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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SNPhood.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SNPhood_1.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SNPhood.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SNPhood/DESCRIPTION’ ... OK
* this is package ‘SNPhood’ version ‘1.29.0’
* 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 ‘SNPhood’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
* 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 startup messages can be suppressed ... 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
.calcBinomTestVector: no visible binding for global variable ‘pp’
Undefined global functions or variables:
  pp
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SNPhood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAndSummarizeAllelicBiasTest
> ### Title: Summarize the allelic bias analysis across SNP regions and bins
> ###   and visualize some of the results.
> ### Aliases: plotAndSummarizeAllelicBiasTest
> 
> ### ** Examples
> 
> data(SNPhood, package="SNPhood")
Warning in data(SNPhood, package = "SNPhood") :
  data set ‘SNPhood’ not found
> SNPhood.o = testForAllelicBiases (SNPhood.o, readGroups = c("maternal", "paternal"))
Warning in value[[3L]](cond) :
  Could not obtain chromosome sizes using GenomeInfoDb, try fallback implementation...

Test allelic bias for dataset GM10847
 Calculating read overlaps for the background distribution... This may take a while
 Read group maternal
 Read group paternal
 Calculate background distribution with 100 repetitions. This may take a while.
Test allelic bias for dataset GM12890
 Calculating read overlaps for the background distribution... This may take a while
 Read group maternal
 Read group paternal
 Calculate background distribution with 100 repetitions. This may take a while.


FINISHED SUCCESSFULLY WITH ALLELIC BIAS TEST.

 Execution time: 35.4 secs
> SNPhood.o = plotAndSummarizeAllelicBiasTest(SNPhood.o)
Warning in plotAndSummarizeAllelicBiasTest(SNPhood.o) :
  Multiple plots will be produced but no PDf filename has been specified (fileToPlot). It might possible that only the last graph is shown.
No id variables; using all as measure variables
Warning: Removed 305 rows containing non-finite values (`stat_bin()`).
Warning: Removed 4 rows containing missing values (`geom_bar()`).
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: plotAndSummarizeAllelicBiasTest ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.data.frame
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘IntroductionToSNPhood.Rmd’ using ‘UTF-8’... OK
  ‘workflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SNPhood
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘SNPhood’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SNPhood)