Question

Error with R package curatedTCGAData while trying to download TCGA MultiAssayExperiments

0

Entering edit mode

svlachavas ▴ 830

@svlachavas-7225

Last seen 6 months ago

Germany/Heidelberg/German Cancer Resear…

Enter the body of text here

Code should be placed in three backticks as shown below

library(curatedTCGAData)
library(TCGAutils)
library(UpSetR)
library(DESeq2)
library(M3C)
luad.mae<- curatedTCGAData(
+     
+     diseaseCode = "LUAD",
+     
+     assays = c(
+         
+         "RPPAArray","Mutation",
+         "RNASeq2GeneNorm", # here perhaps the raw RSEM counts
+         "GISTIC_ThresholdedByGene"
+         
+     ),
+     
+     dry.run = FALSE
+     
+ )
snapshotDate(): 2020-04-27
Working on: LUAD_GISTIC_ThresholdedByGene-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: LUAD_Mutation-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: LUAD_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: LUAD_RPPAArray-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Error in checkSlotAssignment(object, name, value) : 
  assignment of an object of class "NULL" is not valid for slot 'elementMetadata' in an object of class "ExperimentList"; is(value, "DataTable_OR_NULL") is not TRUE

I tried also to remove first and then re-install from Bioc both MAE, curatedTCGA and TCGAutils R packages, but after removing each package I was getting the following warning:

remove.packages("TCGAutils")
Removing package from 'C:/Program Files/R/R-4.0.2/library'
(as 'lib' is unspecified)
Warning messages:
1: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL") 
2: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL") 
3: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL") 
4: multiple methods tables found for ‘rowRanges’ 

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] M3C_1.10.0                  DESeq2_1.28.1               UpSetR_1.4.0               
 [4] TCGAutils_1.8.1             curatedTCGAData_1.10.1      MultiAssayExperiment_1.14.0
 [7] SummarizedExperiment_1.18.2 DelayedArray_0.16.0         MatrixGenerics_1.2.0       
[10] matrixStats_0.57.0          Matrix_1.2-18               Biobase_2.48.0             
[13] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         IRanges_2.24.0             
[16] S4Vectors_0.28.0            BiocGenerics_0.36.0        

loaded via a namespace (and not attached):
  [1] snow_0.4-3                    AnnotationHub_2.20.2         
  [3] BiocFileCache_1.12.1          plyr_1.8.6                   
  [5] lazyeval_0.2.2                splines_4.0.2                
  [7] BiocParallel_1.22.0           usethis_1.6.3                
  [9] ggplot2_3.3.2                 digest_0.6.27                
 [11] foreach_1.5.1                 ensembldb_2.12.1             
 [13] htmltools_0.5.0               matrixcalc_1.0-3             
 [15] fansi_0.4.1                   magrittr_2.0.1               
 [17] memoise_1.1.0                 cluster_2.1.0                
 [19] doParallel_1.0.16             remotes_2.2.0                
 [21] Biostrings_2.56.0             readr_1.4.0                  
 [23] annotate_1.66.0               R.utils_2.10.1               
 [25] askpass_1.1                   prettyunits_1.1.1            
 [27] colorspace_2.0-0              blob_1.2.1                   
 [29] rvest_0.3.6                   rappdirs_0.3.1               
 [31] xfun_0.19                     dplyr_1.0.2                  
 [33] callr_3.5.1                   crayon_1.3.4                 
 [35] RCurl_1.98-1.2                jsonlite_1.7.1               
 [37] genefilter_1.70.0             RaggedExperiment_1.12.0      
 [39] iterators_1.0.13              survival_3.2-7               
 [41] glue_1.4.2                    GenomicDataCommons_1.12.0    
 [43] gtable_0.3.0                  zlibbioc_1.34.0              
 [45] XVector_0.28.0                pkgbuild_1.1.0               
 [47] scales_1.1.1                  DBI_1.1.0                    
 [49] Rcpp_1.0.5                    xtable_1.8-4                 
 [51] progress_1.2.2                reticulate_1.18              
 [53] bit_4.0.4                     umap_0.2.7.0                 
 [55] httr_1.4.2                    RColorBrewer_1.1-2           
 [57] ellipsis_0.3.1                pkgconfig_2.0.3              
 [59] XML_3.99-0.5                  R.methodsS3_1.8.1            
 [61] dbplyr_2.0.0                  locfit_1.5-9.4               
 [63] tidyselect_1.1.0              rlang_0.4.9                  
 [65] later_1.1.0.1                 AnnotationDbi_1.50.3         
 [67] munsell_0.5.0                 BiocVersion_3.11.1           
 [69] tools_4.0.2                   cli_2.2.0                    
 [71] generics_0.1.0                RSQLite_2.2.1                
 [73] ExperimentHub_1.14.2          devtools_2.3.2               
 [75] evaluate_0.14                 stringr_1.4.0                
 [77] fastmap_1.0.1                 yaml_2.2.1                   
 [79] processx_3.4.5                knitr_1.30                   
 [81] bit64_4.0.5                   fs_1.5.0                     
 [83] purrr_0.3.4                   AnnotationFilter_1.12.0      
 [85] mime_0.9                      R.oo_1.24.0                  
 [87] xml2_1.3.2                    biomaRt_2.44.4               
 [89] compiler_4.0.2                rstudioapi_0.13              
 [91] curl_4.3                      interactiveDisplayBase_1.26.3
 [93] testthat_3.0.0                maftools_2.4.12              
 [95] tibble_3.0.4                  geneplotter_1.66.0           
 [97] stringi_1.5.3                 ps_1.5.0                     
 [99] RSpectra_0.16-0               GenomicFeatures_1.40.1       
[101] desc_1.2.0                    lattice_0.20-41              
[103] ProtGenerics_1.20.0           vctrs_0.3.5                  
[105] pillar_1.4.7                  lifecycle_0.2.0              
[107] BiocManager_1.30.10           corpcor_1.6.9                
[109] data.table_1.13.4             bitops_1.0-6                 
[111] httpuv_1.5.4                  rtracklayer_1.48.0           
[113] R6_2.5.0                      promises_1.1.1               
[115] gridExtra_2.3                 codetools_0.2-18             
[117] sessioninfo_1.1.1             assertthat_0.2.1             
[119] pkgload_1.1.0                 openssl_1.4.3                
[121] rprojroot_2.0.2               withr_2.3.0                  
[123] GenomicAlignments_1.24.0      Rsamtools_2.4.0              
[125] GenomeInfoDbData_1.2.3        doSNOW_1.0.19                
[127] hms_0.5.3                     grid_4.0.2                   
[129] rmarkdown_2.5                 Rtsne_0.15                   
[131] shiny_1.5.0                   tinytex_0.27

