build.log

file_808669.txt (text/plain), 6.28 KB, created by Sam James on 2021-08-17 02:47:27 UTC

 * Package:    sci-chemistry/dssp-2.2.1-r2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
Unable to configure loopback interface: Operation not permitted
>>> Unpacking source...
>>> Unpacking dssp-2.2.1.tgz to /var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work
Unable to configure loopback interface: Operation not permitted
>>> Preparing source in /var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work/dssp-2.2.1 ...
 * Applying dssp-2.1.0-gentoo.patch ...
 [ ok ]
 * Applying dssp-2.2.1-boost-1.65-tr1-removal.patch ...
 [ ok ]
>>> Source prepared.
Unable to configure loopback interface: Operation not permitted
>>> Configuring source in /var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work/dssp-2.2.1 ...
>>> Source configured.
Unable to configure loopback interface: Operation not permitted
>>> Compiling source in /var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work/dssp-2.2.1 ...
make -j4 
compiling obj/mkdssp.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/mkdssp.o src/mkdssp.cpp
compiling obj/dssp.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/dssp.o src/dssp.cpp
compiling obj/primitives-3d.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/primitives-3d.o src/primitives-3d.cpp
compiling obj/structure.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/structure.o src/structure.cpp
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/format/alt_sstream.hpp:22,
                 from /usr/include/boost/format/internals.hpp:24,
                 from /usr/include/boost/format.hpp:38,
                 from src/dssp.cpp:15:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind.hpp:30,
                 from src/structure.cpp:14:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
compiling obj/utils.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/utils.o src/utils.cpp
In file included from /usr/include/boost/bind.hpp:30,
                 from src/utils.cpp:11:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
compiling obj/mas.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/mas.o src/mas.cpp
compiling obj/iocif.o
x86_64-pc-linux-gnu-g++ -I"/usr/include" -iquote src -DUSE_COMPRESSION -DLINUX -DVERSION='"2.2.1"' -DNDEBUG -O2 -march=native -pipe -Wall -Wno-multichar -pthread -MD -c -o obj/iocif.o src/iocif.cpp
linking mkdssp
x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -o mkdssp obj/mkdssp.o obj/dssp.o obj/primitives-3d.o obj/structure.o obj/utils.o obj/mas.o obj/iocif.o -L"/usr/lib64" -lboost_thread-mt -lboost_filesystem-mt -lboost_program_options-mt -lboost_iostreams-mt -lboost_system-mt -lz -lbz2 -pthread
/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread-mt
/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_filesystem-mt
/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_program_options-mt
/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_iostreams-mt
/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_system-mt
collect2: error: ld returned 1 exit status
make: *** [makefile:54: mkdssp] Error 1
 * ERROR: sci-chemistry/dssp-2.2.1-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/dssp-2.2.1-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/dssp-2.2.1-r2::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work/dssp-2.2.1'
 * S: '/var/tmp/portage/sci-chemistry/dssp-2.2.1-r2/work/dssp-2.2.1'