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This page was generated on 2023-09-28 11:35:24 -0400 (Thu, 28 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 153/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.6.4  (landing page)
Matteo Calgaro
Snapshot Date: 2023-09-27 14:00:15 -0400 (Wed, 27 Sep 2023)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_17
git_last_commit: c9eb539
git_last_commit_date: 2023-07-22 05:17:46 -0400 (Sat, 22 Jul 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    TIMEOUT  skippedskipped

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.
- 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: 1.6.4
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_1.6.4.tar.gz
StartedAt: 2023-09-27 19:31:17 -0400 (Wed, 27 Sep 2023)
EndedAt: 2023-09-27 20:02:57 -0400 (Wed, 27 Sep 2023)
EllapsedTime: 1900.9 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_1.6.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/benchdamic.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.6.4’
* 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
** inst
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
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)
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
> 
> 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 310 ]
> 
> proc.time()
   user  system elapsed 
170.097   6.068 216.028 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
CAT0.0060.0000.006
DA_ALDEx23.7960.1483.945
DA_ANCOM4.7420.1484.891
DA_DESeq22.570.042.61
DA_MAST1.5370.0151.527
DA_Maaslin20.2420.0160.260
DA_NOISeq1.6630.0881.751
DA_Seurat0.5790.0120.591
DA_ZicoSeq0.6200.0080.628
DA_basic0.0310.0000.031
DA_corncob1.3230.0601.388
DA_dearseq0.0570.0040.060
DA_edgeR0.3150.0000.315
DA_limma0.0730.0000.073
DA_linda0.0270.0040.032
DA_metagenomeSeq0.2430.0000.244
RMSE0.0010.0000.001
addKnowledge0.1600.0080.168
areaCAT3.8310.0723.903
checkNormalization0.0010.0000.000
createColors0.0050.0000.005
createConcordance4.1530.0524.205
createEnrichment0.2380.0040.241
createMocks0.0040.0000.003
createPositives0.7900.0040.794
createSplits0.030.000.03
createTIEC2.4530.0362.489
enrichmentTest0.1130.0000.113
extractDA0.1580.0040.162
extractStatistics0.1570.0000.157
fitDM0.0300.0000.031
fitHURDLE0.6930.0120.706
fitModels2.3720.0322.405
fitNB0.0430.0000.043
fitZIG0.0490.0000.049
fitZINB0.4050.0000.404
getDA0.0740.0080.082
getPositives0.0750.0000.075
getStatistics0.0700.0000.069
get_counts_metadata0.2070.0000.206
iterative_ordering0.0090.0010.010
meanDifferences0.0000.0020.002
norm_CSS0.0640.0000.064
norm_DESeq20.3970.0000.398
norm_TSS0.0280.0000.029
norm_edgeR0.0340.0000.033
plotConcordance4.7650.0844.848
plotContingency1.1940.0201.215
plotEnrichment1.1230.0001.123
plotFDR2.2170.0122.228
plotFPR2.1940.0442.237
plotKS2.2680.0042.271
plotLogP2.1360.0762.212
plotMD3.7090.0683.776
plotMutualFindings1.0920.0081.100
plotPositives0.7990.0000.799
plotQQ2.1290.0282.157
plotRMSE2.9330.0002.933
prepareObserved0.0010.0000.001
runDA0.4610.0000.461
runMocks0.7110.0040.715
runNormalizations0.4340.0000.434
runSplits3.3680.0323.400
setNormalizations0.0010.0000.001
set_ALDEx20.0060.0000.006
set_ANCOM0.0070.0000.007
set_DESeq20.0070.0000.007
set_MAST0.0030.0000.003
set_Maaslin20.0040.0000.004
set_NOISeq0.0030.0000.003
set_Seurat0.0010.0040.005
set_ZicoSeq0.0030.0030.006
set_basic0.0010.0000.002
set_corncob0.0040.0000.003
set_dearseq0.0020.0000.002
set_edgeR0.0020.0080.011
set_limma0.0080.0000.008
set_linda0.0060.0000.005
set_metagenomeSeq0.0050.0000.005
weights_ZINB0.4040.0000.404