{"action":"created","issue":{"url":"https://api.github.com/repos/jhhung/Tailor/issues/6","labels_url":"https://api.github.com/repos/jhhung/Tailor/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/jhhung/Tailor/issues/6/comments","events_url":"https://api.github.com/repos/jhhung/Tailor/issues/6/events","html_url":"https://github.com/jhhung/Tailor/issues/6","id":84247339,"number":6,"title":"possible linker error not solved by switching /lib library files","user":{"login":"warrenmcg","id":6866073,"avatar_url":"https://avatars.githubusercontent.com/u/6866073?v=3","gravatar_id":"","url":"https://api.github.com/users/warrenmcg","html_url":"https://github.com/warrenmcg","followers_url":"https://api.github.com/users/warrenmcg/followers","following_url":"https://api.github.com/users/warrenmcg/following{/other_user}","gists_url":"https://api.github.com/users/warrenmcg/gists{/gist_id}","starred_url":"https://api.github.com/users/warrenmcg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/warrenmcg/subscriptions","organizations_url":"https://api.github.com/users/warrenmcg/orgs","repos_url":"https://api.github.com/users/warrenmcg/repos","events_url":"https://api.github.com/users/warrenmcg/events{/privacy}","received_events_url":"https://api.github.com/users/warrenmcg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-02T22:46:18Z","updated_at":"2015-06-03T22:22:02Z","closed_at":null,"body":"Hi Jui-Hung Hung,\r\n\r\nI’m a graduate student who was introduced to your tool at the RNA Society Meeting last week after your paper was mentioned in a talk by Stefan Ameres. I wanted to try your tool out on a small-RNA-Seq dataset that my lab and collaborators collected.\r\n\r\nI still consider myself a novice to bioinformatics, particularly when it comes to C++. I attempted to install Tailor from the github release, following the instructions on the website, and received an error that I cannot interpret.\r\n\r\nI’m installing on Ubuntu 14.04.2 with boost and gcc. I tried to use the Linux library file (libabwt_table_LINUX.a) instead of the default file, but I received the same error.\r\n\r\nHere is the output from the \"make\" command:\r\n\r\n    /usr/bin/cmake -H/home/warren/Downloads/Tailor-1.0 -B/home/warren/Downloads/Tailor-1.0 --check-build-system CMakeFiles/Makefile.cmake 0\r\n    /usr/bin/cmake -E cmake_progress_start /home/warren/Downloads/Tailor-1.0/CMakeFiles /home/warren/Downloads/Tailor-1.0/CMakeFiles/progress.marks\r\n    make -f CMakeFiles/Makefile2 all\r\n    make[1]: Entering directory `/home/warren/Downloads/Tailor-1.0'\r\n    make -f CMakeFiles/bin/tailor.dir/build.make CMakeFiles/bin/tailor.dir/depend\r\n    make[2]: Entering directory `/home/warren/Downloads/Tailor-1.0'\r\n    cd /home/warren/Downloads/Tailor-1.0 && /usr/bin/cmake -E cmake_depends \"Unix Makefiles\" /home/warren/Downloads/Tailor-1.0 /home/warren/Downloads/Tailor-1.0 /home/warren/Downloads/Tailor-1.0 /home/warren/Downloads/Tailor-1.0 /home/warren/Downloads/Tailor-1.0/CMakeFiles/bin/tailor.dir/DependInfo.cmake --color=\r\n    make[2]: Leaving directory `/home/warren/Downloads/Tailor-1.0'\r\n    make -f CMakeFiles/bin/tailor.dir/build.make CMakeFiles/bin/tailor.dir/build\r\n    make[2]: Entering directory `/home/warren/Downloads/Tailor-1.0'\r\n    Linking CXX executable bin/tailor\r\n    /usr/bin/cmake -E cmake_link_script CMakeFiles/bin/tailor.dir/link.txt --verbose=1\r\n    /usr/bin/c++   -Ofast -std=c++11    CMakeFiles/bin/tailor.dir/src/main.cpp.o  -o bin/tailor -rdynamic /usr/local/lib/libboost_date_time.so /usr/local/lib/libboost_filesystem.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_system.so /usr/local/lib/libboost_filesystem.