{"action":"created","issue":{"url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/88","repository_url":"https://api.github.com/repos/HenrikBengtsson/matrixStats","labels_url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/88/labels{/name}","comments_url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/88/comments","events_url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/88/events","html_url":"https://github.com/HenrikBengtsson/matrixStats/issues/88","id":163927633,"number":88,"title":"Travis fails when trying to install matrixStats","user":{"login":"muschellij2","id":1075118,"avatar_url":"https://avatars.githubusercontent.com/u/1075118?v=3","gravatar_id":"","url":"https://api.github.com/users/muschellij2","html_url":"https://github.com/muschellij2","followers_url":"https://api.github.com/users/muschellij2/followers","following_url":"https://api.github.com/users/muschellij2/following{/other_user}","gists_url":"https://api.github.com/users/muschellij2/gists{/gist_id}","starred_url":"https://api.github.com/users/muschellij2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/muschellij2/subscriptions","organizations_url":"https://api.github.com/users/muschellij2/orgs","repos_url":"https://api.github.com/users/muschellij2/repos","events_url":"https://api.github.com/users/muschellij2/events{/privacy}","received_events_url":"https://api.github.com/users/muschellij2/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-07-05T19:31:36Z","updated_at":"2016-07-05T19:36:02Z","closed_at":null,"body":"I have duplicated this on travis-ci repo:  https://github.com/travis-ci/travis-ci/issues/6267\r\n\r\nI have found Travis fail when trying to installing matrixStats and says biocInstaller is needed.  I don't know if this happens because biocViews is in the `DESCRIPTION` (I doubt it though). \r\n\r\nTo reproduce the error, I created a simple test package (with RStudio/devtools) and only depended on matrixStats and used `devtools::use_travis` and depended on `matrixStats` using `Imports`.  \r\n\r\nThe build log is located at https://travis-ci.org/muschellij2/testmatrixstats, but the main error (on Travis) is:\r\n```\r\n3.10s$ Rscript -e 'deps <- devtools::dev_package_deps(dependencies = TRUE);devtools::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message(\"missing: \", paste(setdiff(deps$package, installed.packages()), collapse=\", \")); q(status = 1, save = \"no\")}'\r\ntrying URL 'https://cloud.r-project.org/src/contrib/matrixStats_0.50.2.tar.gz'\r\nContent type 'application/x-gzip' length 167570 bytes (163 KB)\r\n==================================================\r\ndownloaded 163 KB\r\nInstalling matrixStats\r\nError: ‘BiocInstaller’ must be installed for this functionality.\r\nExecution halted\r\n```\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/comments/230579713","html_url":"https://github.com/HenrikBengtsson/matrixStats/issues/88#issuecomment-230579713","issue_url":"https://api.github.com/repos/HenrikBengtsson/matrixStats/issues/88","id":230579713,"user":{"login":"muschellij2","id":1075118,"avatar_url":"https://avatars.githubusercontent.com/u/1075118?v=3","gravatar_id":"","url":"https://api.github.com/users/muschellij2","html_url":"https://github.com/muschellij2","followers_url":"https://api.github.com/users/muschellij2/followers","following_url":"https://api.github.com/users/muschellij2/following{/other_user}","gists_url":"https://api.github.com/users/muschellij2/gists{/gist_id}","starred_url":"https://api.github.com/users/muschellij2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/muschellij2/subscriptions","organizations_url":"https://api.github.com/users/muschellij2/orgs","repos_url":"https://api.github.com/users/muschellij2/repos","events_url":"https://api.github.com/users/muschellij2/events{/privacy}","received_events_url":"https://api.github.com/users/muschellij2/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T19:36:02Z","updated_at":"2016-07-05T19:36:02Z","body":"Dug a little deeper and realized that when `biocViews` are in the description, `devtools` has the following line in https://github.com/hadley/devtools/blob/master/R/utils.r:\r\n```r\r\nis_bioconductor <- function(x) {\r\n  x$package != \"BiocInstaller\" && !is.null(x$biocviews)\r\n}\r\n```\r\nThus, although not an `Imports` or `Suggests`, `biocInstaller` seems to be a hidden/implicit dependency when installing using `devtools`.  This affects Travis builds.  I will close the comment on travis-ci/travis-ci#6267, but leave it open here an open one on `devtools`."}}
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