* using log directory 'd:/Rcompile/CRANpkg/local/4.5/Tendril.Rcheck' * using R version 4.5.2 (2025-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'Tendril/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Tendril' version '2.0.4' * 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 'Tendril' can be installed ... OK * 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 ... [0s] OK * checking whether the package can be loaded with stated dependencies ... [0s] OK * checking whether the package can be unloaded cleanly ... [0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s] OK * checking whether the namespace can be unloaded cleanly ... [0s] OK * checking loading without being on the library search path ... [0s] 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 ... [4s] OK * checking Rd files ... [1s] NOTE checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly * 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 ... [2s] ERROR Running examples in 'Tendril-Ex.R' failed The error most likely occurred in: > ### Name: Tendril > ### Title: Tendril > ### Aliases: Tendril > > ### ** Examples > > data <- Tendril(mydata = TendrilData, + rotations = Rotations, + AEfreqThreshold=9, + Tag = "Comment", + Treatments = c("placebo", "active"), + Unique.Subject.Identifier = "subjid", + Terms = "ae", + Treat = "treatment", + StartDay = "day", + SubjList = SubjList, + SubjList.subject = "subjid", + SubjList.treatment = "treatment" + ) Error: ! `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... [9s] ERROR Running 'testthat.R' [7s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(Tendril) > > test_check("Tendril") Saving _problems/test_plot_timeseries-21.R Saving _problems/test_tendrilData-251.R Saving _problems/test_tendrilData-337.R Saving _problems/test_tendrilData-365.R Saving _problems/test_tendrilData-395.R Saving _problems/test_tendrilData-426.R Saving _problems/test_tendrilData-458.R Saving _problems/test_tendrilData-492.R Saving _problems/test_tendrilData-522.R Saving _problems/test_tendrilPerm-25.R Saving _problems/test_tendrilPerm-137.R [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_plot_timeseries.R:8:5'): Creation of plot timeseries ─────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test_plot_timeseries.R:7:3 2. │ └─base::withCallingHandlers(...) 3. └─Tendril::Tendril(...) at test_plot_timeseries.R:8:5 4. └─Tendril:::dataSetup(...) 5. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 6. └─dplyr:::lazy_defunct("rename", hint = FALSE) 7. └─lifecycle::deprecate_stop(...) 8. └─lifecycle:::deprecate_stop0(msg) 9. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:238:5'): tendril_result_correct ────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:238:5 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:324:3'): tendril_result_correct_filter_double_events ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:324:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:356:3'): tendril_result_no_SubjList_supplied ───── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:356:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:384:3'): tendril_result_no_SubjList_supplied_single_rotation_factor ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:384:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:413:3'): tendril_proportional_rotation_factor ──── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:413:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:445:3'): tendril_error_event_after_dropout ─────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilData.R:445:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:478:3'): tendril_check_correct_imbalance_and_variable_rotation ── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:478:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilData.R:509:3'): tendril_check_for_presence_of_term ────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. └─Tendril::Tendril(...) at test_tendrilData.R:509:3 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) ── Error ('test_tendrilPerm.R:14:5'): input_perm_valid ───────────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilPerm.R:13:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) at test_tendrilPerm.R:14:5 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) ── Error ('test_tendrilPerm.R:126:5'): output_perm_valid ─────────────────────── Error: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test_tendrilPerm.R:125:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─Tendril::Tendril(...) at test_tendrilPerm.R:126:5 7. └─Tendril:::dataSetup(...) 8. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 9. └─dplyr:::lazy_defunct("rename", hint = FALSE) 10. └─lifecycle::deprecate_stop(...) 11. └─lifecycle:::deprecate_stop0(msg) 12. └─rlang::cnd_signal(...) [ FAIL 11 | WARN 0 | SKIP 0 | PASS 12 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [4s] ERROR Error(s) in re-building vignettes: --- re-building 'TendrilUsage.Rmd' using rmarkdown Quitting from TendrilUsage.Rmd:28-51 [example_plot] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. --- Backtrace: ▆ 1. └─Tendril::Tendril(...) 2. └─Tendril:::dataSetup(...) 3. └─dplyr::rename_(data, Unique.Subject.Identifier = Unique.Subject.Identifier) 4. └─dplyr:::lazy_defunct("rename", hint = FALSE) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'TendrilUsage.Rmd' failed with diagnostics: `rename_()` was deprecated in dplyr 0.7.0 and is now defunct. ℹ Please use `rename()` instead. --- failed re-building 'TendrilUsage.Rmd' SUMMARY: processing the following file failed: 'TendrilUsage.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [33s] OK * checking HTML version of manual ... [7s] OK * DONE Status: 3 ERRORs, 1 NOTE