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 11:39 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 267/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Cardinal 3.9.0 (landing page) Kylie Ariel Bemis
| 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 | 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: 3.9.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Cardinal_3.9.0.tar.gz |
StartedAt: 2024-12-23 20:22:20 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:34:46 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 746.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Cardinal.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Cardinal.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Cardinal_3.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Cardinal.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘Cardinal/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Cardinal’ version ‘3.9.0’ * 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Cardinal-package.Rd: bplapply, simple_logger MSImagingArrays-class.Rd: ImzMeta-class, ProcessingStep-class MSImagingExperiment-class.Rd: ImzMeta-class, ProcessingStep-class MeansTest.Rd: lme, chunkApply, bplapply ResultsList-class.Rd: SimpleList-class SpatialCV.Rd: chunkApply, bplapply, cv_do SpatialDGMM.Rd: chunkApply, bplapply SpatialFastmap.Rd: chunkApply, bplapply SpatialKMeans.Rd: chunkApply, bplapply SpatialPCA.Rd: chunkApply, bplapply, irlba SpatialPLS.Rd: chunkApply, bplapply SpatialResults-class.Rd: DataFrame-class SpatialShrunkenCentroids.Rd: chunkApply, bplapply SpectraArrays-class.Rd: SimpleList-class SpectralImagingArrays-class.Rd: ProcessingStep-class SpectralImagingData-class.Rd: ProcessingStep-class SpectralImagingExperiment-class.Rd: DataFrame-class, ProcessingStep-class XDataFrame-class.Rd: DataFrame-class, DataFrame colocalized.Rd: chunkApply, bplapply estimateDomain.Rd: chunkApply, bplapply, chunkLapply findNeighbors.Rd: sparse_mat-class normalize.Rd: rescale_sum, rescale_rms, rescale_ref peakAlign.Rd: chunkApply, bplapply peakPick.Rd: estnoise_diff, estnoise_sd, estnoise_mad, estnoise_quant, estnoise_filt, findpeaks_cwt peakProcess.Rd: chunkApply, bplapply plot-image.Rd: enhance, filt2, plot_image plot-spectra.Rd: downsample, plot_signal process.Rd: chunkApply, bplapply readMSIData.Rd: matter, chunkApply, bplapply recalibrate.Rd: warp1_loc, warp1_dtw, warp1_cow reduceBaseline.Rd: estbase_loc, estbase_hull, estbase_snip, estbase_med simulateSpectra.Rd: chunkApply, bplapply smooth.Rd: filt1_gauss, filt1_bi, filt1_adapt, filt1_diff, filt1_guide, filt1_pag, filt1_sg, filt1_ma spatialDists.Rd: chunkApply, bplapply spatialWeights.Rd: chunkApply, bplapply, sparse_mat-class spectrapply.Rd: chunkApply, bplapply summarize.Rd: chunkApply, bplapply writeMSIData.Rd: chunkApply, bplapply Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 12.901 0.351 13.252 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/Cardinal.Rcheck/00check.log’ for details.
Cardinal.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Cardinal ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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: BiocParallel 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 Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth 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 > > test_check("Cardinal") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 756 ] > > proc.time() user system elapsed 172.185 4.564 174.981
Cardinal.Rcheck/Cardinal-Ex.timings
name | user | system | elapsed | |
MSImagingArrays-class | 0.506 | 0.076 | 0.582 | |
MSImagingExperiment-class | 0.109 | 0.000 | 0.109 | |
MassDataFrame-class | 0.025 | 0.002 | 0.027 | |
MeansTest | 12.901 | 0.351 | 13.252 | |
PositionDataFrame-class | 0.047 | 0.000 | 0.048 | |
SpatialDGMM | 2.518 | 0.015 | 2.533 | |
SpatialFastmap | 2.114 | 0.051 | 2.166 | |
SpatialKMeans | 2.212 | 0.061 | 2.272 | |
SpatialNMF | 2.074 | 0.009 | 2.083 | |
SpatialPCA | 2.014 | 0.001 | 2.015 | |
SpatialPLS | 2.098 | 0.024 | 2.122 | |
SpatialShrunkenCentroids | 2.835 | 0.046 | 2.881 | |
SpectraArrays-class | 0.008 | 0.001 | 0.009 | |
SpectralImagingArrays-class | 0.061 | 0.006 | 0.067 | |
SpectralImagingExperiment-class | 0.077 | 0.004 | 0.081 | |
XDataFrame-class | 0.026 | 0.000 | 0.027 | |
bin | 0.487 | 0.012 | 0.499 | |
colocalized | 2.590 | 0.037 | 2.627 | |
features | 1.897 | 0.012 | 1.909 | |
findNeighbors | 0.051 | 0.004 | 0.055 | |
normalize | 0.459 | 0.000 | 0.461 | |
peakAlign | 0.604 | 0.001 | 0.606 | |
peakPick | 0.669 | 0.000 | 0.669 | |
peakProcess | 0.621 | 0.001 | 0.622 | |
pixels | 1.904 | 0.021 | 1.925 | |
plot-image | 4.720 | 0.059 | 4.780 | |
plot-spectra | 0.635 | 0.002 | 0.637 | |
process | 0.603 | 0.003 | 0.607 | |
recalibrate | 0.654 | 0.002 | 0.656 | |
reduceBaseline | 0.593 | 0.002 | 0.596 | |
simulateSpectra | 2.247 | 0.006 | 2.253 | |
sliceImage | 1.915 | 0.003 | 1.918 | |
smooth | 0.600 | 0.001 | 0.601 | |
spatialDists | 2.130 | 0.003 | 2.133 | |
spatialWeights | 2.120 | 0.030 | 2.149 | |
spectrapply | 1.915 | 0.004 | 1.919 | |
subset | 2.114 | 0.065 | 2.178 | |
summarize | 2.186 | 0.003 | 2.188 | |