Error: se does not inherit from class SummarizedExperiment

Question

[WUSCHEL]

Hi,

I am using DEP package for analysis of deferentially enriched proteins. I get an error when testing comparisions, this same scripts worked in my old PC.

data_diff_manual <- test_diff(data_imp_knn, type = "manual", 
+                               test = c('mut_0h__vs_WT_0h_', 
+                                        'mut_0h__vs_WT_0h_',
+                                        'mut_0h__vs_WT_0h_'))

Error message:

Error: se does not inherit from class SummarizedExperiment

How can I fix this?

[Friederike]

Which version of DEP are you using? Which type of object is data_imp_knn (e.g., what's the output of class(data_imp_knn), str(data_imp_knn) etc.

Did you generate that object with the workflow detailed in their latest vignette or did you use a previously generate Robject?

[WUSCHEL]

Thank you Friederike :) R = 3.6.1

> class(data_imp_knn)
[1] "SummarizedExperiment"
attr(,"package")
[1] "SummarizedExperiment"


> str(data_imp_knn)
Formal class 'SummarizedExperiment' [package "SummarizedExperiment"] with 5 slots
  ..@ colData        :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots

Seems bioconductor is not compatible with R 3.6.

[Friederike]

Seems bioconductor is not compatible with R 3.6.

What do you mean by that? Have you tried updating all your BioC packages? Which R version are you using?

[WUSCHEL]

version.string R version 3.6.1 (2019-07-05)

Yes I've updates, but getting error Error: Bioconductor version '3.8' requires R version '3.5'; see https://bioconductor.org/install

[Friederike]

3.8 is not the most recent one, as is indicated when you follow the link in the error message.

[WUSCHEL]

Thanks. I've installed everything again, but doesn't help.

I get this warning message. How to resolve this.

> library(DEP)
Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.1)
than is installed on your system (1.0.2). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

[WUSCHEL]

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

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

other attached packages:
 [1] imputeLCMD_2.0              impute_1.58.0               pcaMethods_1.76.0          
 [4] norm_1.0-9.5                tmvtnorm_1.4-10             gmm_1.6-2                  
 [7] sandwich_2.5-1              Matrix_1.2-17               mvtnorm_1.0-11             
[10] SummarizedExperiment_1.14.1 DelayedArray_0.10.0         BiocParallel_1.17.18       
[13] matrixStats_0.54.0          Biobase_2.44.0              GenomicRanges_1.36.0       
[16] GenomeInfoDb_1.20.0         IRanges_2.18.1              S4Vectors_0.22.0           
[19] BiocGenerics_0.30.0         fitdistrplus_1.0-14         npsurv_0.4-0               
[22] lsei_1.2-0                  survival_2.44-1.1           MASS_7.3-51.4              
[25] DEP_1.6.0                   data.table_1.12.2           forcats_0.4.0              
[28] stringr_1.4.0               dplyr_0.8.3                 purrr_0.3.2                
[31] readr_1.3.1                 tidyr_0.8.3                 tibble_2.1.3               
[34] ggplot2_3.2.0               tidyverse_1.2.1            

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1       rjson_0.2.20           circlize_0.4.6         XVector_0.24.0        
 [5] GlobalOptions_0.1.0    clue_0.3-57            rstudioapi_0.10        mzR_2.18.0            
 [9] affyio_1.54.0          DT_0.7                 lubridate_1.7.4        xml2_1.2.1            
[13] splines_3.6.1          codetools_0.2-16       ncdf4_1.16.1           doParallel_1.0.15     
[17] zeallot_0.1.0          jsonlite_1.6           broom_0.5.2            cluster_2.1.0         
[21] vsn_3.52.0             png_0.1-7              shinydashboard_0.7.1   shiny_1.3.2           
[25] BiocManager_1.30.4     compiler_3.6.1         httr_1.4.0             backports_1.1.4       
[29] assertthat_0.2.1       lazyeval_0.2.2         limma_3.40.6           cli_1.1.0             
[33] later_0.8.0            htmltools_0.3.6        tools_3.6.1            gtable_0.3.0          
[37] glue_1.3.1             GenomeInfoDbData_1.2.1 affy_1.62.0            Rcpp_1.0.2            
[41] MALDIquant_1.19.3      cellranger_1.1.0       vctrs_0.2.0            preprocessCore_1.46.0 
[45] nlme_3.1-140           iterators_1.0.12       rvest_0.3.4            mime_0.7              
[49] XML_3.98-1.20          zlibbioc_1.30.0        zoo_1.8-6              scales_1.0.0          
[53] MSnbase_2.10.1         hms_0.5.0              promises_1.0.1         ProtGenerics_1.16.0   
[57] RColorBrewer_1.1-2     ComplexHeatmap_2.0.0   yaml_2.2.0             gridExtra_2.3         
[61] stringi_1.4.3          foreach_1.4.7          shape_1.4.4            rlang_0.4.0           
[65] pkgconfig_2.0.2        bitops_1.0-6           mzID_1.22.0            lattice_0.20-38       
[69] labeling_0.3           htmlwidgets_1.3        tidyselect_0.2.5       plyr_1.8.4            
[73] magrittr_1.5           R6_2.4.0               generics_0.0.2         pillar_1.4.2          
[77] haven_2.1.1            withr_2.1.2            RCurl_1.95-4.12        modelr_0.1.4          
[81] crayon_1.3.4           GetoptLong_0.1.7       grid_3.6.1             readxl_1.3.1          
[85] digest_0.6.20          xtable_1.8-4           httpuv_1.5.1           munsell_0.5.0

[WUSCHEL]

When I try to reinstall, get this error now.

  * installing *source* package 'DEP' ...
    ** using staged installation
    ** R
    Warning: no function found corresponding to methods exports from 'GenomicRanges' for: 'FactorToClass'
    Warning: no function found corresponding to methods exports from 'DelayedArray' for: 'splitAsList'
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
      namespace 'ProtGenerics' 1.16.0 is already loaded, but >= 1.17.2 is required
    Calls: <Anonymous> ... namespaceImport -> loadNamespace -> namespaceImport -> loadNamespace
    Execution halted
    ERROR: lazy loading failed for package 'DEP'
    * removing 'C:/Users/AWY/Documents/R/win-library/3.6/DEP'
    Warning in install.packages :
      installation of package ‘C:/Users/AWY/Desktop/DEP_1.7.0.tar.gz’ had non-zero exit status

[Friederike]

Has the DEP package ever worked for you?

The thing is: it's very difficult for us to diagnose from afar what exactly is going on, there seem to be a couple of clashes of different packages and dependencies, but at this point, it's almost impossible to identify the original culprit. If I were you, I'd probably try to start from a clean slate, i.e. update bioconductor and the re-install DEP. If DEP is the only package throwing an error, it's probably best to reach out to the authors themselves (either via their github page or the bioconductor forum).

[Devon Ryan]

Don't install the development version (1.7.0 has not and will not ever be released as an actual version). Also, don't mix and match packages between bioconductor releases, that is likely to cause problems such as what you're seeing.