Can't get data from ExperimentHub

[lgatto]

While the depmap data is on ExperimentHub, I can't seem to actually download it.

> library(ExperimentHub)
> eh <- ExperimentHub()
snapshotDate(): 2019-04-16
> query(eh, "depmap")
ExperimentHub with 7 records
# snapshotDate(): 2019-04-16 
# $dataprovider: Broad Institute
# $species: Homo sapiens
# $rdataclass: tibble
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH2260"]]' 

           title             
  EH2260 | rnai_19Q1         
  EH2261 | crispr_19Q1       
  EH2262 | copyNumber_19Q1   
  EH2263 | RPPA_19Q1         
  EH2264 | TPM_19Q1          
  EH2265 | mutationCalls_19Q1
  EH2266 | metadata_19Q1     
> eh["EH2260"]
ExperimentHub with 1 record
# snapshotDate(): 2019-04-16 
# names(): EH2260
# package(): depmap
# $dataprovider: Broad Institute
# $species: Homo sapiens
# $rdataclass: tibble
# $rdatadateadded: 2019-04-15
# $title: rnai_19Q1
# $description: (DEMETER2) Batch and off-target corrected RNAi gene knockdow...
# $taxonomyid: 9606
# $genome: 
# $sourcetype: CSV
# $sourceurl: https://ndownloader.figshare.com/files/13515395
# $sourcesize: NA
# $tags: c("ExperimentHub", "ExperimentData", "ReproducibleResearch",
#   "RepositoryData", "AssayDomainData", "CopyNumberVariationData",
#   "DiseaseModel", "CancerData", "BreastCancerData", "ColonCancerData",
#   "KidneyCancerData", "LeukemiaCancerData", "LungCancerData",
#   "OvarianCancerData", "ProstateCancerData", "OrganismData",
#   "Homo_sapiens_Data", "PackageTypeData", "SpecimenSource",
#   "CellCulture", "Genome", "Proteome", "StemCell", "Tissue") 
# retrieve record with 'object[["EH2260"]]' 
> eh[["EH2260"]]
snapshotDate(): 2019-04-16
see ?depmap and browseVignettes('depmap') for documentation
downloading 1 resources
retrieving 1 resource
Downloading: 240 B     
Error: failed to load resource
  name: EH2260
  title: rnai_19Q1
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: ‘https://experimenthub.bioconductor.org/fetch/2260’
  local file path: ‘/home/lgatto/.cache/ExperimentHub/66b14bbce11c_2260’
  reason: Forbidden (HTTP 403). 
2: bfcadd() failed; resource removed
  rid: BFC30
  fpath: ‘https://experimenthub.bioconductor.org/fetch/2260’
  reason: download failed 
3: download failed
  hub path: ‘https://experimenthub.bioconductor.org/fetch/2260’
  cache resource: ‘EH2260 : 2260’
  reason: bfcadd() failed; see warnings() 

@lshep - is this an issue with the depmap package that is still missing something?

This is with

> sessionInfo()
R version 3.6.0 beta (2019-04-15 r76395)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS:   /usr/lib/libblas.so.3.8.0
LAPACK: /usr/lib/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] depmap_0.2.0          dplyr_0.8.0.1         ExperimentHub_1.9.3  
[4] AnnotationHub_2.15.12 BiocFileCache_1.7.9   dbplyr_1.3.0         
[7] BiocGenerics_0.29.2  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1                    later_0.8.0                  
 [3] compiler_3.6.0                pillar_1.3.1                 
 [5] BiocManager_1.30.4            prettyunits_1.0.2            
 [7] remotes_2.0.4                 tools_3.6.0                  
 [9] digest_0.6.18                 pkgbuild_1.0.3               
[11] bit_1.1-14                    RSQLite_2.1.1                
[13] memoise_1.1.0                 tibble_2.1.1                 
[15] pkgconfig_2.0.2               rlang_0.3.4                  
[17] shiny_1.3.1                   DBI_1.0.0                    
[19] cli_1.1.0                     yaml_2.2.0                   
[21] curl_3.3                      withr_2.1.2                  
[23] httr_1.4.0                    IRanges_2.17.5               
[25] S4Vectors_0.21.23             rappdirs_0.3.1               
[27] stats4_3.6.0                  rprojroot_1.3-2              
[29] bit64_0.9-7                   tidyselect_0.2.5             
[31] Biobase_2.43.1                glue_1.3.1                   
[33] R6_2.4.0                      processx_3.3.0               
[35] AnnotationDbi_1.45.1          callr_3.2.0                  
[37] purrr_0.3.2                   blob_1.1.1                   
[39] magrittr_1.5                  promises_1.0.1               
[41] htmltools_0.3.6               backports_1.1.4              
[43] ps_1.3.0                      assertthat_0.2.1             
[45] xtable_1.8-3                  mime_0.6                     
[47] interactiveDisplayBase_1.21.0 httpuv_1.5.1                 
[49] crayon_1.3.4                 

[lshep]

I'll double check that the data is public on S3 and double check the file names.

[lshep]

The RDataPaths in the inst/extdata/metadata.csv file used a capital .Rda while the file names themselves have a lowercase .rda. Do you have a preference? It would be easier for me to rename the files to a capital Rda on S3 but I can do either

[lgatto]

As you prefer.

[lshep]

Please try now, it should be resolved.

[lgatto]

Fantastic, thank you!