Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 2005/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpatialOmicsOverlay 1.7.0 (landing page) Maddy Griswold
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the SpatialOmicsOverlay package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialOmicsOverlay.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. |
Package: SpatialOmicsOverlay |
Version: 1.7.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialOmicsOverlay_1.7.0.tar.gz |
StartedAt: 2024-12-23 21:32:26 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 21:35:24 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 178.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpatialOmicsOverlay.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialOmicsOverlay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialOmicsOverlay_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SpatialOmicsOverlay.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpatialOmicsOverlay/DESCRIPTION’ ... OK * this is package ‘SpatialOmicsOverlay’ version ‘1.7.0’ * 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 ‘SpatialOmicsOverlay’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 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 plotSpatialOverlay: no visible binding for global variable ‘xcoor’ plotSpatialOverlay: no visible binding for global variable ‘ycoor’ plotSpatialOverlay: no visible binding for global variable ‘sampleID’ plotSpatialOverlay: no visible binding for global variable ‘Target’ scaleBarPrinting: no visible binding for global variable ‘X’ scaleBarPrinting: no visible binding for global variable ‘Y’ Undefined global functions or variables: Target X Y sampleID xcoor ycoor * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed add4ChannelImage 7.444 0.574 5.511 cropSamples 4.932 0.460 4.808 readSpatialOverlay 4.961 0.369 4.895 * 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/SpatialOmicsOverlay.Rcheck/00check.log’ for details.
SpatialOmicsOverlay.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialOmicsOverlay ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘SpatialOmicsOverlay’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpatialOmicsOverlay)
SpatialOmicsOverlay.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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(vdiffr) > > options( java.parameters = "-Xmx4g" ) > library( "RBioFormats" ) BioFormats library version 7.3.0 > > library(SpatialOmicsOverlay) > > # #run tests > test_check("SpatialOmicsOverlay") Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: NanoStringNCTools 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: ggplot2 Extracting XML Parsing XML - scan metadata Parsing XML - overlay data Generating Coordinates Extracting XML Parsing XML - scan metadata Parsing XML - overlay data Generating Coordinates Calculating and scaling coordinates Calculating and scaling coordinates [ FAIL 0 | WARN 3 | SKIP 0 | PASS 422 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 422 ] > > > > proc.time() user system elapsed 51.930 4.728 52.742
SpatialOmicsOverlay.Rcheck/SpatialOmicsOverlay-Ex.timings
name | user | system | elapsed | |
add4ChannelImage | 7.444 | 0.574 | 5.511 | |
addImageOmeTiff | 4.424 | 0.315 | 4.019 | |
addPlottingFactor | 0.184 | 0.007 | 0.192 | |
bookendStr | 0.000 | 0.000 | 0.001 | |
changeColoringIntensity | 4.426 | 0.324 | 4.014 | |
changeImageColoring | 4.260 | 0.321 | 4.045 | |
checkValidRes | 0.947 | 0.116 | 0.880 | |
createCoordFile | 1.233 | 0.030 | 1.263 | |
createMask | 2.777 | 0.128 | 2.916 | |
cropSamples | 4.932 | 0.460 | 4.808 | |
cropTissue | 3.922 | 0.395 | 3.819 | |
downloadMouseBrainImage | 0.041 | 0.003 | 0.044 | |
flipX | 3.847 | 0.402 | 3.784 | |
flipY | 3.881 | 0.445 | 3.879 | |
fluorLegend | 0.602 | 0.089 | 0.691 | |
moveCoords | 0.074 | 0.007 | 0.080 | |
parseOverlayAttrs | 1.158 | 0.126 | 1.134 | |
parseScanMetadata | 1.296 | 0.124 | 1.093 | |
plotSpatialOverlay | 0.490 | 0.085 | 0.579 | |
readLabWorksheet | 0.002 | 0.001 | 0.001 | |
readSpatialOverlay | 4.961 | 0.369 | 4.895 | |
recolor | 3.978 | 0.338 | 3.743 | |
removeSample | 0.090 | 0.003 | 0.093 | |
xmlExtraction | 1.084 | 0.102 | 1.060 | |