diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 91193aa7facc..c2d33ef3ce82 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,48 +1,58 @@
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
 DISTVERSION=		0.51.1
 PORTEPOCH=		1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 WWW=		https://pachterlab.github.io/kallisto/about.html
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
 ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le riscv64
 ONLY_FOR_ARCHS_REASON=	Requires a 64-bit processor
 
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
 		libsz.so:science/libaec \
 		libhts.so:biology/htslib
 
 USES=		cmake:noninja compiler:c++11-lang gmake localbase:ldflags
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
 EXTRACT_AFTER_ARGS=	--exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/ext/htslib --no-same-owner --no-same-permissions
 
 SUB_FILES=	kallisto-test
 
 PORTEXAMPLES=		*
 PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
 # hdf5 is being phased out and is no longer built in by default, but is still
 # required for Sleuth (requires kallisto bootstrap estimates) and other
 # downstream tools.  Remove this after Sleuth et al catch up.
 CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
 # WIP: Remove before committing
 CMAKE_ARGS+=		-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 MAKE_JOBS_UNSAFE=	yes
+CXXFLAGS+=		-Wno-unqualified-std-cast-call
 LDFLAGS+=		-lhts -lz
 
 OPTIONS_DEFINE=	EXAMPLES
 
+.include <bsd.port.pre.mk>
+
+# Build fails with clang19, but succeeds with gcc13
+# Have not figured out where this sz_link member is even supposed to come from
+# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
+.if ${OSVERSION} > 1500000
+USE_GCC=	yes
+.endif
+
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
index d25cf028cfdd..c662b37881c9 100644
--- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
+++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
@@ -1,40 +1,41 @@
---- ext/bifrost/CMakeLists.txt.orig	2023-06-27 10:45:00 UTC
+--- ext/bifrost/CMakeLists.txt.orig	2024-09-17 05:40:08 UTC
 +++ ext/bifrost/CMakeLists.txt
-@@ -7,18 +7,12 @@ find_package(Threads REQUIRED)
+@@ -6,18 +6,12 @@ SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX
+ 
  # To enable a larger default k-mer size, replace MAX_KMER_SIZE with a larger multiple of 32: actual maximum k-mer size will be MAX_KMER_SIZE-1.
- SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
  SET(MAX_GMER_SIZE "${MAX_KMER_SIZE}" CACHE STRING "MAX_GMER_SIZE")
 -# Enable architecture optimizations
 -SET(COMPILATION_ARCH "native" CACHE STRING "COMPILATION_ARCH")
 -# Enable AVX2 instructions
 -SET(ENABLE_AVX2 "ON" CACHE STRING "ENABLE_AVX2")
 +SET(CMAKE_VERBOSE_MAKEFILE "ON")
  
  # Set some default compile flags
  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c11")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wno-unqualified-std-cast-call")
  
 -set_property(SOURCE BlockedBloomFilter.cpp APPEND_STRING PROPERTY COMPILE_FLAGS " -funroll-loops")
 -
 -
  #check if we are on arm64 and apple, if so, disable AVX2
  if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
  	message("Disabling AVX2 instructions on arm64")
-@@ -30,8 +24,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+@@ -29,8 +23,6 @@ else(COMPILATION_ARCH MATCHES "OFF")
  	message("Disabling native architecture compilation (including AVX2)")
  else(COMPILATION_ARCH MATCHES "OFF")
  	message("Compilation architecture: ${COMPILATION_ARCH}")
 -	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=${COMPILATION_ARCH}")
 -	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${COMPILATION_ARCH}")
  endif(COMPILATION_ARCH MATCHES "OFF")
  
  if(ENABLE_AVX2 MATCHES "OFF")
-@@ -56,7 +48,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
+@@ -55,7 +47,7 @@ else(CMAKE_BUILD_TYPE MATCHES Debug)
  		set(CMAKE_EXE_LINKER_FLAGS "-pg")
  	else(CMAKE_BUILD_TYPE MATCHES Profile)
  		message("Build type: Release")
 -		add_compile_options(-O3)
 +		add_compile_options(-O2)
  	endif(CMAKE_BUILD_TYPE MATCHES Profile) 
  endif(CMAKE_BUILD_TYPE MATCHES Debug)