Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093

4 files changed, 11 insertions, 21 deletions

diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile
index d906a3428bd8..1a080d9f26b1 100644
--- a/biology/htslib/Makefile
+++ b/biology/htslib/Makefile
@@ -17,10 +17,11 @@ TEST_DEPENDS=	bash:shells/bash
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
 
-USES=		autoreconf gmake perl5 shebangfix
+USES=		autoreconf gmake pathfix perl5 shebangfix
 USE_PERL5=	test
 USE_LDCONFIG=	yes
 GNU_CONFIGURE=	yes
+PATHFIX_MAKEFILEIN=	Makefile
 SHEBANG_FILES=	test/compare_sam.pl test/test.pl
 
 OPTIONS_DEFINE=		CURL
diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
index cb35c2f0f055..3a2b195df912 100644
--- a/biology/htslib/files/patch-Makefile
+++ b/biology/htslib/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2015-12-15 16:34:33 UTC
+--- Makefile.orig	2016-04-22 08:45:12 UTC
 +++ Makefile
 @@ -22,16 +22,7 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
@@ -17,7 +17,7 @@
  
  # For now these don't work too well as samtools also needs to know to
  # add -lbz2 and -llzma if linking against the static libhts.a library.
-@@ -58,16 +49,10 @@ includedir  = $(prefix)/include
+@@ -58,17 +49,11 @@ includedir  = $(prefix)/include
  libdir      = $(exec_prefix)/lib
  libexecdir  = $(exec_prefix)/libexec
  datarootdir = $(prefix)/share
@@ -25,17 +25,17 @@
 +mandir      = $(prefix)/man
  man1dir     = $(mandir)/man1
  man5dir     = $(mandir)/man5
--pkgconfigdir= $(libdir)/pkgconfig
--
+ pkgconfigdir= $(prefix)/libdata/pkgconfig
+ 
 -MKDIR_P = mkdir -p
 -INSTALL = install -p
 -INSTALL_PROGRAM = $(INSTALL)
 -INSTALL_DATA    = $(INSTALL) -m 644
 -INSTALL_DIR     = $(MKDIR_P) -m 755
-+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
- 
+-
  # Set by config.mk if plugins are enabled
  plugindir =
+ 
 @@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
  	test/test-vcf-api \
  	test/test-vcf-sweep
@@ -45,7 +45,7 @@
  
  HTSPREFIX =
  include htslib_vars.mk
-@@ -361,7 +346,7 @@ installdirs:
+@@ -360,7 +345,7 @@ installdirs:
  # and libhts.so.NN (used by client executables at runtime).
  
  install-so: libhts.so installdirs
diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
index 92c3e8e8fb0f..835189d8c0c9 100644
--- a/biology/jellyfish/Makefile
+++ b/biology/jellyfish/Makefile
@@ -17,7 +17,7 @@ BUILD_DEPENDS=	yaggo:devel/yaggo
 GNU_CONFIGURE=	yes
 
 USES=		autoreconf compiler:c++11-lib gmake \
-		libtool pkgconfig
+		libtool pathfix pkgconfig
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
@@ -35,10 +35,4 @@ BROKEN_FreeBSD_9_i386=	multiple code issues on i386 < 10.0-RELEASE
 CONFIGURE_ARGS+=--without-sse
 .endif
 
-# configure does not support --with-pkgconfigdir
-post-patch:
-	@${REINPLACE_CMD} \
-		-e 's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|g' \
-		${WRKSRC}/Makefile.am
-
 .include <bsd.port.post.mk>
diff --git a/biology/libgtextutils/Makefile b/biology/libgtextutils/Makefile
index 1cc106ef7e7d..04037d5c7814 100644
--- a/biology/libgtextutils/Makefile
+++ b/biology/libgtextutils/Makefile
@@ -10,7 +10,7 @@ COMMENT=	Gordon's text utilities
 
 LICENSE=	AGPLv3
 
-USES=		autoreconf libtool pkgconfig
+USES=		autoreconf libtool pathfix pkgconfig
 GNU_CONFIGURE=	yes
 USE_LDCONFIG=	yes
 
@@ -19,9 +19,4 @@ GH_ACCOUNT=	agordon
 
 INSTALL_TARGET=	install-strip
 
-post-patch:
-	@${REINPLACE_CMD} \
-		's|$$(libdir)/pkgconfig|${PREFIX}/libdata/pkgconfig|' \
-		${WRKSRC}/Makefile.am
-
 .include <bsd.port.mk>