Back to Build/check report for BioC 3.15
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-27 11:09:48 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 nebbiolo1


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: 2022-06-26 13:55:11 -0400 (Sun, 26 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

Summary

Package: benchdamic
Version: 1.2.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings benchdamic_1.2.0.tar.gz
StartedAt: 2022-06-26 18:49:46 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 18:58:21 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 515.2 seconds
RetCode: 0
Status:   OK  
CheckDir: benchdamic.Rcheck
Warnings: 0

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.2.0’
* 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 7.418  0.128   7.547
plotConcordance   5.504  0.020   5.524
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL benchdamic
###
##############################################################################
##############################################################################


* installing to library ‘/home/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) -- "Vigorous Calisthenics"
Copyright (C) 2022 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=95.15, log10(eps+1)=Inf, stillActive=88
it= 1, nll=94.57, log10(eps+1)=0.04, stillActive=58
it= 2, nll=92.49, log10(eps+1)=0.05, stillActive=49
it= 3, nll=90.60, log10(eps+1)=0.07, stillActive=39
it= 4, nll=89.62, log10(eps+1)=0.06, stillActive=33
it= 5, nll=88.84, log10(eps+1)=0.09, stillActive=26
it= 6, nll=91.70, log10(eps+1)=0.09, stillActive=9
it= 7, nll=92.56, log10(eps+1)=0.04, stillActive=5
it= 8, nll=93.25, log10(eps+1)=0.02, stillActive=3
it= 9, nll=93.29, log10(eps+1)=0.02, stillActive=3
it=10, nll=93.29, log10(eps+1)=0.03, stillActive=3
it=11, nll=93.37, log10(eps+1)=0.03, stillActive=1
it=12, nll=93.38, log10(eps+1)=0.02, stillActive=1
it=13, nll=93.65, 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 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 127 ]
> 
> proc.time()
   user  system elapsed 
 47.619   2.143  49.729 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx23.4170.3443.762
DA_DESeq23.4930.1483.640
DA_MAST0.7470.0080.754
DA_Seurat2.3950.1202.515
DA_corncob1.2340.0451.283
DA_edgeR0.1870.0040.191
DA_limma0.0840.0000.084
DA_metagenomeSeq0.2340.0080.242
RMSE0.0010.0000.001
addKnowledge0.1250.0040.129
areaCAT4.5710.0844.655
checkNormalization0.0000.0000.001
createColors0.0010.0040.006
createConcordance7.4180.1287.547
createEnrichment0.2290.0000.229
createMocks0.0010.0020.004
createPositives0.6960.0290.725
createSplits0.0390.0000.039
createTIEC1.6710.0721.743
enrichmentTest0.0810.0000.081
extractDA0.1720.0000.172
extractStatistics0.180.000.18
fitDM0.0310.0000.031
fitHURDLE0.3420.0000.342
fitModels1.2810.0121.293
fitNB0.0410.0040.045
fitZIG0.0690.0000.070
fitZINB0.4310.0130.444
getDA0.070.010.08
getPositives0.0670.0040.071
getStatistics0.0650.0040.069
iterative_ordering0.0080.0040.012
meanDifferences0.0000.0020.002
norm_CSS0.0660.0040.070
norm_DESeq20.8040.0040.808
norm_TSS0.0470.0080.056
norm_edgeR0.0540.0030.057
plotConcordance5.5040.0205.524
plotContingency0.8740.0040.878
plotEnrichment0.9140.0120.927
plotFPR1.3840.0161.400
plotKS1.2680.0161.285
plotMD2.4420.0362.477
plotMutualFindings0.8470.0080.855
plotPositives0.6800.0240.704
plotQQ1.3570.0121.368
plotRMSE1.7970.0281.826
prepareObserved0.0000.0010.001
runDA0.8010.0100.811
runMocks0.6640.0200.684
runNormalizations0.5300.0000.529
runSplits3.1100.0643.174
setNormalizations0.0000.0000.001
set_ALDEx20.0050.0000.006
set_DESeq20.0070.0000.008
set_MAST0.0050.0000.006
set_Seurat0.0030.0040.005
set_corncob0.0060.0000.006
set_edgeR0.010.000.01
set_limma0.0080.0000.007
set_metagenomeSeq0.0020.0040.005
weights_ZINB0.3830.0160.400