ncbi-blast+: Patch for RELRO on NetBSD

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Apr 27 12:39:44 2018 -0500
Changeset:	f72f77b1f074b544f7f0b1c864d3f6f2a18c28c1

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

Log Message:
ncbi-blast+: Patch for RELRO on NetBSD

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f72f77b1f074b544f7f0b1c864d3f6f2a18c28c1

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

diffstat:
 ncbi-blast+/distinfo                                 |  1 +
 ...build-system_helpers_Makefile.run__with__lock.app | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+)

diffs:
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index cafc10e425..2823474e3f 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -9,3 +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
diff --git a/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app b/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
new file mode 100644
index 0000000000..300aeca060
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
@@ -0,0 +1,20 @@
+$NetBSD$
+
+# 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
+@@ -6,9 +6,9 @@ CC          = $(CC_FOR_BUILD)
+ CC_WRAPPER  =
+ CXX_WRAPPER =
+ CPP         = $(CPP_FOR_BUILD)
+-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
+ LIBS        = $(C_LIBS)
+ LINK        = $(CC)
+ LINK_WRAPPER =