*/*: sync with upstream

Taken from: HardenedBSD

audio/easytag/files/patch-configure

@@ -0,0 +1,11 @@
+--- configure.orig	2018-03-31 02:06:04 UTC
++++ configure
+@@ -18871,7 +18871,7 @@ return ID3Tag_Link ();
+   return 0;
+ }
+ _ACEOF
+-for ac_lib in '' "id3" "id3 -lstdc++" "id3 -lz" "id3 -lz -lstdc++"; do
++for ac_lib in "id3 -lstdc++" "id3 -lz -lstdc++"; do
+   if test -z "$ac_lib"; then
+     ac_res="none required"
+   else

biology/Makefile

@@ -109,6 +109,7 @@
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += ssaha
+    SUBDIR += stacks
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker

biology/stacks/Makefile

@@ -0,0 +1,20 @@
+# $FreeBSD$
+
+PORTNAME=	stacks
+DISTVERSION=	1.48
+CATEGORIES=	biology
+MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
+
+MAINTAINER=	[email protected]
+COMMENT=	Software pipeline for building loci from short-read sequences
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		gmake python shebangfix
+SHEBANG_FILES=	scripts/*.pl scripts/*.py
+GNU_CONFIGURE=	yes
+
+LDFLAGS+=	-lpthread
+
+.include <bsd.port.mk>

biology/stacks/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1520376299
+SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e
+SIZE (stacks-1.48.tar.gz) = 895195

biology/stacks/files/patch-htslib_Makefile

@@ -0,0 +1,20 @@
+--- htslib/Makefile.orig	2016-09-16 15:40:03 UTC
++++ htslib/Makefile
+@@ -22,13 +22,13 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
++CC     ?= gcc
++AR     ?= ar
++RANLIB ?= ranlib
+
+ CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-CFLAGS   = -g -Wall -O2
++CFLAGS   ?= -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+ LDFLAGS  =
+ LIBS     =

biology/stacks/pkg-descr

@@ -0,0 +1,6 @@
+Stacks is a software pipeline for building loci from short-read sequences, such
+as those generated on the Illumina platform. Stacks was developed to work with
+restriction enzyme-based data, such as RAD-seq, for the purpose of building
+genetic maps and conducting population genomics and phylogeography.
+
+WWW: http://catchenlab.life.illinois.edu/stacks/

biology/stacks/pkg-message

@@ -0,0 +1,16 @@
+===
+
+If you would like to use the stacks web interface, follow the instructions at:
+
+    http://catchenlab.life.illinois.edu/stacks/manual-v1/#install
+
+You will need to install databases/p5-DBD-mysql to allow the optional
+wrapper scripts to interact with the database server.
+
+To set up the web server, you will need an apache server such as www/apache24,
+MySQL server and client packages such as databases/mysql56-client and 
+databases/mysql56-server, and PHP interface modules such as
+databases/php56-mysql (php56 will be automatically installed as a dependency),
+and lastly textproc/p5-Spreadsheet-WriteExcel.
+
+===

