Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1532/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plotgardener 1.6.4  (landing page)
Nicole Kramer
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/plotgardener
git_branch: RELEASE_3_17
git_last_commit: 9340324
git_last_commit_date: 2023-08-04 12:52:12 -0400 (Fri, 04 Aug 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for plotgardener on kjohnson2


To the developers/maintainers of the plotgardener package:
- 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: 1.6.4
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_1.6.4.tar.gz
StartedAt: 2023-10-18 15:05:33 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 15:15:15 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 582.6 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_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/plotgardener.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plotgardener/DESCRIPTION’ ... OK
* this is package ‘plotgardener’ version ‘1.6.4’
* 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 R 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 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 ... OK
* checking Rd files ... OK
* 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      9.970  0.463  15.988
plotIdeogram    5.816  0.495  16.628
plotGenes       5.554  0.191   8.830
annoGenomeLabel 4.226  0.178   6.735
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c checkRow.cpp -o checkRow.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rebinBigwig.cpp -o rebinBigwig.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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, setdiff, sort, 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 22.02.0
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.
signal[signal1_h]
signal[signal1_h]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 118 ]
> 
> proc.time()
   user  system elapsed 
 49.415   2.864  77.521 

Example timings

plotgardener.Rcheck/plotgardener-Ex.timings

nameusersystemelapsed
annoDomains0.8820.0921.513
annoGenomeLabel4.2260.1786.735
annoHeatmapLegend0.6150.0581.024
annoHighlight0.9100.0331.445
annoPixels0.9620.0901.616
annoSegments2.0430.0953.290
annoText1.1000.0431.760
annoXaxis1.6270.0692.583
annoYaxis0.6760.0651.141
annoZoomLines2.8950.1124.596
assembly000
c0.0000.0000.004
calcSignalRange1.1390.0251.779
colorby0.7210.0141.118
defaultPackages0.0120.0010.019
genomes0.0000.0000.001
mapColors0.1030.0050.171
pageCreate0.0500.0040.085
pageGuideHide0.0400.0030.065
pageGuideHorizontal0.0360.0020.056
pageGuideShow0.8690.0911.452
pageGuideVertical0.1120.0060.185
pageLayoutCol0.0010.0010.001
pageLayoutRow0.0010.0000.001
pagePlotPlace0.6270.0610.979
pagePlotRemove0.5480.0540.886
pgParams1.6640.0832.639
plotCircle0.0370.0030.062
plotGG0.3020.0150.486
plotGenes5.5540.1918.830
plotGenomeLabel2.3380.0833.704
plotHicRectangle0.5840.0530.996
plotHicSquare0.7200.0641.193
plotHicTriangle1.3870.0972.265
plotIdeogram 5.816 0.49516.628
plotLegend0.3820.0130.599
plotManhattan2.0430.1073.298
plotMultiSignal2.2280.0553.495
plotPairs0.1420.0080.219
plotPairsArches0.1500.0080.218
plotPolygon0.0600.0040.091
plotRanges0.2000.0080.314
plotRaster 9.970 0.46315.988
plotRect0.6120.0260.969
plotSegments0.0740.0040.111
plotSignal0.8890.0501.420
plotText0.0600.0040.096
plotTranscripts1.1760.0471.881
readBigwig0.3840.0070.602
readHic0.0100.0040.027