Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(arsenal)
  > 
  > test_check("arsenal")
  ── 1. Error: Keep labels in modelsum (@test_keep.labels.R#71)  ─────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(age ~ sex + arm, data = mockstudy, 
         subset = age < 80), text = TRUE)), c("|                        |estimate |std.error |p.value |adj.r.squared |", 
         "|:-----------------------|:--------|:---------|:-------|:-------------|", "|(Intercept)             |59.850   |0.372     |< 0.001 |0.002         |", 
         "|sex Female              |-1.076   |0.595     |0.071   |              |", "|(Intercept)             |59.290   |0.542     |< 0.001 |-0.001        |", 
         "|Treatment Arm F: FOLFOX |0.340    |0.691     |0.623   |              |", "|Treatment Arm G: IROX   |-0.063   |0.792     |0.936   |              |")) at testthat/test_keep.labels.R:71
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(age ~ sex + arm, data = mockstudy, subset = age < 
         80), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(age ~ sex + arm, data = mockstudy, subset = age < 80), text = TRUE)
  11: modelsum(age ~ sex + arm, data = mockstudy, subset = age < 80)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 2. Error: A basic modelsum call--no labels, no missings (@test_modelsum.R#13)
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + time, data = mdat), text = TRUE)), 
         c("|            |estimate |std.error |p.value |adj.r.squared |", "|:-----------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept) |39.826   |0.779     |< 0.001 |-0.011        |", "|Sex Male    |-0.258   |1.115     |0.818   |              |", 
             "|(Intercept) |41.130   |1.197     |< 0.001 |0.009         |", "|time        |-0.371   |0.275     |0.182   |              |")) at testthat/test_modelsum.R:13
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + time, data = mdat), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + time, data = mdat), text = TRUE)
  11: modelsum(Age ~ Sex + time, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 3. Error: A basic modelsum tableby call--labels, no missings (@test_modelsum.
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + trt, data = mdat), text = TRUE)), 
         c("|                |estimate |std.error |p.value |adj.r.squared |", "|:---------------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept)     |39.826   |0.779     |< 0.001 |-0.011        |", "|Sex Male        |-0.258   |1.115     |0.818   |              |", 
             "|(Intercept)     |40.528   |0.874     |< 0.001 |0.006         |", "|Treatment Arm B |-1.380   |1.128     |0.225   |              |")) at testthat/test_modelsum.R:26
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + trt, data = mdat), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + trt, data = mdat), text = TRUE)
  11: modelsum(Age ~ Sex + trt, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 4. Error: A basic modelsum call--adding adjustment (@test_modelsum.R#39)  ───
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, 
         data = mdat), text = TRUE)), c("|                |estimate |std.error |p.value |adj.r.squared |", 
         "|:---------------|:--------|:---------|:-------|:-------------|", "|(Intercept)     |40.632   |1.024     |< 0.001 |-0.005        |", 
         "|Sex Male        |-0.221   |1.112     |0.843   |              |", "|Treatment Arm B |-1.373   |1.135     |0.229   |              |", 
         "|(Intercept)     |41.938   |1.366     |< 0.001 |0.014         |", "|time            |-0.368   |0.275     |0.184   |              |", 
         "|Treatment Arm B |-1.366   |1.123     |0.227   |              |")) at testthat/test_modelsum.R:39
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE)
  11: modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 5. Error: A basic modelsum call--suppressing intercept and/or adjustment vars
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, 
         data = mdat), text = TRUE, show.intercept = FALSE)), c("|                |estimate |std.error |p.value |adj.r.squared |", 
         "|:---------------|:--------|:---------|:-------|:-------------|", "|Sex Male        |-0.221   |1.112     |0.843   |-0.005        |", 
         "|Treatment Arm B |-1.373   |1.135     |0.229   |              |", "|time            |-0.368   |0.275     |0.184   |0.014         |", 
         "|Treatment Arm B |-1.366   |1.123     |0.227   |              |")) at testthat/test_modelsum.R:54
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE, 
         show.intercept = FALSE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE, show.intercept = FALSE)
  11: modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 6. Error: Reordering variables (@test_modelsum.R#90)  ───────────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + Group + time, data = mdat)[c(3, 
         1, 2)], text = TRUE)), c("|            |estimate |std.error |p.value |adj.r.squared |", 
         "|:-----------|:--------|:---------|:-------|:-------------|", "|(Intercept) |41.130   |1.197     |< 0.001 |0.009         |", 
         "|time        |-0.371   |0.275     |0.182   |              |", "|(Intercept) |39.826   |0.779     |< 0.001 |-0.011        |", 
         "|Sex Male    |-0.258   |1.115     |0.818   |              |", "|(Intercept) |40.033   |0.970     |< 0.001 |-0.021        |", 
         "|Group Low   |-0.400   |1.372     |0.771   |              |", "|Group Med   |-0.600   |1.372     |0.663   |              |")) at testthat/test_modelsum.R:90
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + Group + time, data = mdat)[c(3, 1, 2)], 
         text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + Group + time, data = mdat)[c(3, 1, 2)], text = TRUE)
  11: modelsum(Age ~ Sex + Group + time, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 7. Failure: offset() works (@test_modelsum.R#125)  ──────────────────────────
  `summary(...)` threw an error.
