{"action":"created","issue":{"url":"https://api.github.com/repos/sahilseth/flowr/issues/8","labels_url":"https://api.github.com/repos/sahilseth/flowr/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/sahilseth/flowr/issues/8/comments","events_url":"https://api.github.com/repos/sahilseth/flowr/issues/8/events","html_url":"https://github.com/sahilseth/flowr/issues/8","id":94387431,"number":8,"title":"PBS scheduler errors with qsub submission: &amp;&amp; in bash command","user":{"login":"dyndna","id":2738338,"avatar_url":"https://avatars.githubusercontent.com/u/2738338?v=3","gravatar_id":"","url":"https://api.github.com/users/dyndna","html_url":"https://github.com/dyndna","followers_url":"https://api.github.com/users/dyndna/followers","following_url":"https://api.github.com/users/dyndna/following{/other_user}","gists_url":"https://api.github.com/users/dyndna/gists{/gist_id}","starred_url":"https://api.github.com/users/dyndna/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dyndna/subscriptions","organizations_url":"https://api.github.com/users/dyndna/orgs","repos_url":"https://api.github.com/users/dyndna/repos","events_url":"https://api.github.com/users/dyndna/events{/privacy}","received_events_url":"https://api.github.com/users/dyndna/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-10T20:41:45Z","updated_at":"2015-07-10T23:28:20Z","closed_at":null,"body":"dependent jobs are failing because of syntax error while parsing first bash command:\r\n\r\n```\r\nPBS Job Id: 40993.\r\nJob Name:   T95f3A8d9eG_001.job_start-1\r\nExec host:  \r\nExecution terminated\r\nExit_status=2\r\nresources_used.cput=00:00:00\r\nresources_used.mem=0kb\r\nresources_used.vmem=0kb\r\nresources_used.walltime=00:00:01\r\n```\r\n\r\n#### sample 1, command 1:\r\n\r\n    cat ~/flowr/runs/<SAMPLE_ID>/001../job_start_cmd_1.sh \r\n```\r\n## --- command to run comes here (flow_mat)\r\n## ------  \r\n mkdir -p 95f31dd1-0014-4f11-b866-f6bf5cb152c8__8d9ebd2e-9ac6-4d93-81fb-5cfe6f4a4e7a &amp;&amp; touch 95f31dd1-0014-4f11-b866-f6bf5cb152c8__8d9ebd2e-9ac6-4d93-81fb-5cfe6f4a4e7a.running \r\n```\r\n\r\n    cat ~/flowr/runs/<SAMPLE_ID>/001../job_start_cmd_1.out\r\n\r\n```\r\n/var/spool/torque/mom_priv/jobs/40993....SC: line 35: syntax error near unexpected token `;&'\r\n/var/spool/torque/mom_priv/jobs/40993.....SC: line 35: ` mkdir -p 95f31dd1-0014-4f11-b866-f6bf5cb152c8__8d9ebd2e-9ac6-4d93-81fb-5cfe6f4a4e7a &amp;&amp; touch 95f31dd1-0014-4f11-b866-f6bf5cb152c8__8d9ebd2e-9ac6-4d93-81fb-5cfe6f4a4e7a.running '\r\n```\r\n\r\n` &amp;&amp;` was passed in bash command and probable cause of error.\r\n\r\nSubsequent jobs dependent on `job_start_cmd_1` fails:\r\n\r\n```\r\nPBS Job Id: 40994.\r\nJob Name:  2_make_config\r\nAborted by PBS Server \r\nJob deleted as result of dependency on job 40993...\r\n```\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/sahilseth/flowr/issues/comments/120550056","html_url":"https://github.com/sahilseth/flowr/issues/8#issuecomment-120550056","issue_url":"https://api.github.com/repos/sahilseth/flowr/issues/8","id":120550056,"user":{"login":"sahilseth","id":684975,"avatar_url":"https://avatars.githubusercontent.com/u/684975?v=3","gravatar_id":"","url":"https://api.github.com/users/sahilseth","html_url":"https://github.com/sahilseth","followers_url":"https://api.github.com/users/sahilseth/followers","following_url":"https://api.github.com/users/sahilseth/following{/other_user}","gists_url":"https://api.github.com/users/sahilseth/gists{/gist_id}","starred_url":"https://api.github.com/users/sahilseth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sahilseth/subscriptions","organizations_url":"https://api.github.com/users/sahilseth/orgs","repos_url":"https://api.github.com/users/sahilseth/repos","events_url":"https://api.github.com/users/sahilseth/events{/privacy}","received_events_url":"https://api.github.com/users/sahilseth/received_events","type":"User","site_admin":false},"created_at":"2015-07-10T23:28:20Z","updated_at":"2015-07-10T23:28:20Z","body":"Ok, so the second issue was with rendering.\r\n\r\n- Update the package\r\n- replace `{{` with `{{{` as shown in: https://github.com/sahilseth/flowr/commit/f7bf959005b87a14a75102223518d47321a3353d in your torque.sh\r\n\r\nI have tested this:\r\nhttps://github.com/sahilseth/flowr/blob/master/inst/extdata/example1_flow_mat.txt\r\n\r\n"}}