git: 9cb153ab3484 - main - biology/ucsc-userapps: Update to v474

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=9cb153ab34840d98a13cde17c524498a70cdd7f3

commit 9cb153ab34840d98a13cde17c524498a70cdd7f3
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-11-28 15:57:21 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-11-28 15:59:20 +0000

    biology/ucsc-userapps: Update to v474
    
    Several fixes and a few enhancements since v472
    Changes: https://github.com/ucscGenomeBrowser/kent/releases
    
    Reported by:    portscout
---
 biology/ucsc-userapps/Makefile                            | 12 ++++++------
 biology/ucsc-userapps/distinfo                            |  6 +++---
 biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c | 14 --------------
 3 files changed, 9 insertions(+), 23 deletions(-)

diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile
index 5d4fa1eb9df6..35f30e18f80d 100644
--- a/biology/ucsc-userapps/Makefile
+++ b/biology/ucsc-userapps/Makefile
@@ -1,18 +1,20 @@
 PORTNAME=	ucsc-userapps
-DISTVERSION=	472
+DISTVERSION=	474
 CATEGORIES=	biology perl5 python
-MASTER_SITES=	http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
+MASTER_SITES=	https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
 DISTNAME=	userApps.v${DISTVERSION}.src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Command line tools from the UCSC Genome Browser project
 WWW=		https://hgdownload.cse.ucsc.edu/admin/exe/
 
-# Some tools in the source dist are non-free for commercial use.
-# If they are added, the license below must be changed and packaging forbidden.
+# Note: Some tools in the source dist are non-free for commercial use.
+# If they are added to the install, the license below must be changed
+# and packaging forbidden.
 LICENSE=	MIT
 
 BUILD_DEPENDS=	bash:shells/bash
+# FIXME: Switch from mysql to mariadb
 LIB_DEPENDS=	libmysqlclient.so:databases/mysql80-client \
 		libunwind.so:devel/libunwind \
 		libfreetype.so:print/freetype2 \
@@ -21,8 +23,6 @@ RUN_DEPENDS=	bash:shells/bash
 
 USES=		gmake iconv localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz
 
-RESTRICTED=	Redistribution is limited, see license
-
 SHEBANG_FILES=	kent/src/checkUmask.sh \
 		kent/src/utils/bigHeat \
 		kent/src/utils/chromToUcsc/chromToUcsc \
diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo
index e5f22b962d6f..ea61209e348b 100644
--- a/biology/ucsc-userapps/distinfo
+++ b/biology/ucsc-userapps/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1730984296
-SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2
-SIZE (userApps.v472.src.tgz) = 24378966
+TIMESTAMP = 1732796640
+SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7
+SIZE (userApps.v474.src.tgz) = 24402279
diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
deleted file mode 100644
index e75057e7937c..000000000000
--- a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
+++ /dev/null
@@ -1,14 +0,0 @@
---- kent/src/hg/lib/jksql.c.orig	2024-10-16 04:15:27 UTC
-+++ kent/src/hg/lib/jksql.c
-@@ -1128,8 +1128,9 @@ if (sp->verifyServerCert && !sameString(sp->verifyServ
- // If turned on this can defeat Man-In-The-Middle attacks.
- if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0"))
-     {
--    #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000
--    mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED);
-+    #if !defined(MARIADB_BASE_VERSION) && defined(MYSQL_VERSION_ID) && (MYSQL_VERSION_ID >= 80000)
-+    int ssl_mode = SSL_MODE_REQUIRED;
-+    mysql_options(conn, MYSQL_OPT_SSL_MODE, &ssl_mode);
-     #else
-     my_bool flag = TRUE;
-     mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);