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CRAN Package Check Results for Package reportRmd

Last updated on 2026-10-24 17:51:41 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.3 21.78 244.39 266.17 NOTE
r-devel-linux-x86_64-debian-gcc 0.1.3 14.48 155.85 170.33 ERROR
r-devel-linux-x86_64-fedora-clang 0.1.3 17.00 167.65 184.65 ERROR
r-devel-linux-x86_64-fedora-gcc 0.1.3 16.00 169.61 185.61 ERROR
r-devel-windows-x86_64 0.1.3 25.00 258.00 283.00 OK
r-patched-linux-x86_64 0.1.3 21.93 232.05 253.98 OK
r-release-linux-x86_64 0.1.3 22.74 228.85 251.59 OK
r-release-macos-arm64 0.1.3 5.00 77.00 82.00 OK
r-release-macos-x86_64 0.1.3 15.00 348.00 363.00 OK
r-release-windows-x86_64 0.1.3 23.00 254.00 277.00 OK
r-oldrel-macos-arm64 0.1.3 5.00 69.00 74.00 OK
r-oldrel-macos-x86_64 0.1.3 14.00 150.00 164.00 OK
r-oldrel-windows-x86_64 0.1.3 32.00 316.00 348.00 OK

Check Details

Version: 0.1.3
Check: Rd contents
Result: NOTE Rd files without \usage: ‘ggkmcif2_2025.Rd’ \arguments should not be documented without \usage. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: examples
Result: ERROR Running examples in ‘reportRmd-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rm_survtime > ### Title: Display survival rates and events for specified times > ### Aliases: rm_survtime > > ### ** Examples > > # Kaplan-Mieir survival probabilities with time displayed in years > data("pembrolizumab") > rm_survtime(data=pembrolizumab,time='os_time',status='os_status', + strata="cohort",type='KM',survtimes=seq(12,72,12), + survtimesLbls=seq(1,6,1), + survtimeunit='years') <table class="table table" style="margin-left: auto; margin-right: auto; margin-left: auto; margin-right: auto;"> <thead> <tr> <th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;"> Time (years) </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> At Risk </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Events </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Censored </th> <th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;"> Survival Rate (95% CI) </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> Overall </td> <td style="text-align:right;"> 94 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 48 </td> <td style="text-align:right;"> 44 </td> <td style="text-align:right;"> 2 </td> <td style="text-align:right;"> 0.53 (0.44, 0.64) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 24 </td> <td style="text-align:right;"> 17 </td> <td style="text-align:right;"> 7 </td> <td style="text-align:right;"> 0.33 (0.24, 0.44) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 36 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 3 </td> <td style="text-align:right;"> 21 </td> <td style="text-align:right;"> 0.28 (0.20, 0.40) </td> </tr> <tr> <td style="text-align:left;"> A </td> <td style="text-align:right;"> 16 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 10 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0.38 (0.20, 0.71) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 2 </td> <td style="text-align:right;"> 3 </td> <td style="text-align:right;"> 0.23 (0.09, 0.59) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 36 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 0.23 (0.09, 0.59) </td> </tr> <tr> <td style="text-align:left;"> B </td> <td style="text-align:right;"> 18 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 5 </td> <td style="text-align:right;"> 12 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 0.32 (0.16, 0.64) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 4 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 0.06 (9.6e-03, 0.42) </td> </tr> <tr> <td style="text-align:left;"> C </td> <td style="text-align:right;"> 18 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 11 </td> <td style="text-align:right;"> 7 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0.61 (0.42, 0.88) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 8 </td> <td style="text-align:right;"> 3 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0.44 (0.27, 0.74) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 36 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 2 </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.31 (0.15, 0.64) </td> </tr> <tr> <td style="text-align:left;"> D </td> <td style="text-align:right;"> 12 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 8 </td> <td style="text-align:right;"> 4 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0.67 (0.45, 0.99) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 2 </td> <td style="text-align:right;"> 0.67 (0.45, 0.99) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 36 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 6 </td> <td style="text-align:right;"> 0.67 (0.45, 0.99) </td> </tr> <tr> <td style="text-align:left;"> E </td> <td style="text-align:right;"> 30 </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> <td style="text-align:right;"> </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 12 </td> <td style="text-align:right;"> 18 </td> <td style="text-align:right;"> 11 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 0.63 (0.48, 0.83) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 24 </td> <td style="text-align:right;"> 9 </td> <td style="text-align:right;"> 8 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 0.34 (0.20, 0.57) </td> </tr> <tr> <td style="text-align:left;padding-left: 2em;" indentlevel="1"> 36 </td> <td style="text-align:right;"> 0 </td> <td style="text-align:right;"> 1 </td> <td style="text-align:right;"> 8 </td> <td style="text-align:right;"> 0.29 (0.15, 0.53) </td> </tr> </tbody> </table>> > # Cox Proportional Hazards survivial probabilities > rm_survtime(data=pembrolizumab,time='os_time',status='os_status', + strata="cohort",type='PH',survtimes=seq(12,72,12),survtimeunit='months') Error in a$specials[[i]] : subscript out of bounds Calls: rm_survtime ... survfit.coxph -> model.matrix.coxph -> delete.response -> off Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘reportRmd.Rmd’ using rmarkdown Quitting from reportRmd.Rmd:504-507 [unnamed-chunk-48] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `a$specials[[i]]`: ! subscript out of bounds --- Backtrace: ▆ 1. └─reportRmd::rm_survtime(...) 2. ├─survival::survfit(...) 3. └─survival:::survfit.coxph(...) 4. └─survival:::model.matrix.coxph(object, data = mf) 5. └─stats::delete.response(object$terms) 6. └─stats (local) off(a$specials[[i]]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'reportRmd.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘reportRmd.Rmd’ SUMMARY: processing the following file failed: ‘reportRmd.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: tests
Result: ERROR Running ‘testthat.R’ [8s/20s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(reportRmd) > > test_check("reportRmd") Using MC sim. Use set.seed() prior to function for reproducible results. Using MC sim. Use set.seed() prior to function for reproducible results. Saving _problems/test_calculations-348.R boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ── Expected `output[, 2]` to equal `est`. Differences: actual | expected [1] NA | NA [1] [2] "Reference" | "Reference" [2] [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3] [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4] [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5] [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.1.3
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/17s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(reportRmd) > > test_check("reportRmd") Using MC sim. Use set.seed() prior to function for reproducible results. Using MC sim. Use set.seed() prior to function for reproducible results. Saving _problems/test_calculations-348.R boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_calculations.R:348:3'): rm_mvsum outputs glmer binomial model with ORs correctly ── Expected `output[, 2]` to equal `est`. Differences: actual | expected [1] NA | NA [1] [2] "Reference" | "Reference" [2] [3] "0.37 (0.20, 0.68)" - "0.37 (0.20, 0.67)" [3] [4] "0.32 (0.17, 0.61)" | "0.32 (0.17, 0.61)" [4] [5] "0.21 (0.09, 0.48)" - "0.21 (0.09, 0.47)" [5] [ FAIL 1 | WARN 3 | SKIP 0 | PASS 66 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

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