Matteo Calgaro
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: devel |
| git_last_commit: 9f9c589 |
| git_last_commit_date: 2024-11-26 03:11:57 -0500 (Tue, 26 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-04 11:44 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 158/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.13.2 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.13.2 |
| 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_1.13.2.tar.gz |
| StartedAt: 2025-02-03 18:48:19 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 18:52:04 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 224.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: benchdamic.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.13.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.13.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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 ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
fitDM.Rd: MGLMreg
fitHURDLE.Rd: zlm
fitNB.Rd: glmFit
fitZIG.Rd: fitZig
fitZINB.Rd: zinbFit
norm_edgeR.Rd: calcNormFactors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.21-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-arm64/Resources/library’ * installing *source* package ‘benchdamic’ ... ** this is package ‘benchdamic’ version ‘1.13.2’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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
23.748 1.271 27.996
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.002 | 0.001 | 0.007 | |
| DA_ALDEx2 | 2.167 | 0.274 | 3.701 | |
| DA_ANCOM | 0.279 | 0.017 | 0.469 | |
| DA_DESeq2 | 1.796 | 0.019 | 3.010 | |
| DA_MAST | 0.465 | 0.019 | 0.935 | |
| DA_Maaslin2 | 0.126 | 0.024 | 0.141 | |
| DA_NOISeq | 0.664 | 0.014 | 0.811 | |
| DA_Seurat | 1.019 | 0.012 | 1.705 | |
| DA_ZicoSeq | 0.257 | 0.009 | 0.443 | |
| DA_basic | 0.012 | 0.001 | 0.018 | |
| DA_corncob | 0.367 | 0.031 | 0.676 | |
| DA_dearseq | 0.023 | 0.001 | 0.033 | |
| DA_edgeR | 0.072 | 0.002 | 0.122 | |
| DA_limma | 0.029 | 0.001 | 0.049 | |
| DA_linda | 0.021 | 0.001 | 0.026 | |
| DA_metagenomeSeq | 0.116 | 0.002 | 0.211 | |
| DA_mixMC | 0.250 | 0.006 | 0.432 | |
| RMSE | 0.000 | 0.000 | 0.001 | |
| addKnowledge | 0.060 | 0.004 | 0.107 | |
| areaCAT | 1.461 | 0.041 | 2.119 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.002 | 0.000 | 0.052 | |
| createConcordance | 1.829 | 0.043 | 3.084 | |
| createEnrichment | 0.085 | 0.004 | 0.137 | |
| createMocks | 0.001 | 0.000 | 0.004 | |
| createPositives | 0.317 | 0.006 | 0.541 | |
| createSplits | 0.012 | 0.002 | 0.022 | |
| createTIEC | 1.010 | 0.021 | 1.596 | |
| enrichmentTest | 0.037 | 0.002 | 0.053 | |
| extractDA | 0.052 | 0.001 | 0.062 | |
| extractStatistics | 0.050 | 0.002 | 0.052 | |
| fitDM | 0.010 | 0.001 | 0.010 | |
| fitHURDLE | 0.226 | 0.004 | 0.245 | |
| fitModels | 0.725 | 0.010 | 1.203 | |
| fitNB | 0.014 | 0.000 | 0.035 | |
| fitZIG | 0.015 | 0.000 | 0.020 | |
| fitZINB | 0.151 | 0.002 | 0.273 | |
| getDA | 0.026 | 0.003 | 0.055 | |
| getPositives | 0.031 | 0.001 | 0.056 | |
| getStatistics | 0.022 | 0.002 | 0.028 | |
| get_counts_metadata | 0.044 | 0.001 | 0.069 | |
| iterative_ordering | 0.003 | 0.000 | 0.004 | |
| meanDifferences | 0.000 | 0.000 | 0.001 | |
| norm_CSS | 0.048 | 0.002 | 0.104 | |
| norm_DESeq2 | 0.139 | 0.001 | 0.219 | |
| norm_TSS | 0.014 | 0.001 | 0.032 | |
| norm_edgeR | 0.013 | 0.000 | 0.030 | |
| plotConcordance | 1.894 | 0.030 | 3.214 | |
| plotContingency | 0.360 | 0.005 | 0.501 | |
| plotEnrichment | 0.316 | 0.006 | 0.324 | |
| plotFDR | 0.616 | 0.013 | 0.629 | |
| plotFPR | 0.641 | 0.013 | 0.658 | |
| plotKS | 0.713 | 0.018 | 0.737 | |
| plotLogP | 0.639 | 0.027 | 0.667 | |
| plotMD | 0.970 | 0.021 | 1.005 | |
| plotMutualFindings | 0.317 | 0.006 | 0.325 | |
| plotPositives | 0.210 | 0.004 | 0.218 | |
| plotQQ | 0.613 | 0.015 | 0.629 | |
| plotRMSE | 0.782 | 0.007 | 0.789 | |
| prepareObserved | 0 | 0 | 0 | |
| runDA | 0.138 | 0.001 | 0.139 | |
| runMocks | 0.219 | 0.006 | 0.254 | |
| runNormalizations | 0.125 | 0.001 | 0.130 | |
| runSplits | 1.047 | 0.030 | 1.088 | |
| setNormalizations | 0.001 | 0.000 | 0.000 | |
| set_ALDEx2 | 0.002 | 0.000 | 0.002 | |
| set_ANCOM | 0.002 | 0.000 | 0.003 | |
| set_DESeq2 | 0.003 | 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 | 0.003 | 0.000 | 0.003 | |
| set_basic | 0.000 | 0.000 | 0.001 | |
| set_corncob | 0.002 | 0.000 | 0.001 | |
| set_dearseq | 0.000 | 0.001 | 0.001 | |
| set_edgeR | 0.003 | 0.000 | 0.004 | |
| set_limma | 0.002 | 0.000 | 0.003 | |
| set_linda | 0.002 | 0.000 | 0.003 | |
| set_metagenomeSeq | 0.002 | 0.000 | 0.002 | |
| set_mixMC | 0.001 | 0.000 | 0.001 | |
| weights_ZINB | 0.123 | 0.001 | 0.126 | |