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biology/ucsc-userapps: Update to v474

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Several fixes and a few enhancements since v472
Changes: https://github.com/ucscGenomeBrowser/kent/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-11-28 09:57:21 -06:00
parent 6f8be4c065
commit 9cb153ab34
3 changed files with 9 additions and 23 deletions
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12
biology/ucsc-userapps/Makefile
View file

@ -1,18 +1,20 @@
PORTNAME= ucsc-userapps PORTNAME= ucsc-userapps
DISTVERSION= 472 DISTVERSION= 474
CATEGORIES= biology perl5 python 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${DISTVERSION}.src DISTNAME= userApps.v${DISTVERSION}.src
MAINTAINER= jwb@FreeBSD.org MAINTAINER= jwb@FreeBSD.org
COMMENT= Command line tools from the UCSC Genome Browser project COMMENT= Command line tools from the UCSC Genome Browser project
WWW= https://hgdownload.cse.ucsc.edu/admin/exe/ WWW= https://hgdownload.cse.ucsc.edu/admin/exe/
# Some tools in the source dist are non-free for commercial use. # Note: 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. # If they are added to the install, the license below must be changed
# and packaging forbidden.
LICENSE= MIT LICENSE= MIT
BUILD_DEPENDS= bash:shells/bash BUILD_DEPENDS= bash:shells/bash
# FIXME: Switch from mysql to mariadb
LIB_DEPENDS= libmysqlclient.so:databases/mysql80-client \ LIB_DEPENDS= libmysqlclient.so:databases/mysql80-client \
libunwind.so:devel/libunwind \ libunwind.so:devel/libunwind \
libfreetype.so:print/freetype2 \ 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 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 \ SHEBANG_FILES= kent/src/checkUmask.sh \
kent/src/utils/bigHeat \ kent/src/utils/bigHeat \
kent/src/utils/chromToUcsc/chromToUcsc \ kent/src/utils/chromToUcsc/chromToUcsc \

6
biology/ucsc-userapps/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1730984296 TIMESTAMP = 1732796640
SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2 SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7
SIZE (userApps.v472.src.tgz) = 24378966 SIZE (userApps.v474.src.tgz) = 24402279

14
biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
View file

@ -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);