YuLab-SMU
Error in enrichKEGG() function
Hi, I encountered some difficulties using enrichKEGG() function, for the example from document page:
gene <- names(geneList)[abs(geneList) > 2]
kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05)
results show,
--> No gene can be mapped....
--> Expected input gene ID:
--> return NULL...
And my current version of the packages are as below.
> packageVersion("clusterProfiler")
[1] ‘4.8.3’
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.8.3
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.7 rstudioapi_0.15.0 magrittr_2.0.3
[5] farver_2.1.1 fs_1.6.3 zlibbioc_1.46.0 vctrs_0.6.3
[9] memoise_2.0.1 RCurl_1.98-1.12 ggtree_3.8.2 htmltools_0.5.6
[13] usethis_2.2.2 curl_5.0.2 gridGraphics_0.5-1 htmlwidgets_1.6.2
[17] desc_1.4.2 plyr_1.8.8 cachem_1.0.8 createKEGGdb_0.0.3
[21] igraph_1.5.1 mime_0.12 lifecycle_1.0.3 pkgconfig_2.0.3
[25] gson_0.1.0 Matrix_1.5-4.1 R6_2.5.1 fastmap_1.1.1
[29] GenomeInfoDbData_1.2.10 shiny_1.7.5 digest_0.6.33 aplot_0.2.1
[33] enrichplot_1.20.3 colorspace_2.1-0 patchwork_1.1.3 AnnotationDbi_1.62.2
[37] S4Vectors_0.38.1 ps_1.7.5 rprojroot_2.0.3 pkgload_1.3.2.1
[41] RSQLite_2.3.1 fansi_1.0.4 httr_1.4.7 polyclip_1.10-4
[45] compiler_4.3.1 remotes_2.4.2.1 bit64_4.0.5 withr_2.5.0
[49] downloader_0.4 BiocParallel_1.34.2 viridis_0.6.4 DBI_1.1.3
[53] pkgbuild_1.4.2 ggforce_0.4.1 R.utils_2.12.2 MASS_7.3-60
[57] sessioninfo_1.2.2 HDO.db_0.99.1 tools_4.3.1 scatterpie_0.2.1
[61] ape_5.7-1 httpuv_1.6.11 R.oo_1.25.0 glue_1.6.2
[65] callr_3.7.3 nlme_3.1-162 GOSemSim_2.26.1 promises_1.2.1
[69] shadowtext_0.1.2 grid_4.3.1 reshape2_1.4.4 fgsea_1.26.0
[73] generics_0.1.3 gtable_0.3.4 R.methodsS3_1.8.2 tidyr_1.3.0
[77] data.table_1.14.8 tidygraph_1.2.3 utf8_1.2.3 XVector_0.40.0
[81] BiocGenerics_0.46.0 ggrepel_0.9.3 pillar_1.9.0 stringr_1.5.0
[85] yulab.utils_0.1.0 later_1.3.1 splines_4.3.1 dplyr_1.1.3
[89] tweenr_2.0.2 treeio_1.24.3 lattice_0.21-8 bit_4.0.5
[93] tidyselect_1.2.0 GO.db_3.17.0 Biostrings_2.68.1 miniUI_0.1.1.1
[97] gridExtra_2.3 IRanges_2.34.1 stats4_4.3.1 graphlayouts_1.0.1
[101] Biobase_2.60.0 devtools_2.4.5 stringi_1.7.12 lazyeval_0.2.2
[105] ggfun_0.1.3 codetools_0.2-19 ggraph_2.1.0 tibble_3.2.1
[109] qvalue_2.32.0 BiocManager_1.30.22 ggplotify_0.1.2 cli_3.6.1
[113] xtable_1.8-4 munsell_0.5.0 processx_3.8.2 Rcpp_1.0.11
[117] GenomeInfoDb_1.36.3 png_0.1-8 parallel_4.3.1 ellipsis_0.3.2
[121] ggplot2_3.4.3 blob_1.2.4 prettyunits_1.1.1 profvis_0.3.8
[125] DOSE_3.26.1 urlchecker_1.0.1 bitops_1.0-7 tidytree_0.4.5
[129] viridisLite_0.4.2 scales_1.2.1 purrr_1.0.2 crayon_1.5.2
[133] rlang_1.1.1 cowplot_1.1.1 fastmatch_1.1-4 KEGGREST_1.40.0
Additionally, when I ran into trouble when produceing KEGG.db by createKEGGdb package. I can't install KEGG.db.
