Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
benchdamic 1.15.3 (landing page) Matteo Calgaro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.15.3 |
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_1.15.3.tar.gz |
StartedAt: 2025-10-03 19:56:44 -0400 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 20:12:14 -0400 (Fri, 03 Oct 2025) |
EllapsedTime: 929.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: benchdamic.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.15.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/benchdamic.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘benchdamic/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘benchdamic’ version ‘1.15.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 32 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... NOTE Namespace in Imports field not imported from: ‘microbiome’ All declared Imports should be used. * 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'norm_DESeq2.Rd': ‘[DESeq2]{estimateSizeFactors}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 5.150 1.133 6.476 areaCAT 5.122 0.190 11.548 createConcordance 4.879 0.266 13.782 plotConcordance 4.800 0.215 10.766 runSplits 4.252 0.490 9.069 DA_DESeq2 4.230 0.047 6.045 plotMD 3.825 0.294 15.869 createTIEC 3.108 0.251 10.098 plotQQ 3.134 0.092 5.610 plotRMSE 2.551 0.094 5.480 fitModels 2.310 0.100 6.138 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| |------------(25%)----------(50%)----------(75%)----------| [ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_getStatistics_getDA_extractDA.R:160:5'): Extract DA features from a list of methods: using threshold_pvalue and threshold_logfc ── length(unique(t1[[2]]$DA)) not equal to 3. 1/1 mismatches [1] 2 - 3 == -1 [ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ] Error: Test failures Execution halted * 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 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’ * installing *source* package ‘benchdamic’ ... ** this is package ‘benchdamic’ version ‘1.15.3’ ** 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.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 1 | WARN 2 | SKIP 0 | PASS 333 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_getStatistics_getDA_extractDA.R:160:5'): Extract DA features from a list of methods: using threshold_pvalue and threshold_logfc ── length(unique(t1[[2]]$DA)) not equal to 3. 1/1 mismatches [1] 2 - 3 == -1 [ FAIL 1 | WARN 2 | SKIP 0 | PASS 333 ] Error: Test failures Execution halted
benchdamic.Rcheck/benchdamic-Ex.timings
name | user | system | elapsed | |
CAT | 0.004 | 0.002 | 0.011 | |
DA_ALDEx2 | 5.150 | 1.133 | 6.476 | |
DA_ANCOM | 0.991 | 0.022 | 1.027 | |
DA_DESeq2 | 4.230 | 0.047 | 6.045 | |
DA_MAST | 2.091 | 0.044 | 3.868 | |
DA_Maaslin2 | 0.386 | 0.074 | 0.796 | |
DA_NOISeq | 1.337 | 0.023 | 1.531 | |
DA_Seurat | 1.866 | 0.069 | 2.772 | |
DA_ZicoSeq | 0.797 | 0.102 | 1.902 | |
