CRAN Package Check Results for Package popEpi

Last updated on 2018-05-14 01:46:53 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.4 12.76 261.52 274.28 ERROR
r-devel-linux-x86_64-debian-gcc 0.4.4 14.14 150.62 164.76 ERROR
r-devel-linux-x86_64-fedora-clang 0.4.4 282.20 ERROR
r-devel-linux-x86_64-fedora-gcc 0.4.4 254.22 ERROR
r-devel-windows-ix86+x86_64 0.4.4 24.00 247.00 271.00 ERROR
r-patched-linux-x86_64 0.4.4 10.81 181.49 192.30 ERROR
r-patched-solaris-x86 0.4.4 331.80 ERROR
r-release-linux-x86_64 0.4.4 12.69 181.63 194.32 ERROR
r-release-windows-ix86+x86_64 0.4.4 24.00 247.00 271.00 ERROR
r-release-osx-x86_64 0.4.4 OK
r-oldrel-windows-ix86+x86_64 0.4.4 25.00 197.00 222.00 ERROR
r-oldrel-osx-x86_64 0.4.4 OK

Check Details

Version: 0.4.4
Check: examples
Result: ERROR
    Running examples in ‘popEpi-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: makeWeightsDT
    > ### Title: Make a 'data.table' of Tabulated, Aggregated Values and Weights
    > ### Aliases: makeWeightsDT
    >
    > ### ** Examples
    >
    > library(survival)
    > library(data.table)
    >
    > makeWeightsDT <- popEpi:::makeWeightsDT ## this avoids errors during tests
    >
    > sire <- copy(popEpi::sire)
    > set.seed(1L)
    > sire$sex <- rbinom(nrow(sire), 1, 0.5)
    > ag <- lexpand(sire, birth = "bi_date", entry = "dg_date", exit = "ex_date",
    + status = status %in% 1:2, pophaz = popmort, pp = FALSE,
    + aggre = list(sex, agegr = cut(dg_age, c(0,50,75,Inf)), fot),
    + fot = seq(0, 5, 1/12))
    dropped 16 rows where entry == exit
    NOTE: 71 rows in split data had values of 'age' higher than max of pophaz's 'agegroup'; the hazard values at 'agegroup' == 100 were used for these
    > ps <- quote(list(sex, fot))
    > as <- quote(list(agegr))
    > vs <- list(quote(list(pyrs, at.risk)))
    > ws <- list(agegr = c(0.2,0.4,0.4))
    >
    > #### custom.levels usage
    > fb <- seq(0, 5-1/12, 1/12) ## exclude 5 as no row has that value
    > ag2 <- ag[fot > 0.5,]
    > # repeats fot intervals < 0.5 as empty rows
    > # may be the safest way to do this
    > dt <- makeWeightsDT(ag2, print = ps, adjust = as,
    + values = vs, weights = ws,
    + custom.levels = list(fot = fb))
    > ## aggregate from intervals seq(0, 5, 1/12) to 0:5
    > fb2 <- 0:5 ## (this time we include 5 as the roof)
    > dt <- makeWeightsDT(ag2, print = ps, adjust = as,
    + values = vs, weights = ws,
    + custom.levels = list(fot = fb2),
    + custom.levels.cut.low = "fot")
    >
    >
    > #### use of enclos
    > TF <- environment()
    > gender <- factor(ag$sex)
    > dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    + values = vs, weights = ws, enclos = TF)
    > ## or NULL: uses calling frame by default.
    > dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    + values = vs, weights = ws,
    + enclos = NULL)
    > ## passing parent.fram(1) is the same thing (as below),
    > ## but won't pass in testing these examples somehow (but work in real life)
    > # dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    > # values = vs, weights = ws,
    > # enclos = NULL)
    >
    > #### formula usage
    > form <- Surv(fot, factor(from0to1))~gender
    > dt <- makeWeightsDT(ag, formula = form, Surv.response = TRUE,
    + adjust = as, values = vs, weights = ws,
    + enclos = NULL)
    Error in as.data.table.array(xi, keep.rownames = keep.rownames) :
     as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
    Calls: makeWeightsDT ... Surv2DT -> data.table -> as.data.table -> as.data.table.array
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [136s/64s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.4.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Quitting from lines 38-67 (survtab_examples.Rmd)
    Error: processing vignette ‘survtab_examples.Rmd’ failed with diagnostics:
    as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [56s/80s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.4.4
Check: examples
Result: ERROR
    Running examples in ‘popEpi-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: makeWeightsDT
    > ### Title: Make a 'data.table' of Tabulated, Aggregated Values and Weights
    > ### Aliases: makeWeightsDT
    >
    > ### ** Examples
    >
    > library(survival)
    > library(data.table)
    >
    > makeWeightsDT <- popEpi:::makeWeightsDT ## this avoids errors during tests
    >
    > sire <- copy(popEpi::sire)
