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Empty bin after compilation

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Empty bin after compilation

Dear Rosetta Users,

I downloaded the most recent release rosetta2014.52 and compiled the source code on a Linux 64 bit machine with the command: ./ -j4 mode=release bin. The compilation seemed successful as I saw the "scons: done building targets" message. But the bin/ was empty though the build/src contains newly generated files. Looking at the log file, I found these lines:

g++ -o build/src/debug/linux/2.6/64/x86/gcc/4.4/default/devel/svn_version.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -Wno-uninitialized -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DPTR_BOOST -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include src/devel/
g++ -o build/src/debug/linux/2.6/64/x86/gcc/4.4/default/ -Wl,-rpath=/home/svu/bchyuk/rosetta/main/source/build/external/debug/linux/2.6/64/x86/gcc/4.4/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/src/debug/linux/2.6/64/x86/gcc/4.4/default/devel/init.os build/src/debug/linux/2.6/64/x86/gcc/4.4/default/devel/svn_version.os -Lexternal/lib -Lbuild/src/debug/linux/2.6/64/x86/gcc/4.4/default -Lsrc -Lbuild/external/debug/linux/2.6/64/x86/gcc/4.4/default -Lexternal -L/usr/lib -L/usr/local/lib -lprotocols.7 -lprotocols.6 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols_h.4 -lprotocols_g.4 -lprotocols_f.4 -lprotocols_e.4 -lprotocols_d.4 -lprotocols_c.4 -lprotocols_b.4 -lprotocols_a.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3
/usr/bin/ld: skipping incompatible /usr/lib/ when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/ when searching for -lc
scons: done building targets.

I guess there is a linking error here, which failed to create a symlink under bin/. How do I solve this problem?

Post Situation: 
Fri, 2015-01-09 18:58

The message output would indicate to me that it didn't recognize the "bin" on the commandline. What's more, it doesn't look like it's even recognizing the "mode=release" -- it's building in debug directories.

What happens if you re-run the scons command (try re-typing it)? What happens if you use a specific program name instead of bin? (e.g. "./ -j4 mode=release relax" or "./ -j4 mode=release rosetta_scripts" or "./ -j4 mode=release score_jd2")

Mon, 2015-01-19 16:18

Sorry, turns out I was recompiling in an old Rosetta folder(rookie mistake), with the bin directory cleaned some time before. But it was still a mystery why it is not taking the commandline. Everything just goes to debug dir even I used a specific application name.

Never mind. I just ignored this and compiled with the right download, and it worked fine. Thanks for your help!

Wed, 2015-01-21 23:34