Pull Request

Closes #44

Part of https://github.com/insightsengineering/coredev-tasks/issues/546

Upstream bug: https://github.com/r-lib/pkgdepends/issues/367

Changes description:

Removes sources links that include "src/contrib/Archive"
- When {pkgdepends} attempts to download the tarball, it will try all sources and archive-based sources are only source-code
Re-downloads tarball using mirror.
- Last attempt to explicitly use ppm snapshot mirror

Testing

Install or load this branch
- renv::install("insightsengineering/verdepcheck@fix-random-download%40main")
Clone {tmc}
- checkout 546-fix-verdepcheck@main branch
Run all strategies:
- verdepcheck::min_cohort_deps_check("/path/to/tmc")
- verdepcheck::min_isolated_deps_check("/path/to/tmc")
- verdepcheck::release_deps_check("/path/to/tmc")
- verdepcheck::max_deps_check("/path/to/tmc")

Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  ------------------------
R/check.R                            73      73  0.00%    26-220
R/deps_installation_proposal.R      139     139  0.00%    58-269
R/desc_utils.R                       71      43  39.44%   15-32, 108, 117-168, 186
R/get_ref.R                         239     238  0.42%    13-473, 492-535
R/solve.R                            84      84  0.00%    9-170
R/utils.R                            66      42  36.36%   3-23, 41, 47, 57-104
TOTAL                               672     619  7.89%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
R/check.R       +36     +36  +100.00%
TOTAL           +36     +36  -0.45%

Results for commit: 9374e2abf7bc7e40dbe5a2cd64fc9a7f0aa91655

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

Unit Tests Summary

1 files 4 suites 1s :stopwatch: 41 tests 13 :white_check_mark: 28 :zzz: 0 :x: 94 runs 65 :white_check_mark: 29 :zzz: 0 :x:

Results for commit 9374e2ab.

:recycle: This comment has been updated with latest results.

This is what I get

> verdepcheck::min_cohort_deps_check(".")
✔ Loading metadata database ... done
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc20ee461a
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc7c785e66
✔ Updated metadata database: 5.22 MB in 7 files.                                 
✔ Updating metadata database ... done                                      
Error : ! Could not solve package dependencies:                             
* deps::C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc20ee461a:
  * Can't install dependency rtables=insightsengineering/rtables (>= 0.6.7.9003)
  * Can't install dependency rtables=insightsengineering/rtables
* rtables=insightsengineering/rtables: Can't install dependency formatters (>= 0.5.7.9000)

we are trying to pull rtables from github, but rtables also should get formatters from github : )

I see the same for min_isolated_deps_check

> verdepcheck::min_isolated_deps_check(".")
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc1f0d5dfc
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc6a102857
Error : ! Could not solve package dependencies:                                  
* deps::C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc1f0d5dfc: Can't install dependency rtables=insightsengineering/rtables (>= 0.6.7.9003)
* rtables=insightsengineering/rtables: Can't install dependency formatters (>= 0.5.7.9000)

It's caused by this rtables dependency on formatters. Should be resolved once 0.5.7 formatters is released to CRAN

Last two give similar issues

> verdepcheck::release_deps_check(".")
✔ Updated metadata database: 2.20 MB in 2 files.                          
✔ Updating metadata database ... done                                     
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc10a36729
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc26fd7ec9
Error : ! Could not solve package dependencies:                            
* deps::C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc10a36729: Can't install dependency rtables (>= 0.6.7.9003)
> verdepcheck::max_deps_check(".")
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc10285add
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc64711b56
Error : ! Could not solve package dependencies:                              
* deps::C:\Users\kosinsm4\AppData\Local\Temp\RtmpUp5Hbc\file62bc10285add:
  * Can't install dependency rtables (>= 0.6.7.9003)
  * Can't install dependency insightsengineering/tern
  * Can't install dependency insightsengineering/rlistings
  * Can't install dependency insightsengineering/rtables
* insightsengineering/tern: Can't install dependency formatters (>= 0.5.7.9000)
* insightsengineering/rlistings: Can't install dependency formatters (>= 0.5.7.9000)
* insightsengineering/rtables: Can't install dependency formatters (>= 0.5.7.9000)

My bad, please try using the 546-fix-verdepcheck@main branch that:

Doesn't have the most recent change
It also has a fix for a package version

we are trying to pull rtables from github, but rtables also should get formatters from github : )

This is a slippery slope as we would have to include secondary dependencies github repos in the DESCRIPTION file and that would grow very fast. (would we do that all the 188 primary and secondary+ dependency?)

We have to stop somewhere and for now we are only keeping primary. There's an argument though to include secondary insightengineering deps :thinking:

Retried with 546-fix-verdepcheck@main branch for teal.modules.clinical

Looks like I dont have LaTeX but everything else went fine for the first strategy that I tried

