Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:37:31 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 153/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.8.2 (landing page) Matteo Calgaro
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the benchdamic package: - 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 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: benchdamic |
Version: 1.8.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.8.2.tar.gz |
StartedAt: 2024-03-27 23:42:21 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-28 00:12:05 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 1784.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings benchdamic_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/benchdamic.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.8.2’ * 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 DA_ALDEx2 11.939 1.571 14.473 plotConcordance 10.748 0.114 11.078 createConcordance 10.458 0.137 11.028 areaCAT 9.114 0.164 9.503 DA_ANCOM 8.547 0.096 8.976 plotMD 8.393 0.062 9.458 runSplits 7.548 0.101 7.760 plotRMSE 6.639 0.069 7.127 DA_DESeq2 6.255 0.142 7.540 fitModels 5.997 0.074 6.243 createTIEC 5.850 0.059 6.031 plotFPR 4.850 0.045 5.474 plotLogP 4.823 0.050 5.420 plotKS 4.805 0.047 5.165 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘benchdamic’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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 1 | PASS 310 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_DA_paired.R:3:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 310 ] > > proc.time() user system elapsed 394.458 9.129 545.321
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.009 | 0.002 | 0.011 | |
DA_ALDEx2 | 11.939 | 1.571 | 14.473 | |
DA_ANCOM | 8.547 | 0.096 | 8.976 | |
DA_DESeq2 | 6.255 | 0.142 | 7.540 | |
DA_MAST | 3.240 | 0.113 | 3.862 | |
DA_Maaslin2 | 0.506 | 0.069 | 0.696 | |
DA_NOISeq | 1.916 | 0.028 | 2.117 | |
DA_Seurat | 3.237 | 0.064 | 3.514 | |
DA_ZicoSeq | 1.793 | 0.036 | 1.884 | |
DA_basic | 0.070 | 0.003 | 0.074 | |
DA_dearseq | 0.114 | 0.004 | 0.122 | |
DA_edgeR | 0.464 | 0.015 | 0.517 | |
DA_limma | 0.152 | 0.011 | 0.177 | |
DA_linda | 0.073 | 0.005 | 0.117 | |
DA_metagenomeSeq | 0.538 | 0.032 | 0.599 | |
DA_mixMC | 0.814 | 0.044 | 0.916 | |
RMSE | 0.002 | 0.000 | 0.002 | |
addKnowledge | 0.343 | 0.013 | 0.390 | |
areaCAT | 9.114 | 0.164 | 9.503 | |
checkNormalization | 0.000 | 0.001 | 0.001 | |
createColors | 0.008 | 0.001 | 0.010 | |
createConcordance | 10.458 | 0.137 | 11.028 | |
createEnrichment | 0.545 | 0.013 | 0.575 | |
createMocks | 0.007 | 0.004 | 0.010 | |
createPositives | 1.941 | 0.045 | 2.026 | |
createSplits | 0.068 | 0.002 | 0.071 | |
createTIEC | 5.850 | 0.059 | 6.031 | |
enrichmentTest | 0.255 | 0.009 | 0.267 | |
extractDA | 0.472 | 0.015 | 0.497 | |
extractStatistics | 0.395 | 0.006 | 0.409 | |
fitDM | 0.074 | 0.002 | 0.079 | |
fitHURDLE | 1.612 | 0.008 | 1.654 | |
fitModels | 5.997 | 0.074 | 6.243 | |
fitNB | 0.101 | 0.001 | 0.103 | |
fitZIG | 0.115 | 0.001 | 0.118 | |
fitZINB | 1.019 | 0.007 | 1.042 | |
getDA | 0.173 | 0.020 | 0.197 | |
getPositives | 0.176 | 0.006 | 0.185 | |
getStatistics | 0.158 | 0.013 | 0.174 | |
get_counts_metadata | 0.424 | 0.006 | 0.436 | |
iterative_ordering | 0.022 | 0.002 | 0.025 | |
meanDifferences | 0.004 | 0.001 | 0.005 | |
norm_CSS | 0.149 | 0.002 | 0.155 | |
norm_DESeq2 | 1.000 | 0.005 | 1.017 | |
norm_TSS | 0.070 | 0.002 | 0.077 | |
norm_edgeR | 0.156 | 0.004 | 0.178 | |
plotConcordance | 10.748 | 0.114 | 11.078 | |
plotContingency | 2.412 | 0.036 | 2.500 | |
plotEnrichment | 2.286 | 0.023 | 2.385 | |
plotFDR | 4.763 | 0.039 | 4.915 | |
plotFPR | 4.850 | 0.045 | 5.474 | |
plotKS | 4.805 | 0.047 | 5.165 | |
plotLogP | 4.823 | 0.050 | 5.420 | |
plotMD | 8.393 | 0.062 | 9.458 | |
plotMutualFindings | 2.380 | 0.024 | 2.667 | |
plotPositives | 1.646 | 0.017 | 1.752 | |
plotQQ | 4.711 | 0.048 | 4.860 | |
plotRMSE | 6.639 | 0.069 | 7.127 | |
prepareObserved | 0.003 | 0.001 | 0.017 | |
runDA | 1.152 | 0.017 | 1.197 | |
runMocks | 1.561 | 0.027 | 1.628 | |
runNormalizations | 1.063 | 0.008 | 1.085 | |
runSplits | 7.548 | 0.101 | 7.760 | |
setNormalizations | 0.000 | 0.001 | 0.001 | |
set_ALDEx2 | 0.015 | 0.001 | 0.018 | |
set_ANCOM | 0.018 | 0.002 | 0.020 | |
set_DESeq2 | 0.019 | 0.001 | 0.021 | |
set_MAST | 0.008 | 0.001 | 0.010 | |
set_Maaslin2 | 0.011 | 0.001 | 0.011 | |
set_NOISeq | 0.008 | 0.000 | 0.009 | |
set_Seurat | 0.015 | 0.001 | 0.016 | |
set_ZicoSeq | 0.017 | 0.001 | 0.018 | |
set_basic | 0.004 | 0.000 | 0.006 | |
set_dearseq | 0.004 | 0.001 | 0.006 | |
set_edgeR | 0.033 | 0.001 | 0.035 | |
set_limma | 0.020 | 0.001 | 0.021 | |
set_linda | 0.012 | 0.000 | 0.012 | |
set_metagenomeSeq | 0.012 | 0.001 | 0.013 | |
set_mixMC | 0.006 | 0.001 | 0.007 | |
weights_ZINB | 1.097 | 0.010 | 1.120 | |