diff options
| author | bacon <bacon@pkgsrc.org> | 2018-05-22 21:37:29 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2018-05-22 21:37:29 +0000 |
| commit | 46fe6025310f7c52e784441c4f40ec5d713f2fea (patch) | |
| tree | 3bf4903900ef32eaece8659858f7e209a42de1f2 /biology | |
| parent | 6b4d4d03b7b6e61f5d82ddc6138b407f09015985 (diff) | |
| download | pkgsrc-46fe6025310f7c52e784441c4f40ec5d713f2fea.tar.gz | |
biology/ncbi-blast+: Respect env to support PKGSRC_USE_RELRO
Fix a previous patch that hard-coded relro support by patching in pkgsrc
CFLAGS, CXXFLAGS, and LDFLAGS instead.
OK wiz@
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/ncbi-blast+/Makefile | 3 | ||||
| -rw-r--r-- | biology/ncbi-blast+/distinfo | 4 | ||||
| -rw-r--r-- | biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app | 10 |
3 files changed, 9 insertions, 8 deletions
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index bb84df1728c..84edbc1649a 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,7 +1,8 @@ -# $NetBSD: Makefile,v 1.1 2018/04/27 20:28:28 bacon Exp $ +# $NetBSD: Makefile,v 1.2 2018/05/22 21:37:29 bacon Exp $ DISTNAME= ncbi-blast-${PV}+-src PKGNAME= ncbi-blast+-${PV} +PKGREVISION= 1 CATEGORIES= biology MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/ diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo index a2df99c4125..a1780471f2b 100644 --- a/biology/ncbi-blast+/distinfo +++ b/biology/ncbi-blast+/distinfo @@ -1,4 +1,4 @@ -$NetBSD: distinfo,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: distinfo,v 1.2 2018/05/22 21:37:29 bacon Exp $ SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8 RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd @@ -9,4 +9,4 @@ SHA1 (patch-src_algo_blast_core_blast__kappa.c) = a580a5fb2d5a3af04c27dd63a7edd3 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01 SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97 SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6 -SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = 0fb99ac4e582938fd47e66c146da71695f009b98 +SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app b/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app index 55539d225a0..036b153d872 100644 --- a/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app +++ b/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app @@ -1,9 +1,9 @@ -$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.2 2018/05/22 21:37:29 bacon Exp $ # Missing RELRO for this one binary # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820959 ---- src/build-system/helpers/Makefile.run_with_lock.app.orig 2018-04-27 16:21:07.000000000 +0000 +--- src/build-system/helpers/Makefile.run_with_lock.app.orig 2016-02-23 17:06:47.000000000 +0000 +++ src/build-system/helpers/Makefile.run_with_lock.app @@ -6,9 +6,9 @@ CC = $(CC_FOR_BUILD) CC_WRAPPER = @@ -12,9 +12,9 @@ $NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.1 2018/ -CFLAGS = $(CFLAGS_FOR_BUILD) -CPPFLAGS = $(CPPFLAGS_FOR_BUILD) -LDFLAGS = $(LDFLAGS_FOR_BUILD) -+CFLAGS = $(CFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now -+CPPFLAGS = $(CPPFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now -+LDFLAGS = $(LDFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now ++CFLAGS := $(CFLAGS_FOR_BUILD) $(CFLAGS) ++CPPFLAGS := $(CPPFLAGS_FOR_BUILD) $(CPPFLAGS) ++LDFLAGS := $(LDFLAGS_FOR_BUILD) $(LDFLAGS) LIBS = $(C_LIBS) LINK = $(CC) LINK_WRAPPER = |