You receive this bug because this package does not respect my system's CC ( x86_64-pc-linux-gnu-gcc - /usr/bin/x86_64-pc-linux-gnu-gcc ) and calls directly gcc -/usr/bin/gcc The possible solutions to fix this issue are: 1)Fix the buildsystem, if you can 2)inherit toolchain-funcs and use tc-export CC 3)inherit toolchain-funcs and use emake CC="$(tc-getCC)" gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNDEBUG -O3 -D_LARGE_FILE -c -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF pattern.c
+*ncbi-tools-2.2.26-r2 (01 Mar 2013) + + 01 Mar 2013; Justin Lecher <jlec@gentoo.org> -ncbi-tools-2.2.26-r1.ebuild, + +ncbi-tools-2.2.26-r2.ebuild: + Fix all config files, #459720, #459726, #459878 + Please test and reopen if needed