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| author | mat <mat@FreeBSD.org> | 2016-10-21 23:21:13 +0800 |
|---|---|---|
| committer | mat <mat@FreeBSD.org> | 2016-10-21 23:21:13 +0800 |
| commit | 60e51bda11dcc0742419f2a459990d0d81cb07d8 (patch) | |
| tree | a5029ff30555b3a7ee0621f4dd5aacb832fde1d8 /biology | |
| parent | 3432585b4743642027fc2b3af5eac2780fc2c4cd (diff) | |
| download | freebsd-ports-gnome-60e51bda11dcc0742419f2a459990d0d81cb07d8.tar.gz freebsd-ports-gnome-60e51bda11dcc0742419f2a459990d0d81cb07d8.tar.zst freebsd-ports-gnome-60e51bda11dcc0742419f2a459990d0d81cb07d8.zip | |
Use USES=pathfix where applicable.
PR: 213195
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D8093
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/htslib/Makefile | 3 | ||||
| -rw-r--r-- | biology/htslib/files/patch-Makefile | 14 | ||||
| -rw-r--r-- | biology/jellyfish/Makefile | 8 | ||||
| -rw-r--r-- | biology/libgtextutils/Makefile | 7 |
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> |