verdepcheck::min_cohort_deps_check(".")
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\RtmpkZuXze\file5ebc52714aaf
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\RtmpkZuXze\file5ebc49f57c33
✔ Updated metadata database: 5.23 MB in 8 files.                           
✔ Updating metadata database ... done                                      
ℹ Getting 180 pkgs (185.16 MB), 8 (25.09 MB) cached                         
✔ Got assertthat 0.2.1 (i386+x86_64-w64-mingw32) (56.02 kB)                                    
✔ Got base64enc 0.1-3 (i386+x86_64-w64-mingw32) (32.80 kB)                                     
✔ Got crul 1.4.2 (i386+x86_64-w64-mingw32) (676.83 kB)                                         
✔ Got abind 1.4-5 (i386+x86_64-w64-mingw32) (64.68 kB)                                         
✔ Got anytime 0.3.9 (i386+x86_64-w64-mingw32) (715.95 kB)                                      
✔ Got askpass 1.2.0 (i386+x86_64-w64-mingw32) (74.42 kB)                                       
✔ Got backports 1.4.1 (i386+x86_64-w64-mingw32) (105.18 kB)                                    
✔ Got brio 1.1.4 (i386+x86_64-w64-mingw32) (40.80 kB)                                          
✔ Got broom 1.0.5 (i386+x86_64-w64-mingw32) (1.94 MB)                                          
✔ Got commonmark 1.9.1 (i386+x86_64-w64-mingw32) (141.95 kB)                                   
✔ Got crayon 1.5.2 (i386+x86_64-w64-mingw32) (165.39 kB)                                       
✔ Got curl 5.2.1 (i386+x86_64-w64-mingw32) (3.22 MB)                                           
✔ Got data.table 1.15.4 (i386+x86_64-w64-mingw32) (2.41 MB)                                    
✔ Got fansi 1.0.6 (i386+x86_64-w64-mingw32) (320.43 kB)                                        
✔ Got fastmap 1.1.1 (i386+x86_64-w64-mingw32) (133.42 kB)                                      
✔ Got farver 2.1.1 (i386+x86_64-w64-mingw32) (1.51 MB)                                         
✔ Got flextable 0.9.5 (i386+x86_64-w64-mingw32) (1.38 MB)                                      
✔ Got glue 1.7.0 (i386+x86_64-w64-mingw32) (163.13 kB)                                         
✔ Got gridExtra 2.3 (i386+x86_64-w64-mingw32) (1.11 MB)                                        
✔ Got gtable 0.3.4 (i386+x86_64-w64-mingw32) (227.93 kB)                                       
✔ Got haven 2.5.4 (i386+x86_64-w64-mingw32) (755.93 kB)                                        
✔ Got magrittr 2.0.3 (i386+x86_64-w64-mingw32) (229.11 kB)                                     
✔ Got MatrixModels 0.5-3 (i386+x86_64-w64-mingw32) (422.45 kB)                                 
✔ Got memoise 2.0.1 (i386+x86_64-w64-mingw32) (51.62 kB)                                       
✔ Got mime 0.12 (i386+x86_64-w64-mingw32) (40.68 kB)                                           
✔ Got minqa 1.2.6 (i386+x86_64-w64-mingw32) (438.21 kB)                                        
✔ Got shinyWidgets 0.8.5 (i386+x86_64-w64-mingw32) (1.54 MB)                                   
✔ Got rbibutils 2.2.16 (i386+x86_64-w64-mingw32) (759.04 kB)                                   
✔ Got shinyvalidate 0.1.3 (i386+x86_64-w64-mingw32) (193.77 kB)                                
✔ Got sourcetools 0.1.7-1 (i386+x86_64-w64-mingw32) (126.84 kB)                                
✔ Got MESS 0.5.12 (i386+x86_64-w64-mingw32) (3.58 MB)                                          
✔ Got ragg 1.3.0 (i386+x86_64-w64-mingw32) (1.91 MB)                                           
✔ Got systemfonts 1.0.6 (i386+x86_64-w64-mingw32) (1.30 MB)                                    
✔ Got teal.code 0.5.0 (i386+x86_64-w64-mingw32) (204.73 kB)                                    
✔ Got teal 0.15.2 (i386+x86_64-w64-mingw32) (2.19 MB)                                          
✔ Got urltools 1.7.3 (i386+x86_64-w64-mingw32) (612.00 kB)                                     
✔ Got utf8 1.2.4 (i386+x86_64-w64-mingw32) (149.20 kB)                                         
✔ Got uuid 1.2-0 (i386+x86_64-w64-mingw32) (51.47 kB)                                          
✔ Got vctrs 0.6.5 (i386+x86_64-w64-mingw32) (1.34 MB)                                          
✔ Got viridisLite 0.4.2 (i386+x86_64-w64-mingw32) (1.30 MB)                                    
✔ Got crosstalk 1.2.1 (i386+x86_64-w64-mingw32) (416.80 kB)                                    
✔ Got diffobj 0.3.5 (i386+x86_64-w64-mingw32) (1.03 MB)                                        
✔ Got digest 0.6.35 (i386+x86_64-w64-mingw32) (217.29 kB)                                      
✔ Got cowplot 1.1.3 (i386+x86_64-w64-mingw32) (1.38 MB)                                        
✔ Got dplyr 1.1.4 (i386+x86_64-w64-mingw32) (1.59 MB)                                          
✔ Got DT 0.33 (i386+x86_64-w64-mingw32) (2.03 MB)                                              
✔ Got generics 0.1.3 (i386+x86_64-w64-mingw32) (83.89 kB)                                      
✔ Got gfonts 0.2.0 (i386+x86_64-w64-mingw32) (2.87 MB)                                         
✔ Got ggformula 0.12.0 (i386+x86_64-w64-mingw32) (1.83 MB)                                     
✔ Got nestcolor 0.1.2 (i386+x86_64-w64-mingw32) (441.81 kB)                                    
✔ Got nloptr 2.0.3 (i386+x86_64-w64-mingw32) (1.01 MB)                                         
✔ Got numDeriv 2016.8-1.1 (i386+x86_64-w64-mingw32) (117.50 kB)                                
✔ Got officer 0.6.5 (i386+x86_64-w64-mingw32) (1.73 MB)                                        
✔ Got R.methodsS3 1.8.2 (i386+x86_64-w64-mingw32) (85.30 kB)                                   
✔ Got RColorBrewer 1.1-3 (i386+x86_64-w64-mingw32) (54.57 kB)                                  
✔ Got quadprog 1.5-8 (i386+x86_64-w64-mingw32) (36.87 kB)                                      
✔ Got R.cache 0.16.0 (i386+x86_64-w64-mingw32) (114.60 kB)                                     
✔ Got stringr 1.5.1 (i386+x86_64-w64-mingw32) (324.14 kB)                                      
✔ Got quantreg 5.97 (i386+x86_64-w64-mingw32) (1.57 MB)                                        
✔ Got vroom 1.6.5 (i386+x86_64-w64-mingw32) (1.26 MB)                                          
✔ Got waldo 0.5.2 (i386+x86_64-w64-mingw32) (106.31 kB)                                        
✔ Got shinytest2 0.3.1 (i386+x86_64-w64-mingw32) (3.16 MB)                                     
✔ Got websocket 1.4.1 (i386+x86_64-w64-mingw32) (2.80 MB)                                      
✔ Got ellipsis 0.3.2 (i386+x86_64-w64-mingw32) (40.88 kB)                                      
✔ Got estimability 1.5 (i386+x86_64-w64-mingw32) (54.12 kB)                                    
✔ Got emmeans 1.10.1 (i386+x86_64-w64-mingw32) (2.22 MB)                                       
✔ Got htmltools 0.5.8.1 (i386+x86_64-w64-mingw32) (364.88 kB)                                  
✔ Got htmlwidgets 1.6.4 (i386+x86_64-w64-mingw32) (814.05 kB)                                  
✔ Got httpcode 0.3.0 (i386+x86_64-w64-mingw32) (35.56 kB)                                      
✔ Got httpuv 1.6.15 (i386+x86_64-w64-mingw32) (977.03 kB)                                      
✔ Got mosaicCore 0.9.4.0 (i386+x86_64-w64-mingw32) (200.94 kB)                                 
✔ Got munsell 0.5.1 (i386+x86_64-w64-mingw32) (246.01 kB)                                      
✔ Got mvtnorm 1.2-4 (i386+x86_64-w64-mingw32) (755.23 kB)                                      
✔ Got pbkrtest 0.5.2 (i386+x86_64-w64-mingw32) (194.83 kB)                                     
✔ Got mmrm 0.3.11 (i386+x86_64-w64-mingw32) (2.61 MB)                                          
✔ Got rematch2 2.1.2 (i386+x86_64-w64-mingw32) (49.10 kB)                                      
✔ Got rlang 1.1.3 (i386+x86_64-w64-mingw32) (1.61 MB)                                          
✔ Got rmarkdown 2.26 (i386+x86_64-w64-mingw32) (2.70 MB)                                       
✔ Got textshaping 0.3.7 (i386+x86_64-w64-mingw32) (1.19 MB)                                    
✔ Got rlistings 0.2.8 (i386+x86_64-w64-mingw32) (3.22 MB)                                      
✔ Got testthat 3.2.1.1 (i386+x86_64-w64-mingw32) (2.23 MB)                                     
✔ Got forcats 1.0.0 (i386+x86_64-w64-mingw32) (429.40 kB)                                      
✔ Got foreach 1.5.2 (i386+x86_64-w64-mingw32) (150.03 kB)                                      
✔ Got colorspace 2.1-0 (i386+x86_64-w64-mingw32) (2.64 MB)                                     
✔ Got globals 0.16.3 (i386+x86_64-w64-mingw32) (110.63 kB)                                     
✔ Got iterators 1.0.14 (i386+x86_64-w64-mingw32) (355.59 kB)                                   
✔ Got jquerylib 0.1.4 (i386+x86_64-w64-mingw32) (526.15 kB)                                    
✔ Got jsonlite 1.8.8 (i386+x86_64-w64-mingw32) (1.11 MB)                                       
✔ Got stringi 1.8.3 (i386+x86_64-w64-mingw32) (15.01 MB)                                       
✔ Got pingr 2.0.3 (i386+x86_64-w64-mingw32) (60.49 kB)                                         
✔ Got pkgbuild 1.4.4 (i386+x86_64-w64-mingw32) (205.26 kB)                                     
✔ Got pkgconfig 2.0.3 (i386+x86_64-w64-mingw32) (23.00 kB)                                     
✔ Got pkgload 1.3.4 (i386+x86_64-w64-mingw32) (182.59 kB)                                      
✔ Got plotly 4.10.4 (i386+x86_64-w64-mingw32) (3.24 MB)                                        
✔ Got scales 1.3.0 (i386+x86_64-w64-mingw32) (721.01 kB)                                       
✔ Got selectr 0.4-2 (i386+x86_64-w64-mingw32) (497.94 kB)                                      
✔ Got shape 1.4.6.1 (i386+x86_64-w64-mingw32) (755.56 kB)                                      
✔ Got shinybusy 0.3.3 (i386+x86_64-w64-mingw32) (624.45 kB)                                    
✔ Got xtable 1.8-4 (i386+x86_64-w64-mingw32) (711.34 kB)                                       
✔ Got yaml 2.3.8 (i386+x86_64-w64-mingw32) (116.77 kB)                                         
✔ Got zip 2.3.1 (i386+x86_64-w64-mingw32) (432.09 kB)                                          
✔ Got cachem 1.0.8 (i386+x86_64-w64-mingw32) (73.54 kB)                                        
✔ Got geeasy 0.1.1 (i386+x86_64-w64-mingw32) (127.54 kB)                                       
✔ Got geeM 0.10.1 (i386+x86_64-w64-mingw32) (82.07 kB)                                         
✔ Got geepack 1.3.10 (i386+x86_64-w64-mingw32) (693.40 kB)                                     
✔ Got shiny 1.8.1.1 (i386+x86_64-w64-mingw32) (4.84 MB)                                       
✔ Got glmnet 4.1-8 (i386+x86_64-w64-mingw32) (2.43 MB)                                
✔ Got processx 3.8.4 (i386+x86_64-w64-mingw32) (685.53 kB)                            
✔ Got ps 1.7.6 (i386+x86_64-w64-mingw32) (555.70 kB)                                  
✔ Got bslib 0.7.0 (i386+x86_64-w64-mingw32) (5.57 MB)                                 
✔ Got promises 1.3.0 (i386+x86_64-w64-mingw32) (2.01 MB)                              
✔ Got tern.mmrm 0.3.0 (i386+x86_64-w64-mingw32) (568.88 kB)                           
✔ Got tinytex 0.50 (i386+x86_64-w64-mingw32) (142.93 kB)                              
✔ Got triebeard 0.4.1 (i386+x86_64-w64-mingw32) (499.03 kB)                           
✔ Got TMB 1.9.11 (i386+x86_64-w64-mingw32) (1.95 MB)                                 
✔ Got highr 0.10 (i386+x86_64-w64-mingw32) (46.92 kB)                       
✔ Got kinship2 1.9.6.1 (i386+x86_64-w64-mingw32) (563.84 kB)                
✔ Got knitr 1.46 (i386+x86_64-w64-mingw32) (1.09 MB)                        
✔ Got hms 1.1.3 (i386+x86_64-w64-mingw32) (105.79 kB)                       
✔ Got fontquiver 0.2.1 (i386+x86_64-w64-mingw32) (2.28 MB)                  
✔ Got later 1.3.2 (i386+x86_64-w64-mingw32) (441.09 kB)                     
✔ Got pillar 1.9.0 (i386+x86_64-w64-mingw32) (663.49 kB)                    
✔ Got praise 1.0.0 (i386+x86_64-w64-mingw32) (20.25 kB)                     
✔ Got R.oo 1.26.0 (i386+x86_64-w64-mingw32) (1.00 MB)                       
✔ Got rvest 1.0.4 (i386+x86_64-w64-mingw32) (309.79 kB)                     
✔ Got shinyjs 2.1.0 (i386+x86_64-w64-mingw32) (1.11 MB)                     
✔ Got Rcpp 1.0.12 (i386+x86_64-w64-mingw32) (2.87 MB)                       
✔ Got teal.widgets 0.4.2 (i386+x86_64-w64-mingw32) (201.66 kB)              
✔ Got sass 0.4.9 (i386+x86_64-w64-mingw32) (2.61 MB)                        
✔ Got teal.transform 0.5.0 (i386+x86_64-w64-mingw32) (2.34 MB)              
✔ Got checkmate 2.3.1 (i386+x86_64-w64-mingw32) (746.81 kB)                 
✔ Got cli 3.6.2 (i386+x86_64-w64-mingw32) (1.36 MB)                         
✔ Got fontBitstreamVera 0.1.1 (i386+x86_64-w64-mingw32) (697.83 kB)         
✔ Got evaluate 0.23 (i386+x86_64-w64-mingw32) (85.94 kB)                    
✔ Got logger 0.3.0 (i386+x86_64-w64-mingw32) (757.59 kB)                   
✔ Got lubridate 1.9.3 (i386+x86_64-w64-mingw32) (989.98 kB)               
✔ Got R6 2.5.1 (i386+x86_64-w64-mingw32) (85.25 kB)                       
✔ Got rappdirs 0.3.3 (i386+x86_64-w64-mingw32) (52.48 kB)                 
✔ Got SparseM 1.81 (i386+x86_64-w64-mingw32) (1.05 MB)                    
✔ Got R.utils 2.12.3 (i386+x86_64-w64-mingw32) (1.46 MB)                  
✔ Got tern.gee 0.1.3 (i386+x86_64-w64-mingw32) (435.96 kB)                
✔ Got timechange 0.3.0 (i386+x86_64-w64-mingw32) (507.92 kB)              
✔ Got bit 4.0.5 (i386+x86_64-w64-mingw32) (1.15 MB)                       
✔ Got tzdb 0.4.0 (i386+x86_64-w64-mingw32) (1.00 MB)                      
✔ Got car 3.1-2 (i386+x86_64-w64-mingw32) (1.73 MB)                       
✔ Got clipr 0.8.0 (i386+x86_64-w64-mingw32) (55.88 kB)                    
✔ Got desc 1.4.3 (i386+x86_64-w64-mingw32) (339.25 kB)                    
✔ Got callr 3.7.6 (i386+x86_64-w64-mingw32) (474.57 kB)                   
✔ Got fs 1.6.3 (i386+x86_64-w64-mingw32) (397.49 kB)                      
✔ Got formatters 0.5.6 (i386+x86_64-w64-mingw32) (4.56 MB)                
✔ Got parallelly 1.37.1 (i386+x86_64-w64-mingw32) (367.60 kB)             
✔ Got lazyeval 0.2.2 (i386+x86_64-w64-mingw32) (162.48 kB)                
