Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:05:08 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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:
- 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: 2022-01-18 01:55:07 -0500 (Tue, 18 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings benchdamic_1.0.0.tar.gz
StartedAt: 2022-01-18 06:25:27 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 06:33:10 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 462.8 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings benchdamic_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/benchdamic.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 7.534  0.032   7.566
areaCAT           6.528  0.028   6.557
DA_DESeq2         5.844  0.156   6.000
plotConcordance   5.764  0.023   5.788
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)
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=95.09, log10(eps+1)=Inf, stillActive=88
it= 1, nll=94.73, log10(eps+1)=0.04, stillActive=58
it= 2, nll=92.59, log10(eps+1)=0.05, stillActive=49
it= 3, nll=90.84, log10(eps+1)=0.09, stillActive=38
it= 4, nll=89.71, log10(eps+1)=0.10, stillActive=33
it= 5, nll=89.60, log10(eps+1)=0.06, stillActive=28
it= 6, nll=90.70, log10(eps+1)=0.07, stillActive=13
it= 7, nll=90.70, log10(eps+1)=0.07, stillActive=8
it= 8, nll=91.34, log10(eps+1)=0.02, stillActive=5
it= 9, nll=91.62, log10(eps+1)=0.03, stillActive=4
it=10, nll=91.57, log10(eps+1)=0.03, stillActive=4
it=11, nll=91.36, log10(eps+1)=0.05, stillActive=4
it=12, nll=91.67, log10(eps+1)=0.07, stillActive=2
it=13, nll=91.57, log10(eps+1)=0.06, stillActive=2
it=14, nll=91.60, log10(eps+1)=0.06, stillActive=1
it=15, nll=91.63, 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 5 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
 48.170   1.272  49.399 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx23.9700.1314.104
DA_DESeq25.8440.1566.000
DA_MAST0.9010.0470.949
DA_Seurat0.7410.0170.756
DA_corncob1.3220.0081.340
DA_edgeR0.3290.0000.329
DA_limma0.1590.0000.159
DA_metagenomeSeq0.2360.0000.236
RMSE0.0010.0000.001
addKnowledge0.130.000.13
areaCAT6.5280.0286.557
checkNormalization000
createColors0.0050.0000.004
createConcordance7.5340.0327.566
createEnrichment0.1930.0000.193
createMocks0.0020.0000.002
createPositives0.6950.0000.695
createSplits0.0340.0000.034
createTIEC1.5030.0041.507
enrichmentTest0.070.000.07
extractDA0.1680.0000.168
extractStatistics0.1720.0000.172
fitDM0.0340.0000.034
fitHURDLE0.5450.0000.545
fitModels1.3800.0041.384
fitNB0.0480.0000.048
fitZIG0.0450.0030.049
fitZINB0.2340.0010.235
getDA0.0570.0000.058
getPositives0.0570.0000.057
getStatistics0.0480.0020.051
iterative_ordering0.0060.0000.007
meanDifferences0.0010.0000.001
norm_CSS0.0570.0000.056
norm_DESeq20.7330.0000.733
norm_TSS0.0260.0000.025
norm_edgeR0.0280.0000.027
plotConcordance5.7640.0235.788
plotContingency0.7970.0010.797
plotEnrichment0.7520.0080.760
plotFPR1.2240.0041.228
plotKS1.2320.0121.245
plotMD2.2930.0112.306
plotMutualFindings0.7170.0010.717
plotPositives0.6090.0000.609
plotQQ1.1980.0001.206
plotRMSE1.7760.0201.796
prepareObserved0.0020.0000.002
runDA0.8280.0000.827
runMocks0.6140.0030.619
runNormalizations0.8170.0000.817
runSplits3.0010.0003.001
setNormalizations000
set_ALDEx20.0050.0000.005
set_DESeq20.0070.0000.007
set_MAST0.0050.0000.005
set_Seurat0.0060.0000.006
set_corncob0.0060.0000.006
set_edgeR0.0060.0040.010
set_limma0.0070.0000.007
set_metagenomeSeq0.0050.0000.005
weights_ZINB0.2570.0000.257