mhekkel
commented
3 years ago Hi Jarek,
So you're using Ubuntu 20, right. Curious.
Could you please send the config.log file in the directory where you tried to configure dssp? Perhaps that file can tell me what is going on.
regards, -maarten
Op 21-5-2021 om 15:32 schreef Jvdjvdjvd:
System: "Ubuntu 20.04.1 LTS" Thank you for sharing this program. Unfortunately I am having problems installing it. Could you help me? I installed mrc and libcif++ but my the dssp configuration has trouble finding this libcif++ install.
|(base) @.***:~/Documents/dssp$ sudo ./configure checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ supports C++17 features with -std=c++17... yes checking whether C++ compiler accepts -fstandalone-debug... no checking for a BSD-compatible install... /usr/bin/install -c checking for pkg-config... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for a sed that does not truncate output... /usr/bin/sed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for mrc... /usr/local/bin/mrc checking how to run the C++ preprocessor... g++ -std=c++17 -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking filesystem usability... yes checking filesystem presence... yes checking for filesystem... yes checking for boostlib >= 1.65.1 (106501)... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Program_Options library is available... yes checking for exit in -lboost_program_options... yes checking whether the Boost::Date_Time library is available... yes checking for exit in -lboost_date_time... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking need to link zlib... no checking need to link bzip2... no checking cif++/Cif++.hpp usability... yes checking cif++/Cif++.hpp presence... yes checking for cif++/Cif++.hpp... yes checking for cif++/Cif++.hpp... (cached) yes checking for main in -lcifpp... no configure: error: libcif++ not found |
The installation of libcif++ seemed successful:
./configure checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ supports C++17 features with -std=c++17... yes checking whether C++ compiler accepts -fstandalone-debug... no checking how to run the C++ preprocessor... g++ -std=c++17 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking filesystem usability... yes checking filesystem presence... yes checking for filesystem... yes checking for a BSD-compatible install... /usr/bin/install -c checking for pkg-config... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for a sed that does not truncate output... /usr/bin/sed checking how to run the C preprocessor... gcc -E checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -std=c++17 -E checking for ld used by g++ -std=c++17... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=c++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=c++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=c++17 static flag -static works... yes checking if g++ -std=c++17 supports -c -o file.o... yes checking if g++ -std=c++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for mrc... /usr/local/bin/mrc checking for filesystem... (cached) yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strchr... yes checking for strerror... yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking termios.h usability... yes checking termios.h presence... yes checking for termios.h... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for ptrdiff_t... yes checking whether make sets $(MAKE)... yes checking for boostlib >= 1.71 (107100)... