{"action":"created","issue":{"url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/2","repository_url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs","labels_url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/2/comments","events_url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/2/events","html_url":"https://github.com/smussmann82/BayesAss3-SNPs/issues/2","id":321868128,"number":2,"title":"BayesAss3-SNPs compilation error","user":{"login":"milaja","id":38856355,"avatar_url":"https://avatars3.githubusercontent.com/u/38856355?v=4","gravatar_id":"","url":"https://api.github.com/users/milaja","html_url":"https://github.com/milaja","followers_url":"https://api.github.com/users/milaja/followers","following_url":"https://api.github.com/users/milaja/following{/other_user}","gists_url":"https://api.github.com/users/milaja/gists{/gist_id}","starred_url":"https://api.github.com/users/milaja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/milaja/subscriptions","organizations_url":"https://api.github.com/users/milaja/orgs","repos_url":"https://api.github.com/users/milaja/repos","events_url":"https://api.github.com/users/milaja/events{/privacy}","received_events_url":"https://api.github.com/users/milaja/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"smussmann82","id":17727337,"avatar_url":"https://avatars1.githubusercontent.com/u/17727337?v=4","gravatar_id":"","url":"https://api.github.com/users/smussmann82","html_url":"https://github.com/smussmann82","followers_url":"https://api.github.com/users/smussmann82/followers","following_url":"https://api.github.com/users/smussmann82/following{/other_user}","gists_url":"https://api.github.com/users/smussmann82/gists{/gist_id}","starred_url":"https://api.github.com/users/smussmann82/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smussmann82/subscriptions","organizations_url":"https://api.github.com/users/smussmann82/orgs","repos_url":"https://api.github.com/users/smussmann82/repos","events_url":"https://api.github.com/users/smussmann82/events{/privacy}","received_events_url":"https://api.github.com/users/smussmann82/received_events","type":"User","site_admin":false},"assignees":[{"login":"smussmann82","id":17727337,"avatar_url":"https://avatars1.githubusercontent.com/u/17727337?v=4","gravatar_id":"","url":"https://api.github.com/users/smussmann82","html_url":"https://github.com/smussmann82","followers_url":"https://api.github.com/users/smussmann82/followers","following_url":"https://api.github.com/users/smussmann82/following{/other_user}","gists_url":"https://api.github.com/users/smussmann82/gists{/gist_id}","starred_url":"https://api.github.com/users/smussmann82/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smussmann82/subscriptions","organizations_url":"https://api.github.com/users/smussmann82/orgs","repos_url":"https://api.github.com/users/smussmann82/repos","events_url":"https://api.github.com/users/smussmann82/events{/privacy}","received_events_url":"https://api.github.com/users/smussmann82/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-05-10T09:30:43Z","updated_at":"2018-05-11T13:40:30Z","closed_at":null,"author_association":"NONE","body":"Hi Steve,\r\n\r\nThank you for putting this program out there!\r\n\r\nHowever, we have a problem trying to compile the program on a university computer cluster (Linux). The cluster manager forwarded me the error, he was using gcc 4.9.3 when compiling. I hope you can help.\r\n\r\nThe error:\r\ng++ -O3 -Wall -c main.cpp\r\nmain.cpp: In function ‘int main(int, char**)’:\r\nmain.cpp:1153:19: warning: narrowing conversion of ‘l’ from ‘unsigned int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing]\r\n     char targ[]={l}, targ2[]={j};\r\n                   ^\r\nmain.cpp:1153:32: warning: narrowing conversion of ‘j’ from ‘unsigned int’ to ‘char’ inside { } is ill-formed in C++11 [-Wnarrowing]\r\n     char targ[]={l}, targ2[]={j};\r\n                                ^\r\nmain.cpp:1174:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n       if(iterAllele->second == sampleIndiv[l]->getAllele(j,m))\r\n                             ^\r\nmain.cpp: In function ‘void readInputFile(Indiv**, unsigned int&, unsigned int&, unsigned int&, unsigned int*, std::string&, int)’:\r\nmain.cpp:1257:7: warning: unused variable ‘lastChar’ [-Wunused-variable]\r\n  char lastChar='a', nextChar;\r\n       ^\r\nmain.cpp:1257:21: warning: variable ‘nextChar’ set but not used [-Wunused-but-set-variable]\r\n  char lastChar='a', nextChar;\r\n                     ^\r\nmain.cpp: In function ‘void getEmpiricalAlleleFreqs(double***, Indiv**, unsigned int*, unsigned