osca-source/osca.intro

Introduction to the OSCA book.

osca.intro's Issues

Build failure because problem downloading E-MTAB-5522 data from ArrayExpress

The latest build on BioC 3.15 is failing because a download used in the 'The SingleCellExperiment class' (inst/book/sce-class.Rmd) returns a 404 error ¹.

OSCA.intro/inst/book/sce-class.Rmd

Lines 63 to 64 in 3687787

	lun.zip <- bfcrpath(bfc, file.path("https://www.ebi.ac.uk/arrayexpress/files",
	"E-MTAB-5522/E-MTAB-5522.processed.1.zip"))

download.file(
  "https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip", 
  tempfile())
#> Warning in download.file("https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/
#> E-MTAB-5522.processed.1.zip", : cannot open URL 'https://www.ebi.ac.uk/
#> biostudies/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip': HTTP status was '404
#> Not Found'
#> Error in download.file("https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip", : cannot open URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5522/E-MTAB-5522.processed.1.zip'

^{Created on 2022-10-15 with reprex v2.0.2}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23)
#>  os       macOS Big Sur ... 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_AU.UTF-8
#>  ctype    en_AU.UTF-8
#>  tz       Australia/Melbourne
#>  date     2022-10-15
#>  pandoc   2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P cli           3.4.1   2022-09-23 [?] CRAN (R 4.2.0)
#>  P digest        0.6.29  2021-12-01 [?] CRAN (R 4.2.0)
#>  P evaluate      0.17    2022-10-07 [?] CRAN (R 4.2.0)
#>  P fansi         1.0.3   2022-03-24 [?] CRAN (R 4.2.0)
#>  P fastmap       1.1.0   2021-01-25 [?] CRAN (R 4.2.0)
#>  P fs            1.5.2   2021-12-08 [?] CRAN (R 4.2.0)
#>  P glue          1.6.2   2022-02-24 [?] CRAN (R 4.2.0)
#>  P highr         0.9     2021-04-16 [?] CRAN (R 4.2.0)
#>  P htmltools     0.5.3   2022-07-18 [?] CRAN (R 4.2.0)
#>  P knitr         1.40    2022-08-24 [?] CRAN (R 4.2.0)
#>  P lifecycle     1.0.3   2022-10-07 [?] CRAN (R 4.2.0)
#>  P magrittr      2.0.3   2022-03-30 [?] CRAN (R 4.2.0)
#>  P pillar        1.8.1   2022-08-19 [?] CRAN (R 4.2.0)
#>  P pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 4.2.0)
#>  P purrr         0.3.5   2022-10-06 [?] CRAN (R 4.2.0)
#>    R.cache       0.16.0  2022-07-21 [3] CRAN (R 4.2.0)
#>  P R.methodsS3   1.8.2   2022-06-13 [?] CRAN (R 4.2.0)
#>  P R.oo          1.25.0  2022-06-12 [?] CRAN (R 4.2.0)
#>  P R.utils       2.12.0  2022-06-28 [?] CRAN (R 4.2.0)
#>  P reprex        2.0.2   2022-08-17 [?] CRAN (R 4.2.0)
#>  P rlang         1.0.6   2022-09-24 [?] CRAN (R 4.2.0)
#>  P rmarkdown     2.17    2022-10-07 [?] CRAN (R 4.2.0)
#>  P rstudioapi    0.14    2022-08-22 [?] CRAN (R 4.2.0)
#>    sessioninfo   1.2.2   2021-12-06 [3] CRAN (R 4.2.0)
#>  P stringi       1.7.8   2022-07-11 [?] CRAN (R 4.2.0)
#>  P stringr       1.4.1   2022-08-20 [?] CRAN (R 4.2.0)
#>    styler        1.7.0   2022-03-13 [3] CRAN (R 4.2.0)
#>  P tibble        3.1.8   2022-07-22 [?] CRAN (R 4.2.0)
#>  P utf8          1.2.2   2021-07-24 [?] CRAN (R 4.2.0)
#>  P vctrs         0.4.2   2022-09-29 [?] CRAN (R 4.2.0)
#>  P withr         2.5.0   2022-03-03 [?] CRAN (R 4.2.0)
#>  P xfun          0.33    2022-09-12 [?] CRAN (R 4.2.0)
#>  P yaml          2.3.5   2022-02-21 [?] CRAN (R 4.2.0)
#> 
#>  [1] /Users/Peter/Library/Caches/org.R-project.R/R/renv/library/OSCA.intro-6bfda6b6/R-4.2/x86_64-apple-darwin17.0
#>  [2] /Users/Peter/GitHub/OSCA.intro/renv/sandbox/R-4.2/x86_64-apple-darwin17.0/84ba8b13
#>  [3] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Visiting the ArrayExpress page for that resource (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-5522) I'm able to download the data in a web browser by pointing and clicking², but I can't find or figure out the URL for direct download.
So rather than this being caused by an intermittent unavailability of the download, perhaps ArrayExpress have removed this ability to point to a URL for a download?

@LTLA Do you know if this has happened before and if the data are available elsewhere?

Footnotes

1. The same error also occurs the latest build on BioC 3.16. ↩

2. Clicking the 'download' button next to 'Processed Data' and then clicking the 'Download' button under 'Download as a ZIP file' box that pops up. ↩