Your message dated Tue, 31 Mar 2009 09:47:18 +0000
with message-id <e1loayw-00026y...@ries.debian.org>
and subject line Bug#521996: fixed in emboss 6.0.1-8
has caused the Debian Bug report #521996,
regarding jemboss build-depends on openjdk-6-jre
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
521996: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=521996
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
package: jemboss
version: 6.0.1-6
severity: serious
tags: patch
In -7 openjdk-6-jdk was moved from build-depends-indep to the
build-depends. This makes it impossible to build the architecture
dependent packages on hppa and hence prevents emboss from migrating to
testing.
The following patch (based on -6 as -7 hadn't hit the mirrors yet plus
it'll probablly be a smaller diff ;) ) allows the architecture specific
binaries (which afaict have nothing to do with java) to be built without
needing openjdk-6-jdk installed. It also fixes a FTBFS if built twice in
a row issue I ran into while working on the patch.
diff -ur emboss-6.0.1/debian/rules emboss-6.0.1.new/debian/rules
--- emboss-6.0.1/debian/rules 2009-03-31 04:10:30.000000000 +0100
+++ emboss-6.0.1.new/debian/rules 2009-03-31 02:51:13.000000000 +0100
@@ -11,15 +11,21 @@
AJAX = $(CURDIR)/debian/libajax6
NUCLEUS = $(CURDIR)/debian/libnucleus6
+CONFFLAGS = --prefix=/usr --bindir=/usr/lib/emboss
+
+#if openjdk-6-jdk is not installed don't tell configure to use it
+#this allows binary-arch builds to be performed without openjdk
+#installed
+ifneq ($(wildcard /usr/lib/jvm/java-6-openjdk/include/classfile_constants.h),)
+ CONFFLAGS += --with-java=/usr/lib/jvm/java-6-openjdk/include
+ CONFFLAGS += --with-javaos=/usr/lib/jvm/java-6-openjdk/include/linux
+endif
+
config.status:
dh_testdir
ln -sf /usr/share/misc/config.sub .
ln -sf /usr/share/misc/config.guess .
- ./configure \
- --prefix=/usr \
- --bindir=/usr/lib/emboss \
- --with-java=/usr/lib/jvm/java-6-openjdk/include \
- --with-javaos=/usr/lib/jvm/java-6-openjdk/include/linux
+ ./configure $(CONFFLAGS)
include /usr/share/quilt/quilt.make
@@ -47,7 +53,7 @@
find jemboss/ -type f -name "*.class" | xargs -r rm -f
- $(RM) debian/emboss_tmp
+ rm -rf debian/emboss_tmp
$(RM) config.status install-stamp
--- End Message ---
--- Begin Message ---
Source: emboss
Source-Version: 6.0.1-8
We believe that the bug you reported is fixed in the latest version of
emboss, which is due to be installed in the Debian FTP archive:
emboss-data_6.0.1-8_all.deb
to pool/main/e/emboss/emboss-data_6.0.1-8_all.deb
emboss-doc_6.0.1-8_all.deb
to pool/main/e/emboss/emboss-doc_6.0.1-8_all.deb
emboss-lib_6.0.1-8_powerpc.deb
to pool/main/e/emboss/emboss-lib_6.0.1-8_powerpc.deb
emboss-test_6.0.1-8_all.deb
to pool/main/e/emboss/emboss-test_6.0.1-8_all.deb
emboss_6.0.1-8.diff.gz
to pool/main/e/emboss/emboss_6.0.1-8.diff.gz
emboss_6.0.1-8.dsc
to pool/main/e/emboss/emboss_6.0.1-8.dsc
emboss_6.0.1-8_powerpc.deb
to pool/main/e/emboss/emboss_6.0.1-8_powerpc.deb
jemboss_6.0.1-8_all.deb
to pool/main/e/emboss/jemboss_6.0.1-8_all.deb
libajax6-dev_6.0.1-8_powerpc.deb
to pool/main/e/emboss/libajax6-dev_6.0.1-8_powerpc.deb
libajax6_6.0.1-8_powerpc.deb
to pool/main/e/emboss/libajax6_6.0.1-8_powerpc.deb
libnucleus6-dev_6.0.1-8_powerpc.deb
to pool/main/e/emboss/libnucleus6-dev_6.0.1-8_powerpc.deb
libnucleus6_6.0.1-8_powerpc.deb
to pool/main/e/emboss/libnucleus6_6.0.1-8_powerpc.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 521...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated emboss package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Tue, 31 Mar 2009 14:26:55 +0900
Source: emboss
Binary: emboss emboss-data emboss-doc emboss-test emboss-lib jemboss libajax6
libajax6-dev libnucleus6 libnucleus6-dev
Architecture: source all powerpc
Version: 6.0.1-8
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Charles Plessy <ple...@debian.org>
Description:
emboss - the european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc - documentation for EMBOSS
emboss-lib - EMBOSS Libraries
emboss-test - test files for the EMBOSS package
jemboss - graphical user interface to EMBOSS
libajax6 - EMBOSS library for commands
libajax6-dev - development files for libajax
libnucleus6 - EMBOSS library for molecular sequence analysis
libnucleus6-dev - development files for libnucleus
Closes: 521996
Changes:
emboss (6.0.1-8) unstable; urgency=low
.
* debian/rules:
- Do not pass java options to the configure script if openjdk is not
installed (Closes: #521996, thanks to Peter Green).
