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:
- update these build columns
- add a
build_check_date column to the getStudies(cbio, buildReport = TRUE) output, providing the date when these builds were checked
- document how to update the build columns (in README.Rmd?)
- 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)
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#> tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.0)
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#> 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)
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#>
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#> * ── Packages attached to the search path.
#>
#> ──────────────────────────────────────────────────────────────────────────────
Created on 2025-07-02 with reprex v2.1.1
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 ininst/scripts/buildStudieswere run so that they haven't been tested? It would be good to:build_check_datecolumn to thegetStudies(cbio, buildReport = TRUE)output, providing the date when these builds were checkedsuppressPackageStartupMessages({ 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 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