  Message: there is no package called 'broom'
  Class:   error/condition
  
  ── 8. Error: strata() works (@test_modelsum.R#132)  ────────────────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Surv(time, status) ~ ethan, adjust = ~strata(Sex), 
         data = mdat, family = "survival"), text = TRUE)), c("|              |HR    |CI.lower.HR |CI.upper.HR |p.value |concordance |Nmiss |", 
         "|:-------------|:-----|:-----------|:-----------|:-------|:-----------|:-----|", 
         "|ethan Heinzen |1.051 |0.549       |2.014       |0.880   |0.499       |3     |")) at testthat/test_modelsum.R:132
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Surv(time, status) ~ ethan, adjust = ~strata(Sex), 
         data = mdat, family = "survival"), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Surv(time, status) ~ ethan, adjust = ~strata(Sex), data = mdat, 
         family = "survival"), text = TRUE)
  11: modelsum(Surv(time, status) ~ ethan, adjust = ~strata(Sex), data = mdat, family = "survival")
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 9. Error: 'weights=' works (@test_modelsum.R#143)  ──────────────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex, data = mdat, weights = weights))), 
         c("|             |estimate |std.error |p.value |adj.r.squared |", "|:------------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept)  |39.826   |0.889     |< 0.001 |0.020         |", "|**Sex Male** |1.953    |1.167     |0.098   |              |")) at testthat/test_modelsum.R:143
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex, data = mdat, weights = weights)))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex, data = mdat, weights = weights))
  11: modelsum(Age ~ Sex, data = mdat, weights = weights)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 10. Error: ordinal works (@test_modelsum.R#158)  ────────────────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Sat ~ Infl, adjust = ~Type + Cont, 
         weights = Freq, data = housing, family = "ordinal"))), c("|                   |OR    |CI.lower.OR |CI.upper.OR |p.value |", 
         "|:------------------|:-----|:-----------|:-----------|:-------|", "|Low&#124;Medium    |NA    |NA          |NA          |< 0.001 |", 
         "|Medium&#124;High   |NA    |NA          |NA          |< 0.001 |", "|**Cont High**      |1.434 |1.189       |1.730       |< 0.001 |", 
         "|**Infl High**      |3.628 |2.832       |4.663       |< 0.001 |", "|**Infl Medium**    |1.762 |1.436       |2.164       |< 0.001 |", 
         "|**Type Apartment** |0.564 |0.446       |0.712       |< 0.001 |", "|**Type Atrium**    |0.693 |0.511       |0.940       |0.018   |", 
         "|**Type Terrace**   |0.336 |0.249       |0.451       |< 0.001 |")) at testthat/test_modelsum.R:158
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Sat ~ Infl, adjust = ~Type + Cont, weights = Freq, 
         data = housing, family = "ordinal")))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Sat ~ Infl, adjust = ~Type + Cont, weights = Freq, data = housing, 
         family = "ordinal"))
  11: modelsum(Sat ~ Infl, adjust = ~Type + Cont, weights = Freq, data = housing, family = "ordinal")
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 11. Error: negbin works (@test_modelsum.R#204)  ─────────────────────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(fu.time ~ sex, adjust = ~age + arm, 
         data = mockstudy, family = negbin), negbin.stats = c("estimate", "p.value", "theta"), 
         text = TRUE, digits = 5)), c("|                        |estimate |p.value |theta   |", 
         "|:-----------------------|:--------|:-------|:-------|", "|(Intercept)             |6.52819  |< 0.001 |1.84776 |", 
         "|sex Female              |-0.02370 |0.545   |        |", "|Age in Years            |-0.00342 |0.039   |        |", 
         "|Treatment Arm F: FOLFOX |0.28161  |< 0.001 |        |", "|Treatment Arm G: IROX   |0.09396  |0.071   |        |")) at testthat/test_modelsum.R:204
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(fu.time ~ sex, adjust = ~age + arm, data = mockstudy, 
         family = negbin), negbin.stats = c("estimate", "p.value", "theta"), text = TRUE, 
         digits = 5))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(fu.time ~ sex, adjust = ~age + arm, data = mockstudy, family = negbin), 
         negbin.stats = c("estimate", "p.value", "theta"), text = TRUE, digits = 5)
