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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:esetVis.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings esetVis_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/esetVis.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘esetVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esetVis’ version ‘1.25.0’
* 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 ‘esetVis’ 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
ggvisPlotEset: no visible global function definition for ‘:=’
ggvisPlotEset: no visible binding for global variable ‘fill’
ggvisPlotEset: no visible binding for global variable ‘shape’
ggvisPlotEset: no visible binding for global variable ‘size’
ggvisPlotEset: no visible binding for global variable ‘opacity’
Undefined global functions or variables:
  := fill opacity shape size
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘esetVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGeneSetsForPlot
> ### Title: get gene sets for plot of eSet object.
> ### Aliases: getGeneSetsForPlot
> 
> ### ** Examples
> 
> # example dataset
> library(ALL)
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")'.

> data(ALL)
> 
> # get gene annotation from probe IDs
> library("hgu95av2.db")
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: org.Hs.eg.db


> probeIDs <- featureNames(ALL)
> geneInfo <- select(hgu95av2.db, probeIDs,"ENTREZID", "PROBEID")
'select()' returned 1:many mapping between keys and columns
> 
> # get pathway annotation for the genes contained in the ALL dataset (can take a few minutes)
> geneSets <- getGeneSetsForPlot(entrezIdentifiers = geneInfo$ENTREZID, species = "Human", 
+ 	geneSetSource = 'GOBP',
+ 	useDescription = FALSE, trace = TRUE)
Loading required namespace: GO.db
Failed with error:  ‘there is no package called ‘GO.db’’
Error in getGeneSets(species = species, geneSetSource = db, entrezIdentifiers = entrezIdentifiers) : 
  Package 'GO.db' should be available for the extraction of pathways from: GOBP.
Calls: getGeneSetsForPlot -> system.time -> lapply -> FUN -> getGeneSets
Timing stopped at: 0.002 0.001 0.002
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘esetVis-vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘esetVis-vignette.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GO.db''
Quitting from lines 392-399 (esetVis-vignette.Rmd) 
Error: processing vignette 'esetVis-vignette.Rmd' failed with diagnostics:
Package 'GO.db' should be available for the extraction of pathways from: GOBP.
--- failed re-building ‘esetVis-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘esetVis-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL esetVis
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘esetVis’ ...
** using staged installation
** R
** 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 (esetVis)