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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BEAT.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BEAT_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BEAT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BEAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BEAT’ version ‘1.40.0’
* 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 ‘BEAT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
koeff: no visible global function definition for ‘dbinom’
positionsReadCSV: no visible global function definition for ‘read.csv’
printEpimutStats: no visible global function definition for ‘median’
priorr: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta dbinom median read.csv
Consider adding
  importFrom("stats", "dbeta", "dbinom", "median")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BEAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: epimutation_calls
> ### Title: Returns epimutation rates and sites.
> ### Aliases: epimutation_calls
> ### Keywords: BEAT
> 
> ### ** Examples
> 
> # Local working directory
> localpath <- system.file('extdata', package = 'BEAT')
> # Names of samples, expected filenames are e.g. reference.positions.csv
> sampNames <- c("reference", "sample")
> # Empirical BS-conversion rates, e.g. estimated from non-CpG methylation
> convrates <- c(0.8,0.5)
> # Vector denoting reference vs. single-cell status of given samples
> is.reference <- c(TRUE,FALSE)
> params <- makeParams(localpath, sampNames, convrates, is.reference, pminus = 0.2, regionSize = 10000, minCounts = 5, verbose = TRUE, computeRegions = TRUE, computeMatrices = TRUE, writeEpicallMatrix = TRUE)
> # pool CG positions into regions
> positions_to_regions(params)
Sample: reference.positions.csv regionSize: 10000 minCounts: 5
Processed reference.positions.csv, yielding 16728 regions of 10000 nt
Sample: sample.positions.csv regionSize: 10000 minCounts: 5
Processed sample.positions.csv, yielding 15948 regions of 10000 nt
> # compute model statistics
> generate_results(params)
Sample: reference
Generating conversion matrix...
Adding methylation states and 9 matrices...
Sample: sample
Generating conversion matrix...
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BEAT.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BEAT
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘BEAT’ ...
** using staged installation
** R
** data
** 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 (BEAT)