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Update api_build and pack_build #84

Description

@lwaldron

Not time-critical, but there are 115 NA values in the getStudies(cbio, buildReport = TRUE) api_build and pack_build columns. I'm guessing these are studies added to cBioPortal since the last time the scripts in inst/scripts/buildStudies were run so that they haven't been tested? It would be good to:

  1. update these build columns
  2. add a build_check_date column to the getStudies(cbio, buildReport = TRUE) output, providing the date when these builds were checked
  3. document how to update the build columns (in README.Rmd?)
  4. perhaps add it to @jwokaty's pre-release TODO list along with bugsigdb-related data updates
suppressPackageStartupMessages({
  library(cBioPortalData)
})
cbio <- cBioPortal()
studies <- getStudies(cbio, buildReport = TRUE)
summary(studies$api_build)
#>    Mode   FALSE    TRUE    NA's 
#> logical      40     339     115
summary(studies$pack_build)
#>    Mode   FALSE    TRUE    NA's 
#> logical      27     352     115
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.5.0 (2025-04-11)
#>  os       macOS Sequoia 15.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Rome
#>  date     2025-07-02
#>  pandoc   3.4 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#>  quarto   1.7.30 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package              * version   date (UTC) lib source
#>  abind                  1.4-8     2024-09-12 [1] CRAN (R 4.5.0)
#>  AnnotationDbi          1.70.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  AnVIL                * 1.20.1    2025-05-22 [1] Bioconductor 3.21 (R 4.5.0)
#>  AnVILBase            * 1.2.0     2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  Biobase              * 2.68.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  BiocBaseUtils          1.10.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  BiocFileCache          2.16.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  BiocGenerics         * 0.54.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  BiocIO                 1.18.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  BiocParallel           1.42.1    2025-05-29 [1] Bioconductor 3.21 (R 4.5.0)
#>  Biostrings             2.76.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  bit                    4.6.0     2025-03-06 [1] CRAN (R 4.5.0)
#>  bit64                  4.6.0-1   2025-01-16 [1] CRAN (R 4.5.0)
#>  bitops                 1.0-9     2024-10-03 [1] CRAN (R 4.5.0)
#>  blob                   1.2.4     2023-03-17 [1] CRAN (R 4.5.0)
#>  cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.5.0)
#>  cBioPortalData       * 2.20.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  cli                    3.6.5     2025-04-23 [1] CRAN (R 4.5.0)
#>  codetools              0.2-20    2024-03-31 [1] CRAN (R 4.5.0)
#>  crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.5.0)
#>  curl                   6.4.0     2025-06-22 [1] CRAN (R 4.5.0)
#>  data.table             1.17.6    2025-06-17 [1] CRAN (R 4.5.0)
#>  DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.5.0)
#>  dbplyr                 2.5.0     2024-03-19 [1] CRAN (R 4.5.0)
#>  DelayedArray           0.34.1    2025-04-17 [1] Bioconductor 3.21 (R 4.5.0)
#>  devtools               2.4.5     2022-10-11 [1] CRAN (R 4.5.0)
#>  digest                 0.6.37    2024-08-19 [1] CRAN (R 4.5.0)
#>  dplyr                * 1.1.4     2023-11-17 [1] CRAN (R 4.5.0)
#>  DT                     0.33      2024-04-04 [1] CRAN (R 4.5.0)
#>  ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.5.0)
#>  evaluate               1.0.4     2025-06-18 [1] CRAN (R 4.5.0)
#>  fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.5.0)
#>  filelock               1.0.3     2023-12-11 [1] CRAN (R 4.5.0)
#>  formatR                1.14      2023-01-17 [1] CRAN (R 4.5.0)
#>  fs                     1.6.6     2025-04-12 [1] CRAN (R 4.5.0)
#>  futile.logger          1.4.3     2016-07-10 [1] CRAN (R 4.5.0)
#>  futile.options         1.0.1     2018-04-20 [1] CRAN (R 4.5.0)
#>  generics             * 0.1.4     2025-05-09 [1] CRAN (R 4.5.0)
#>  GenomeInfoDb         * 1.44.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  GenomeInfoDbData       1.2.14    2025-05-13 [1] Bioconductor
#>  GenomicAlignments      1.44.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  GenomicDataCommons     1.32.1    2025-05-22 [1] Bioconductor 3.21 (R 4.5.0)
#>  GenomicFeatures        1.60.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  GenomicRanges        * 1.60.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  glue                   1.8.0     2024-09-30 [1] CRAN (R 4.5.0)
#>  hms                    1.1.3     2023-03-21 [1] CRAN (R 4.5.0)
#>  htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.5.0)
#>  htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.5.0)
#>  httpuv                 1.6.16    2025-04-16 [1] CRAN (R 4.5.0)
