Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 273/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Cardinal 3.6.4 (landing page) Kylie Ariel Bemis
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the Cardinal package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.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: Cardinal |
Version: 3.6.4 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Cardinal_3.6.4.tar.gz |
StartedAt: 2024-07-21 22:25:33 -0400 (Sun, 21 Jul 2024) |
EndedAt: 2024-07-21 22:32:06 -0400 (Sun, 21 Jul 2024) |
EllapsedTime: 393.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Cardinal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Cardinal_3.6.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Cardinal.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘Cardinal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cardinal’ version ‘3.6.4’ * 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 ‘Cardinal’ can be installed ... OK * 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 loading without being on the library search path ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘Cardinal’ ... ** 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 (Cardinal)
Cardinal.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(Cardinal) Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: BiocParallel 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 Cardinal v3.6 is a major update. Use vignette('Cardinal3-guide') to see what's new. > > test_check("Cardinal") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 713 ] > > proc.time() user system elapsed 101.492 1.351 102.836
Cardinal.Rcheck/Cardinal-Ex.timings
name | user | system | elapsed | |
MSImagingArrays-class | 0.287 | 0.008 | 0.295 | |
MSImagingExperiment-class | 0.413 | 0.020 | 0.433 | |
MassDataFrame-class | 0.025 | 0.000 | 0.025 | |
PositionDataFrame-class | 0.044 | 0.000 | 0.044 | |
SpatialNMF | 0.891 | 0.088 | 0.979 | |
SpatialPCA | 1.032 | 0.024 | 1.056 | |
SpatialPLS | 0.706 | 0.012 | 0.718 | |
SpectraArrays-class | 0.009 | 0.000 | 0.009 | |
SpectralImagingArrays-class | 0.055 | 0.000 | 0.055 | |
SpectralImagingExperiment-class | 0.063 | 0.004 | 0.067 | |
XDataFrame-class | 0.024 | 0.000 | 0.024 | |
bin | 0.484 | 0.036 | 0.520 | |
colocalized | 0.686 | 0.008 | 0.694 | |
features | 0.543 | 0.060 | 0.603 | |
findNeighbors | 0.044 | 0.004 | 0.049 | |
meansTest | 3.162 | 0.056 | 3.218 | |
normalize | 0.434 | 0.000 | 0.434 | |
peakAlign | 0.628 | 0.000 | 0.628 | |
peakPick | 0.707 | 0.044 | 0.751 | |
peakProcess | 0.658 | 0.000 | 0.658 | |
pixels | 0.526 | 0.008 | 0.533 | |
plot-image | 1.124 | 0.012 | 1.135 | |
plot-spectra | 0.660 | 0.000 | 0.659 | |
process | 0.643 | 0.008 | 0.651 | |
recalibrate | 0.699 | 0.000 | 0.699 | |
reduceBaseline | 0.602 | 0.000 | 0.602 | |
simulateSpectra | 1.142 | 0.088 | 1.231 | |
slice | 0.580 | 0.012 | 0.593 | |
smooth | 0.583 | 0.000 | 0.584 | |
spatialDGMM | 1.029 | 0.008 | 1.037 | |
spatialFastmap | 0.704 | 0.004 | 0.707 | |
spatialKMeans | 0.803 | 0.000 | 0.802 | |
spatialShrunkenCentroids | 1.740 | 0.028 | 1.768 | |
spatialWeights | 0.605 | 0.016 | 0.621 | |
spectrapply | 0.525 | 0.000 | 0.524 | |
subset | 0.711 | 0.008 | 0.719 | |
summarize | 0.716 | 0.052 | 0.768 | |