  11: modelsum(fu.time ~ sex, adjust = ~age + arm, data = mockstudy, family = negbin)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 12. Error: 01/26/2017: Brendan Broderick's Bold Text Wrapping Problem (@test_
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(short.name ~ really.long.name + as.long.as.this, 
         adjust = ~why.would.you.name.something, data = dat))), c("|                                 |estimate |std.error |p.value |adj.r.squared |", 
         "|:--------------------------------|:--------|:---------|:-------|:-------------|", 
         "|(Intercept)                      |0.035    |0.099     |0.721   |-0.001        |", 
         "|**really.long.name**             |0.099    |0.099     |0.319   |              |", 
         "|**why.would.you.name.something** |-0.083   |0.090     |0.361   |              |", 
         "|(Intercept)                      |0.048    |0.097     |0.624   |0.023         |", 
         "|**as.long.as.this**              |0.198    |0.106     |0.066   |              |", 
         "|**why.would.you.name.something** |-0.090   |0.089     |0.314   |              |")) at testthat/test_modelsum.R:230
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(short.name ~ really.long.name + as.long.as.this, adjust = ~why.would.you.name.something, 
         data = dat)))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(short.name ~ really.long.name + as.long.as.this, adjust = ~why.would.you.name.something, 
         data = dat))
  11: modelsum(short.name ~ really.long.name + as.long.as.this, adjust = ~why.would.you.name.something, 
         data = dat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 13. Failure: 02/07/2017: Ryan Lennon's R Markdown spacing problem. Also 02/14
  `capture.kable(...)` threw an error.
  Message: there is no package called 'broom'
  Class:   error/condition
  
  ── 14. Error: 02/13/2017: Krista Goergen's survival subset and NA problems (@tes
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(form, data = mdat.tmp, subset = Group == 
         "High", family = "survival"), text = TRUE)), capture.kable(summary(modelsum(form, 
         data = mdat.tmp[mdat.tmp$Group == "High", ], family = "survival"), text = TRUE))) at testthat/test_modelsum.R:260
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(form, data = mdat.tmp, subset = Group == "High", family = "survival"), 
         text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(form, data = mdat.tmp, subset = Group == "High", family = "survival"), 
         text = TRUE)
  11: modelsum(form, data = mdat.tmp, subset = Group == "High", family = "survival")
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 15. Error: 04/12/2017: ... vs modelsum.control (@test_modelsum.R#288)  ──────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, 
         data = mdat, show.adjust = FALSE, control = modelsum.control()), text = TRUE)), 
         c("|            |estimate |std.error |p.value |adj.r.squared |", "|:-----------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept) |40.632   |1.024     |< 0.001 |-0.005        |", "|Sex Male    |-0.221   |1.112     |0.843   |              |", 
             "|(Intercept) |41.938   |1.366     |< 0.001 |0.014         |", "|time        |-0.368   |0.275     |0.184   |              |")) at testthat/test_modelsum.R:288
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat, show.adjust = FALSE, 
         control = modelsum.control()), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat, show.adjust = FALSE, 
         control = modelsum.control()), text = TRUE)
  11: modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat, show.adjust = FALSE, control = modelsum.control())
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 16. Error: 08/01/2017: Beth Atkinson's subset problem (@test_modelsum.R#306) 
  there is no package called 'pROC'
  1: expect_identical(capture.kable(summary(modelsum(form, data = mockstudy, subset = idx, 
         adjust = ~arm, family = "binomial"), text = TRUE)), capture.kable(summary(modelsum(form, 
         data = mockstudy, subset = sex == "Male", adjust = ~arm, family = "binomial"), 
         text = TRUE))) at testthat/test_modelsum.R:306
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, 
         family = "binomial"), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, family = "binomial"), 
         text = TRUE)
  11: modelsum(form, data = mockstudy, subset = idx, adjust = ~arm, family = "binomial")
