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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ATACseqQC.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ATACseqQC_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ATACseqQC.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-22 01:29:30 UTC
* checking for file ‘ATACseqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ATACseqQC’ version ‘1.36.0’
* 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 ‘ATACseqQC’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    extdata  11.6Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readBamFile.Rd: Rsamtools
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ‘ATACseqQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: factorFootprints
> ### Title: plot ATAC-seq footprints infer factor occupancy genome wide
> ### Aliases: factorFootprints
> 
> ### ** Examples
> 
> 
> bamfile <- system.file("extdata", "GL1.bam",
+                        package="ATACseqQC")
> library(MotifDb)
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Seqinfo
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

> CTCF <- query(MotifDb, c("CTCF"))
> CTCF <- as.list(CTCF)
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
> factorFootprints(bamfile, pfm=CTCF[[1]],
+                 genome=Hsapiens,
+                 min.score="95%", seqlev="chr1",
+                 upstream=100, downstream=100)
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
  cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES'
Warning: package 'grImport2' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Loading required namespace: Cairo
Failed with error:  'there is no package called 'Cairo''
Warning in checkValidSVG(doc, warn = warn) :
  This picture may not have been generated by Cairo graphics; errors may result
Loading required namespace: Cairo
Failed with error:  'there is no package called 'Cairo''
Warning in checkValidSVG(doc, warn = warn) :
  This picture may not have been generated by Cairo graphics; errors may result
Loading required namespace: Cairo
Failed with error:  'there is no package called 'Cairo''
Warning in checkValidSVG(doc, warn = warn) :
  This picture may not have been generated by Cairo graphics; errors may result
no slot of name "content" for this object of class "Picture"> ##### Using user defined binding sites #####
> bds <- readRDS(system.file("extdata", "jolma2013.motifs.bindingList.95.rds",
+                           package="ATACseqQC"))
> bindingSites <- bds[["Hsapiens-jolma2013-CTCF"]]
> seqlev <- "chr1" #seqlevels(bindingSites)
> ff <- factorFootprints(bamfile, pfm=CTCF[[1]],
+                 bindingSites=bindingSites,
+                 seqlev=seqlev,
+                 upstream=100, downstream=100)
no slot of name "content" for this object of class "Picture"> ##### normalize the plot by distal signals #####
> library(motifStack)
Loading required package: grid
> Profile <- lapply(ff$signal, function(.ele) colMeans(.ele, na.rm = TRUE))
> pfm <- new('pfm', mat=as.matrix(CTCF[[1]]), name='CTCF')
> plotFootprints(Profile=c(Profile[["+"]], Profile[["-"]]),
+               Mlen=ff$Mlen,
+               motif=pfm,
+               segmentation=ff$Profile.segmentation,
+               reNormalizeByDistalSig=TRUE)
Error in lapply(object@content, grobify, defs = object@defs, gpFUN = gpFUN,  : 
  no slot of name "content" for this object of class "Picture"
Calls: plotFootprints ... pictureGrob -> grobify -> grobify -> .local -> lapply
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
enrichedFragments 199.100  2.723 201.843
distanceDyad       22.021  0.681  22.709
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ATACseqQC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ATACseqQC
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ATACseqQC’ ...
** this is package ‘ATACseqQC’ version ‘1.36.0’
** 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 (ATACseqQC)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.

> require("ATACseqQC") || stop("unable to load Package:ATACseqQC")
Loading required package: ATACseqQC
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

[1] TRUE
> require("GenomicAlignments") || stop("unable to load Package:GenomicAlignments")
Loading required package: GenomicAlignments
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
[1] TRUE
> require("BSgenome") || stop("unable to load Package:BSgenome")
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer
[1] TRUE
> require("rtracklayer") || stop("unable to load Package:rtracklayer")
[1] TRUE
> require("utils") || stop("unable to load Package:utils")
[1] TRUE
> require("testthat") || stop("unable to load testthat")
Loading required package: testthat
[1] TRUE
> test_check("ATACseqQC")

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[ FAIL 0 | WARN 20 | SKIP 1 | PASS 25 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_factorFootprints.R:1:1'

[ FAIL 0 | WARN 20 | SKIP 1 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
 61.402   2.182  63.583