Last updated on 2024-07-24 12:21:19 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| cards | 1 | 12 | |
| cardx | 13 | ||
| dcurves | 13 | ||
| ggsurvfit | 13 | ||
| gtsummary | 6 | 7 | |
| rstudio.prefs | 13 | ||
| starter | 8 | 5 | |
| tidycmprsk | 1 | 12 | |
| updater | 13 |
Current CRAN status: NOTE: 1, OK: 12
Version: 0.1.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ard_stack.Rd: dyn-dots
bind_ard.Rd: dyn-dots
eval_capture_conditions.Rd: eval_tidy
get_ard_statistics.Rd: dyn-dots
print.card.Rd: dyn-dots
process_selectors.Rd: dyn-dots
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavor: r-devel-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 6, OK: 7
Version: 1.7.2
Check: Rd files
Result: NOTE
checkRd: (-1) as_flex_table.Rd:24: Lost braces; missing escapes or markup?
24 | A {flextable} object
| ^
checkRd: (-1) as_hux_table.Rd:37: Lost braces; missing escapes or markup?
37 | A {huxtable} object
| ^
checkRd: (-1) as_kable_extra.Rd:42: Lost braces; missing escapes or markup?
42 | and {kableExtra}; \code{as_kable_extra()} supports arguments in \code{knitr::kable()}.
| ^
checkRd: (-1) as_kable_extra.Rd:37: Lost braces; missing escapes or markup?
37 | A {kableExtra} table
| ^
checkRd: (-1) select_helpers.Rd:53: Lost braces; missing escapes or markup?
53 | Set of functions to supplement the {tidyselect} set of
| ^
checkRd: (-1) tbl_summary.Rd:91: Lost braces; missing escapes or markup?
91 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
| ^
checkRd: (-1) tbl_summary.Rd:91: Lost braces; missing escapes or markup?
91 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
| ^
checkRd: (-1) tbl_svysummary.Rd:183: Lost braces; missing escapes or markup?
183 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
| ^
checkRd: (-1) tbl_svysummary.Rd:183: Lost braces; missing escapes or markup?
183 | from the \\{tidyselect\\} package and \\{gtsummary\\} package are available to
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 1.7.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘gallery.Rmd’ using rmarkdown
--- finished re-building ‘gallery.Rmd’
--- re-building ‘gtsummary_definition.Rmd’ using rmarkdown
Quitting from lines 312-331 [unnamed-chunk-12] (gtsummary_definition.Rmd)
Error: processing vignette 'gtsummary_definition.Rmd' failed with diagnostics:
The package "katex" (>= 1.4.1) is required to render equations in HTML
tables.
--- failed re-building ‘gtsummary_definition.Rmd’
--- re-building ‘inline_text.Rmd’ using rmarkdown
--- finished re-building ‘inline_text.Rmd’
--- re-building ‘rmarkdown.Rmd’ using rmarkdown
--- finished re-building ‘rmarkdown.Rmd’
--- re-building ‘tbl_regression.Rmd’ using rmarkdown
--- finished re-building ‘tbl_regression.Rmd’
--- re-building ‘tbl_summary.Rmd’ using rmarkdown
--- finished re-building ‘tbl_summary.Rmd’
--- re-building ‘themes.Rmd’ using rmarkdown
--- finished re-building ‘themes.Rmd’
SUMMARY: processing the following file failed:
‘gtsummary_definition.Rmd’
Error: Vignette re-building failed.
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: 1.7.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'gallery.Rmd' using rmarkdown
--- finished re-building 'gallery.Rmd'
--- re-building 'gtsummary_definition.Rmd' using rmarkdown
Quitting from lines 312-331 [unnamed-chunk-12] (gtsummary_definition.Rmd)
Error: processing vignette 'gtsummary_definition.Rmd' failed with diagnostics:
The package "katex" (>= 1.4.1) is required to render equations in HTML
tables.
--- failed re-building 'gtsummary_definition.Rmd'
--- re-building 'inline_text.Rmd' using rmarkdown
--- finished re-building 'inline_text.Rmd'
--- re-building 'rmarkdown.Rmd' using rmarkdown
--- finished re-building 'rmarkdown.Rmd'
--- re-building 'tbl_regression.Rmd' using rmarkdown
--- finished re-building 'tbl_regression.Rmd'
--- re-building 'tbl_summary.Rmd' using rmarkdown
--- finished re-building 'tbl_summary.Rmd'
--- re-building 'themes.Rmd' using rmarkdown
--- finished re-building 'themes.Rmd'
SUMMARY: processing the following file failed:
'gtsummary_definition.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 8, OK: 5
Version: 0.1.15
Check: HTML version of manual
Result: NOTE
Found the following HTML validation problems:
create_symlink.html:55:1 (create_symlink.Rd:17): Warning: trimming empty <dt>
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [23s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidycmprsk)
>
> test_check("tidycmprsk")
11 cases omitted due to missing values
-- crr() -----------------------------------------------------------------------
* Call Surv(ttdeath, death_cr) ~ age
* Failure type of interest "death from cancer"
Variable Coef SE HR 95% CI p-value
age 0.006 0.010 1.01 0.99, 1.03 0.55
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
x There was an error evaluating the LHS of the formula.
-- cuminc() --------------------------------------------------------------------
* Failure type "death from cancer"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.000 0.000 NA, NA
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.071 0.026 0.031, 0.134
Drug A 20.0 61 0.173 0.039 0.106, 0.255
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.039 0.019 0.013, 0.090
Drug B 15.0 75 0.167 0.037 0.102, 0.246
Drug B 20.0 55 0.255 0.043 0.175, 0.343
* Failure type "death other causes"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.010 0.010 0.001, 0.050
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.082 0.028 0.038, 0.147
Drug A 20.0 61 0.204 0.041 0.131, 0.289
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.029 0.017 0.008, 0.077
Drug B 15.0 75 0.098 0.030 0.050, 0.165
Drug B 20.0 55 0.206 0.040 0.133, 0.289
* Tests
outcome statistic df p.value
death from cancer 1.99 1.00 0.16
death other causes 0.089 1.00 0.77
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-tbl_cuminc.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gtsummary.R:2:3'): gtsummary tables work with crr() output ───
`crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:2:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:7:3'): gtsummary tables work with crr() output ───
``%>%`(...)` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:7:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:12:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:12:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:17:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:17:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:29:3'): gtsummary tables work with crr() output ──
`... <- NULL` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:29:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ grade, trial_contr) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Error ('test-gtsummary.R:35:3'): gtsummary tables work with crr() output ────
Error in `eval(code, test_env)`: object 'contr_sum' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-gtsummary.R:35:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::unique(contr_sum$table_body$contrasts_type)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 13