Date: Mon, 13 Apr 2026 13:22:16 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 945218c4828c - main - biology/gffread: Update to 0.12.9 Message-ID: <69dcee08.41908.38394ca0@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=945218c4828c359874c330b64c173a84b61dca53 commit 945218c4828c359874c330b64c173a84b61dca53 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2026-04-13 13:20:48 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2026-04-13 13:20:48 +0000 biology/gffread: Update to 0.12.9 Fix buffer overflow Changes: https://github.com/gpertea/gffread/releases Reported by: portscout --- biology/gffread/Makefile | 6 +++--- biology/gffread/distinfo | 10 +++++----- biology/gffread/pkg-descr | 7 ++++++- 3 files changed, 14 insertions(+), 9 deletions(-) diff --git a/biology/gffread/Makefile b/biology/gffread/Makefile index ed622c0c85e7..eb96cebdf8cb 100644 --- a/biology/gffread/Makefile +++ b/biology/gffread/Makefile @@ -1,11 +1,11 @@ PORTNAME= gffread DISTVERSIONPREFIX= v -DISTVERSION= 0.12.7 +DISTVERSION= 0.12.9 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= GFF/GTF format conversions, filtering, FASTA extraction, etc -WWW= http://ccb.jhu.edu/software/stringtie/gff.shtml\#gffread +WWW= https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE @@ -14,7 +14,7 @@ USES= gmake USE_GITHUB= yes GH_ACCOUNT= gpertea -GH_TUPLE= gpertea:gclib:v${DISTVERSION}:gpertea/gclib +GH_TUPLE= gpertea:gclib:v0.12.8:gpertea/gclib INSTALL_TARGET= install-strip diff --git a/biology/gffread/distinfo b/biology/gffread/distinfo index 14af8eee92bf..74f937f72767 100644 --- a/biology/gffread/distinfo +++ b/biology/gffread/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1636511584 -SHA256 (gpertea-gffread-v0.12.7_GH0.tar.gz) = 6f3417090b3beb74f435bf5d462c87475b3c704a8a0d71821f6c1321c47dbbbe -SIZE (gpertea-gffread-v0.12.7_GH0.tar.gz) = 403734 -SHA256 (gpertea-gclib-v0.12.7_GH0.tar.gz) = 9c74db64c4ee1fb93a6c02fa227258baafc337303f26ce3ba0cf37dfc1ba687f -SIZE (gpertea-gclib-v0.12.7_GH0.tar.gz) = 259314 +TIMESTAMP = 1776080973 +SHA256 (gpertea-gffread-v0.12.9_GH0.tar.gz) = 92eb4a52fdd14c5fd3684041ef2d040c44d7414d076467a326eea2efa087a085 +SIZE (gpertea-gffread-v0.12.9_GH0.tar.gz) = 408710 +SHA256 (gpertea-gclib-v0.12.8_GH0.tar.gz) = a8dea4d273d6802f77f26a5394b1d66dfc1aba46a725c61e4c7399b756fb75e3 +SIZE (gpertea-gclib-v0.12.8_GH0.tar.gz) = 262545 diff --git a/biology/gffread/pkg-descr b/biology/gffread/pkg-descr index def9446aacb9..2971ed7cbfaf 100644 --- a/biology/gffread/pkg-descr +++ b/biology/gffread/pkg-descr @@ -1,2 +1,7 @@ GFF/GTF utility providing format conversions, filtering, FASTA sequence -extraction and more. +extraction and more. The program gffread can be used to validate, +filter, convert and perform various other operations on GFF files. +Because the program shares the same GFF parser code with Cufflinks, +Stringtie, and gffcompare, it could be used to verify that a GFF file +from a certain annotation source is correctly "understood" by these +programs.home | help
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