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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings EnrichmentBrowser_2.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/EnrichmentBrowser.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.29.0’
* package encoding: UTF-8
* 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 ‘EnrichmentBrowser’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
Undefined global functions or variables:
  go_linkage_type
* 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 ‘EnrichmentBrowser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ebrowser
> ### Title: Seamless navigation through enrichment analysis results
> ### Aliases: ebrowser
> 
> ### ** Examples
> 
> 
>     # expression data from file
>     exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
>     cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
>     rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
>     
>     # getting all human KEGG gene sets
>     # hsa.gs <- getGenesets(org="hsa", db="kegg")
>     gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
>     hsa.gs <- getGenesets(gs.file)
> 
>     # output destination 
>     out.dir <- configEBrowser("OUTDIR.DEFAULT") 
> 
>     # set-based enrichment analysis
>     ebrowser( meth="ora", perm=0,
+             exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, 
+             gs=hsa.gs, org="hsa", nr.show=3,
+             out.dir=out.dir, report.name="oraReport")
Read expression data ...
Normalize ...
Excluding 211 genes not satisfying min.cpm threshold

Attaching package: 'Biostrings'

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

    complement

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

    strsplit


Attaching package: 'ShortRead'

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

    basePath, name

DE analysis ...
Execute ORA ...
Creating gene report ...
Creating set view ...
Creating kegg view ...
##############################################################################
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).
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Annotating genes ...
Genewise differential expression written to /home/biocbuild/.local/share/R/EnrichmentBrowser/results/de.txt
Your output files are in /home/biocbuild/.local/share/R/EnrichmentBrowser/results
Produce html report ...
> 
>     # compile a gene regulatory network from KEGG pathways
>     hsa.grn <- compileGRN(org="hsa", db="kegg")
>    
>     # network-based enrichment analysis
>     ebrowser(   meth="ggea", 
+             exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, 
+             gs=hsa.gs, grn=hsa.grn, org="hsa", nr.show=3,
+             out.dir=out.dir, report.name="ggeaReport")
Read expression data ...
Normalize ...
Excluding 211 genes not satisfying min.cpm threshold
DE analysis ...
Execute GGEA ...
Creating gene report ...
Creating set view ...
Creating kegg view ...
Creating graph view ...
Annotating genes ...
Genewise differential expression written to /home/biocbuild/.local/share/R/EnrichmentBrowser/results/de.txt
Your output files are in /home/biocbuild/.local/share/R/EnrichmentBrowser/results
Produce html report ...
> 
>     # combining results
>     ebrowser( meth=c("ora", "ggea"), perm=0, comb=TRUE,
+             exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, 
+             gs=hsa.gs, grn=hsa.grn, org="hsa", nr.show=3,
+             out.dir=out.dir, report.name="combReport")
Read expression data ...
Normalize ...
Excluding 211 genes not satisfying min.cpm threshold
DE analysis ...
Execute ORA ...
Creating gene report ...
Creating set view ...
Creating kegg view ...
Creating graph view ...
Execute GGEA ...
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘EnrichmentBrowser.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘EnrichmentBrowser.Rnw’ using knitr
Killed

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

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

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