Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:20:00 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 benchdamic package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.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 140/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.2.5 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: benchdamic |
Version: 1.2.5 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings benchdamic_1.2.5.tar.gz |
StartedAt: 2022-10-18 18:41:41 -0400 (Tue, 18 Oct 2022) |
EndedAt: 2022-10-18 18:50:26 -0400 (Tue, 18 Oct 2022) |
EllapsedTime: 524.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings benchdamic_1.2.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.2.5’ * 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 ‘benchdamic’ 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 LazyData ... 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 areaCAT 6.209 0.147 6.357 DA_ALDEx2 5.000 0.452 5.453 plotConcordance 5.272 0.047 5.320 DA_ANCOM 1.042 0.007 15.880 * 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: OK
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-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(benchdamic) > > test_check("benchdamic") |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 0 | WARN 0 | SKIP 0 | PASS 273 ] > > proc.time() user system elapsed 48.162 2.170 64.850
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.005 | 0.000 | 0.005 | |
DA_ALDEx2 | 5.000 | 0.452 | 5.453 | |
DA_ANCOM | 1.042 | 0.007 | 15.880 | |
DA_DESeq2 | 3.325 | 0.063 | 3.389 | |
DA_MAST | 0.690 | 0.013 | 0.702 | |
DA_NOISeq | 2.054 | 0.088 | 2.146 | |
DA_Seurat | 0.919 | 0.032 | 0.951 | |
DA_basic | 0.03 | 0.00 | 0.03 | |
DA_dearseq | 0.059 | 0.003 | 0.062 | |
DA_edgeR | 0.188 | 0.012 | 0.200 | |
DA_limma | 0.075 | 0.003 | 0.079 | |
DA_metagenomeSeq | 0.293 | 0.013 | 0.304 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.479 | 0.008 | 0.487 | |
areaCAT | 6.209 | 0.147 | 6.357 | |
checkNormalization | 0.000 | 0.000 | 0.001 | |
createColors | 0.001 | 0.003 | 0.005 | |
createConcordance | 4.644 | 0.100 | 4.744 | |
createEnrichment | 0.262 | 0.000 | 0.263 | |
createMocks | 0.004 | 0.000 | 0.004 | |
createPositives | 0.929 | 0.008 | 0.938 | |
createSplits | 0.027 | 0.003 | 0.032 | |
createTIEC | 1.907 | 0.036 | 1.943 | |
enrichmentTest | 0.120 | 0.001 | 0.120 | |
extractDA | 0.172 | 0.000 | 0.172 | |
extractStatistics | 0.164 | 0.004 | 0.168 | |
fitDM | 0.028 | 0.004 | 0.031 | |
fitHURDLE | 0.372 | 0.004 | 0.377 | |
fitModels | 1.363 | 0.007 | 1.371 | |
fitNB | 0.045 | 0.000 | 0.045 | |
fitZIG | 0.053 | 0.004 | 0.057 | |
fitZINB | 0.430 | 0.004 | 0.434 | |
getDA | 0.082 | 0.003 | 0.086 | |
getPositives | 0.082 | 0.000 | 0.083 | |
getStatistics | 0.064 | 0.007 | 0.072 | |
get_counts_metadata | 0.183 | 0.001 | 0.183 | |
iterative_ordering | 0.011 | 0.000 | 0.011 | |
meanDifferences | 0.002 | 0.000 | 0.003 | |
norm_CSS | 0.067 | 0.007 | 0.074 | |
norm_DESeq2 | 0.491 | 0.005 | 0.495 | |
norm_TSS | 0.032 | 0.000 | 0.032 | |
norm_edgeR | 0.053 | 0.000 | 0.053 | |
plotConcordance | 5.272 | 0.047 | 5.320 | |
plotContingency | 1.109 | 0.004 | 1.114 | |
plotEnrichment | 1.032 | 0.001 | 1.032 | |
plotFPR | 1.814 | 0.027 | 1.843 | |
plotKS | 1.893 | 0.012 | 1.906 | |
plotLogP | 1.769 | 0.012 | 1.782 | |
plotMD | 2.447 | 0.044 | 2.491 | |
plotMutualFindings | 0.937 | 0.012 | 0.950 | |
plotPositives | 0.729 | 0.012 | 0.741 | |
plotQQ | 1.668 | 0.052 | 1.720 | |
plotRMSE | 1.677 | 0.016 | 1.693 | |
prepareObserved | 0.000 | 0.001 | 0.001 | |
runDA | 0.483 | 0.009 | 0.493 | |
runMocks | 0.680 | 0.016 | 0.696 | |
runNormalizations | 0.552 | 0.004 | 0.556 | |
runSplits | 3.591 | 0.088 | 3.679 | |
setNormalizations | 0 | 0 | 0 | |
set_ALDEx2 | 0.007 | 0.000 | 0.006 | |
set_ANCOM | 0.005 | 0.000 | 0.005 | |
set_DESeq2 | 0.007 | 0.000 | 0.007 | |
set_MAST | 0.003 | 0.000 | 0.003 | |
set_NOISeq | 0.004 | 0.000 | 0.004 | |
set_Seurat | 0.006 | 0.000 | 0.006 | |
set_basic | 0.001 | 0.000 | 0.002 | |
set_dearseq | 0.002 | 0.000 | 0.002 | |
set_edgeR | 0.01 | 0.00 | 0.01 | |
set_limma | 0.007 | 0.000 | 0.007 | |
set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
weights_ZINB | 0.455 | 0.000 | 0.455 | |