invalid class "DESeqDataSet" object error

[elenichri]

I am trying to run proActiv with 174 TCGA GBM junction files. Everything goes smoothly until the calculation reaches its end. I get the following error:

File loaded into memory
Calculating junction counts
Calculating normalized read counts...
converting counts to integer mode
Error in validObject(.Object) : 
  invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class

I tried installing proActiv via Bioconductor and via devtools/github, but I get the error in both cases. I ran BiocManager::valid() and got 1 too new package and 18 out of date. It is strange because the out_of_date packages are the ones that I have just installed/updated!

What trouble me most is the too new package

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

         Version LibPath                                           
proActiv "1.3.4" "/home/chr.elen/R/x86_64-pc-linux-gnu-library/4.0"

This is weird because my sessionInfo() tells me that I am running proActiv 1.1.6.

R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /data/apps/R/4.0.0/lib64/R/lib/libRblas.so
LAPACK: /data/apps/R/4.0.0/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] devtools_2.4.2         usethis_2.0.1          proActiv_1.1.6         TCGAbiolinks_2.18.0   
 [5] GenomicFeatures_1.42.3 AnnotationDbi_1.52.0   Biobase_2.50.0         GenomicRanges_1.42.0  
 [9] GenomeInfoDb_1.26.7    IRanges_2.24.1         S4Vectors_0.28.1       BiocGenerics_0.36.1   

loaded via a namespace (and not attached):
  [1] backports_1.2.1             Hmisc_4.5-0                 BiocFileCache_1.14.0       
  [4] plyr_1.8.6                  lazyeval_0.2.2              splines_4.0.0              
  [7] BiocParallel_1.24.1         ggplot2_3.3.5               digest_0.6.27              
 [10] ensembldb_2.14.1            htmltools_0.5.1.1           fansi_0.5.0                
 [13] magrittr_2.0.1              checkmate_2.0.0             memoise_2.0.0              
 [16] BSgenome_1.58.0             cluster_2.1.2               remotes_2.4.0              
 [19] Biostrings_2.58.0           readr_1.4.0                 annotate_1.68.0            
 [22] matrixStats_0.59.0          R.utils_2.10.1              askpass_1.1                
 [25] prettyunits_1.1.1           jpeg_0.1-8.1                colorspace_2.0-2           
 [28] blob_1.2.1                  rvest_1.0.0                 rappdirs_0.3.3             
 [31] xfun_0.24                   dplyr_1.0.7                 callr_3.7.0                
 [34] crayon_1.4.1                RCurl_1.98-1.3              jsonlite_1.7.2             
 [37] genefilter_1.72.1           survival_3.2-11             VariantAnnotation_1.36.0   
 [40] glue_1.4.2                  gtable_0.3.0                zlibbioc_1.36.0            
 [43] XVector_0.30.0              DelayedArray_0.16.3         pkgbuild_1.2.0             
 [46] scales_1.1.1                DBI_1.1.1                   Rcpp_1.0.7                 
 [49] xtable_1.8-4                progress_1.2.2              htmlTable_2.2.1            
 [52] foreign_0.8-81              bit_4.0.4                   Formula_1.2-4              
 [55] htmlwidgets_1.5.3           httr_1.4.2                  RColorBrewer_1.1-2         
 [58] ellipsis_0.3.2              pkgconfig_2.0.3             XML_3.99-0.6               
 [61] R.methodsS3_1.8.1           Gviz_1.34.1                 nnet_7.3-16                
 [64] dbplyr_2.1.1                locfit_1.5-9.4              utf8_1.2.1                 
 [67] tidyselect_1.1.1            rlang_0.4.11                munsell_0.5.0              
 [70] tools_4.0.0                 cachem_1.0.5                downloader_0.4             
 [73] cli_3.0.0                   generics_0.1.0              RSQLite_2.2.7              
 [76] stringr_1.4.0               fastmap_1.1.0               processx_3.5.2             
 [79] knitr_1.33                  bit64_4.0.5                 fs_1.5.0                   
 [82] purrr_0.3.4                 AnnotationFilter_1.14.0     packrat_0.6.0              
 [85] R.oo_1.24.0                 xml2_1.3.2                  biomaRt_2.46.3             
 [88] compiler_4.0.0              rstudioapi_0.13             curl_4.3.2                 
 [91] png_0.1-7                   testthat_3.0.4              tibble_3.1.2               
 [94] geneplotter_1.68.0          stringi_1.7.2               ps_1.6.0                   
 [97] desc_1.3.0                  lattice_0.20-44             ProtGenerics_1.22.0        
[100] Matrix_1.3-4                vctrs_0.3.8                 pillar_1.6.1               
[103] lifecycle_1.0.0             BiocManager_1.30.16         data.table_1.14.0          
[106] bitops_1.0-7                rtracklayer_1.50.0          R6_2.5.0                   
[109] latticeExtra_0.6-29         gridExtra_2.3               sessioninfo_1.1.1          
[112] dichromat_2.0-0             assertthat_0.2.1            pkgload_1.2.1              
[115] SummarizedExperiment_1.20.0 rprojroot_2.0.2             openssl_1.4.4              
[118] DESeq2_1.30.1               withr_2.4.2                 GenomicAlignments_1.26.0   
[121] Rsamtools_2.6.0             GenomeInfoDbData_1.2.4      hms_1.1.0                  
[124] grid_4.0.0                  rpart_4.1-15                tidyr_1.1.3                
[127] biovizBase_1.38.0           base64enc_0.1-3            

Could you please help me resolve the problem?

Thank you very much !

[jleechung]

Hi @elenichri , thanks for your interest in proActiv! If you're installing the github version or the one from the Bioconductor development branch you should be seeing 1.3.4. Either way I've not seen this error before. I suppose you are using standard STAR / TopHat2 junction files?

[elenichri]

Thank you @jleechung for your prompt reply! It is weird that I see v1.1.6. If I go into the R library folder, it is indeed v1.3.4. So why do I see v 1.1.6 in my sessionInfo()? And, anyway, why is proActiv v1.3.4 labelled as too new? Please note that I run this on a server, where I don't have admin rights.

Yes, I use TopHat2 junction files.

[jleechung]

@elenichri I see. You can try calling library(proActiv, lib.loc = ...) to load the proActiv from a specific location and see if you then get 1.3.4 in the sess info.

Too new might be because 1.3.4 is from the dev version of Bioconductor but I'm not entirely sure.

[elenichri]

@jleechung I did so and indeed, proActiv 1.3.4 was loaded in the R environment. However, it is still considered too new and I still get the same error when I run proActiv invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class I will try to completely remove proActiv by deleting the respective R library and then try to load an older version. I hope this will work.

[jleechung]

@elenichri Sure. It's also possible that packages from different Bioconductor releases are installed and loaded at the same time. In any case you can perhaps try to process one or two files locally and see if you can reproduce the error.

[elenichri]

Thanks @jleechung . It was a Bioconductor package clash on the server I am using. Problem solved :)