{"action":"opened","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1282","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1282/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1282/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1282/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1282","id":142419514,"number":1282,"title":"Looking for summary.pdf and error rendering R report","user":{"login":"pfujita","id":3877668,"avatar_url":"https://avatars.githubusercontent.com/u/3877668?v=3","gravatar_id":"","url":"https://api.github.com/users/pfujita","html_url":"https://github.com/pfujita","followers_url":"https://api.github.com/users/pfujita/followers","following_url":"https://api.github.com/users/pfujita/following{/other_user}","gists_url":"https://api.github.com/users/pfujita/gists{/gist_id}","starred_url":"https://api.github.com/users/pfujita/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pfujita/subscriptions","organizations_url":"https://api.github.com/users/pfujita/orgs","repos_url":"https://api.github.com/users/pfujita/repos","events_url":"https://api.github.com/users/pfujita/events{/privacy}","received_events_url":"https://api.github.com/users/pfujita/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-03-21T17:42:01Z","updated_at":"2016-03-21T17:42:01Z","closed_at":null,"body":"Hello bcbio team,\r\n\r\nThank you for your excellent work on this resource. We are in the process of updating to the latest stable version of bcbio (0.9.6) and have most of it working. I am seeing two issues with our installation which I'm hoping are related. \r\n\r\nThe old version we were running generates a summary pdf in the main results folder - typically [samplename]-summary.pdf. Our test runs seem to complete successfully, with one small R rendering error (the vcfs and bams look fine and other files are as expected). I'm wondering if that R error is precluding generation of this pdf, or, if things have changed enough since the old version that this pdf is no longer a part of the final results directory, or has been deprecated?\r\n\r\nThe R report rendering error - which may also be related to #1122 - is as follows:\r\n\r\nQuitting from lines 54-158 (report-ready.Rmd)\r\nError in file(file, \"rt\") : cannot open the connection\r\nCalls: render ... withCallingHandlers -> withVisible -> eval -> eval -> read.table -> file\r\nIn addition: Warning message:\r\nIn file(file, \"rt\") :\r\n  cannot open file '/test_dir/report/metrics/metrics.tsv': No such file or directory\r\n\r\nExecution halted\r\n' returned non-zero exit status 1\r\n\r\nThe file: /test_dir/report/metrics/metrics.tsv does exist though, so I'm not sure why it's complaining. I also tried rerunning report-ready.Rmd outside bcbio but I get the same error. Any ideas? Could this be fixed by updating to the most recent dev version?\r\n\r\nThanks for your help,\r\n\r\nPauline\r\n"}}