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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GenVisR_1.43.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GenVisR.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 ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.43.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘GenVisR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildWaterfallPlot,WaterfallData: no visible global function definition
  for ‘tail’
setTierTwo,data.table: no visible global function definition for ‘tail’
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
  missingINdex tail tmp
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) lohSpec.Rd:46: Lost braces; missing escapes or markup?
    46 | consisting of elements from the set {"M", "F"}. Used to suppress the plotting
       |                                     ^
* 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 ‘GenVisR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genCov
> ### Title: Construct a region of interest coverage plot
> ### Aliases: genCov
> 
> ### ** Examples
> 
> # Load transcript meta data
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
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

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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")'.

> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> 
> # Load BSgenome
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
> genome <- BSgenome.Hsapiens.UCSC.hg19
> 
> # Define a region of interest
> gr <- GRanges(seqnames=c("chr10"),
+ ranges=IRanges(start=c(89622195), end=c(89729532)), strand=strand(c("+")))
> 
> # Create Data for input
> start <- c(89622194:89729524)
> end <- c(89622195:89729525)
> chr <- 10
> cov <- c(rnorm(100000, mean=40), rnorm(7331, mean=10))
> cov_input_A <- as.data.frame(cbind(chr, start, end, cov))
> 
> start <- c(89622194:89729524)
> end <- c(89622195:89729525)
> chr <- 10
> cov <- c(rnorm(50000, mean=40), rnorm(7331, mean=10), rnorm(50000, mean=40))
> cov_input_A <- as.data.frame(cbind(chr, start, end, cov))
> 
> # Define the data as a list
> data <- list("Sample A"=cov_input_A)
> 
> # Call genCov
> genCov(data, txdb, gr, genome, gene_labelTranscriptSize=3)
Obtaining CDS Coordinates
'select()' returned 1:many mapping between keys and columns
Obtaining UTR Coordinates
'select()' returned 1:many mapping between keys and columns
Error in if (is.na(UTR)) { : the condition has length > 1
Calls: genCov -> geneViz -> geneViz_formatUTR
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
Lolliplot-class 24.730  2.456  33.591
cnSpec           5.528  0.139   5.655
cnFreq           5.437  0.176   5.614
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GenVisR
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GenVisR’ ...
** this is package ‘GenVisR’ version ‘1.43.0’
** 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 (GenVisR)

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(GenVisR)
> 
> test_check("GenVisR")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 510 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 510 ]
> 
> proc.time()
   user  system elapsed 
109.078   7.159 127.140