Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:54 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the diffcyt package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffcyt.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 505/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
diffcyt 1.14.0 (landing page) Lukas M. Weber
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: diffcyt |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffcyt_1.14.0.tar.gz |
StartedAt: 2022-04-12 12:34:55 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 12:41:42 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 406.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: diffcyt.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffcyt.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffcyt_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘diffcyt/DESCRIPTION’ ... OK * this is package ‘diffcyt’ version ‘1.14.0’ * 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 ‘diffcyt’ 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 ... NOTE calcCounts: no visible binding for global variable ‘cluster_id’ calcCounts: no visible binding for global variable ‘sample_id’ calcMedians: no visible binding for global variable ‘cluster_id’ calcMedians: no visible binding for global variable ‘sample_id’ calcMedians: no visible binding for global variable ‘value’ calcMediansByClusterMarker: no visible binding for global variable ‘cluster_id’ calcMediansByClusterMarker: no visible binding for global variable ‘marker_id’ calcMediansByClusterMarker: no visible binding for global variable ‘value’ calcMediansBySampleMarker: no visible binding for global variable ‘sample_id’ calcMediansBySampleMarker: no visible binding for global variable ‘marker_id’ calcMediansBySampleMarker: no visible binding for global variable ‘value’ Undefined global functions or variables: cluster_id marker_id sample_id value * 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 diffcyt 16.706 0.172 16.891 testDA_GLMM 16.491 0.072 16.591 plotHeatmap 10.181 0.105 10.299 topTable 7.647 0.063 7.717 testDS_LMM 7.580 0.045 7.631 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffcyt.Rcheck/00check.log’ for details.
diffcyt.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL diffcyt ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘diffcyt’ ... ** 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 (diffcyt)
diffcyt.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(diffcyt) > > test_check("diffcyt") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ] > > proc.time() user system elapsed 16.020 0.777 16.783
diffcyt.Rcheck/diffcyt-Ex.timings
name | user | system | elapsed | |
calcCounts | 2.978 | 0.067 | 3.048 | |
calcMedians | 2.941 | 0.107 | 3.050 | |
calcMediansByClusterMarker | 2.037 | 0.059 | 2.097 | |
calcMediansBySampleMarker | 1.665 | 0.032 | 1.700 | |
createContrast | 0.000 | 0.001 | 0.000 | |
createDesignMatrix | 0.012 | 0.002 | 0.014 | |
createFormula | 0.005 | 0.001 | 0.006 | |
diffcyt | 16.706 | 0.172 | 16.891 | |
generateClusters | 1.601 | 0.035 | 1.637 | |
plotHeatmap | 10.181 | 0.105 | 10.299 | |
prepareData | 0.052 | 0.001 | 0.053 | |
testDA_GLMM | 16.491 | 0.072 | 16.591 | |
testDA_edgeR | 2.984 | 0.018 | 3.006 | |
testDA_voom | 2.951 | 0.033 | 2.993 | |
testDS_LMM | 7.580 | 0.045 | 7.631 | |
testDS_limma | 4.660 | 0.045 | 4.709 | |
topTable | 7.647 | 0.063 | 7.717 | |
transformData | 0.078 | 0.001 | 0.079 | |