• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘clinUtils/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘clinUtils’ version ‘0.2.2’
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 serialization versions ... OK
• checking whether package ‘clinUtils’ 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 ... [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 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 ... [8s/10s] OK
• checking Rd files ... [0s/1s] 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 ... [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 ... [1s/1s] ERROR Running examples in ‘clinUtils-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compareTables > ### Title: Compare tables > ### Aliases: compareTables > > ### ** Examples > > ## Example 1 > # In this case the referenceVar 'a' is the same > # the comparison highlights only as change in the variables 'c' and 'd' > newData <- data.frame( + "a" = c(1, 2, 3, 4), + "b" = c(5, 6, 7, 8), + "c" = rep(1, 4), + "d" = rep(2, 4) + ) > oldData <- data.frame( + "a" = c(1, 2, 3, 4), + "b" = c(3, 4, 7, 8), + "c" = rep(2, 4), + "d" = rep(1, 4) + ) > compareTables( + newData = newData, + oldData = oldData, + referenceVars = "a", + changeableVars = c("c", "d") + ) Error in `[.data.table`(diffDataDetailed, , `:=`((colsDiff), { :   attempt access index 5/5 in VECTOR_ELT Calls: compareTables ... exportDiffData -> formatDetailsComparison -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [10s/13s] ERROR   Running ‘testthat.R’ [10s/12s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(clinUtils)   >   > test_check("clinUtils")   Saving _problems/test_compareTables-121.R   [ FAIL 6 | WARN 1 | SKIP 2 | PASS 289 ]      ══ Skipped tests (2) ═══════════════════════════════════════════════════════════   • On CRAN (2): 'test_getClinDT.R:838:7', 'test_getClinDT.R:855:7'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_compareTables.R:118:7'): When reference columns are not specified, all columns are used as the reference ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_equal(...) at test_compareTables.R:118:7    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. └─clinUtils::compareTables(newData, oldData)    5. └─clinUtils::exportDiffData(...)    6. └─clinUtils:::formatDetailsComparison(...)    7. ├─...[]    8. └─data.table:::`[.data.table`(...)   ── Error ('test_compareTables.R:266:7'): The difference dataset is exported correctly to an interactive table ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_silent(res <- exportDiffData(diffData)) at test_compareTables.R:266:7     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─clinUtils::exportDiffData(diffData)    10. └─clinUtils:::formatDetailsComparison(...)    11. ├─...[]    12. └─data.table:::`[.data.table`(...)   ── Error ('test_compareTables.R:292:7'): The merged product of the difference dataset and new dataset is exported correctly to an interactive table ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_silent(res <- exportDiffData(diffData, newDataDiff = newDataDiff)) at test_compareTables.R:292:7     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─clinUtils::exportDiffData(diffData, newDataDiff = newDataDiff)    10. └─clinUtils:::formatDetailsComparison(...)    11. ├─...[]    12. └─data.table:::`[.data.table`(...)   ── Error ('test_compareTables.R:316:7'): The merged product of the difference dataset and old dataset is exported correctly to an interactive table ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_silent(...) at test_compareTables.R:316:7     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─clinUtils::compareTables(...)    10. └─clinUtils::exportDiffData(...)    11. └─clinUtils:::formatDetailsComparison(...)    12. ├─...[]    13. └─data.table:::`[.data.table`(...)   ── Error ('test_compareTables.R:357:7'): A placeholder is displayed in the interactive table if there is no difference between the new and old data ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 3/3 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_silent(res <- exportDiffData(diffData)) at test_compareTables.R:357:7     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─clinUtils::exportDiffData(diffData)    10. └─clinUtils:::formatDetailsComparison(...)    11. ├─...[]    12. └─data.table:::`[.data.table`(...)   ── Error ('test_compareTables.R:378:7'): Column names are renamed correctly in the interactive difference data table ──   Error in ``[.data.table`(diffDataDetailed, , `:=`((colsDiff), { if (all(`Comparison type` == "Addition")) { as.list(rep("+", length(cols))) } else if (all(`Comparison type` == "Removal")) { as.list(rep("-", length(cols))) } else { lapply(.SD, function(x) { ifelse(uniqueN(x) == 1, "==", "!=") }) } }), .SDcols = cols, by = referenceVars)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_silent(...) at test_compareTables.R:378:7     2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)     3. │ ├─testthat (local) .capture(...)     4. │ │ ├─withr::with_output_sink(...)     5. │ │ │ └─base::force(code)     6. │ │ ├─base::withCallingHandlers(...)     7. │ │ └─base::withVisible(code)     8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     9. └─clinUtils::exportDiffData(...)    10. └─clinUtils:::formatDetailsComparison(...)    11. ├─...[]    12. └─data.table:::`[.data.table`(...)      [ FAIL 6 | WARN 1 | SKIP 2 | PASS 289 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [10s/13s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘clinUtils-vignette.Rmd’ using rmarkdown Quitting from clinUtils-vignette.Rmd:339-366 [compareTables] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 8/8 in VECTOR_ELT --- Backtrace:     ▆  1. └─clinUtils::compareTables(...)  2. └─clinUtils::exportDiffData(...)  3. └─clinUtils:::formatDetailsComparison(...)  4. ├─...[]  5. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'clinUtils-vignette.Rmd' failed with diagnostics: attempt access index 8/8 in VECTOR_ELT --- failed re-building ‘clinUtils-vignette.Rmd’ SUMMARY: processing the following file failed:   ‘clinUtils-vignette.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [3s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs