{"action":"created","issue":{"url":"https://api.github.com/repos/statgen/Minimac4/issues/14","repository_url":"https://api.github.com/repos/statgen/Minimac4","labels_url":"https://api.github.com/repos/statgen/Minimac4/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/statgen/Minimac4/issues/14/comments","events_url":"https://api.github.com/repos/statgen/Minimac4/issues/14/events","html_url":"https://github.com/statgen/Minimac4/issues/14","id":383706206,"node_id":"MDU6SXNzdWUzODM3MDYyMDY=","number":14,"title":"install failed","user":{"login":"yutoubb","id":15372439,"node_id":"MDQ6VXNlcjE1MzcyNDM5","avatar_url":"https://avatars2.githubusercontent.com/u/15372439?v=4","gravatar_id":"","url":"https://api.github.com/users/yutoubb","html_url":"https://github.com/yutoubb","followers_url":"https://api.github.com/users/yutoubb/followers","following_url":"https://api.github.com/users/yutoubb/following{/other_user}","gists_url":"https://api.github.com/users/yutoubb/gists{/gist_id}","starred_url":"https://api.github.com/users/yutoubb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yutoubb/subscriptions","organizations_url":"https://api.github.com/users/yutoubb/orgs","repos_url":"https://api.github.com/users/yutoubb/repos","events_url":"https://api.github.com/users/yutoubb/events{/privacy}","received_events_url":"https://api.github.com/users/yutoubb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-11-23T05:18:39Z","updated_at":"2018-11-23T15:11:04Z","closed_at":null,"author_association":"NONE","body":"Scanning dependencies of target minimac4\r\n[  8%] Building CXX object CMakeFiles/minimac4.dir/src/Analysis.cpp.o\r\n[ 16%] Building CXX object CMakeFiles/minimac4.dir/src/AnalysisChunks.cpp.o\r\n[ 25%] Building CXX object CMakeFiles/minimac4.dir/src/DosageData.cpp.o\r\n[ 33%] Building CXX object CMakeFiles/minimac4.dir/src/HaplotypeSet.cpp.o\r\n[ 41%] Building CXX object CMakeFiles/minimac4.dir/src/Imputation.cpp.o\r\n[ 50%] Building CXX object CMakeFiles/minimac4.dir/src/ImputationStatistics.cpp.o\r\n[ 58%] Building CXX object CMakeFiles/minimac4.dir/src/Main.cpp.o\r\n[ 66%] Building CXX object CMakeFiles/minimac4.dir/src/MarkovModel.cpp.o\r\n[ 75%] Building CXX object CMakeFiles/minimac4.dir/src/MarkovParameters.cpp.o\r\n[ 83%] Building CXX object CMakeFiles/minimac4.dir/src/Unique.cpp.o\r\n[ 91%] Building CXX object CMakeFiles/minimac4.dir/src/Estimation.cpp.o\r\n[100%] Linking CXX executable minimac4\r\nCMakeFiles/minimac4.dir/src/Analysis.cpp.o: In function `Analysis::CheckGeneticMapFile()':\r\nAnalysis.cpp:(.text+0x1abe): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nCMakeFiles/minimac4.dir/src/Analysis.cpp.o: In function `Analysis::readm3vcfFileChunk(int, HaplotypeSet&)':\r\nAnalysis.cpp:(.text+0x2871): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nCMakeFiles/minimac4.dir/src/Analysis.cpp.o: In function `Analysis::InitializeRefFileStream(String&)':\r\nAnalysis.cpp:(.text+0x32ff): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nAnalysis.cpp:(.text+0x3340): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nAnalysis.cpp:(.text+0x378b): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nCMakeFiles/minimac4.dir/src/Analysis.cpp.o:Analysis.cpp:(.text+0x40b0): more undefined references to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' follow\r\nCMakeFiles/minimac4.dir/src/HaplotypeSet.cpp.o: In function `HaplotypeSet::GetVariantInfofromVCFFile(String&, String, AllVariable&)':\r\nHaplotypeSet.cpp:(.text+0xad0f): undefined reference to `VcfRecordFilter::getString(int)'\r\nCMakeFiles/minimac4.dir/src/HaplotypeSet.cpp.o: In function `HaplotypeSet::readm3vcfFile(String, String, int, int, int)':\r\nHaplotypeSet.cpp:(.text+0xc406): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nHaplotypeSet.cpp:(.text+0xc52c): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nHaplotypeSet.cpp:(.text+0xcfd2): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nHaplotypeSet.cpp:(.text+0xdb78): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nCMakeFiles/minimac4.dir/src/Estimation.cpp.o: In function `Estimation::readm3vcfFileChunk(int, HaplotypeSet&)':\r\nEstimation.cpp:(.text+0x1de9): undefined reference to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)'\r\nCMakeFiles/minimac4.dir/src/Estimation.cpp.o:Estimation.cpp:(.text+0x5bcd): more undefined references to `InputFile::readLine(std::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' follow\r\ncollect2: ld returned 1 exit status\r\nmake[2]: *** [minimac4] Error 1\r\nmake[1]: *** [CMakeFiles/minimac4.dir/all] Error 2\r\nmake: *** [all] Error 2\r\nBinary created at /release-build/minimac4\r\n"},"comment":{"url":"https://api.github.com/repos/statgen/Minimac4/issues/comments/441264355","html_url":"https://github.com/statgen/Minimac4/issues/14#issuecomment-441264355","issue_url":"https://api.github.com/repos/statgen/Minimac4/issues/14","id":441264355,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTI2NDM1NQ==","user":{"login":"jonathonl","id":4069894,"node_id":"MDQ6VXNlcjQwNjk4OTQ=","avatar_url":"https://avatars3.githubusercontent.com/u/4069894?v=4","gravatar_id":"","url":"https://api.github.com/users/jonathonl","html_url":"https://github.com/jonathonl","followers_url":"https://api.github.com/users/jonathonl/followers","following_url":"https://api.github.com/users/jonathonl/following{/other_user}","gists_url":"https://api.github.com/users/jonathonl/gists{/gist_id}","starred_url":"https://api.github.com/users/jonathonl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jonathonl/subscriptions","organizations_url":"https://api.github.com/users/jonathonl/orgs","repos_url":"https://api.github.com/users/jonathonl/repos","events_url":"https://api.github.com/users/jonathonl/events{/privacy}","received_events_url":"https://api.github.com/users/jonathonl/received_events","type":"User","site_admin":false},"created_at":"2018-11-23T15:11:04Z","updated_at":"2018-11-23T15:11:04Z","author_association":"CONTRIBUTOR","body":"Can you please provide the OS version you are running?\r\n\r\nThe problem is that libStatGen cannot be found for linking. I'm assuming you ran the install.sh script and there are error messages in that script's log files. I would recommend not using that script. Instead you can run the following from the Minimac4 source directory:\r\n```\r\ncget install -f ./requirements.txt\r\nmkdir build && cd build\r\ncmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. \r\nmake\r\n```\r\n\r\nAlternatively, there are binary packages in the releases section. There are system dependent ways to extract into a non-root directory. For Debian it will look something like `dpkg -x pkg.deb dest_dir`.\r\n\r\nSide note: you do not need a virtual environment to install cget without root. Instead run `pip install --user cget`."}}
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