Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:07:29 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 machv2


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? here 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 139/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.0.0  (landing page)
Matteo Calgaro
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_14
git_last_commit: 5175773
git_last_commit_date: 2021-10-26 13:13:35 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: benchdamic
Version: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2022-01-13 10:28:02 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 10:40:53 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 771.1 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/benchdamic.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.0.0’
* 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
createConcordance 14.239  0.127  14.393
DA_DESeq2          9.415  0.329   9.782
plotConcordance    9.445  0.100   9.756
areaCAT            8.275  0.119   8.679
runSplits          5.943  0.049   6.008
DA_ALDEx2          4.891  0.619   5.523
* 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/4.1/Resources/library’
* installing *source* package ‘benchdamic’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (benchdamic)

Tests output

benchdamic.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
> 
> test_check("benchdamic")
it= 0, nll=95.20, log10(eps+1)=Inf, stillActive=88
it= 1, nll=94.90, log10(eps+1)=0.04, stillActive=57
it= 2, nll=93.07, log10(eps+1)=0.04, stillActive=49
it= 3, nll=91.44, log10(eps+1)=0.06, stillActive=39
it= 4, nll=89.76, log10(eps+1)=0.07, stillActive=34
it= 5, nll=88.81, log10(eps+1)=0.07, stillActive=33
it= 6, nll=89.93, log10(eps+1)=0.06, stillActive=16
it= 7, nll=89.35, log10(eps+1)=0.09, stillActive=14
it= 8, nll=90.06, log10(eps+1)=0.07, stillActive=9
it= 9, nll=90.03, log10(eps+1)=0.09, stillActive=8
it=10, nll=90.20, log10(eps+1)=0.00, stillActive=5
it=11, nll=90.21, log10(eps+1)=0.00, stillActive=5
it=12, nll=90.23, log10(eps+1)=0.00, stillActive=1
it=13, nll=90.25, log10(eps+1)=0.01, stillActive=1
it=14, nll=90.27, log10(eps+1)=0.02, stillActive=1
it=15, nll=90.24, log10(eps+1)=0.04, stillActive=1
it=16, nll=90.12, log10(eps+1)=0.09, stillActive=1
it=17, nll=90.51, log10(eps+1)=0.00, stillActive=0
|------------(25%)----------(50%)----------(75%)----------|
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

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      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      + Running now: norm_CSS 
        Parameters: method=median 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      + Running now: norm_CSS 
        Parameters: method=median 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      + Running now: norm_CSS 
        Parameters: method=median 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=CSSmedian, weights=FALSE 
      * Running now: DA_limma 
        Parameters: pseudo_count=FALSE, design=~1 + HMP_BODY_SUBSITE, coef=2, norm=TMM, weights=FALSE 
      + Running now: norm_edgeR 
        Parameters: method=TMM 
      + Running now: norm_DESeq2 
        Parameters: method=poscounts 
      + Running now: norm_CSS 
        Parameters: method=default 
      + Running now: norm_TSS 
        Parameters: method=TSS 
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
 85.806   2.914  88.896 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx24.8910.6195.523
DA_DESeq29.4150.3299.782
DA_MAST1.3080.0121.324
DA_Seurat1.0490.0251.075
DA_corncob1.9990.0792.104
DA_edgeR0.4320.0100.444
DA_limma0.1090.0030.113
DA_metagenomeSeq0.3390.0060.782
RMSE0.0010.0010.002
addKnowledge1.4970.0121.513
areaCAT8.2750.1198.679
checkNormalization000
createColors0.0060.0000.006
createConcordance14.239 0.12714.393
createEnrichment0.2910.0050.297
createMocks0.0030.0020.004
createPositives1.1890.0111.202
createSplits0.0840.0030.086
createTIEC2.4760.0262.511
enrichmentTest0.1430.0060.149
extractDA0.3260.0040.329
extractStatistics0.3290.0040.333
fitDM0.0610.0010.062
fitHURDLE0.7930.0060.799
fitModels1.9900.0112.001
fitNB0.0710.0010.072
fitZIG0.0950.0010.097
fitZINB0.5380.0050.543
getDA0.1150.0130.128
getPositives0.1110.0030.115
getStatistics0.1210.0070.130
iterative_ordering0.0180.0010.019
meanDifferences0.0030.0010.004
norm_CSS0.1030.0020.104
norm_DESeq21.4520.0341.681
norm_TSS0.0580.0010.060
norm_edgeR0.0560.0010.058
plotConcordance9.4450.1009.756
plotContingency1.4120.0171.433
plotEnrichment1.3980.0201.425
plotFPR2.4690.0302.507
plotKS2.3290.0252.361
plotMD4.4900.0244.521
plotMutualFindings1.6080.0091.620
plotPositives1.2000.0061.212
plotQQ2.5470.0272.594
plotRMSE3.2880.0293.373
prepareObserved0.0010.0010.002
runDA1.7130.0071.721
runMocks1.3520.0131.365
runNormalizations1.4970.0021.501
runSplits5.9430.0496.008
setNormalizations0.0000.0000.001
set_ALDEx20.0100.0010.011
set_DESeq20.0150.0010.015
set_MAST0.0110.0000.013
set_Seurat0.0110.0000.011
set_corncob0.0120.0010.012
set_edgeR0.0280.0010.146
set_limma0.0170.0010.018
set_metagenomeSeq0.0120.0000.012
weights_ZINB0.5510.0040.556