| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 1532/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plotgardener 1.6.4 (landing page) Nicole Kramer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
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. |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
plotgardener.Rcheck/plotgardener-Ex.timings
| name | user | system | elapsed | |
| annoDomains | 0.882 | 0.092 | 1.513 | |
| annoGenomeLabel | 4.226 | 0.178 | 6.735 | |
| annoHeatmapLegend | 0.615 | 0.058 | 1.024 | |
| annoHighlight | 0.910 | 0.033 | 1.445 | |
| annoPixels | 0.962 | 0.090 | 1.616 | |
| annoSegments | 2.043 | 0.095 | 3.290 | |
| annoText | 1.100 | 0.043 | 1.760 | |
| annoXaxis | 1.627 | 0.069 | 2.583 | |
| annoYaxis | 0.676 | 0.065 | 1.141 | |
| annoZoomLines | 2.895 | 0.112 | 4.596 | |
| assembly | 0 | 0 | 0 | |
| c | 0.000 | 0.000 | 0.004 | |
| calcSignalRange | 1.139 | 0.025 | 1.779 | |
| colorby | 0.721 | 0.014 | 1.118 | |
| defaultPackages | 0.012 | 0.001 | 0.019 | |
| genomes | 0.000 | 0.000 | 0.001 | |
| mapColors | 0.103 | 0.005 | 0.171 | |
| pageCreate | 0.050 | 0.004 | 0.085 | |
| pageGuideHide | 0.040 | 0.003 | 0.065 | |
| pageGuideHorizontal | 0.036 | 0.002 | 0.056 | |
| pageGuideShow | 0.869 | 0.091 | 1.452 | |
| pageGuideVertical | 0.112 | 0.006 | 0.185 | |
| pageLayoutCol | 0.001 | 0.001 | 0.001 | |
| pageLayoutRow | 0.001 | 0.000 | 0.001 | |
| pagePlotPlace | 0.627 | 0.061 | 0.979 | |
| pagePlotRemove | 0.548 | 0.054 | 0.886 | |
| pgParams | 1.664 | 0.083 | 2.639 | |
| plotCircle | 0.037 | 0.003 | 0.062 | |
| plotGG | 0.302 | 0.015 | 0.486 | |
| plotGenes | 5.554 | 0.191 | 8.830 | |
| plotGenomeLabel | 2.338 | 0.083 | 3.704 | |
| plotHicRectangle | 0.584 | 0.053 | 0.996 | |
| plotHicSquare | 0.720 | 0.064 | 1.193 | |
| plotHicTriangle | 1.387 | 0.097 | 2.265 | |
| plotIdeogram | 5.816 | 0.495 | 16.628 | |
| plotLegend | 0.382 | 0.013 | 0.599 | |
| plotManhattan | 2.043 | 0.107 | 3.298 | |
| plotMultiSignal | 2.228 | 0.055 | 3.495 | |
| plotPairs | 0.142 | 0.008 | 0.219 | |
| plotPairsArches | 0.150 | 0.008 | 0.218 | |
| plotPolygon | 0.060 | 0.004 | 0.091 | |
| plotRanges | 0.200 | 0.008 | 0.314 | |
| plotRaster | 9.970 | 0.463 | 15.988 | |
| plotRect | 0.612 | 0.026 | 0.969 | |
| plotSegments | 0.074 | 0.004 | 0.111 | |
| plotSignal | 0.889 | 0.050 | 1.420 | |
| plotText | 0.060 | 0.004 | 0.096 | |
| plotTranscripts | 1.176 | 0.047 | 1.881 | |
| readBigwig | 0.384 | 0.007 | 0.602 | |
| readHic | 0.010 | 0.004 | 0.027 | |