Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:07:05 -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 merida1


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: /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_1.2.0.tar.gz
StartedAt: 2022-06-23 23:48:57 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-24 00:06:03 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 1026.3 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.2.0’
* 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 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 18.174  0.132  18.730
plotConcordance   12.166  0.085  12.494
areaCAT           10.744  0.143  11.029
DA_DESeq2          6.907  0.278   7.238
runSplits          7.111  0.072   7.370
DA_ALDEx2          5.977  0.743   6.973
plotMD             5.679  0.037   6.039
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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=95.21, log10(eps+1)=Inf, stillActive=88
it= 1, nll=95.00, log10(eps+1)=0.04, stillActive=55
it= 2, nll=92.99, log10(eps+1)=0.05, stillActive=45
it= 3, nll=91.27, log10(eps+1)=0.06, stillActive=36
it= 4, nll=89.73, log10(eps+1)=0.07, stillActive=32
it= 5, nll=89.24, log10(eps+1)=0.07, stillActive=27
it= 6, nll=89.44, log10(eps+1)=0.06, stillActive=13
it= 7, nll=89.12, log10(eps+1)=0.08, stillActive=10
it= 8, nll=90.03, log10(eps+1)=0.07, stillActive=5
it= 9, nll=89.94, log10(eps+1)=0.02, stillActive=4
it=10, nll=89.89, log10(eps+1)=0.03, stillActive=3
it=11, nll=89.63, log10(eps+1)=0.07, stillActive=3
it=12, nll=89.60, log10(eps+1)=0.10, stillActive=2
it=13, nll=89.74, log10(eps+1)=0.09, stillActive=1
it=14, nll=90.05, 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 
 97.285   3.586 111.648 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx25.9770.7436.973
DA_DESeq26.9070.2787.238
DA_MAST1.2940.0131.309
DA_Seurat1.2050.0191.236
DA_corncob4.0480.1004.245
DA_edgeR0.3420.0070.353
DA_limma0.1520.0040.156
DA_metagenomeSeq0.4620.0060.469
RMSE0.0010.0000.002
addKnowledge0.2350.0080.244
areaCAT10.744 0.14311.029
checkNormalization0.0000.0000.001
createColors0.0090.0000.009
createConcordance18.174 0.13218.730
createEnrichment0.4250.0060.447
createMocks0.0060.0020.007
createPositives1.6400.0201.754
createSplits0.1110.0030.124
createTIEC3.4840.0383.642
enrichmentTest0.1670.0040.173
extractDA0.3900.0050.400
extractStatistics0.3840.0060.394
fitDM0.0710.0010.072
fitHURDLE0.7460.0050.755
fitModels2.7740.0182.811
fitNB0.0890.0000.090
fitZIG0.1060.0000.107
fitZINB0.9780.0030.990
getDA0.1600.0060.168
getPositives0.1590.0030.163
getStatistics0.1400.0050.145
iterative_ordering0.0210.0010.021
meanDifferences0.0030.0000.004
norm_CSS0.1380.0010.141
norm_DESeq21.0490.0061.063
norm_TSS0.0720.0000.073
norm_edgeR0.0750.0010.076
plotConcordance12.166 0.08512.494
plotContingency2.0240.0142.098
plotEnrichment1.9080.0111.946
plotFPR2.9450.0192.977
plotKS3.1730.0323.433
plotMD5.6790.0376.039
plotMutualFindings2.0070.0142.131
plotPositives1.4500.0091.536
plotQQ3.2170.0233.602
plotRMSE4.0420.0214.337
prepareObserved0.0030.0000.003
runDA1.2910.0111.399
runMocks1.7920.0361.930
runNormalizations1.1870.0041.257
runSplits7.1110.0727.370
setNormalizations0.0010.0010.001
set_ALDEx20.0130.0000.013
set_DESeq20.0170.0000.017
set_MAST0.0140.0010.014
set_Seurat0.0150.0000.016
set_corncob0.0140.0000.014
set_edgeR0.0310.0010.032
set_limma0.0150.0010.016
set_metagenomeSeq0.0130.0000.014
weights_ZINB0.9760.0030.983