+# Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031
+ default-jdk,
+ ant
#Build-Depends-Indep: default-jdk
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/emboss.git
@@ -115,8 +117,9 @@ Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
emboss,
- default-jre,
- tcsh | csh | c-shell
+ emboss-data,
+ default-jre
+# libgnujaf-java
Description: graphical user interface to EMBOSS
Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular
Biology Open Software Suite. It is part of the EMBOSS distribution.
diff --git a/debian/jemboss.desktop b/debian/jemboss.desktop
index d6facc6..ec41abc 100644
--- a/debian/jemboss.desktop
+++ b/debian/jemboss.desktop
@@ -1,8 +1,8 @@
[Desktop Entry]
Version=1.0
Terminal=false
-Icon=jemboss
-Exec=runJemboss.sh
+Icon=/usr/share/EMBOSS/jemboss/images/jemboss_icon.png
+Exec=jemboss
Name=Jemboss
GenericName=GUI for EMBOSS
Comment=Graphical user interface for the European Molecular Biology Open Software Suite.
diff --git a/debian/jemboss.install b/debian/jemboss.install
index ebf6376..81e3afd 100644
--- a/debian/jemboss.install
+++ b/debian/jemboss.install
@@ -1 +1,2 @@
debian/jemboss.desktop usr/share/applications
+debian/jemboss_icon.png usr/share/EMBOSS/jemboss/images/
diff --git a/debian/jemboss.links b/debian/jemboss.links
new file mode 100644
index 0000000..fc20c71
--- /dev/null
+++ b/debian/jemboss.links
@@ -0,0 +1 @@
+/usr/bin/runJemboss.sh /usr/bin/jemboss
diff --git a/debian/jemboss_icon.png b/debian/jemboss_icon.png
new file mode 100644
index 0000000..cda22c4
Binary files /dev/null and b/debian/jemboss_icon.png differ
diff --git a/debian/patches/no_makejar.patch b/debian/patches/no_makejar.patch
new file mode 100644
index 0000000..00150fe
--- /dev/null
+++ b/debian/patches/no_makejar.patch
@@ -0,0 +1,46 @@
+This started out as a patch to remove makeJar.csh but as I dug deeper into the
+mess it's gathered other Java fixups. When I actually get the thing straight
+I will give it a proper name.
+TIM
+--- a/jemboss/utils/Makefile.am
++++ b/jemboss/utils/Makefile.am
+@@ -5,7 +5,6 @@
+ jembossutils_DATA = \
+ install-jemboss-server.sh \
+ keys.sh \
+-makeJar.csh \
+ makeJNLP.sh \
+ makeFileManagerJNLP.sh \
+ template.html \
+--- a/jemboss/runJemboss.sh.in
++++ b/jemboss/runJemboss.sh.in
+@@ -28,6 +28,8 @@
+ CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/axis/saaj.jar";
+ CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/axis/wsdl4j.jar";
+
++CLASSPATH="${CLASSPATH}:/usr/share/EMBOSS/data/"
++
+ cd "${JEMBOSS_HOME}";
+
+ # Add local to run Jemboss in 'standalone' mode:
+--- a/jemboss/lib/Makefile.am
++++ b/jemboss/lib/Makefile.am
+@@ -6,7 +6,6 @@
+
+ jembosslib_DATA = \
+ README \
+-activation.jar \
+ jakarta-regexp-1.2.jar \
+ mail.jar \
+ jalviewApplet.jar \
+--- a/jemboss/runJemboss.sh
++++ b/jemboss/runJemboss.sh
+@@ -11,7 +11,7 @@
+
+ export CLASSPATH="";
+
+-CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/activation.jar";
++#CLASSPATH="${CLASSPATH}:/usr/share/java/activation.jar";
+ CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/client.jar";
+ CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/jakarta-regexp-1.2.jar";
+ CLASSPATH="${CLASSPATH}:${JEMBOSS_HOME}/lib/jalviewApplet.jar";
diff --git a/debian/patches/path_max.patch b/debian/patches/path_max.patch
index 8364ddd..4fd1057 100644
--- a/debian/patches/path_max.patch
+++ b/debian/patches/path_max.patch
@@ -3,8 +3,8 @@ Last-Update: Wed, 24 Sep 2014 10:36:02 UTC
Bug-Debian: http://bugs.debian.org/762673
Description: PATH_MAX is missing on Hurd so avoid this
---- a/ajax/core/ajfile.c.orig 2013-07-15 23:25:29.000000000 +0200
-+++ b/ajax/core/ajfile.c 2014-09-24 11:01:42.000000000 +0200
+--- a/ajax/core/ajfile.c
++++ b/ajax/core/ajfile.c
@@ -8574,9 +8574,9 @@
const AjPStr ajFileValueCwd(void)
diff --git a/debian/patches/series b/debian/patches/series
index 41c77d7..a711ad9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ bashism.patch
plplotP-correct-padding.patch
remove_non-free_doc.patch
path_max.patch
+no_makejar.patch
diff --git a/debian/rules b/debian/rules
index 46f2ba9..b8a697c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,11 @@
export DH_VERBOSE=1
+# TODO - migrate all binary JARs to use the packaged versions instead.