  12: pROC::roc
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 17. Error: 07/27/2017: Too many adjustment vars in as.data.frame.modelsum (#1
  there is no package called 'broom'
  1: expect_equal(nrow(as.data.frame(modelsum(y ~ x1, adjust = ~x7 + x2 + x3 + x5 + x8, 
         data = df))), 10L) at testthat/test_modelsum.R:326
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: nrow(as.data.frame(modelsum(y ~ x1, adjust = ~x7 + x2 + x3 + x5 + x8, data = df)))
  5: as.data.frame(modelsum(y ~ x1, adjust = ~x7 + x2 + x3 + x5 + x8, data = df))
  6: modelsum(y ~ x1, adjust = ~x7 + x2 + x3 + x5 + x8, data = df)
  7: broom::tidy
  8: getExportedValue(pkg, name)
  9: asNamespace(ns)
  10: getNamespace(ns)
  11: loadNamespace(name)
  12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  13: withOneRestart(expr, restarts[[1L]])
  14: doWithOneRestart(return(expr), restart)
  
  ── 18. Error: 07/27/2017: modelsum labels (#13) (@test_modelsum.R#332)  ────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(bmi ~ age, adjust = ~sex, data = mockstudy), 
         labelTranslations = list(sexFemale = "Female", age = "Age, yrs"), text = TRUE)), 
         c("|            |estimate |std.error |p.value |adj.r.squared |", "|:-----------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept) |26.793   |0.766     |< 0.001 |0.004         |", "|Age, yrs    |0.012    |0.012     |0.348   |              |", 
             "|Female      |-0.718   |0.291     |0.014   |              |")) at testthat/test_modelsum.R:332
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(bmi ~ age, adjust = ~sex, data = mockstudy), labelTranslations = list(sexFemale = "Female", 
         age = "Age, yrs"), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(bmi ~ age, adjust = ~sex, data = mockstudy), labelTranslations = list(sexFemale = "Female", 
         age = "Age, yrs"), text = TRUE)
  11: modelsum(bmi ~ age, adjust = ~sex, data = mockstudy)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 19. Error: 12/23/2017: non-syntactic names (#44, #45) (@test_modelsum.R#355) 
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(y ~ x1x, data = dat))), c("|            |estimate |std.error |p.value |adj.r.squared |", 
         "|:-----------|:--------|:---------|:-------|:-------------|", "|(Intercept) |3.000    |0.707     |0.003   |0.727         |", 
         "|**x1x B**   |5.000    |1.000     |0.001   |              |")) at testthat/test_modelsum.R:355
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(y ~ x1x, data = dat)))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(y ~ x1x, data = dat))
  11: modelsum(y ~ x1x, data = dat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 20. Error: 01/05/2018: leading/trailing whitespace (#48) (@test_modelsum.R#37
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(age ~ arm, data = set_labels(mockstudy, 
         list(arm = " Arm "))))), c("|                   |estimate |std.error |p.value |adj.r.squared |", 
         "|:------------------|:--------|:---------|:-------|:-------------|", "|(Intercept)        |59.673   |0.557     |< 0.001 |-0.001        |", 
         "|**Arm  F: FOLFOX** |0.628    |0.709     |0.376   |              |", "|**Arm  G: IROX**   |0.090    |0.812     |0.912   |              |")) at testthat/test_modelsum.R:376
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(age ~ arm, data = set_labels(mockstudy, list(arm = " Arm ")))))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(age ~ arm, data = set_labels(mockstudy, list(arm = " Arm "))))
  11: modelsum(age ~ arm, data = set_labels(mockstudy, list(arm = " Arm ")))
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 21. Error: 02/23/2018: wrapping long labels (#59) (@test_modelsum.R#404)  ───
  there is no package called 'broom'
  1: expect_identical(capture.kable(print(summary(modelsum(Age ~ Group + time + dt, data = set_labels(mdat, 
         labs)), text = TRUE), width = 30)), c("|                               |estimate |std.error |p.value |adj.r.squared |", 
         "|:------------------------------|:--------|:---------|:-------|:-------------|", 
         "|(Intercept)                    |40.033   |0.970     |< 0.001 |-0.021        |", 
         "|This is a really long label    |-0.400   |1.372     |0.771   |              |", 
         "|for the Group variable Low     |         |          |        |              |", 