- Recursive removal of emboss_tmp (to build the package twice in a row).
- Removed one `dh binary-indep` instance that strangely sneaked in after
running `svn update`.
* debian/control:
- Moved again openjdk-6-jdk to Build-Depends-Indep.
- Added debhelper's ${misc:Depends} substitution variable to the packages
that did not already depend on it.
Checksums-Sha1:
9e58460c4f8fa5044121025f4d71cb0c79f71c8f 1614 emboss_6.0.1-8.dsc
fa2514710edb15b1c62ad3bed0243acf23c80a4a 252573 emboss_6.0.1-8.diff.gz
86dd4b35abc996e255b5c078915bd00b9da18599 827496 emboss-data_6.0.1-8_all.deb
0311bcdd84f210830097957d68ff9e0ba5a73471 5210384 emboss-doc_6.0.1-8_all.deb
fcf2905c4782182978ad8655dbc2f93c15eef67a 5667914 emboss-test_6.0.1-8_all.deb
5608345e9d92152973a53714d48a5bbecdaddb71 4479582 jemboss_6.0.1-8_all.deb
807153e3cea80128c8934f5c66df6b63b0e3c836 1079448 emboss_6.0.1-8_powerpc.deb
fcbf90e553368c1cae9c655d8d51e92145b8b398 466060 emboss-lib_6.0.1-8_powerpc.deb
7f5197ef967d54312d139b0fcd03ad12be2ab977 790664 libajax6_6.0.1-8_powerpc.deb
bcda19226020ebe82290aa771c9437c655f85562 986126
libajax6-dev_6.0.1-8_powerpc.deb
c71ed8532563a1ff996d2055cfbe5e581a716846 204620 libnucleus6_6.0.1-8_powerpc.deb
12144d27087c1e1ff5ea4ea6f55f73428324614b 228158
libnucleus6-dev_6.0.1-8_powerpc.deb
Checksums-Sha256:
aae57001f3b94f3feacfe06204c10ea2b4d97c7b7316cb341e6d2d40d6db12d5 1614
emboss_6.0.1-8.dsc
d595dff9289fa7743245a95b3ab759b667427026304b2921bc940da913155f19 252573
emboss_6.0.1-8.diff.gz
f34b24ec826286abc0aa2cc806967519e84b1d4c81db206c7b3e78b5fc16d5db 827496
emboss-data_6.0.1-8_all.deb
11a963aaf88a2150f2c0b13564212eacd9716b296dacd29362f2f378ceb219ca 5210384
emboss-doc_6.0.1-8_all.deb
c963d18e63196850c1654128a980c4867f225f2ece54eba761a1f94022fa4e43 5667914
emboss-test_6.0.1-8_all.deb
d5394624f995fd31a826300340db8bf74b36002ef61177386aede6443e45ad5f 4479582
jemboss_6.0.1-8_all.deb
64d5e295478045d101b94d11aaaa348a699a78bfbb16bd558697b83a1810805a 1079448
emboss_6.0.1-8_powerpc.deb
e9dcb7d58e9b9cc8a6adaf44ab39df2b2d25f212ac15c8441ae54cbdad51b50b 466060
emboss-lib_6.0.1-8_powerpc.deb
c61789d72025205ba53a0a1661703bceed99f4de344404669c079617902252f4 790664
libajax6_6.0.1-8_powerpc.deb
e3252eca5458e8f19f30ff65afdb8e7dc98331da7d7e0f050186c70d3642b753 986126
libajax6-dev_6.0.1-8_powerpc.deb
34d74212432e91b2bbb579d9a3adf56acc7b409b8f5abdda715eb4e54386224f 204620
libnucleus6_6.0.1-8_powerpc.deb
a16bc72a6dabffd863f8f39af5a6b7509b2327391b4e187ea1cad7119e6d766f 228158
libnucleus6-dev_6.0.1-8_powerpc.deb
Files:
79ebdd3141222cb221d658a2d9830811 1614 science optional emboss_6.0.1-8.dsc
ee8e11ea6dbc0e58d52ad00b25914026 252573 science optional emboss_6.0.1-8.diff.gz
37fbb5f14bc96164483d23145f8d2e31 827496 science optional
emboss-data_6.0.1-8_all.deb
04416b907c3a0bd6978e3f7d477bbc73 5210384 doc optional
emboss-doc_6.0.1-8_all.deb
d13f462bc32fffa29ec9ff6166612d94 5667914 misc optional
emboss-test_6.0.1-8_all.deb
da93ac9535ce76ab5d3edcd3aaf477e3 4479582 science optional
jemboss_6.0.1-8_all.deb
7001fd76eb5e4f9e90bd82a1f814b07d 1079448 science optional
emboss_6.0.1-8_powerpc.deb
42cfc64ee98aad4af2a91ed8b77be60c 466060 libs optional
emboss-lib_6.0.1-8_powerpc.deb
6c3d9858eaba261cb915d71ca655504a 790664 libs optional
libajax6_6.0.1-8_powerpc.deb
617dba469024e114ac144a156a45cfc4 986126 libdevel optional
libajax6-dev_6.0.1-8_powerpc.deb
b43d9e7b7478203dda0974b5f0b07643 204620 libs optional
libnucleus6_6.0.1-8_powerpc.deb
0c02930e257bc5f3faf7e2b0b82a1600 228158 libdevel optional
libnucleus6-dev_6.0.1-8_powerpc.deb
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--- End Message ---