DA_basic | 0.048 | 0.007 | 0.101 | |
DA_corncob | 1.039 | 0.163 | 2.295 | |
DA_dearseq | 0.054 | 0.003 | 0.071 | |
DA_edgeR | 0.159 | 0.009 | 0.209 | |
DA_limma | 0.061 | 0.003 | 0.094 | |
DA_linda | 0.046 | 0.004 | 0.068 | |
DA_maaslin3 | 0.489 | 0.027 | 2.444 | |
DA_metagenomeSeq | 0.346 | 0.014 | 1.799 | |
DA_mixMC | 0.763 | 0.029 | 1.477 | |
RMSE | 0.001 | 0.001 | 0.001 | |
addKnowledge | 0.224 | 0.019 | 1.150 | |
areaCAT | 5.122 | 0.190 | 11.548 | |
checkNormalization | 0 | 0 | 0 | |
createColors | 0.003 | 0.001 | 0.004 | |
createConcordance | 4.879 | 0.266 | 13.782 | |
createEnrichment | 0.214 | 0.011 | 0.404 | |
createMocks | 0.001 | 0.002 | 0.004 | |
createPositives | 1.044 | 0.096 | 3.924 | |
createSplits | 0.027 | 0.002 | 0.226 | |
createTIEC | 3.108 | 0.251 | 10.098 | |
enrichmentTest | 0.153 | 0.007 | 0.312 | |
extractDA | 0.244 | 0.009 | 0.531 | |
extractStatistics | 0.203 | 0.011 | 0.648 | |
fitDM | 0.041 | 0.009 | 0.480 | |
fitHURDLE | 0.729 | 0.156 | 4.739 | |
fitModels | 2.310 | 0.100 | 6.138 | |
fitNB | 0.035 | 0.001 | 0.036 | |
fitZIG | 0.039 | 0.001 | 0.039 | |
fitZINB | 0.352 | 0.004 | 0.443 | |
getDA | 0.064 | 0.007 | 0.138 | |
getPositives | 0.060 | 0.003 | 0.087 | |
getStatistics | 0.053 | 0.004 | 0.133 | |
get_counts_metadata | 0.123 | 0.010 | 0.293 | |
iterative_ordering | 0.009 | 0.003 | 0.059 | |
meanDifferences | 0.002 | 0.000 | 0.017 | |
norm_CSS | 0.062 | 0.008 | 0.150 | |
norm_DESeq2 | 0.384 | 0.033 | 1.197 | |
norm_TSS | 0.026 | 0.001 | 0.030 | |
norm_edgeR | 0.036 | 0.002 | 0.039 | |
plotConcordance | 4.800 | 0.215 | 10.766 | |
plotContingency | 1.590 | 0.064 | 2.184 | |
plotEnrichment | 1.531 | 0.123 | 2.782 | |
plotFDR | 2.532 | 0.052 | 2.747 | |
plotFPR | 2.749 | 0.056 | 2.921 | |
plotKS | 2.872 | 0.055 | 4.060 | |
plotLogP | 2.186 | 0.038 | 2.905 | |
plotMD | 3.825 | 0.294 | 15.869 | |
plotMutualFindings | 1.279 | 0.025 | 1.768 | |
plotPositives | 0.804 | 0.019 | 1.146 | |
plotQQ | 3.134 | 0.092 | 5.610 | |
plotRMSE | 2.551 | 0.094 | 5.480 | |
prepareObserved | 0.002 | 0.001 | 0.001 | |
runDA | 0.715 | 0.024 | 1.638 | |
runMocks | 0.743 | 0.018 | 1.044 | |
runNormalizations | 0.535 | 0.008 | 0.705 | |
runSplits | 4.252 | 0.490 | 9.069 | |
setNormalizations | 0.000 | 0.000 | 0.001 | |
set_ALDEx2 | 0.005 | 0.001 | 0.007 | |
set_ANCOM | 0.007 | 0.003 | 0.027 | |
set_DESeq2 | 0.007 | 0.000 | 0.009 | |
set_MAST | 0.002 | 0.000 | 0.003 | |
set_Maaslin2 | 0.004 | 0.001 | 0.005 | |
set_NOISeq | 0.004 | 0.000 | 0.004 | |
set_Seurat | 0.009 | 0.002 | 0.020 | |
set_ZicoSeq | 0.009 | 0.001 | 0.012 | |
set_basic | 0.003 | 0.001 | 0.007 | |
set_corncob | 0.006 | 0.004 | 0.016 | |
set_dearseq | 0.002 | 0.000 | 0.003 | |
set_edgeR | 0.014 | 0.001 | 0.016 | |
set_limma | 0.007 | 0.000 | 0.009 | |
set_linda | 0.008 | 0.001 | 0.009 | |
set_maaslin3 | 0.006 | 0.004 | 0.045 | |
set_metagenomeSeq | 0.005 | 0.001 | 0.005 | |
set_mixMC | 0.003 | 0.001 | 0.003 | |
weights_ZINB | 0.519 | 0.015 | 0.583 | |