Answers.Body: <p>Compile with gcc or remove <code>inline</code> from <code>librna/fold.c:776</code> and <code>librna/fold.c:846</code>.</p>
  
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Answers.Body: <p>The other option would be to use RNAz via a docker container instead on installing it directly.  The docker container can be downloaded from <a href="https://quay.io/repository/biocontainers/rnaz" rel="nofollow noreferrer">biocontainers</a>.  If you are new to docker here is a <a href="https://docs.docker.com/docker-for-mac/" rel="nofollow noreferrer">tutorial for mac</a>.</p>
  
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Answers.Body: <p>The first thing to try is to perform the install as sudo.</p>
  
  <pre><code>sudo ./configure # definitely
  sudo make ... sudo make install # possibly (?)
  </code></pre>
  
  <p>The clang++ compiler may be using a path that is not setup in your profile and sudo will overcome this. If sudo works you know what the problem is and its a case of changing permissions and configurations accordingly. There is a good chance this will resolve the matter.</p>
  
  <p>There are other possibilities, it could be the compiler. It looks like the compiler is fine however looking at the config file and the check. The final issue is it could be the program ;-)</p>
  
  <blockquote>
    <p>Tried this. Same result. Will continue scratching head</p>
  </blockquote>
  
  <p>Try an installation on Linux</p>
  
  <p>Otherwise its usual stuff, namely upgrading Xtools</p>
  
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Answers.Text: Tried this. Same result. Will continue scratching head.
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Answers.Text: Xtools or Linux ... Linux has a better chance
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Answers.Text: Xtools is current. Yeah. I know things will likely compile A-OK with Linux. Will try that too. Thanks.
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Body: <p>Having trouble building RNAz 2.1 on MacOS. Following instructions at <a href="https://www.tbi.univie.ac.at/software/RNAz/" rel="nofollow noreferrer">https://www.tbi.univie.ac.at/software/RNAz/</a></p>
  
  <pre><code>tar -xzf RNAz-2.1-tar.gz
  cd RNAz-2.1
  ./configure
  make
  </code></pre>
  
  <p><code>make</code> fails with </p>
  
  <pre><code>/usr/bin/clang++ -o RNAz RNAz.o rnaz_utils.o svm_helper.o zscore.o cmdline.o strand.o svm.o -L../librna -lRNA -lm 
  Undefined symbols for architecture x86_64:
    "_HairpinE", referenced from:
        _alifold in libRNA.a(alifold.o)
        _fill_arrays in libRNA.a(fold.o)
        _backtrack in libRNA.a(fold.o)
        _stack_energy in libRNA.a(fold.o)
    "_LoopEnergy", referenced from:
        _alifold in libRNA.a(alifold.o)
        _fill_arrays in libRNA.a(fold.o)
        _backtrack in libRNA.a(fold.o)
        _stack_energy in libRNA.a(fold.o)
  ld: symbol(s) not found for architecture x86_64
  </code></pre>
  
  <p>Thinking that compiling for 32-bit might work I tried setting </p>
  
  <pre><code>CXXFLAGS = -m32
  LDFLAGS = -m32
  </code></pre>
  
  <p>without success (same result). Same result with <code>gmake</code>.</p>
  
  <p><strong>Configure</strong>
  Configure checks for <code>gcc</code></p>
  
  <pre><code>...
  checking for gcc... gcc
  checking whether the C compiler works... yes
  ...
  </code></pre>
  
  <p><strong>Makefile</strong></p>
  
  <p>Makefile specifies the following:</p>
  
  <pre><code>CC = gcc
  CCDEPMODE = depmode=gcc3
  CFLAGS = -g -O2
  CPP = gcc -E
  CPPFLAGS = 
  CXX = g++
  CXXDEPMODE = depmode=gcc3
  CXXFLAGS = -g -O2
  </code></pre>
  
  <p><strong>Compiler</strong></p>
  
  <p>Apple LLVM version 10.0.0 (clang-1000.11.45.5)</p>
  
  <p>Target: x86_64-apple-darwin18.2.0</p>
  
  <p>Thread model: posix</p>
  
  <p>InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin</p>
  
  <p>Has anyone built this successfully on MacOS? Or perhaps suggestions as to how I might build this successfully? I'm at a loss.</p>
  
Tags: <rna>
Title: Building RNAz on MacOS
ThreadText: # Building RNAz on MacOS
  
  (Asked by: username_0 on 2019-02-01)
  
  Having trouble building RNAz 2.1 on MacOS. Following instructions at <https://www.tbi.univie.ac.at/software/RNAz/>
  
  ```
  tar -xzf RNAz-2.1-tar.gz
  cd RNAz-2.1
  ./configure
  make
  
  ```
  
  `make` fails with
  
  ```
  /usr/bin/clang++ -o RNAz RNAz.o rnaz_utils.o svm_helper.o zscore.o cmdline.o strand.o svm.o -L../librna -lRNA -lm 
  Undefined symbols for architecture x86_64:
    "_HairpinE", referenced from:
        _alifold in libRNA.a(alifold.o)
        _fill_arrays in libRNA.a(fold.o)
        _backtrack in libRNA.a(fold.o)
        _stack_energy in libRNA.a(fold.o)
    "_LoopEnergy", referenced from:
        _alifold in libRNA.a(alifold.o)
        _fill_arrays in libRNA.a(fold.o)
        _backtrack in libRNA.a(fold.o)
        _stack_energy in libRNA.a(fold.o)
  ld: symbol(s) not found for architecture x86_64
  
  ```
  
  Thinking that compiling for 32-bit might work I tried setting
  
  ```
  CXXFLAGS = -m32
  LDFLAGS = -m32
  
  ```
  
  without success (same result). Same result with `gmake`.
  
  **Configure**
  Configure checks for `gcc`
  
  ```
  ...
  checking for gcc... gcc
  checking whether the C compiler works... yes
  ...
  
  ```
  
  **Makefile**
  
  Makefile specifies the following:
  
  ```
  CC = gcc
  CCDEPMODE = depmode=gcc3
  CFLAGS = -g -O2
  CPP = gcc -E
  CPPFLAGS = 
  CXX = g++
  CXXDEPMODE = depmode=gcc3
  CXXFLAGS = -g -O2
  
  ```
  
  **Compiler**
  
  Apple LLVM version 10.0.0 (clang-1000.11.45.5)
  
  Target: x86\_64-apple-darwin18.2.0
  
  Thread model: posix
  
  InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
  
  Has anyone built this successfully on MacOS? Or perhaps suggestions as to how I might build this successfully? I'm at a loss.
  
  **Tags:** rna
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2019-02-01. Score: 3 | Accepted answer
  
  Compile with gcc or remove `inline` from `librna/fold.c:776` and `librna/fold.c:846`.
  
  
  ---
  
  ### Answer by username_2 on 2019-02-01. Score: 2
  
  The other option would be to use RNAz via a docker container instead on installing it directly. The docker container can be downloaded from [biocontainers](https://quay.io/repository/biocontainers/rnaz). If you are new to docker here is a [tutorial for mac](https://docs.docker.com/docker-for-mac/).
  
  
  ---
  
  ### Answer by username_3 on 2019-02-01. Score: 1
  
  The first thing to try is to perform the install as sudo.
  
  ```
  sudo ./configure # definitely
  sudo make ... sudo make install # possibly (?)
  
  ```
  
  The clang++ compiler may be using a path that is not setup in your profile and sudo will overcome this. If sudo works you know what the problem is and its a case of changing permissions and configurations accordingly. There is a good chance this will resolve the matter.
  
  There are other possibilities, it could be the compiler. It looks like the compiler is fine however looking at the config file and the check. The final issue is it could be the program ;-)
  
  > Tried this. Same result. Will continue scratching head
  
  Try an installation on Linux
  
  Otherwise its usual stuff, namely upgrading Xtools
  
  > **Comments:**
  > **username_0**: Tried this. Same result. Will continue scratching head.  
  > **username_3**: Xtools or Linux ... Linux has a better chance  
  > **username_0**: Xtools is current. Yeah. I know things will likely compile A-OK with Linux. Will try that too. Thanks.  
  
  ---
  
  