Back to Multiple platform build/check report for BioC 3.15
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:22:36 -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 merida1


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: /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_1.2.5.tar.gz
StartedAt: 2022-10-18 23:37:48 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 23:54:29 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 1000.8 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.2.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 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 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         10.507  1.024  12.056
createConcordance  9.359  0.119   9.534
areaCAT            9.217  0.195   9.444
plotConcordance    8.788  0.062   8.875
runSplits          6.634  0.046   6.693
DA_DESeq2          5.772  0.055   5.857
plotMD             5.033  0.024   5.105
DA_ANCOM           2.216  0.015  28.551
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 93.834   3.358 135.639 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0080.0000.009
DA_ALDEx210.507 1.02412.056
DA_ANCOM 2.216 0.01528.551
DA_DESeq25.7720.0555.857
DA_MAST1.1520.0141.167
DA_NOISeq1.5740.0131.594
DA_Seurat1.0160.0281.052
DA_basic0.0590.0010.060
DA_dearseq0.0950.0030.099
DA_edgeR0.3050.0100.318
DA_limma0.1180.0040.123
DA_metagenomeSeq0.5000.0140.518
RMSE0.0010.0010.002
addKnowledge0.5500.0160.567
areaCAT9.2170.1959.444
checkNormalization000
createColors0.0100.0010.011
createConcordance9.3590.1199.534
createEnrichment0.4860.0070.495
createMocks0.0040.0010.005
createPositives1.7580.0471.827
createSplits0.0670.0030.070
createTIEC3.7200.0573.804
enrichmentTest0.2140.0050.218
extractDA0.3420.0050.347
extractStatistics0.3370.0030.341
fitDM0.0680.0010.069
fitHURDLE0.6660.0050.675
fitModels2.5400.0252.575
fitNB0.0890.0010.090
fitZIG0.0870.0010.088
fitZINB0.9220.0110.941
getDA0.1580.0090.167
getPositives0.1550.0050.161
getStatistics0.1430.0070.150
get_counts_metadata0.3540.0050.360
iterative_ordering0.0210.0010.021
meanDifferences0.0030.0000.004
norm_CSS0.1380.0010.141
norm_DESeq20.8940.0080.908
norm_TSS0.0590.0010.061
norm_edgeR0.0750.0010.076
plotConcordance8.7880.0628.875
plotContingency2.2360.0202.264
plotEnrichment2.2600.0212.305
plotFPR3.9530.0274.150
plotKS3.8330.0323.914
plotLogP3.6430.0343.688
plotMD5.0330.0245.105
plotMutualFindings2.0130.0132.032
plotPositives1.5000.0091.513
plotQQ3.3950.0303.439
plotRMSE3.6120.0193.643
prepareObserved0.0020.0000.002
runDA0.9260.0050.933
runMocks1.2750.0091.286
runNormalizations1.0060.0051.013
runSplits6.6340.0466.693
setNormalizations0.0000.0000.001
set_ALDEx20.0100.0010.010
set_ANCOM0.0090.0000.009
set_DESeq20.0130.0010.014
set_MAST0.0060.0000.006
set_NOISeq0.0060.0000.007
set_Seurat0.010.000.01
set_basic0.0030.0000.003
set_dearseq0.0030.0000.003
set_edgeR0.0250.0000.025
set_limma0.0170.0010.016
set_metagenomeSeq0.0110.0000.012
weights_ZINB0.8190.0020.823