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 <[email protected]> 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 <[email protected]. Uploaders: Andreas Tille <[email protected]> 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 <[email protected]> +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@abs_top_srcdir@ -I@abs_top_srcdir@/src -I@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@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt `pkg-config --cflags libGkArrays` ++AM_CPPFLAGS = -I@abs_top_srcdir@ -I@abs_srcdir@/karkkainen_bwt $(GKARRAYS_CFLAGS) + AM_LDFLAGS = -lm -lpthread -lSSA -L@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 You're receiving this email because of your account on salsa.debian.org.
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