Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-16 11:47 -0400 (Wed, 16 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4473 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4730 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4478 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
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 158/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.11.1 (landing page) Matteo Calgaro
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 1.11.1 |
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_1.11.1.tar.gz |
StartedAt: 2024-10-15 19:33:25 -0400 (Tue, 15 Oct 2024) |
EndedAt: 2024-10-15 19:37:34 -0400 (Tue, 15 Oct 2024) |
EllapsedTime: 248.7 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_1.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/benchdamic.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.11.1’ * 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 code 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 ... NOTE checkRd: (-1) DA_Seurat.Rd:29-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:33-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:45-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:47-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:57-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:59-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:62-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:64-67: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) DA_Seurat.Rd:71-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) areaCAT.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:24-28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) areaCAT.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createConcordance.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createEnrichment.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:20-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:24-27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) createTIEC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) enrichmentTest.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) extractDA.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getDA.Rd:63-66: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_counts_metadata.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotConcordance.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) plotConcordance.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) set_Seurat.Rd:26-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:29-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:31-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:43-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:46-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:48-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:64-66: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:68-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) set_Seurat.Rd:72: Lost braces in \itemize; meant \describe ? * 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 ... 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-3.20-bioc/meat/benchdamic.Rcheck/00check.log’ for details.
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** testing if installed package can be loaded from final location Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** testing if installed package keeps a record of temporary installation path * DONE (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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) Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'spam' > > 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 322 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_DA_paired.R:3:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 322 ] > > proc.time() user system elapsed 28.492 1.161 36.780
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.002 | 0.000 | 0.002 | |
DA_ALDEx2 | 1.838 | 0.281 | 2.123 | |
DA_ANCOM | 0.469 | 0.020 | 0.490 | |
DA_DESeq2 | 0.843 | 0.013 | 0.857 | |
DA_MAST | 0.367 | 0.007 | 0.373 | |
DA_Maaslin2 | 0.108 | 0.012 | 0.154 | |
DA_NOISeq | 0.663 | 0.014 | 0.745 | |
DA_Seurat | 1.015 | 0.014 | 1.086 | |
DA_ZicoSeq | 0.202 | 0.005 | 0.208 | |
DA_basic | 0.010 | 0.001 | 0.010 | |
DA_corncob | 0.294 | 0.017 | 0.329 | |
DA_dearseq | 0.020 | 0.000 | 0.022 | |
DA_edgeR | 0.062 | 0.002 | 0.064 | |
DA_limma | 0.026 | 0.001 | 0.032 | |
DA_linda | 0.015 | 0.001 | 0.016 | |
DA_metagenomeSeq | 0.074 | 0.001 | 0.077 | |
DA_mixMC | 0.090 | 0.007 | 0.102 | |
RMSE | 0 | 0 | 0 | |
addKnowledge | 0.056 | 0.003 | 0.059 | |
areaCAT | 1.162 | 0.029 | 1.239 | |
checkNormalization | 0 | 0 | 0 | |
createColors | 0.002 | 0.000 | 0.002 | |
createConcordance | 1.321 | 0.029 | 1.423 | |
createEnrichment | 0.074 | 0.002 | 0.082 | |
createMocks | 0.000 | 0.000 | 0.001 | |
createPositives | 0.245 | 0.005 | 0.266 | |
createSplits | 0.009 | 0.001 | 0.010 | |
createTIEC | 0.780 | 0.017 | 0.828 | |
enrichmentTest | 0.035 | 0.001 | 0.036 | |
extractDA | 0.048 | 0.001 | 0.053 | |
extractStatistics | 0.048 | 0.002 | 0.050 | |
fitDM | 0.010 | 0.000 | 0.011 | |
fitHURDLE | 0.241 | 0.006 | 0.253 | |
fitModels | 0.686 | 0.013 | 0.712 | |
fitNB | 0.012 | 0.000 | 0.012 | |
fitZIG | 0.015 | 0.000 | 0.014 | |
fitZINB | 0.138 | 0.002 | 0.139 | |
getDA | 0.023 | 0.003 | 0.026 | |
getPositives | 0.022 | 0.002 | 0.024 | |
getStatistics | 0.019 | 0.002 | 0.021 | |
get_counts_metadata | 0.048 | 0.001 | 0.049 | |
iterative_ordering | 0.004 | 0.000 | 0.005 | |
meanDifferences | 0.001 | 0.000 | 0.001 | |
norm_CSS | 0.019 | 0.000 | 0.024 | |
norm_DESeq2 | 0.122 | 0.001 | 0.157 | |
norm_TSS | 0.009 | 0.000 | 0.009 | |
norm_edgeR | 0.01 | 0.00 | 0.01 | |
plotConcordance | 1.354 | 0.040 | 1.401 | |
plotContingency | 0.298 | 0.005 | 0.343 | |
plotEnrichment | 0.310 | 0.007 | 0.338 | |
plotFDR | 0.608 | 0.012 | 0.675 | |
plotFPR | 0.733 | 0.028 | 0.837 | |
plotKS | 0.625 | 0.009 | 0.693 | |
plotLogP | 0.621 | 0.010 | 0.728 | |
plotMD | 0.948 | 0.008 | 0.958 | |
plotMutualFindings | 0.295 | 0.006 | 0.302 | |
plotPositives | 0.191 | 0.003 | 0.195 | |
plotQQ | 0.602 | 0.010 | 0.613 | |
plotRMSE | 0.834 | 0.006 | 0.840 | |
prepareObserved | 0 | 0 | 0 | |
runDA | 0.134 | 0.001 | 0.134 | |
runMocks | 0.203 | 0.003 | 0.206 | |
runNormalizations | 0.127 | 0.001 | 0.128 | |
runSplits | 1.027 | 0.024 | 1.051 | |
setNormalizations | 0 | 0 | 0 | |
set_ALDEx2 | 0.001 | 0.000 | 0.002 | |
set_ANCOM | 0.002 | 0.000 | 0.002 | |
set_DESeq2 | 0.002 | 0.000 | 0.003 | |
set_MAST | 0.001 | 0.000 | 0.001 | |
set_Maaslin2 | 0.001 | 0.000 | 0.001 | |
set_NOISeq | 0.001 | 0.000 | 0.001 | |
set_Seurat | 0.001 | 0.000 | 0.002 | |
set_ZicoSeq | 0.002 | 0.000 | 0.002 | |
set_basic | 0.000 | 0.000 | 0.001 | |
set_corncob | 0.002 | 0.000 | 0.001 | |
set_dearseq | 0.000 | 0.000 | 0.001 | |
set_edgeR | 0.004 | 0.000 | 0.004 | |
set_limma | 0.002 | 0.000 | 0.003 | |
set_linda | 0.001 | 0.000 | 0.001 | |
set_metagenomeSeq | 0.002 | 0.000 | 0.001 | |
set_mixMC | 0.000 | 0.000 | 0.001 | |
weights_ZINB | 0.120 | 0.000 | 0.121 | |