Running ‘test_base.R’ [50s/68s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  1. Error: qmatrix.msm for psor model, defaults (@test_models.r#255) ------------
  Function 'c' is not in the derivatives table
  1: expect_warning(qmatrix.msm(psor.msm, covariates = list(foo = 1)), "ignoring") at testthat/test_models.r:255
  2: capture_warnings(object)
  3: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  4: qmatrix.msm(psor.msm, covariates = list(foo = 1))
  5: deltamethod(form, ests, cov)
  6: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  7: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  8: lapply(X = X, FUN = FUN, ...)
  9: FUN(X[[i]], ...)
  10: eval(deriv(form, syms))
  11: deriv(form, syms)
  12: deriv.formula(form, syms)
  
  2. Error: qmatrix.msm with supplied covariates (@test_models.r#264) ------------
  Function 'c' is not in the derivatives table
  1: qmatrix.msm(psor.msm, covariates = list(ollwsdrt = 0.1, hieffusn = 0.4)) at testthat/test_models.r:264
  2: deltamethod(form, ests, cov)
  3: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  4: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  5: lapply(X = X, FUN = FUN, ...)
  6: FUN(X[[i]], ...)
  7: eval(deriv(form, syms))
  8: deriv(form, syms)
  9: deriv.formula(form, syms)
  
  3. Error: qmatrix.msm with non-default confidence limits (@test_models.r#271) --
  Function 'c' is not in the derivatives table
  1: qmatrix.msm(psor.msm, covariates = list(ollwsdrt = 0.1, hieffusn = 0.4), cl = 0.99) at testthat/test_models.r:271
  2: deltamethod(form, ests, cov)
  3: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  4: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  5: lapply(X = X, FUN = FUN, ...)
  6: FUN(X[[i]], ...)
  7: eval(deriv(form, syms))
  8: deriv(form, syms)
  9: deriv.formula(form, syms)
  
  4. Error: qmatrix.msm sojourn component (@test_models.r#276) -------------------
  Function 'c' is not in the derivatives table
  1: qmatrix.msm(psor.msm, covariates = list(ollwsdrt = 0.1, hieffusn = 0.4), sojourn = TRUE) at testthat/test_models.r:276
  2: deltamethod(form, ests, cov)
  3: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  4: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  5: lapply(X = X, FUN = FUN, ...)
  6: FUN(X[[i]], ...)
  7: eval(deriv(form, syms))
  8: deriv(form, syms)
  9: deriv.formula(form, syms)
  
  5. Error: qmatrix.msm bug for user-supplied covariates fixed in 1.1.3 (@test_models.r#291) 
  Function 'c' is not in the derivatives table
  1: expect_equal(qmatrix.msm(psor.nocen.msm, covariates = "mean")$SE[1, 2], qmatrix.msm(psor.nocen.msm, 
         covariates = list(hieffusn = cm["hieffusn"], ollwsdrt = cm["ollwsdrt"]))$SE[1, 
         2]) at testthat/test_models.r:291
  2: compare(object, expected, ...)
  3: qmatrix.msm(psor.nocen.msm, covariates = "mean")
  4: deltamethod(form, ests, cov)
  5: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  6: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  7: lapply(X = X, FUN = FUN, ...)
  8: FUN(X[[i]], ...)
  9: eval(deriv(form, syms))
  10: deriv(form, syms)
  11: deriv.formula(form, syms)
  
  6. Error: qmatrix.msm: unspecified covariate values default to zero (@test_models.r#297) 
  Function 'c' is not in the derivatives table
  1: expect_equal(qmatrix.msm(psor.msm, covariates = list(hieffusn = 0)), qmatrix.msm(psor.msm, 
         covariates = list(ollwsdrt = 0, hieffusn = 0))) at testthat/test_models.r:297
  2: compare(object, expected, ...)
  3: qmatrix.msm(psor.msm, covariates = list(hieffusn = 0))
  4: deltamethod(form, ests, cov)
  5: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  6: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  7: lapply(X = X, FUN = FUN, ...)
  8: FUN(X[[i]], ...)
  9: eval(deriv(form, syms))
  10: deriv(form, syms)
  11: deriv.formula(form, syms)
  
  7. Error: sojourn.msm (@test_models.r#306) -------------------------------------
  Function 'c' is not in the derivatives table
  1: sojourn.msm(psor.msm, covariates = list(ollwsdrt = 0.1, hieffusn = 0.4)) at testthat/test_models.r:306
  2: qmatrix.msm(x, covariates, sojourn = TRUE, ci = ci, cl = cl, B = B)
  3: deltamethod(form, ests, cov)
  4: t(sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     }))
  5: sapply(g, function(form) {
         as.numeric(attr(eval(deriv(form, syms)), "gradient"))
     })
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: eval(deriv(form, syms))
  9: deriv(form, syms)
  10: deriv.formula(form, syms)
  
  testthat results ================================================================
  OK: 2142 SKIPPED: 0 FAILED: 7
  1. Error: qmatrix.msm for psor model, defaults (@test_models.r#255) 
  2. Error: qmatrix.msm with supplied covariates (@test_models.r#264) 
  3. Error: qmatrix.msm with non-default confidence limits (@test_models.r#271) 
  4. Error: qmatrix.msm sojourn component (@test_models.r#276) 
  5. Error: qmatrix.msm bug for user-supplied covariates fixed in 1.1.3 (@test_models.r#291) 
  6. Error: qmatrix.msm: unspecified covariate values default to zero (@test_models.r#297) 
  7. Error: sojourn.msm (@test_models.r#306) 
  
  Error: testthat unit tests failed
  Execution halted