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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Motif2Site.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Motif2Site_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Motif2Site.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 ‘Motif2Site/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Motif2Site’ version ‘1.3.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .gitignoreommit
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Motif2Site’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ‘Motif2Site-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DetectBindingSitesBed
> ### Title: Detect binding sites from bed motif input
> ### Aliases: DetectBindingSitesBed
> 
> ### ** Examples
> 
> 
> # FUR candidate motifs in NC_000913 E. coli
> FurMotifs=system.file("extdata", "FurMotifs.bed", package="Motif2Site")
> 
> # ChIP-seq datasets in bed single end format
> IPFe <- c(system.file("extdata", "FUR_fe1.bed", package="Motif2Site"),
+         system.file("extdata", "FUR_fe2.bed", package="Motif2Site"))
> Inputs <- c(system.file("extdata", "Input1.bed", package="Motif2Site"),
+             system.file("extdata", "Input2.bed", package="Motif2Site"))
> FURfeBedInputStats <- 
+   DetectBindingSitesBed(BedFile=FurMotifs,
+                         IPfiles=IPFe, 
+                         BackgroundFiles=Inputs, 
+                         genome="Ecoli",
+                         genomeBuild="20080805",
+                         DB="NCBI",
+                         expName="FUR_Fe_BedInput",
+                         format="BEDSE"
+                        )
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Warning in densfun(x, parm[1], parm[2], ...) : NaNs produced
Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘Motif2Site.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Motif2Site.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Motif2Site
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Motif2Site’ ...
** 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 (Motif2Site)