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error installing nauty package on mac osx 10.7

asked 2013-05-07 15:25:36 -0500

vermette gravatar image

updated 2015-10-22 14:36:51 -0500

FrédéricC gravatar image

I am attempting to install the nauty package for Sage on my Mac OSX 10.7.5. The Sage version is Sage-5.9-OSX-64bit-10.7-x86_64-Darwin-app.dmg. Everything seems to work fine in Sage.

However, upon running install_package('nauty'), I get an error. The full output is here, I think the relevant part is this:

checking build system type... i686-apple-darwin11.4.2

checking host system type... i686-apple-darwin11.4.2

checking for gcc... gcc

checking whether the C compiler works... no

configure: error: in



configure: error: C compiler cannot create executables

See 'config.log' for more details.

Error configuring nauty.

The config.log which it references is here. Any help would be much appreciated. Also, let me know if there is a more preferred place to host a text file in the future.

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answered 2013-05-07 15:34:52 -0500

kcrisman gravatar image

You need a C compiler for this. What happens in the terminal when you do

which gcc


gcc -v

Thankfully, we just updated the installation from source documentation to mention how to get this on Mac.

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The `config.log` file posted by vermette seems to indicate `gcc -v` finds gcc 4.7.2 (shipped with Sage). Can you use Sage's gcc from a binary when you don't have Apple's command line tools installed? Does it matter that the "Configured with" info in the output of `gcc -v` has bits of paths from where the binary was compiled (that was actually on my computer), that are meaningless on vermette's computer?

slelievre gravatar imageslelievre ( 2013-05-08 05:00:50 -0500 )edit

No, Sage's gcc still needs, I think, libraries and header files that get installed system-wide when you install the command line tools.

John Palmieri gravatar imageJohn Palmieri ( 2013-05-08 05:35:45 -0500 )edit

Installing Command Line Tools from XCode's Downloads preference pane (as advised in the link you provided) did the trick. I found a dozen places advising to install XCode, but none mentioned that I'd also need to go into the preferences and install anything else (namely, the Command Line Tools). Thanks for your quick and accurate response!

vermette gravatar imagevermette ( 2013-05-08 08:37:33 -0500 )edit

No problem! I have to say that it is only with newer Macs that the command line tools aren't just automatically part of Xcode (grumble, grumble) but glad it worked out for you.

kcrisman gravatar imagekcrisman ( 2013-05-08 10:13:33 -0500 )edit

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Asked: 2013-05-07 15:25:36 -0500

Seen: 447 times

Last updated: May 08 '13