git: ddc812686212 - main - biology/kallisto: Clean up build
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Date: Mon, 24 Jul 2023 15:46:19 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=ddc812686212150df9dd26893ec936b26102aff2
commit ddc812686212150df9dd26893ec936b26102aff2
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-07-24 15:44:58 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-07-24 15:44:58 +0000
biology/kallisto: Clean up build
Silence warnings due to detected compiler standards
Enable BAM support in cmake
Patch out remaining aggressive optimizations
---
biology/kallisto/Makefile | 8 ++++--
biology/kallisto/files/patch-CMakeLists.txt | 27 +++++++++++++++++-
.../files/patch-ext_bifrost_CMakeLists.txt | 33 ++++++++++++++++++++--
biology/kallisto/files/patch-src_CMakeLists.txt | 12 ++++----
4 files changed, 69 insertions(+), 11 deletions(-)
diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index ea7cb1a53596..4ae2b8bd94ec 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,7 +1,7 @@
PORTNAME= kallisto
DISTVERSIONPREFIX= v
DISTVERSION= 0.50.0
-PORTREVISION= 1
+PORTREVISION= 2
PORTEPOCH= 1
CATEGORIES= biology
@@ -12,8 +12,8 @@ WWW= https://pachterlab.github.io/kallisto/about.html
LICENSE= BSD2CLAUSE
LICENSE_FILE= ${WRKSRC}/license.txt
-# Requires a 64-bit processor
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64
+ONLY_FOR_ARCHS_REASON= Requires a 64-bit processor
LIB_DEPENDS= libhdf5.so:science/hdf5 \
libsz.so:science/libaec \
@@ -32,7 +32,9 @@ EXAMPLES_PLIST_FILES= bin/kallisto-test
# hdf5 is being phased out and is no longer built in by default, but is still
# required for Sleuth (requires kallisto bootstrap estimates) and other
# downstream tools. Remove this after Sleuth et al catch up.
-CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON
+CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
+# WIP: Remove before committing
+CMAKE_ARGS+= -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
MAKE_JOBS_UNSAFE= yes
LDFLAGS+= -lhts -lz
diff --git a/biology/kallisto/files/patch-CMakeLists.txt b/biology/kallisto/files/patch-CMakeLists.txt
index 7c6d4c95b51e..0eff9653f86c 100644
--- a/biology/kallisto/files/patch-CMakeLists.txt
+++ b/biology/kallisto/files/patch-CMakeLists.txt
@@ -1,6 +1,31 @@
--- CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
+++ CMakeLists.txt
-@@ -56,42 +56,16 @@ ENDIF(LINK MATCHES static)
+@@ -33,10 +33,11 @@ if(${CMAKE_VERSION} VERSION_LESS 3.1)
+ # remove this block once CMake >=3.1 has fixated in the ecosystem
+ add_compile_options(-std=c++11)
+ else()
++ # Use c++11 to silence warnings
+ include(CheckCXXCompilerFlag)
+- check_cxx_compiler_flag(-std=c++17 COMPILER_SUPPORTS_CXX17)
++ check_cxx_compiler_flag(-std=c++11 COMPILER_SUPPORTS_CXX17)
+ if(COMPILER_SUPPORTS_CXX17)
+- set(CMAKE_CXX_STANDARD 17)
++ set(CMAKE_CXX_STANDARD 11)
+ else()
+ set(CMAKE_CXX_STANDARD 11)
+ endif()
+@@ -44,9 +45,7 @@ else()
+ set(CMAKE_CXX_EXTENSIONS OFF)
+ endif()
+
+-#add_compile_options(-Wall -Wno-unused-function)
+-add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
+-set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-subobject-linkage -Wno-return-type") # Suppress bifrost warning
++set(PROJECT_BIFROST_CMAKE_CXX_FLAGS "-Wno-return-type") # Suppress bifrost warning
+
+ if(LINK MATCHES static)
+ message("static build")
+@@ -56,42 +55,16 @@ ENDIF(LINK MATCHES static)
include(ExternalProject)
diff --git a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
index c4c22a5e0666..d25cf028cfdd 100644
--- a/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
+++ b/biology/kallisto/files/patch-ext_bifrost_CMakeLists.txt
@@ -1,6 +1,26 @@
---- ext/bifrost/CMakeLists.txt.orig 2023-07-14 14:27:24 UTC
+--- ext/bifrost/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
+++ ext/bifrost/CMakeLists.txt
-@@ -30,8 +30,6 @@ if(COMPILATION_ARCH MATCHES "OFF")
+@@ -7,18 +7,12 @@ 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_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_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")
message("Disabling native architecture compilation (including AVX2)")
else(COMPILATION_ARCH MATCHES "OFF")
message("Compilation architecture: ${COMPILATION_ARCH}")
@@ -9,3 +29,12 @@
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)
+
diff --git a/biology/kallisto/files/patch-src_CMakeLists.txt b/biology/kallisto/files/patch-src_CMakeLists.txt
index c7927b9e1478..87cd4b49b02d 100644
--- a/biology/kallisto/files/patch-src_CMakeLists.txt
+++ b/biology/kallisto/files/patch-src_CMakeLists.txt
@@ -1,6 +1,6 @@
---- src/CMakeLists.txt.orig 2023-07-06 14:07:38 UTC
+--- src/CMakeLists.txt.orig 2023-06-27 10:45:00 UTC
+++ src/CMakeLists.txt
-@@ -3,10 +3,6 @@ file(GLOB headers *.h *.hpp)
+@@ -3,12 +3,6 @@ file(GLOB headers *.h *.hpp)
list(REMOVE_ITEM sources main.cpp)
@@ -8,10 +8,12 @@
-include_directories(../ext/htslib)
-endif(USE_BAM)
-
- add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
-
+-add_compile_options(-Wno-subobject-linkage) # Suppress bifrost warning
+-
add_library(kallisto_core ${sources} ${headers})
-@@ -17,7 +13,7 @@ add_executable(kallisto main.cpp)
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+
+@@ -17,7 +11,7 @@ add_executable(kallisto main.cpp)
find_package( Threads REQUIRED )
ExternalProject_Get_Property(bifrost install_dir)
if (USE_BAM)