git: 12191baead85 - main - biology/checkm: Remove expired port

The branch main has been updated by rene:

URL: https://cgit.FreeBSD.org/ports/commit/?id=12191baead8520b49266479d22c09dffef583ae9

commit 12191baead8520b49266479d22c09dffef583ae9
Author:     Rene Ladan <rene@FreeBSD.org>
AuthorDate: 2025-06-02 17:02:45 +0000
Commit:     Rene Ladan <rene@FreeBSD.org>
CommitDate: 2025-06-02 17:02:45 +0000

    biology/checkm: Remove expired port
    
    2025-06-01 biology/checkm: Depends on expired science/py-DendroPy
---
 MOVED                    |  1 +
 biology/Makefile         |  1 -
 biology/checkm/Makefile  | 30 ------------------------------
 biology/checkm/distinfo  |  3 ---
 biology/checkm/pkg-descr | 13 -------------
 5 files changed, 1 insertion(+), 47 deletions(-)

diff --git a/MOVED b/MOVED
index a392845a827f..a80c087b36ef 100644
--- a/MOVED
+++ b/MOVED
@@ -4459,3 +4459,4 @@ textproc/py-textract||2025-06-02|Has expired: Depends on expiring textproc/py-ex
 databases/py-fastapi-users-db-ormar||2025-06-02|Has expired: Depends on expiring www/py-fastapi-users
 www/py-fastapi-users||2025-06-02|Has expired: Depends on expired devel/py-makefun
 multimedia/ffsubsync||2025-06-02|Has expired: Depends on expired multimedia/py-ffmpeg-python
+biology/checkm||2025-06-02|Has expired: Depends on expired science/py-DendroPy
diff --git a/biology/Makefile b/biology/Makefile
index ea85f35b064d..9f2f693fcfc5 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -37,7 +37,6 @@
     SUBDIR += canu
     SUBDIR += cd-hit
     SUBDIR += cdbfasta
-    SUBDIR += checkm
     SUBDIR += chip-seq
     SUBDIR += clustal-omega
     SUBDIR += clustalw
diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile
deleted file mode 100644
index cb7cc7108d4a..000000000000
--- a/biology/checkm/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-PORTNAME=	CheckM
-DISTVERSIONPREFIX=	v
-DISTVERSION=	1.2.3
-PORTREVISION=	1
-CATEGORIES=	biology python
-
-MAINTAINER=	yuri@FreeBSD.org
-COMMENT=	Quality assessment tool for the microbial genomes
-WWW=		https://ecogenomics.github.io/CheckM/
-
-LICENSE=	GPLv3
-LICENSE_FILE=	${WRKSRC}/LICENSE
-
-DEPRECATED=	Depends on expired science/py-DendroPy
-EXPIRATION_DATE=2025-06-01
-
-RUN_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}DendroPy>0:science/py-DendroPy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
-
-USES=		dos2unix python
-USE_GITHUB=	yes
-GH_ACCOUNT=	Ecogenomics
-USE_PYTHON=	distutils noflavors autoplist
-
-NO_ARCH=	yes
-
-.include <bsd.port.mk>
diff --git a/biology/checkm/distinfo b/biology/checkm/distinfo
deleted file mode 100644
index c1da8633ab00..000000000000
--- a/biology/checkm/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-TIMESTAMP = 1730733018
-SHA256 (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 5f8340e71d3256ba8cf407d27bdc7914d1aa86b14b2d63d1e32cceb325e5aa82
-SIZE (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 1017616
diff --git a/biology/checkm/pkg-descr b/biology/checkm/pkg-descr
deleted file mode 100644
index 4238256d225a..000000000000
--- a/biology/checkm/pkg-descr
+++ /dev/null
@@ -1,13 +0,0 @@
-CheckM provides a set of tools for assessing the quality of genomes recovered
-from isolates, single cells, or metagenomes.
-
-It provides robust estimates of genome completeness and contamination by using
-collocated sets of genes that are ubiquitous and single-copy within a
-phylogenetic lineage.
-
-Assessment of genome quality can also be examined using plots depicting key
-genomic characteristics (e.g., GC, coding density) which highlight sequences
-outside the expected distributions of a typical genome. CheckM also provides
-tools for identifying genome bins that are likely candidates for merging based
-on marker set compatibility, similarity in genomic characteristics, and
-proximity within a reference genome tree.