Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-14 13:06:03 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:benchdamic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings benchdamic_1.0.0.tar.gz
StartedAt: 2022-01-13 15:56:09 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 16:10:23 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 853.5 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:benchdamic.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings benchdamic_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/benchdamic.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
createConcordance 9.00   0.06    9.06
DA_DESeq2         6.94   0.92    7.86
plotConcordance   5.28   0.13    5.41
areaCAT           5.31   0.03    5.34
DA_corncob        1.78   0.16    8.79
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
createConcordance 8.61   0.00    8.61
DA_DESeq2         6.88   0.03    6.90
plotConcordance   6.36   0.00    6.36
areaCAT           5.03   0.00    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/benchdamic_1.0.0.tar.gz && rm -rf benchdamic.buildbin-libdir && mkdir benchdamic.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=benchdamic.buildbin-libdir benchdamic_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL benchdamic_1.0.0.zip && rm benchdamic_1.0.0.tar.gz benchdamic_1.0.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  221k  100  221k    0     0  1396k      0 --:--:-- --:--:-- --:--:-- 1404k

install for i386

* 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
  converting help for package 'benchdamic'
    finding HTML links ... done
    DA_ALDEx2                               html  
    DA_DESeq2                               html  
    DA_MAST                                 html  
    DA_Seurat                               html  
    DA_corncob                              html  
    DA_edgeR                                html  
    DA_limma                                html  
    DA_metagenomeSeq                        html  
    RMSE                                    html  
    addKnowledge                            html  
    areaCAT                                 html  
    checkNormalization                      html  
    createColors                            html  
    createConcordance                       html  
    createEnrichment                        html  
    createMocks                             html  
    createPositives                         html  
    createSplits                            html  
    createTIEC                              html  
    enrichmentTest                          html  
    extractDA                               html  
    extractStatistics                       html  
    fitDM                                   html  
    finding level-2 HTML links ... done

    fitHURDLE                               html  
    fitModels                               html  
    fitNB                                   html  
    fitZIG                                  html  
    fitZINB                                 html  
    getDA                                   html  
    getPositives                            html  
    getStatistics                           html  
    iterative_ordering                      html  
    meanDifferences                         html  
    microbial_metabolism                    html  
    norm_CSS                                html  
    norm_DESeq2                             html  
    norm_TSS                                html  
    norm_edgeR                              html  
    plotConcordance                         html  
    plotConcordanceDendrogram               html  
    plotConcordanceHeatmap                  html  
    plotContingency                         html  
    plotEnrichment                          html  
    plotFPR                                 html  
    plotKS                                  html  
    plotMD                                  html  
    plotMutualFindings                      html  
    plotPositives                           html  
    plotQQ                                  html  
    plotRMSE                                html  
    prepareObserved                         html  
    ps_plaque_16S                           html  
    ps_stool_16S                            html  
    runDA                                   html  
    runMocks                                html  
    runNormalizations                       html  
    runSplits                               html  
    setNormalizations                       html  
    set_ALDEx2                              html  
    set_DESeq2                              html  
    set_MAST                                html  
    set_Seurat                              html  
    set_corncob                             html  
    set_edgeR                               html  
    set_limma                               html  
    set_metagenomeSeq                       html  
    weights_ZINB                            html  
** 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

install for x64

* installing *source* package 'benchdamic' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'benchdamic' as benchdamic_1.0.0.zip
* DONE (benchdamic)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'benchdamic' successfully unpacked and MD5 sums checked

Tests output

benchdamic.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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=95.21, log10(eps+1)=Inf, stillActive=88
it= 1, nll=94.79, log10(eps+1)=0.04, stillActive=58
it= 2, nll=93.02, log10(eps+1)=0.06, stillActive=46
it= 3, nll=91.76, log10(eps+1)=0.06, stillActive=35
it= 4, nll=90.46, log10(eps+1)=0.06, stillActive=32
it= 5, nll=90.20, log10(eps+1)=0.07, stillActive=29
it= 6, nll=92.27, log10(eps+1)=0.05, stillActive=15
it= 7, nll=91.82, log10(eps+1)=0.06, stillActive=14
it= 8, nll=91.10, log10(eps+1)=0.08, stillActive=14
it= 9, nll=91.39, log10(eps+1)=0.06, stillActive=10
it=10, nll=91.38, log10(eps+1)=0.06, stillActive=9
it=11, nll=91.34, log10(eps+1)=0.03, stillActive=8
it=12, nll=91.56, log10(eps+1)=0.06, stillActive=6
it=13, nll=91.53, log10(eps+1)=0.03, stillActive=6
it=14, nll=91.86, log10(eps+1)=0.00, stillActive=5
it=15, nll=91.90, log10(eps+1)=0.00, stillActive=5
it=16, nll=91.94, log10(eps+1)=0.00, stillActive=5
it=17, nll=91.98, log10(eps+1)=0.00, stillActive=5
it=18, nll=92.01, log10(eps+1)=0.00, stillActive=5
it=19, nll=92.04, log10(eps+1)=0.00, stillActive=5
it=20, nll=92.07, log10(eps+1)=0.00, stillActive=5
it=21, nll=92.08, log10(eps+1)=0.00, stillActive=5
it=22, nll=92.08, log10(eps+1)=0.01, stillActive=5
it=23, nll=92.01, log10(eps+1)=0.02, stillActive=5
it=24, nll=91.78, log10(eps+1)=0.06, stillActive=5
it=25, nll=91.55, log10(eps+1)=0.10, stillActive=4
it=26, nll=91.43, log10(eps+1)=0.09, stillActive=3
it=27, nll=92.34, 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
      + 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 
  53.45    5.73   61.09 