✔ Got lifecycle 1.0.4 (i386+x86_64-w64-mingw32) (141.91 kB)               
✔ Got teal.logger 0.2.0 (i386+x86_64-w64-mingw32) (54.20 kB)              
✔ Got teal.reporter 0.3.1 (i386+x86_64-w64-mingw32) (674.21 kB)           
✔ Got lme4 1.1-35.3 (i386+x86_64-w64-mingw32) (4.55 MB)                   
✔ Got openssl 2.1.1 (i386+x86_64-w64-mingw32) (3.18 MB)                   
✔ Got chromote 0.2.0 (i386+x86_64-w64-mingw32) (386.45 kB)                
✔ Got xml2 1.3.6 (i386+x86_64-w64-mingw32) (1.61 MB)                      
✔ Got gdtools 0.3.7 (i386+x86_64-w64-mingw32) (2.19 MB)                   
✔ Got labelled 2.12.0 (i386+x86_64-w64-mingw32) (324.21 kB)               
✔ Got ggrepel 0.9.5 (i386+x86_64-w64-mingw32) (594.13 kB)                 
✔ Got tern 0.9.4 (i386+x86_64-w64-mingw32) (5.61 MB)                      
✔ Got ggridges 0.5.6 (i386+x86_64-w64-mingw32) (2.27 MB)                  
✔ Got sys 3.4.2 (i386+x86_64-w64-mingw32) (46.89 kB)                      
✔ Got shinycssloaders 1.0.0 (i386+x86_64-w64-mingw32) (141.29 kB)         
✔ Got teal.slice 0.5.0 (i386+x86_64-w64-mingw32) (1.68 MB)                
✔ Got teal.data 0.5.0 (i386+x86_64-w64-mingw32) (2.17 MB)                 
✔ Got xfun 0.43 (i386+x86_64-w64-mingw32) (499.55 kB)                     
✔ Got fontawesome 0.5.2 (i386+x86_64-w64-mingw32) (1.35 MB)               
✔ Got httr 1.4.7 (i386+x86_64-w64-mingw32) (497.92 kB)                    
✔ Got styler 1.10.3 (i386+x86_64-w64-mingw32) (864.41 kB)                 
✔ Got tibble 3.2.1 (i386+x86_64-w64-mingw32) (695.40 kB)                  
✔ Got tidyselect 1.2.1 (i386+x86_64-w64-mingw32) (229.99 kB)              
✔ Got fontLiberation 0.1.0 (i386+x86_64-w64-mingw32) (4.53 MB)            
✔ Got tidyr 1.3.1 (i386+x86_64-w64-mingw32) (1.27 MB)                     
✔ Got vistime 1.2.4 (i386+x86_64-w64-mingw32) (2.00 MB)                   
✔ Got rprojroot 2.0.4 (i386+x86_64-w64-mingw32) (115.37 kB)               
✔ Got bit64 4.0.5 (i386+x86_64-w64-mingw32) (501.75 kB)                   
✔ Got rtables 0.6.7 (i386+x86_64-w64-mingw32) (3.83 MB)                   
✔ Got withr 3.0.0 (i386+x86_64-w64-mingw32) (250.88 kB)                   
✔ Got labeling 0.4.3 (i386+x86_64-w64-mingw32) (63.85 kB)                 
✔ Got carData 3.0-5 (i386+x86_64-w64-mingw32) (1.71 MB)                   
✔ Got isoband 0.2.7 (i386+x86_64-w64-mingw32) (1.93 MB)                   
✔ Got purrr 1.0.2 (i386+x86_64-w64-mingw32) (511.30 kB)                   
✔ Got Rdpack 2.6 (i386+x86_64-w64-mingw32) (760.35 kB)                    
✔ Got readr 2.1.5 (i386+x86_64-w64-mingw32) (1.18 MB)                     
✔ Got ggplot2 3.5.0 (i386+x86_64-w64-mingw32) (4.88 MB)                   
✔ Downloaded 188 packages (211.02 MB) in 4m 15.2s                         
✔ Installed abind 1.4-5  (1.2s)                                                       
✔ Installed anytime 0.3.9  (1.5s)                      
✔ Installed askpass 1.2.0  (2.3s)                      
✔ Installed assertthat 0.2.1  (2.5s)                   
✔ Installed backports 1.4.1  (2.8s)                   
✔ Installed base64enc 0.1-3  (3.2s)                   
✔ Installed bit 4.0.5  (3.5s)                         
✔ Installed bit64 4.0.5  (3.9s)                       
✔ Installed brio 1.1.4  (4.3s)                        
✔ Installed broom 1.0.5  (5s)                                                              
✔ Installed cachem 1.0.8  (5.2s)                                                         
✔ Installed bslib 0.7.0  (6s)                                                              
✔ Installed callr 3.7.6  (1.4s)                                                              
✔ Installed car 3.1-2  (1.5s)                         
✔ Installed carData 3.0-5  (2s)                       
✔ Installed checkmate 2.3.1  (2s)                     
✔ Installed chromote 0.2.0  (2.4s)                    
✔ Installed cli 3.6.2  (2.7s)                         
✔ Installed clipr 0.8.0  (3.2s)                        
✔ Installed commonmark 1.9.1  (3s)                     
✔ Installed colorspace 2.1-0  (3.9s)                   
✔ Installed cowplot 1.1.3  (4s)                        
✔ Installed crayon 1.5.2  (4s)                         
✔ Installed crosstalk 1.2.1  (4.4s)                    
✔ Installed crul 1.4.2  (4.6s)                         
✔ Installed curl 5.2.1  (5.3s)                         
✔ Installed desc 1.4.3  (5.1s)                         
✔ Installed data.table 1.15.4  (5.8s)                  
✔ Installed diffobj 0.3.5  (5.8s)                      
✔ Installed digest 0.6.35  (6.2s)                      
✔ Installed dplyr 1.1.4  (6.3s)                        
✔ Installed ellipsis 0.3.2  (6.3s)                     
✔ Installed DT 0.33  (7.4s)                            
✔ Installed emmeans 1.10.1  (6.8s)                     
✔ Installed estimability 1.5  (7.1s)                   
✔ Installed evaluate 0.23  (6.9s)                      
✔ Installed fansi 1.0.6  (6.9s)                        
✔ Installed farver 2.1.1  (6.7s)                       
✔ Installed fastmap 1.1.1  (6.8s)                      
✔ Installed flextable 0.9.5  (6.9s)                    
✔ Installed fontawesome 0.5.2  (6.9s)                  
✔ Installed generics 0.1.3  (274ms)                    
✔ Installed fontBitstreamVera 0.1.1  (7.5s)            
✔ Installed fontLiberation 0.1.0  (7.5s)               
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✔ Installed ggrepel 0.9.5  (245ms)                     
✔ Installed forcats 1.0.0  (7.8s)                      
✔ Installed foreach 1.5.2  (7.8s)                      
✔ Installed formatters 0.5.6  (7.5s)                   
✔ Installed fs 1.6.3  (7.7s)                           
✔ Installed gdtools 0.3.7  (7.5s)                      
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✔ Installed geeM 0.10.1  (7.5s)                        
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✔ Installed gfonts 0.2.0  (6.5s)                       
✔ Installed ggformula 0.12.0  (6.6s)                   
✔ Installed ggplot2 3.5.0  (6.5s)                      
✔ Installed ggridges 0.5.6  (5.9s)                     
✔ Installed glmnet 4.1-8  (5.9s)                       
✔ Installed globals 0.16.3  (6.2s)                     
✔ Installed glue 1.7.0  (6.2s)                         
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✔ Installed highr 0.10  (6.1s)                         
✔ Installed hms 1.1.3  (6.2s)                          
✔ Installed htmltools 0.5.8.1  (6.1s)                  
✔ Installed htmlwidgets 1.6.4  (6s)                    
✔ Installed httpcode 0.3.0  (6.1s)                     
✔ Installed httpuv 1.6.15  (6s)                        
✔ Installed lifecycle 1.0.4  (249ms)                   
✔ Installed httr 1.4.7  (6.6s)                         
✔ Installed isoband 0.2.7  (6.1s)                      
✔ Installed iterators 1.0.14  (6.1s)                   
✔ Installed jquerylib 0.1.4  (6.1s)                    
✔ Installed jsonlite 1.8.8  (6s)                       
✔ Installed kinship2 1.9.6.1  (6s)                     
✔ Installed knitr 1.46  (6.2s)                         
✔ Installed labeling 0.4.3  (6.1s)                     
✔ Installed labelled 2.12.0  (6.1s)                    
✔ Installed later 1.3.2  (6.1s)                        
✔ Installed lazyeval 0.2.2  (6.2s)                     
✔ Installed mosaicCore 0.9.4.0  (480ms)                
✔ Installed lme4 1.1-35.3  (5.9s)                      
✔ Installed logger 0.3.0  (5.9s)                       
✔ Installed lubridate 1.9.3  (6s)                      
✔ Installed magrittr 2.0.3  (6.1s)                     
✔ Installed MatrixModels 0.5-3  (6.1s)                 
✔ Installed memoise 2.0.1  (6.3s)                      
✔ Installed MESS 0.5.12  (6.2s)                        
✔ Installed mime 0.12  (6s)                             
✔ Installed minqa 1.2.6  (6s)                           
✔ Installed mmrm 0.3.11  (6.1s)                         
✔ Installed munsell 0.5.1  (5.6s)                       
✔ Installed mvtnorm 1.2-4  (5.6s)                       
✔ Installed nestcolor 0.1.2  (5.5s)                     
✔ Installed nloptr 2.0.3  (5.6s)                        
✔ Installed numDeriv 2016.8-1.1  (5.9s)                 
✔ Installed officer 0.6.5  (5.8s)                       
✔ Installed openssl 2.1.1  (5.8s)                       
✔ Installed parallelly 1.37.1  (5.6s)                   
✔ Installed pbkrtest 0.5.2  (5.6s)                      
✔ Installed pillar 1.9.0  (5.6s)                        
✔ Installed pingr 2.0.3  (5.5s)                         
✔ Installed pkgbuild 1.4.4  (5.5s)                      
✔ Installed pkgconfig 2.0.3  (5.1s)                     
✔ Installed pkgload 1.3.4  (5.2s)                       
✔ Installed plotly 4.10.4  (5.2s)                       
✔ Installed praise 1.0.0  (5.1s)                        
✔ Installed processx 3.8.4  (5.2s)                      
✔ Installed promises 1.3.0  (5.3s)                      
✔ Installed ps 1.7.6  (5.2s)                            
✔ Installed purrr 1.0.2  (5.3s)                         
✔ Installed quadprog 1.5-8  (5.3s)                      
✔ Installed quantreg 5.97  (5.9s)                       
✔ Installed R.cache 0.16.0  (5.9s)                      
✔ Installed R.methodsS3 1.8.2  (5.9s)                   
✔ Installed R.oo 1.26.0  (6s)                           
✔ Installed R.utils 2.12.3  (6s)                        
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✔ Installed ragg 1.3.0  (6.2s)                          
✔ Installed rappdirs 0.3.3  (6.2s)                      
✔ Installed rbibutils 2.2.16  (6.1s)                    
✔ Installed RColorBrewer 1.1-3  (6.2s)                  
✔ Installed Rdpack 2.6  (5.8s)                          
✔ Installed readr 2.1.5  (5.1s)                         
✔ Installed rematch2 2.1.2  (5.1s)                      
✔ Installed rlang 1.1.3  (5.1s)                         
✔ Installed Rcpp 1.0.12  (8.2s)                         
✔ Installed rlistings 0.2.8  (5.7s)                     
✔ Installed rmarkdown 2.26  (5.6s)                      
✔ Installed rprojroot 2.0.4  (5.6s)                     
✔ Installed rtables 0.6.7  (5.4s)                       
✔ Installed rvest 1.0.4  (5.4s)                         
✔ Installed sass 0.4.9  (5.4s)                          
✔ Installed scales 1.3.0  (5.3s)                        
✔ Installed selectr 0.4-2  (5.3s)                       
✔ Installed shape 1.4.6.1  (5.4s)                       
✔ Installed shiny 1.8.1.1  (5.5s)                       
✔ Installed shinybusy 0.3.3  (5.2s)                     
✔ Installed shinycssloaders 1.0.0  (5.1s)               
✔ Installed shinyjs 2.1.0  (5.1s)                       
✔ Installed shinytest2 0.3.1  (5s)                      
✔ Installed shinyvalidate 0.1.3  (5s)                   
✔ Installed sourcetools 0.1.7-1  (4.5s)                 
✔ Installed SparseM 1.81  (4.4s)                        
✔ Installed shinyWidgets 0.8.5  (5.9s)                  
✔ Installed stringi 1.8.3  (4.9s)                       
✔ Installed stringr 1.5.1  (5s)                         
✔ Installed styler 1.10.3  (4.8s)                       
✔ Installed sys 3.4.2  (4.8s)                           
✔ Installed systemfonts 1.0.6  (4.8s)                   
✔ Installed teal 0.15.2  (4.9s)                         
✔ Installed teal.code 0.5.0  (4.8s)                     
✔ Installed teal.data 0.5.0  (5s)                       
✔ Installed teal.logger 0.2.0  (5.1s)                   
✔ Installed teal.reporter 0.3.1  (5s)                   
✔ Installed teal.slice 0.5.0  (5s)                      
✔ Installed teal.transform 0.5.0  (4.8s)                
✔ Installed teal.widgets 0.4.2  (4.9s)                  
✔ Installed tern 0.9.4  (4.8s)                          
✔ Installed tern.gee 0.1.3  (5s)                        
✔ Installed tern.mmrm 0.3.0  (5s)                       
✔ Installed testthat 3.2.1.1  (5.1s)                    
✔ Installed textshaping 0.3.7  (5.1s)                   
✔ Installed tibble 3.2.1  (5.1s)                        
✔ Installed tidyr 1.3.1  (5s)                           
✔ Installed tidyselect 1.2.1  (5s)                      
✔ Installed timechange 0.3.0  (5.1s)                    
✔ Installed tinytex 0.50  (5.1s)                        
✔ Installed waldo 0.5.2  (479ms)                        
✔ Installed TMB 1.9.11  (5.5s)                          
✔ Installed triebeard 0.4.1  (5.5s)                     
✔ Installed tzdb 0.4.0  (5.5s)                          
✔ Installed urltools 1.7.3  (5.4s)                      
✔ Installed utf8 1.2.4  (5.3s)                          
✔ Installed uuid 1.2-0  (5.5s)                          
✔ Installed vctrs 0.6.5  (5.6s)                         
✔ Installed viridisLite 0.4.2  (5.4s)                   
✔ Installed vistime 1.2.4  (5.5s)                      
✔ Installed vroom 1.6.5  (5.5s)                        
✔ Installed websocket 1.4.1  (4.8s)                    
✔ Installed withr 3.0.0  (5s)                          
✔ Installed xfun 0.43  (5.1s)                                                                  
✔ Installed xml2 1.3.6  (5s)                                                                 
✔ Installed xtable 1.8-4  (4.9s)                                                       
✔ Installed yaml 2.3.8  (4.8s)                                                   
✔ Installed zip 2.3.1  (4.7s)                                            
── R CMD build ───────────────────────────────────────────────────────────────────────────────
pdflatex not found! Not building PDF manual.
✔  checking for file 'C:\Rprojects\teal.modules.clinical/DESCRIPTION' ...
─  preparing 'teal.modules.clinical': (31.9s)
✔  checking DESCRIPTION meta-information ... 
─  installing the package to build vignettes (2s)
✔  creating vignettes (26.5s)
─  checking for LF line-endings in source and make files and shell scripts (2.4s)
─  checking for empty or unneeded directories
   Removed empty directory 'teal.modules.clinical/Include'
─  building 'teal.modules.clinical_0.9.1.9006.tar.gz'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py'

