{"action":"created","issue":{"url":"https://api.github.com/repos/cmbi/xssp/issues/94","repository_url":"https://api.github.com/repos/cmbi/xssp","labels_url":"https://api.github.com/repos/cmbi/xssp/issues/94/labels{/name}","comments_url":"https://api.github.com/repos/cmbi/xssp/issues/94/comments","events_url":"https://api.github.com/repos/cmbi/xssp/issues/94/events","html_url":"https://github.com/cmbi/xssp/issues/94","id":332740232,"node_id":"MDU6SXNzdWUzMzI3NDAyMzI=","number":94,"title":"installation on OSX","user":{"login":"ppxasjsm","id":3668316,"node_id":"MDQ6VXNlcjM2NjgzMTY=","avatar_url":"https://avatars2.githubusercontent.com/u/3668316?v=4","gravatar_id":"","url":"https://api.github.com/users/ppxasjsm","html_url":"https://github.com/ppxasjsm","followers_url":"https://api.github.com/users/ppxasjsm/followers","following_url":"https://api.github.com/users/ppxasjsm/following{/other_user}","gists_url":"https://api.github.com/users/ppxasjsm/gists{/gist_id}","starred_url":"https://api.github.com/users/ppxasjsm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ppxasjsm/subscriptions","organizations_url":"https://api.github.com/users/ppxasjsm/orgs","repos_url":"https://api.github.com/users/ppxasjsm/repos","events_url":"https://api.github.com/users/ppxasjsm/events{/privacy}","received_events_url":"https://api.github.com/users/ppxasjsm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":18,"created_at":"2018-06-15T11:31:53Z","updated_at":"2018-10-13T06:59:14Z","closed_at":null,"author_association":"NONE","body":"I am trying to used Biopython to compute some DSSP values for a bunch of pdbs (https://biopython.org/DIST/docs/api/Bio.PDB.DSSP%27-module.html). \r\nI seem to struggle to install DSSP though. \r\nNaively, following the instructions and standard ways of installing on a unix system, I went ahead and cloned the repository:\r\n\r\n```\r\ngit clone https://github.com/cmbi/xssp.git   \r\ncd xssp\r\n./configure    \r\nmake    \r\nmake install\r\n```\r\n\r\nThe error I get is:\r\n```\r\n./configure: No such file or directory\r\n```\r\n\r\nNot really sure how to trouble shoot this. "},"comment":{"url":"https://api.github.com/repos/cmbi/xssp/issues/comments/429517155","html_url":"https://github.com/cmbi/xssp/issues/94#issuecomment-429517155","issue_url":"https://api.github.com/repos/cmbi/xssp/issues/94","id":429517155,"node_id":"MDEyOklzc3VlQ29tbWVudDQyOTUxNzE1NQ==","user":{"login":"YoshitakaMo","id":16487484,"node_id":"MDQ6VXNlcjE2NDg3NDg0","avatar_url":"https://avatars1.githubusercontent.com/u/16487484?v=4","gravatar_id":"","url":"https://api.github.com/users/YoshitakaMo","html_url":"https://github.com/YoshitakaMo","followers_url":"https://api.github.com/users/YoshitakaMo/followers","following_url":"https://api.github.com/users/YoshitakaMo/following{/other_user}","gists_url":"https://api.github.com/users/YoshitakaMo/gists{/gist_id}","starred_url":"https://api.github.com/users/YoshitakaMo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/YoshitakaMo/subscriptions","organizations_url":"https://api.github.com/users/YoshitakaMo/orgs","repos_url":"https://api.github.com/users/YoshitakaMo/repos","events_url":"https://api.github.com/users/YoshitakaMo/events{/privacy}","received_events_url":"https://api.github.com/users/YoshitakaMo/received_events","type":"User","site_admin":false},"created_at":"2018-10-13T06:59:14Z","updated_at":"2018-10-13T06:59:14Z","author_association":"NONE","body":"I changed `src/progress.h` as you wrote and then tried compilation. However, another issue occurred. When using Apple LLVM 10.0.0 compiler, \r\n```\r\n$ ./configure --prefix=/Users/hogehoge/xssp/3.0.3 CC=/usr/bin/gcc CXX=/usr/bin/g++ LDFLAGS=-L/Users/hogehoge/apps/libzeep CPPFLAGS='-I/Users/hogehoge/apps/libzeep'\r\n\r\n$ make clean ; make -j4\r\ntest -z \"mkdssp mkhssp hsspconv test_fasta test_conv test_readpdb\" || rm -f mkdssp mkhssp hsspconv test_fasta test_conv test_readpdb\r\ntest -z \"mtrx/matrices.h\" || rm -f mtrx/matrices.h\r\nrm -f *.o\r\nrm -f src/*.o\r\nrm -f tests/*.o\r\nperl mtrx/mkmat_h.pl mtrx/\r\n/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am\r\ndepbase=`echo src/iocif.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/iocif.o -MD -MP -MF $depbase.Tpo -c -o src/iocif.o src/iocif.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/mas.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mas.o -MD -MP -MF $depbase.Tpo -c -o src/mas.o src/mas.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/primitives-3d.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/primitives-3d.o -MD -MP -MF $depbase.Tpo -c -o src/primitives-3d.o src/primitives-3d.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/structure.