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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:eegc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings eegc_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/eegc.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eegc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eegc’ version ‘1.26.0’
* 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 ‘eegc’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data  10.5Mb
* 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 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
categorizeGene : <anonymous>: no visible global function definition for
  ‘quantile’
densityPlot: no visible binding for global variable ‘density’
densityPlot: no visible global function definition for ‘lines’
densityPlot: no visible global function definition for ‘axis’
densityPlot: no visible global function definition for ‘adjustcolor’
densityPlot: no visible global function definition for ‘legend’
densityPlot : <anonymous>: no visible global function definition for
  ‘quantile’
densityPlot: no visible global function definition for ‘text’
densityPlot: no visible global function definition for ‘dev.copy2pdf’
diffGene: no visible global function definition for ‘model.matrix’
diffGene: no visible binding for global variable ‘treat’
diffGene: no visible binding for global variable ‘control’
diffGene: no visible global function definition for ‘results’
diffGene: no visible global function definition for ‘p.adjust’
dotPercentage: no visible global function definition for ‘lines’
dotPercentage: no visible global function definition for ‘axis’
dotPercentage: no visible global function definition for ‘text’
dotPercentage: no visible global function definition for ‘par’
enrichment : enrichment : <anonymous>: no visible global function
  definition for ‘phyper’
enrichment : enrichment: no visible global function definition for
  ‘p.adjust’
functionEnrich: no visible global function definition for ‘is’
grnPlot: no visible global function definition for ‘title’
grnPlot: no visible global function definition for ‘legend’
markerScatter: no visible global function definition for
  ‘colorRampPalette’
markerScatter: no visible global function definition for ‘points’
markerScatter: no visible global function definition for ‘lm’
markerScatter: no visible global function definition for ‘abline’
markerScatter: no visible global function definition for ‘text’
markerScatter: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline adjustcolor axis colorRampPalette control density dev.copy2pdf
  is legend lines lm model.matrix p.adjust par phyper points quantile
  results text title treat
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette",
             "dev.copy2pdf")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points", "text", "title")
  importFrom("methods", "is")
  importFrom("stats", "density", "lm", "model.matrix", "p.adjust",
             "phyper", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'barplotEnrich.Rd':
  ‘[DOSE]{barplot.enrichResult}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... WARNING
  LazyData DB of 10.5 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘eegc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: functionEnrich
> ### Title: Funtional Enrichment Analysis
> ### Aliases: functionEnrich
> 
> ### ** Examples
> 
> data(cate.gene)
> # result in "enrichResult" class by specifying TRUE to enrichResult parameter
> goenrichraw = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
+                              GO = TRUE, KEGG = FALSE, enrichResult = TRUE)
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

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

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

'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  12.9% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  14.16% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.48% of input gene IDs are fail to map...
'select()' returned 1:many mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  11.28% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.13% of input gene IDs are fail to map...
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
> 
> # result of the summary of "enrichResult" by specifying FALSE to enrichResult parameter
> # GO enrichment
> goenrich = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
+                           GO = TRUE, KEGG = FALSE, enrichResult = FALSE)
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  12.9% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  14.16% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.48% of input gene IDs are fail to map...
'select()' returned 1:many mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  11.28% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.13% of input gene IDs are fail to map...
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
Warning in FUN(X[[i]], ...) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
> 
> # KEGG enrichment
> keggenrich = functionEnrich(cate.gene, organism = "human", pAdjustMethod = "fdr",
+                             GO = FALSE, KEGG = TRUE, enrichResult = FALSE)
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  12.9% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  14.16% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.48% of input gene IDs are fail to map...
'select()' returned 1:many mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  11.28% of input gene IDs are fail to map...
'select()' returned 1:1 mapping between keys and columns
Warning in bitr(x, fromType = from, toType = c("ENTREZID"), OrgDb = OrgDb) :
  9.13% of input gene IDs are fail to map...
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Warning in download.file(url, method = method, ...) :
  cannot open URL 'https://rest.kegg.jp/link/hsa/pathway': HTTP status was '403 Forbidden'
fail to download KEGG data...
Error in download.KEGG.Path(species) : 
  Failed to download KEGG data. Wrong 'species' or the network is unreachable. The 'species' should be one of organisms listed in 'https://www.genome.jp/kegg/catalog/org_list.html'
Calls: functionEnrich ... prepare_KEGG -> download_KEGG -> download.KEGG.Path
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL eegc
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘eegc’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (eegc)