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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EGSEA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings EGSEA_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EGSEA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘EGSEA/DESCRIPTION’ ... OK
* this is package ‘EGSEA’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘EGSEA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’
buildMSigDBIdx: no visible binding for global variable ‘msigdb’
generateSummaryPlots: no visible binding for global variable ‘x.data’
generateSummaryPlots: no visible binding for global variable ‘y.data’
generateSummaryPlots: no visible binding for global variable ‘gsSize’
generateSummaryPlots: no visible binding for global variable ‘id’
generateSummaryPlots: no visible binding for global variable ‘sig’
loadKeggData: no visible binding for global variable ‘kegg.pathways’
Undefined global functions or variables:
  GOTERM gsSize id kegg.pathways msigdb sig x.data y.data
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘arraydata’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘Glimma’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘EGSEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: egsea
> ### Title: Core functions to perform ensemble of gene set enrichment
> ###   analysis (EGSEA)
> ### Aliases: egsea egsea,egsea-main egsea.cnt egsea.cnt,egsea-main
> ###   egsea.ora egsea.ora,egsea-main egsea.cnt egsea.ma
> ###   egsea.cnt,egsea-main
> 
> ### ** Examples
> 
> # Example of egsea
> library(EGSEAdata)
> data(il13.data)
> v = il13.data$voom
> contrasts = il13.data$contra
> gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", 
+ msigdb.gsets="none", 
+          kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
[1] "Building KEGG pathways annotation object ... "
> # set report = TRUE to generate the EGSEA interactive report
> gsa = egsea(voom.results=v, contrasts=contrasts,  gs.annots=gs.annots, 
+          symbolsMap=v$genes, baseGSEAs=egsea.base()[-c(2,5,6,9,12)], 
+ 			display.top = 5, sort.by="avg.rank", 
+ 			report.dir="./il13-egsea-report", 
+          num.threads = 2, report = FALSE)
EGSEA analysis has started
##------ Sun Oct 15 21:09:44 2023 ------##
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and kegg collection
...safe*....zscore*..globaltest*camera*..gage*...gsva*..ora*
##------ Sun Oct 15 21:09:52 2023 ------##
EGSEA analysis took 7.72000000000003 seconds.
EGSEA analysis has completed
> topSets(gsa) 
Extracting the top gene sets of the collection 
KEGG Pathways for the contrast X24IL13-X24
 Sorted by avg.rank
 [1] "Intestinal immune network for IgA production"             
 [2] "Asthma"                                                   
 [3] "Amoebiasis"                                               
 [4] "Hematopoietic cell lineage"                               
 [5] "HTLV-I infection"                                         
 [6] "Viral myocarditis"                                        
 [7] "Malaria"                                                  
 [8] "Endocrine and other factor-regulated calcium reabsorption"
 [9] "Legionellosis"                                            
[10] "Proteoglycans in cancer"                                  
> 
> # Example of egsea.cnt
> library(EGSEAdata)
> data(il13.data.cnt)
> cnt = il13.data.cnt$counts
> group = il13.data.cnt$group
> design = il13.data.cnt$design
> contrasts = il13.data.cnt$contra
> genes = il13.data.cnt$genes
> gs.annots = buildIdx(entrezIDs=rownames(cnt), species="human", 
+ msigdb.gsets="none",
+          kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
[1] "Building KEGG pathways annotation object ... "
> # set report = TRUE to generate the EGSEA interactive report
> gsa = egsea.cnt(counts=cnt, group=group, design=design, contrasts=contrasts, 
+          gs.annots=gs.annots, 
+          symbolsMap=genes, baseGSEAs=egsea.base()[-c(2,5,6,9,12)], 
+ display.top = 5,
+           sort.by="avg.rank", 
+ report.dir="./il13-egsea-cnt-report", 
+          num.threads = 2, report = FALSE)
EGSEA analysis has started
##------ Sun Oct 15 21:09:53 2023 ------##
Log fold changes are estimated using limma package ... 
limma DE analysis is carried out ... 
EGSEA is running on the provided data and kegg collection
...safe*....zscore*..globaltest*camera*..gage*...gsva*..ora*
##------ Sun Oct 15 21:10:01 2023 ------##
EGSEA analysis took 7.97499999999999 seconds.
EGSEA analysis has completed
> topSets(gsa) 
Extracting the top gene sets of the collection 
KEGG Pathways for the contrast X24IL13-X24
 Sorted by avg.rank
 [1] "Intestinal immune network for IgA production"             
 [2] "Asthma"                                                   
 [3] "Amoebiasis"                                               
 [4] "Malaria"                                                  
 [5] "Hematopoietic cell lineage"                               
 [6] "HTLV-I infection"                                         
 [7] "Viral myocarditis"                                        
 [8] "Endocrine and other factor-regulated calcium reabsorption"
 [9] "Legionellosis"                                            
[10] "Prion diseases"                                           
> 
> # Example of egsea.ora
> library(EGSEAdata)
> data(il13.data)
> voom.results = il13.data$voom
> contrast = il13.data$contra
> library(limma)

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

> vfit = lmFit(voom.results, voom.results$design)
> vfit = contrasts.fit(vfit, contrast)
> vfit = eBayes(vfit)
> top.Table = topTable(vfit, coef=1, number=Inf, p.value=0.05, lfc=1)
> deGenes = as.character(top.Table$FeatureID)
> logFC =  top.Table$logFC
> names(logFC) = deGenes
> gs.annots = buildIdx(entrezIDs=deGenes, species="human", 
+ msigdb.gsets="none",
+          kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
[1] "Building KEGG pathways annotation object ... "
> # set report = TRUE to generate the EGSEA interactive report
> gsa = egsea.ora(geneIDs=deGenes, universe= 
+ as.character(voom.results$genes[,1]),
+              logFC =logFC, title="X24IL13-X24",  
+ gs.annots=gs.annots, 
+              symbolsMap=top.Table[, c(1,2)], display.top = 5,
+               report.dir="./il13-egsea-ora-report", num.threads = 2, 
+ 				report = FALSE)
EGSEA analysis has started
##------ Sun Oct 15 21:10:03 2023 ------##
EGSEA is running on the provided data and kegg collection
.ora*
##------ Sun Oct 15 21:10:03 2023 ------##
EGSEA analysis took 0.138000000000005 seconds.
EGSEA analysis has completed
> topSets(gsa) 
Extracting the top gene sets of the collection 
KEGG Pathways for the contrast X24IL13X24
 Sorted by p.adj
 [1] "Hematopoietic cell lineage"            
 [2] "Staphylococcus aureus infection"       
 [3] "Cytokine-cytokine receptor interaction"
 [4] "Phagosome"                             
 [5] "Tuberculosis"                          
 [6] "Leishmaniasis"                         
 [7] "Cell adhesion molecules (CAMs)"        
 [8] "Rheumatoid arthritis"                  
 [9] "Asthma"                                
[10] "Type I diabetes mellitus"              
> 
> # Example of egsea.ma
> library(Glimma)
Error in library(Glimma) : there is no package called ‘Glimma’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘EGSEA.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/EGSEA.Rcheck/00check.log’
for details.