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/structure.o -MD -MP -MF $depbase.Tpo -c -o src/structure.o src/structure.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/utils.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/utils.o -MD -MP -MF $depbase.Tpo -c -o src/utils.o src/utils.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/blast.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/blast.o -MD -MP -MF $depbase.Tpo -c -o src/blast.o src/blast.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/fasta.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/fasta.o -MD -MP -MF $depbase.Tpo -c -o src/fasta.o src/fasta.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/fetchdbrefs.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/fetchdbrefs.o -MD -MP -MF $depbase.Tpo -c -o src/fetchdbrefs.o src/fetchdbrefs.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/hssp-nt.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/hssp-nt.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-nt.o src/hssp-nt.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/matrix.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/matrix.o -MD -MP -MF $depbase.Tpo -c -o src/matrix.o src/matrix.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/mkhssp.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mkhssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkhssp.o src/mkhssp.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/progress.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/progress.o -MD -MP -MF $depbase.Tpo -c -o src/progress.o src/progress.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\nsrc/hssp-nt.cpp:1085:25: error: cannot increment value of type 'MCounter' (aka 'boost::detail::atomic_count')\r\n        uint64 next = ix++;\r\n                      ~~^\r\ndepbase=`echo src/hssp-convert-3to1.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/bin/g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/hssp-convert-3to1.o -MD -MP -MF $depbase.Tpo -c -o src/hssp-convert-3to1.o src/hssp-convert-3to1.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\n1 error generated.\r\nmake[1]: *** [src/hssp-nt.o] Error 1\r\nmake[1]: *** Waiting for unfinished jobs....\r\nsrc/progress.cpp:183:23: error: no viable overloaded '+='\r\n    (mImpl->mConsumed += inConsumed) >= mImpl->mMax and\r\n     ~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~\r\nsrc/progress.cpp:194:23: error: no viable overloaded '='\r\n    (mImpl->mConsumed = inProgress) >= mImpl->mMax and\r\n     ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~\r\n/usr/local/include/boost/smart_ptr/detail/atomic_count_std_atomic.hpp:51:20: note: candidate function not viable: no known conversion\r\n      from 'int64' (aka 'long long') to 'const boost::detail::atomic_count' for 1st argument\r\n    atomic_count & operator=(atomic_count const &);\r\n                   ^\r\n2 errors generated.\r\nmake[1]: *** [src/progress.o] Error 1\r\n```\r\nthe Apple clang compiler couldn't compile them.\r\n\r\nI found that this issue didn't occur when compiling with GNU compiler 6 or 8 installed by Homebrew. However, there remains some boost issue... \r\n```\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo tests/test_readpdb.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT tests/test_readpdb.o -MD -MP -MF $depbase.Tpo -c -o tests/test_readpdb.o tests/test_readpdb.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/dssp.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/dssp.o -MD -MP -MF $depbase.Tpo -c -o src/dssp.o src/dssp.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\ndepbase=`echo src/mkdssp.o | sed 's|[^/]*$|.deps/&|;s|\\.o$||'`;\\\r\n        /usr/local/bin/g++-6 -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Werror -Wno-reorder -pthread -I/usr/local/include -I./src/ -I/Users/hogehoge/apps/libzeep  -g -O2 -MT src/mkdssp.o -MD -MP -MF $depbase.Tpo -c -o src/mkdssp.o src/mkdssp.cpp &&\\\r\n        mv -f $depbase.Tpo $depbase.Po\r\n/usr/local/bin/g++-6  -g -O2  -L/Users/hogehoge/apps/libzeep -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread-mt -lpthread -lboost_unit_test_framework-mt\r\nUndefined symbols for architecture x86_64:\r\n  \"boost::unit_test::ut_detail::normalize_test_case_name[abi:cxx11](boost::unit_test::basic_cstring<char const>)\", referenced from:\r\n      boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long) in test_fasta.o\r\nld: symbol(s) not found for architecture x86_64\r\ncollect2: error: ld returned 1 exit status\r\nmake[1]: *** [test_fasta] Error 1\r\nmake[1]: *** Waiting for unfinished jobs....\r\nmake: *** [all] Error 2\r\n```\r\n"}}
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