zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

bcl2fastq2: patch for compiling on aarch64 (#40195)

Browse Source
This commit is contained in:
snehring 2023-09-25 23:26:19 -05:00 committed by GitHub
parent 550613ee3a
commit 9fda22d942
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 13 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
var/spack/repos/builtin/packages/bcl2fastq2/cxxConfigure-aarch64.patch Normal file
View File

@ -0,0 +1,11 @@
--- a/src/cmake/cxxConfigure.cmake 2017-06-22 12:14:50.000000000 -0500
+++ b/src/cmake/cxxConfigure.cmake 2023-09-25 11:50:55.819690648 -0500
@@ -118,7 +118,7 @@
set(BCL2FASTQ_DEP_LIB ${BCL2FASTQ_DEP_LIB} "${LIBEXSLT_LIBRARIES}" "${LIBXSLT_LIBRARIES}" "${LIBXML2_LIBRARIES}")
#set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -fopenmp -msse2 -Werror -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
-set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -std=c++11 -fopenmp -msse2 -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
+set (CMAKE_CXX_FLAGS "$ENV{CXX_FLAGS} $ENV{CXXFLAGS} -std=c++11 -fopenmp -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith" CACHE STRING "g++ flags" FORCE)
#set (CMAKE_CXX_FLAGS_DEBUG "-O0 -g -pg -fprofile-arcs -ftest-coverage -D_GLIBCXX_DEBUG" CACHE STRING "g++ flags" FORCE)
set (CMAKE_CXX_FLAGS_DEBUG "-O0 -std=c++11 -g -pg -fprofile-arcs -ftest-coverage" CACHE STRING "g++ flags" FORCE)
#set (CMAKE_CXX_FLAGS_DEBUG "-std=c++11 -O0 -g -pg -fprofile-arcs -ftest-coverage" CACHE STRING "g++ flags" FORCE)

2
var/spack/repos/builtin/packages/bcl2fastq2/package.py
View File

@ -49,6 +49,8 @@ class Bcl2fastq2(Package):
# After finding the libxslt bits, cmake still needs to wire in the # After finding the libxslt bits, cmake still needs to wire in the
# libexslt bits. # libexslt bits.
patch("cxxConfigure-cmake.patch") patch("cxxConfigure-cmake.patch")
# -msse2 isn't valid for arm
patch("cxxConfigure-aarch64.patch", when="target=aarch64:")
root_cmakelists_dir = "src" root_cmakelists_dir = "src"