Answers.Body: <p>You need to install GCC, or a newer version of Clang.</p>
  
  <p>Your compiler — though the binary is called <code>gcc</code> — is actually Clang, and the Clang version that’s shipping with macOS/Xcode still does not support OpenMP.</p>
  
  <p>The easiest course of action is probably to install GCC via Homebrew (<code>brew install gcc</code>) and then configure Sniffles to use Homebrew’s GCC (i.e. setting the <code>CMAKE_C*_COMPILER</code> paths to <code>/usr/local/bin/g{cc,++}-$version</code>).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-13T21:28:38.073Z
Answers.Text: I have tried what you said, unsuccessfully. I have updated my original question.
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-13T12:42:05.560Z
Answers.LastActivityDate: 2018-06-13T12:42:05.560Z
Answers.UserDisplayName: Konrad Rudolph
Body: <p>I have followed the steps described <a href="https://github.com/fritzsedlazeck/Sniffles/wiki#how-to-build-sniffles" rel="nofollow noreferrer">here</a> to install Sniffles on my Mac Book Pro running macOS High Sierra.</p>
  
  <p>However, I am struggling with this step:</p>
  
  <pre><code>cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 
  </code></pre>
  
  <p>I do not have an /opt folder, so I get the following output:</p>
  
  <pre><code>-- The C compiler identification is unknown
  -- The CXX compiler identification is unknown
  CMake Error at CMakeLists.txt:2 (project):
    The CMAKE_C_COMPILER:
  
      /opt/local/bin/gcc-mp-4.7
  
    is not a full path to an existing compiler tool.
  
    Tell CMake where to find the compiler by setting either the environment
    variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
    the compiler, or to the compiler name if it is in the PATH.
  
  
  CMake Error at CMakeLists.txt:2 (project):
    The CMAKE_CXX_COMPILER:
  
      /opt/local/bin/g++-mp-4.7
  
    is not a full path to an existing compiler tool.
  
    Tell CMake where to find the compiler by setting either the environment
    variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
    to the compiler, or to the compiler name if it is in the PATH.
  
  
  -- Configuring incomplete, errors occurred!
  See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeOutput.log".
  See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeError.log".
  </code></pre>
  
  <p>Unsurprisingly, the error file says that /opt/local/bin/gcc-mp-4.7 does not exist.</p>
  
  <p>So I tried:</p>
  
  <pre><code>cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/gcc ..
  </code></pre>
  
  <p>I get another long message but the most important bit is:</p>
  
  <pre><code>CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
    Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
  </code></pre>
  
  <p>I do not know what to do to solve this error.</p>
  
  <p>I do have gcc here: /usr/bin/gcc and cmake version 3.8.1.</p>
  
  <p>I have created an issue on the <a href="https://github.com/fritzsedlazeck/Sniffles/issues/80" rel="nofollow noreferrer">Sniffles GitHub repository</a>.</p>
  
  <h3>Update 13th June 2018</h3>
  
  <p>I installed the latest version of gcc:</p>
  
  <pre><code>brew install gcc
  Warning: gcc 8.1.0 is already installed and up-to-date
  To reinstall 8.1.0, run `brew reinstall gcc`
  </code></pre>
  
  <p>Then, I tried to make cmake use gcc and g++ in the /usr/local/bin folder. </p>
  
  <pre><code>cmake -D CMAKE_C_COMPILER=/usr/local/bin/gcc-8 -D CMAKE_CXX_COMPILER=/usr/local/bin/g++-8 ..
  </code></pre>
  
  <p>This recreated the same problem:</p>
  
  <pre><code>CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
    Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
  </code></pre>
  
  <p>Do I need to set the OpenMP_C*_FLAGS to something?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-13T10:26:32.863Z
Comments.Text: Do you have OpenMP installed? It's required.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-13T12:38:59.723Z
Comments.Text: @DevonRyan OpenMP is installed as part of GCC. The problem is that OP isn’t using GCC.
Comments.UserDisplayName: Konrad Rudolph
Tags: <software-installation>
Title: Problem installing last build of Sniffles
ThreadText: # Problem installing last build of Sniffles
  
  (Asked by: username_0 on 2018-06-13)
  
  I have followed the steps described [here](https://github.com/fritzsedlazeck/Sniffles/wiki#how-to-build-sniffles) to install Sniffles on my Mac Book Pro running macOS High Sierra.
  
