The items in "qvalue" column by enrichKEGG （enrichGO-BP-CC-MF） are all "NA"

[Roner2022]

GO_kk=enrichGO(gene,OrgDb = org.Hs.eg.db, pvalueCutoff =1,qvalueCutoff = 1, ont="ALL", readable =T)

错误于get("GO2ONT", envir = GO_DATA): 'envir'参数无效

GO_BP=enrichGO(gene,OrgDb = org.Hs.eg.db, pvalueCutoff =1, qvalueCutoff = 1, ont="BP", readable =T)

GO_MF=enrichGO(gene,OrgDb = org.Hs.eg.db, pvalueCutoff =1, qvalueCutoff = 1, ont="MF", readable =T)

GO_CC=enrichGO(gene,OrgDb = org.Hs.eg.db, pvalueCutoff =1, pAdjustMethod ="BH", qvalueCutoff = 1, ont="CC", readable =T)

GO_BP = GO_BP@result
GO_MF = GO_MF@result
GO_CC = GO_CC@result
GO_enrich = rbind(GO_BP,GO_MF,GO_CC)

 

| >

KEGG_kk <- enrichKEGG(gene, organism = "hsa",pvalueCutoff =1, qvalueCutoff =1) 警告信息: 1: In grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), : Viewport has zero dimension(s)

2: In grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), :
Viewport has zero dimension(s)

3: In grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), :
Viewport has zero dimension(s)

4: In file(file, "rt") :
URL 'https://raw.githubusercontent.com/YuLab-SMU/clusterProfiler/refs/heads/gh-pages/md5.txt': status was 'Could not resolve hostname'

[guidohooiveld]

Is there any reason you are using the development/GitHub version of clusterPofiler?

I am asking because everything works fine when using the release version and the example data set. See code below. When using the example code, does it work for you?

Also, if you really would like to use the GitHub version, please check here to make sure that you install all required GitHub packages in the proper order as well!
See under point 4. here: #804 (comment)

Gene Ontology (ALL)

> library(clusterProfiler)
> library(enrichplot)
> library(DOSE)
> 
> data(geneList)
> de <- names(geneList)[1:100]
> 
> x <- enrichGO(de, 'org.Hs.eg.db', pvalueCutoff = 1,
+               qvalueCutoff = 1, ont="ALL", readable =TRUE)

> 
> as.data.frame(x)[1:5,]
           ONTOLOGY         ID                          Description GeneRatio
GO:0007059       BP GO:0007059               chromosome segregation     34/99
GO:0098813       BP GO:0098813       nuclear chromosome segregation     31/99
GO:0000819       BP GO:0000819         sister chromatid segregation     28/99
GO:0000070       BP GO:0000070 mitotic sister chromatid segregation     26/99
GO:0140014       BP GO:0140014             mitotic nuclear division     29/99
             BgRatio RichFactor FoldEnrichment   zScore       pvalue
GO:0007059 434/18860 0.07834101       14.92436 21.31834 5.455834e-31
GO:0098813 323/18860 0.09597523       18.28377 22.75982 6.626003e-31
GO:0000819 233/18860 0.12017167       22.89331 24.42682 1.189654e-30
GO:0000070 192/18860 0.13541667       25.79756 25.08763 7.632382e-30
GO:0140014 281/18860 0.10320285       19.66066 22.89381 8.511544e-30
               p.adjust       qvalue
GO:0007059 5.655293e-28 4.537068e-28
GO:0098813 5.655293e-28 4.537068e-28
GO:0000819 6.769131e-28 5.430666e-28
GO:0000070 2.905841e-27 2.331267e-27
GO:0140014 2.905841e-27 2.331267e-27
                                                                                                                                                                                                             geneID
GO:0007059 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/HJURP/SKA1/NUSAP1/TPX2/TACC3/NEK2/CENPM/CENPN/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA
GO:0098813                   CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA
GO:0000819                                    CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/TOP2A/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B
GO:0000070                                                CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B
GO:0140014                              CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA
           Count
GO:0007059    34
GO:0098813    31
GO:0000819    28
GO:0000070    26
GO:0140014    29
> 

KEGG

> y <- enrichKEGG(de, organism = "hsa", pvalueCutoff = 1, qvalueCutoff =1)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> as.data.frame(y)[1:5,]
                   category           subcategory       ID
hsa04110 Cellular Processes Cell growth and death hsa04110
hsa04218 Cellular Processes Cell growth and death hsa04218
hsa04814 Cellular Processes         Cell motility hsa04814
hsa04114 Cellular Processes Cell growth and death hsa04114
hsa04657 Organismal Systems         Immune system hsa04657
                     Description GeneRatio  BgRatio RichFactor FoldEnrichment
hsa04110              Cell cycle     12/59 158/9522 0.07594937      12.257455
hsa04218     Cellular senescence      7/59 157/9522 0.04458599       7.195725
hsa04814          Motor proteins      7/59 197/9522 0.03553299       5.734664
hsa04114          Oocyte meiosis      6/59 139/9522 0.04316547       6.966468
hsa04657 IL-17 signaling pathway      5/59  95/9522 0.05263158       8.494202
            zScore       pvalue     p.adjust       qvalue
hsa04110 11.266550 1.636065e-10 2.061443e-08 1.894392e-08
hsa04218  6.180747 4.815436e-05 3.033725e-03 2.787884e-03
hsa04814  5.302134 2.001221e-04 6.528682e-03 5.999624e-03
hsa04114  5.595085 2.072597e-04 6.528682e-03 5.999624e-03
hsa04657  5.796332 2.908514e-04 7.329455e-03 6.735506e-03
                                                             geneID Count
hsa04110 8318/991/9133/10403/890/983/4085/81620/7272/9212/1111/9319    12
hsa04218                          2305/4605/9133/890/983/51806/1111     7
hsa04814                     9493/1062/81930/3832/3833/146909/10112     7
hsa04114                               991/9133/983/4085/51806/6790     6
hsa04657                                   4312/6280/6279/6278/3627     5
> 

> sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
[1] DOSE_4.4.0             enrichplot_1.30.4      clusterProfiler_4.18.4

loaded via a namespace (and not attached):
  [1] DBI_1.2.3               gson_0.1.0              rlang_1.1.7            
  [4] magrittr_2.0.4          compiler_4.5.1          RSQLite_2.4.5          
  [7] png_0.1-8               systemfonts_1.3.1       vctrs_0.7.0            
 [10] reshape2_1.4.5          stringr_1.6.0           pkgconfig_2.0.3        
 [13] crayon_1.5.3            fastmap_1.2.0           XVector_0.50.0         
 [16] purrr_1.2.1             bit_4.6.0               cachem_1.1.0           
 [19] aplot_0.2.9             jsonlite_2.0.0          blob_1.3.0             
 [22] tidydr_0.0.6            BiocParallel_1.44.0     tweenr_2.0.3           
 [25] parallel_4.5.1          cluster_2.1.8.1         R6_2.6.1               
 [28] stringi_1.8.7           RColorBrewer_1.1-3      GOSemSim_2.36.0        
 [31] Rcpp_1.1.1              Seqinfo_1.0.0           ggtangle_0.1.1         
 [34] R.utils_2.13.0          IRanges_2.44.0          Matrix_1.7-4           
 [37] splines_4.5.1           igraph_2.2.1            tidyselect_1.2.1       
 [40] qvalue_2.42.0           dichromat_2.0-0.1       codetools_0.2-20       
 [43] lattice_0.22-7          tibble_3.3.1            plyr_1.8.9             
 [46] Biobase_2.70.0          treeio_1.34.0           withr_3.0.2            
 [49] KEGGREST_1.50.0         S7_0.2.1                gridGraphics_0.5-1     
 [52] scatterpie_0.2.6        polyclip_1.10-7         Biostrings_2.78.0      
 [55] pillar_1.11.1           ggtree_4.0.4            stats4_4.5.1           
 [58] ggfun_0.2.0             generics_0.1.4          S4Vectors_0.48.0       
 [61] ggplot2_4.0.1           scales_1.4.0            tidytree_0.4.7         
 [64] glue_1.8.0              gdtools_0.4.4           lazyeval_0.2.2         
 [67] tools_4.5.1             ggnewscale_0.5.2        data.table_1.18.0      
 [70] fgsea_1.36.2            ggiraph_0.9.3           fs_1.6.6               
 [73] fastmatch_1.1-8         cowplot_1.2.0           grid_4.5.1             
 [76] tidyr_1.3.2             ape_5.8-1               AnnotationDbi_1.72.0   
 [79] nlme_3.1-168            patchwork_1.3.2         ggforce_0.5.0          
 [82] cli_3.6.5               rappdirs_0.3.4          fontBitstreamVera_0.1.1
 [85] dplyr_1.1.4             gtable_0.3.6            R.methodsS3_1.8.2      
 [88] yulab.utils_0.2.3       digest_0.6.39           fontquiver_0.2.1       
 [91] BiocGenerics_0.56.0     ggrepel_0.9.6           ggplotify_0.1.3        
 [94] org.Hs.eg.db_3.22.0     htmlwidgets_1.6.4       farver_2.1.2           
 [97] memoise_2.0.1           htmltools_0.5.9         R.oo_1.27.1            
[100] lifecycle_1.0.5         httr_1.4.7              GO.db_3.22.0           
[103] fontLiberation_0.1.0    bit64_4.6.0-1           MASS_7.3-65            
>

[Roner2022]

I occasionally browsed GitHub, discovered a new version, and wanted to try it for routine analysis, but encountered unexpected issues. However, following your advice, everything is now working normally. Thank you !

[GuangchuangYu]

the github version of enrichit fixes this issue.