Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:34 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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 nebbiolo2


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 153/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.5.2  (landing page)
Matteo Calgaro
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 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  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

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: 2023-04-12 04:52:02 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 05:24:36 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 1953.2 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) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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) (2023-02-14 r83833) -- "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 
 69.659   3.515  87.846 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0050.0000.005
DA_ALDEx23.6190.1163.736
DA_ANCOM1.4140.0801.495
DA_DESeq24.0010.0964.097
DA_MAST0.5820.0120.594
DA_NOISeq1.5120.0481.561
DA_Seurat0.7770.0040.781
DA_basic0.0280.0000.027
DA_corncob1.1160.0121.137
DA_dearseq0.1400.0040.144
DA_edgeR0.1600.0000.161
DA_limma0.0650.0000.066
DA_metagenomeSeq0.2570.0000.256
RMSE0.0010.0000.000
addKnowledge0.1590.0000.158
areaCAT3.7290.0483.776
checkNormalization0.0010.0000.000
createColors0.0050.0000.004
createConcordance4.2760.0724.348
createEnrichment0.2420.0000.241
createMocks0.0020.0010.002
createPositives0.7830.0060.790
createSplits0.0280.0000.028
createTIEC2.5200.0442.564
enrichmentTest0.1520.0000.152
extractDA0.1680.0000.168
extractStatistics0.1660.0000.167
fitDM0.0290.0000.029
fitHURDLE0.3530.0040.357
fitModels1.2310.0361.266
fitNB0.0430.0000.043
fitZIG0.0520.0000.052
fitZINB0.4330.0080.441
getDA0.0690.0080.078
getPositives0.0810.0000.081
getStatistics0.0580.0080.066
get_counts_metadata0.2210.0000.221
iterative_ordering0.010.000.01
meanDifferences0.0020.0000.001
norm_CSS0.0720.0000.072
norm_DESeq20.4460.0000.446
norm_TSS0.0460.0000.046
norm_edgeR0.0360.0000.036
plotConcordance4.7380.1124.850
plotContingency1.0670.0001.068
plotEnrichment1.0710.0001.071
plotFDR2.0730.0042.076
plotFPR2.0790.0082.088
plotKS2.0670.0282.095
plotLogP2.1960.0162.213
plotMD2.6730.0282.701
plotMutualFindings1.2130.0321.244
plotPositives0.7950.0120.807
plotQQ2.1850.0162.200
plotRMSE1.9470.0642.011
prepareObserved0.0010.0000.001
runDA0.5190.0000.520
runMocks0.7520.0000.753
runNormalizations0.5180.0000.518
runSplits3.8190.1003.919
setNormalizations000
set_ALDEx20.0080.0000.008
set_ANCOM0.0080.0000.008
set_DESeq20.0080.0000.008
set_MAST0.0030.0000.003
set_NOISeq0.0030.0000.003
set_Seurat0.0060.0000.006
set_basic0.0020.0000.002
set_corncob0.0040.0000.004
set_dearseq0.0020.0000.002
set_edgeR0.0120.0000.012
set_limma0.0080.0000.008
set_metagenomeSeq0.0050.0000.005
weights_ZINB0.4280.0000.428