int, unsigned int, unsigned int, bool)’:\r\nmain.cpp:1505:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n       if (sampleIndiv[m]->getAllele(j,0) == k)\r\n                                          ^\r\nmain.cpp:1508:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n       if (sampleIndiv[m]->getAllele(j,1) == k)\r\n                                          ^\r\nmain.cpp: In function ‘void parseComLine(int, char**, std::string&, int&, unsigned int&, unsigned int&, unsigned int&, std::string&, double&, double&, double&, bool&, bool&, bool&, bool&, bool&, bool&, int&)’:\r\nmain.cpp:1735:47: error: ‘class boost::program_options::typed_value<std::basic_string<char>, char>’ has no member named ‘required’\r\n   (\"file,F\", opt::value<string>(&infileName)->required(), \"Specify input file\")\r\n                                               ^\r\nmain.cpp:1736:41: error: ‘class boost::program_options::typed_value<int, char>’ has no member named ‘required’\r\n   (\"loci,l\", opt::value<int>(&MAXLOCI)->required(), \"Specify number of loci in input file\")\r\n                                         ^\r\nmain.cpp:1768:13: error: ‘required_option’ in namespace ‘opt’ does not name a type\r\n  catch(opt::required_option& e) //catch errors resulting from required options\r\n             ^\r\nmain.cpp:1770:42: error: ‘e’ was not declared in this scope\r\n   std::cerr << std::endl << \"ERROR: \" << e.what() << std::endl << std::endl;\r\n                                          ^\r\nmake: *** [main.o] Error 1\r\n\r\nMany thanks,\r\nMilaja"},"comment":{"url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/comments/388366663","html_url":"https://github.com/smussmann82/BayesAss3-SNPs/issues/2#issuecomment-388366663","issue_url":"https://api.github.com/repos/smussmann82/BayesAss3-SNPs/issues/2","id":388366663,"user":{"login":"milaja","id":38856355,"avatar_url":"https://avatars3.githubusercontent.com/u/38856355?v=4","gravatar_id":"","url":"https://api.github.com/users/milaja","html_url":"https://github.com/milaja","followers_url":"https://api.github.com/users/milaja/followers","following_url":"https://api.github.com/users/milaja/following{/other_user}","gists_url":"https://api.github.com/users/milaja/gists{/gist_id}","starred_url":"https://api.github.com/users/milaja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/milaja/subscriptions","organizations_url":"https://api.github.com/users/milaja/orgs","repos_url":"https://api.github.com/users/milaja/repos","events_url":"https://api.github.com/users/milaja/events{/privacy}","received_events_url":"https://api.github.com/users/milaja/received_events","type":"User","site_admin":false},"created_at":"2018-05-11T13:40:29Z","updated_at":"2018-05-11T13:40:29Z","author_association":"NONE","body":"Hi Steve,\n\nAnd thanks for the extremely fast response!\n\nI have forwarded your reply to our cluster manager, he has had a brief look\nand he says that the boost libraries version 1.60 is installed as a\ndefault. But he didn't have time to test the other options you mentioned\nand he will have a proper look later. I'll let you know if we continue\nhaving problems getting it compiled.\n\nThanks again and have a nice weekend!\n\nCheers,\nMilaja\n\n2018-05-10 11:24 GMT+01:00 Steve Mussmann <notifications@github.com>:\n\n> Hello Milaja,\n>\n> The error that caused compilation to fail seems to be related to the boost\n> program_options library which I used for handling command line input. I\n> have seen a similar error previously when there was a problem with the C++\n> Boost libraries installation.\n>\n> What version of the Boost libraries do you have installed? I think the\n> oldest version I have tested is 1.54 and the most recent is 1.60. Also, I\n> once encountered a problem where the program_options library did not\n> install alongside the rest of the Boost installation. I fixed this by\n> either downloading the source for Boost and compiling, or specifically\n> installing the library from my system's package manager. For example, under\n> Ubuntu this would be:\n> sudo apt-get install libboost-program-options-dev\n>\n> I hope that helps. Let me know if you encounter any more issues,\n>\n> -Steve\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/smussmann82/BayesAss3-SNPs/issues/2#issuecomment-388015314>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AlDmo68usUnnZwx_Vpaqb2X_JsA71p05ks5txBVugaJpZM4T5ng6>\n> .\n>\n\n\n\n-- \nDr Milaja Nykanen\nSchool of Biological, Earth and Environmental Sciences,\nUniversity College Cork\nCork, Ireland\n\nMobile: +353 (0)85 110 1466\n"}}
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