Compilation fails on Mac OSX

[lrvdijk]

Hi,

I'm trying to compile the latest Bifrost on Mac OS X (MacBook M1 pro, OS X 13.4), but for some reason I get the error it is unable to find the function mkdtemp

/Users/ldijk/Library/Mobile Documents/com~apple~CloudDocs/programming/bioinformatics/gatk-bacteria/bifrost/src/CompactedDBG.tcc:2801:17: error: use of undeclared identifier 'mkdtemp'
/Users/ldijk/Library/Mobile Documents/com~apple~CloudDocs/programming/bioinformatics/gatk-bacteria/bifrost/src/CompactedDBG.tcc:2801:17:             if (mkdtemp(tmp_dir) == nullptr) {error:
                ^use of undeclared identifier 'mkdtemp'

            if (mkdtemp(tmp_dir) == nullptr) {

I am a bit suprised by this, because I see that unistd.h gets included (which is where that function is defined on OS X). I also tried to run with cmake .. -D_DARWIN_C_SOURCE to no avail (a suggestion I found by googling a bit).

Full compilation log using a cmake generated verbose makefile: log.txt

Any ideas how to fix this?

[GuillaumeHolley]

Hi @lrvdijk,

I appreciate the feedback, thanks. I also thought that mkdtemp was part of unistd.h (and of course it compiles just fine on UNIX platforms) but a bit of googling indicates that it is actually part of stdlib.h (see here). So this might be the issue?

I don't have a Mac OS X machine to try this, would you mind giving it a shot? Just add #include <stdlib.h> at the top of CompactedDBG.hpp with the other includes, rerun cmake with a new build directory and hopefully this should work.

Crossing my fingers but in any case, let me know if it worked. Guillaume

[lrvdijk]

Just tried it, but no luck unfortunately. I'd also have assumed the #include <cstdlib> would have provided that function in that case.

[GuillaumeHolley]

Good point, #include <cstdlib> should be enough. I was just hoping this could have been something as simple to fix as a missing include since the clang error message was kind of hinting in that direction. To be honest, I have no idea what is going on right now. I'll try to find a Macbook asap and install Bifrost on it to see what's wrong.

[GuillaumeHolley]

Hi again @lrvdijk,

@pmelsted worked his magic and made a fix for MacOS. Furthermore, the Cmake files shouldn't give any troubles to MacOS anymore. The fix is on the mac_fix branch, could you give it a shot first on your side? I'll try it on my side as well tonight and merge with main if we both green light this.

Guillaume

[lrvdijk]

I successfully compiled Bifrost! Thanks for the quick response!

[GuillaumeHolley]

@lrvdijk Compilation fix for MacOS fully integrated in v1.3.1 release :)