##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings BindingSiteFinder_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.2.0’
* 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 ‘BindingSiteFinder’ 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 code 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘BindingSiteFinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateBsFoldChange
> ### Title: Compute fold-changes per binding site
> ### Aliases: calculateBsFoldChange
> 
> ### ** Examples
> 
> # load clip data
> files <- system.file("extdata", package="BindingSiteFinder")
> load(list.files(files, pattern = ".rda$", full.names = TRUE))
> load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
> 
> # make example dataset
> bds = makeBindingSites(bds, bsSize = 7)
> bds = assignToGenes(bds, anno.genes = gns)
8.97% (443/4939) of binding sites overlap with multiple anno.genes in the given gene annotation. 
Apply 'frequency' solution
> bds = imputeBsDifferencesForTestdata(bds)
> bds = calculateBsBackground(bds, anno.genes = gns)
Warning in calculateBsBackground(bds, anno.genes = gns) :
  Found 114 binding sites with 'NA' as geneID. 
Removing those keeps 4939 binding sites remaining. 

> 
> # calculate fold changes - no shrinkage
> bds = calculateBsFoldChange(bds)
1) Testing binding sites 
2) Testing genes 
> 
> # calculate fold changes - with shrinkage
> bds = calculateBsFoldChange(bds, use.lfc.shrinkage = TRUE)
1) Testing binding sites 
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL BindingSiteFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘BindingSiteFinder’ ...
** 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 (BindingSiteFinder)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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("BindingSiteFinder")
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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> test_check("BindingSiteFinder")
[1] "make bs"
[1] "calc ratio"
[1] "make bs"
[1] "calc ratio"
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]
> 
> proc.time()
   user  system elapsed 
378.927  24.166 472.047