head	1.4;
access;
symbols
	pkgsrc-2026Q1:1.4.0.6
	pkgsrc-2026Q1-base:1.4
	pkgsrc-2025Q4:1.4.0.4
	pkgsrc-2025Q4-base:1.4
	pkgsrc-2025Q3:1.4.0.2
	pkgsrc-2025Q3-base:1.4
	pkgsrc-2025Q2:1.3.0.8
	pkgsrc-2025Q2-base:1.3
	pkgsrc-2025Q1:1.3.0.6
	pkgsrc-2025Q1-base:1.3
	pkgsrc-2024Q4:1.3.0.4
	pkgsrc-2024Q4-base:1.3
	pkgsrc-2024Q3:1.3.0.2
	pkgsrc-2024Q3-base:1.3
	pkgsrc-2024Q2:1.1.0.6
	pkgsrc-2024Q2-base:1.1
	pkgsrc-2024Q1:1.1.0.4
	pkgsrc-2024Q1-base:1.1
	pkgsrc-2023Q4:1.1.0.2
	pkgsrc-2023Q4-base:1.1;
locks; strict;
comment	@# @;


1.4
date	2025.08.19.08.13.21;	author wiz;	state Exp;
branches;
next	1.3;
commitid	9Dod5X444bbvBj7G;

1.3
date	2024.09.20.00.03.15;	author bacon;	state Exp;
branches;
next	1.2;
commitid	vGzFMkGm3GMJAtqF;

1.2
date	2024.07.27.12.22.54;	author bacon;	state Exp;
branches;
next	1.1;
commitid	OLdxWtcRDO02stjF;

1.1
date	2023.11.04.14.35.07;	author bacon;	state Exp;
branches;
next	;
commitid	1gIhLVph3euAJiLE;


desc
@@


1.4
log
@kallisto: fix build with cmake 4
@
text
@$NetBSD: patch-ext_bifrost_CMakeLists.txt,v 1.3 2024/09/20 00:03:15 bacon Exp $

Fix build with cmake 4

# Respect pkgsrc build flags

--- ext/bifrost/CMakeLists.txt.orig	2024-09-17 05:40:08.000000000 +0000
+++ ext/bifrost/CMakeLists.txt
@@@@ -1,4 +1,4 @@@@
-cmake_minimum_required(VERSION 3.0.0)
+cmake_minimum_required(VERSION 3.5)
 
 project(Bifrost)
 
@@@@ -6,18 +6,12 @@@@ find_package(Threads REQUIRED)
 
 # 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_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_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")
@@@@ -25,20 +19,6 @@@@ if(APPLE AND CMAKE_SYSTEM_PROCESSOR MATC
 	set(COMPILATION_ARCH "OFF")
 endif(APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm")
 
-if(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=${COMPILATION_ARCH}")
-endif(COMPILATION_ARCH MATCHES "OFF")
-
-if(ENABLE_AVX2 MATCHES "OFF")
-	message("Disabling AVX2 instructions")
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mno-avx2")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mno-avx2")
-endif(ENABLE_AVX2 MATCHES "OFF")
-
 # Manages build types
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "Release")
@


1.3
log
@biology/kallisto: Update to 0.51.1

Enhancements to ir-kallisto and pseudoalignments

Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
@
text
@d1 3
a3 1
$NetBSD$
d7 1
a7 1
--- ext/bifrost/CMakeLists.txt.orig	2024-07-23 11:56:13.172038229 +0000
d9 6
@


1.2
log
@biology/kallisto: Update to 0.51.0,1

Add support for long reads to kallisto bus and kallisto quant-tcc

Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout
@
text
@@


1.1
log
@biology/kallisto: Update to 0.50.1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases
@
text
@d3 1
a3 1
# Portability
d5 1
a5 1
--- ext/bifrost/CMakeLists.txt.orig	2023-06-27 10:45:00.000000000 +0000
d7 2
a8 1
@@@@ -7,18 +7,12 @@@@ find_package(Threads REQUIRED)
a9 1
 SET(MAX_KMER_SIZE "32" CACHE STRING "MAX_KMER_SIZE")
d27 8
a34 4
@@@@ -30,8 +24,6 @@@@ if(COMPILATION_ARCH MATCHES "OFF")
 	message("Disabling native architecture compilation (including AVX2)")
 else(COMPILATION_ARCH MATCHES "OFF")
 	message("Compilation architecture: ${COMPILATION_ARCH}")
d37 11
a47 12
 endif(COMPILATION_ARCH MATCHES "OFF")
 
 if(ENABLE_AVX2 MATCHES "OFF")
@@@@ -56,7 +48,7 @@@@ 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)
 
@