git: 18cabe581ff1 - main - biology/kallisto: Unbreak build on 15-CURRENT

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=18cabe581ff1d41153e070ce37aed797b9118f00

commit 18cabe581ff1d41153e070ce37aed797b9118f00
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-05-15 11:45:07 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-05-15 11:45:07 +0000

    biology/kallisto: Unbreak build on 15-CURRENT
    
    Unable to identify the cause, use GCC as a workaround for now
    No change on other FreeBSD versions
---
 biology/kallisto/Makefile                               | 12 +++++++++++-
 biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt | 13 +++++++------
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 91193aa7facc..c2d33ef3ce82 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -37,12 +37,22 @@ 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
@@ -1,8 +1,8 @@
---- 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")
@@ -12,7 +12,8 @@
  
  # 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")
 -
@@ -20,7 +21,7 @@
  #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}")
@@ -29,7 +30,7 @@
  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")