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###
### Running command:
###
###   /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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL EGSEA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘EGSEA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (EGSEA)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(EGSEA)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: gage

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

The following object is masked from 'package:gage':

    geneData

Loading required package: pathview

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################




> 
> test_check("EGSEA")
[1] "Created the User-Defined Gene Sets collection ... "
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
 13.806   0.835  14.630