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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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error in evaluating the argument 'x' in selecting a method for function 'get': argument is of length zero #74

Closed dpolychr closed 2 years ago

dpolychr commented 2 years ago

Hi,

Many thanks for this useful package. I have installed it successfully however when I am trying to download and cache datasets using ExperimentHub I am getting the following error:

crispr <- eh[["EH2261"]]
see ?depmap and browseVignettes('depmap') for documentation
downloading 1 resources
retrieving 1 resource
  |=================================================================================================================================================================================| 100%

loading from cache
Error: failed to load resource
  name: EH2261
  title: crispr_19Q1
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': argument is of length zero

Could you please advise?

Many thanks, Dimitris

lgatto commented 2 years ago

It works here.

> library(depmap)
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

snapshotDate(): 2021-10-19
This is depmap release 21Q3
> crispr_19Q1()
see ?depmap and browseVignettes('depmap') for documentation
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
# A tibble: 9,839,772 × 6
   depmap_id  cell_line                    gene   gene_name entrez_id dependency
   <chr>      <chr>                        <chr>  <chr>     <chr>          <dbl>
 1 ACH-000004 HEL_HAEMATOPOIETIC_AND_LYMP… A1BG … A1BG      1             0.135 
 2 ACH-000005 HEL9217_HAEMATOPOIETIC_AND_… A1BG … A1BG      1            -0.212 
 3 ACH-000007 LS513_LARGE_INTESTINE        A1BG … A1BG      1             0.0433
 4 ACH-000009 C2BBE1_LARGE_INTESTINE       A1BG … A1BG      1             0.0705
 5 ACH-000011 253J_URINARY_TRACT           A1BG … A1BG      1             0.191 
 6 ACH-000012 HCC827_LUNG                  A1BG … A1BG      1            -0.0104
 7 ACH-000013 ONCODG1_OVARY                A1BG … A1BG      1             0.0210
 8 ACH-000014 HS294T_SKIN                  A1BG … A1BG      1             0.113 
 9 ACH-000015 NCIH1581_LUNG                A1BG … A1BG      1            -0.0742
10 ACH-000017 SKBR3_BREAST                 A1BG … A1BG      1             0.133 
# … with 9,839,762 more rows
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

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

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

other attached packages:
[1] depmap_1.8.0 dplyr_1.0.7 

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0               tidyselect_1.1.1             
 [3] BiocVersion_3.14.0            purrr_0.3.4                  
 [5] vctrs_0.3.8                   generics_0.1.1               
 [7] htmltools_0.5.2               stats4_4.1.2                 
 [9] BiocFileCache_2.2.0           yaml_2.2.1                   
[11] utf8_1.2.2                    interactiveDisplayBase_1.32.0
[13] blob_1.2.2                    rlang_0.4.12                 
[15] pillar_1.6.4                  later_1.3.0                  
[17] withr_2.4.3                   glue_1.6.0                   
[19] DBI_1.1.2                     rappdirs_0.3.3               
[21] BiocGenerics_0.40.0           bit64_4.0.5                  
[23] dbplyr_2.1.1                  GenomeInfoDbData_1.2.7       
[25] lifecycle_1.0.1               zlibbioc_1.40.0              
[27] ExperimentHub_2.2.0           Biostrings_2.62.0            
[29] memoise_2.0.1                 Biobase_2.54.0               
[31] IRanges_2.28.0                fastmap_1.1.0                
[33] httpuv_1.6.4                  GenomeInfoDb_1.30.0          
[35] curl_4.3.2                    fansi_0.5.0                  
[37] AnnotationDbi_1.56.2          Rcpp_1.0.7                   
[39] xtable_1.8-4                  promises_1.2.0.1             
[41] filelock_1.0.2                BiocManager_1.30.16          
[43] cachem_1.0.6                  S4Vectors_0.32.3             
[45] XVector_0.34.0                mime_0.12                    
[47] bit_4.0.4                     AnnotationHub_3.2.0          
[49] png_0.1-7                     digest_0.6.29                
[51] shiny_1.7.1                   cli_3.1.0                    
[53] tools_4.1.2                   bitops_1.0-7                 
[55] magrittr_2.0.1                RCurl_1.98-1.5               
[57] tibble_3.1.6                  RSQLite_2.2.9                
[59] crayon_1.4.2                  pkgconfig_2.0.3              
[61] ellipsis_0.3.2                assertthat_0.2.1             
[63] httr_1.4.2                    R6_2.5.1                     
[65] compiler_4.1.2

Make sure you use R >= 4.1 and update your packages.

dpolychr commented 2 years ago

Thanks @lgatto works now - I've updated to R 4.1 (I was 4.0), removed the old cache from ExperimentHub (otherwise library depmap was failing to install) and all good now

lgatto commented 2 years ago

Excellent!