0
$\begingroup$

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.

$\endgroup$
0
3
$\begingroup$

Compile with gcc or remove inline from librna/fold.c:776 and librna/fold.c:846.

$\endgroup$
2
$\begingroup$

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. If you are new to docker here is a tutorial for mac.

$\endgroup$
1
$\begingroup$

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

$\endgroup$
3
  • 1
    $\begingroup$ Tried this. Same result. Will continue scratching head. $\endgroup$ – PartialOrder Feb 1 '19 at 17:24
  • $\begingroup$ Xtools or Linux ... Linux has a better chance $\endgroup$ – M__ Feb 1 '19 at 17:28
  • 1
    $\begingroup$ Xtools is current. Yeah. I know things will likely compile A-OK with Linux. Will try that too. Thanks. $\endgroup$ – PartialOrder Feb 1 '19 at 17:29

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.