Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:46 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the NormalyzerDE package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NormalyzerDE.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1351/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
NormalyzerDE 1.17.0 (landing page) Jakob Willforss
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: NormalyzerDE |
Version: 1.17.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NormalyzerDE_1.17.0.tar.gz |
StartedAt: 2023-02-28 09:56:52 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 10:05:43 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 531.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: NormalyzerDE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:NormalyzerDE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings NormalyzerDE_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/NormalyzerDE.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘NormalyzerDE/DESCRIPTION’ ... OK * this is package ‘NormalyzerDE’ version ‘1.17.0’ * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘NormalyzerDE’ 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 R 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 ... 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 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 generatePlots 19.348 0.304 19.656 NormalyzerEvaluationResults 7.373 0.315 7.690 analyzeNormalizations 6.160 0.072 6.233 writeNormalizedDatasets 6.139 0.012 6.151 getSmoothedRTNormalizedMatrix 5.701 0.024 5.725 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/NormalyzerDE.Rcheck/00check.log’ for details.
NormalyzerDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL NormalyzerDE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘NormalyzerDE’ ... ** 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 (NormalyzerDE)
NormalyzerDE.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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(NormalyzerDE) > test_check("NormalyzerDE") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ] > > proc.time() user system elapsed 41.417 0.964 42.372
NormalyzerDE.Rcheck/NormalyzerDE-Ex.timings
name | user | system | elapsed | |
NormalyzerEvaluationResults | 7.373 | 0.315 | 7.690 | |
NormalyzerResults | 0.115 | 0.000 | 0.115 | |
NormalyzerStatistics | 0.018 | 0.000 | 0.018 | |
analyzeNormalizations | 6.160 | 0.072 | 6.233 | |
calculateContrasts | 0.124 | 0.004 | 0.127 | |
generateAnnotatedMatrix | 0.065 | 0.000 | 0.065 | |
generatePlots | 19.348 | 0.304 | 19.656 | |
generateStatsReport | 3.181 | 0.028 | 3.210 | |
getRTNormalizedMatrix | 3.727 | 0.080 | 3.807 | |
getSmoothedRTNormalizedMatrix | 5.701 | 0.024 | 5.725 | |
getVerifiedNormalyzerObject | 0.06 | 0.00 | 0.06 | |
globalIntensityNormalization | 0.005 | 0.000 | 0.005 | |
loadData | 0.001 | 0.000 | 0.001 | |
loadDesign | 0 | 0 | 0 | |
meanNormalization | 0.005 | 0.000 | 0.005 | |
medianNormalization | 0.004 | 0.000 | 0.004 | |
normMethods | 2.568 | 0.024 | 2.592 | |
normalyzer | 0 | 0 | 0 | |
normalyzerDE | 1.455 | 0.008 | 1.464 | |
performCyclicLoessNormalization | 0.011 | 0.000 | 0.011 | |
performGlobalRLRNormalization | 0.021 | 0.000 | 0.021 | |
performQuantileNormalization | 0.001 | 0.001 | 0.002 | |
performSMADNormalization | 0.000 | 0.002 | 0.002 | |
performVSNNormalization | 0.023 | 0.000 | 0.024 | |
reduceTechnicalReplicates | 0.036 | 0.003 | 0.039 | |
setupJobDir | 0.000 | 0.000 | 0.001 | |
setupRawContrastObject | 0.019 | 0.000 | 0.019 | |
setupRawDataObject | 0.023 | 0.000 | 0.023 | |
setupTestData | 0.002 | 0.000 | 0.001 | |
writeNormalizedDatasets | 6.139 | 0.012 | 6.151 | |