── R CMD check ───────────────────────────────────────────────────────────────────────────────
─  using log directory 'C:/Users/kosinsm4/AppData/Local/Temp/RtmpkZuXze/file5ebc110f7f05/teal.modules.clinical.Rcheck' (503ms)
─  using R version 4.4.0 (2024-04-24 ucrt)
─  using platform: x86_64-w64-mingw32
─  R was compiled by
       gcc.exe (GCC) 13.2.0
       GNU Fortran (GCC) 13.2.0
─  running under: Windows 11 x64 (build 22621)
─  using session charset: UTF-8
✔  checking for file 'teal.modules.clinical/DESCRIPTION' (4.1s)
─  this is package 'teal.modules.clinical' version '0.9.1.9006'
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (1.7s)
✔  checking if this is a source package ... 
✔  checking if there is a namespace
W  checking for executable files (29.9s)
   Found the following executable files:
     Lib/site-packages/pip/_vendor/distlib/t32.exe
     Lib/site-packages/pip/_vendor/distlib/t64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/t64.exe
     Lib/site-packages/pip/_vendor/distlib/w32.exe
     Lib/site-packages/pip/_vendor/distlib/w64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/w64.exe
     Lib/site-packages/setuptools/cli-32.exe
     Lib/site-packages/setuptools/cli-64.exe
     Lib/site-packages/setuptools/cli-arm64.exe
     Lib/site-packages/setuptools/cli.exe
     Lib/site-packages/setuptools/gui-32.exe
     Lib/site-packages/setuptools/gui-64.exe
     Lib/site-packages/setuptools/gui-arm64.exe
     Lib/site-packages/setuptools/gui.exe
     Scripts/pip-3.11.exe
     Scripts/pip.exe
     Scripts/pip3.11.exe
     Scripts/pip3.exe
     Scripts/python.exe
     Scripts/pythonw.exe
     Scripts/wheel-3.11.exe
     Scripts/wheel.exe
     Scripts/wheel3.11.exe
     Scripts/wheel3.exe
   Source packages should not contain undeclared executable files.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking for hidden files and directories ... 
W  checking for portable file names ... 
   Found the following files with non-portable file names:
     Lib/site-packages/setuptools/command/launcher manifest.xml
     Lib/site-packages/setuptools/script (dev).tmpl
   These are not fully portable file names.
   See section 'Package structure' in the 'Writing R Extensions' manual.
   Found the following non-portable file paths:
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py

