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NOTE: I write these examples exactly the way they worked for me. No guarantees whatsoever, etc, etc.

OK. I updated my machines to Yosemite, and, of course, you’re curious about BLAST. Right? Story short: You have to do exactly the very same thing as I did under Mavericks. I know, the errors given if you don’t do any of this look different to the errors under Mavericks. I know, I know. But the thing compiles all right doing exactly the same. Here what I did in just one terminal because today I don’t feel like showing you the errors, trials and tribulations (maybe another day):

% mkdir BUILD
% cd BUILD
% tar zxvf ../ncbi-blast-2.2.29+-src.tar.gz | tail -5
ncbi-blast-2.2.29+-src/c++/compilers/msvc1000_prj/dll/build/all_gui.bat
ncbi-blast-2.2.29+-src/c++/compilers/msvc1000_prj/dll/third_party_msvcdll_install.vcxproj
ncbi-blast-2.2.29+-src/c++/compilers/msvc1000_prj/dll/dll_main.cpp
ncbi-blast-2.2.29+-src/c++/compilers/msvc1000_prj/dll/third_party_dll_install.mak
ncbi-blast-2.2.29+-src/c++/configure.orig
% cd ncbi-blast-2.2.29+-src/c++/
% setenv CC '/sw/bin/gcc-4'
% setenv CXX '/sw/bin/g++-4'
% setenv CFLAGS '-O3'
% setenv CXXFLAGS '-O3'
%
%  ./configure --without-debug --with-strip --with-mt --with-build-root=ReleaseMT --with-static --with-static-exe --prefix=/usr/local/ncbi |& tail -5
To build everything:  cd /Users/gmh/BUILD/ncbi-blast-2.2.29+-src/c++/ReleaseMT/build && make all_r
or simply run make in the current directory

******* CONFIGURATION SUCCESSFUL *******
%
% perl -i.bak -pe 's{\s+\-std=\S+}{}' ReleaseMT/build/Makefile.mk
% make -j4
... output not shown for brevity ...
% sudo make install

That’s it for now ladies and gentlemen!

Have fun,

-SuperGabo

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