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reese3928 / methylGSA

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing
https://bioconductor.org/packages/release/bioc/html/methylGSA.html
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'runExample' is not an exported object from 'namespace:methylGSA' #3

Open sam0per opened 3 years ago

sam0per commented 3 years ago

Hi there,

After following your guidelines on how to launch the Shiny app, I am getting the following error

'runExample' is not an exported object from 'namespace:methylGSA'

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] shinydashboard_0.7.1  methylGSA_1.2.3       shinycssloaders_1.0.0
[4] DT_0.18               shiny_1.6.0          

loaded via a namespace (and not attached):
  [1] utf8_1.2.1                                         
  [2] tidyselect_1.1.1                                   
  [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
  [4] RSQLite_2.2.7                                      
  [5] AnnotationDbi_1.46.1                               
  [6] htmlwidgets_1.5.3                                  
  [7] grid_3.6.3                                         
  [8] BiocParallel_1.18.1                                
  [9] munsell_0.5.0                                      
 [10] codetools_0.2-18                                   
 [11] preprocessCore_1.46.0                              
 [12] statmod_1.4.36                                     
 [13] colorspace_2.0-1                                   
 [14] GOSemSim_2.10.0                                    
 [15] Biobase_2.44.0                                     
 [16] stats4_3.6.3                                       
 [17] DOSE_3.10.2                                        
 [18] urltools_1.7.3                                     
 [19] GenomeInfoDbData_1.2.1                             
 [20] polyclip_1.10-0                                    
 [21] bit64_4.0.5                                        
 [22] farver_2.1.0                                       
 [23] rhdf5_2.28.1                                       
 [24] vctrs_0.3.8                                        
 [25] generics_0.1.0                                     
 [26] R6_2.5.0                                           
 [27] GenomeInfoDb_1.20.0                                
 [28] illuminaio_0.26.0                                  
 [29] graphlayouts_0.7.1                                 
 [30] locfit_1.5-9.4                                     
 [31] bitops_1.0-7                                       
 [32] cachem_1.0.5                                       
 [33] reshape_0.8.8                                      
 [34] fgsea_1.10.1                                       
 [35] gridGraphics_0.5-1                                 
 [36] DelayedArray_0.10.0                                
 [37] assertthat_0.2.1                                   
 [38] promises_1.2.0.1                                   
 [39] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 
 [40] scales_1.1.1                                       
 [41] ggraph_2.0.5                                       
 [42] enrichplot_1.4.0                                   
 [43] gtable_0.3.0                                       
 [44] methylumi_2.30.0                                   
 [45] tidygraph_1.2.0                                    
 [46] rlang_0.4.11                                       
 [47] genefilter_1.66.0                                  
 [48] splines_3.6.3                                      
 [49] rtracklayer_1.44.4                                 
 [50] GEOquery_2.52.0                                    
 [51] europepmc_0.4                                      
 [52] BiocManager_1.30.15                                
 [53] reshape2_1.4.4                                     
 [54] GenomicFeatures_1.36.4                             
 [55] httpuv_1.6.1                                       
 [56] qvalue_2.16.0                                      
 [57] clusterProfiler_3.12.0                             
 [58] tools_3.6.3                                        
 [59] ggplotify_0.0.7                                    
 [60] nor1mix_1.3-0                                      
 [61] ggplot2_3.3.3                                      
 [62] ellipsis_0.3.2                                     
 [63] RColorBrewer_1.1-2                                 
 [64] BiocGenerics_0.30.0                                
 [65] siggenes_1.58.0                                    
 [66] ggridges_0.5.3                                     
 [67] Rcpp_1.0.6                                         
 [68] plyr_1.8.6                                         
 [69] progress_1.2.2                                     
 [70] zlibbioc_1.30.0                                    
 [71] purrr_0.3.4                                        
 [72] RCurl_1.98-1.3                                     
 [73] BiasedUrn_1.07                                     
 [74] prettyunits_1.1.1                                  
 [75] openssl_1.4.4                                      
 [76] IlluminaHumanMethylationEPICmanifest_0.3.0         
 [77] viridis_0.6.1                                      
 [78] cowplot_1.1.1                                      
 [79] bumphunter_1.26.0                                  
 [80] S4Vectors_0.22.1                                   
