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pharmaverse / admiral

ADaM in R Asset Library
https://pharmaverse.github.io/admiral
Apache License 2.0
222 stars 62 forks source link

pre-CRAN release check (2h) #852

Closed koegerr closed 2 years ago

koegerr commented 2 years ago
bms63 commented 2 years ago

@konstantinakoukR As of February 3rd, if I do a Pull Request of develinto mainthese are all the files that have changed. Maybe this is what we can focus our review on - since these are the ones that have changed since the last release?

Probably should get an updated list below on February 9th.

  1.  .Rbuildignore
  2. +1 −0  .github/.gitignore
  3. +17 −0  .github/pull_request_template.md
  4. +3 −0  .github/workflows/R-CMD-check.yml
  5. +70 −0  .github/workflows/check_templates.yml
  6. +11 −1  .github/workflows/lintr.yaml
  7. +14 −9  DESCRIPTION
  8. +15 −1  NAMESPACE
  9. +22 −0  NEWS.md
  10. +1 −1  R/admiral-package.R
  11. +28 −7  R/assertions.R
  12. +177 −0  R/compat_friendly_type.R
  13. +6 −6  R/data.R
  14. +0 −146  R/derive_baseline.R
  15. +120 −10  R/derive_date_vars.R
  16. +58 −23  R/{derive_params_exposure.R → derive_param_exposure.R}
  17. +140 −0  R/derive_var_base.R
  18. +86 −0  R/{derive_disposition_dt.R → derive_var_disposition_dt.R}
  19. +146 −22  R/{derive_disposition_status.R → derive_var_disposition_status.R}
  20. +54 −22  R/derive_var_dthcaus.R
  21. +315 −10  R/{derive_extreme_flag.R → derive_var_extreme_flag.R}
  22. +141 −17  R/{derive_last_dose.R → derive_var_last_dose.R}
  23. +90 −0  R/derive_var_last_dose_amt.R
  24. +84 −0  R/derive_var_last_dose_date.R
  25. +104 −0  R/derive_var_last_dose_grp.R
  26. +58 −19  R/derive_var_lstalvdt.R
  27. +78 −0  R/{derive_obs_number.R → derive_var_obs_number.R}
  28. +41 −14  R/derive_var_ontrtfl.R
  29. +101 −13  R/derive_vars_aage.R
  30. +188 −29  R/{derive_disposition_reason.R → derive_vars_disposition_reason.R}
  31. +219 −0  R/derive_vars_last_dose.R
  32. +2 −2  R/filter_extreme.R
  33. +7 −1  R/globals.R
  34. +30 −2  R/utils.R
  35. +7 −2  README.md
  36. +2 −1  _pkgdown.yml
  37. +5 −7  inst/templates/ad_adae.R
  38. +1 −1  inst/templates/ad_adcm.R
  39. +11 −7  inst/templates/ad_adeg.R
  40. +3 −3  inst/templates/ad_adex.R
  41. +22 −18  inst/templates/ad_adsl.R
  42. +12 −8  inst/templates/ad_advs.R
  43. +1 −1  man/adae.Rd
  44. +1 −1  man/adcm.Rd
  45. +1 −1  man/adex.Rd
  46. +6 −0  man/admiral-package.Rd
  47. +1 −1  man/adsl.Rd
  48. +1 −1  man/advs.Rd
  49. +4 −0  man/assert_varval_list.Rd
  50. +10 −1  man/compute_tmf.Rd
  51. +95 −0  man/convert_date_to_dtm.Rd
  52. +6 −4  man/derive_agegr_fda.Rd
  53. +6 −39  man/derive_baseline.Rd
  54. +3 −1  man/derive_disposition_dt.Rd
  55. +3 −1  man/derive_disposition_reason.Rd
  56. +3 −1  man/derive_disposition_status.Rd
  57. +3 −1  man/derive_extreme_flag.Rd
  58. +2 −2  man/derive_last_dose.Rd
  59. +3 −1  man/derive_obs_number.Rd
  60. +153 −0  man/derive_param_exposure.Rd
  61. +5 −77  man/derive_params_exposure.Rd
  62. +81 −0  man/derive_var_agegr_fda.Rd
  63. +62 −19  man/derive_var_base.Rd
  64. +4 −26  man/derive_var_basec.Rd
  65. +88 −0  man/derive_var_disposition_dt.Rd
  66. +121 −0  man/derive_var_disposition_status.Rd
  67. +18 −10  man/derive_var_dthcaus.Rd
  68. +173 −0  man/derive_var_extreme_flag.Rd
  69. +136 −0  man/derive_var_last_dose.Rd
  70. +110 −0  man/derive_var_last_dose_amt.Rd
  71. +96 −0  man/derive_var_last_dose_date.Rd
  72. +120 −0  man/derive_var_last_dose_grp.Rd
  73. +28 −14  man/derive_var_lstalvdt.Rd
  74. +78 −0  man/derive_var_obs_number.Rd
  75. +22 −0  man/derive_var_ontrtfl.Rd
  76. +149 −0  man/derive_var_worst_flag.Rd
  77. +157 −0  man/derive_vars_disposition_reason.Rd
  78. +33 −1  man/derive_vars_dtm.Rd
