{"action":"opened","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1083","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1083/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1083/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1083/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1083","id":113701180,"number":1083,"title":"Install: R errors are silent","user":{"login":"lbeltrame","id":25192,"avatar_url":"https://avatars.githubusercontent.com/u/25192?v=3","gravatar_id":"","url":"https://api.github.com/users/lbeltrame","html_url":"https://github.com/lbeltrame","followers_url":"https://api.github.com/users/lbeltrame/followers","following_url":"https://api.github.com/users/lbeltrame/following{/other_user}","gists_url":"https://api.github.com/users/lbeltrame/gists{/gist_id}","starred_url":"https://api.github.com/users/lbeltrame/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbeltrame/subscriptions","organizations_url":"https://api.github.com/users/lbeltrame/orgs","repos_url":"https://api.github.com/users/lbeltrame/repos","events_url":"https://api.github.com/users/lbeltrame/events{/privacy}","received_events_url":"https://api.github.com/users/lbeltrame/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-27T22:13:19Z","updated_at":"2015-10-27T22:13:19Z","closed_at":null,"body":"While upgrading the pipeline, I noticed that a few R packages failed to install (glibc version mismatch), but the installation went on nevertheless. Like all the other steps, install failures should abort the install / upgrade."}}