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

Mon May 14 07:14:18 BST 2018

Hi Andreas,

there were some changes in data.table that is breaking some popEpi functionality... you may want to try to install an older version of data.table. I'll try to get a fix out pretty soon though.

Sincerely,
Joonas Miettinen
Epidemiologinen tutkija - Epidemiological researcher
Suomen Syöpärekisteri  - Finnish Cancer Registry 
Institute for Statistical and Epidemiological Cancer Research 
Unioninkatu 22, 00130 Helsinki, Finland

-----Original Message-----
From: Andreas Tille [mailto:andreas at an3as.eu] 
Sent: 12. toukokuuta 2018 23:44
To: Joonas Miettinen <Joonas.Miettinen at cancer.fi>; Debian R Packages Maintainers <r-pkg-team at alioth-lists.debian.net>
Subject: Some failed tests in popEpi

Hi Joonas,

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

BEGIN TEST testthat.R

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help.
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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.

--
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