{"action":"created","issue":{"url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/35","repository_url":"https://api.github.com/repos/KlugerLab/FIt-SNE","labels_url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/35/comments","events_url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/35/events","html_url":"https://github.com/KlugerLab/FIt-SNE/issues/35","id":361323754,"node_id":"MDU6SXNzdWUzNjEzMjM3NTQ=","number":35,"title":"Installation problems on Linux","user":{"login":"lmweber","id":8062417,"node_id":"MDQ6VXNlcjgwNjI0MTc=","avatar_url":"https://avatars3.githubusercontent.com/u/8062417?v=4","gravatar_id":"","url":"https://api.github.com/users/lmweber","html_url":"https://github.com/lmweber","followers_url":"https://api.github.com/users/lmweber/followers","following_url":"https://api.github.com/users/lmweber/following{/other_user}","gists_url":"https://api.github.com/users/lmweber/gists{/gist_id}","starred_url":"https://api.github.com/users/lmweber/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lmweber/subscriptions","organizations_url":"https://api.github.com/users/lmweber/orgs","repos_url":"https://api.github.com/users/lmweber/repos","events_url":"https://api.github.com/users/lmweber/events{/privacy}","received_events_url":"https://api.github.com/users/lmweber/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-09-18T14:10:08Z","updated_at":"2018-10-12T19:31:46Z","closed_at":"2018-09-23T18:46:23Z","author_association":"NONE","body":"Hi, I had some difficulties installing FIt-SNE on our Linux server, which I thought I would mention here in case others have the same problems.\r\n\r\nFirst, I installed FFTW from source, using the source tarball from the provided link. I installed it into my home directory using the standard commands `./configure --prefix=$HOME`, `make`, and `make install`.\r\n\r\nThen, I cloned the FIt-SNE GitHub repository and tried running the `g++` compiler command provided on the readme page. However, this gave the following errors:\r\n\r\n```\r\nIn file included from src/tsne.cpp:39:0:\r\nsrc/nbodyfft.h:7:19: fatal error: fftw3.h: No such file or directory\r\ncompilation terminated.\r\nIn file included from src/nbodyfft.cpp:3:0:\r\nsrc/nbodyfft.h:7:19: fatal error: fftw3.h: No such file or directory\r\ncompilation terminated.\r\n```\r\n\r\nand\r\n\r\n```\r\n/usr/bin/ld: cannot find -lfftw3\r\ncollect2: error: ld returned 1 exit status\r\n```\r\n\r\nI managed to fix this by adding extra arguments to specify the `include` and `lib` directories (where the FFTW files were installed) in the `g++` call, as follows:\r\n\r\n`g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp -I<path_to_include_directory> -L<path_to_lib_directory> -o bin/fast_tsne -pthread -lfftw3 -lm`\r\n\r\nI think it would be helpful to include a few comments on this on the readme page, for users who do not have a lot of experience using compilers."},"comment":{"url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/comments/429437426","html_url":"https://github.com/KlugerLab/FIt-SNE/issues/35#issuecomment-429437426","issue_url":"https://api.github.com/repos/KlugerLab/FIt-SNE/issues/35","id":429437426,"node_id":"MDEyOklzc3VlQ29tbWVudDQyOTQzNzQyNg==","user":{"login":"yimingli","id":4153781,"node_id":"MDQ6VXNlcjQxNTM3ODE=","avatar_url":"https://avatars0.githubusercontent.com/u/4153781?v=4","gravatar_id":"","url":"https://api.github.com/users/yimingli","html_url":"https://github.com/yimingli","followers_url":"https://api.github.com/users/yimingli/followers","following_url":"https://api.github.com/users/yimingli/following{/other_user}","gists_url":"https://api.github.com/users/yimingli/gists{/gist_id}","starred_url":"https://api.github.com/users/yimingli/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yimingli/subscriptions","organizations_url":"https://api.github.com/users/yimingli/orgs","repos_url":"https://api.github.com/users/yimingli/repos","events_url":"https://api.github.com/users/yimingli/events{/privacy}","received_events_url":"https://api.github.com/users/yimingli/received_events","type":"User","site_admin":false},"created_at":"2018-10-12T19:31:46Z","updated_at":"2018-10-12T19:31:46Z","author_association":"NONE","body":"I installed `fftw` using `conda` as suggested here: https://github.com/KlugerLab/pyFIt-SNE. But saw the same `fftw3.h: No such file or directory` error. Had to specify the fftw paths to make it work. Took me a while to find this post; I think it would be helpful to add some comments or a link to this issue."}}
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