Matteo Calgaro
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: RELEASE_3_19 |
| git_last_commit: f1bb951 |
| git_last_commit_date: 2024-09-23 11:21:25 -0400 (Mon, 23 Sep 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 155/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.10.1 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 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: 1.10.1 |
| 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_1.10.1.tar.gz |
| StartedAt: 2024-10-17 13:27:36 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 13:42:02 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 866.4 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_1.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.10.1’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DA_ALDEx2 6.426 0.804 7.468
plotConcordance 5.133 0.091 5.474
createConcordance 4.732 0.136 5.376
plotMD 4.036 0.054 7.663
runSplits 3.661 0.114 6.991
plotRMSE 3.039 0.038 6.061
plotFPR 2.683 0.054 5.524
plotLogP 2.533 0.058 5.164
plotKS 2.535 0.048 5.048
plotFDR 2.482 0.050 5.026
* 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-3.19-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
98.917 6.923 168.357
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.006 | 0.000 | 0.006 | |
| DA_ALDEx2 | 6.426 | 0.804 | 7.468 | |
| DA_ANCOM | 1.890 | 0.069 | 2.048 | |
| DA_DESeq2 | 3.313 | 0.090 | 3.516 | |
| DA_MAST | 1.446 | 0.036 | 1.549 | |
| DA_Maaslin2 | 0.299 | 0.045 | 0.397 | |
| DA_NOISeq | 2.069 | 0.028 | 2.211 | |
| DA_Seurat | 3.375 | 0.057 | 3.568 | |
| DA_ZicoSeq | 0.700 | 0.021 | 0.754 | |
| DA_basic | 0.034 | 0.002 | 0.038 | |
| DA_corncob | 1.090 | 0.083 | 1.239 | |
| DA_dearseq | 0.069 | 0.003 | 0.076 | |
| DA_edgeR | 0.232 | 0.009 | 0.247 | |
| DA_limma | 0.092 | 0.004 | 0.098 | |
| DA_linda | 0.053 | 0.004 | 0.059 | |
| DA_metagenomeSeq | 0.289 | 0.009 | 0.311 | |
| DA_mixMC | 0.331 | 0.033 | 0.396 | |
| RMSE | 0.001 | 0.000 | 0.001 | |
| addKnowledge | 0.198 | 0.011 | 0.218 | |
| areaCAT | 4.435 | 0.158 | 4.912 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.006 | 0.001 | 0.009 | |
| createConcordance | 4.732 | 0.136 | 5.376 | |
| createEnrichment | 0.273 | 0.009 | 0.297 | |
| createMocks | 0.003 | 0.001 | 0.006 | |
| createPositives | 0.994 | 0.038 | 1.103 | |
| createSplits | 0.033 | 0.002 | 0.053 | |
| createTIEC | 2.861 | 0.065 | 3.911 | |
| enrichmentTest | 0.125 | 0.005 | 0.160 | |
| extractDA | 0.189 | 0.006 | 0.241 | |
| extractStatistics | 0.188 | 0.008 | 0.247 | |
| fitDM | 0.033 | 0.003 | 0.044 | |
| fitHURDLE | 0.940 | 0.018 | 1.186 | |
| fitModels | 2.578 | 0.051 | 3.159 | |
| fitNB | 0.050 | 0.001 | 0.058 | |
| fitZIG | 0.057 | 0.001 | 0.058 | |
| fitZINB | 0.509 | 0.006 | 0.543 | |
| getDA | 0.080 | 0.010 | 0.091 | |
| getPositives | 0.080 | 0.005 | 0.093 | |
| getStatistics | 0.073 | 0.006 | 0.084 | |
| get_counts_metadata | 0.202 | 0.004 | 0.221 | |
| iterative_ordering | 0.012 | 0.001 | 0.014 | |
| meanDifferences | 0.002 | 0.000 | 0.003 | |
| norm_CSS | 0.075 | 0.001 | 0.080 | |
| norm_DESeq2 | 0.510 | 0.005 | 0.556 | |
| norm_TSS | 0.030 | 0.001 | 0.034 | |
| norm_edgeR | 0.040 | 0.001 | 0.043 | |
| plotConcordance | 5.133 | 0.091 | 5.474 | |
| plotContingency | 1.252 | 0.021 | 2.209 | |
| plotEnrichment | 1.179 | 0.017 | 2.433 | |
| plotFDR | 2.482 | 0.050 | 5.026 | |
| plotFPR | 2.683 | 0.054 | 5.524 | |
| plotKS | 2.535 | 0.048 | 5.048 | |
| plotLogP | 2.533 | 0.058 | 5.164 | |
| plotMD | 4.036 | 0.054 | 7.663 | |
| plotMutualFindings | 1.199 | 0.023 | 2.307 | |
| plotPositives | 0.465 | 0.008 | 1.098 | |
| plotQQ | 2.322 | 0.050 | 4.539 | |
| plotRMSE | 3.039 | 0.038 | 6.061 | |
| prepareObserved | 0.001 | 0.000 | 0.002 | |
| runDA | 0.538 | 0.202 | 1.315 | |
| runMocks | 0.791 | 0.068 | 1.726 | |
| runNormalizations | 0.585 | 0.029 | 1.217 | |
| runSplits | 3.661 | 0.114 | 6.991 | |
| setNormalizations | 0.000 | 0.000 | 0.021 | |
| set_ALDEx2 | 0.006 | 0.000 | 0.010 | |
| set_ANCOM | 0.009 | 0.001 | 0.011 | |
| set_DESeq2 | 0.010 | 0.000 | 0.019 | |
| set_MAST | 0.004 | 0.000 | 0.004 | |
| set_Maaslin2 | 0.002 | 0.000 | 0.004 | |
| set_NOISeq | 0.002 | 0.000 | 0.005 | |
| set_Seurat | 0.003 | 0.001 | 0.015 | |
| set_ZicoSeq | 0.004 | 0.000 | 0.009 | |
| set_basic | 0.001 | 0.000 | 0.001 | |
| set_corncob | 0.003 | 0.000 | 0.024 | |
| set_dearseq | 0.001 | 0.001 | 0.002 | |
| set_edgeR | 0.008 | 0.000 | 0.010 | |
| set_limma | 0.009 | 0.000 | 0.123 | |
| set_linda | 0.005 | 0.000 | 0.009 | |
| set_metagenomeSeq | 0.003 | 0.000 | 0.017 | |
| set_mixMC | 0.004 | 0.000 | 0.163 | |
| weights_ZINB | 0.464 | 0.011 | 0.901 | |