• using R version 4.5.2 Patched (2026-01-31 r89374)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• 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 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 ‘Tendril’ 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 ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/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 ... [6s/9s] OK
• checking Rd files ... [0s/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 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/2s] ERROR Running examples in ‘Tendril-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### 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 ... [4s/6s] ERROR   Running ‘testthat.R’ [4s/5s] 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 ───────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ──────────────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ──   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ─────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ──   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ───────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ──   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ──────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ─────────────────────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ───────────────────────   <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>   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 ... [2s/2s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘TendrilUsage.Rmd’ using rmarkdown Quitting from TendrilUsage.Rmd:28-51 [example_plot] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/lifecycle_error_deprecated> 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 ... [4s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs, 1 NOTE