         "|This is a really long label    |-0.600   |1.372     |0.663   |              |", 
         "|for the Group variable Med     |         |          |        |              |", 
         "|(Intercept)                    |41.130   |1.197     |< 0.001 |0.009         |", 
         "|Another really long label.     |-0.371   |0.275     |0.182   |              |", 
         "|Can you believe how long this  |         |          |        |              |", 
         "|is                             |         |          |        |              |", 
         "|(Intercept)                    |41.531   |2.017     |< 0.001 |-0.001        |", 
         "|ThisLabelHasNoSpacesSoLetsSeeH |0.000    |0.000     |0.348   |              |", 
         "|owItBehaves                    |         |          |        |              |")) at testthat/test_modelsum.R:404
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(print(summary(modelsum(Age ~ Group + time + dt, data = set_labels(mdat, 
         labs)), text = TRUE), width = 30))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: print(summary(modelsum(Age ~ Group + time + dt, data = set_labels(mdat, labs)), text = TRUE), 
         width = 30)
  11: summary(modelsum(Age ~ Group + time + dt, data = set_labels(mdat, labs)), text = TRUE)
  12: modelsum(Age ~ Group + time + dt, data = set_labels(mdat, labs))
  13: broom::tidy
  14: getExportedValue(pkg, name)
  15: asNamespace(ns)
  16: getNamespace(ns)
  17: loadNamespace(name)
  18: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  19: withOneRestart(expr, restarts[[1L]])
  20: doWithOneRestart(return(expr), restart)
  
  ── 22. Error: 05/31/2018: similar column names (#98) (@test_modelsum.R#433)  ───
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(y ~ b, adjust = ~a + aa, data = dat))), 
         c("|            |estimate |std.error |p.value |adj.r.squared |", "|:-----------|:--------|:---------|:-------|:-------------|", 
             "|(Intercept) |0.417    |0.295     |0.208   |0.984         |", "|**b b**     |-0.467   |0.548     |0.427   |              |", 
             "|**a**       |-0.083   |0.217     |0.714   |              |", "|**aa**      |1.250    |0.183     |< 0.001 |              |")) at testthat/test_modelsum.R:433
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(y ~ b, adjust = ~a + aa, data = dat)))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(y ~ b, adjust = ~a + aa, data = dat))
  11: modelsum(y ~ b, adjust = ~a + aa, data = dat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 23. Error: 05/31/2018: similar column names (#100) (@test_modelsum.R#453)  ──
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(y ~ a, adjust = ~d, data = set_labels(dat, 
         list(a = "A", d = "D"))), text = TRUE)), c("|            |estimate |std.error |p.value |adj.r.squared |", 
         "|:-----------|:--------|:---------|:-------|:-------------|", "|(Intercept) |8.000    |1.000     |< 0.001 |0.688         |", 
         "|A a         |-5.000   |1.091     |0.003   |              |", "|D d         |-0.000   |1.091     |1.000   |              |")) at testthat/test_modelsum.R:453
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(y ~ a, adjust = ~d, data = set_labels(dat, list(a = "A", 
         d = "D"))), text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(y ~ a, adjust = ~d, data = set_labels(dat, list(a = "A", d = "D"))), 
         text = TRUE)
  11: modelsum(y ~ a, adjust = ~d, data = set_labels(dat, list(a = "A", d = "D")))
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 24. Error: 06/19/2018: term.name (#109) (@test_modelsum.R#467)  ─────────────
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, 
         data = mdat), text = TRUE, term.name = "Term")), c("|Term            |estimate |std.error |p.value |adj.r.squared |", 
         "|:---------------|:--------|:---------|:-------|:-------------|", "|(Intercept)     |40.632   |1.024     |< 0.001 |-0.005        |", 
         "|Sex Male        |-0.221   |1.112     |0.843   |              |", "|Treatment Arm B |-1.373   |1.135     |0.229   |              |", 
         "|(Intercept)     |41.938   |1.366     |< 0.001 |0.014         |", "|time            |-0.368   |0.275     |0.184   |              |", 
         "|Treatment Arm B |-1.366   |1.123     |0.227   |              |")) at testthat/test_modelsum.R:467
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE, 