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_program_options.so -lpthread -lz lib/libabwt_table.a /usr/local/lib/libboost_serialization.so /usr/local/lib/libboost_regex.so /usr/local/lib/libboost_thread.so /usr/local/lib/libboost_iostreams.so /usr/local/lib/libboost_program_options.so -lpthread -lz lib/libabwt_table.a -Wl,-rpath,/usr/local/lib \r\n    lib/libabwt_table.a(abwt_table.o): In function `ABWT_table::readBWT(std::string)':\r\n    abwt_table.cpp:(.text+0xbfd): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'\r\n    abwt_table.cpp:(.text+0xc34): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'\r\n    lib/libabwt_table.a(abwt_table.o): In function `ABWT_table::readSEQ(std::string, ABSequence<std::string>&)':\r\n    abwt_table.cpp:(.text+0xd1d): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'\r\n    abwt_table.cpp:(.text+0xd53): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'\r\n    lib/libabwt_table.a(abwt_table.o): In function `ABWT_table::createAllTable(ABSequence<std::string>&, std::vector<std::string, std::allocator<std::string> >&)':\r\n    abwt_table.cpp:(.text+0x3e8c): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'\r\n    abwt_table.cpp:(.text+0x5824): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'\r\n    lib/libabwt_table.a(abwt_table.o): In function `ABWT_table::readTable(std::string)':\r\n    abwt_table.cpp:(.text+0x5f56): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'\r\n    abwt_table.cpp:(.text+0x618f): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'\r\n    lib/libabwt_table.a(abwt_table.o): In function `ABWT_table::readNPosLen(std::string const&)':\r\n    abwt_table.cpp:(.text+0x6c81): undefined reference to `boost::archive::detail::shared_ptr_helper::shared_ptr_helper()'\r\n    abwt_table.cpp:(.text+0x6ccc): undefined reference to `boost::archive::detail::shared_ptr_helper::~shared_ptr_helper()'\r\n    collect2: error: ld returned 1 exit status\r\n    make[2]: *** [bin/tailor] Error 1\r\n    make[2]: Leaving directory `/home/warren/Downloads/Tailor-1.0'\r\n    make[1]: *** [CMakeFiles/bin/tailor.dir/all] Error 2\r\n    make[1]: Leaving directory `/home/warren/Downloads/Tailor-1.0'\r\n    make: *** [all] Error 2\r\n\r\nLet me know what can be done to fix this error.\r\n\r\nThanks,\r\nWarren"},"comment":{"url":"https://api.github.com/repos/jhhung/Tailor/issues/comments/108631363","html_url":"https://github.com/jhhung/Tailor/issues/6#issuecomment-108631363","issue_url":"https://api.github.com/repos/jhhung/Tailor/issues/6","id":108631363,"user":{"login":"warrenmcg","id":6866073,"avatar_url":"https://avatars.githubusercontent.com/u/6866073?v=3","gravatar_id":"","url":"https://api.github.com/users/warrenmcg","html_url":"https://github.com/warrenmcg","followers_url":"https://api.github.com/users/warrenmcg/followers","following_url":"https://api.github.com/users/warrenmcg/following{/other_user}","gists_url":"https://api.github.com/users/warrenmcg/gists{/gist_id}","starred_url":"https://api.github.com/users/warrenmcg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/warrenmcg/subscriptions","organizations_url":"https://api.github.com/users/warrenmcg/orgs","repos_url":"https://api.github.com/users/warrenmcg/repos","events_url":"https://api.github.com/users/warrenmcg/events{/privacy}","received_events_url":"https://api.github.com/users/warrenmcg/received_events","type":"User","site_admin":false},"created_at":"2015-06-03T22:22:02Z","updated_at":"2015-06-03T22:22:02Z","body":"I'm using the source code from the latest release. Is the \"tailor_v.1.0_linux_static\" the binary? I downloaded that, but it wasn't executable and had no file extension, so I'm not sure its purpose is. Otherwise, I was attempting to install from the source code using your instructions. I also am using the latest version of boost (v. 1.58.0). I did not post the output from the cmake step above (sorry!), but I can show it below:\r\n\r\n    -- Boost version: 1.58.0\r\n    -- Boost version: 1.58.0\r\n    -- Found the following Boost libraries:\r\n    --   date_time\r\n    --   filesystem\r\n    --   system\r\n    --   serialization\r\n    --   system\r\n    --   filesystem\r\n    --   regex\r\n    --   thread\r\n    --   iostreams\r\n    --   program_options\r\n    -- Configuring done\r\n    -- Generating done\r\n    -- Build files have been written to: /home/warren/Downloads/Tailor-1.0\r\n\r\nWhat are the next steps?"}}