Error installing rosetta2014.35 on Ubuntu14.04

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    • October 31, 2014 at 7:25 pm #2050
      Anonymous

        Hello,

        I am trying to install rosetta2014.35 on ubuntu14.04.
        I installed the last versions of gcc and clang compilers, namely gcc-4.8 and clang-3.5

        I installed the following packages and libraries as reccommanded

        sudo apt-get install build-essential
        sudo apt-get install zlib1g-dev
        sudo apt-get update

        and executed the commands

        cd main/source/
        scons bin mode=release

        but unsuccessfully!! I always receive the same error (see below)

        Also I updated g++ compilers on tools/build/site.setting. topsail file

        #####################
        import os
        settings = {
        “site” : {
        “prepends” : {
        “program_path” : os.environ[“PATH”].split(“:”),
        # “include_path” : os.environ[“INCLUDE”].split(“:”),
        # “library_path” : os.environ[“LD_LIBRARY_PATH”].split(“:”),
        },
        “appends” : {
        },
        “overrides” : {
        “cc”:”gcc-4.8″,
        “cxx”:”g++-4.8″,
        },
        “removes” : {
        },
        },
        }
        #####################################

        Here is the error I currently receive:

        annalisa@annalisa-CG5275:~/rosetta_2014.35.57232_bundle/main/source$ scons bin mode=release
        scons: Reading SConscript files …
        Running versioning script … Done. (0.0 seconds)
        Number of option files updated: 0
        Total 2998 options.
        Finished updating ResidueType properties — no changes needed
        scons: done reading SConscript files.
        scons: Building targets …
        g++-4.8 -o build/src/release/linux/3.13/64/x86/gcc/4.8/default/apps/public/AbinitioRelax.o -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/apps/public/AbinitioRelax.cc
        g++-4.8 -o build/src/release/linux/3.13/64/x86/gcc/4.8/default/devel/init.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/init.cc
        g++-4.8 -o build/src/release/linux/3.13/64/x86/gcc/4.8/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 -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -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/svn_version.cc

        Hope to solve it soon!

        Thanks a lot in advance.

        Annalisa

      • October 31, 2014 at 7:52 pm #10512
        Anonymous

          I don’t see any errors listed there. What you’ve posted is the normal output from the Rosetta compile process. You’ll get a large number of such lines, as it takes quite a while for Rosetta to compile. (If you have multiple processors you can devote to compiling, you can pass the -jX flag to scons, where X is the number of processors to use: e.g. -j4 on a quad-core machine.)

          If there is an error in compiling, you should see a line which actually says “Error”, as well as something like “building terminated because of errors”, followed by the compilation terminating. If the compilation is successful, you’ll see the line “done building targets” printed instead.

          Note that the compilation process should be interruptible – simply restart with the exact same commandline, and the compilation should pick up where it left off. This is often a good way to check if compiling finished successfully. If it did, there should be a very simple output. (Mostly “up to date” messages.) If not, you’ll see the failing compilation command printed again, along with the error message.

        • November 1, 2014 at 5:06 pm #10513
          Anonymous

            Installed and up-to-date correctly.

            Thanks a lot!

            Annalisa

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