##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:nullranges.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings nullranges_1.17.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/nullranges.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘nullranges/DESCRIPTION’ ... OK
* this is package ‘nullranges’ version ‘1.17.1’
* 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 ‘nullranges’ 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 ... NOTE
bootRanges: no visible global function definition for ‘filter’
plotSegment: no visible global function definition for ‘%>%’
plotSegment: no visible global function definition for ‘group_by’
plotSegment: no visible global function definition for ‘summarise’
segmentDensity: no visible global function definition for ‘filter’
Undefined global functions or variables:
  %>% filter group_by summarise
Consider adding
  importFrom("stats", "filter")
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘nullranges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSegment
> ### Title: Plot genome segmentation
> ### Aliases: plotSegment
> 
> ### ** Examples
> 
> 
> example("segmentDensity")

sgmntD> n <- 10000

sgmntD> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: Seqinfo

sgmntD> gr <- GRanges("chr1", IRanges(round(
sgmntD+   c(runif(n/4,1,991), runif(n/4,1001,3991),
sgmntD+     runif(n/4,4001,4991), runif(n/4,7001,9991))),
sgmntD+   width=10), seqlengths=c(chr1=10000))

sgmntD> gr <- sort(gr)

sgmntD> exclude <- GRanges("chr1", IRanges(5001,6000), seqlengths=c(chr1=10000))

sgmntD> seg <- segmentDensity(gr, n=3, L_s=100, exclude=exclude, type="cbs")
Error in storage.mode(x) <- "double" : 
  no method for coercing this S4 class to a vector
Calls: example ... withVisible -> eval -> eval -> segmentDensity -> filter
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Saving _problems/test_matchRanges-57.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_matchRanges.R:57:3'): Coerce MatchIt to Matched subclasses ─────
  Error in `coerceToRanges(d, ranges, keep_mcols, "GRanges")`: The 'mariner' package is required for this function.
  Backtrace:
      ▆
   1. └─nullranges:::as_MatchedGRanges(m, ranges = NULL, keep_mcols = TRUE) at test_matchRanges.R:57:3
   2.   └─nullranges:::coerceToRanges(d, ranges, keep_mcols, "GRanges")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/nullranges.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL nullranges
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘nullranges’ ...
** this is package ‘nullranges’ version ‘1.17.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (nullranges)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(nullranges)
> 
> test_check("nullranges")
Saving _problems/test_matchRanges-57.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_matchRanges.R:57:3'): Coerce MatchIt to Matched subclasses ─────
Error in `coerceToRanges(d, ranges, keep_mcols, "GRanges")`: The 'mariner' package is required for this function.
Backtrace:
    ▆
 1. └─nullranges:::as_MatchedGRanges(m, ranges = NULL, keep_mcols = TRUE) at test_matchRanges.R:57:3
 2.   └─nullranges:::coerceToRanges(d, ranges, keep_mcols, "GRanges")

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
Error:
! Test failures.
Execution halted