   Tarballs are only required to store paths of up to 100 bytes and cannot
   store those of more than 256 bytes, with restrictions including to 100
   bytes for the final component.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking whether package 'teal.modules.clinical' can be installed (16.4s)
✔  checking installed package size (1.3s)
✔  checking package directory
✔  checking 'build' directory
✔  checking DESCRIPTION meta-information ... 
✔  checking top-level files
✔  checking for left-over files ...
✔  checking index information ... 
✔  checking package subdirectories (1.4s)
✔  checking code files for non-ASCII characters ... 
✔  checking R files for syntax errors ... 
✔  checking whether the package can be loaded (2s)
✔  checking whether the package can be loaded with stated dependencies (2.1s)
✔  checking whether the package can be unloaded cleanly (2s)
✔  checking whether the namespace can be loaded with stated dependencies (1.8s)
✔  checking whether the namespace can be unloaded cleanly (2.1s)
✔  checking loading without being on the library search path (2.4s)
✔  checking whether startup messages can be suppressed (4.1s)
✔  checking dependencies in R code (3.2s)
✔  checking S3 generic/method consistency (2s)
✔  checking replacement functions (1.9s)
✔  checking foreign function calls (2.7s)
✔  checking R code for possible problems (13.6s)
✔  checking Rd files (2.1s)
✔  checking Rd metadata ... 
✔  checking Rd cross-references (552ms)
✔  checking for missing documentation entries (2.1s)
✔  checking for code/documentation mismatches (6.5s)
✔  checking Rd \usage sections (2.9s)
✔  checking Rd contents (666ms)
✔  checking for unstated dependencies in examples (1.8s)
✔  checking contents of 'data' directory ... 
✔  checking data for non-ASCII characters (442ms)
✔  checking LazyData
✔  checking data for ASCII and uncompressed saves ... 
✔  checking installed files from 'inst/doc' (464ms)
✔  checking files in 'vignettes' ... 
✔  checking examples (10.3s)
✔  checking for unstated dependencies in 'tests' ... 
─  checking tests (428ms)
✔  Running 'testthat.R' (17.1s)
✔  checking for unstated dependencies in vignettes (558ms)
✔  checking package vignettes ... 
✔  checking re-building of vignette outputs (13.4s)
W  checking PDF version of manual (4.6s)
   LaTeX errors when creating PDF version.
   This typically indicates Rd problems.
E  checking PDF version of manual without index (4.1s)
   Re-running with no redirection of stdout/stderr.
   Hmm ... looks like a package
   Converting parsed Rd's to LaTeX ...........
   Creating pdf output from LaTeX ...
   Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
     pdflatex is not available
   Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
     pdflatex is not available
   Error in running tools::texi2pdf()
   You may want to clean up by 'rm -Rf C:/Users/kosinsm4/AppData/Local/Temp/RtmpaSmdmg/Rd2pdfb005fdf22c7'

