• using R Under development (unstable) (2025-02-02 r87676)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.6 (1+b1)     Debian flang-new version 19.1.6 (1+b1)
• running under: Debian GNU/Linux trixie/sid
• 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 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 ‘teal.modules.clinical’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [5s/7s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/8s] OK
• checking whether the package can be unloaded cleanly ... [5s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [5s/8s] OK
• checking loading without being on the library search path ... [5s/6s] OK
• checking whether startup messages can be suppressed ... [5s/7s] 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 ... [55s/70s] OK
• checking Rd files ... [2s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   split_choices.Rd: choices_selected   template_coxreg_m.Rd: control_coxreg   template_coxreg_u.Rd: control_coxreg   tm_t_tte.Rd: data_extract_spec, coxph_pairwise, surv_timepoint,     surv_time Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• 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/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 ... [6s/7s] ERROR Running examples in ‘teal.modules.clinical-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [13s/16s] OK   Running ‘testthat.R’ [12s/16s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [17s/28s] OK
• checking PDF version of manual ... [13s/16s] OK
• checking HTML version of manual ... [9s/13s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE