Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-09-23 12:03 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1592/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plotgardener 1.15.1  (landing page)
Nicole Kramer
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/plotgardener
git_branch: devel
git_last_commit: 2bc0a3e
git_last_commit_date: 2025-04-16 16:49:52 -0400 (Wed, 16 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for plotgardener on nebbiolo2

To the developers/maintainers of the plotgardener package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plotgardener.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: plotgardener
Version: 1.15.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings plotgardener_1.15.1.tar.gz
StartedAt: 2025-09-23 02:53:51 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 03:02:11 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 499.5 seconds
RetCode: 0
Status:   OK  
CheckDir: plotgardener.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings plotgardener_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/plotgardener.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘plotgardener/DESCRIPTION’ ... OK
* this is package ‘plotgardener’ version ‘1.15.1’
* 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 ‘plotgardener’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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
checkRd: (-1) annoDomains.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoDomains.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoGenomeLabel.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoHeatmapLegend.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoPixels.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoSegments.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoXaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) annoYaxis.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGenomeLabel.Rd:81-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicRectangle.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicSquare.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotHicTriangle.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotIdeogram.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLegend.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotManhattan.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotMultiSignal.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotPairsArches.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotRanges.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSegments.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSignal.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:95-96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readBigwig.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) readHic.Rd:70: Lost braces in \itemize; meant \describe ?
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
plotRaster   19.903  0.962  20.866
plotIdeogram  5.068  0.242   5.730
readCool      0.842  0.323  49.808
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/plotgardener.Rcheck/00check.log’
for details.


Installation output

plotgardener.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL plotgardener
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘plotgardener’ ...
** this is package ‘plotgardener’ version ‘1.15.1’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c checkRow.cpp -o checkRow.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c rebinBigwig.cpp -o rebinBigwig.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o plotgardener.so RcppExports.o checkRow.o rebinBigwig.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-plotgardener/00new/plotgardener/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (plotgardener)

Tests output

plotgardener.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(plotgardener)

Attaching package: 'plotgardener'

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

    c

> 
> test_check("plotgardener")
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")'.


Using poppler version 24.02.0
Loading required package: BiocFileCache
Loading required package: dbplyr

Attaching package: 'AnnotationHub'

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

    cache

pairs[pairs1]
arches[arches1]
ranges[ranges1]
transcripts[transcripts1]
start, endLoading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Read in hic file with KR normalization at 1e+05 BP resolution.
trying URL 'https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool'
Content type 'binary/octet-stream' length 4103444 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

trying URL 'https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1'
Content type 'application/octet-stream' length 55194561 bytes (52.6 MB)
==================================================
downloaded 52.6 MB

signal[signal1_h]
signal[signal1_h]
transcripts[transcripts1]
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 133 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-transcriptFilter.R:4:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 133 ]
> 
> proc.time()
   user  system elapsed 
 46.618   2.062  98.428 

Example timings

plotgardener.Rcheck/plotgardener-Ex.timings

nameusersystemelapsed
annoDomains0.6770.0430.722
annoGenomeLabel2.4340.1442.578
annoHeatmapLegend1.5040.1391.644
annoHighlight0.6970.0300.726
annoPixels0.8350.0370.873
annoSegments1.7220.0471.770
annoText0.7870.0200.807
annoXaxis1.3370.0251.362
annoYaxis0.5340.0080.541
annoZoomLines2.3460.0582.405
assembly0.0010.0000.000
c000
calcSignalRange0.2820.0040.287
colorby0.5400.0090.548
defaultPackages0.0080.0000.009
genomes0.0000.0000.001
mapColors0.1430.0020.144
pageCreate0.0390.0000.039
pageGuideHide0.0330.0000.032
pageGuideHorizontal0.0280.0000.028
pageGuideShow0.7340.0080.742
pageGuideVertical0.0900.0010.091
pageLayoutCol0.0010.0000.001
pageLayoutRow0.0000.0000.001
pagePlotPlace0.5540.0050.559
pagePlotRemove0.4310.0030.434
pgParams2.8290.1032.940
plotCircle0.0290.0000.029
plotGG0.2820.0020.284
plotGenes3.7050.0723.778
plotGenomeLabel1.6910.0321.724
plotHicRectangle0.5130.0150.528
plotHicSquare0.5790.0170.597
plotHicTriangle1.1830.0191.201
plotIdeogram5.0680.2425.730
plotLegend0.3260.0050.331
plotManhattan1.7660.0191.785
plotMultiSignal1.6350.0691.704
plotPairs0.1450.0010.146
plotPairsArches0.1370.0020.139
plotPolygon0.0440.0000.044
plotRanges0.1560.0000.156
plotRaster19.903 0.96220.866
plotRect0.5010.0170.518
plotSegments0.0580.0000.060
plotSignal0.7210.0290.749
plotText0.0470.0000.047
plotTranscripts0.9090.0070.916
readBigwig0.2440.0340.278
readCool 0.842 0.32349.808
readHic0.0070.0020.009