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This page was generated on 2023-03-30 12:33:41 -0400 (Thu, 30 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
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 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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 152/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.5.2  (landing page)
Matteo Calgaro
Snapshot Date: 2023-03-29 14:00:20 -0400 (Wed, 29 Mar 2023)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: devel
git_last_commit: 224bcad
git_last_commit_date: 2022-11-21 11:52:14 -0400 (Mon, 21 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: benchdamic
Version: 1.5.2
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.5.2.tar.gz
StartedAt: 2023-03-29 18:48:13 -0400 (Wed, 29 Mar 2023)
EndedAt: 2023-03-29 19:20:19 -0400 (Wed, 29 Mar 2023)
EllapsedTime: 1926.0 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings benchdamic_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.5.2’
* 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 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 ... 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
* 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 ...
  ‘intro.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

benchdamic.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1 | SKIP 0 | PASS 292 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 292 ]
> 
> proc.time()
   user  system elapsed 
 65.149   3.024  82.238 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0050.0000.005
DA_ALDEx23.7260.2123.938
DA_ANCOM1.5450.0801.625
DA_DESeq24.3800.0764.456
DA_MAST0.5880.0080.595
DA_NOISeq1.5700.0041.574
DA_Seurat0.7860.0160.802
DA_basic0.030.000.03
DA_corncob1.3220.0451.369
DA_dearseq0.1670.0040.171
DA_edgeR0.1830.0040.187
DA_limma0.0710.0080.079
DA_metagenomeSeq0.2970.0000.297
RMSE0.0010.0000.001
addKnowledge0.1760.0080.184
areaCAT4.4140.4884.902
checkNormalization000
createColors0.0020.0030.006
createConcordance4.4510.3604.812
createEnrichment0.2390.0120.250
createMocks0.0000.0040.004
createPositives0.8010.0560.857
createSplits0.030.000.03
createTIEC2.4010.1402.540
enrichmentTest0.1180.0080.126
extractDA0.2110.0120.224
extractStatistics0.2140.0240.238
fitDM0.0350.0000.035
fitHURDLE0.3470.0240.371
fitModels1.2250.0721.298
fitNB0.0480.0000.048
fitZIG0.0550.0000.055
fitZINB0.3790.0240.402
getDA0.0640.0160.081
getPositives0.0740.0000.075
getStatistics0.0650.0040.068
get_counts_metadata0.2190.0120.231
iterative_ordering0.0110.0000.011
meanDifferences0.0020.0000.002
norm_CSS0.0730.0030.077
norm_DESeq20.4160.0000.416
norm_TSS0.030.000.03
norm_edgeR0.0340.0000.034
plotConcordance4.4760.2684.744
plotContingency1.1120.0081.119
plotEnrichment1.1170.0401.157
plotFDR2.1090.0882.197
plotFPR2.0960.0642.159
plotKS2.070.042.11
plotLogP2.0630.0762.138
plotMD2.4600.1322.592
plotMutualFindings1.1310.0321.163
plotPositives0.7160.0040.720
plotQQ2.1670.0282.195
plotRMSE1.7980.0241.822
prepareObserved0.0010.0000.002
runDA0.4950.0200.515
runMocks0.7060.0200.726
runNormalizations0.5050.0040.509
runSplits3.4830.1483.631
setNormalizations000
set_ALDEx20.0060.0000.007
set_ANCOM0.0030.0040.008
set_DESeq20.0070.0000.007
set_MAST0.0030.0000.003
set_NOISeq0.0000.0040.003
set_Seurat0.0020.0040.005
set_basic0.0020.0000.002
set_corncob0.0040.0000.004
set_dearseq0.0020.0000.002
set_edgeR0.0110.0000.011
set_limma0.0070.0000.008
set_metagenomeSeq0.0010.0040.005
weights_ZINB0.3960.0000.397