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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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Cannot connect to ExperimentHub server #87

Closed shitiezhu closed 8 months ago

shitiezhu commented 1 year ago

Hi, I got an error when I install the "depmap 1.14.0" r package in R 4.3.1. The error is 

`* installing *source* package 'depmap' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
Error: package or namespace load failed for 'depmap':
 .onLoad failed in loadNamespace() for 'depmap', details:
  call: FUN(X[[i]], ...)
  error: 'copyNumber_22Q1' not found in ExperimentHub
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/Users/shiti/AppData/Local/R/win-library/4.3/depmap'

The downloaded source packages are in
    ‘C:\Users\shiti\AppData\Local\Temp\RtmpwL6nHF\downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘depmap’ had non-zero exit status`
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] miniUI_0.1.1.1        BiocManager_1.30.21.1 compiler_4.3.1        crayon_1.5.2         
 [5] promises_1.2.0.1      Rcpp_1.0.11           stringr_1.5.0         callr_3.7.3          
 [9] later_1.3.1           fastmap_1.1.1         mime_0.12             R6_2.5.1             
[13] htmlwidgets_1.6.2     profvis_0.3.8         shiny_1.7.4.1         rlang_1.1.1          
[17] cachem_1.0.8          stringi_1.7.12        httpuv_1.6.11         fs_1.6.3             
[21] pkgload_1.3.2.1       memoise_2.0.1         cli_3.6.1             magrittr_2.0.3       
[25] ps_1.7.5              digest_0.6.33         processx_3.8.2        rstudioapi_0.15.0    
[29] xtable_1.8-4          remotes_2.4.2.1       devtools_2.4.5        lifecycle_1.0.3      
[33] prettyunits_1.1.1     vctrs_0.6.3           glue_1.6.2            urlchecker_1.0.1     
[37] sessioninfo_1.2.2     pkgbuild_1.4.2        purrr_1.0.1           usethis_2.2.2        
[41] tools_4.3.1           ellipsis_0.3.2        htmltools_0.5.5
lgatto commented 1 year ago

What version of ExperimentHub do you have - the latest is 2.8.1.

Could you check and, if needed, install/update it with BiocManager::install("ExperimentHub") and then try again installing depmap.

lgatto commented 1 year ago

Here's copyNumber_22Q1 in ExperimentHub 2.8.1:

> eh <- ExperimentHub()
snapshotDate(): 2023-04-24
> query(eh, "copyNumber_22Q1")
ExperimentHub with 1 record
# snapshotDate(): 2023-04-24
# names(): EH7524
# package(): depmap
# $dataprovider: Broad Institute
# $species: Homo sapiens
# $rdataclass: tibble
# $rdatadateadded: 2022-04-26
# $title: copyNumber_22Q1
# $description: WES log copy number data for 25368 genes, 1754 cell lines, 35 primary diseases and 38 lineages.
# $taxonomyid: 9606
# $genome: 
# $sourcetype: CSV
# $sourceurl: https://ndownloader.figshare.com/files/34008428
# $sourcesize: NA
# $tags: c("AssayDomainData", "BreastCancerData", "CancerData", "CellCulture", "ColonCancerData",
#   "CopyNumberVariationData", "DiseaseModel", "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", "Genome", "Homo_sapiens_Data", "KidneyCancerData",
#   "LeukemiaCancerData", "LungCancerData", "OrganismData", "OvarianCancerData", "ProstateCancerData",
#   "Proteome", "RepositoryData", "ReproducibleResearch", "StemCell", "Tissue") 
# retrieve record with 'object[["EH7524"]]' 
> eh[["EH7524"]]
snapshotDate(): 2023-04-24
see ?depmap and browseVignettes('depmap') for documentation
downloading 1 resources
retrieving 1 resource
  |===========================================================================================================| 100%

loading from cache
# A tibble: 44,495,472 × 6
   depmap_id  gene            log_copy_number entrez_id gene_name cell_line                                    
   <chr>      <chr>                     <dbl>     <int> <chr>     <chr>                                        
 1 ACH-001533 DDX11L1 (84771)           1.02      84771 DDX11L1   KARPAS1718_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE
 2 ACH-000934 DDX11L1 (84771)           0.855     84771 DDX11L1   MDAMB361_BREAST                              
 3 ACH-000653 DDX11L1 (84771)           1.07      84771 DDX11L1   JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE      
 4 ACH-001497 DDX11L1 (84771)           1.04      84771 DDX11L1   ESO51_OESOPHAGUS                             
 5 ACH-000888 DDX11L1 (84771)           0.701     84771 DDX11L1   NCIH1793_LUNG                                
 6 ACH-000433 DDX11L1 (84771)           0.982     84771 DDX11L1   CAKI1_KIDNEY                                 
 7 ACH-002004 DDX11L1 (84771)           1.03      84771 DDX11L1   UACC62_SKIN_CJ1_RESISTANT                    
 8 ACH-000717 DDX11L1 (84771)           0.759     84771 DDX11L1   COLO680N_OESOPHAGUS                          
 9 ACH-002154 DDX11L1 (84771)           1.14      84771 DDX11L1   LB647SCLC_LUNG                               
10 ACH-002200 DDX11L1 (84771)           1.05      84771 DDX11L1   SW962_VULVA                                  
# ℹ 44,495,462 more rows
# ℹ Use `print(n = ...)` to see more rows
> packageVersion("ExperimentHub")
[1] ‘2.8.1’
YanlanSun commented 9 months ago

I also face this problem, can you give me some suggestions? Thank you very much!

ExperimentHub related information image

lgatto commented 9 months ago

This is linked to ExperimentHub. Try to load it to create a cache and/or see message in installation error.