  79. +141 −0  man/derive_vars_last_dose.Rd
  80. +2 −2  man/derive_worst_flag.Rd
  81. +6 −2  man/dthcaus_source.Rd
  82. +1 −1  man/ex_single.Rd
  83. +1 −1  man/format_eoxxstt_default.Rd
  84. +1 −1  man/format_reason_default.Rd
  85. +24 −0  man/get_source_vars.Rd
  86. +6 −2  man/lstalvdt_source.Rd
  87. +24 −0  man/replace_values_by_names.Rd
  88. +27 −0  tests/testthat/test-convert_date_to_dtm.R
  89. +317 −16  tests/testthat/test-deprecation.R
  90. +6 −6  tests/testthat/test-derive_aage.R
  91. +1 −2  tests/testthat/test-derive_param_bmi.R
  92. +6 −6  tests/testthat/{test-derive_params_exposure.R → test-derive_param_exposure.R}
  93. +4 −38  tests/testthat/{test_derive_baseline.R → test-derive_var_base.R}
  94. +5 −3  tests/testthat/{test-derive_disposition_dt.R → test-derive_var_disposition_dt.R}
  95. +4 −2  tests/testthat/{test-derive_disposition_status.R → test-derive_var_disposition_status.R}
  96. +43 −19  tests/testthat/test-derive_var_dthcaus.R
  97. +14 −12  tests/testthat/{test-derive_extreme_flag.R → test-derive_var_extreme_flag.R}
  98. +14 −12  tests/testthat/{test-derive_last_dose.R → test-derive_var_last_dose.R}
  99. +74 −0  tests/testthat/test-derive_var_last_dose_amt.R
  100. +115 −0  tests/testthat/test-derive_var_last_dose_date.R
  101. +51 −0  tests/testthat/test-derive_var_last_dose_grp.R
  102. +25 −43  tests/testthat/test-derive_var_lstalvdt.R
  103. +2 −0  tests/testthat/{test-derive_obs_number.R → test-derive_var_obs_number.R}
  104. +70 −0  tests/testthat/test-derive_var_ontrtfl.R
  105. +6 −4  tests/testthat/{test-derive_disposition_reason.R → test-derive_vars_disposition_reason.R}
  106. +131 −1  tests/testthat/test-derive_vars_dtm.R
  107. +176 −0  tests/testthat/test-derive_vars_last_dose.R
  108. +1 −2  tests/testthat/test-user_helpers.R
  109. +2 −1  vignettes/admiral.Rmd
  110. +114 −74  vignettes/adsl.Rmd
  111. +3 −3  vignettes/bds_exposure.Rmd
  112. +60 −20  vignettes/bds_finding.Rmd
  113. +24 −2  vignettes/bds_tte.Rmd
  114. +8 −12  vignettes/contribution_model.Rmd
  115. +38 −0  vignettes/development_process.Rmd
  116. +9 −7  vignettes/faq.Rmd
  117. +115 −27  vignettes/git_usage.Rmd
  118. BIN  vignettes/github_committ.png
  119. BIN  vignettes/github_conflicts.png
  120. BIN  vignettes/github_create_pr.png
  121. BIN  vignettes/github_delete_branch.png
  122. BIN  vignettes/github_feature_branch.png
  123. BIN  vignettes/github_linked_issues.png
  124. BIN  vignettes/github_sprint_done.png
  125. +12 −12  vignettes/occds.Rmd
  126. +17 −26  vignettes/programming_strategy.Rmd
  127. +20 −5  vignettes/unit_test_guidance.Rmd
  128. +7 −7  vignettes/writing_vignettes.Rmd
konstantinakoukR commented 2 years ago

Hi @bms63! Thank you so much for the inclusive list you provided! @koegerr, pretty helpful checklist! It seems that we have a clear strategy to start with! Thank you both!

bms63 commented 2 years ago

I was playing around with this linkchecking program in RStudio. You have to run the python kernal as it is a python package. https://pypi.org/project/LinkChecker/. It has spotted a few broken links, but it is not catching them all. Maybe something to look into more for automated checks on links.

konstantinakoukR commented 2 years ago

Regarding the spelling check, I had a look in the spelling package here. You can perform a spell check on specific document files or package description, documentation, and vignettes. There is option of setting CMD check as well. Maybe we can have a more detailed look into this.

bms63 commented 2 years ago

Hi all,

We have done all the pre-release checks for the task list. Everything is in Pull Request Review. Going to close this thread since it is not tied to a PR. Please re-open if you have concerns