ncib-blast+: Fix build on Darwin

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Oct 14 08:33:14 2019 -0500
Changeset:	5cc0b5263cc522683ed734b891964f65c8320491

Modified Files:
	ncbi-blast+/Makefile
	ncbi-blast+/distinfo
	ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
	ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
	ncbi-blast+/patches/patch-src_build-system_configure
	ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h

Log Message:
ncib-blast+: Fix build on Darwin

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5cc0b5263cc522683ed734b891964f65c8320491

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

diffstat:
 ncbi-blast+/Makefile                               |  6 +++--
 ncbi-blast+/distinfo                               |  4 +--
 .../patch-src_algo_blast_core_blast__kappa.c       |  2 +-
 .../patch-src_build-system_cmake_cmake-cfg-unix.sh |  2 +-
 .../patches/patch-src_build-system_configure       | 31 ++++++++++++++++++----
 .../patch-src_util_checksum_farmhash_farmhash.h    |  2 +-
 6 files changed, 35 insertions(+), 12 deletions(-)

diffs:
diff --git a/ncbi-blast+/Makefile b/ncbi-blast+/Makefile
index 183f1d375a..f92396e7bb 100644
--- a/ncbi-blast+/Makefile
+++ b/ncbi-blast+/Makefile
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.4 2018/07/20 03:34:03 ryoon Exp $
+# $NetBSD: Makefile,v 1.11 2019/08/11 13:18:00 wiz Exp $
 
 DISTNAME=	ncbi-blast-2.8.1+-src
 PKGNAME=	${DISTNAME:S/+-src//:S/blast/blast+/}
+PKGREVISION=	5
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
@@ -20,9 +21,10 @@ SUBST_SED.configure+=	-e '/--infodir=DIR/d'
 SUBST_SED.configure+=	-e '/--mandir=DIR/d'
 SUBST_FILES.configure+=	${WRKSRC}/src/build-system/configure
 
-USE_TOOLS+=	bash gmake
+USE_TOOLS+=	bash gmake perl
 USE_LANGUAGES=	c c++
 GNU_CONFIGURE=	yes
+GNU_CONFIGURE_STRICT=	no	# doesn't know --enable-option-checking
 REPLACE_BASH=	scripts/common/impl/define_random_macros.sh
 REPLACE_BASH+=	src/app/blast/get_species_taxids.sh
 REPLACE_PERL=	src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
index a46bb8c1b0..dd5de1e83b 100644
--- a/ncbi-blast+/distinfo
+++ b/ncbi-blast+/distinfo
@@ -1,4 +1,4 @@
-$NetBSD$
+$NetBSD: distinfo,v 1.3 2019/01/07 15:00:10 bacon Exp $
 
 SHA1 (ncbi-blast-2.8.1+-src.tar.gz) = 16573b642d7861d0bed67f3eb1174fc646819eec
 RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd
@@ -9,6 +9,6 @@ SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de
 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
-SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6
+SHA1 (patch-src_build-system_configure) = a50fffa8239120100483e10a35f9e083ac354f63
 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd
 SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b
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 9151cc267c..b5ee840aba 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
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 bacon Exp $
+$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.2 2019/01/07 15:00:10 bacon Exp $
 
 # Work around NetBSD stderr def choking macro
 
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
index c51cfed7ca..0e184ea4af 100644
--- a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
+++ b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
@@ -1,4 +1,4 @@
-$NetBSD$
+$NetBSD: patch-src_build-system_cmake_cmake-cfg-unix.sh,v 1.1 2019/01/07 15:00:10 bacon Exp $
 
 # Portability
 
diff --git a/ncbi-blast+/patches/patch-src_build-system_configure b/ncbi-blast+/patches/patch-src_build-system_configure
index 466f7b69c5..81ac8c292e 100644
--- a/ncbi-blast+/patches/patch-src_build-system_configure
+++ b/ncbi-blast+/patches/patch-src_build-system_configure
@@ -1,15 +1,36 @@
-$NetBSD: patch-src_build-system_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $
+$NetBSD$
 
-# Fix support for localstatedir
+# Fix support for localstatedir and with-libiconv-prefix
 
---- src/build-system/configure.orig	2018-02-19 01:32:40 UTC
+--- src/build-system/configure.orig	2018-11-13 14:37:02.000000000 +0000
 +++ src/build-system/configure
-@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
+@@ -1783,8 +1783,8 @@ for x_arg in "$@" ; do
+       | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
        | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
        | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
-       | --datadir=* | --sysconfdir=* | --localstatedir=* \
+-      | --datadir=* | --sysconfdir=* | --localstatedir=* \
 -      | --with-runpath=* | --with-relative-runpath=* \
++      | --datadir=* | --sysconfdir=* | --localstatedir=* | --with-libiconv-prefix=* \
 +      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
        | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
        | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
        | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
+@@ -1857,9 +1857,7 @@ Fine tuning of the installation director
+   --oldincludedir=DIR    C header files for non-gcc [/usr/include]
+   --datarootdir=DIR      read-only arch.-independent data root [PREFIX/share]
+   --datadir=DIR          read-only architecture-independent data [DATAROOTDIR]
+-  --infodir=DIR          info documentation [DATAROOTDIR/info]
+   --localedir=DIR        locale-dependent data [DATAROOTDIR/locale]
+-  --mandir=DIR           man documentation [DATAROOTDIR/man]
+   --docdir=DIR           documentation root [DATAROOTDIR/doc/ncbi-tools--]
+   --htmldir=DIR          html documentation [DOCDIR]
+   --dvidir=DIR           dvi documentation [DOCDIR]
+@@ -8250,7 +8248,7 @@ case "$host_os:$compiler" in
+ esac
+ 
+ if test "$with_mt" != "no" ; then
+-   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE"
++   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL"
+    LIBS="$LIBS $THREAD_LIBS"
+    case "$host_os:$compiler" in
+      solaris2.??:* | solaris*:GCC | *:Compaq | irix* | aix* | darwin* | cygwin*)
diff --git a/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h b/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
index 89e72bd212..dcd0a43378 100644
--- a/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
+++ b/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
@@ -1,4 +1,4 @@
-$NetBSD$
+$NetBSD: patch-src_util_checksum_farmhash_farmhash.h,v 1.1 2019/01/07 15:00:11 bacon Exp $
 
 # __GNUC__ does not imply location of endian.h.  Check for BSD first.