CVS commit: pkgsrc/biology/ncbi-blast+

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue May 22 21:37:29 UTC 2018

Modified Files:
        pkgsrc/biology/ncbi-blast+: Makefile distinfo
        pkgsrc/biology/ncbi-blast+/patches:
            patch-src_build-system_helpers_Makefile.run__with__lock.app

Log Message:
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@


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/ncbi-blast+/Makefile \
    pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.1 pkgsrc/biology/ncbi-blast+/Makefile:1.2
--- pkgsrc/biology/ncbi-blast+/Makefile:1.1     Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/Makefile Tue May 22 21:37:29 2018
@@ -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+/${PV}/
Index: pkgsrc/biology/ncbi-blast+/distinfo
diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.1 pkgsrc/biology/ncbi-blast+/distinfo:1.2
--- pkgsrc/biology/ncbi-blast+/distinfo:1.1     Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/distinfo Tue May 22 21:37:29 2018
@@ -1,4 +1,4 @@
-$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__k
 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

Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.1 
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.2
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.1  Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app      Tue May 22 21:37:29 2018
@@ -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_
 -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 =