freebsd update to 1.86

.gitignore

@@ -1 +1,5 @@
 *~
+pooler/128.h
+pooler/32-64.h
+pooler/32.h
+pooler/pooler

freebsd/Makefile

@@ -1,14 +1,16 @@
 PORTNAME=		pooler
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.85
+DISTVERSION=		1.86
 CATEGORIES=		biology
 
 MAINTAINER=	[email protected]
 COMMENT=	Optimise DNA sequencing primer-set combinations
+WWW=		https://ssb22.user.srcf.net/pooler/
 
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKDIR}/${GH_PROJECT}-${PORTVERSION}/LICENSE
 
+USES=		desktop-file-utils
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	ssb22

freebsd/README.md

@@ -2,17 +2,19 @@ FreeBSD port
 ============
 
 This was [committed to FreeBSD's ports tree](https://svnweb.freebsd.org/ports?view=revision&revision=555418)
-under `/usr/ports/biology/pooler` (porting discussion was on [issue 251065](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=251065),
+under `/usr/ports/biology/pooler`, porting discussion was on [issue 251065](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=251065),
 v1.77 update was [472c25a](https://cgit.freebsd.org/ports/commit/?id=472c25aa5d8dc3268fc5476b53100872d1900467)
-discussed at [257975](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=257975)),
+discussed at [257975](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=257975),
 v1.78 update was [541454f](https://cgit.FreeBSD.org/ports/commit/?id=541454f9939d3836bc1bcf642f8c748a1d04bb80)
 discussed at [258120](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=258120),
 v1.82 update was [8d34513](https://cgit.freebsd.org/ports/commit/?id=8d34513c3f7ac851134d8452109c28497f0442cb)
 discussed at [261741](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=261741),
 v1.84 update was [3b861fa](https://cgit.freebsd.org/ports/commit/?id=3b861fa65fe8386404132158eb153378007483bf)
 discussed at [262498](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262498),
-and
 1.85 update was [bcc206f](https://cgit.freebsd.org/ports/commit/?id=bcc206f2be0cca24bf8688ab6d81c351ccbc98d3)
-discussed at [265163](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=265163)
+discussed at [265163](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=265163),
+and
+1.86 update was [a75fab4](https://cgit.freebsd.org/ports/commit/?id=a75fab4072ee1d5d0c5f8240986c016f123a97fd)
+discussed at [268445](https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=268445).
 
 FreeBSD users should be able to install it via `pkg install pooler`

freebsd/pkg-descr

@@ -18,5 +18,3 @@ Primer Pooler can:
   sequencing applications)
 
 * Do all of the above with degenerate primers too.
-
-WWW: http://ssb22.user.srcf.net/pooler/

freebsd/update.sh

@@ -1,5 +1,4 @@
 #!/bin/bash
-# ssh freebsd svn switch https://svn.FreeBSD.org/ports/head /usr/ports # TODO: how to migrate this to git? (2021q3 branch is OK for now)
 # ssh freebsd pkg install portlint
 # ssh freebsd "echo 'DEVELOPER=yes' >> /etc/make.conf"
 ssh freebsd 'cd /usr/ports/biology/pooler/ && rm -f Makefile pkg-descr && wget https://cgit.freebsd.org/ports/plain/biology/pooler/Makefile https://cgit.freebsd.org/ports/plain/biology/pooler/pkg-descr' || exit 1
@@ -14,5 +13,5 @@ if ! ssh freebsd 'cd /usr/ports/biology/pooler/ && rm -f distinfo && make makesu
 fi
 ssh freebsd 'cd /usr/ports/biology/pooler/ && git commit * -m "biology/pooler: update to '"$(grep -m 1 '^#.*Program_Version' ../pooler/version.h|cut -d ' ' -f5|tr -d '"')"'"' &&
 ssh freebsd 'cd /usr/ports && git format-patch --stdout -1' > pooler.mbox &&
-echo "pooler.mbox to https://bugs.freebsd.org/bugzilla/enter_bug.cgi (as plain-text attachment + set URL to http://ssb22.user.srcf.net/pooler/#changes )"
+echo "pooler.mbox to https://bugs.freebsd.org/bugzilla/enter_bug.cgi (as plain-text attachment + set URL to http://ssb22.user.srcf.net/pooler/#changes + set maintainer-approval flag)"
 echo "If the diff is wrong and we need to re-run update.sh after a change, first do: ssh freebsd 'cd /usr/ports;git reset --hard HEAD~1'"

pooler/Makefile

@@ -23,8 +23,10 @@ win-crosscompile: pooler.exe pooler64.exe
 .PHONY: win-crosscompile mingw publish
 pooler.exe: 128.h 32.h 32-64.h mingw
 	i686-w64-mingw32-gcc $(WinFlags) *.c -l comdlg32 -o pooler.exe -lm
+	chmod -x pooler.exe
 pooler64.exe: 128.h 32.h 32-64.h mingw
 	x86_64-w64-mingw32-gcc $(WinFlags) *.c -l comdlg32 -o pooler64.exe -lm
+	chmod -x pooler64.exe
 mingw:
 	@if ! which x86_64-w64-mingw32-gcc >/dev/null; then if which apt-get >/dev/null; then echo "Installing the cross-compiler with apt-get..."; sudo apt-get install gcc-mingw-w64; elif which yum >/dev/null; then echo "Installing the cross-compiler with yum..."; sudo yum install mingw32-gcc mingw64-gcc mingw32-libgomp mingw64-libgomp mingw32-winpthreads-static mingw64-winpthreads-static; else echo "Cannot find the cross-compiler or how to install it"; exit 1; fi; fi