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Gentoo's Bugzilla – Attachment 409052 Details for
Bug 557822
sci-chemistry/autodock_vina-1.1.2 : ld: cannot find -lboost_thread
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sci-chemistry:autodock_vina-1.1.2:20150815-060622.log
sci-chemistry:autodock_vina-1.1.2:20150815-060622.log (text/plain), 6.67 KB, created by
Toralf Förster
on 2015-08-15 08:29:22 UTC
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Description:
sci-chemistry:autodock_vina-1.1.2:20150815-060622.log
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Creator:
Toralf Förster
Created:
2015-08-15 08:29:22 UTC
Size:
6.67 KB
patch
obsolete
> * Package: sci-chemistry/autodock_vina-1.1.2 > * Repository: gentoo > * Maintainer: jlec@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux pie ssp userland_GNU > * FEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking autodock_vina_1_1_2.tgz to /var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work/autodock_vina_1_1_2/build/linux/release ... > * Applying 1.1.2-gentoo.patch ... > [ ok ] > * Applying autodock_vina-1.1.2-boost-filesystem.patch ... > [ ok ] >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work/autodock_vina_1_1_2/build/linux/release ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work/autodock_vina_1_1_2/build/linux/release ... >make -j1 BASE=/usr/ GPP=x86_64-pc-linux-gnu-g++ C_OPTIONS=-DNDEBUG >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -I ../../../src/lib -o main.o -c ../../../src/main/main.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o cache.o -c ../../../src/lib/cache.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o coords.o -c ../../../src/lib/coords.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o current_weights.o -c ../../../src/lib/current_weights.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o everything.o -c ../../../src/lib/everything.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o grid.o -c ../../../src/lib/grid.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o szv_grid.o -c ../../../src/lib/szv_grid.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o manifold.o -c ../../../src/lib/manifold.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o model.o -c ../../../src/lib/model.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o monte_carlo.o -c ../../../src/lib/monte_carlo.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o mutate.o -c ../../../src/lib/mutate.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o my_pid.o -c ../../../src/lib/my_pid.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o naive_non_cache.o -c ../../../src/lib/naive_non_cache.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o non_cache.o -c ../../../src/lib/non_cache.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o parallel_mc.o -c ../../../src/lib/parallel_mc.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o parse_pdbqt.o -c ../../../src/lib/parse_pdbqt.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o pdb.o -c ../../../src/lib/pdb.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o quasi_newton.o -c ../../../src/lib/quasi_newton.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o quaternion.o -c ../../../src/lib/quaternion.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o random.o -c ../../../src/lib/random.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o ssd.o -c ../../../src/lib/ssd.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o terms.o -c ../../../src/lib/terms.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -march=native -O2 -pipe -DBOOST_FILESYSTEM_VERSION=3 -o weighted_terms.o -c ../../../src/lib/weighted_terms.cpp >x86_64-pc-linux-gnu-g++ -pthread -ansi -Wno-long-long -DNDEBUG -I/usr//include -Wl,-O1 -Wl,--as-needed -L. -o vina main.o cache.o coords.o current_weights.o everything.o grid.o szv_grid.o manifold.o model.o monte_carlo.o mutate.o my_pid.o naive_non_cache.o non_cache.o parallel_mc.o parse_pdbqt.o pdb.o quasi_newton.o quaternion.o random.o ssd.o terms.o weighted_terms.o -lboost_system -lboost_thread -lboost_serialization -lboost_filesystem -lboost_program_options -lpthread >/usr/lib/gcc/x86_64-pc-linux-gnu/4.8.4/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread >collect2: error: ld returned 1 exit status >../../makefile_common:34: recipe for target 'vina' failed >make: *** [vina] Error 1 > * ERROR: sci-chemistry/autodock_vina-1.1.2::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-chemistry/autodock_vina-1.1.2::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/autodock_vina-1.1.2::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-chemistry:autodock_vina-1.1.2:20150815-060622.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work/autodock_vina_1_1_2/build/linux/release' > * S: '/var/tmp/portage/sci-chemistry/autodock_vina-1.1.2/work/autodock_vina_1_1_2/build/linux/release'
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