Question: install augustus on MAC
1
gravatar for qwzhang0601
2.2 years ago by
qwzhang060160
United States
qwzhang060160 wrote:

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
augustus • 951 views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 2.2 years ago by qwzhang060160
0
gravatar for cmdcolin
2.2 years ago by
cmdcolin1.1k
United States
cmdcolin1.1k wrote:

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

ADD COMMENTlink written 2.2 years ago by cmdcolin1.1k

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.

ADD REPLYlink written 2.2 years ago by qwzhang060160

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

ADD REPLYlink written 2.2 years ago by cmdcolin1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 828 users visited in the last hour