 [81] SummarizedExperiment_1.14.1                        
 [82] ggrepel_0.9.1                                      
 [83] magrittr_2.0.1                                     
 [84] data.table_1.14.0                                  
 [85] DO.db_2.9                                          
 [86] triebeard_0.3.0                                    
 [87] reactome.db_1.68.0                                 
 [88] packrat_0.6.0                                      
 [89] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
 [90] matrixStats_0.58.0                                 
 [91] missMethyl_1.18.0                                  
 [92] hms_1.1.0                                          
 [93] mime_0.10                                          
 [94] xtable_1.8-4                                       
 [95] XML_3.99-0.3                                       
 [96] RobustRankAggreg_1.1                               
 [97] mclust_5.4.7                                       
 [98] IRanges_2.18.3                                     
 [99] gridExtra_2.3                                      
[100] compiler_3.6.3                                     
[101] biomaRt_2.40.5                                     
[102] minfi_1.30.0                                       
[103] tibble_3.1.2                                       
[104] crayon_1.4.1                                       
[105] htmltools_0.5.1.1                                  
[106] later_1.2.0                                        
[107] tidyr_1.1.3                                        
[108] DBI_1.1.1                                          
[109] tweenr_1.0.2                                       
[110] MASS_7.3-54                                        
[111] Matrix_1.3-3                                       
[112] readr_1.4.0                                        
[113] cli_2.5.0                                          
[114] quadprog_1.5-8                                     
[115] parallel_3.6.3                                     
[116] igraph_1.2.6                                       
[117] GenomicRanges_1.36.1                               
[118] pkgconfig_2.0.3                                    
[119] rvcheck_0.1.8                                      
[120] GenomicAlignments_1.20.1                           
[121] IlluminaHumanMethylation450kmanifest_0.4.0         
[122] xml2_1.3.2                                         
[123] foreach_1.5.1                                      
[124] annotate_1.62.0                                    
[125] rngtools_1.5                                       
[126] multtest_2.40.0                                    
[127] beanplot_1.2                                       
[128] XVector_0.24.0                                     
[129] ruv_0.9.7.1                                        
[130] doRNG_1.8.2                                        
[131] scrime_1.3.5                                       
[132] stringr_1.4.0                                      
[133] digest_0.6.27                                      
[134] Biostrings_2.52.0                                  
[135] base64_2.0                                         
[136] fastmatch_1.1-0                                    
[137] DelayedMatrixStats_1.6.1                           
[138] Rsamtools_2.0.3                                    
[139] lifecycle_1.0.0                                    
[140] nlme_3.1-152                                       
[141] jsonlite_1.7.2                                     
[142] Rhdf5lib_1.6.3                                     
[143] viridisLite_0.4.0                                  
[144] askpass_1.1                                        
[145] limma_3.40.6                                       
[146] fansi_0.5.0                                        
[147] pillar_1.6.1                                       
[148] lattice_0.20-44                                    
[149] fastmap_1.1.0                                      
[150] httr_1.4.2                                         
[151] survival_3.2-11                                    
[152] GO.db_3.8.2                                        
[153] glue_1.4.2                                         
[154] UpSetR_1.4.0                                       
[155] iterators_1.0.13                                   
[156] bit_4.0.4                                          
[157] ggforce_0.3.3                                      
[158] stringi_1.6.2                                      
[159] HDF5Array_1.12.3                                   
[160] blob_1.2.1                                         
[161] org.Hs.eg.db_3.8.2                                 
[162] memoise_2.0.0                                      
[163] dplyr_1.0.6

I can launch a Shiny app example runExample("01_hello") but it does not work with methylGSA. Probably, I am missing something and I hope that someone can help me with this issue.

reese3928 commented 3 years ago

Hi,

Is it possible for you to install a later version of methylGSA? In your current session, methylGSA version 1.2.3 is loaded. Shiny app is not supported for that version.

Package can be update by: BiocManager::install("methylGSA")

sam0per commented 3 years ago

I have tried to update the package as you have suggested but nothing changes incuding the version of the package in my local. Is it because I would need to update R too (version 3.6 to version 4)?