ncbi-blast+: Patches for CentOS 7

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 2 09:07:42 2019 -0600
Changeset:	767e0ec35abde549e2c7099d56e2688456e33714

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/distinfo
	ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c

Log Message:
ncbi-blast+: Patches for CentOS 7

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=767e0ec35abde549e2c7099d56e2688456e33714

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

diffstat:
 ncbi-blast+/Makefile                                         | 9 ++++++++-
 ncbi-blast+/distinfo                                         | 2 +-
 ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c | 2 ++
 3 files changed, 11 insertions(+), 2 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index faf3d8622d..1be09dce43 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -20,9 +20,16 @@ SUBST_SED.configure+=	-e '/--infodir=DIR/d'
 SUBST_SED.configure+=	-e '/--mandir=DIR/d'
 SUBST_FILES.configure+=	${WRKSRC}/src/build-system/configure
 
-USE_TOOLS+=	gmake
+# Can't use a patch due to RCS tags in the script
+SUBST_CLASSES+=		random
+SUBST_STAGE.random=	pre-configure
+SUBST_SED.random=	-e 's|/bin/sh|/usr/bin/env bash|'
+SUBST_FILES.random=	${WRKSRC}/scripts/common/impl/define_random_macros.sh
+
+USE_TOOLS+=	bash gmake
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
+REPLACE_BASH=	scripts/common/impl/define_random_macros.sh
 REPLACE_PERL=	src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
 REPLACE_PYTHON=	src/app/winmasker/windowmasker_2.2.22_adapter.py
 
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 5781af9568..8695e2816e 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -5,7 +5,7 @@ RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd
 SHA512 (ncbi-blast-2.8.1+-src.tar.gz) = 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f
 Size (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 bytes
 SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
-SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 29108a2922ae9f48996ff60f7eed90cad0108a6f
+SHA1 (patch-src_algo_blast_core_blast__kappa.c) = bf434d830a6bb7e9089c7ff1870aae0d8c82ce67
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
 SHA1 (patch-src_build-system_cmake_cmake-cfg-unix.sh) = 90468f3109800e01fc7351926adb331919a12fb2
 SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97
diff --git a/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c b/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
index 0de6982b37..4c731c9b5a 100644
--- a/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
+++ b/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Macro chokes on NetBSD's way of defining stderr
+
 --- src/algo/blast/core/blast_kappa.c.orig	2019-01-02 04:00:17.000000000 +0000
 +++ src/algo/blast/core/blast_kappa.c
 @@ -32,6 +32,7 @@