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I am trying to download Paprica onto my Mac, https://www.polarmicrobes.org/installing-paprica-on-mac-osx/

The steps that I have completed are listed below

  1. Install Python modules

     pip3 install numpy
 pip3 install biopython
 pip3 install joblib
 pip3 install pandas
 pip3 install seqmagick

  2. Show import modules in python3 shell

     import numpy
 import Bio
 import joblib
 import pandas

  3. Demonstrate that seqmagick works

     seqmagick

  4. Using homebrew installed:

     brew install wget

  5. Installed Infernal, placer, and 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

  6. Then I installed gappa

    git clone --recursive https://github.com/lczech/gappa.git
cd gappa
make
cd ~

This is where things stop working. When I run make in the gappa directory I get the output listed below. I have tried several different methods for getting OpenMP to work, but have not had any success. Any help that folks could give would be highly appreciated! :)

`(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
Gabe
  • 1
  • It looks like you didn't actually install infernal. You just unpacked the code and moved it. The documentation (http://eddylab.org/infernal/Userguide.pdf) says you still need to run `.configure` and `make`. Or just install it through homebrew since you used it for other packages. You are also clearly missing OpenMP. – sweenish Jan 28 '21 at 20:30
  • You are using Clang from Apple's Xcode collection. It supports OpenMP but does not provide the runtime library and its header file. That can be fixed by installing `libomp` from Homebrew - see [here](https://stackoverflow.com/a/61871393/1374437). You need to add `-lomp` to the link flags. Alternatively, install GCC from Homebrew and use it to compile the code. – Hristo Iliev Jan 29 '21 at 07:40

0 Answers0