Check results for 'admiralophtha'

using R Under development (unstable) (2026-01-13 r89301)
using platform: x86_64-pc-linux-gnu
R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
running under: Fedora Linux 42 (Workstation Edition)
using session charset: UTF-8
using option ‘--no-stop-on-test-error’
checking for file ‘admiralophtha/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘admiralophtha’ version ‘1.3.0’
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 ‘admiralophtha’ can be installed ... [18s/23s] OK See the install log for details.
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 ... OK
checking whether the package can be loaded with stated dependencies ... OK
checking whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... 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 ... OK
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd line widths ... 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 ... 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 ... ERROR Running examples in ‘admiralophtha-Ex.R’ failed The error most likely occurred in: > ### Name: derive_var_studyeye > ### Title: Derive Study Eye > ### Aliases: derive_var_studyeye > ### Keywords: der_adsl > > ### ** Examples > > library(tibble) > library(admiral) > > adsl <- tribble( + ~STUDYID, ~USUBJID, + "XXX001", "P01", + "XXX001", "P02", + "XXX001", "P03", + "XXX001", "P04", + "XXX001", "P05" + ) > > sc <- tribble( + ~STUDYID, ~USUBJID, ~SCTESTCD, ~SCSTRESC, + "XXX001", "P01", "FOCID", "OS", + "XXX001", "P01", "ACOHORT", "COHORT1", + "XXX001", "P02", "FOCID", "OD", + "XXX001", "P02", "ACOHORT", "COHORT3", + "XXX001", "P04", "FOCID", "OU", + "XXX001", "P05", "FOCID", "OD", + "XXX001", "P06", "FOCID", "OS" + ) > > derive_var_studyeye(adsl, sc) Error in left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship) : could not find function "left_join" Calls: derive_var_studyeye ... tryCatch -> tryCatchList -> tryCatchOne -> doTryCatch Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... ERROR Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(admiralophtha) > > test_check("admiralophtha") Saving _problems/test-derive_var_studyeye-29.R Saving _problems/test-derive_var_studyeye-66.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 8 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-derive_var_studyeye.R:26:3'): derive_var_studyeye Test 1: STUDYEYE is derived correctly in normal case ── Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join" Backtrace: ▆ 1. ├─expected_output1 %>% select(-STUDYEYE) %>% ... at test-derive_var_studyeye.R:26:3 2. ├─admiralophtha::derive_var_studyeye(., sc1) 3. │ ├─... %>% mutate(STUDYEYE = seye_cat(STUDYEYE)) 4. │ └─admiral::derive_vars_merged(...) 5. │ └─base::tryCatch(...) 6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 9. └─dplyr::mutate(., STUDYEYE = seye_cat(STUDYEYE)) ── Error ('test-derive_var_studyeye.R:63:3'): derive_var_studyeye Test 2: STUDYEYE is derived correctly when parsing non-standard SCTESTCD ── Error in `left_join(dataset, add_data, by = vars2chr(by_vars), relationship = relationship)`: could not find function "left_join" Backtrace: ▆ 1. ├─expected_output2 %>% select(-STUDYEYE) %>% ... at test-derive_var_studyeye.R:63:3 2. ├─admiralophtha::derive_var_studyeye(., sc2, "STDEYE") 3. │ ├─... %>% mutate(STUDYEYE = seye_cat(STUDYEYE)) 4. │ └─admiral::derive_vars_merged(...) 5. │ └─base::tryCatch(...) 6. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 7. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 8. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 9. └─dplyr::mutate(., STUDYEYE = seye_cat(STUDYEYE)) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 8 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [25s/26s] OK
checking PDF version of manual ... OK
checking HTML version of manual ... OK
checking for non-standard things in the check directory ... OK
checking for detritus in the temp directory ... OK
DONE

Status: 2 ERRORs