ncbi-blast+: Clean up, add bl3

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

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Apr 25 11:41:45 2018 -0500
Changeset:	5997d4f1bf8481313aaa9791aef0e7d73bc221fd

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/distinfo
	ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
	ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
	ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
	ncbi-blast+/patches/patch-src_build-system_configure
Added Files:
	ncbi-blast+/buildlink3.mk

Log Message:
ncbi-blast+: Clean up, add bl3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5997d4f1bf8481313aaa9791aef0e7d73bc221fd

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

diffstat:
 ncbi-blast+/Makefile                               | 42 +++++++++-------------
 ncbi-blast+/buildlink3.mk                          | 13 +++++++
 ncbi-blast+/distinfo                               |  8 ++---
 .../patches/patch-compilers_xcode30__prj_configure |  1 +
 .../patch-src_algo_blast_core_blast__kappa.c       |  1 +
 .../patch-src_build-system_cmake_cmake-configure   |  1 +
 .../patches/patch-src_build-system_configure       |  1 +
 7 files changed, 37 insertions(+), 30 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index 96a422e9b2..8d477b89a8 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,18 +1,10 @@
 # $NetBSD$
-#
-###########################################################
-#                  Generated by fbsd2pkg                  #
-#              Mon Mar 26 08:34:17 CDT 2018               #
-###########################################################
 
-# LIB_DEPENDS=
-#		libtspi.so:security/trousers \
-
-DISTNAME=	ncbi-blast-${PORTVERSION}+-src
-PKGNAME=	ncbi-blast+-${PORTVERSION}
+DISTNAME=	ncbi-blast-${PV}+-src
+PKGNAME=	ncbi-blast+-${PV}
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
-		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
+		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://blast.ncbi.nlm.nih.gov/
@@ -20,42 +12,40 @@ COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
 LICENSE=	public-domain
 
 # Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
-# Fix unknown options in configure
-SUBST_CLASSES+=		thread
-SUBST_STAGE.thread=	post-patch
-SUBST_SED.thread+=	-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
-SUBST_SED.thread+=	-e '/--infodir=DIR/d'
-SUBST_SED.thread+=	-e '/--mandir=DIR/d'
-SUBST_FILES.thread+=	${WRKSRC}/src/build-system/configure
+# Fix "unknown options" in configure
+SUBST_CLASSES+=		configure
+SUBST_STAGE.configure=	post-patch
+SUBST_SED.configure+=	-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
+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
+USE_TOOLS+=	gmake strip
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
 REPLACE_BASH=	compilers/xcode30_prj/configure
 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
 
-WRKSRC=			${WRKDIR}/${DISTNAME}/c++
-
 # The test for amq can hang, but amq is not needed so just avoid the test
 # configure chooses /usr/local/bin/ar with no flags
 # Resolve a conflict with libproj by moving libs to a subdir
 CONFIGURE_ENV=		ncbi_cv_prog_amq_w=no
 CONFIGURE_ARGS+=	AR="ar cr" --without-boost
 CONFIGURE_ARGS+=	--libdir=${PREFIX}/lib/ncbi-tools++
-
-MAKE_JOBS_SAFE=	no	# Intermittent issues
-
-PORTVERSION=	2.7.1
+MAKE_JOBS_SAFE=		no	# Intermittent issues
+WRKSRC=			${WRKDIR}/${DISTNAME}/c++
 
 .include "../../mk/bsd.prefs.mk"
 
 .if ${OPSYS} == NetBSD
 # statfs is deprecated on NetBSD, but still exists in libc
 # configure checks only for undefined reference, not for usability
-CONFIGURE_ENV+=         ac_cv_func_statfs=no
+CONFIGURE_ENV+=		ac_cv_func_statfs=no
 .endif
 
+PV=	2.7.1
+
 post-install:
 	${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
 	${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
diff --git a/ncbi-blast+/buildlink3.mk b/ncbi-blast+/buildlink3.mk
new file mode 100644
index 0000000000..929b9a9e70
--- /dev/null
+++ b/ncbi-blast+/buildlink3.mk
@@ -0,0 +1,13 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	ncbi-blast+
+
+.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
+NCBI_BLAST+_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.ncbi-blast++=	ncbi-blast+>=2.7.1
+BUILDLINK_PKGSRCDIR.ncbi-blast+?=	../../wip/ncbi-blast+
+
+.endif	# NCBI_BLAST+_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-ncbi-blast+
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index 92229cd1d8..2f28dd2490 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -4,8 +4,8 @@ SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8
 RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd
 SHA512 (ncbi-blast-2.7.1+-src.tar.gz) = e4b3914f51165ae4c82051068ed9d3470687a4e0f1df6274018c0ba14b241666a570d72265c7d167b8ce2a9075652744244a00e3e95c00c4252da0fbd80d17c6
 Size (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 bytes
-SHA1 (patch-compilers_xcode30__prj_configure) = d6bf60c1a12ef1ddd93af1bce87543a1d5156bea
-SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 0d0492bbb93d9ac48a9456bb5762c923ae84ffb9
+SHA1 (patch-compilers_xcode30__prj_configure) = c7d1a489176853663ccc7354796fb490d69ead91
+SHA1 (patch-src_algo_blast_core_blast__kappa.c) = a580a5fb2d5a3af04c27dd63a7edd349b7ae1be7
 SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
-SHA1 (patch-src_build-system_cmake_cmake-configure) = e120568c934342c8003f89470d78b28f87ae48c4
-SHA1 (patch-src_build-system_configure) = cd2cffb73da34806c189f871799960f78a1a5a4d
+SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97
+SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6
diff --git a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
index e04dbbad6c..0d69fa8b8c 100644
--- a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
+++ b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # Fix portibility
+
 --- compilers/xcode30_prj/configure.orig	2018-03-26 14:12:13.368983690 +0000
 +++ compilers/xcode30_prj/configure
 @@ -1,2 +1,2 @@
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 939e2f7b16..2565da87a3 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
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # Work around NetBSD stderr def choking macro
+
 --- src/algo/blast/core/blast_kappa.c.orig	2018-03-26 21:55:44.000000000 +0000
 +++ src/algo/blast/core/blast_kappa.c
 @@ -32,6 +32,7 @@
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
index a2b48f44b9..9d165fba9c 100644
--- a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
+++ b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # Fix portability issue
+
 --- src/build-system/cmake/cmake-configure.orig	2018-03-26 14:13:44.229849356 +0000
 +++ src/build-system/cmake/cmake-configure
 @@ -468,7 +468,7 @@ fi
diff --git a/ncbi-blast+/patches/patch-src_build-system_configure b/ncbi-blast+/patches/patch-src_build-system_configure
index 366e19784a..26493f44d3 100644
--- a/ncbi-blast+/patches/patch-src_build-system_configure
+++ b/ncbi-blast+/patches/patch-src_build-system_configure
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # Fix support for localstatedir
+
 --- src/build-system/configure.orig	2018-02-19 01:32:40 UTC
 +++ src/build-system/configure
 @@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do