search

luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
302 stars 38 forks source link

Problem installing on macOS 10.15.3 #126

Closed nuin closed 4 years ago

nuin commented 4 years ago

Describe the bug

I have tried all possible ways to compile on macOS (including some tips from previous issues I've opened) and nothing seems to work.

I tried the develop branch as per install instructions and then release/7.0.0 as it worked before for me on previous versions of macOS and compilers.

Command Command line to install octopus:

$ ./scripts/install.py
$ ./scripts/install.py --threads 1
$ ./scripts/install.py -c /usr/local/Cellar/llvm/10.0.0_3/bin/clang -cxx /usr/local/Cellar/llvm/10.0.0_3/bin/clang++

among others

Additional context

stderr and stdout of the last command run are attached. These files are a little shorted with only three errors. With a regular install with no parameters, I can get up to 30 errors. stderr.txt stdout.txt

dancooke commented 4 years ago

Which commit are you using?

Have you tried using the --dependencies option (i.e. the recommended way to install)?

$ ./scripts/install.py --dependencies

What error do you get when you try this?

nuin commented 4 years ago

Hi @dancooke

Latest I tried, which is worked on other similar machines (with an older version of macOS) is

9222d54d864c5a13364c848fb0bd0df5f63e8f26

tagged as release/0.7.0.

I also tried with the --dependecies parameter, with similar results. Any other relevant information that I can give you? I had tried the same approach you mentioned on an older ticket I opened, and didn't work.

Thanks

dancooke commented 4 years ago

Sorry for the delay. Can you try the latest develop branch?

nuin commented 4 years ago

Hi

Compilation seems to work fine with

./scripts/install.py -c /usr/local/Cellar/llvm/10.0.0_3/bin/clang -cxx /usr/local/Cellar/llvm/10.0.0_3/bin/clang++

but when trying to execute

[100%] Linking CXX executable octopus
[100%] Built target octopus
Install the project...
-- Install configuration: "Release"
-- Installing: /Users/nuin/octopus/bin/octopus
❯ bin/octopus
dyld: Library not loaded: /usr/local/opt/icu4c/lib/libicudata.64.dylib
  Referenced from: /usr/local/opt/boost/lib/libboost_log-mt.dylib
  Reason: image not found
[1]    65645 abort      bin/octopus

./scripts/install.py --dependencies -c /usr/local/Cellar/llvm/10.0.0_3/bin/clang -cxx /usr/local/Cellar/llvm/10.0.0_3/bin/clang++

to make re-install dependencies and make it work properly.