The configure process for the latest ATLAS snapshot (3.11.22) does not recognize the compiler that I'm specifying with a -C alg option as GCC -- it gives me an UNKNOWN COMPILER error and tells me I need to specify flags.
The problem traces to the CompIsGcc function in atlconf_misc.c -- specifically, the conditional made up of various strstr() calls at line 778.
My compiler's version string is (with some details redacted):
"x86_64-grtev3-linux-gnu-gcc (Google_...) 4.8.x-google 2013... (prerelease)\n"
None of the conditionals match this. As mentioned in the comments, CompIsGcc does not search for "gcc" as that matches "pgcc" among others -- but my compiler version string doesn't match any of the strstr patterns, nor does it start with "gcc" because it's set up as a cross-compiler.
Might I suggest adding "-gcc " to the set of patterns you check for?
I've confirmed that adding this gets me a successful configuration, and the leading "-" avoids matching "pgcc".