#>  httr                   1.4.7     2023-08-15 [1] CRAN (R 4.5.0)
#>  httr2                  1.1.2     2025-03-26 [1] CRAN (R 4.5.0)
#>  IRanges              * 2.42.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  jsonlite               2.0.0     2025-03-27 [1] CRAN (R 4.5.0)
#>  KEGGREST               1.48.1    2025-06-19 [1] Bioconductor 3.21 (R 4.5.1)
#>  knitr                  1.50      2025-03-16 [1] CRAN (R 4.5.0)
#>  lambda.r               1.2.4     2019-09-18 [1] CRAN (R 4.5.0)
#>  later                  1.4.2     2025-04-08 [1] CRAN (R 4.5.0)
#>  lattice                0.22-7    2025-04-02 [1] CRAN (R 4.5.0)
#>  lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.5.0)
#>  magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.5.0)
#>  Matrix                 1.7-3     2025-03-11 [1] CRAN (R 4.5.0)
#>  MatrixGenerics       * 1.20.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  matrixStats          * 1.5.0     2025-01-07 [1] CRAN (R 4.5.0)
#>  memoise                2.0.1     2021-11-26 [1] CRAN (R 4.5.0)
#>  mime                   0.13      2025-03-17 [1] CRAN (R 4.5.0)
#>  miniUI                 0.1.2     2025-04-17 [1] CRAN (R 4.5.0)
#>  MultiAssayExperiment * 1.34.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  pillar                 1.10.2    2025-04-05 [1] CRAN (R 4.5.0)
#>  pkgbuild               1.4.8     2025-05-26 [1] CRAN (R 4.5.0)
#>  pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.5.0)
#>  pkgload                1.4.0     2024-06-28 [1] CRAN (R 4.5.0)
#>  png                    0.1-8     2022-11-29 [1] CRAN (R 4.5.0)
#>  profvis                0.4.0     2024-09-20 [1] CRAN (R 4.5.0)
#>  promises               1.3.3     2025-05-29 [1] CRAN (R 4.5.0)
#>  purrr                  1.0.4     2025-02-05 [1] CRAN (R 4.5.0)
#>  R6                     2.6.1     2025-02-15 [1] CRAN (R 4.5.0)
#>  RaggedExperiment       1.32.2    2025-05-08 [1] Bioconductor 3.21 (R 4.5.0)
#>  rapiclient             0.1.8     2024-09-30 [1] CRAN (R 4.5.0)
#>  rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.5.0)
#>  Rcpp                   1.0.14    2025-01-12 [1] CRAN (R 4.5.0)
#>  RCurl                  1.98-1.17 2025-03-22 [1] CRAN (R 4.5.0)
#>  readr                  2.1.5     2024-01-10 [1] CRAN (R 4.5.0)
#>  remotes                2.5.0     2024-03-17 [1] CRAN (R 4.5.0)
#>  reprex                 2.1.1     2024-07-06 [1] CRAN (R 4.5.0)
#>  restfulr               0.0.15    2022-06-16 [1] CRAN (R 4.5.0)
#>  rjson                  0.2.23    2024-09-16 [1] CRAN (R 4.5.0)
#>  RJSONIO                2.0.0     2025-04-05 [1] CRAN (R 4.5.0)
#>  rlang                  1.1.6     2025-04-11 [1] CRAN (R 4.5.0)
#>  rmarkdown              2.29      2024-11-04 [1] CRAN (R 4.5.0)
#>  Rsamtools              2.24.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  RSQLite                2.4.1     2025-06-08 [1] CRAN (R 4.5.0)
#>  rstudioapi             0.17.1    2024-10-22 [1] CRAN (R 4.5.0)
#>  RTCGAToolbox           2.38.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  rtracklayer            1.68.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  rvest                  1.0.4     2024-02-12 [1] CRAN (R 4.5.0)
#>  S4Arrays               1.8.1     2025-05-29 [1] Bioconductor 3.21 (R 4.5.0)
#>  S4Vectors            * 0.46.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  sessioninfo            1.2.3     2025-02-05 [1] CRAN (R 4.5.0)
#>  shiny                  1.10.0    2024-12-14 [1] CRAN (R 4.5.0)
#>  SparseArray            1.8.0     2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  stringi                1.8.7     2025-03-27 [1] CRAN (R 4.5.0)
#>  stringr                1.5.1     2023-11-14 [1] CRAN (R 4.5.0)
#>  SummarizedExperiment * 1.38.1    2025-04-28 [1] Bioconductor 3.21 (R 4.5.0)
#>  TCGAutils              1.28.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  tibble                 3.3.0     2025-06-08 [1] CRAN (R 4.5.0)
#>  tidyr                  1.3.1     2024-01-24 [1] CRAN (R 4.5.0)
#>  tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.5.0)
#>  tzdb                   0.5.0     2025-03-15 [1] CRAN (R 4.5.0)
#>  UCSC.utils             1.4.0     2025-04-17 [1] Bioconductor 3.21 (R 4.5.0)
#>  urlchecker             1.0.1     2021-11-30 [1] CRAN (R 4.5.0)
#>  usethis                3.1.0     2024-11-26 [1] CRAN (R 4.5.0)
#>  vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.5.0)
#>  withr                  3.0.2     2024-10-28 [1] CRAN (R 4.5.0)
#>  xfun                   0.52      2025-04-02 [1] CRAN (R 4.5.0)
#>  XML                    3.99-0.18 2025-01-01 [1] CRAN (R 4.5.0)
#>  xml2                   1.3.8     2025-03-14 [1] CRAN (R 4.5.0)
#>  xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.5.0)
#>  XVector                0.48.0    2025-04-15 [1] Bioconductor 3.21 (R 4.5.0)
#>  yaml                   2.3.10    2024-07-26 [1] CRAN (R 4.5.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Created on 2025-07-02 with reprex v2.1.1

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