   See
     'C:/Users/kosinsm4/AppData/Local/Temp/RtmpkZuXze/file5ebc110f7f05/teal.modules.clinical.Rcheck/00check.log'
   for details.

Ok I run this with LaTeX installed and worked

verdepcheck::min_cohort_deps_check(".")
✔ Updated metadata database: 2.20 MB in 2 files.
✔ Updating metadata database ... done
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c30f66fb7
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c54d8598f
✔ Loading metadata database ... done
ℹ Getting 180 pkgs (185.16 MB), 8 (25.09 MB) cached                  
✔ Cached copy of abind 1.4-5 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of anytime 0.3.9 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of askpass 1.2.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of assertthat 0.2.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of backports 1.4.1 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of base64enc 0.1-3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of bit 4.0.5 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of bit64 4.0.5 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of brio 1.1.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of broom 1.0.5 (i386+x86_64-w64-mingw32) is the latest build
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── R CMD build ───────────────────────────────────────────────────── 
✔  checking for file 'C:\Rprojects\teal.modules.clinical/DESCRIPTION'
─  preparing 'teal.modules.clinical': (8.2s)
✔  checking DESCRIPTION meta-information ... 
─  installing the package to build vignettes (2.2s)
✔  creating vignettes (22.5s)
─  checking for LF line-endings in source and make files and shell scripts (3.6s)
─  checking for empty or unneeded directories
   Removed empty directory 'teal.modules.clinical/Include'
─  building 'teal.modules.clinical_0.9.1.9006.tar.gz'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py'

── R CMD check ─────────────────────────────────────────────────────
─  using log directory 'C:/Users/kosinsm4/AppData/Local/Temp/Rtmp84khcL/file97c14113ad9/teal.modules.clinical.Rcheck' (455ms)
─  using R version 4.4.0 (2024-04-24 ucrt)
─  using platform: x86_64-w64-mingw32
─  R was compiled by
       gcc.exe (GCC) 13.2.0
       GNU Fortran (GCC) 13.2.0
─  running under: Windows 11 x64 (build 22621)
─  using session charset: UTF-8
✔  checking for file 'teal.modules.clinical/DESCRIPTION' (2.3s)
─  this is package 'teal.modules.clinical' version '0.9.1.9006'
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (1s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
W  checking for executable files (28.1s)
   Found the following executable files:
     Lib/site-packages/pip/_vendor/distlib/t32.exe
     Lib/site-packages/pip/_vendor/distlib/t64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/t64.exe
     Lib/site-packages/pip/_vendor/distlib/w32.exe
     Lib/site-packages/pip/_vendor/distlib/w64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/w64.exe
     Lib/site-packages/setuptools/cli-32.exe
     Lib/site-packages/setuptools/cli-64.exe
     Lib/site-packages/setuptools/cli-arm64.exe
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     Lib/site-packages/setuptools/gui.exe
     Scripts/pip-3.11.exe
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     Scripts/wheel-3.11.exe
     Scripts/wheel.exe
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   Source packages should not contain undeclared executable files.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking for hidden files and directories ... 
W  checking for portable file names ... 
   Found the following files with non-portable file names:
     Lib/site-packages/setuptools/command/launcher manifest.xml
     Lib/site-packages/setuptools/script (dev).tmpl
   These are not fully portable file names.
   See section 'Package structure' in the 'Writing R Extensions' manual.
   Found the following non-portable file paths:
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py