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking whether the Boost::Date_Time library is available... yes checking for exit in -lboost_date_time... yes checking whether the Boost::Regex library is available... yes checking for exit in -lboost_regex... yes checking need to link zlib... no checking need to link bzip2... no configure: creating ./config.status config.status: creating GNUmakefile config.status: creating libcifpp.pc config.status: creating tools/update-dictionary-script config.status: creating src/Config.hpp config.status: executing libtool commands (base) @.:~/Documents/libcifpp$ make mkdir -p obj >> src/AtomType.cpp >> src/BondMap.cpp >> src/Cif2PDB.cpp >> src/Cif++.cpp >> src/CifParser.cpp rm -f version-info-.txt >> src/CifUtils.cpp >> src/CifValidator.cpp >> src/Compound.cpp >> src/PDB2Cif.cpp >> src/PDB2CifRemark3.cpp >> src/Point.cpp >> src/Secondary.cpp >> src/Structure.cpp >> src/Symmetry.cpp >> src/TlsParser.cpp /bin/sh /home/jarek/Documents/libcifpp/libtool --silent --tag=CXX --mode=link g++ -std=c++17 -I/usr/include -g -O2 -pthread -Wall -Wno-multichar -I include -O2 -DCACHE_DIR='"/var/cache/libcifpp"' -DDATA_DIR='"/usr/local/share/libcifpp"' -DUSE_RSRC=1 -DNDEBUG -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -version-info 1:1:1 -o libcifpp.la -rpath /usr/local/lib obj/AtomType.lo obj/BondMap.lo obj/Cif2PDB.lo obj/Cif++.lo obj/CifParser.lo obj/CifUtils.lo obj/CifValidator.lo obj/Compound.lo obj/PDB2Cif.lo obj/PDB2CifRemark3.lo obj/Point.lo obj/Secondary.lo obj/Structure.lo obj/Symmetry.lo obj/TlsParser.lo -lboost_iostreams -lboost_date_time -lboost_regex -lz -lbz2 (base) **@.***:~/Documents/libcifpp$ sudo make install mkdir -p data wget -O data/components.cif.gz ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz --2021-05-21 15:04:31-- ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz => ‘data/components.cif.gz’ Resolving ftp.wwpdb.org (ftp.wwpdb.org)... 128.6.158.66 Connecting to ftp.wwpdb.org (ftp.wwpdb.org) 128.6.158.66 :21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/pdb/data/monomers ... done. ==> SIZE components.cif.gz ... 78506636 ==> PASV ... done. ==> RETR components.cif.gz ... done. Length: 78506636 (75M) (unauthoritative) components.cif.gz 100%[====================================================================================>] 74,87M 1,30MB/s in 59s 2021-05-21 15:05:32 (1,27 MB/s) - ‘data/components.cif.gz’ saved [78506636] install -d /usr/local/share/libcifpp install -m644 data/components.cif.gz /usr/local/share/libcifpp/ install -d /usr/local/lib /bin/sh /home/jarek/Documents/libcifpp/libtool --mode=install install libcifpp.la /usr/local/lib libtool: install: install .libs/libcifpp.lai /usr/local/lib/libcifpp.la libtool: install: install .libs/libcifpp.a /usr/local/lib/libcifpp.a libtool: install: chmod 644 /usr/local/lib/libcifpp.a libtool: install: ranlib /usr/local/lib/libcifpp.a libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/sbin" ldconfig -n /usr/local/lib Libraries have been installed in: /usr/local/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages.
install -d /usr/local/share/libcifpp for d in mmcif_ddl.dic mmcif_pdbx_v50.dic; do \ install -m644 rsrc/$d /usr/local/share/libcifpp; \ gzip -f /usr/local/share/libcifpp/$d; \ done install -d /var/cache/libcifpp install -d /etc/cron.weekly if [ ! -f /etc/libcifpp.conf ] ; then \ echo "# Uncomment the next line to enable automatic updates" > /etc/libcifpp.conf; \ echo "# update=true"
/etc/libcifpp.conf; \ echo ""; \ echo "Update the /etc/libcifpp.conf file to enable automatic updates"; \ echo ""; \ fi install -m755 tools/update-dictionary-script /etc/cron.weekly/libcifpp install -d /usr/local/include/cif++ for f in AtomType.hpp BondMap.hpp CifParser.hpp Compound.hpp PDB2CifRemark3.hpp Structure.hpp Cif2PDB.hpp CifUtils.hpp Point.hpp Symmetry.hpp Cif++.hpp CifValidator.hpp PDB2Cif.hpp Secondary.hpp TlsParser.hpp; do install include/cif++/$f /usr/local/include/cif++/$f; done install -d /usr/local/lib/pkgconfig install -m 644 libcifpp.pc /usr/local/lib/pkgconfig/libcifpp.pc |
Do you have a suggestion on how to install the dssp? Kind regards, Jarek
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Jvdjvdjvd
System: "Ubuntu 20.04.1 LTS" Thank you for sharing this program. Unfortunately I am having problems installing it. Could you help me? I installed mrc and libcif++ but my the dssp configuration has trouble finding this libcif++ install.
The installation of libcif++ seemed successful:
Do you have a suggestion on how to install the dssp? Kind regards, Jarek