[med-svn] [Git][med-team/hmmer2][master] 6 commits: Add patch to fix FTBFS

[Nilesh Patra (@nilesh)]

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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