[R-pkg-team] Some failed tests in popEpi

[Andreas Tille]

Hi Joonas,

I intend to package popEpi for Debian.  When running the test suite I
get:


BEGIN TEST testthat.R

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> library(testthat)
> library(popEpi)
> test_check("popEpi")
NOTE: entry.status has been set to 0 for all.
NOTE: entry.status has been set to "DM" for all.
-- 1. Error: removing consecutively bad surv.ints is logical w/ & w/out adjustin
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: expect_message({
       st1 <- survtab(Surv(fot, lex.Xst) ~ agegr, subset = !(agegr == 1L & fot > 8.49), 
           data = x, surv.type = "surv.obs")
   }, regexp = NA) at testthat/test_survtab_bad_surv_ints.R:16
2: quasi_capture(enquo(object), capture_messages, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, message = function(condition) {
       out$push(condition)
       invokeRestart("muffleMessage")
   })
5: eval_bare(get_expr(quo), get_env(quo))
6: survtab(Surv(fot, lex.Xst) ~ agegr, subset = !(agegr == 1L & fot > 8.49), data = x, 
       surv.type = "surv.obs") at testthat/test_survtab_bad_surv_ints.R:17
7: usePopFormula(form = formula, adjust = adjust, data = x, enclos = PF, Surv.response = "either")
8: evalPopFormula(formula = al$arg, data = data, enclos = enclos, Surv.response = Surv.response)
9: Surv2DT(y)
10: data.table(dt)
11: as.data.table(xi, keep.rownames = keep.rownames)
12: as.data.table.array(xi, keep.rownames = keep.rownames)
13: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

-- 2. Error: survtab_ag messages & results due to non-consecutively bad surv.int
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: expect_message(eval(tf1), msgs[1], ignore.case = TRUE) at testthat/test_survtab_bad_surv_ints.R:69
2: quasi_capture(enquo(object), capture_messages, label = label)
3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
4: withCallingHandlers(code, message = function(condition) {
       out$push(condition)
       invokeRestart("muffleMessage")
   })
5: eval_bare(get_expr(quo), get_env(quo))
6: eval(tf1)
7: eval(tf1)
8: survtab(Surv(fot, lex.Xst) ~ 1, data = x, surv.type = "surv.obs", subset = !(fot >= 
       5 & fot < 7))
9: usePopFormula(form = formula, adjust = adjust, data = x, enclos = PF, Surv.response = "either")
10: evalPopFormula(formula = al$arg, data = data, enclos = enclos, Surv.response = Surv.response)
11: Surv2DT(y)
12: data.table(dt)
13: as.data.table(xi, keep.rownames = keep.rownames)
14: as.data.table.array(xi, keep.rownames = keep.rownames)
15: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

-- 3. Error: surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johan
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: survtab(Surv(fot, event = lex.Xst) ~ 1, data = x, surv.type = "cif.obs") at testthat/test_survtab_observed.R:14
2: usePopFormula(form = formula, adjust = adjust, data = x, enclos = PF, Surv.response = "either")
3: evalPopFormula(formula = al$arg, data = data, enclos = enclos, Surv.response = Surv.response)
4: Surv2DT(y)
5: data.table(dt)
6: as.data.table(xi, keep.rownames = keep.rownames)
7: as.data.table.array(xi, keep.rownames = keep.rownames)
8: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

-- 4. Error: survtab works with more complicated estimation (@test_survtab_obser
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: survtab(Surv(time = FUT, event = lex.Xst) ~ factor(sex, 0:1, c("male", "female")) + 
       period + adjust(agegr), data = xl, weights = list(agegr = as.numeric(table(x$agegr))), 
       surv.type = "surv.obs", breaks = list(FUT = seq(0, 5, 1/12))) at testthat/test_survtab_observed.R:112
2: usePopFormula(form = formula, adjust = adjust, data = x, enclos = PF, Surv.response = "either")
3: evalPopFormula(formula = al$arg, data = data, enclos = enclos, Surv.response = Surv.response)
4: Surv2DT(y)
5: data.table(dt)
6: as.data.table(xi, keep.rownames = keep.rownames)
7: as.data.table.array(xi, keep.rownames = keep.rownames)
8: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

-- 5. Error: relative survivals about the same as relsurv's (@test_survtab_relat
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: survtab(Surv(fot, event = lex.Xst) ~ 1, data = x, surv.type = "surv.rel", relsurv.method = "e2", 
       pophaz = pm, breaks = list(fot = fb)) at testthat/test_survtab_relative.R:57
2: usePopFormula(form = formula, adjust = adjust, data = x, enclos = PF, Surv.response = "either")
3: evalPopFormula(formula = al$arg, data = data, enclos = enclos, Surv.response = Surv.response)
4: Surv2DT(y)
5: data.table(dt)
6: as.data.table(xi, keep.rownames = keep.rownames)
7: as.data.table.array(xi, keep.rownames = keep.rownames)
8: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

-- 6. Error: evalPopFormula & usePopFormula output is stable (@test_utils.R#251)
as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
1: evalPopFormula(f1a, data = x, enclos = TF, Surv.response = TRUE) at testthat/test_utils.R:251
2: Surv2DT(y)
3: data.table(dt)
4: as.data.table(xi, keep.rownames = keep.rownames)
5: as.data.table.array(xi, keep.rownames = keep.rownames)
6: stop("as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used")

== testthat results  ===========================================================
OK: 215 SKIPPED: 41 FAILED: 6
1. Error: removing consecutively bad surv.ints is logical w/ & w/out adjusting (@test_survtab_bad_surv_ints.R#16) 
2. Error: survtab_ag messages & results due to non-consecutively bad surv.ints are OK (@test_survtab_bad_surv_ints.R#69) 
3. Error: surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen (@test_survtab_observed.R#14) 
4. Error: survtab works with more complicated estimation (@test_survtab_observed.R#112) 
5. Error: relative survivals about the same as relsurv's (@test_survtab_relative.R#57) 
6. Error: evalPopFormula & usePopFormula output is stable (@test_utils.R#251) 

Error: testthat unit tests failed
Execution halted


Is there anything I might miss when running the test suite?

Kind regards

       Andreas.

-- 
http://fam-tille.de