Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:39 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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? 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 140/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.2.0  (landing page)
Matteo Calgaro
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: RELEASE_3_15
git_last_commit: a0ce080
git_last_commit_date: 2022-04-26 12:19:21 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: benchdamic
Version: 1.2.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.2.0.tar.gz
StartedAt: 2022-06-23 23:04:13 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:14:39 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 625.9 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:benchdamic.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings benchdamic_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.2.0'
* 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
* 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 9.21   0.14    9.39
plotConcordance   6.64   0.13    6.77
areaCAT           5.97   0.07    6.06
DA_ALDEx2         4.00   1.36    5.41
DA_corncob        3.17   0.08    7.50
* 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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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=95.21, log10(eps+1)=Inf, stillActive=88
it= 1, nll=94.89, log10(eps+1)=0.04, stillActive=57
it= 2, nll=92.75, log10(eps+1)=0.05, stillActive=48
it= 3, nll=90.88, log10(eps+1)=0.07, stillActive=40
it= 4, nll=89.59, log10(eps+1)=0.08, stillActive=35
it= 5, nll=89.27, log10(eps+1)=0.06, stillActive=30
it= 6, nll=89.32, log10(eps+1)=0.08, stillActive=16
it= 7, nll=88.91, log10(eps+1)=0.08, stillActive=13
it= 8, nll=89.39, log10(eps+1)=0.08, stillActive=5
it= 9, nll=90.41, log10(eps+1)=0.01, stillActive=2
it=10, nll=90.48, log10(eps+1)=0.02, stillActive=2
it=11, nll=90.60, log10(eps+1)=0.01, stillActive=1
it=12, nll=90.69, 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 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
  55.81    3.81   59.62 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx24.001.365.41
DA_DESeq23.970.184.14
DA_MAST0.720.010.75
DA_Seurat0.910.000.90
DA_corncob3.170.087.50
DA_edgeR0.220.000.22
DA_limma0.110.000.11
DA_metagenomeSeq0.300.020.31
RMSE000
addKnowledge0.190.000.19
areaCAT5.970.076.06
checkNormalization000
createColors0.010.000.02
createConcordance9.210.149.39
createEnrichment0.290.020.31
createMocks000
createPositives0.940.030.97
createSplits0.060.000.06
createTIEC2.050.022.06
enrichmentTest0.110.000.11
extractDA0.170.030.21
extractStatistics0.190.010.20
fitDM0.030.000.03
fitHURDLE0.410.000.41
fitModels1.560.021.57
fitNB0.040.000.05
fitZIG0.080.000.08
fitZINB0.410.000.40
getDA0.080.000.08
getPositives0.080.010.10
getStatistics0.10.00.1
iterative_ordering0.020.000.02
meanDifferences000
norm_CSS0.090.000.09
norm_DESeq20.620.000.62
norm_TSS0.040.000.04
norm_edgeR0.040.000.04
plotConcordance6.640.136.77
plotContingency1.210.061.28
plotEnrichment1.040.061.11
plotFPR1.800.041.94
plotKS1.500.042.15
plotMD3.050.033.08
plotMutualFindings1.120.041.16
plotPositives0.850.030.87
plotQQ2.200.012.23
plotRMSE2.300.023.69
prepareObserved000
runDA0.880.000.87
runMocks0.950.030.99
runNormalizations0.830.000.83
runSplits4.400.064.47
setNormalizations000
set_ALDEx20.020.000.01
set_DESeq20.020.000.02
set_MAST0.010.000.01
set_Seurat000
set_corncob0.020.000.02
set_edgeR0.010.000.01
set_limma0.020.000.02
set_metagenomeSeq0.010.000.02
weights_ZINB0.410.000.40