Jellyfish Installation Question

Question

[nai2364]

Hello,

I'm a student trying to install jellyfish (2.2.4), and the configure step went fine. However, the next step (make) sends an error and I'm not quite sure how to deal with it - I tried commenting out the mentioned section but since I'm not really aware of what that code is doing I'm hesitant to proceed. Anyway, here's the original error message

Username-MacBook-Pro:jellyfish-2.2.4 Username$ ./configure

all the checks, went well

Username-MacBook-Pro:jellyfish-2.2.4 Username$ make
make  all-am
  CXX      lib/misc.lo
lib/misc.cc:86:11: error: no member named 'all_of' in namespace 'std'
  if(std::all_of(arg.begin(), arg.end(), isblunt))
     ~~~~~^
1 error generated.
make[1]: *** [lib/misc.lo] Error 1
make: *** [all] Error 2

If anyone has an idea how how to fix this problem I'd very much appreciate it!

[chjiao3456]

I am trying to install Jellyfish, however I was stuck in the first step for there is no configure file at all...

Answer 1

[Jon]

I noticed that you are on a Mac. You will save yourself a lot of time and headache by installing the homebrew package manager and then homebrew science repository.

#install home-brew
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

#tap science home-brew repo
brew tap homebrew/science

#install jellyfish
brew install jellyfish

[nai2364]

Hi - this seemed to be working but somehow I ended up with exactly the same error, I looked at the troubleshooting issues pages but it seems to be something jellyfish-related and not homebrew related so I'm still not really sure what is going on

=> ./configure --prefix=/usr/local/Cellar/jellyfish/2.1.4
==> make
Last 15 lines from /Users/Username/Library/Logs/Homebrew/jellyfish/02.make:
/usr/bin/make  all-am
  CXX    lib/rectangular_binary_matrix.lo
  CXX    lib/mer_dna.lo
  CXX    lib/storage.lo
  CXX    lib/allocators_mmap.lo
  CXX    lib/misc.lo
  CXX    lib/int128.lo
  CXX    lib/thread_exec.lo
lib/misc.cc:86:11: error: no member named 'all_of' in namespace 'std'
  if(std::all_of(arg.begin(), arg.end(), isblunt))
     ~~~~~^
1 error generated.
make[1]: *** [lib/misc.lo] Error 1
make[1]: *** Waiting for unfinished jobs....
make: *** [all] Error 2

READ THIS: https://git.io/brew-troubleshooting
If reporting this issue please do so at (not Homebrew/homebrew):
  https://github.com/homebrew/homebrew-science/issues

[Jon]

It might be related to the C compiler that you have on Mac - clang versus GCC or perhaps a missing dependency. Usually homebrew sorts out the missing dependencies for you. You can install GCC with homebrew as well and then try to build with the GCC instead of clang (default on mac). I think that homebrew usually installs the compiled binary by default, but you can also force it to install by passing the --build-from-source argument, i.e. brew install jellyfish --build-from-source But I'm not really sure if that is the problem. Homebrew installed jellyfish on my system without any problems, however I do have GCC-4.8 and GCC-5 installed on my system.

[Jon]

Did you try this fix? Jellyfish v2.1.4 make error