Error: package or namespace load failed for ‘EGSEA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

Question

I am currently trying to use this library for a phosphoproteomics data analysis, which is suggested by a paper on an phosphoproteomics analysis tool.

When I use this

library(EGSEA)

I get this

Error: package or namespace load failed for ‘EGSEA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘KEGGdzPathwaysGEO’

How can I resolve this issue? I've tried reinstalling this package many times and even tried updating to a new R version.

SessionInfo()

R version 4.0.3 (2020-10-10)
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] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] pathview_1.30.1      topGO_2.42.0         SparseM_1.78         GO.db_3.12.1        
[5] graph_1.68.0         AnnotationDbi_1.52.0 IRanges_2.24.1       S4Vectors_0.28.1    
[9] gage_2.40.1          rmotifx_1.0          devtools_2.3.2       usethis_2.0.0       
[13] ggseqlogo_0.1        shinydashboard_0.7.1 cowplot_1.1.1        shiny_1.6.0         
[17] reshape2_1.4.4       heatmaply_1.1.1      viridis_0.5.1        viridisLite_0.3.0   
[21] plotly_4.9.3         forcats_0.5.1        stringr_1.4.0        dplyr_1.0.3         
[25] purrr_0.3.4          readr_1.4.0          tidyr_1.1.2          tibble_3.0.5        
[29] ggplot2_3.3.3        tidyverse_1.3.0      Biobase_2.50.0       BiocGenerics_0.36.0 
[33] limma_3.46.0        
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0            RSQLite_2.2.3               htmlwidgets_1.5.3          
[4] grid_4.0.3                  TSP_1.1-10                  BiocParallel_1.24.1        
[7] R2HTML_2.3.2                munsell_0.5.0               codetools_0.2-18           
[10] DT_0.17                     withr_2.4.1                 colorspace_2.0-0           
[13] rstudioapi_0.13             MatrixGenerics_1.2.0        KEGGgraph_1.50.0           
[16] GenomeInfoDbData_1.2.4      hwriter_1.3.2               bit64_4.0.5                
[19] rprojroot_2.0.2             vctrs_0.3.6                 generics_0.1.0             
[22] R6_2.5.0                    GenomeInfoDb_1.26.2         Glimma_2.0.0               
[25] seriation_1.2-9             locfit_1.5-9.4              bitops_1.0-6               
[28] DelayedArray_0.16.1         assertthat_0.2.1            promises_1.1.1             
[31] scales_1.1.1                gtable_0.3.0                processx_3.4.5             
[34] rlang_0.4.10                genefilter_1.72.1           splines_4.0.3              
[37] lazyeval_0.2.2              broom_0.7.3                 yaml_2.2.1                 
[40] BiocManager_1.30.10         modelr_0.1.8                backports_1.2.1            
[43] httpuv_1.5.5                tools_4.0.3                 ellipsis_0.3.1             
[46] gplots_3.1.1                RColorBrewer_1.1-2          HTMLUtils_0.1.7            
[49] sessioninfo_1.1.1           Rcpp_1.0.6                  plyr_1.8.6                 
[52] zlibbioc_1.36.0             RCurl_1.98-1.2              ps_1.5.0                   
[55] prettyunits_1.1.1           SummarizedExperiment_1.20.0 haven_2.3.1                
[58] fs_1.5.0                    magrittr_2.0.1              data.table_1.13.6          
[61] reprex_1.0.0                matrixStats_0.57.0          pkgload_1.1.0              
[64] hms_1.0.0                   mime_0.9                    GSVA_1.38.0                
[67] xtable_1.8-4                XML_3.99-0.5                readxl_1.3.1               
[70] gridExtra_2.3               EGSEAdata_1.18.0            testthat_3.0.1             
[73] compiler_4.0.3              KernSmooth_2.23-18          crayon_1.3.4               
[76] htmltools_0.5.1.1           later_1.1.0.1               geneplotter_1.68.0         
[79] lubridate_1.7.9.2           DBI_1.1.1                   dbplyr_2.0.0               
[82] Matrix_1.3-2                cli_2.2.0                   GenomicRanges_1.42.0       
[85] pkgconfig_2.0.3             registry_0.5-1              xml2_1.3.2                 
[88] foreach_1.5.1               annotate_1.68.0             webshot_0.5.2              
[91] XVector_0.30.0              rvest_0.3.6                 callr_3.5.1                
[94] digest_0.6.27               Biostrings_2.58.0           cellranger_1.1.0           
[97] dendextend_1.14.0           edgeR_3.32.1                GSEABase_1.52.1           
[100] curl_4.3                    gtools_3.8.2                lifecycle_0.2.0          
[103] jsonlite_1.7.2              desc_1.2.0                  fansi_0.4.2              
[106] pillar_1.4.7                lattice_0.20-41             KEGGREST_1.30.1            
[109] fastmap_1.1.0               httr_1.4.2                  pkgbuild_1.2.0             
[112] survival_3.2-7              glue_1.4.2                  remotes_2.2.0              
[115] png_0.1-7                   iterators_1.0.13            bit_4.0.4                  
[118] Rgraphviz_2.34.0            stringi_1.5.3               blob_1.2.1                 
[121] DESeq2_1.30.0               org.Hs.eg.db_3.12.0         caTools_1.18.1             
[124] memoise_2.0.0

Install the required package: `if (!requireNamespace("BiocManager", quietly = TRUE)); install.packages("BiocManager"); BiocManager::install("KEGGdzPathwaysGEO")` (per https://bioconductor.org/packages/release/data/experiment/html/KEGGdzPathwaysGEO.html) — jared_mamrot, Feb 01 '21 at 08:56
@jared_mamrot Thanks! I installed the package as what you've suggested, but when I load the EGSEA library again, a similar error message pops out `Error: package or namespace load failed for ‘EGSEA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘hgu133a.db’` This has happened quite a few times after I personally install all of the packages required. — Phoebe Chair, Feb 02 '21 at 03:52
Hmm... How did you install EGSEA? `BiocManager::install("EGSEA")`? It looks like the packages you are having trouble with are compiled from source, rather than binaries downloaded from bioconductor; perhaps you're having issues compiling packages... Do you have xcode (and the xcode command line tools) installed? See https://support.rstudio.com/hc/en-us/articles/200486498-Package-Development-Prerequisites — jared_mamrot, Feb 02 '21 at 05:09
@jared_mamrot Yes, `if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("EGSEA")` I used this. I do not have xcode installed, I guess you'd recommend to download this app and give it a try? Based on your answer given below, I've also tried selecting 'yes' when asked to update all packages during the installation of EGSEA. I will have to update my macOs software and download xcode to give it a try. Thanks so much! — Phoebe Chair, Feb 03 '21 at 06:45

score 0 · Answer 1 · answered Feb 02 '21 at 05:45

Running these commands and selecting "yes" when asked if I wanted to update all packages fixed the issue for me:

BiocManager::install("EGSEA")
BiocManager::install("KEGGdzPathwaysGEO")
library(EGSEA)

Installing the dependencies for EGSEA (especially KEGGdzPathwaysGEO, which had to be installed separately) required me to compile some of them from source. To compile R packages you may need to 'jump through some hoops' e.g. see https://stackoverflow.com/a/65334247/12957340 for compiling packages from source in macOS Big Sur.

Error: package or namespace load failed for ‘EGSEA’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):

1 Answers1