Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1565/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plotgardener 1.12.0  (landing page)
Nicole Kramer
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/plotgardener
git_branch: RELEASE_3_20
git_last_commit: d40c62a
git_last_commit_date: 2024-10-29 11:03:25 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-12-20 07:44:21 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:56:53 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 751.9 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/plotgardener.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.12.0’
* 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      14.639  0.956  15.848
plotGenes       10.140  0.191  10.472
plotIdeogram     8.694  0.736  13.253
annoGenomeLabel  5.198  0.276   5.537
readCool         1.618  0.629   8.655
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘plotgardener’ ...
** 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/4.4-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/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, saveRDS, 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")'.


Using poppler version 23.04.0
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]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 133 ]
> 
> proc.time()
   user  system elapsed 
 87.344   5.695 105.056 

Example timings

plotgardener.Rcheck/plotgardener-Ex.timings

nameusersystemelapsed
annoDomains2.2910.0932.394
annoGenomeLabel5.1980.2765.537
annoHeatmapLegend2.0350.0762.229
annoHighlight1.4070.0661.581
annoPixels1.9150.1452.166
annoSegments3.0010.1503.314
annoText1.5040.0731.690
annoXaxis3.0700.0753.294
annoYaxis1.1670.0901.299
annoZoomLines4.2190.1764.438
assembly0.0010.0010.001
c0.0010.0010.001
calcSignalRange0.4730.0270.503
colorby0.9280.0200.953
defaultPackages0.0520.0050.057
genomes0.0000.0010.001
mapColors0.2050.0070.212
pageCreate0.1130.0030.159
pageGuideHide0.0990.0030.102
pageGuideHorizontal0.0880.0020.091
pageGuideShow1.5670.1331.735
pageGuideVertical0.1820.0070.195
pageLayoutCol0.0010.0000.002
pageLayoutRow0.0010.0010.002
pagePlotPlace1.1680.0961.319
pagePlotRemove0.8660.0560.928
pgParams4.1560.1914.389
plotCircle0.0740.0030.078
plotGG0.4930.0120.507
plotGenes10.140 0.19110.472
plotGenomeLabel3.9020.1104.075
plotHicRectangle0.9630.0631.047
plotHicSquare1.2190.0961.331
plotHicTriangle2.4390.1032.673
plotIdeogram 8.694 0.73613.253
plotLegend0.6890.0240.744
plotManhattan2.9290.1533.099
plotMultiSignal2.9390.0713.029
plotPairs0.2960.0080.305
plotPairsArches0.3070.0090.350
plotPolygon0.1180.0030.120
plotRanges0.4110.0150.430
plotRaster14.639 0.95615.848
plotRect0.8730.0531.021
plotSegments0.1450.0060.155
plotSignal1.4390.0931.635
plotText0.1160.0060.213
plotTranscripts2.0720.0882.393
readBigwig0.6900.0520.763
readCool1.6180.6298.655
readHic0.0160.0050.022