[med-svn] [Git][med-team/hmmer2][master] 6 commits: Add patch to fix FTBFS
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Mar 25 10:44:38 GMT 2024
Nilesh Patra pushed to branch master at Debian Med / hmmer2
Commits:
ca3a07cd by Nilesh Patra at 2024-03-25T13:08:20+05:30
Add patch to fix FTBFS
- - - - -
f6d21537 by Nilesh Patra at 2024-03-25T10:07:54+00:00
Pass GNU Test macro to resolve implicit function warning with pthread
- - - - -
5d9277d3 by Nilesh Patra at 2024-03-25T10:20:03+00:00
Also run dh_clean in addition to overriden ops
- - - - -
e63c921f by Nilesh Patra at 2024-03-25T10:31:21+00:00
Change exercises.sqc post installation - do not change files in source root
- - - - -
1a577145 by Nilesh Patra at 2024-03-25T16:09:07+05:30
Move from pkg-config => pkgconf
- - - - -
04766961 by Nilesh Patra at 2024-03-25T16:10:02+05:30
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fixup-implicit-function-declaration.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+hmmer2 (2.3.2+dfsg-9) unstable; urgency=medium
+
+ * Team Upload.
+ * Add patch to fix FTBFS due to implicit-function-decl
+ * Pass GNU Test macro to resolve implicit function
+ warning with pthread. (Closes: #1066436)
+ * Also run dh_clean in addition to overridden ops
+ * Change exercises.sqc post installation - do not
+ change files in source root (Closes: #1046065, #1049476)
+ * Move from pkg-config => pkgconf
+
+ -- Nilesh Patra <nilesh at iki.fi> Mon, 25 Mar 2024 16:09:47 +0530
+
hmmer2 (2.3.2+dfsg-8) unstable; urgency=medium
* Provide configure.ac as source for configure
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
libperl4-corelibs-perl,
libsquid-dev,
- pkg-config,
+ pkgconf,
dh-exec,
rename
Standards-Version: 4.6.1
=====================================
debian/patches/fixup-implicit-function-declaration.patch
=====================================
@@ -0,0 +1,12 @@
+--- a/src/funcs.h
++++ b/src/funcs.h
+@@ -171,6 +171,9 @@
+ /* mathsupport.c
+ * Much of this code deals with Dirichlet prior mathematics.
+ */
++
++extern double Gammln(double x);
++extern double IncompleteGamma(double a, double x);
+ extern int Prob2Score(float p, float null);
+ extern float Score2Prob(int sc, float null);
+ extern float Scorify(int sc);
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ spelling.patch
use_debian_packaged_biosquid.patch
build_libhmmer.a_with-fPIC.patch
add-runstatedir-option.patch
+fixup-implicit-function-declaration.patch
=====================================
debian/rules
=====================================
@@ -15,8 +15,9 @@ export AUTOHEADER = 'true'
dh $@
override_dh_clean:
+ dh_clean
if [ -e configure_not_used ] ; then mv configure_not_used configure; fi
- rm -f configure.ac
+ rm -f configure.ac src/config.h
# Trying to address #1025739 but the resulting configure file does not work
override_dh_autoreconf:
@@ -27,7 +28,7 @@ override_dh_autoreconf:
dh_autoreconf
override_dh_auto_configure:
- dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm
+ dh_auto_configure -- --enable-threads --enable-lfs PTHREAD_CFLAGS="-D_XOPEN_SOURCE=500" # --enable-pvm
# avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together)
sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \
-e '/^#define PACKAGE_NAME /a #endif' \
@@ -68,9 +69,9 @@ endif
override_dh_installexamples:
dh_installexamples
mkdir -p $(sampledir);
- sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
cp -a testsuite/* $(sampledir)/;
mkdir $(sampledir)/tutorial;
cp -a tutorial/* $(sampledir)/tutorial;
+ sed -i "s#hmm#hmm2#g" $(sampledir)/exercises.sqc
sed -i "s#../tut#./tut#g" $(sampledir)/exercises.sqc
find $(sampledir) -name 'Makefile' | xargs sed -i "s^$(CURDIR)^.^g"
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/fd3eb0a0d832a592bb9521d51a3da9b1f9dd6f19...04766961c8a832c97312b22a09f0dd61bc098504
--
View it on GitLab: https://salsa.debian.org/med-team/hmmer2/-/compare/fd3eb0a0d832a592bb9521d51a3da9b1f9dd6f19...04766961c8a832c97312b22a09f0dd61bc098504
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