diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile
index 7994bb0f8748..cb7cc7108d4a 100644
--- a/biology/checkm/Makefile
+++ b/biology/checkm/Makefile
@@ -1,27 +1,30 @@
 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>