Any ideas or suggestions why this is happening ? The only recent updates were some R packages like S4Vectors that were updated/re-install due to the github installation of the R package MOFA2-

Best,

Efstathios

MultiAssayExperiment curatedTCGAData TCGAutils • 1.8k views

ADD COMMENT • link 3.4 years ago svlachavas ▴ 830

1

Entering edit mode

Make sure that your Bioconductor installation is up-to-date. Use BiocManager::valid() to check.

It looks like you may be mixing Bioconductor versions because the current release of XVector is 0.30.0 and not 0.28.0 as listed here.

See the BiocManager vignette for working with multiple versions of Bioconductor (if needed).

ADD REPLY • link 3.4 years ago Marcel Ramos 690

0

Entering edit mode

Dear Marcel,

thank you for the immediate feedback and suggestions-I was currently investigating into that, and when performed the suggestions of BiocManager::valid(), again I noticed the following:

 BiocManager::valid()

* sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
 [1] BiocManager_1.30.10 compiler_4.0.2      assertthat_0.2.1    Matrix_1.2-18      
 [5] cli_2.2.0           tools_4.0.2         glue_1.4.2          rstudioapi_0.13    
 [9] yaml_2.2.1          crayon_1.3.4        fansi_0.4.1         grid_4.0.2         
[13] rlang_0.4.9         lattice_0.20-41    

Bioconductor version '3.11'

  * 0 packages out-of-date
  * 3 packages too new

create a valid installation with

  BiocManager::install(c(
    "DelayedArray", "IRanges", "S4Vectors"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
0 packages out-of-date; 3 packages too new 
> library(MultiAssayExperiment)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Error: package 'BiocGenerics' 0.34.0 is loaded, but >= 0.35.0 is required by 'S4Vectors'
In addition: Warning messages:
1: multiple methods tables found for 'which' 
2: undefined slot classes in definition of "XRaw": elementMetadata(class "DataTable_OR_NULL") 
3: undefined slot classes in definition of "XInteger": elementMetadata(class "DataTable_OR_NULL") 
4: undefined slot classes in definition of "XDouble": elementMetadata(class "DataTable_OR_NULL") 
5: multiple methods tables found for 'which' 
6: multiple methods tables found for 'rowRanges' 
7: package 'S4Vectors' was built under R version 4.0.3 
> library(curatedTCGAData)
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: S4Vectors
Error: package 'BiocGenerics' 0.34.0 is loaded, but >= 0.35.0 is required by 'S4Vectors'
In addition: Warning message:
package 'S4Vectors' was built under R version 4.0.3

You think that I should remove and re-install S4Vectors from the Bioc version ? or you think BiocGenerics should be removed and re-installed ?

ADD REPLY • link 3.4 years ago svlachavas ▴ 830

1

Entering edit mode

It seems that you are mixing different versions of binary packages in the same repository; hence, you get the message package 'S4Vectors' was built under R version 4.0.3.

Install only packages for your particular R version. I would recommend that you use R 4.0.3 with Bioconductor 3.12 and only download packages for that R version.

Alternatively, you may be able to check existing version mismatches by doing:

BiocManager::install(c(
    "DelayedArray", "IRanges", "S4Vectors"
  ), update = TRUE, ask = FALSE, checkBuilt = TRUE)

ADD REPLY • link 3.4 years ago Marcel Ramos 690

1

Entering edit mode

Small update-had to remove manually IRanges, S4Vectors and DelayedArrray-then re-install with Bioc and the errors were removed

Thank you one more time for your valuable help !!!

ADD REPLY • link 3.4 years ago svlachavas ▴ 830