default version number?

[lwaldron]

Seems like there should be a default version number (probably 2.0.1, which would be the default preference for most users), so that the default invocation doesn't result in error. Why not?

suppressPackageStartupMessages(library(curatedTCGAData))
curatedTCGAData()
#> Error in curatedTCGAData(): 'version' is not '1.1.38' or '2.0.1'; see '?curatedTCGAData'

^{Created on 2021-05-28 by the reprex package (v2.0.0)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.0 (2021-05-18) #> os Ubuntu 18.04.5 LTS #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/New_York #> date 2021-05-28 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib source #> AnnotationDbi 1.54.0 2021-05-19 [1] Bioconductor #> AnnotationHub 3.0.0 2021-05-19 [1] Bioconductor #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) #> backports 1.2.1 2020-12-09 [1] CRAN (R 4.0.3) #> Biobase * 2.52.0 2021-05-19 [1] Bioconductor #> BiocFileCache 2.0.0 2021-05-19 [1] Bioconductor #> BiocGenerics * 0.38.0 2021-05-19 [1] Bioconductor #> BiocManager 1.30.15 2021-05-11 [1] CRAN (R 4.1.0) #> BiocVersion 3.13.1 2021-03-19 [1] Bioconductor #> Biostrings 2.60.0 2021-05-19 [1] Bioconductor #> bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2) #> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2) #> bitops 1.0-7 2021-04-24 [1] CRAN (R 4.0.5) #> blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0) #> cachem 1.0.5 2021-05-15 [1] CRAN (R 4.1.0) #> cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.5) #> crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.4) #> curatedTCGAData * 1.14.0 2021-05-20 [1] Bioconductor #> curl 4.3.1 2021-04-30 [1] CRAN (R 4.1.0) #> DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.4) #> dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.0.5) #> DelayedArray 0.18.0 2021-05-19 [1] Bioconductor #> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3) #> dplyr 1.0.6 2021-05-05 [1] CRAN (R 4.1.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0) #> ExperimentHub 2.0.0 2021-05-19 [1] Bioconductor #> fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.4) #> filelock 1.0.2 2018-10-05 [1] CRAN (R 4.1.0) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) #> generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3) #> GenomeInfoDb * 1.28.0 2021-05-19 [1] Bioconductor #> GenomeInfoDbData 1.2.6 2021-05-25 [1] Bioconductor #> GenomicRanges * 1.44.0 2021-05-19 [1] Bioconductor #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) #> highr 0.9 2021-04-16 [1] CRAN (R 4.0.5) #> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.4) #> httpuv 1.6.1 2021-05-07 [1] CRAN (R 4.1.0) #> httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) #> interactiveDisplayBase 1.30.0 2021-05-19 [1] Bioconductor #> IRanges * 2.26.0 2021-05-19 [1] Bioconductor #> KEGGREST 1.32.0 2021-05-19 [1] Bioconductor #> knitr 1.33 2021-04-24 [1] CRAN (R 4.0.5) #> later 1.2.0 2021-04-23 [1] CRAN (R 4.0.5) #> lattice 0.20-44 2021-05-02 [2] CRAN (R 4.1.0) #> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.4) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3) #> Matrix 1.3-3 2021-05-04 [2] CRAN (R 4.0.5) #> MatrixGenerics * 1.4.0 2021-05-19 [1] Bioconductor #> matrixStats * 0.58.0 2021-01-29 [1] CRAN (R 4.0.4) #> memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.4) #> mime 0.10 2021-02-13 [1] CRAN (R 4.0.4) #> MultiAssayExperiment * 1.18.0 2021-05-19 [1] Bioconductor #> pillar 1.6.1 2021-05-16 [1] CRAN (R 4.1.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0) #> promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.4) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0) #> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3) #> rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.0.4) #> Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.4) #> RCurl 1.98-1.3 2021-03-16 [1] CRAN (R 4.0.4) #> reprex 2.0.0 2021-04-02 [1] CRAN (R 4.0.5) #> rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0) #> rmarkdown 2.8 2021-05-07 [1] CRAN (R 4.1.0) #> RSQLite 2.2.7 2021-04-22 [1] CRAN (R 4.0.5) #> S4Vectors * 0.30.0 2021-05-19 [1] Bioconductor #> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) #> shiny 1.6.0 2021-01-25 [1] CRAN (R 4.0.4) #> stringi 1.6.2 2021-05-17 [1] CRAN (R 4.1.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) #> styler 1.4.1 2021-03-30 [1] CRAN (R 4.0.5) #> SummarizedExperiment * 1.22.0 2021-05-19 [1] Bioconductor #> tibble 3.1.2 2021-05-16 [1] CRAN (R 4.1.0) #> tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0) #> utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.4) #> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0) #> withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.5) #> xfun 0.23 2021-05-15 [1] CRAN (R 4.1.0) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0) #> XVector 0.32.0 2021-05-19 [1] Bioconductor #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0) #> zlibbioc 1.38.0 2021-05-19 [1] Bioconductor #> #> [1] /usr/local/lib/R/site-library #> [2] /usr/lib/R/library ```

[LiNk-NY]

Hi Levi, @lwaldron

I wanted this to be a conscious choice for the user since there are some significant additions / changes to the data. A 2.0.1 version may disturb the older workflows that use the older 1.1.38 data.

If you feel strongly about this, I can make the change and include a warning about it.

Best, Marcel

[DarioS]

Vignette has

2 Data Versions curatedTCGAData now has a version 2.0.1 set of data with a number of improvements and bug fixes.

but the latest version on Bioconductor is 1.20.0. What is it lower than mentioned in vignette? Does the improvements refer to the harmonisation done in 2016 and available from Genomic Data Commons?

[LiNk-NY]

Hi Dario, @DarioS Data and package versions are not the same. The improvements do not include the harmonization done by the GDC. Please refer to the GenomicDataCommons package for GDC data. Best, Marcel

[kjiojio]

suppressPackageStartupMessages(library(curatedTCGAData)) curatedTCGAData()

> Error in curatedTCGAData(): 'version' is not '1.1.38' or '2.0.1'; see '?curatedTCGAData'

this question doesn't fix?

[LiNk-NY]

You have to pick a version. See the version section in the ?curatedTCGAData.