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 11:35:47 -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: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings benchdamic_1.8.2.tar.gz |
StartedAt: 2024-03-27 20:20:49 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 20:39:28 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 1118.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: benchdamic.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings benchdamic_1.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/benchdamic.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 ... ‘intro.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-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 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 158.648 5.056 202.487
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.005 | 0.000 | 0.005 | |
DA_ALDEx2 | 3.833 | 0.259 | 4.093 | |
DA_ANCOM | 3.341 | 0.069 | 3.410 | |
DA_DESeq2 | 2.558 | 0.028 | 2.586 | |
DA_MAST | 1.283 | 0.048 | 1.305 | |
DA_Maaslin2 | 0.214 | 0.020 | 0.235 | |
DA_NOISeq | 1.343 | 0.100 | 1.443 | |
DA_Seurat | 2.205 | 0.112 | 2.317 | |
DA_ZicoSeq | 0.653 | 0.016 | 0.670 | |
DA_basic | 0.030 | 0.000 | 0.031 | |
DA_dearseq | 0.057 | 0.004 | 0.061 | |
DA_edgeR | 0.244 | 0.004 | 0.248 | |
DA_limma | 0.068 | 0.004 | 0.072 | |
DA_linda | 0.033 | 0.000 | 0.032 | |
DA_metagenomeSeq | 0.229 | 0.007 | 0.237 | |
DA_mixMC | 0.401 | 0.029 | 0.462 | |
RMSE | 0.001 | 0.000 | 0.001 | |
addKnowledge | 0.168 | 0.020 | 0.189 | |
areaCAT | 3.740 | 0.336 | 4.076 | |
checkNormalization | 0.000 | 0.001 | 0.000 | |
createColors | 0.002 | 0.003 | 0.005 | |
createConcordance | 4.020 | 0.264 | 4.284 | |
createEnrichment | 0.225 | 0.012 | 0.237 | |
createMocks | 0.002 | 0.000 | 0.002 | |
createPositives | 0.777 | 0.092 | 0.869 | |
createSplits | 0.03 | 0.00 | 0.03 | |
createTIEC | 2.312 | 0.112 | 2.424 | |
enrichmentTest | 0.103 | 0.004 | 0.107 | |
extractDA | 0.155 | 0.008 | 0.163 | |
extractStatistics | 0.191 | 0.028 | 0.219 | |
fitDM | 0.027 | 0.004 | 0.031 | |
fitHURDLE | 0.662 | 0.064 | 0.726 | |
fitModels | 2.228 | 0.096 | 2.324 | |
fitNB | 0.046 | 0.000 | 0.046 | |
fitZIG | 0.091 | 0.012 | 0.103 | |
fitZINB | 0.364 | 0.004 | 0.368 | |
getDA | 0.063 | 0.004 | 0.067 | |
getPositives | 0.066 | 0.012 | 0.078 | |
getStatistics | 0.058 | 0.008 | 0.065 | |
get_counts_metadata | 0.154 | 0.020 | 0.174 | |
iterative_ordering | 0.01 | 0.00 | 0.01 | |
meanDifferences | 0.002 | 0.000 | 0.002 | |
norm_CSS | 0.063 | 0.000 | 0.063 | |
norm_DESeq2 | 0.399 | 0.004 | 0.403 | |
norm_TSS | 0.03 | 0.00 | 0.03 | |
norm_edgeR | 0.030 | 0.004 | 0.034 | |
plotConcordance | 4.144 | 0.164 | 4.308 | |
plotContingency | 1.113 | 0.060 | 1.173 | |
plotEnrichment | 0.915 | 0.036 | 0.951 | |
plotFDR | 1.913 | 0.121 | 2.033 | |
plotFPR | 1.863 | 0.052 | 1.915 | |
plotKS | 1.952 | 0.020 | 1.973 | |
plotLogP | 1.907 | 0.052 | 1.959 | |
plotMD | 3.258 | 0.116 | 3.374 | |
plotMutualFindings | 0.917 | 0.024 | 0.941 | |
plotPositives | 0.693 | 0.016 | 0.709 | |
plotQQ | 1.900 | 0.016 | 1.916 | |
plotRMSE | 2.669 | 0.020 | 2.689 | |
prepareObserved | 0.002 | 0.000 | 0.002 | |
runDA | 0.454 | 0.016 | 0.470 | |
runMocks | 0.644 | 0.008 | 0.653 | |
runNormalizations | 0.464 | 0.003 | 0.468 | |
runSplits | 3.190 | 0.113 | 3.302 | |
setNormalizations | 0.001 | 0.000 | 0.001 | |
set_ALDEx2 | 0.006 | 0.000 | 0.006 | |
set_ANCOM | 0.007 | 0.000 | 0.007 | |
set_DESeq2 | 0.006 | 0.000 | 0.006 | |
set_MAST | 0.002 | 0.000 | 0.003 | |
set_Maaslin2 | 0.004 | 0.000 | 0.004 | |
set_NOISeq | 0.003 | 0.000 | 0.003 | |
set_Seurat | 0.005 | 0.000 | 0.005 | |
set_ZicoSeq | 0.006 | 0.000 | 0.006 | |
set_basic | 0.000 | 0.001 | 0.001 | |
set_dearseq | 0.000 | 0.001 | 0.002 | |
set_edgeR | 0.01 | 0.00 | 0.01 | |
set_limma | 0.007 | 0.000 | 0.007 | |
set_linda | 0.005 | 0.000 | 0.005 | |
set_metagenomeSeq | 0.005 | 0.000 | 0.005 | |
set_mixMC | 0.002 | 0.000 | 0.003 | |
weights_ZINB | 0.37 | 0.00 | 0.37 | |