Unable to build RNAz on macOS 13 Ventura

[iljungr]

I am trying to build RNAz-2.1 on macOS 13 Ventura. I first installed ViennaRNA-2.5.1. It was failing compilation with "zscore.c:354:21: error: call to undeclared function 'time'". I was able to work around this by adding #include <time.h> to zscore.c. Now it is failing trying to link, complaining:
Undefined symbols for architecture arm64:
"_HairpinE", referenced from:
_alifold in libRNA.a(alifold.o)
_fold in libRNA.a(fold.o)
_stack_energy in libRNA.a(fold.o)
"_LoopEnergy", referenced from:
_alifold in libRNA.a(alifold.o)
_fold in libRNA.a(fold.o)
_stack_energy in libRNA.a(fold.o)
ld: symbol(s) not found for architecture arm64

I tried ./configure CFLAGS="-std=gnu89 -g -O2" as suggested in issue #8, but that didn't help.

How can I build RNAz-2.1 on macOS 13 Ventura?

[iljungr]

I was able to build by remove the "inline" from the declarations and definitions of HairpinE and LoopEnergy in librna/fold.c (as well as adding "#inclusion <time.h>" to score.c).

If this is the "correct" fix, then those two files should be updated on github. If it isn't the correct fix then what is?

[svenderheld]

Dear iljungr,

The old source code on the RNAz web page is not mantained anymore. Please use the software avialable on github.

I'm not familiar with MacOS at all but was able to use a Mac of one of my colleagues. It was the older version of macOS Big Sur (version 11.6).

I cloned the repository

'git clone git@github.com:ViennaRNA/RNAz.git'

and had to install few things in order to run the autogen.sh script

'brew install readline; brew install automake'

'autoupdate'

'./autogen.sh'

This gave a configure file that had a newline issue in 4842. Fixing that adding a ")" and removing the newline therefore moving line 4843 one up resulted in an additional ")" on line 5740 which I removed. Using this edited version made it possible to run

'configure'

and

'make'

Unfortunately, I could therefore not reproduce your issue. I assigened the main developer of the ViennaRNA package if he is aware of similar issues.

Best,
Sven