Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-20 11:37:13 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4666 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4401 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4428 |
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 266/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Cardinal 3.7.0 (landing page) Kylie Ariel Bemis
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
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: 3.7.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cardinal_3.7.0.tar.gz |
StartedAt: 2024-05-18 00:59:24 -0400 (Sat, 18 May 2024) |
EndedAt: 2024-05-18 01:09:53 -0400 (Sat, 18 May 2024) |
EllapsedTime: 629.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Cardinal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Cardinal_3.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Cardinal.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Cardinal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cardinal’ version ‘3.7.0’ * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed meansTest 8.663 0.071 9.523 spatialShrunkenCentroids 5.407 0.075 5.986 * 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: OK
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 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(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 696 ] > > proc.time() user system elapsed 264.049 4.445 291.142
Cardinal.Rcheck/Cardinal-Ex.timings
name | user | system | elapsed | |
MSImagingArrays-class | 0.555 | 0.010 | 0.612 | |
MSImagingExperiment-class | 0.680 | 0.005 | 0.742 | |
MassDataFrame-class | 0.063 | 0.002 | 0.067 | |
PositionDataFrame-class | 0.126 | 0.002 | 0.136 | |
SpatialNMF | 2.396 | 0.150 | 2.731 | |
SpatialPCA | 2.244 | 0.041 | 2.421 | |
SpatialPLS | 1.925 | 0.034 | 2.127 | |
SpectraArrays-class | 0.024 | 0.002 | 0.027 | |
SpectralImagingArrays-class | 0.153 | 0.002 | 0.169 | |
SpectralImagingExperiment-class | 0.160 | 0.003 | 0.175 | |
XDataFrame-class | 0.068 | 0.002 | 0.074 | |
bin | 1.388 | 0.012 | 1.470 | |
colocalized | 1.838 | 0.070 | 2.024 | |
features | 1.479 | 0.044 | 1.647 | |
findNeighbors | 0.128 | 0.010 | 0.149 | |
meansTest | 8.663 | 0.071 | 9.523 | |
normalize | 1.216 | 0.009 | 1.381 | |
peakAlign | 1.791 | 0.013 | 2.007 | |
peakPick | 2.100 | 0.014 | 2.484 | |
peakProcess | 1.934 | 0.012 | 2.181 | |
pixels | 1.445 | 0.010 | 1.625 | |
plot-image | 2.964 | 0.066 | 3.443 | |
plot-spectra | 1.805 | 0.038 | 2.047 | |
process | 1.944 | 0.020 | 2.195 | |
recalibrate | 1.854 | 0.019 | 2.103 | |
reduceBaseline | 1.905 | 0.017 | 2.155 | |
simulateSpectra | 1.981 | 0.036 | 2.234 | |
slice | 1.662 | 0.036 | 1.790 | |
smooth | 1.827 | 0.015 | 1.914 | |
spatialDGMM | 2.958 | 0.031 | 3.170 | |
spatialFastmap | 1.949 | 0.019 | 2.030 | |
spatialKMeans | 2.291 | 0.023 | 2.497 | |
spatialShrunkenCentroids | 5.407 | 0.075 | 5.986 | |
spatialWeights | 1.630 | 0.055 | 1.777 | |
spectrapply | 1.420 | 0.013 | 1.485 | |
subset | 2.331 | 0.025 | 2.479 | |
summarize | 1.932 | 0.024 | 2.060 | |