> remotes::install_github('YuLab-SMU/createKEGGdb')
Downloading GitHub repo YuLab-SMU/createKEGGdb@HEAD
Skipping 1 packages not available: clusterProfiler
-- R CMD build ----------------------------------------------------------------------------------------------
v checking for file 'C:\Users\hoffnungslos\AppData\Local\Temp\RtmpCAhIOd\remotes2c5464656e92\YuLab-SMU-createKEGGdb-c7f6308/DESCRIPTION' (396ms)
- preparing 'createKEGGdb':
v checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION
- building 'createKEGGdb_0.0.3.tar.gz'
将程序包安装入‘C:/Users/hoffnungslos/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
* installing *source* package 'createKEGGdb' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (createKEGGdb)
> createKEGGdb::create_kegg_db(c('hsa','mmu'))
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/mmu"...
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
2023-09-22 15:33:54.101141 Getting KEGG data of hsa.
2023-09-22 15:33:54.155461 KEGG data of hsa has been downloaded.
2023-09-22 15:33:54.21737 KEGG data of hsa has been added to the sqlite database.
Reading KEGG annotation online: "https://rest.kegg.jp/link/mmu/pathway"...
2023-09-22 15:33:54.667968 Getting KEGG data of mmu.
2023-09-22 15:33:54.752116 KEGG data of mmu has been downloaded.
2023-09-22 15:33:54.795117 KEGG data of mmu has been added to the sqlite database.
-- R CMD build ----------------------------------------------------------------------------------------------
v checking for file 'C:\Users\hoffnungslos\AppData\Local\Temp\RtmpCAhIOd\file2c54748ccb7/DESCRIPTION' (369ms)
- preparing 'KEGG.db':
v checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'KEGG.db_1.0.tar.gz'
[1] "./KEGG.db_1.0.tar.gz"
Warning messages:
1: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
2: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
3: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
4: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
> install.packages('KEGG.db_1.0.tar.gz',type = 'source')
将程序包安装入‘C:/Users/hoffnungslos/AppData/Local/R/win-library/4.3’
(因为‘lib’没有被指定)
Warning in install.packages :
package ‘KEGG.db_1.0.tar.gz’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
> library(KEGG.db)
Error in library(KEGG.db) : 不存在叫‘KEGG.db’这个名字的程辑包
Looking forward to your reply!
I have the same troble, are you resolve that? Is there some thing wrong with our Internet issue？
I have the same troble, are you resolve that? Is there some thing wrong with our Internet issue？
no, I just put aside this R package for the time being.
@BIGRICEgo
- Please make sure you have the KEGG.db_1.0.tar.gz file in your working directory
- Or use the latest version of clusterProfiler.
Dear all,
I have the same problem. My ClusterProfiler Version should be uptodate. How can I check whether the automatic download has worked?
> head (gene.Entrez)
13024 12575 11815 20716 19215 57435
3.058626 2.888222 2.861515 2.474483 2.081870 2.034194
> enrichWP(gene.Entrez, organism = "Mus musculus")
--> No gene can be mapped....
--> Expected input gene ID: 16453,15519,18024,13871,209357,69227
--> return NULL...
NULL
sessionInfo() R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale: [1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 [4] LC_NUMERIC=C LC_TIME=German_Germany.utf8
time zone: Europe/Berlin tzcode source: internal
