我正在尝试将 Paprica 下载到我的 Mac 上，https://www.polarmicrobes.org/installing-paprica-on-mac-osx/
我已经完成的步骤如下
安装 Python 模块
pip3 install numpy
pip3 install biopython
pip3 install joblib
pip3 install pandas
pip3 install seqmagick
在python3 shell中显示导入模块
import numpy
import Bio
import joblib
import pandas
证明 seqmagick 有效
seqmagick
使用安装的自制软件：
brew install wget
安装 Infernal、placer 和 epa-ng
wget http://eddylab.org/infernal/infernal-1.1.1-macosx-intel.tar.gz
tar -xzvf infernal-1.1.1-macosx-intel.tar.gz
mv infernal-1.1.1-macosx-intel infernal
然后我安装了gappa
git clone --recursive https://github.com/lczech/gappa.git
cd gappa
make
cd ~
这就是事情停止的地方。当我在 gappa 目录中运行 make 时，我得到下面列出的输出。我尝试了几种不同的方法来让 OpenMP 工作，但没有任何成功。人们可以提供的任何帮助将不胜感激！ :)
`(base) Gabriels-MacBook-Air:gappa gabrielprice$ make
Running CMake...
CMake Deprecation Warning at CMakeLists.txt:26 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The CXX compiler identification is AppleClang 11.0.0.11000033
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Gappa build type: RELEASE
-- Static linking of system libraries: OFF
CMake Deprecation Warning at libs/genesis/CMakeLists.txt:28 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Configuring Genesis
-- CMake version 3.19.3
-- The C compiler identification is AppleClang 11.0.0.11000033
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Genesis version: v0.24.0
-- Building Genesis as a dependency
-- Build type: RELEASE
-- Unity build: FULL
-- C++ compiler: AppleClang 11.0.0.11000033 at /Library/Developer/CommandLineTools/usr/bin/c++
-- C compiler : AppleClang 11.0.0.11000033 at /Library/Developer/CommandLineTools/usr/bin/cc
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for zlib
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libz.tbd (found version "1.2.11")
-- Found zlib: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include 1.2.11
-- Using zlib
-- Looking for Threads
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found Threads:
-- Using Threads
-- Looking for OpenMP
-- Using find_package( OpenMP ) patch
-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp=libiomp5]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp=libomp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Xpreprocessor -fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Xclang -fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
CMake Warning (dev) at /usr/local/Cellar/cmake/3.19.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:426 (message):
The package name passed to `find_package_handle_standard_args` (OpenMP)
does not match the name of the calling package (OpenMP_patch). This can
lead to problems in calling code that expects `find_package` result
variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
libs/genesis/tools/cmake/FindOpenMP_patch.cmake:384 (find_package_handle_standard_args)
libs/genesis/CMakeLists.txt:332 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
-- Found OpenMP_C: -Xclang -fopenmp (found version "3.1")
-- Found OpenMP_CXX: -Xclang -fopenmp (found version "3.1")
-- Found OpenMP: TRUE (found version "3.1")
-- Found OpenMP: -Xclang -fopenmp
-- Using OpenMP
-- Building static lib
-- Final build flags:
-- CMAKE_CXX_FLAGS : -std=c++11 -Wall -Wextra -Wno-unknown-pragmas -pedantic - pedantic-errors -std=c++11 -Wall -Wextra -Wno-unknown-pragmas -pedantic -pedantic-errors -Xclang -fopenmp
-- CMAKE_CXX_FLAGS_RELEASE : -O2 -DNDEBUG -O2 -DNDEBUG
-- GENESIS_CXX_FLAGS : -Xclang -fopenmp
-- GENESIS_EXE_LINKER_FLAGS:
-- GENESIS_LINK_LIBRARIES :
-- Finished configuring Genesis
-- CMAKE_EXE_LINKER_FLAGS
-- GENESIS_LINK_LIBRARIES /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libz.tbd;genesis_lib_static
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/gabrielprice/gappa/build
Running make...
/Library/Developer/CommandLineTools/usr/bin/make -s -C build
Scanning dependencies of target genesis_lib_static
[ 2%] Building CXX object libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/__/__/__/__/genesis_unity_sources/lib /all.cpp.o
/Users/gabrielprice/gappa/build/genesis_unity_sources/lib/all.cpp:172:13: fatal error: 'omp.h' file not found
# include <omp.h>
^~~~~~~
1 error generated.
make[3]: *** [libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/__/__/__/__/genesis_unity_sources/li. b/all.cpp.o] Error 1
make[2]: *** [libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [build] Error 2