benchdamic.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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=95.25, log10(eps+1)=Inf, stillActive=88
it= 1, nll=95.13, log10(eps+1)=0.04, stillActive=56
it= 2, nll=93.22, log10(eps+1)=0.05, stillActive=48
it= 3, nll=91.40, log10(eps+1)=0.06, stillActive=41
it= 4, nll=90.45, log10(eps+1)=0.06, stillActive=32
it= 5, nll=89.55, log10(eps+1)=0.07, stillActive=28
it= 6, nll=90.81, log10(eps+1)=0.06, stillActive=12
it= 7, nll=90.14, log10(eps+1)=0.10, stillActive=9
it= 8, nll=90.39, log10(eps+1)=0.07, stillActive=5
it= 9, nll=90.10, log10(eps+1)=0.06, stillActive=5
it=10, nll=90.38, log10(eps+1)=0.07, stillActive=3
it=11, nll=90.69, log10(eps+1)=0.01, stillActive=2
it=12, nll=91.00, log10(eps+1)=0.00, stillActive=1
it=13, nll=91.03, log10(eps+1)=0.00, stillActive=1
it=14, nll=91.06, log10(eps+1)=0.00, stillActive=1
it=15, nll=91.08, log10(eps+1)=0.00, stillActive=1
it=16, nll=91.10, log10(eps+1)=0.00, stillActive=1
it=17, nll=91.11, log10(eps+1)=0.00, stillActive=1
it=18, nll=91.12, log10(eps+1)=0.00, stillActive=1
it=19, nll=91.11, log10(eps+1)=0.01, stillActive=1
it=20, nll=91.09, log10(eps+1)=0.02, stillActive=1
it=21, nll=91.15, 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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |================                                                      |  22%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================                |  78%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |======================================================================| 100%

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
      + 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 
  57.92    2.50   61.18 

Example timings

benchdamic.Rcheck/examples_i386/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx22.921.094.02
DA_DESeq26.940.927.86
DA_MAST0.700.150.84
DA_Seurat0.690.090.79
DA_corncob1.780.168.79
DA_edgeR0.490.010.50
DA_limma0.110.000.11
DA_metagenomeSeq0.280.000.28
RMSE000
addKnowledge0.140.020.16
areaCAT5.310.035.34
checkNormalization000
createColors0.020.000.02
createConcordance9.000.069.06
createEnrichment0.220.000.22
createMocks000
createPositives0.870.030.91
createSplits0.030.000.03
createTIEC1.670.081.75
enrichmentTest0.110.000.11
extractDA0.220.000.22
extractStatistics0.180.020.21
fitDM0.040.000.03
fitHURDLE0.450.000.45
fitModels1.360.001.36
fitNB0.050.000.05
fitZIG0.060.000.06
fitZINB0.330.000.33
getDA0.060.010.07
getPositives0.060.020.08
getStatistics0.060.010.08
iterative_ordering000
meanDifferences0.020.000.02
norm_CSS0.060.000.06
norm_DESeq20.770.030.80
norm_TSS0.030.000.03
norm_edgeR0.050.000.04
plotConcordance5.280.135.41
plotContingency0.790.010.81
plotEnrichment0.800.020.82
plotFPR1.380.001.37
plotKS1.560.021.80
plotMD2.580.002.58
plotMutualFindings1.250.001.29
plotPositives0.900.010.92
plotQQ1.390.001.39
plotRMSE1.750.021.77
prepareObserved000
runDA0.850.000.84
runMocks0.640.000.64
runNormalizations0.810.000.82
runSplits3.220.063.28
setNormalizations000
set_ALDEx2000
set_DESeq20.010.000.01
set_MAST000
set_Seurat0.020.000.02
set_corncob000
set_edgeR0.020.000.02
set_limma0.010.000.01
set_metagenomeSeq000
weights_ZINB0.340.000.34

benchdamic.Rcheck/examples_x64/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx22.370.943.49
DA_DESeq26.880.036.90
DA_MAST0.680.050.74
DA_Seurat0.600.020.61
DA_corncob1.500.061.82
DA_edgeR0.200.000.21
DA_limma0.100.000.09
DA_metagenomeSeq0.260.000.27
RMSE000
addKnowledge0.160.000.15
areaCAT5.030.005.03
checkNormalization000
createColors000
createConcordance8.610.008.61
createEnrichment0.200.000.21
createMocks000
createPositives0.890.030.92
createSplits0.080.000.08
createTIEC2.340.022.36
enrichmentTest0.130.010.14
extractDA0.20.00.2
extractStatistics0.190.000.19
fitDM0.030.000.03
fitHURDLE0.480.000.48
fitModels1.440.001.44
fitNB0.050.000.05
fitZIG0.050.000.04
fitZINB0.340.000.35
getDA0.110.000.11
getPositives0.090.000.09
getStatistics0.070.000.06
iterative_ordering0.010.000.02
meanDifferences000
norm_CSS0.080.000.08
norm_DESeq20.920.000.92
norm_TSS0.050.000.05
norm_edgeR0.030.000.03
plotConcordance6.360.006.36
plotContingency0.940.000.93
plotEnrichment0.870.000.88
plotFPR1.720.002.03
plotKS1.530.021.55
plotMD2.50.02.5
plotMutualFindings0.860.010.87
plotPositives0.750.000.75
plotQQ1.390.001.39
plotRMSE2.240.002.24
prepareObserved000
runDA1.090.001.09
runMocks0.830.000.83
runNormalizations0.970.000.97
runSplits3.930.003.94
setNormalizations000
set_ALDEx2000
set_DESeq2000
set_MAST0.010.000.02
set_Seurat000
set_corncob0.020.000.01
set_edgeR0.020.000.02
set_limma0.010.000.02
set_metagenomeSeq0.000.010.02
weights_ZINB0.560.000.56