    > set.seed(1L)
    > sire$sex <- rbinom(nrow(sire), 1, 0.5)
    > ag <- lexpand(sire, birth = "bi_date", entry = "dg_date", exit = "ex_date",
    + status = status %in% 1:2, pophaz = popmort, pp = FALSE,
    + aggre = list(sex, agegr = cut(dg_age, c(0,50,75,Inf)), fot),
    + fot = seq(0, 5, 1/12))
    dropped 16 rows where entry == exit
    NOTE: 71 rows in split data had values of 'age' higher than max of pophaz's 'agegroup'; the hazard values at 'agegroup' == 100 were used for these
    > ps <- quote(list(sex, fot))
    > as <- quote(list(agegr))
    > vs <- list(quote(list(pyrs, at.risk)))
    > ws <- list(agegr = c(0.2,0.4,0.4))
    >
    > #### custom.levels usage
    > fb <- seq(0, 5-1/12, 1/12) ## exclude 5 as no row has that value
    > ag2 <- ag[fot > 0.5,]
    > # repeats fot intervals < 0.5 as empty rows
    > # may be the safest way to do this
    > dt <- makeWeightsDT(ag2, print = ps, adjust = as,
    + values = vs, weights = ws,
    + custom.levels = list(fot = fb))
    > ## aggregate from intervals seq(0, 5, 1/12) to 0:5
    > fb2 <- 0:5 ## (this time we include 5 as the roof)
    > dt <- makeWeightsDT(ag2, print = ps, adjust = as,
    + values = vs, weights = ws,
    + custom.levels = list(fot = fb2),
    + custom.levels.cut.low = "fot")
    >
    >
    > #### use of enclos
    > TF <- environment()
    > gender <- factor(ag$sex)
    > dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    + values = vs, weights = ws, enclos = TF)
    > ## or NULL: uses calling frame by default.
    > dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    + values = vs, weights = ws,
    + enclos = NULL)
    > ## passing parent.fram(1) is the same thing (as below),
    > ## but won't pass in testing these examples somehow (but work in real life)
    > # dt <- makeWeightsDT(ag, print = quote(gender), adjust = as,
    > # values = vs, weights = ws,
    > # enclos = NULL)
    >
    > #### formula usage
    > form <- Surv(fot, factor(from0to1))~gender
    > dt <- makeWeightsDT(ag, formula = form, Surv.response = TRUE,
    + adjust = as, values = vs, weights = ws,
    + enclos = NULL)
    Error in as.data.table.array(xi, keep.rownames = keep.rownames) :
     as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
    Calls: makeWeightsDT ... Surv2DT -> data.table -> as.data.table -> as.data.table.array
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [107s/94s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(popEpi)
     > test_check("popEpi")
     OMP: Warning #96: Cannot form a team with 10 threads, using 2 instead.
     OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
     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
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.4.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    OMP: Warning #96: Cannot form a team with 10 threads, using 2 instead.
    OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
    Quitting from lines 38-67 (survtab_examples.Rmd)
    Error: processing vignette 'survtab_examples.Rmd' failed with diagnostics:
    as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [87s/123s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.4.4
Check: tests
Result: ERROR
     Running 'testthat.R' [78s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > 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
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [72s/94s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-patched-linux-x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [121s/145s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-patched-solaris-x86

Version: 0.4.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 38-67 (survtab_examples.Rmd)
    Error: processing vignette 'survtab_examples.Rmd' failed with diagnostics:
    as.data.table.array method should be only called for arrays with 3+ dimensions, for 2 dimensions matrix method should be used
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.4.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [72s/93s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > 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
Flavor: r-release-linux-x86_64

Version: 0.4.4
Check: tests
Result: ERROR
     Running 'testthat.R' [65s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > 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
Flavor: r-oldrel-windows-ix86+x86_64