biology/stacks/pkg-plist

@@ -0,0 +1,70 @@
+bin/clone_filter
+bin/count_fixed_catalog_snps.py
+bin/cstacks
+bin/denovo_map.pl
+bin/exec_velvet.pl
+bin/export_sql.pl
+bin/genotypes
+bin/index_radtags.pl
+bin/integrate_alignments.py
+bin/kmer_filter
+bin/load_radtags.pl
+bin/load_sequences.pl
+bin/phasedstacks
+bin/populations
+bin/process_radtags
+bin/process_shortreads
+bin/pstacks
+bin/ref_map.pl
+bin/rxstacks
+bin/sort_read_pairs.pl
+bin/sstacks
+bin/stacks_export_notify.pl
+bin/ustacks
+%%DATADIR%%/php/CatalogClass.php
+%%DATADIR%%/php/Locus.php
+%%DATADIR%%/php/ajax.js
+%%DATADIR%%/php/annotate.js
+%%DATADIR%%/php/annotate_marker.php
+%%DATADIR%%/php/catalog.php
+%%DATADIR%%/php/catalog_genotypes.php
+%%DATADIR%%/php/constants.php.dist
+%%DATADIR%%/php/correct_genotype.php
+%%DATADIR%%/php/correct_genotypes.php
+%%DATADIR%%/php/db_functions.php
+%%DATADIR%%/php/export.js
+%%DATADIR%%/php/export_batch.php
+%%DATADIR%%/php/fst_view.php
+%%DATADIR%%/php/hapstat_view.php
+%%DATADIR%%/php/header.php
+%%DATADIR%%/php/images/caret-d.png
+%%DATADIR%%/php/images/caret-u.png
+%%DATADIR%%/php/images/excel_icon.png
+%%DATADIR%%/php/images/l-arrow-disabled.png
+%%DATADIR%%/php/images/l-arrow.png
+%%DATADIR%%/php/images/r-arrow-disabled.png
+%%DATADIR%%/php/images/r-arrow.png
+%%DATADIR%%/php/images/stacks_bg.png
+%%DATADIR%%/php/images/stacks_logo_rev_small.png
+%%DATADIR%%/php/index.php
+%%DATADIR%%/php/last_modified.php
+%%DATADIR%%/php/phist_view.php
+%%DATADIR%%/php/pop_view.php
+%%DATADIR%%/php/population_view.js
+%%DATADIR%%/php/samples.php
+%%DATADIR%%/php/sequence_blast.php
+%%DATADIR%%/php/stack_view.php
+%%DATADIR%%/php/stacks.css
+%%DATADIR%%/php/stacks.js
+%%DATADIR%%/php/stacks_functions.php
+%%DATADIR%%/php/sumstat_view.php
+%%DATADIR%%/php/tag.php
+%%DATADIR%%/php/tags.php
+%%DATADIR%%/php/version.php
+%%DATADIR%%/php/view_sequence.php
+%%DATADIR%%/sql/catalog_index.sql
+%%DATADIR%%/sql/chr_index.sql
+%%DATADIR%%/sql/mysql.cnf.dist
+%%DATADIR%%/sql/stacks.sql
+%%DATADIR%%/sql/tag_index.sql
+@dir %%DATADIR%%/php/export

converters/p5-Unicode-String/Makefile

@@ -10,6 +10,9 @@ PKGNAMEPREFIX=	p5-
 MAINTAINER=	[email protected]
 COMMENT=	Perl5 modules to handle various Unicode issues
 
+LICENSE=	ART10 GPLv1+
+LICENSE_COMB=	dual
+
 USES=		perl5
 USE_PERL5=	configure
 

databases/memcached/Makefile

@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	memcached
-PORTVERSION=	1.5.6
+PORTVERSION=	1.5.7
 CATEGORIES=	databases
 MASTER_SITES=	http://www.memcached.org/files/ \
 		GENTOO

databases/memcached/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1519944014
-SHA256 (memcached-1.5.6.tar.gz) = 9675ee859d7d81f7a950f190a6812720b26f08228d356044ec517d4d5af25f03
-SIZE (memcached-1.5.6.tar.gz) = 452038
+TIMESTAMP = 1522358405
+SHA256 (memcached-1.5.7.tar.gz) = 5bb706a8fc7ae7461a6788eaddd85e4a4e84e952d3a80c21926342c2838f4e46
+SIZE (memcached-1.5.7.tar.gz) = 458062

databases/p5-DBD-CSV/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	DBD-CSV
-PORTVERSION=	0.49
+PORTVERSION=	0.51
 PORTEPOCH=	1
 CATEGORIES=	databases perl5
 MASTER_SITES=	CPAN

databases/p5-DBD-CSV/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1466507621
-SHA256 (DBD-CSV-0.49.tgz) = 86fcea010571a6f774344c920c23619c899f8aee30d2961fe2716306a95e9a80
-SIZE (DBD-CSV-0.49.tgz) = 39271
+TIMESTAMP = 1522513695
+SHA256 (DBD-CSV-0.51.tgz) = 603d9756a07e9fc0483d45ef92601319f71dffc7ec490d79680f756dfdc73a08
+SIZE (DBD-CSV-0.51.tgz) = 39260

databases/pglogical/Makefile

@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	pglogical
-PORTVERSION=	2.1.1
+PORTVERSION=	2.2.0
 CATEGORIES=	databases
 
 MAINTAINER=	[email protected]
@@ -16,7 +16,7 @@ WANT_PGSQL=	client server
 USE_GITHUB=	yes
 GH_ACCOUNT=	2ndQuadrant
 GH_PROJECT=	pglogical pglogical_dump:dump
-GH_TAGNAME=	REL2_1_1 9f3b0b1:dump
+GH_TAGNAME=	REL2_2_0 f66606d:dump
 GH_SUBDIR=	pglogical_dump:dump
 
