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waldronlab / cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
https://waldronlab.io/cBioPortalData/
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clinicalData() .cache, db_collect #76

Closed kmezhoud closed 7 months ago

kmezhoud commented 7 months ago

Hi @LiNk-NY , I am facing this issue with clinicalData function. Thanks!

> cgds <- cBioPortal(
    hostname = "www.cbioportal.org",
    protocol = "https",
    api = "/api/v2/api-docs"
)
Warning message:
In .service_validate_md5sum(api_reference_url, api_reference_md5sum,  :
  service version differs from validated version
    service url: https://www.cbioportal.org/api/v2/api-docs
    observed md5sum: 7314de5c5e8056e4e07b411b3e5a0cb9
    expected md5sum: 07ceb76cc5afcf54a9cf2e1a689b18f7
>  cBioPortalData::getStudies(cgds)
# A tibble: 398 × 13
   name          description publicStudy pmid  citation groups status importDate
   <chr>         <chr>       <lgl>       <chr> <chr>    <chr>   <int> <chr>     
 1 Adenoid Cyst… Whole exom… TRUE        2609… Martelo… ACYC;…      0 2023-12-0…
 2 Adenoid Cyst… Whole-exom… TRUE        2368… Ho et a… ACYC;…      0 2023-12-0…
 3 Adenoid Cyst… Targeted S… TRUE        2441… Ross et… ACYC;…      0 2023-12-0…
 4 Adenoid Cyst… Whole-geno… TRUE        2686… Rettig … ACYC;…      0 2023-12-0…
 5 Adenoid Cyst… WGS of 21 … TRUE        2663… Mitani … ACYC;…      0 2023-12-0…
 6 Adenoid Cyst… Whole-geno… TRUE        2682… Drier e… ACYC        0 2023-12-0…
 7 Adenoid Cyst… Whole exom… TRUE        2377… Stephen… ACYC;…      0 2023-12-0…
 8 Adenoid Cyst… Multi-Inst… TRUE        3148… Allen e… ACYC;…      0 2023-12-0…
 9 Basal Cell C… Whole-exom… TRUE        2695… Bonilla… PUBLIC      0 2023-12-0…
10 Acute Lympho… Comprehens… TRUE        2573… Anderss… PUBLIC      0 2023-12-0…
# ℹ 388 more rows
# ℹ 5 more variables: allSampleCount <int>, readPermission <lgl>,
#   studyId <chr>, cancerTypeId <chr>, referenceGenome <chr>
# ℹ Use `print(n = ...)` to see more rows
> clinicalData(cgds, "gbm_tcga_pub")
Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.
> clinicalData(cgds, "gbm_tcga_pub")
/home/kirus/.cache/R/cBioPortalData
  does not exist, create directory? (yes/no): yes
Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Africa/Tunis
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] cBioPortalData_2.12.0       MultiAssayExperiment_1.26.0
 [3] SummarizedExperiment_1.30.2 Biobase_2.60.0             
 [5] GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [7] IRanges_2.34.1              S4Vectors_0.38.2           
 [9] BiocGenerics_0.46.0         MatrixGenerics_1.12.3      
[11] matrixStats_1.2.0           AnVIL_1.12.4               
[13] dplyr_1.1.4                

loaded via a namespace (and not attached):
 [1] DBI_1.2.1                 bitops_1.0-7             
 [3] formatR_1.14              biomaRt_2.56.1           
 [5] rlang_1.1.3               magrittr_2.0.3           
 [7] compiler_4.3.2            RSQLite_2.3.5            
 [9] GenomicFeatures_1.52.2    png_0.1-8                
[11] vctrs_0.6.5               rvest_1.0.3              
[13] stringr_1.5.1             pkgconfig_2.0.3          
[15] crayon_1.5.2              fastmap_1.1.1            
[17] dbplyr_2.4.0              XVector_0.40.0           
[19] ellipsis_0.3.2            utf8_1.2.4               
[21] Rsamtools_2.16.0          promises_1.2.1           
[23] tzdb_0.4.0                purrr_1.0.2              
[25] bit_4.0.5                 zlibbioc_1.46.0          
[27] cachem_1.0.8              jsonlite_1.8.8           
[29] progress_1.2.3            blob_1.2.4               
[31] later_1.3.2               DelayedArray_0.26.7      
[33] BiocParallel_1.34.2       parallel_4.3.2           
[35] prettyunits_1.2.0         R6_2.5.1                 
[37] stringi_1.8.3             rtracklayer_1.60.1       
[39] Rcpp_1.0.12               readr_2.1.5              
[41] httpuv_1.6.14             Matrix_1.6-3             
[43] tidyselect_1.2.0          abind_1.4-5              
[45] yaml_2.3.8                codetools_0.2-19         
[47] miniUI_0.1.1.1            curl_5.2.0               
[49] lattice_0.22-5            tibble_3.2.1             
[51] shiny_1.8.0               KEGGREST_1.40.1          
[53] lambda.r_1.2.4            futile.logger_1.4.3      
[55] BiocFileCache_2.8.0       xml2_1.3.6               
[57] Biostrings_2.68.1         pillar_1.9.0             
[59] filelock_1.0.3            DT_0.31                  
[61] TCGAutils_1.20.4          RCircos_1.2.2            
[63] generics_0.1.3            RCurl_1.98-1.14          
[65] hms_1.1.3                 xtable_1.8-4             
[67] RTCGAToolbox_2.30.0       glue_1.7.0               
[69] tools_4.3.2               BiocIO_1.10.0            
[71] data.table_1.15.0         GenomicAlignments_1.36.0 
[73] rapiclient_0.1.3          XML_3.99-0.16.1          
[75] grid_4.3.2                tidyr_1.3.1              
[77] AnnotationDbi_1.62.2      GenomeInfoDbData_1.2.10  
[79] RaggedExperiment_1.24.2   RJSONIO_1.3-1.9          
[81] restfulr_0.0.15           cli_3.6.2                
[83] rappdirs_0.3.3            futile.options_1.0.1     
[85] fansi_1.0.6               GenomicDataCommons_1.24.3
[87] S4Arrays_1.0.6            digest_0.6.34            
[89] rjson_0.2.21              htmlwidgets_1.6.4        
[91] memoise_2.0.1             htmltools_0.5.7          
[93] lifecycle_1.0.4           httr_1.4.7               
[95] mime_0.12                 bit64_4.0.5
LiNk-NY commented 7 months ago

Hi Karim! @kmezhoud

Thank you for spotting this.

Unfortunately the version of cBioPortalData posted is too old and there have been some changes to the API. Please use either the current Bioconductor release RELEASE_3_18 or devel.

Best regards, Marcel

kmezhoud commented 7 months ago

yes, Bioconductor packages are not updated! It is done! and it works. Thanks!