Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:08 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for benchdamic on palomino3


To the developers/maintainers of the benchdamic package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 140/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.2.5  (landing page)
Matteo Calgaro
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_15
git_last_commit: a9a5cda
git_last_commit_date: 2022-09-10 09:20:25 -0400 (Sat, 10 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: benchdamic
Version: 1.2.5
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.2.5.tar.gz
StartedAt: 2022-10-18 22:15:01 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:26:19 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 677.6 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'benchdamic/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'benchdamic' version '1.2.5'
* 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 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 R 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 ... OK
* 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         6.75   1.50    8.25
plotConcordance   6.55   0.03    6.61
createConcordance 6.04   0.08    6.13
areaCAT           5.39   0.08    5.49
DA_DESeq2         5.33   0.03    5.36
DA_ANCOM          1.56   0.07   18.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

benchdamic.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'benchdamic' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (benchdamic)

Tests output

benchdamic.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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)
> 
> test_check("benchdamic")
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
|------------(25%)----------(50%)----------(75%)----------|
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 273 ]
> 
> proc.time()
   user  system elapsed 
  54.78    3.64   80.84 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT000
DA_ALDEx26.751.508.25
DA_ANCOM 1.56 0.0718.75
DA_DESeq25.330.035.36
DA_MAST0.820.000.83
DA_NOISeq1.630.011.65
DA_Seurat0.640.001.72
DA_basic0.030.000.03
DA_dearseq0.060.000.11
DA_edgeR0.210.000.22
DA_limma0.080.030.11
DA_metagenomeSeq0.290.000.44
RMSE000
addKnowledge0.460.000.51
areaCAT5.390.085.49
checkNormalization000
createColors0.000.000.01
createConcordance6.040.086.13
createEnrichment0.280.020.29
createMocks000
createPositives1.070.061.22
createSplits0.040.000.05
createTIEC2.530.042.59
enrichmentTest0.150.000.14
extractDA0.340.000.35
extractStatistics0.260.020.28
fitDM0.070.000.08
fitHURDLE0.450.020.48
fitModels1.640.011.69
fitNB0.050.000.05
fitZIG0.040.000.04
fitZINB0.410.000.41
getDA0.090.020.11
getPositives0.100.000.09
getStatistics0.090.000.10
get_counts_metadata0.240.000.23
iterative_ordering0.020.000.03
meanDifferences000
norm_CSS0.080.000.08
norm_DESeq20.460.000.47
norm_TSS0.070.000.06
norm_edgeR0.040.000.05
plotConcordance6.550.036.61
plotContingency1.470.051.52
plotEnrichment1.220.061.28
plotFPR2.270.012.88
plotKS2.520.072.58
plotLogP2.700.032.87
plotMD2.920.063.00
plotMutualFindings1.340.032.28
plotPositives0.910.020.92
plotQQ2.400.112.55
plotRMSE2.250.042.29
prepareObserved0.020.000.02
runDA0.470.020.48
runMocks0.860.011.32
runNormalizations0.540.000.54
runSplits4.160.044.19
setNormalizations000
set_ALDEx2000
set_ANCOM0.010.000.02
set_DESeq2000
set_MAST000
set_NOISeq000
set_Seurat000
set_basic000
set_dearseq0.020.000.02
set_edgeR000
set_limma0.020.000.01
set_metagenomeSeq000
weights_ZINB0.450.020.47