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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:chromswitch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings chromswitch_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/chromswitch.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 ‘chromswitch/DESCRIPTION’ ... OK
* this is package ‘chromswitch’ version ‘1.21.0’
* 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 ‘chromswitch’ 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 ... 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 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 ‘chromswitch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callSummary
> ### Title: callSummary
> ### Aliases: callSummary
> 
> ### ** Examples
> 
> 
> samples <- c("E068", "E071", "E074", "E101", "E102", "E110")
> bedfiles <- system.file("extdata", paste0(samples, ".H3K4me3.bed"),
+ package = "chromswitch")
> Conditions <- c(rep("Brain", 3), rep("Other", 3))
> 
> metadata <- data.frame(Sample = samples,
+     H3K4me3 = bedfiles,
+     Condition = Conditions,
+     stringsAsFactors = FALSE)
> 
> regions <- GRanges(seqnames = c("chr19", "chr19"),
+     ranges = IRanges(start = c(54924104, 54874318),
+                                 end = c(54929104, 54877536)))
> 
> callSummary(query = regions,
+                 metadata = metadata,
+                 peaks = H3K4me3,
+                 normalize_columns = c("qValue", "pValue", "signalValue"),
+                 mark = "H3K4me3",
+                 summarize_columns = c("pValue", "qValue", "signalValue"),
+                 heatmap = FALSE,
+                 BPPARAM = BiocParallel::SerialParam())
Warning: `select_()` was deprecated in dplyr 0.7.0.
ℹ Please use `select()` instead.
ℹ The deprecated feature was likely used in the chromswitch package.
  Please report the issue at <https://github.com/sjessa/chromswitch/issues>.
Warning: `funs()` was deprecated in dplyr 0.8.0.
ℹ Please use a list of either functions or lambdas:

# Simple named list: list(mean = mean, median = median)

# Auto named with `tibble::lst()`: tibble::lst(mean, median)

# Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
ℹ The deprecated feature was likely used in the chromswitch package.
  Please report the issue at <https://github.com/sjessa/chromswitch/issues>.
Killed
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘chromswitch_intro.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL chromswitch
###
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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 ‘chromswitch’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (chromswitch)

R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(chromswitch)
Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("chromswitch")
[ FAIL 0 | WARN 39 | SKIP 0 | PASS 93 ]

[ FAIL 0 | WARN 39 | SKIP 0 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
 69.380  21.279  69.321