 MAKE_ARGS=	USE_PGXS=1

databases/pglogical/distinfo

@@ -1,5 +1,5 @@
-TIMESTAMP = 1515711146
-SHA256 (2ndQuadrant-pglogical-2.1.1-REL2_1_1_GH0.tar.gz) = 5f9f9059d36bebb57d567c108a33aa8273d3525dd9e755ac44c71f249c33785f
-SIZE (2ndQuadrant-pglogical-2.1.1-REL2_1_1_GH0.tar.gz) = 244676
-SHA256 (2ndQuadrant-pglogical_dump-9f3b0b1_GH0.tar.gz) = 915250bf63f3b309228c5a2bbd9bfc7df3e1e5e2b54e89f3c52e722797b7b8aa
-SIZE (2ndQuadrant-pglogical_dump-9f3b0b1_GH0.tar.gz) = 206704
+TIMESTAMP = 1521278458
+SHA256 (2ndQuadrant-pglogical-2.2.0-REL2_2_0_GH0.tar.gz) = 47c5091f18194899abea70b902bbbd38f7ac18192cf618b90faa618f013d8d4b
+SIZE (2ndQuadrant-pglogical-2.2.0-REL2_2_0_GH0.tar.gz) = 251121
+SHA256 (2ndQuadrant-pglogical_dump-f66606d_GH0.tar.gz) = 09666d5927fe071c9a2ef64eb7028f793cfea10510a3d17e8ef4335349291e63
+SIZE (2ndQuadrant-pglogical_dump-f66606d_GH0.tar.gz) = 206722

databases/pglogical/files/patch-pglogical__fe.c

@@ -0,0 +1,11 @@
+--- pglogical_fe.c.orig	2018-03-17 09:48:56 UTC
++++ pglogical_fe.c
+@@ -10,6 +10,8 @@
+  *
+  *-------------------------------------------------------------------------
+  */
++#include <sys/wait.h>
++
+ #include "postgres_fe.h"
+
+ #include "pglogical_fe.h"

databases/pglogical/pkg-plist

@@ -15,7 +15,8 @@ share/postgresql/extension/pglogical--2.0.0--2.0.1.sql
 share/postgresql/extension/pglogical--2.0.0--2.1.0.sql
 share/postgresql/extension/pglogical--2.0.1--2.1.0.sql
 share/postgresql/extension/pglogical--2.1.0--2.1.1.sql
-share/postgresql/extension/pglogical--2.1.1.sql
+share/postgresql/extension/pglogical--2.1.1--2.2.0.sql
+share/postgresql/extension/pglogical--2.2.0.sql
 share/postgresql/extension/pglogical.control
 share/postgresql/extension/pglogical_origin--1.0.0.sql
 share/postgresql/extension/pglogical_origin.control

devel/Makefile

@@ -1664,7 +1664,6 @@
     SUBDIR += lua-gettext
     SUBDIR += lua-lgi
     SUBDIR += lua-lpeg
-    SUBDIR += lua-lpeg51
     SUBDIR += lua-luacheck
     SUBDIR += lua-luarocks
     SUBDIR += lua-lunit
@@ -4208,6 +4207,7 @@
     SUBDIR += py-PyExecJS
     SUBDIR += py-PyLD
     SUBDIR += py-PyODE
+    SUBDIR += py-PyUtilib
     SUBDIR += py-QtPy
     SUBDIR += py-RPyC
     SUBDIR += py-Record

devel/apr2/Makefile

@@ -29,6 +29,7 @@ CPE_VERSION=	${PORTVERSION:S|.${SNAPDATE}||}
 USE_PERL5=		build
 USE_LDCONFIG=		yes
 GNU_CONFIGURE=		yes
+TEST_TARGET=		test
 
 OPTIONS_SUB=		yes
 OPTIONS_DEFINE=		DEVELOPER_ONLY
@@ -125,9 +126,4 @@ pre-install:
 post-install:
 	${FIND} ${STAGEDIR}/${PREFIX}/lib -name \*.so | ${XARGS} ${STRIP_CMD}
 
-test:	build
-	@-make test -C ${WRKSRC}
-
-#regression-test:	test
-
 .include <bsd.port.mk>

devel/ga/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	ga
 DISTVERSIONPREFIX=	v
-DISTVERSION=	5.6.4
+DISTVERSION=	5.6.5
 CATEGORIES=	devel
 
 MAINTAINER=	[email protected]

devel/ga/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1522000478
-SHA256 (GlobalArrays-ga-v5.6.4_GH0.tar.gz) = f1e2e92e0ab76f58d7f8afde633b7614dc120f35a99b6880e7320b1dd7e8e652
-SIZE (GlobalArrays-ga-v5.6.4_GH0.tar.gz) = 4958446
+TIMESTAMP = 1522394877
+SHA256 (GlobalArrays-ga-v5.6.5_GH0.tar.gz) = abeb6e105e1a39e9ceb092c5d301f0cb6fa9bf5ce480bd5dd54ac87d86a20346
+SIZE (GlobalArrays-ga-v5.6.5_GH0.tar.gz) = 4963339

devel/ga/pkg-descr

@@ -8,4 +8,4 @@ obtained and taken advantage of whenever data locality is important. The
 primary target architectures for which GA was developed are massively-parallel
 distributed-memory and scalable shared-memory systems.
 
