[med-svn] [Git][med-team/beast-mcmc][master] 3 commits: d/watch: version=5

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / beast-mcmc


Commits:
44528309 by Andreas Tille at 2025-12-22T19:25:54+01:00
d/watch: version=5

- - - - -
a9917487 by Andreas Tille at 2025-12-22T19:26:32+01:00
d/copyright: Cleanup Files-Excluded

- - - - -
0ffd7868 by Andreas Tille at 2025-12-22T19:47:41+01:00
Honor CFLAGS Closes: #1107598

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- + debian/patches/build-flags.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+beast-mcmc (1.10.4+dfsg-8) UNRELEASED; urgency=medium
+
+  * d/watch: version=5
+  * d/copyright: Cleanup Files-Excluded
+  * Honor CFLAGS
+    Closes: #1107598
+
+ -- Andreas Tille <tille at debian.org>  Mon, 22 Dec 2025 19:21:46 +0100
+
 beast-mcmc (1.10.4+dfsg-7) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/copyright
=====================================
@@ -4,8 +4,6 @@ Upstream-Contact: Alexei Drummond <alexei at cs.auckland.ac.nz>,
                   Andrew Rambaut <a.rambaut at ed.ac.uk>
 Source: https://github.com/beast-dev/beast-mcmc
 Files-Excluded: *.jar
-                *.so
-                *.o
                 *.jnilib
                 release*/Mac
                 release*/Windows


=====================================
debian/patches/build-flags.patch
=====================================
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2025-12-22
+Bug-Debian: https://bugs.debian.org/1107598
+Description: Honor CFLAGS
+
+--- a/native/Makefile.linux
++++ b/native/Makefile.linux
+@@ -1,11 +1,11 @@
+ CC=gcc
+-CFLAGS=-O2 -funroll-loops
++CFLAGS+=-O2 -funroll-loops
+ INCLUDES=-I${JAVA_HOME}/include/ -I${JAVA_HOME}/include/linux
+ 
+ OBJS = NucleotideLikelihoodCore.o
+ 
+ .c.o:
+-	${CC} ${CFLAGS} ${INCLUDES} -c $*.c
++	${CC} ${CPPLAGS} ${CFLAGS} ${INCLUDES} -c $*.c
+ 
+ libNucleotideLikelihoodCore.so: ${OBJS}
+-	${CC} ${CFLAGS} ${INCLUDES} -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 ${OBJS}
++	${CC} ${CPPFLAGS} ${CFLAGS} ${INCLUDES} -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 ${OBJS} ${LDFLAGS}


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ create_soname.patch
 fix_encoding.patch
 ignore_mac_install.patch
 update-ejml.patch
+build-flags.patch


=====================================
debian/watch
=====================================
@@ -1,5 +1,8 @@
-version=4
+Version: 5
 
-opts="repacksuffix=+dfsg,dversionmangle=auto,searchmode=plain" \
-        https://api.github.com/repos/beast-dev/@PACKAGE@/releases \
-        https://github.com/beast-dev/@PACKAGE@/releases/download/v\d[\d.-]+/BEAST[^v]*v(\d[\d.-]+)\.tgz
+Template: Github
+Owner: @PACKAGE@
+Project: @PACKAGE@
+Uversion-Mangle: s/^/1./;s/-beta/~beta/
+Repack-Suffix: +dfsg
+Dversion-Mangle: auto



View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/ec33e8bba692d25f84bd0983fe46bda770ec4fcf...0ffd7868f1e2a071d88531a1a31d45a35f9681f7

-- 
View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/ec33e8bba692d25f84bd0983fe46bda770ec4fcf...0ffd7868f1e2a071d88531a1a31d45a35f9681f7
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