- using R version 4.4.2 (2024-10-31 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'teal.modules.clinical/DESCRIPTION' ... OK
- this is package 'teal.modules.clinical' version '0.9.1'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'teal.modules.clinical' can be installed ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [4s] OK
- checking whether the package can be loaded with stated dependencies ... [4s] OK
- checking whether the package can be unloaded cleanly ... [4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s] OK
- checking whether the namespace can be unloaded cleanly ... [4s] OK
- checking loading without being on the library search path ... [4s] OK
- checking whether startup messages can be suppressed ... [4s] OK
- checking use of S3 registration ... 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 ... [27s] OK
- checking Rd files ... [3s] 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 ... [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 ... [8s] ERROR
Running examples in 'teal.modules.clinical-Ex.R' failed
The error most likely occurred in:
> ### Name: tm_a_gee
> ### Title: teal Module: Generalized Estimating Equations (GEE) analysis
> ### Aliases: tm_a_gee
>
> ### ** Examples
>
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
> data <- teal_data()
> data <- within(data, {
+ ADSL <- tmc_ex_adsl
+ ADQS <- tmc_ex_adqs %>%
+ filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+ mutate(
+ AVISIT = as.factor(AVISIT),
+ AVISITN = rank(AVISITN) %>%
+ as.factor() %>%
+ as.numeric() %>%
+ as.factor(),
+ AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
+ ) %>%
+ droplevels()
+ })
> datanames <- c("ADSL", "ADQS")
> datanames(data) <- datanames
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
`teal_data`. See ?names.teal_data
> join_keys(data) <- default_cdisc_join_keys[datanames]
>
> app <- init(
+ data = data,
+ modules = modules(
+ tm_a_gee(
+ label = "GEE",
+ dataname = "ADQS",
+ aval_var = choices_selected("AVALBIN", fixed = TRUE),
+ id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+ arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
+ visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+ paramcd = choices_selected(
+ choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
+ selected = "FKSI-FWB"
+ ),
+ cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
+ )
+ )
+ )
Initializing tm_a_gee (prototype)
Error in as.list(data@env) :
no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [11s] OK
Running 'testthat.R' [11s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [16s] OK
- checking PDF version of manual ... [30s] OK
- checking HTML version of manual ... [26s] OK
- DONE
Status: 1 ERROR