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Author: Helmut Grohne <helmut@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@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
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