{"action":"opened","issue":{"url":"https://api.github.com/repos/joshuaschwab/ltmle/issues/13","labels_url":"https://api.github.com/repos/joshuaschwab/ltmle/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/joshuaschwab/ltmle/issues/13/comments","events_url":"https://api.github.com/repos/joshuaschwab/ltmle/issues/13/events","html_url":"https://github.com/joshuaschwab/ltmle/issues/13","id":73345893,"number":13,"title":"Examples and tests fail when suggested packages are not installed","user":{"login":"hadley","id":4196,"avatar_url":"https://avatars.githubusercontent.com/u/4196?v=3","gravatar_id":"","url":"https://api.github.com/users/hadley","html_url":"https://github.com/hadley","followers_url":"https://api.github.com/users/hadley/followers","following_url":"https://api.github.com/users/hadley/following{/other_user}","gists_url":"https://api.github.com/users/hadley/gists{/gist_id}","starred_url":"https://api.github.com/users/hadley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hadley/subscriptions","organizations_url":"https://api.github.com/users/hadley/orgs","repos_url":"https://api.github.com/users/hadley/repos","events_url":"https://api.github.com/users/hadley/events{/privacy}","received_events_url":"https://api.github.com/users/hadley/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-05-05T15:27:33Z","updated_at":"2015-05-05T15:27:33Z","closed_at":null,"body":"```\r\nchecking examples ... ERROR\r\nRunning examples in ‘ltmle-Ex.R’ failed\r\nThe error most likely occurred in:\r\n\r\n> base::assign(\".ptime\", proc.time(), pos = \"CheckExEnv\")\r\n> ### Name: deterministic.g.function_template\r\n> ### Title: Deterministic g/Q functions - examples and templates\r\n> ### Aliases: MaintainTreatment MaintainControl\r\n> ###   deterministic.g.function_template deterministic.Q.function_template\r\n> \r\n> ### ** Examples\r\n> \r\n>  #Show a template for a deterministic.g.function\r\n>  deterministic.g.function_template\r\nfunction (data, current.node, nodes) \r\n{\r\n    is.deterministic <- stop(\"replace me!\")\r\n    prob1 <- stop(\"replace me!\")\r\n    return(list(is.deterministic = is.deterministic, prob1 = prob1))\r\n}\r\n<environment: namespace:ltmle>\r\n>  \r\n>  #Show a template for a deterministic.Q.function\r\n>  deterministic.Q.function_template\r\nfunction (data, current.node, nodes, called.from.estimate.g) \r\n{\r\n    is.deterministic <- stop(\"replace me!\")\r\n    Q.value <- stop(\"replace me!\")\r\n    return(list(is.deterministic = is.deterministic, Q.value = Q.value))\r\n}\r\n<environment: namespace:ltmle>\r\n>  \r\n>  #Use MaintainControl\r\n>  set.seed(1)\r\n>  rexpit <- function(x) rbinom(n=length(x), size=1, prob=plogis(x))\r\n>  n <- 100\r\n>  W <- rnorm(n)\r\n>  A1 <- rexpit(W)\r\n>  A2 <- as.numeric(rexpit(W) | A1)  #treatment at time 1 implies treatment at time 2\r\n>  Y <- rexpit(W + A1 + A2 + rnorm(n))\r\n>  data <- data.frame(W, A1, A2, Y)\r\n> \r\n>  result <- ltmle(data, Anodes=c(\"A1\", \"A2\"), Ynodes=\"Y\", abar=c(1, 1), \r\n+    SL.library=c(\"SL.glm\", \"SL.step\", \"SL.mean\"), \r\n+    deterministic.g.function=MaintainTreatment)\r\nError in library(\"SuperLearner\") : \r\n  there is no package called ‘SuperLearner’\r\nCalls: ltmle -> ltmleMSM.private -> CheckInputs -> library\r\nExecution halted\r\n```\r\n```\r\nchecking tests ... ERROR\r\nRunning the tests in ‘tests/test-all.R’ failed.\r\nLast 13 lines of output:\r\n  + }\r\n  Loading required package: ltmle\r\n  The influence curve based variance estimator implemented in this package provides \r\n  asymptotically conservative standard error estimates when the treatment mechanism is \r\n  estimated with MLE using a correctly specific parametric model. However, we have found \r\n  in simulations that in finite samples this variance estimator may be substantially\r\n  anti-conservative in settings where the outcome is rare or there are positivity \r\n  violations. An improved variance estimator addressing these challenges is currently \r\n  under development and will be released in a subsequent version of the package.\r\n  \r\n  Error in library(tmle) : there is no package called 'tmle'\r\n  Calls: test_check ... lapply -> FUN -> sys.source2 -> eval -> eval -> library\r\n  Execution halted\r\n```"}}