Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-10-19 11:46 -0400 (Sat, 19 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4474
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4733
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4479
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4509
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (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 158/2273HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.11.1  (landing page)
Matteo Calgaro
Snapshot Date: 2024-10-18 13:40 -0400 (Fri, 18 Oct 2024)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: devel
git_last_commit: 7686034
git_last_commit_date: 2024-09-23 11:05:57 -0400 (Mon, 23 Sep 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped


CHECK results for benchdamic on teran2

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: 1.11.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings benchdamic_1.11.1.tar.gz
StartedAt: 2024-10-18 22:27:32 -0400 (Fri, 18 Oct 2024)
EndedAt: 2024-10-18 23:02:08 -0400 (Fri, 18 Oct 2024)
EllapsedTime: 2076.3 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings benchdamic_1.11.1.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/benchdamic.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotConcordance 3.472 44.054 250.949
createTIEC      2.810  3.412  34.414
DA_ALDEx2       3.828  0.503   6.993
DA_Seurat       2.559  0.000   5.607
* 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
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/benchdamic.Rcheck/00check.log’
for details.


Installation output

benchdamic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 66.412   2.324  88.075 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0040.0010.013
DA_ALDEx23.8280.5036.993
DA_ANCOM1.7600.0922.960
DA_DESeq22.3450.1144.490
DA_MAST2.1440.0202.179
DA_Maaslin20.1670.0230.323
DA_NOISeq1.8400.0033.710
DA_Seurat2.5590.0005.607
DA_ZicoSeq0.8040.0021.266
DA_basic0.0210.0010.030
DA_corncob0.7130.0101.305
DA_dearseq0.0430.0000.088
DA_edgeR0.1420.0020.319
DA_limma0.0550.0010.125
DA_linda0.0370.0000.096
DA_metagenomeSeq0.1850.0010.411
DA_mixMC0.5430.0101.200
RMSE0.0010.0000.002
addKnowledge0.1160.0000.121
areaCAT2.7750.0822.874
checkNormalization000
createColors0.0010.0030.010
createConcordance3.5690.1354.749
createEnrichment0.1700.0020.183
createMocks0.0020.0000.001
createPositives0.5620.0050.602
createSplits0.0200.0000.031
createTIEC 2.810 3.41234.414
enrichmentTest0.1310.0030.142
extractDA0.1210.0000.122
extractStatistics0.1180.0000.118
fitDM0.0220.0010.029
fitHURDLE0.5080.0020.518
fitModels2.4570.0072.493
fitNB0.0300.0020.034
fitZIG0.0350.0010.041
fitZINB0.2950.0040.305
getDA0.0550.0020.064
getPositives0.0530.0010.054
getStatistics0.0460.0010.046
get_counts_metadata0.1210.0020.128
iterative_ordering0.0090.0000.018
meanDifferences0.0010.0000.003
norm_CSS0.0480.0000.055
norm_DESeq20.2900.0020.307
norm_TSS0.0230.0010.090
norm_edgeR0.0250.0000.025
plotConcordance 3.472 44.054250.949
plotContingency0.7350.0010.749
plotEnrichment0.7700.0000.781
plotFDR1.9910.2942.204
plotFPR1.5080.0001.528
plotKS1.8860.0001.887
plotLogP1.6940.0001.699
plotMD3.0590.0003.063
plotMutualFindings0.7230.0000.723
plotPositives0.560.000.56
plotQQ1.6040.0251.628
plotRMSE2.120.002.12
prepareObserved0.0020.0000.001
runDA0.3350.0000.335
runMocks0.4890.0010.490
runNormalizations0.3090.0000.309
runSplits2.7080.0002.708
setNormalizations0.0000.0000.001
set_ALDEx20.0050.0000.005
set_ANCOM0.0070.0000.015
set_DESeq20.0050.0000.005
set_MAST0.0030.0000.002
set_Maaslin20.0030.0000.003
set_NOISeq0.0030.0000.002
set_Seurat0.0050.0000.004
set_ZicoSeq0.0050.0000.005
set_basic0.0010.0000.001
set_corncob0.0030.0000.003
set_dearseq0.0010.0000.002
set_edgeR0.0080.0000.009
set_limma0.0060.0000.006
set_linda0.0030.0000.004
set_metagenomeSeq0.0030.0000.004
set_mixMC0.0010.0000.002
weights_ZINB0.3580.0000.364