compareCluster returns errors with version 3.17.0

[YulongNiu]

Hi,

I want to report the errors from compareCluster() with latest version (3.17.0) of clusterProfiler package. kall.RData is a example input list that can be downloaded.

library('clusterProfiler')
library('org.At.tair.db')

load('kall.RData')

kallGOBP <- compareCluster(geneCluster = kall[1:2],
                           fun = 'enrichGO',
                           OrgDb = 'org.At.tair.db',
                           keyType= 'TAIR',
                           ont = 'BP',
                           universe = keys(org.At.tair.db),
                           pAdjustMethod = 'BH',
                           pvalueCutoff=0.05,
                           qvalueCutoff=0.1)

I got errors like:

. + Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “NULL” is not valid for @‘fun’ in an object of class “compareClusterResult”; is(value, "character") is not TRUE

But when I run the GO enrichment for single cluster, it works:

enrichGO(kall[[1]],
         OrgDb = 'org.At.tair.db',
         keyType= 'TAIR',
         ont = 'BP',
         universe = keys(org.At.tair.db),
         pAdjustMethod = 'BH',
         pvalueCutoff=0.05,
         qvalueCutoff=0.1)

Running environment is:

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 32 (Thirty Two)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.9.so

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

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

other attached packages:
[1] org.At.tair.db_3.11.4  AnnotationDbi_1.50.1   IRanges_2.22.2        
[4] S4Vectors_0.26.1       Biobase_2.48.0         BiocGenerics_0.34.0   
[7] clusterProfiler_3.17.0

loaded via a namespace (and not attached):
 [1] viridis_0.5.1       httr_1.4.1          tidyr_1.1.0        
 [4] tidygraph_1.2.0     bit64_0.9-7         jsonlite_1.7.0     
 [7] viridisLite_0.3.0   splines_4.0.2       ggraph_2.0.3       
[10] DO.db_2.9           BiocManager_1.30.10 rvcheck_0.1.8      
[13] triebeard_0.3.0     urltools_1.7.3      blob_1.2.1         
[16] progress_1.2.2      ggrepel_0.8.2       pillar_1.4.6       
[19] RSQLite_2.2.0       lattice_0.20-41     glue_1.4.1         
[22] downloader_0.4      digest_0.6.25       RColorBrewer_1.1-2 
[25] polyclip_1.10-0     qvalue_2.20.0       colorspace_1.4-1   
[28] cowplot_1.0.0       Matrix_1.2-18       plyr_1.8.6         
[31] pkgconfig_2.0.3     purrr_0.3.4         GO.db_3.11.4       
[34] scales_1.1.1        ggplotify_0.0.5     europepmc_0.4      
[37] tweenr_1.0.1        enrichplot_1.9.1    BiocParallel_1.22.0
[40] ggforce_0.3.2       tibble_3.0.3        generics_0.0.2     
[43] farver_2.0.3        ggplot2_3.3.2       ellipsis_0.3.1     
[46] magrittr_1.5        crayon_1.3.4        memoise_1.1.0      
[49] DOSE_3.15.0         MASS_7.3-51.6       xml2_1.3.2         
[52] tools_4.0.2         data.table_1.12.8   prettyunits_1.1.1  
[55] hms_0.5.3           lifecycle_0.2.0     stringr_1.4.0      
[58] munsell_0.5.0       compiler_4.0.2      gridGraphics_0.5-0 
[61] rlang_0.4.7         ggridges_0.5.2      grid_4.0.2         
[64] igraph_1.2.5        gtable_0.3.0        DBI_1.1.0          
[67] reshape2_1.4.4      graphlayouts_0.7.0  R6_2.4.1           
[70] gridExtra_2.3       dplyr_1.0.0         bit_1.1-15.2       
[73] fastmatch_1.1-0     fgsea_1.14.0        GOSemSim_2.15.0    
[76] stringi_1.4.6       Rcpp_1.0.5          vctrs_0.3.1        
[79] scatterpie_0.1.4    tidyselect_1.1.0   

[EvelynZav]

Hi, did you ever figure this out? I keep getting the error message "assignment of an object of class “NULL” is not valid for @‘fun’ in an object of class “compareClusterResult”; is(value, "character") is not TRUE" however none of my objects are NULL..

[YulongNiu]

Hi, did you ever figure this out? I keep getting the error message "assignment of an object of class “NULL” is not valid for @‘fun’ in an object of class “compareClusterResult”; is(value, "character") is not TRUE" however none of my objects are NULL..

It works on R 3.6.3. The error is associated the R > 4.0.0.

[EvelynZav]

Ah thank you! I have been trying to find R 3.6.3 for Mac OS... I am pretty new to R still.

[PFRoux]

Hi there !

I am still having the exact same issue despite using the GitHub version.

Thanks a lot for your help.

