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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2024-11-28 15:57:21 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2024-11-28 15:59:20 +0000 |
| commit | 9cb153ab34840d98a13cde17c524498a70cdd7f3 (patch) | |
| tree | f82d63d868d510bad8cf6211b8897f99d0b906f0 | |
| parent | 6f8be4c065a80c1c8bbd3fb56e82a673bfc7ce7f (diff) | |
| download | ports-9cb153ab34840d98a13cde17c524498a70cdd7f3.tar.gz ports-9cb153ab34840d98a13cde17c524498a70cdd7f3.zip | |
biology/ucsc-userapps: Update to v474
Several fixes and a few enhancements since v472
Changes: https://github.com/ucscGenomeBrowser/kent/releases
Reported by: portscout
| -rw-r--r-- | biology/ucsc-userapps/Makefile | 12 | ||||
| -rw-r--r-- | biology/ucsc-userapps/distinfo | 6 | ||||
| -rw-r--r-- | 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); |