Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1595/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plotgardener 1.14.0  (landing page)
Nicole Kramer
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/plotgardener
git_branch: RELEASE_3_21
git_last_commit: f5d39c8
git_last_commit_date: 2025-04-15 12:37:13 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for plotgardener on merida1

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: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plotgardener_1.14.0.tar.gz
StartedAt: 2025-10-14 08:18:09 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 08:32:59 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 889.9 seconds
RetCode: 0
Status:   OK  
CheckDir: plotgardener.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plotgardener.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plotgardener_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/plotgardener.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plotgardener/DESCRIPTION’ ... OK
* this is package ‘plotgardener’ version ‘1.14.0’
* 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 ‘plotgardener’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTranscripts.Rd:91-92: 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      16.017  0.996  17.167
plotGenes       10.288  0.383  10.796
plotIdeogram     9.105  0.830  10.464
annoGenomeLabel  5.204  0.248   5.576
readCool         1.522  0.551  50.820
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/plotgardener.Rcheck/00check.log’
for details.


Installation output

plotgardener.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plotgardener
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘plotgardener’ ...
** this is package ‘plotgardener’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c checkRow.cpp -o checkRow.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rebinBigwig.cpp -o rebinBigwig.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o plotgardener.so RcppExports.o checkRow.o rebinBigwig.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: 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")'.


Using poppler version 25.09.1
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]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 133 ]
> 
> proc.time()
   user  system elapsed 
 85.837   5.588 180.551 

Example timings

plotgardener.Rcheck/plotgardener-Ex.timings

nameusersystemelapsed
annoDomains1.5070.1461.825
annoGenomeLabel5.2040.2485.576
annoHeatmapLegend2.1370.0752.217
annoHighlight1.3140.0581.377
annoPixels1.7670.1281.911
annoSegments2.9480.1373.098
annoText1.3780.0501.435
annoXaxis2.8160.0842.906
annoYaxis1.1310.0911.228
annoZoomLines4.0770.1534.250
assembly0.0010.0000.001
c0.0000.0010.001
calcSignalRange0.5250.0280.556
colorby0.9190.0240.957
defaultPackages0.0200.0020.022
genomes0.0010.0010.002
mapColors0.2200.0090.231
pageCreate0.1020.0030.107
pageGuideHide0.0950.0040.100
pageGuideHorizontal0.0860.0020.089
pageGuideShow1.5110.1261.674
pageGuideVertical0.1840.0070.216
pageLayoutCol0.0010.0010.001
pageLayoutRow0.0020.0000.002
pagePlotPlace1.1660.0951.266
pagePlotRemove0.8420.0580.905
pgParams4.2170.2434.475
plotCircle0.0770.0040.081
plotGG0.6670.0090.679
plotGenes10.288 0.38310.796
plotGenomeLabel3.8430.1083.975
plotHicRectangle0.9380.0621.006
plotHicSquare1.2280.0901.328
plotHicTriangle2.4070.0932.518
plotIdeogram 9.105 0.83010.464
plotLegend0.7350.0370.778
plotManhattan3.0770.1583.259
plotMultiSignal3.0780.0883.195
plotPairs0.2980.0100.309
plotPairsArches0.3210.0120.336
plotPolygon0.1260.0050.133
plotRanges0.3740.0100.388
plotRaster16.017 0.99617.167
plotRect0.8880.0480.941
plotSegments0.1480.0060.154
plotSignal1.4160.0991.539
plotText0.1130.0050.119
plotTranscripts1.9650.0712.050
readBigwig0.6590.0210.687
readCool 1.522 0.55150.820
readHic0.0150.0040.021