[med-svn] [Git][med-team/crac][master] 3 commits: Do not use pkg-config in Makefile.am to enable cross building

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / crac


Commits:
8256fd70 by Andreas Tille at 2019-07-26T20:39:23Z
Do not use pkg-config in Makefile.am to enable cross building

- - - - -
adf640fc by Andreas Tille at 2019-07-26T20:39:48Z
debhelper-compat 12

- - - - -
5265461c by Andreas Tille at 2019-07-26T20:43:00Z
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/cross.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+crac (2.5.2+dfsg-2) unstable; urgency=medium
+
+  [ Helmut Grohne ]
+  * Do not use pkg-config in Makefile.am to enable cross building
+    Closes: #933024
+
+  [ Andreas Tille ]
+  * debhelper-compat 12
+
+ -- Andreas Tille <tille at debian.org>  Fri, 26 Jul 2019 22:40:52 +0200
+
 crac (2.5.2+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                zlib1g-dev,
                libhts-dev,
                libjellyfish-2.0-dev,


=====================================
debian/patches/cross.patch
=====================================
@@ -0,0 +1,68 @@
+Author: Helmut Grohne <helmut at subdivi.de>
+Last-Update: Thu, 25 Jul 2019 21:31:15 +0200
+Bug-Debian: https://bugs.debian.org/933024
+Description: crac fails to cross build from source, because it uses the build
+ architecture pkg-config in its Makefile.am files. Doing so is an
+ anti-pattern. You should never call pkg-config from a Makefile.am.
+ Instead such checks should be performed at configure time. The attached
+ patch implements that and makes crac cross buildable. Please consider
+ applying it.
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -282,6 +282,7 @@ AC_ARG_WITH([libProgressBar-prefix],
+             [with_libProgressBar_prefix=""])
+ 
+ dnl Check if we need included ProgressBar library.
++PKG_CHECK_MODULES([PROGRESSBAR],[libProgressBar])
+ PB_OK=0
+ AS_IF([test "x$with_included_ProgressBar" == "xcheck"],
+       [AS_IF([test "x$with_libProgressBar_prefix" != "x"],
+@@ -315,6 +316,7 @@ AC_CHECK_LIB([z], [gzread], ,
+ AC_CHECK_LIB([hts], [hts_hopen], ,
+              [AC_MSG_ERROR([htslib not found, see http://www.htslib.org/])])
+ 
++PKG_CHECK_MODULES([GKARRAYS],[libGkArrays])
+ GK_OK=1
+ AS_IF([test "x$with_included_GkArrays" != "xyes"],
+       [AC_CHECK_LIB([GkArrays],
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -149,11 +149,11 @@ if INCLUDED_JELLYFISH
+ endif
+ 
+ if INCLUDED_GKARRAYS
+-  AM_LDFLAGS += `pkg-config --libs libGkArrays`
+-  AM_CPPFLAGS += `pkg-config --cflags libGkArrays`
++  AM_LDFLAGS += $(GKARRAYS_LIBS)
++  AM_CPPFLAGS += $(GKARRAYS_CFLAGS)
+ if INCLUDED_PROGRESSBAR
+-  AM_LDFLAGS += `pkg-config --libs libProgressBar`
+-  AM_CPPFLAGS += `pkg-config --cflags libProgressBar`
++  AM_LDFLAGS += $(PROGRESSBAR_LIBS)
++  AM_CPPFLAGS += $(PROGRESSBAR_CFLAGS)
+ endif
+ endif
+ 
+--- a/src/libReadsInfo/Makefile.am
++++ b/src/libReadsInfo/Makefile.am
+@@ -124,7 +124,7 @@ libReadsInfo_a_SOURCES =
+ 
+ libReadsInfo_a_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_top_srcdir@/src -I at abs_top_srcdir@/src/libSSA 
+ if INCLUDED_GKARRAYS
+-  libReadsInfo_a_CPPFLAGS += `pkg-config --cflags libGkArrays`
++  libReadsInfo_a_CPPFLAGS += $(GKARRAYS_CFLAGS)
+ endif
+ 
+ 
+--- a/src/libSSA/Makefile.am
++++ b/src/libSSA/Makefile.am
+@@ -101,7 +101,7 @@
+ bin_PROGRAMS = crac-index
+ crac_index_SOURCES = cracIndex.cpp cracIndex.h
+ 
+-AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@/karkkainen_bwt `pkg-config --cflags libGkArrays`
++AM_CPPFLAGS = -I at abs_top_srcdir@ -I at abs_srcdir@/karkkainen_bwt $(GKARRAYS_CFLAGS)
+ AM_LDFLAGS = -lm -lpthread -lSSA -L at abs_builddir@/
+ LDADD = libSSA.a
+ 


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ use_debian_packaged_libjellyfish.patch
 skip_failed_test_bug-14958.patch
 use_debian_packages_libgtarrays.patch
 reproducible_build.patch
+cross.patch



View it on GitLab: https://salsa.debian.org/med-team/crac/compare/8192f40745e6008a626099572afac523a972c56b...5265461c6841d37655adb143bc2a45e2866c4d17

-- 
View it on GitLab: https://salsa.debian.org/med-team/crac/compare/8192f40745e6008a626099572afac523a972c56b...5265461c6841d37655adb143bc2a45e2866c4d17
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