   Tarballs are only required to store paths of up to 100 bytes and cannot
   store those of more than 256 bytes, with restrictions including to 100
   bytes for the final component.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking whether package 'teal.modules.clinical' can be installed (12s)
✔  checking installed package size (1.2s)
✔  checking package directory
✔  checking 'build' directory
✔  checking DESCRIPTION meta-information ... 
✔  checking top-level files
✔  checking for left-over files ... 
✔  checking index information ... 
✔  checking package subdirectories (1.6s)
✔  checking code files for non-ASCII characters ... 
✔  checking R files for syntax errors ... 
✔  checking whether the package can be loaded (1.5s)
✔  checking whether the package can be loaded with stated dependencies (1.5s)
✔  checking whether the package can be unloaded cleanly (1.8s)
✔  checking whether the namespace can be loaded with stated dependencies (1.6s)
✔  checking whether the namespace can be unloaded cleanly (1.9s)
✔  checking loading without being on the library search path (2.3s)
✔  checking whether startup messages can be suppressed (3.7s)
✔  checking dependencies in R code (2.9s)
✔  checking S3 generic/method consistency (1.7s)
✔  checking replacement functions (1.6s)
✔  checking foreign function calls (2.3s)
✔  checking R code for possible problems (11.9s)
✔  checking Rd files (1.8s)
✔  checking Rd metadata ... 
✔  checking Rd cross-references (459ms)
✔  checking for missing documentation entries (2s)
✔  checking for code/documentation mismatches (6.4s)
✔  checking Rd \usage sections (2.8s)
✔  checking Rd contents (726ms)
✔  checking for unstated dependencies in examples (1.8s)
✔  checking contents of 'data' directory ... 
✔  checking data for non-ASCII characters ... 
✔  checking LazyData
✔  checking data for ASCII and uncompressed saves ... 
✔  checking installed files from 'inst/doc' (456ms)
✔  checking files in 'vignettes' ... 
✔  checking examples (9.4s)
✔  checking for unstated dependencies in 'tests' ... 
─  checking tests ...
✔  Running 'testthat.R' (24.2s)
✔  checking for unstated dependencies in vignettes (514ms)
✔  checking package vignettes ... 
✔  checking re-building of vignette outputs (12.2s)
✔  checking PDF version of manual (2m 8.8s)

   See
     'C:/Users/kosinsm4/AppData/Local/Temp/Rtmp84khcL/file97c14113ad9/teal.modules.clinical.Rcheck/00check.log'
   for details.

min_isolated failed - unsure if this is what suppose to happen

verdepcheck::min_isolated_deps_check(".")
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c4f183ab0
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c612e3a38
✔ Loading metadata database ... done
ℹ Getting 150 pkgs (143.06 MB), 37 (65.60 MB) cached                
✔ Cached copy of zip 2.3.1 (i386+x86_64-w64-mingw32) is the latest build                                               
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ℹ Building lubridate 1.7.9                              
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✖ Failed to build lubridate 1.7.9 (3.9s)                                                                          
! Failed to build source package lubridate., stdout + stderr:                                  

OE> Error in rawToChar(block[seq_len(ns)]) : 
OE>   embedded nul in string: 'PK\003\004\n\0\0\0\0\0Nj\xc5X\0\0\0\0\0\0\0\0\0\0\0\0\n\0\0\0lubridate/PK\003\004\024\0\002\0\b\0Hj\xc5Xf\x97\x96J\xc9\0\0\0s\001\0\0\021\0\0\0lubridate/cctz.shM\x90\xbdn\xc30\f\x84w>\005\x9bz'
Error in "stop_task_build(state, worker)" : 
  ! Failed to build source package lubridate.

release_deps was proper

verdepcheck::release_deps_check(".")
ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c67e211a4
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c9fc3b2b
ℹ Getting 147 pkgs (132.02 MB), 40 (78.20 MB) cached                        
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✔ Cached copy of plotly 4.10.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of praise 1.0.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of promises 1.3.0 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of ps 1.7.6 (i386+x86_64-w64-mingw32) is the latest build 
✔ Cached copy of purrr 1.0.2 (i386+x86_64-w64-mingw32) is the latest build
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✔ Cached copy of urltools 1.7.3 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of utf8 1.2.4 (i386+x86_64-w64-mingw32) is the latest build
✔ Cached copy of uuid 1.2-0 (i386+x86_64-w64-mingw32) is the latest build
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✔ Got car 3.1-2 (i386+x86_64-w64-mingw32) (1.73 MB)                                                                     
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✔ Got cowplot 1.1.3 (i386+x86_64-w64-mingw32) (1.38 MB)                              
✔ Got htmltools 0.5.8.1 (i386+x86_64-w64-mingw32) (364.88 kB)                        
✔ Got htmlwidgets 1.6.4 (i386+x86_64-w64-mingw32) (814.05 kB)                        
✔ Got shinybusy 0.3.3 (i386+x86_64-w64-mingw32) (624.45 kB)                          
✔ Got shinycssloaders 1.0.0 (i386+x86_64-w64-mingw32) (141.29 kB)                    
✔ Got shinyjs 2.1.0 (i386+x86_64-w64-mingw32) (1.11 MB)                              
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✔ Got tern.mmrm 0.3.0 (i386+x86_64-w64-mingw32) (568.88 kB)                          
✔ Got ggplot2 3.5.1 (i386+x86_64-w64-mingw32) (5.02 MB)                              
✔ Got processx 3.8.4 (i386+x86_64-w64-mingw32) (685.53 kB)                           
✔ Got rappdirs 0.3.3 (i386+x86_64-w64-mingw32) (52.48 kB)                            
✔ Got pingr 2.0.3 (i386+x86_64-w64-mingw32) (60.49 kB)                               
✔ Got crayon 1.5.2 (i386+x86_64-w64-mingw32) (165.39 kB)                             
✔ Got crosstalk 1.2.1 (i386+x86_64-w64-mingw32) (416.80 kB)                          
✔ Got flextable 0.9.6 (i386+x86_64-w64-mingw32) (3.24 MB)                            
✔ Got lubridate 1.9.3 (i386+x86_64-w64-mingw32) (989.98 kB)                          
✔ Got logger 0.3.0 (i386+x86_64-w64-mingw32) (757.59 kB)                             
✔ Got websocket 1.4.1 (i386+x86_64-w64-mingw32) (2.80 MB)                            
✔ Got lme4 1.1-35.3 (i386+x86_64-w64-mingw32) (4.55 MB)                              
✔ Got stringi 1.8.4 (i386+x86_64-w64-mingw32) (15.01 MB)                             
✔ Downloaded 23 packages (46.21 MB) in 56.7s                                         
✔ Installed abind 1.4-5  (627ms)                                                                             
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✔ Installed shinycssloaders 1.0.0  (5.2s)               
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✔ Installed shinyvalidate 0.1.3  (5s)                   
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✔ Installed SparseM 1.83  (4.8s)                        
✔ Installed stringi 1.8.4  (4.9s)                       
✔ Installed stringr 1.5.1  (4.9s)                       
✔ Installed styler 1.10.3  (4.8s)                       
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✔ Installed teal 0.15.2  (4.8s)                         
✔ Installed teal.code 0.5.0  (4.8s)                     
✔ Installed teal.data 0.6.0  (4.9s)                     
✔ Installed teal.logger 0.2.0  (4.8s)                   
✔ Installed teal.reporter 0.3.1  (4.8s)                 
✔ Installed teal.slice 0.5.1  (4.7s)                    
✔ Installed teal.transform 0.5.0  (4.7s)                
✔ Installed teal.widgets 0.4.2  (4.5s)                  
✔ Installed tern 0.9.4  (4.5s)                          
✔ Installed tern.gee 0.1.3  (4.6s)                      
✔ Installed tern.mmrm 0.3.0  (4.6s)                     
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✔ Installed tibble 3.2.1  (5.1s)                        
✔ Installed tidyr 1.3.1  (4.9s)                         
✔ Installed tidyselect 1.2.1  (5.1s)                    
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✔ Installed tinytex 0.51  (5.3s)                        
✔ Installed triebeard 0.4.1  (5s)                       
✔ Installed TMB 1.9.11  (5.9s)                          
✔ Installed tzdb 0.4.0  (5.5s)                          
✔ Installed urltools 1.7.3  (5.5s)                      
✔ Installed utf8 1.2.4  (5.5s)                          
✔ Installed uuid 1.2-0  (5.5s)                          
✔ Installed vctrs 0.6.5  (5.3s)                         
✔ Installed viridisLite 0.4.2  (5.1s)                   
✔ Installed vistime 1.2.4  (5.1s)                       
✔ Installed vroom 1.6.5  (4.9s)                        
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✔ Installed websocket 1.4.1  (4.7s)                                                                                   
✔ Installed withr 3.0.0  (4.6s)                                                                                
✔ Installed xfun 0.44  (4.6s)                                                                       
✔ Installed xml2 1.3.6  (4.5s)                                                               
✔ Installed xtable 1.8-4  (4.3s)                                                       
✔ Installed yaml 2.3.8  (4.2s)                                                   
✔ Installed zip 2.3.1  (4s)                                              
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file 'C:\Rprojects\teal.modules.clinical/DESCRIPTION' ...
─  preparing 'teal.modules.clinical': (5.2s)
✔  checking DESCRIPTION meta-information ... 
─  installing the package to build vignettes (2.2s)
✔  creating vignettes (24.5s)
─  checking for LF line-endings in source and make files and shell scripts (2.2s)
─  checking for empty or unneeded directories
   Removed empty directory 'teal.modules.clinical/Include'
─  building 'teal.modules.clinical_0.9.1.9006.tar.gz'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py'
   Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
     storing paths of more than 100 bytes is not portable:
     'teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py'

── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory 'C:/Users/kosinsm4/AppData/Local/Temp/Rtmp84khcL/file97c8d73e0e/teal.modules.clinical.Rcheck' (502ms)
─  using R version 4.4.0 (2024-04-24 ucrt)
─  using platform: x86_64-w64-mingw32
─  R was compiled by
       gcc.exe (GCC) 13.2.0
       GNU Fortran (GCC) 13.2.0
─  running under: Windows 11 x64 (build 22621)
─  using session charset: UTF-8
✔  checking for file 'teal.modules.clinical/DESCRIPTION' (2.3s)
─  this is package 'teal.modules.clinical' version '0.9.1.9006'
─  package encoding: UTF-8
✔  checking package namespace information
✔  checking package dependencies (1.3s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
W  checking for executable files (28.3s)
   Found the following executable files:
     Lib/site-packages/pip/_vendor/distlib/t32.exe
     Lib/site-packages/pip/_vendor/distlib/t64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/t64.exe
     Lib/site-packages/pip/_vendor/distlib/w32.exe
     Lib/site-packages/pip/_vendor/distlib/w64-arm.exe
     Lib/site-packages/pip/_vendor/distlib/w64.exe
     Lib/site-packages/setuptools/cli-32.exe
     Lib/site-packages/setuptools/cli-64.exe
     Lib/site-packages/setuptools/cli-arm64.exe
     Lib/site-packages/setuptools/cli.exe
     Lib/site-packages/setuptools/gui-32.exe
     Lib/site-packages/setuptools/gui-64.exe
     Lib/site-packages/setuptools/gui-arm64.exe
     Lib/site-packages/setuptools/gui.exe
     Scripts/pip-3.11.exe
     Scripts/pip.exe
     Scripts/pip3.11.exe
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     Scripts/python.exe
     Scripts/pythonw.exe
     Scripts/wheel-3.11.exe
     Scripts/wheel.exe
     Scripts/wheel3.11.exe
     Scripts/wheel3.exe
   Source packages should not contain undeclared executable files.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking for hidden files and directories ... 
W  checking for portable file names ... 
   Found the following files with non-portable file names:
     Lib/site-packages/setuptools/command/launcher manifest.xml
     Lib/site-packages/setuptools/script (dev).tmpl
   These are not fully portable file names.
   See section 'Package structure' in the 'Writing R Extensions' manual.
   Found the following non-portable file paths:
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py
     teal.modules.clinical/Lib/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py

   Tarballs are only required to store paths of up to 100 bytes and cannot
   store those of more than 256 bytes, with restrictions including to 100
   bytes for the final component.
   See section 'Package structure' in the 'Writing R Extensions' manual.
✔  checking whether package 'teal.modules.clinical' can be installed (18.9s)
✔  checking installed package size (1.5s)
✔  checking package directory
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✔  checking package subdirectories (1.8s)
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✔  checking whether the package can be loaded (1.7s)
✔  checking whether the package can be loaded with stated dependencies (2s)
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✔  checking whether the namespace can be unloaded cleanly (2.3s)
✔  checking loading without being on the library search path (2.6s)
✔  checking whether startup messages can be suppressed (4.1s)
✔  checking dependencies in R code (3s)
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✔  checking R code for possible problems (14.6s)
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✔  checking Rd metadata ... 
✔  checking Rd cross-references (443ms)
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✔  checking Rd contents (555ms)
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─  checking tests (711ms)
✔  Running 'testthat.R' (30.5s)
✔  checking for unstated dependencies in vignettes (733ms)
✔  checking package vignettes (339ms)
✔  checking re-building of vignette outputs (14.7s)
✔  checking PDF version of manual (12.8s)

   See
     'C:/Users/kosinsm4/AppData/Local/Temp/Rtmp84khcL/file97c8d73e0e/teal.modules.clinical.Rcheck/00check.log'
   for details.

max_deps_check failed

ℹ Creating temporary DESCRIPTION file: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c1df03357
ℹ Creating library directory: C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c71f7309c
Error : ! Could not solve package dependencies:                              
* deps::C:\Users\kosinsm4\AppData\Local\Temp\Rtmp84khcL\file97c1df03357:
  * Can't install dependency insightsengineering/tern
  * Can't install dependency insightsengineering/rlistings
  * Can't install dependency insightsengineering/rtables
* insightsengineering/tern: Can't install dependency formatters (>= 0.5.7.9000)
* insightsengineering/rlistings: Can't install dependency formatters (>= 0.5.7.9000)
* insightsengineering/rtables: Can't install dependency formatters (>= 0.5.7.9000)

insightsengineering / verdepcheck