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8

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

other attached packages:
 [1] devtools_2.3.1         usethis_1.6.1          ReactomePA_1.32.0      clusterProfiler_3.16.0 qusage_2.22.0         
 [6] plotrix_3.7-8          data.table_1.13.0      ggrepel_0.8.2          sva_3.36.0             BiocParallel_1.22.0   
[11] genefilter_1.70.0      mgcv_1.8-31            nlme_3.1-148           pheatmap_1.0.12        gridExtra_2.3         
[16] ggplot2_3.3.2          reshape2_1.4.4         magick_2.4.0           hgug4112a.db_3.2.3     org.Hs.eg.db_3.11.4   
[21] AnnotationDbi_1.50.1   IRanges_2.22.2         S4Vectors_0.26.1       Biobase_2.48.0         BiocGenerics_0.34.0   
[26] limma_3.44.3          

loaded via a namespace (and not attached):
  [1] backports_1.1.8     fastmatch_1.1-0     plyr_1.8.6          igraph_1.2.5        splines_4.0.0       TH.data_1.0-10     
  [7] urltools_1.7.3      digest_0.6.25       htmltools_0.5.0     GOSemSim_2.14.0     viridis_0.5.1       GO.db_3.11.4       
 [13] fansi_0.4.1         magrittr_1.5        checkmate_2.0.0     memoise_1.1.0       remotes_2.2.0       annotate_1.66.0    
 [19] graphlayouts_0.7.0  matrixStats_0.56.0  sandwich_2.5-1      enrichplot_1.8.1    prettyunits_1.1.1   colorspace_1.4-1   
 [25] blob_1.2.1          rappdirs_0.3.1      xfun_0.15           dplyr_1.0.0         callr_3.4.3         crayon_1.3.4       
 [31] RCurl_1.98-1.2      jsonlite_1.7.0      graph_1.66.0        scatterpie_0.1.4    survival_3.2-3      zoo_1.8-8          
 [37] glue_1.4.1          polyclip_1.10-0     gtable_0.3.0        emmeans_1.4.8       pkgbuild_1.1.0      graphite_1.34.0    
 [43] scales_1.1.1        DOSE_3.14.0         mvtnorm_1.1-1       DBI_1.1.0           edgeR_3.30.3        Rcpp_1.0.5         
 [49] viridisLite_0.3.0   xtable_1.8-4        progress_1.2.2      gridGraphics_0.5-0  bit_1.1-15.2        reactome.db_1.70.0 
 [55] europepmc_0.4       httr_1.4.1          fgsea_1.14.0        RColorBrewer_1.1-2  ellipsis_0.3.1      pkgconfig_2.0.3    
 [61] XML_3.99-0.4        farver_2.0.3        locfit_1.5-9.4      ggplotify_0.0.5     tidyselect_1.1.0    labeling_0.3       
 [67] rlang_0.4.6         munsell_0.5.0       tools_4.0.0         cli_2.0.2           downloader_0.4      generics_0.0.2     
 [73] RSQLite_2.2.0       ggridges_0.5.2      evaluate_0.14       stringr_1.4.0       yaml_2.2.1          processx_3.4.3     
 [79] fs_1.4.2            knitr_1.29          bit64_0.9-7         tidygraph_1.2.0     purrr_0.3.4         ggraph_2.0.3       
 [85] DO.db_2.9           xml2_1.3.2          BiocStyle_2.16.0    compiler_4.0.0      rstudioapi_0.11     curl_4.3           
 [91] testthat_2.3.2      tibble_3.0.2        tweenr_1.0.1        stringi_1.4.6       ps_1.3.3            desc_1.2.0         
 [97] lattice_0.20-41     Matrix_1.2-18       fftw_1.0-6          vctrs_0.3.1         pillar_1.4.6        lifecycle_0.2.0    
[103] BiocManager_1.30.10 triebeard_0.3.0     estimability_1.3    cowplot_1.0.0       bitops_1.0-6        qvalue_2.20.0      
[109] R6_2.4.1            sessioninfo_1.1.1   codetools_0.2-16    pkgload_1.1.0       assertthat_0.2.1    MASS_7.3-51.6      
[115] rprojroot_1.3-2     withr_2.2.0         multcomp_1.4-13     hms_0.5.3           grid_4.0.0          tidyr_1.1.0        
[121] coda_0.19-3         rmarkdown_2.3       rvcheck_0.1.8       ggforce_0.3.2      

[huerqiang]

@PFRoux
Please use the latest version of the clusterProfiler(3.17.1) in Github

[PFRoux]

Thanks a lot for your feedback. But how to select to version on GitHub ? Best Pierre-François Roux De : Erqiang Hu <notifications@github.com> Répondre à : YuLab-SMU/clusterProfiler <reply@reply.github.com> Date : mercredi 26 août 2020 à 12:30 À : YuLab-SMU/clusterProfiler <clusterProfiler@noreply.github.com> Cc : PFRoux <pierre-francois.roux@orange.fr>, Mention <mention@noreply.github.com> Objet : Re: [YuLab-SMU/clusterProfiler] compareCluster returns errors with version 3.17.0 (#282) @PFRoux Please use the latest version of the clusterProfiler(3.17.1) in Github — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.