  However, I am struggling with this step:
  
  ```
  cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 
  
  ```
  
  I do not have an /opt folder, so I get the following output:
  
  ```
  -- The C compiler identification is unknown
  -- The CXX compiler identification is unknown
  CMake Error at CMakeLists.txt:2 (project):
    The CMAKE_C_COMPILER:
  
      /opt/local/bin/gcc-mp-4.7
  
    is not a full path to an existing compiler tool.
  
    Tell CMake where to find the compiler by setting either the environment
    variable "CC" or the CMake cache entry CMAKE_C_COMPILER to the full path to
    the compiler, or to the compiler name if it is in the PATH.
  
  CMake Error at CMakeLists.txt:2 (project):
    The CMAKE_CXX_COMPILER:
  
      /opt/local/bin/g++-mp-4.7
  
    is not a full path to an existing compiler tool.
  
    Tell CMake where to find the compiler by setting either the environment
    variable "CXX" or the CMake cache entry CMAKE_CXX_COMPILER to the full path
    to the compiler, or to the compiler name if it is in the PATH.
  
  -- Configuring incomplete, errors occurred!
  See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeOutput.log".
  See also "/Users/xxx/Documents/xxx/xxx/Sniffles-master/build/CMakeFiles/CMakeError.log".
  
  ```
  
  Unsurprisingly, the error file says that /opt/local/bin/gcc-mp-4.7 does not exist.
  
  So I tried:
  
  ```
  cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_CXX_COMPILER=/usr/bin/gcc ..
  
  ```
  
  I get another long message but the most important bit is:
  
  ```
  CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
    Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
  
  ```
  
  I do not know what to do to solve this error.
  
  I do have gcc here: /usr/bin/gcc and cmake version 3.8.1.
  
  I have created an issue on the [Sniffles GitHub repository](https://github.com/fritzsedlazeck/Sniffles/issues/80).
  
  ### Update 13th June 2018
  
  I installed the latest version of gcc:
  
  ```
  brew install gcc
  Warning: gcc 8.1.0 is already installed and up-to-date
  To reinstall 8.1.0, run `brew reinstall gcc`
  
  ```
  
  Then, I tried to make cmake use gcc and g++ in the /usr/local/bin folder.
  
  ```
  cmake -D CMAKE_C_COMPILER=/usr/local/bin/gcc-8 -D CMAKE_CXX_COMPILER=/usr/local/bin/g++-8 ..
  
  ```
  
  This recreated the same problem:
  
  ```
  CMake Error at /usr/local/Cellar/cmake/3.8.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
    Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)
  
  ```
  
  Do I need to set the OpenMP\_C\*\_FLAGS to something?
  
  **Tags:** software-installation
  
  > **Comments:**
  > **username_1**: Do you have OpenMP installed? It's required.  
  > **username_2**: @username_1 OpenMP is installed as part of GCC. The problem is that OP isn’t using GCC.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-06-13. Score: 4
  
  You need to install GCC, or a newer version of Clang.
  
  Your compiler — though the binary is called `gcc` — is actually Clang, and the Clang version that’s shipping with macOS/Xcode still does not support OpenMP.
  
  The easiest course of action is probably to install GCC via Homebrew (`brew install gcc`) and then configure Sniffles to use Homebrew’s GCC (i.e. setting the `CMAKE_C*_COMPILER` paths to `/usr/local/bin/g{cc,++}-$version`).
  
  > **Comments:**
  > **username_0**: I have tried what you said, unsuccessfully. I have updated my original question.  
  
  ---
  
  