On Mac 10.12.1 - there is no bottle for Sierra in the formula and building from source apparent fails. I also tried the more recent version available with similar errors. $ brew doctor Your system is ready to brew. $ brew update Already up-to-date.
Full build from here $ brew install GMAP-GSNAP Updating Homebrew. So I've had this problem now with a few other formulas as well, I think that some external configure scripts are getting perl/python versions from elsewhere and not using the same method as brew config. Thus if you have installed necessary perl modules in your brewed version of perl ( /usr/local/bin/perl), they aren't available to system perl when building the formula.
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Any ideas on how I can change this? /usr/local/bin is in front of /usr/bin in my $PATH. Here's another example when trying to install bcftools, Note that the perl and python paths are different. It seems like in the util folder of gmap-gsnap are several perl scripts.