-WWW: https://github.com/GlobalArrays/ga
+WWW: http://hpc.pnl.gov/globalarrays/

devel/ga/pkg-plist

@@ -46,4 +46,4 @@ lib/libcomex.so.0
 lib/libcomex.so.0.0.0
 lib/libga.so
 lib/libga.so.1
-lib/libga.so.1.0.4
+lib/libga.so.1.0.5

devel/jenkins/Makefile

@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	jenkins
-PORTVERSION=	2.112
+PORTVERSION=	2.113
 CATEGORIES=	devel java
 MASTER_SITES=	http://mirrors.jenkins-ci.org/war/${PORTVERSION}/
 DISTNAME=	jenkins

devel/jenkins/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1521523660
-SHA256 (jenkins/2.112/jenkins.war) = 085f597edeb0d49d54d7653f3742ba31ed72b8a1a2b053d2eb23fd806c6a5393
-SIZE (jenkins/2.112/jenkins.war) = 74601396
+TIMESTAMP = 1522421016
+SHA256 (jenkins/2.113/jenkins.war) = 3c443d9aeb178058287d12bb5b81b330e78e83ea949069b82c780257ce301390
+SIZE (jenkins/2.113/jenkins.war) = 74584533

devel/llvm-cheri/Makefile

@@ -2,6 +2,7 @@
 
 PORTNAME=	llvm
 PORTVERSION=	${LLVM_MAJOR}.d${SNAPDATE}
+PORTREVISION=	1
 CATEGORIES=	devel lang
 PKGNAMESUFFIX=	${LLVM_SUFFIX}
 

devel/llvm-cheri/files/llvm-wrapper.sh.in

@@ -4,7 +4,8 @@
 LLVM_PREFIX="%%LLVM_PREFIX%%"
 LLVM_SUFFIX="%%LLVM_SUFFIX%%"
 
-tool=$(basename $0)
+tool=$(/bin/realpath $0)
+tool=${tool##*/}
 tool="${LLVM_PREFIX}/bin/${tool%${LLVM_SUFFIX}}"
 LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}${LLVM_PREFIX}/lib" \
     "${tool}" "${@}"

devel/llvm33/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	llvm
 PORTVERSION=	3.3
-PORTREVISION=	13
+PORTREVISION=	14
 CATEGORIES=	devel lang
 MASTER_SITES=	http://llvm.org/releases/${PORTVERSION}/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src

devel/llvm33/files/llvm-wrapper.sh.in

@@ -4,7 +4,8 @@
 LLVM_PREFIX="%%LLVM_PREFIX%%"
 LLVM_SUFFIX="%%LLVM_SUFFIX%%"
 
-tool=$(basename $0)
+tool=$(/bin/realpath $0)
+tool=${tool##*/}
 tool="${LLVM_PREFIX}/bin/${tool%${LLVM_SUFFIX}}"
 LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}${LLVM_PREFIX}/lib" \
     "${tool}" "${@}"

devel/llvm34/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	llvm
 PORTVERSION=	3.4.2
-PORTREVISION=	8
+PORTREVISION=	9
 CATEGORIES=	devel lang
 MASTER_SITES=	http://llvm.org/releases/${PORTVERSION}/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src

devel/llvm34/files/llvm-wrapper.sh.in

@@ -4,7 +4,8 @@
 LLVM_PREFIX="%%LLVM_PREFIX%%"
 LLVM_SUFFIX="%%LLVM_SUFFIX%%"
 
-tool=$(basename $0)
+tool=$(/bin/realpath $0)
+tool=${tool##*/}
 tool="${LLVM_PREFIX}/bin/${tool%${LLVM_SUFFIX}}"
 LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}${LLVM_PREFIX}/lib" \
     "${tool}" "${@}"

devel/llvm35/Makefile

@@ -2,7 +2,7 @@
 
 PORTNAME=	llvm
 DISTVERSION=	3.5.2
-PORTREVISION=	6
+PORTREVISION=	7
 CATEGORIES=	devel lang
 MASTER_SITES=	http://llvm.org/releases/3.5.2/
 DISTNAME=	${PORTNAME}-${DISTVERSION}.src