{"action":"created","issue":{"url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/6","repository_url":"https://api.github.com/repos/OHDSI/StudyProtocols","labels_url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/6/comments","events_url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/6/events","html_url":"https://github.com/OHDSI/StudyProtocols/issues/6","id":155974256,"number":6,"title":"Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  :    vmode 'character' not implemented","user":{"login":"cahilton","id":5701610,"avatar_url":"https://avatars.githubusercontent.com/u/5701610?v=3","gravatar_id":"","url":"https://api.github.com/users/cahilton","html_url":"https://github.com/cahilton","followers_url":"https://api.github.com/users/cahilton/followers","following_url":"https://api.github.com/users/cahilton/following{/other_user}","gists_url":"https://api.github.com/users/cahilton/gists{/gist_id}","starred_url":"https://api.github.com/users/cahilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cahilton/subscriptions","organizations_url":"https://api.github.com/users/cahilton/orgs","repos_url":"https://api.github.com/users/cahilton/repos","events_url":"https://api.github.com/users/cahilton/events{/privacy}","received_events_url":"https://api.github.com/users/cahilton/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":30,"created_at":"2016-05-20T14:21:47Z","updated_at":"2016-06-27T11:37:07Z","closed_at":null,"body":"I'm still running keppra on Oracle, and ran into another bug. \r\n\r\nHere's the error:\r\n```\r\nNo outcome specified so not creating outcome and time variables\r\nError in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : \r\n  vmode 'character' not implemented\r\nCalls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff\r\nIn addition: Warning message:\r\nreplacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’ \r\nExecution halted\r\n```\r\n\r\n\r\nFull log:\r\n```\r\n\r\nR version 3.3.0 (2016-05-03) -- \"Supposedly Educational\"\r\nCopyright (C) 2016 The R Foundation for Statistical Computing\r\nPlatform: x86_64-pc-linux-gnu (64-bit)\r\n\r\nR is free software and comes with ABSOLUTELY NO WARRANTY.\r\nYou are welcome to redistribute it under certain conditions.\r\nType 'license()' or 'licence()' for distribution details.\r\n\r\n  Natural language support but running in an English locale\r\n\r\nR is a collaborative project with many contributors.\r\nType 'contributors()' for more information and\r\n'citation()' on how to cite R or R packages in publications.\r\n\r\nType 'demo()' for some demos, 'help()' for on-line help, or\r\n'help.start()' for an HTML browser interface to help.\r\nType 'q()' to quit R.\r\n\r\n> library(KeppraAngioedema)\r\nLoading required package: DatabaseConnector\r\nLoading required package: RJDBC\r\nLoading required package: DBI\r\nLoading required package: rJava\r\n> \r\n> # cohortTable = paste(\"ohdsi_keppra\", Sys.getpid(), sep=\"_\")\r\n> cohortTable = \"ohdsi_keppra_19239\"\r\n> print(paste(\"Cohort Table - \", cohortTable))\r\n[1] \"Cohort Table -  ohdsi_keppra_19239\"\r\n> \r\n> # outputDir = paste(\"/home/chilton/ohdsi_keppra/run\", Sys.getpid(), sep=\"_\")\r\n> outputDir = \"/home/chilton/ohdsi_keppra/run_19239\"\r\n> print(paste(\"Output Dir - \", outputDir))\r\n[1] \"Output Dir -  /home/chilton/ohdsi_keppra/run_19239\"\r\n> \r\n> connectionDetails <- createConnectionDetails(dbms = \"oracle\",\r\n+                                              user = \"OHDSI\",\r\n+                                              port = \"1521\",\r\n+                                              password = \"xxx\",\r\n+                                              server = \"sasridg02.uits.iupui.edu/I2B21STG\")\r\n> \r\n> execute(connectionDetails,\r\n+         cdmDatabaseSchema = \"OMOPV5_DE\",\r\n+         workDatabaseSchema = \"OHDSI\",\r\n+         studyCohortTable = cohortTable,\r\n+         oracleTempSchema = \"OHDSI\",\r\n+         outputFolder = outputDir,\r\n+         maxCores = 4,\r\n+         createCohorts = FALSE)\r\nRunning analyses\r\n*** Creating cohortMethodData objects ***\r\nLoading required package: CohortMethod\r\nLoading required package: Cyclops\r\nLoading required package: FeatureExtraction\r\nConnecting using Oracle driver\r\n\r\nConstructing treatment and comparator cohorts\r\n  |                                                                            \r\n  |                                                                      |   0%\r\n  |                                                                            \r\n  |===================================                                   |  50%\r\n  |                                                                            \r\n  |======================================================================| 100%\r\nAnalysis took 23.5 secs\r\nFetching cohorts from server\r\nFetching cohorts took 0.729 secs\r\nConstructing default covariates\r\n  |                                                                            \r\n  |                                                                      |   0%\r\n  |                                                                            \r\n  |=                                                                     |   1%\r\n  |                                                                            \r\n  |=    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98%\r\n  |                                                                            \r\n  |===================================================================== |  99%\r\n  |                                                                            \r\n  |======================================================================| 100%\r\nAnalysis took 13.5 hours\r\nDone\r\nFetching data from server\r\nLoading took 24.8 secs\r\nRemoving redundant covariates\r\nRemoving redundant covariates took 22.3 secs\r\nNormalizing covariates\r\nFetching outcomes from server\r\nFetching outcomes took 0.617 secs\r\n*** Creating study populations ***\r\n  |                                                                            \r\n  |                                                                      |   0%\r\n  |                                                                            \r\n  |=                                                                     |   1%\r\n  |                     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|====================================================================  |  97%\r\n  |                                                                            \r\n  |====================================================================  |  98%\r\n  |                                                                            \r\n  |===================================================================== |  98%\r\n  |                                                                            \r\n  |===================================================================== |  99%\r\n  |                                                                            \r\n  |======================================================================| 100%\r\n*** Fitting shared propensity score models ***\r\nRemoving subject that are in both cohorts (if any)\r\nNo outcome specified so skipping removing people with prior outcomes\r\nRemoving subjects with less than 1 day(s) at risk (if any)\r\nNo outcome specified so not creating outcome and time variables\r\nError in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : \r\n  vmode 'character' not implemented\r\nCalls: execute ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff\r\nIn addition: Warning message:\r\nreplacing previous import ‘Rcpp::LdFlags’ by ‘RcppParallel::LdFlags’ when loading ‘Cyclops’ \r\nExecution halted\r\n```\r\n\r\nAlso, if I rerun it (after it's fixed), can I start from createCohorts = FALSE, or do I need to start over? \r\n\r\nThanks."},"comment":{"url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/comments/228721929","html_url":"https://github.com/OHDSI/StudyProtocols/issues/6#issuecomment-228721929","issue_url":"https://api.github.com/repos/OHDSI/StudyProtocols/issues/6","id":228721929,"user":{"login":"aperotte","id":77780,"avatar_url":"https://avatars.githubusercontent.com/u/77780?v=3","gravatar_id":"","url":"https://api.github.com/users/aperotte","html_url":"https://github.com/aperotte","followers_url":"https://api.github.com/users/aperotte/followers","following_url":"https://api.github.com/users/aperotte/following{/other_user}","gists_url":"https://api.github.com/users/aperotte/gists{/gist_id}","starred_url":"https://api.github.com/users/aperotte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aperotte/subscriptions","organizations_url":"https://api.github.com/users/aperotte/orgs","repos_url":"https://api.github.com/users/aperotte/repos","events_url":"https://api.github.com/users/aperotte/events{/privacy}","received_events_url":"https://api.github.com/users/aperotte/received_events","type":"User","site_admin":false},"created_at":"2016-06-27T11:37:07Z","updated_at":"2016-06-27T11:37:07Z","body":"Great!  Also, thanks to @mark-velez for the runas solution."}}
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