- using R version 4.3.3 (2024-02-29)
- using platform: x86_64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘admiralonco/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘admiralonco’ version ‘1.1.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘admiralonco’ can be installed ... [4s/6s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [3s/4s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [10s/15s] ERROR
Running examples in ‘admiralonco-Ex.R’ failed
The error most likely occurred in:
> ### Name: rsp_y
> ### Title: Pre-Defined Response Event Objects
> ### Aliases: rsp_y no_data_n cb_y bor_cr bor_pr bor_sd bor_non_crpd bor_pd
> ### bor_ne no_data_missing crsp_y_cr crsp_y_pr cbor_cr cbor_pr
> ### Keywords: source_specifications
>
> ### ** Examples
>
> # This shows the definition of all pre-defined `event` objects that ship
> # with {admiralonco}
> exports <- sort(getNamespaceExports("admiralonco"))
> for (obj_name in exports) {
+ obj <- getExportedValue("admiralonco", obj_name)
+ if (inherits(obj, "event_def")) {
+ cat("\n", obj_name, ":\n", sep = "")
+ print(obj, indent = 2)
+ }
+ }
bor_cr:
<event> object
description: "Define complete response (CR) for best overall response (BOR)"
dataset_name: "ovr"
condition: AVALC == "CR"
mode: NULL
order: NULL
set_values_to:
Error in is_named(list[[name]]) : could not find function "is_named"
Calls: print -> print.source -> print_named_list
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [23s/37s] OK
Running ‘testthat.R’ [22s/37s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [16s/25s] ERROR
Errors in running code in vignettes:
when running code in ‘adrs.Rmd’
...
+ case_when(arg == "NE" ~ 1, arg == "CR" ~ 2, arg == "PR" ~
+ 3, arg == "SD" ~ 4, arg == "NON-CR/NON-PD" .... [TRUNCATED]
> adrs <- adrs %>% restrict_derivation(derivation = derive_var_extreme_flag,
+ args = params(by_vars = c(get_admiral_option("subject_keys"),
+ .... [TRUNCATED]
When sourcing ‘adrs.R’:
Error: could not find function "is_named"
Execution halted
when running code in ‘adrs_basic.Rmd’
...
+ case_when(arg == "NE" ~ 1, arg == "CR" ~ 2, arg == "PR" ~
+ 3, arg == "SD" ~ 4, arg == "NON-CR/NON-PD" .... [TRUNCATED]
> adrs <- adrs %>% restrict_derivation(derivation = derive_var_extreme_flag,
+ args = params(by_vars = c(get_admiral_option("subject_keys"),
+ .... [TRUNCATED]
When sourcing ‘adrs_basic.R’:
Error: could not find function "is_named"
Execution halted
when running code in ‘adrs_imwg.Rmd’
...
> if (nrow(many_nes) > 0) {
+ cli_warn("There are subjects with more than three NEs in a row.")
+ }
> adrs_imwg <- adrs_imwg %>% restrict_derivation(derivation = derive_var_extreme_flag,
+ args = params(by_vars = exprs(!!!get_admiral_option("sub ..." ... [TRUNCATED]
When sourcing ‘adrs_imwg.R’:
Error: could not find function "is_named"
Execution halted
when running code in ‘adtr.Rmd’
...
> adtr_sum <- adtr_sum %>% derive_var_merged_summary(dataset_add = adtr,
+ by_vars = get_admiral_option("subject_keys"), filter_add = AVISIT ==
.... [TRUNCATED]
> adtr_sum <- adtr_sum %>% restrict_derivation(derivation = derive_var_extreme_flag,
+ args = params(by_vars = get_admiral_option("subject_keys") .... [TRUNCATED]
When sourcing ‘adtr.R’:
Error: could not find function "is_named"
Execution halted
when running code in ‘irecist.Rmd’
...
|01-701-1115 |WEEK 6 |OVR |Overall Response by Investigator |iUPD |iUPD | 2|
|01-701-1118 |WEEK 6 |OVR |Overall Response by Investigator |iUPD |iUPD | 2|
> adrs <- adrs %>% restrict_derivation(derivation = derive_var_extreme_flag,
+ args = params(by_vars = c(get_admiral_option("subject_keys"),
+ .... [TRUNCATED]
When sourcing ‘irecist.R’:
Error: could not find function "is_named"
Execution halted
‘admiralonco.Rmd’ using ‘UTF-8’... [1s/2s] OK
‘adrs.Rmd’ using ‘UTF-8’... failed
‘adrs_basic.Rmd’ using ‘UTF-8’... failed
‘adrs_imwg.Rmd’ using ‘UTF-8’... failed
‘adtr.Rmd’ using ‘UTF-8’... failed
‘adtte.Rmd’ using ‘UTF-8’... [4s/6s] OK
‘irecist.Rmd’ using ‘UTF-8’... failed
‘nactdt.Rmd’ using ‘UTF-8’... [2s/3s] OK
- checking re-building of vignette outputs ... [34s/52s] NOTE
Error(s) in re-building vignettes:
--- re-building ‘admiralonco.Rmd’ using rmarkdown
--- finished re-building ‘admiralonco.Rmd’
--- re-building ‘adrs.Rmd’ using rmarkdown
Quitting from lines 233-256 [unnamed-chunk-11] (adrs.Rmd)
Error: processing vignette 'adrs.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘adrs.Rmd’
--- re-building ‘adrs_basic.Rmd’ using rmarkdown
Quitting from lines 232-255 [unnamed-chunk-11] (adrs_basic.Rmd)
Error: processing vignette 'adrs_basic.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘adrs_basic.Rmd’
--- re-building ‘adrs_imwg.Rmd’ using rmarkdown
Quitting from lines 558-569 [unnamed-chunk-17] (adrs_imwg.Rmd)
Error: processing vignette 'adrs_imwg.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘adrs_imwg.Rmd’
--- re-building ‘adtr.Rmd’ using rmarkdown
Quitting from lines 355-369 [unnamed-chunk-16] (adtr.Rmd)
Error: processing vignette 'adtr.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘adtr.Rmd’
--- re-building ‘adtte.Rmd’ using rmarkdown
--- finished re-building ‘adtte.Rmd’
--- re-building ‘irecist.Rmd’ using rmarkdown
Quitting from lines 243-254 [unnamed-chunk-11] (irecist.Rmd)
Error: processing vignette 'irecist.Rmd' failed with diagnostics:
could not find function "is_named"
--- failed re-building ‘irecist.Rmd’
--- re-building ‘nactdt.Rmd’ using rmarkdown
--- finished re-building ‘nactdt.Rmd’
SUMMARY: processing the following files failed:
‘adrs.Rmd’ ‘adrs_basic.Rmd’ ‘adrs_imwg.Rmd’ ‘adtr.Rmd’ ‘irecist.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [6s/10s] OK
- DONE
Status: 2 ERRORs, 1 NOTE
- using check arguments '--no-clean-on-error '