install augustus on MAC

Question

[qwzhang0601]

I am trying to install augustus3.2.3 on my Mac with system (macOS Sierra, version 10.12.2). When I "make" it, it reports the following errors. Any suggestions? Many thanks

 "vtable for std::basic_streambuf<char, std::char_traits<char> >", referenced from:

      itoa(int) in augustus-6ce428.o
      GBProcessor::getSequence(GBPositions&) in genbank.o
      itoa(int) in genbank.o
      GBFeature::GBFeature(char const*) in genbank.o
      GBSplitter::GBSplitter(std::string) in genbank.o
      GBSplitter::determineFileType() in genbank.o
      GBSplitter::~GBSplitter() in genbank.o
      ...
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
  "vtable for std::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >", referenced from:

      itoa(int) in augustus-6ce428.o
      GBProcessor::getSequence(GBPositions&) in genbank.o
      itoa(int) in genbank.o
      GBFeature::GBFeature(char const*) in genbank.o
      GBSplitter::GBSplitter(std::string) in genbank.o
      GBSplitter::determineFileType() in genbank.o
      GBSplitter::~GBSplitter() in genbank.o
      ...
  NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.

ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [augustus] Error 1

And then using "clang -v" I got the following message

zhang$ clang -v
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin16.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Answer 1

[cmdcolin]

It is hard to read these error messages, but in general, I would suggest installing augustus with Homebrew. See http://brew.sh/

brew install homebrew/science/augustus

You can also look at the "formula" that Homebrew uses to install augustus and it's dependencies in detail here

https://github.com/Homebrew/homebrew-science/blob/master/augustus.rb

[qwzhang0601]

Thank you for your suggestions. But there are still problems. Any ideas about this? Thanks

zhang$ brew install homebrew/science/augustus ==> Installing augustus from homebrew/science Error: You must brew link cmake before homebrew/science/augustus can be installed

zhang$ brew link cmake Linking /usr/local/Cellar/cmake/3.7.2... Error: Could not symlink share/emacs/site-lisp/cmake /usr/local/share/emacs/site-lisp is not writable.

[cmdcolin]

In general with homebrew you don't want to use sudo to install things anymore, so you can use sudo chown -R username:admin /usr/local/ which will try to reset permissions to you in /usr/local. You can also run brew doctor which will probably tell you to run something similar