printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild dssp 2>&1 The package 'dssp' will be built without being installed. Reading build dependency for dssp-2.2.1-1... Reading dependency for dssp-2.2.1-1... Reading build conflict for dssp-2.2.1-1... The package 'bzip2-dev' will be installed. Reading dependency for bzip2-dev-1.0.6-1... Reading runtime dependency for bzip2-dev-1.0.6-1... The package 'boost1.53.nopython' will be installed. Reading dependency for boost1.53.nopython-1.53.0-2... Reading runtime dependency for boost1.53.nopython-1.53.0-2... The package 'boost1.53.nopython-shlibs' will be installed. Reading dependency for boost1.53.nopython-shlibs-1.53.0-2... Reading runtime dependency for boost1.53.nopython-shlibs-1.53.0-2... The following package will be rebuilt: dssp The following 3 additional packages will be installed: boost1.53.nopython boost1.53.nopython-shlibs bzip2-dev Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/dssp-2.2.1.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 47141 100 47141 0 0 105k 0 --:--:-- --:--:-- --:--:-- 105k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/boost1.53.nopython_1.53.0-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/boost1.53.nopython-shlibs_1.53.0-2_darwin-x86_64.deb Selecting previously deselected package boost1.53.nopython. (Reading database ... 4296 files and directories currently installed.) Unpacking boost1.53.nopython (from .../boost1.53.nopython_1.53.0-2_darwin-x86_64.deb) ... Selecting previously deselected package boost1.53.nopython-shlibs. Unpacking boost1.53.nopython-shlibs (from .../boost1.53.nopython-shlibs_1.53.0-2_darwin-x86_64.deb) ... Setting up boost1.53.nopython-shlibs (1.53.0-2) ... Setting up boost1.53.nopython (1.53.0-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/bzip2-dev_1.0.6-1_darwin-x86_64.deb Selecting previously deselected package bzip2-dev. (Reading database ... 48238 files and directories currently installed.) Unpacking bzip2-dev (from .../bzip2-dev_1.0.6-1_darwin-x86_64.deb) ... Setting up bzip2-dev (1.0.6-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-dssp-2.2.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-dssp-2.2.1-1' in `/sw/build.build/fink-buildlock-dssp-2.2.1-1_2014.07.31-14.21.20_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-dssp-2.2.1-1_2014.07.31-14.21.20_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-dssp-2.2.1-1. (Reading database ... 48245 files and directories currently installed.) Unpacking fink-buildlock-dssp-2.2.1-1 (from .../fink-buildlock-dssp-2.2.1-1_2014.07.31-14.21.20_darwin-x86_64.deb) ... Setting up fink-buildlock-dssp-2.2.1-1 (2014.07.31-14.21.20) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.WI_0_ env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/dssp-2.2.1.tgz dssp-2.2.1/ dssp-2.2.1/makefile dssp-2.2.1/changelog dssp-2.2.1/src/ dssp-2.2.1/src/structure.h dssp-2.2.1/src/iocif.cpp dssp-2.2.1/src/matrix.h dssp-2.2.1/src/mas.h dssp-2.2.1/src/utils.cpp dssp-2.2.1/src/mkdssp.cpp dssp-2.2.1/src/primitives-3d.h dssp-2.2.1/src/iocif.h dssp-2.2.1/src/structure.cpp dssp-2.2.1/src/align-2d.h dssp-2.2.1/src/mas.cpp dssp-2.2.1/src/dssp.cpp dssp-2.2.1/src/buffer.h dssp-2.2.1/src/matrix.inl dssp-2.2.1/src/utils.h dssp-2.2.1/src/dssp.h dssp-2.2.1/src/primitives-3d.cpp dssp-2.2.1/doc/ dssp-2.2.1/doc/mkdssp.1 dssp-2.2.1/LICENSE_1_0.txt dssp-2.2.1/README.txt sudo -u fink-bld [ENV] sh -c /tmp/fink.KuyAm sed -i.old -e s/-static// makefile sed -i.old -e 's|man/man1|share/man/man1|' makefile sudo -u fink-bld [ENV] sh -c /tmp/fink._UVCf /tmp/fink.thcTG #!/bin/sh -ev echo "BOOST_LIB_SUFFIX = -mt-1_53" >make.config echo "BOOST_LIB_DIR = /sw/lib" >>make.config echo "BOOST_INC_DIR = /sw/include/boost-1_53" >>make.config DEST_DIR=/sw make makefile:55: obj/mkdssp.d: No such file or directory makefile:55: obj/dssp.d: No such file or directory makefile:55: obj/primitives-3d.d: No such file or directory makefile:55: obj/structure.d: No such file or directory makefile:55: obj/utils.d: No such file or directory makefile:55: obj/mas.d: No such file or directory makefile:55: obj/iocif.d: No such file or directory compiling obj/mkdssp.o compiling obj/dssp.o compiling obj/primitives-3d.o compiling obj/structure.o compiling obj/utils.o compiling obj/mas.o compiling obj/iocif.o In file included from src/utils.cpp:12: In file included from /sw/include/boost-1_53/boost/thread.hpp:13: In file included from /sw/include/boost-1_53/boost/thread/thread.hpp:17: In file included from /sw/include/boost-1_53/boost/thread/pthread/thread_data.hpp:12: In file included from /sw/include/boost-1_53/boost/thread/lock_types.hpp:18: In file included from /sw/include/boost-1_53/boost/thread/thread_time.hpp:9: In file included from /sw/include/boost-1_53/boost/date_time/time_clock.hpp:17: In file included from /sw/include/boost-1_53/boost/shared_ptr.hpp:17: /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:491:41: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr( std::unique_ptr< Y, D > && r ): px( r.get() ), pn() ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:556:51: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr & operator=( std::unique_ptr && r ) ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:558:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions] this_type( static_cast< std::unique_ptr && >( r ) ).swap(*this); ^ In file included from src/structure.cpp:15: In file included from /sw/include/boost-1_53/boost/format.hpp:38: In file included from /sw/include/boost-1_53/boost/format/internals.hpp:23: In file included from /sw/include/boost-1_53/boost/format/alt_sstream.hpp:21: In file included from /sw/include/boost-1_53/boost/shared_ptr.hpp:17: /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:491:41: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr( std::unique_ptr< Y, D > && r ): px( r.get() ), pn() ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:556:51: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr & operator=( std::unique_ptr && r ) ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:558:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions] this_type( static_cast< std::unique_ptr && >( r ) ).swap(*this); ^ In file included from src/dssp.cpp:15: In file included from /sw/include/boost-1_53/boost/format.hpp:38: In file included from /sw/include/boost-1_53/boost/format/internals.hpp:23: In file included from /sw/include/boost-1_53/boost/format/alt_sstream.hpp:21: In file included from /sw/include/boost-1_53/boost/shared_ptr.hpp:17: /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:491:41: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr( std::unique_ptr< Y, D > && r ): px( r.get() ), pn() ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:556:51: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr & operator=( std::unique_ptr && r ) ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:558:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions] this_type( static_cast< std::unique_ptr && >( r ) ).swap(*this); ^ In file included from src/iocif.cpp:9: In file included from /sw/include/boost-1_53/boost/iostreams/copy.hpp:28: In file included from /sw/include/boost-1_53/boost/iostreams/chain.hpp:37: In file included from /sw/include/boost-1_53/boost/shared_ptr.hpp:17: /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:491:41: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr( std::unique_ptr< Y, D > && r ): px( r.get() ), pn() ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:556:51: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr & operator=( std::unique_ptr && r ) ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:558:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions] this_type( static_cast< std::unique_ptr && >( r ) ).swap(*this); ^ In file included from src/mkdssp.cpp:17: In file included from /sw/include/boost-1_53/boost/program_options.hpp:15: In file included from /sw/include/boost-1_53/boost/program_options/options_description.hpp:16: In file included from /sw/include/boost-1_53/boost/shared_ptr.hpp:17: /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:491:41: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr( std::unique_ptr< Y, D > && r ): px( r.get() ), pn() ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:556:51: warning: rvalue references are a C++11 extension [-Wc++11-extensions] shared_ptr & operator=( std::unique_ptr && r ) ^ /sw/include/boost-1_53/boost/smart_ptr/shared_ptr.hpp:558:55: warning: rvalue references are a C++11 extension [-Wc++11-extensions] this_type( static_cast< std::unique_ptr && >( r ) ).swap(*this); ^ 3 warnings generated. 3 warnings generated. src/structure.cpp:35:2: warning: unused variable 'kSSBridgeDistance' [-Wunused-const-variable] kSSBridgeDistance = 3.0, ^ 3 warnings generated. 3 warnings generated. 4 warnings generated. linking mkdssp clang: warning: argument unused during compilation: '-pthread' /bin/rm -rf /sw/build.build/root-dssp-2.2.1-1 /bin/mkdir -p /sw/build.build/root-dssp-2.2.1-1/sw /bin/mkdir -p /sw/build.build/root-dssp-2.2.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-dssp-2.2.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.zCW8C /tmp/fink.eyOqN #!/bin/sh -ev DEST_DIR=/sw/build.build/root-dssp-2.2.1-1/sw make install install -d /sw/build.build/root-dssp-2.2.1-1/sw/bin /sw/build.build/root-dssp-2.2.1-1/sw/share/man/man1 install -m 755 mkdssp /sw/build.build/root-dssp-2.2.1-1/sw/bin/mkdssp install doc/mkdssp.1 /sw/build.build/root-dssp-2.2.1-1/sw/share/man/man1/mkdssp.1 sudo -u fink-bld [ENV] sh -c /tmp/fink.ujvn9 /usr/bin/install -d -m 700 /sw/build.build/root-dssp-2.2.1-1/sw/share/doc/dssp /bin/cp -r changelog /sw/build.build/root-dssp-2.2.1-1/sw/share/doc/dssp/ /bin/cp -r LICENSE_1_0.txt /sw/build.build/root-dssp-2.2.1-1/sw/share/doc/dssp/ /bin/cp -r README.txt /sw/build.build/root-dssp-2.2.1-1/sw/share/doc/dssp/ /bin/chmod -R go=u-w /sw/build.build/root-dssp-2.2.1-1/sw/share/doc/dssp /bin/rm -f /sw/build.build/root-dssp-2.2.1-1/sw/info/dir /sw/build.build/root-dssp-2.2.1-1/sw/info/dir.old /sw/build.build/root-dssp-2.2.1-1/sw/share/info/dir /sw/build.build/root-dssp-2.2.1-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-dssp-2.2.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `dssp' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/dssp_2.2.1-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-dssp-2.2.1-1 (Reading database ... 48246 files and directories currently installed.) Removing fink-buildlock-dssp-2.2.1-1 ...