Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 155/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.10.0  (landing page)
Matteo Calgaro
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_19
git_last_commit: 8e9ad07
git_last_commit_date: 2024-04-30 11:38:25 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    TIMEOUT  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for benchdamic on nebbiolo1

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.

raw results


Summary

Package: benchdamic
Version: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings benchdamic_1.10.0.tar.gz
StartedAt: 2024-06-16 20:54:08 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 21:28:15 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 2047.5 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings benchdamic_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.10.0’
* 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 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/benchdamic.Rcheck/00check.log’
for details.


Installation output

benchdamic.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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
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)

Tests output

benchdamic.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 84.879   4.061 107.167 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0050.0000.005
DA_ALDEx23.6530.1963.851
DA_ANCOM1.4310.0921.525
DA_DESeq22.5120.0162.530
DA_MAST1.2490.0201.243
DA_Maaslin20.2560.0160.274
DA_NOISeq1.5350.0641.601
DA_Seurat2.3370.0722.409
DA_ZicoSeq0.5890.0080.597
DA_basic0.0300.0000.031
DA_corncob0.8890.0320.928
DA_dearseq0.0520.0030.054
DA_edgeR0.1830.0040.188
DA_limma0.0710.0040.076
DA_linda0.0480.0000.049
DA_metagenomeSeq0.2450.0040.249
DA_mixMC0.3210.0050.410
RMSE0.0010.0000.001
addKnowledge0.1580.0080.166
areaCAT3.7010.3804.081
checkNormalization000
createColors0.0000.0050.005
createConcordance4.1850.2024.386
createEnrichment0.2330.0000.234
createMocks0.0030.0000.004
createPositives0.8130.0160.830
createSplits0.0280.0000.028
createTIEC2.3710.0242.396
enrichmentTest0.1080.0040.112
extractDA0.1640.0000.164
extractStatistics0.1650.0000.165
fitDM0.0350.0000.034
fitHURDLE0.7540.0280.782
fitModels2.2580.0882.346
fitNB0.0430.0000.043
fitZIG0.0440.0040.048
fitZINB0.4350.0320.467
getDA0.0700.0120.082
getPositives0.0710.0040.075
getStatistics0.0570.0160.073
get_counts_metadata0.1540.0040.158
iterative_ordering0.0050.0040.009
meanDifferences0.0000.0020.002
norm_CSS0.0560.0060.062
norm_DESeq20.4020.0040.406
norm_TSS0.0280.0040.032
norm_edgeR0.0370.0000.037
plotConcordance4.1790.0804.260
plotContingency1.0140.0121.026
plotEnrichment0.9020.0000.902
plotFDR1.8520.0201.872
plotFPR2.1020.0322.154
plotKS1.8960.0361.932
plotLogP1.9010.0481.949
plotMD3.2130.0963.310
plotMutualFindings0.9790.0200.999
plotPositives0.6600.0200.679
plotQQ1.9480.0321.980
plotRMSE2.6670.0202.687
prepareObserved0.0000.0010.002
runDA0.5690.0140.583
runMocks0.6800.0080.687
runNormalizations0.4430.0000.443
runSplits3.4840.0243.508
setNormalizations000
set_ALDEx20.0060.0000.006
set_ANCOM0.0080.0000.008
set_DESeq20.0070.0000.007
set_MAST0.0040.0000.004
set_Maaslin20.0050.0000.005
set_NOISeq0.0040.0000.004
set_Seurat0.0020.0040.006
set_ZicoSeq0.0070.0000.006
set_basic0.0020.0000.002
set_corncob0.0000.0040.004
set_dearseq0.0020.0000.002
set_edgeR0.0100.0000.011
set_limma0.0080.0000.008
set_linda0.0030.0020.006
set_metagenomeSeq0.0020.0030.005
set_mixMC0.0020.0020.002
weights_ZINB0.4480.0080.456