bug in gdcdata?

[LiNk-NY]

Hi Sean, @seandavi

I am getting an error in both release and devel using the gdcdata download function. Was there a change to the API with accessing legacy archive data? :thinking:

library(GenomicDataCommons)
#> Loading required package: magrittr
#> 
#> Attaching package: 'GenomicDataCommons'
#> The following object is masked from 'package:stats':
#> 
#>     filter

query <- files(legacy = TRUE) %>%
    filter( ~ cases.project.project_id == "TCGA-COAD" &
        data_category == "Gene expression" &
        data_type == "Exon quantification")

gdc_set_cache(directory = tempdir())
#> GDC Cache directory set to: /tmp/RtmpZy8SUZ
qu <- manifest(query)
qq <- gdcdata(qu$id[1:4])
#> Error: '{"data": {"hits": [], "pagination": {"sort": "", "page": 0, "total": 0, "size": 0, "from": 0, "count": 0, "pages": 0}}, "warnings": {}}' does not exist in current working directory ('/tmp/Rtmpepf3MV/reprex2b61675e2b76').

^{Created on 2020-09-14 by the reprex package (v0.3.0)}

http://bioconductor.org/checkResults/devel/bioc-LATEST/TCGAutils/malbec1-buildsrc.html http://bioconductor.org/checkResults/release/bioc-LATEST/TCGAutils/malbec2-buildsrc.html

Thanks!

[LiNk-NY]

Hi Sean, @seandavi This may be related? The package is not passing on Linux: http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicDataCommons/nebbiolo1-checksrc.html

The source package is not available: http://bioconductor.org/packages/3.13/bioc/html/GenomicDataCommons.html

This is the error from the build report:

> # and get the data, placing it into the gdc_cache() directory
> fpaths <- gdcdata(uuids, use_cached=TRUE)
Error in (function (uri, destination, overwrite, progress, token = NULL,  : 
  Unavailable For Legal Reasons (Internet draft) (HTTP 451).
Calls: gdcdata -> mapply -> <Anonymous> -> stop_for_status
Execution halted