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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings plotgardener_1.11.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘plotgardener/DESCRIPTION’ ... OK
* this is package ‘plotgardener’ version ‘1.11.3’
* 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 ‘plotgardener’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 whether startup messages can be suppressed ... 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
.checkCool: no visible binding for global variable ‘name’
pgParams: no visible binding for global variable ‘width’
pgParams: no visible binding for global variable ‘strand’
Undefined global functions or variables:
  name strand width
* checking Rd files ... NOTE
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* 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘plotgardener-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotIdeogram
> ### Title: Plot a chromosome ideogram with or without cytobands
> ### Aliases: plotIdeogram
> 
> ### ** Examples
> 
> ## Load Giemsa stain band information and genomic
> ## annotation data for hg19 genome assembly
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: GenomicFeatures
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
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: GenomeInfoDb
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")'.

> library(AnnotationHub)
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: ‘AnnotationHub’

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

    cache

> 
> ## Create page
> pageCreate(width = 4.5, height = 1, default.units = "inches")
> 
> ## Plot and place ideogram
> ideogramPlot <- plotIdeogram(
+     chrom = "chr2", assembly = "hg19",
+     x = 0.25, y = 0.25, width = 4, height = 0.3,
+     just = c("left", "top"),
+     default.units = "inches"
+ )
Error: failed to load resource
  name: AH53177
  title: UCSC cytoBand track for hg19
  reason: unknown input format
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:
    5.     ├─base::as.data.frame(suppressMessages(cytobands[[AH_id]]))
    6.     ├─base::suppressMessages(cytobands[[AH_id]])
    7.     │ └─base::withCallingHandlers(...)
    8.     ├─cytobands[[AH_id]]
    9.     └─cytobands[[AH_id]]
   10.       └─AnnotationHub (local) .local(x, i, j = j, ...)
   11.         └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   12.           └─base::tryCatch(...)
   13.             └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14.               └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   15.                 └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 132 ]
  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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck/00check.log’
for details.