Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1871/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scDiagnostics 1.0.0 (landing page) Anthony Christidis
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the scDiagnostics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDiagnostics.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: scDiagnostics |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scDiagnostics_1.0.0.tar.gz |
StartedAt: 2024-11-20 09:08:34 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 09:18:28 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 593.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scDiagnostics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scDiagnostics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scDiagnostics_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scDiagnostics.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘scDiagnostics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scDiagnostics’ version ‘1.0.0’ * 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 ‘scDiagnostics’ 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 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... NOTE 'LazyDataCompression' is specified without 'LazyData' * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotCellTypeMDS 14.098 0.128 18.326 calculateCellDistances 12.417 0.405 15.936 calculateCramerPValue 6.591 0.042 7.724 calculateCellDistancesSimilarity 4.559 0.232 6.459 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/scDiagnostics.Rcheck/00check.log’ for details.
scDiagnostics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scDiagnostics ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘scDiagnostics’ ... ** using staged installation ** R ** data ** 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 (scDiagnostics)
scDiagnostics.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(scDiagnostics) > > test_check("scDiagnostics") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 276 ] > > proc.time() user system elapsed 109.543 7.434 136.874
scDiagnostics.Rcheck/scDiagnostics-Ex.timings
name | user | system | elapsed | |
boxplotPCA | 1.301 | 0.156 | 1.576 | |
calculateAveragePairwiseCorrelation | 2.821 | 0.052 | 3.208 | |
calculateCategorizationEntropy | 0.007 | 0.000 | 0.015 | |
calculateCellDistances | 12.417 | 0.405 | 15.936 | |
calculateCellDistancesSimilarity | 4.559 | 0.232 | 6.459 | |
calculateCellSimilarityPCA | 1.443 | 0.059 | 1.370 | |
calculateCramerPValue | 6.591 | 0.042 | 7.724 | |
calculateDiscriminantSpace | 3.442 | 0.050 | 4.780 | |
calculateHVGOverlap | 1.250 | 0.015 | 2.478 | |
calculateHotellingPValue | 1.044 | 0.007 | 1.232 | |
calculateNearestNeighborProbabilities | 2.871 | 0.003 | 3.345 | |
calculateSIRSpace | 2.586 | 0.005 | 3.523 | |
calculateVarImpOverlap | 3.285 | 0.063 | 3.836 | |
calculateWassersteinDistance | 1.838 | 0.178 | 4.031 | |
compareCCA | 0.729 | 0.013 | 1.485 | |
comparePCA | 1.051 | 0.014 | 1.924 | |
comparePCASubspace | 0.958 | 0.011 | 1.941 | |
detectAnomaly | 1.798 | 0.029 | 2.350 | |
histQCvsAnnotation | 0.420 | 0.002 | 0.422 | |
plot.calculateWassersteinDistanceObject | 1.557 | 0.163 | 2.713 | |
plotCellTypeMDS | 14.098 | 0.128 | 18.326 | |
plotCellTypePCA | 0.927 | 0.014 | 0.983 | |
plotGeneExpressionDimred | 1.334 | 0.011 | 1.386 | |
plotGeneSetScores | 0.704 | 0.004 | 0.751 | |
plotMarkerExpression | 0.377 | 0.005 | 0.390 | |
plotPairwiseDistancesDensity | 0.763 | 0.010 | 0.776 | |
plotQCvsAnnotation | 0.147 | 0.002 | 0.187 | |
projectPCA | 0.204 | 0.004 | 0.209 | |
projectSIR | 0.977 | 0.003 | 1.045 | |
qc_data | 0.027 | 0.001 | 0.030 | |
query_data | 0.024 | 0.001 | 0.027 | |
reference_data | 0.056 | 0.001 | 0.060 | |
regressPC | 1.151 | 0.006 | 1.176 | |