+# activation.jar never used?? Or sould we use the system version?
+# Note activation.jar was included in upstream but unused.
+#export CLASSPATH=/usr/share/java/activation.jar:
+
%:
dh $@ --with autotools-dev,autoreconf
@@ -32,16 +37,24 @@ DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)
override_dh_auto_configure:
dh_autotools-dev_updateconfig
dh_auto_configure -- $(CONFFLAGS)
-
+
override_dh_auto_build:
dh_auto_build -- AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(DEB_LDFLAGS)"
+ # Add 2 extra files wanted in jemboss.jar
+ cd jemboss/lib && make jemboss.jar
+ cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties
override_dh_clean:
dh_autotools-dev_restoreconfig
- rm --force --recursive debian/emboss_tmp
- find jemboss/ -type f -name "*.class" | xargs -r rm -f
+ rm -rf debian/emboss_tmp
+ find jemboss/ -type f -name "*.class" -delete
[ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )
dh_clean --exclude=feattext.html~ config.status test-stamp install-stamp
+ rm -f jemboss/runJemboss.sh
+ rm -f jemboss/utils/makeJar.csh
+ rm -f jemboss/lib/jemboss.jar jemboss/resources/resources.jar jemboss/lib/activation.jar
+ find test '(' -name 'Makefile' -o -name 'Makefile.in' ')' -delete
+ rm -f config.guess
override_dh_auto_install-arch:
### Binaries and data go to a temporary dir before being moved to their own package ###
@@ -66,25 +79,27 @@ override_dh_auto_install-arch:
### Documentation goes in emboss-doc. ###
$(MAKE) -C doc install DESTDIR=$(CURDIR)/debian/emboss-doc
- antiword $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.doc > $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.txt
+ antiword debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.doc > debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.txt
# Remove this file when the relicenced file becomes part of the upstream tarball.
- uudecode -o $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf $(CURDIR)/debian/EMBOSS_qg_new.pdf.uu
+ uudecode -o debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf debian/EMBOSS_qg_new.pdf.uu
override_dh_auto_install-indep:
$(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss bindir=/usr/bin
# install target seems to remove executable flag which is claimed by lintian
- find $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \;
+ find debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \;
# dangling LICEN[CS]E FILE
- rm $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE
+ rm debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE
+ # resources.jar not needed as we use the data files in /usr/share/EMBOSS/data/
+ rm -f debian/jemboss/usr/share/EMBOSS/jemboss/resources/resources.jar
### Installation of the test suite
- cp -a test $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/
- sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
- sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc
- mv $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc $(CURDIR)/debian/emboss-test/etc/emboss/embossrc.d/emboss-test
- find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/data -executable -type f -exec chmod a-x \{\} \;
- find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test -type d -name CVS | xargs rm -rf
- find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete
+ cp -a test debian/emboss-test/usr/share/EMBOSS/
+ sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+ sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" debian/emboss-test/usr/share/EMBOSS/test/.embossrc
+ mv debian/emboss-test/usr/share/EMBOSS/test/.embossrc debian/emboss-test/etc/emboss/embossrc.d/emboss-test
+ find debian/emboss-test/usr/share/EMBOSS/test/data -executable -type f -exec chmod a-x \{\} \;
+ find debian/emboss-test/usr/share/EMBOSS/test -type d -name CVS | xargs rm -rf
+ find debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete
override_dh_auto_test:
$(RM) test-stamp
@@ -95,16 +110,16 @@ override_dh_auto_test:
echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc
echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc
cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh
-
+
override_dh_installchangelogs:
dh_installchangelogs -k ChangeLog
-
+
override_dh_installman:
dh_installman -a -p emboss
for i in $(RENAMED) ; \
do dh_link usr/share/man/man1/$$i.1e.gz usr/share/man/man1/em_$$i.1e.gz ; \
done
-
+
override_dh_builddeb:
dh_builddeb -- -Z xz
diff --git a/debian/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..7f5adc6
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/jemboss_icon.png
--
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