attached base packages: [1] grid stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] openxlsx_4.2.5.2 VennDiagram_1.7.3 futile.logger_1.4.3 scales_1.3.0
[5] ggplot2_3.5.1 Seurat_5.1.0 pathview_1.44.0 gprofiler2_0.2.3
[9] DOSE_3.30.1 enrichplot_1.24.0 org.Mm.eg.db_3.19.1 AnnotationDbi_1.66.0
[13] IRanges_2.38.0 S4Vectors_0.42.0 Biobase_2.64.0 BiocGenerics_0.50.0
[17] clusterProfiler_4.12.0 SeuratObject_5.0.2 sp_2.1-4
loaded via a namespace (and not attached):
[1] fs_1.6.4 matrixStats_1.3.0 spatstat.sparse_3.0-3
[4] bitops_1.0-7 HDO.db_0.99.1 httr_1.4.7
[7] RColorBrewer_1.1-3 Rgraphviz_2.48.0 tools_4.4.0
[10] sctransform_0.4.1 utf8_1.2.4 R6_2.5.1
[13] lazyeval_0.2.2 uwot_0.2.2 withr_3.0.0
[16] gridExtra_2.3 progressr_0.14.0 cli_3.6.2
[19] formatR_1.14 spatstat.explore_3.2-7 fastDummies_1.7.3
[22] scatterpie_0.2.2 labeling_0.4.3 KEGGgraph_1.64.0
[25] spatstat.data_3.0-4 ggridges_0.5.6 pbapply_1.7-2
[28] yulab.utils_0.1.4 gson_0.1.0 parallelly_1.37.1
[31] RSQLite_2.3.7 generics_0.1.3 gridGraphics_0.5-1
[34] ica_1.0-3 spatstat.random_3.2-3 dplyr_1.1.4
[37] zip_2.3.1 GO.db_3.19.1 Matrix_1.7-0
[40] fansi_1.0.6 abind_1.4-5 lifecycle_1.0.4
[43] SummarizedExperiment_1.34.0 qvalue_2.36.0 SparseArray_1.4.5
[46] Rtsne_0.17 blob_1.2.4 promises_1.3.0
[49] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.22-6
[52] cowplot_1.1.3 KEGGREST_1.44.0 pillar_1.9.0
[55] fgsea_1.30.0 GenomicRanges_1.56.0 future.apply_1.11.2
[58] codetools_0.2-20 fastmatch_1.1-4 leiden_0.4.3.1
[61] glue_1.7.0 ggfun_0.1.4 data.table_1.15.4
[64] remotes_2.5.0 vctrs_0.6.5 png_0.1-8
[67] treeio_1.28.0 spam_2.10-0 gtable_0.3.5
[70] cachem_1.1.0 S4Arrays_1.4.1 mime_0.12
[73] tidygraph_1.3.1 survival_3.6-4 fitdistrplus_1.1-11
[76] ROCR_1.0-11 nlme_3.1-164 ggtree_3.12.0
[79] bit64_4.0.5 RcppAnnoy_0.0.22 GenomeInfoDb_1.40.0
[82] irlba_2.3.5.1 KernSmooth_2.23-24 colorspace_2.1-0
[85] DBI_1.2.2 DESeq2_1.44.0 tidyselect_1.2.1
[88] bit_4.0.5 compiler_4.4.0 graph_1.82.0
[91] DelayedArray_0.30.1 plotly_4.10.4 shadowtext_0.1.3
[94] lmtest_0.9-40 stringr_1.5.1 digest_0.6.35
[97] goftest_1.2-3 spatstat.utils_3.0-4 XVector_0.44.0
[100] htmltools_0.5.8.1 pkgconfig_2.0.3 MatrixGenerics_1.16.0
[103] fastmap_1.2.0 rlang_1.1.3 htmlwidgets_1.6.4
[106] UCSC.utils_1.0.0 shiny_1.8.1.1 farver_2.1.2
[109] zoo_1.8-12 jsonlite_1.8.8 BiocParallel_1.38.0
[112] GOSemSim_2.30.0 RCurl_1.98-1.14 magrittr_2.0.3
[115] GenomeInfoDbData_1.2.12 ggplotify_0.1.2 dotCall64_1.1-1
[118] patchwork_1.2.0 munsell_0.5.1 Rcpp_1.0.12
[121] ape_5.8 ggnewscale_0.4.10 viridis_0.6.5
[124] reticulate_1.37.0 stringi_1.8.4 ggraph_2.2.1
[127] zlibbioc_1.50.0 MASS_7.3-60.2 plyr_1.8.9
[130] org.Hs.eg.db_3.19.1 parallel_4.4.0 listenv_0.9.1
[133] ggrepel_0.9.5 deldir_2.0-4 Biostrings_2.72.0
[136] graphlayouts_1.1.1 splines_4.4.0 tensor_1.5
[139] locfit_1.5-9.9 igraph_2.0.3 spatstat.geom_3.2-9
[142] RcppHNSW_0.6.0 reshape2_1.4.4 futile.options_1.0.1
[145] XML_3.99-0.16.1 lambda.r_1.2.4 renv_1.0.7
[148] BiocManager_1.30.23 tweenr_2.0.3 httpuv_1.6.15
[151] RANN_2.6.1 tidyr_1.3.1 purrr_1.0.2
[154] polyclip_1.10-6 future_1.33.2 scattermore_1.2
[157] ggforce_0.4.2 xtable_1.8-4 RSpectra_0.16-1
[160] tidytree_0.4.6 later_1.3.2 viridisLite_0.4.2
[163] snow_0.4-4 tibble_3.2.1 aplot_0.2.2
[166] memoise_2.0.1 cluster_2.1.6 globals_0.16.3
Best and thanks, Nina