         term.name = "Term"))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat), text = TRUE, term.name = "Term")
  11: modelsum(Age ~ Sex + time, adjust = ~trt, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 25. Error: 08/24/2018: latex (#123) (@test_modelsum.R#484)  ─────────────────
  there is no package called 'broom'
  1: expect_identical(capture.output(summary(modelsum(Age ~ Sex, adjust = ~trt, data = mdat), 
         text = "latex")), c("", "\\begin{tabular}{l|l|l|l|l}", "\\hline", " & estimate & std.error & p.value & adj.r.squared\\\\", 
         "\\hline", "(Intercept) & 40.632 & 1.024 & < 0.001 & -0.005\\\\", "\\hline", 
         "\\textbf{Sex Male} & -0.221 & 1.112 & 0.843 & \\\\", "\\hline", "\\textbf{Treatment Arm B} & -1.373 & 1.135 & 0.229 & \\\\", 
         "\\hline", "\\end{tabular}", "")) at testthat/test_modelsum.R:484
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.output(summary(modelsum(Age ~ Sex, adjust = ~trt, data = mdat), text = "latex"))
  5: evalVis(expr)
  6: withVisible(eval(expr, pf))
  7: eval(expr, pf)
  8: eval(expr, pf)
  9: summary(modelsum(Age ~ Sex, adjust = ~trt, data = mdat), text = "latex")
  10: modelsum(Age ~ Sex, adjust = ~trt, data = mdat)
  11: broom::tidy
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: loadNamespace(name)
  16: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  17: withOneRestart(expr, restarts[[1L]])
  18: doWithOneRestart(return(expr), restart)
  
  ── 26. Error: 09/05/2018: correctly label contrasts for ordinal variables (#133)
  there is no package called 'broom'
  1: expect_identical(capture.kable(summary(modelsum(Age ~ Phase, adjust = ~Group.ord + 
         trt + ht_in, data = mdat), text = TRUE)), c("|                 |estimate |std.error |p.value |adj.r.squared |", 
         "|:----------------|:--------|:---------|:-------|:-------------|", "|(Intercept)      |47.686   |7.301     |< 0.001 |-0.019        |", 
         "|Phase .L         |-0.679   |1.152     |0.557   |              |", "|Phase .Q         |-1.044   |0.960     |0.280   |              |", 
         "|Group.ord .L     |0.243    |0.977     |0.804   |              |", "|Group.ord .Q     |0.410    |1.069     |0.702   |              |", 
         "|Treatment Arm B  |-1.460   |1.159     |0.211   |              |", "|Height in Inches |-0.112   |0.110     |0.314   |              |")) at testthat/test_modelsum.R:507
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: capture.kable(summary(modelsum(Age ~ Phase, adjust = ~Group.ord + trt + ht_in, data = mdat), 
         text = TRUE))
  5: capture.output(x) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/arsenal.Rcheck/tests/testthat/helper-script.R:4
  6: evalVis(expr)
  7: withVisible(eval(expr, pf))
  8: eval(expr, pf)
  9: eval(expr, pf)
  10: summary(modelsum(Age ~ Phase, adjust = ~Group.ord + trt + ht_in, data = mdat), text = TRUE)
  11: modelsum(Age ~ Phase, adjust = ~Group.ord + trt + ht_in, data = mdat)
  12: broom::tidy
  13: getExportedValue(pkg, name)
  14: asNamespace(ns)
  15: getNamespace(ns)
  16: loadNamespace(name)
  17: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  18: withOneRestart(expr, restarts[[1L]])
  19: doWithOneRestart(return(expr), restart)
  
  ── 27. Error: write2.list (summary objects) -> PDF (@test_write2.R#50)  ────────
  there is no package called 'broom'
  1: summary(modelsum(age ~ sex, data = mockstudy), title = "A Title for modelsum") at testthat/test_write2.R:50
  2: modelsum(age ~ sex, data = mockstudy)
  3: broom::tidy
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: loadNamespace(name)
  8: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
  9: withOneRestart(expr, restarts[[1L]])
  10: doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 182 SKIPPED: 10 FAILED: 27
  1. Error: Keep labels in modelsum (@test_keep.labels.R#71) 
  2. Error: A basic modelsum call--no labels, no missings (@test_modelsum.R#13) 
  3. Error: A basic modelsum tableby call--labels, no missings (@test_modelsum.R#26) 
  4. Error: A basic modelsum call--adding adjustment (@test_modelsum.R#39) 
  5. Error: A basic modelsum call--suppressing intercept and/or adjustment vars (@test_modelsum.R#54) 
  6. Error: Reordering variables (@test_modelsum.R#90) 
  7. Failure: offset() works (@test_modelsum.R#125) 
  8. Error: strata() works (@test_modelsum.R#132) 
  9. Error: 'weights=' works (@test_modelsum.R#143) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted