enrichKegg Description is <NA>

[llrs]

In the recent versions of clusterProfiler I have found that all my pathways are NA see:

               ID Description GeneRatio BgRatio       pvalue  p.adjust     qvalue
hsa00603 hsa00603        <NA>      2/20 14/5869 0.0009797338 0.0305606 0.02680754
hsa00511 hsa00511        <NA>      2/20 17/5869 0.0014552666 0.0305606 0.02680754
            geneID Count
hsa00603 2717/3074     2
hsa00511 2519/3074     2

Also, have a look at the example, it doesn't return any significant pathway, which may not be what you wanted to show :D

R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.2 LTS

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

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

other attached packages: [1] BiocInstaller_1.24.0 clusterProfiler_3.2.10 DOSE_3.0.9

loaded via a namespace (and not attached): [1] qvalue_2.6.0 gtools_3.5.0 fgsea_1.0.2
[4] reshape2_1.4.2 splines_3.3.2 colorspace_1.3-0
[7] graphite_1.20.1 stats4_3.3.2 hash_2.2.6
[10] chron_2.3-47 DBI_0.5-1 BiocParallel_1.8.1
[13] rappdirs_0.3.1 BiocGenerics_0.20.0 RColorBrewer_1.1-2
[16] gsubfn_0.6-6 KEGG.db_3.2.3 plyr_1.8.4
[19] stringr_1.1.0 STRINGdb_1.14.0 munsell_0.4.3
[22] GOSemSim_2.0.3 gtable_0.2.0 caTools_1.17.1
[25] Biobase_2.34.0 IRanges_2.8.1 parallel_3.3.2
[28] AnnotationDbi_1.36.0 proto_1.0.0 Rcpp_0.12.8
[31] KernSmooth_2.23-15 reactome.db_1.58.0 scales_0.4.1
[34] ReactomePA_1.18.1 gdata_2.17.0 plotrix_3.6-3
[37] DO.db_2.9 S4Vectors_0.12.0 graph_1.52.0
[40] gplots_3.0.1 gridExtra_2.2.1 fastmatch_1.0-4
[43] ggplot2_2.2.0 png_0.1-7 stringi_1.1.2
[46] grid_3.3.2 tools_3.3.2 bitops_1.0-6
[49] magrittr_1.5 sqldf_0.4-10 lazyeval_0.2.0
[52] RCurl_1.95-4.8 tibble_1.2 RSQLite_1.0.0
[55] GO.db_3.4.0 tidyr_0.6.0 data.table_1.9.8
[58] assertthat_0.1 igraph_1.0.1

[GuangchuangYu]

> require(clusterProfiler)
Loading required package: clusterProfiler
Loading required package: DOSE

DOSE v3.0.9  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

clusterProfiler v3.2.10  For help: https://guangchuangyu.github.io/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
> data(geneList)
> de = names(geneList)
> de = names(geneList)[1:100]
> x = enrichKEGG(de)
> x
#
# over-representation test
#
#...@organism    hsa 
#...@ontology    KEGG 
#...@keytype     kegg 
#...@gene    chr [1:100] "4312" "8318" "10874" "55143" "55388" "991" ...
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...3 enriched terms found
'data.frame':   3 obs. of  9 variables:
 $ ID         : chr  "hsa04110" "hsa04114" "hsa04115"
 $ Description: chr  "Cell cycle" "Oocyte meiosis" "p53 signaling pathway"
 $ GeneRatio  : chr  "8/41" "6/41" "4/41"
 $ BgRatio    : chr  "124/7176" "124/7176" "69/7176"
 $ pvalue     : num  3.76e-07 6.46e-05 6.06e-04
 $ p.adjust   : num  3.72e-05 3.20e-03 2.00e-02
 $ qvalue     : num  3.48e-05 2.99e-03 1.87e-02
 $ geneID     : chr  "8318/991/9133/890/983/4085/7272/1111" "991/9133/983/4085/51806/6790" "9133/6241/983/1111"
 $ Count      : int  8 6 4
#...Citation
  Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
  clusterProfiler: an R package for comparing biological themes among
  gene clusters. OMICS: A Journal of Integrative Biology
  2012, 16(5):284-287 

I can't reproduce your issue, and thanks for pointing out the example.

[llrs]

Strange, after three trials I finally could print the description. It might be a problem with my setup... Thanks for your quick response

[GuangchuangYu]

and also might be a problem of the KEGG web site.