Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:27 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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? 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 136/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
benchdamic 1.1.0  (landing page)
Matteo Calgaro
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/benchdamic
git_branch: master
git_last_commit: 7854ed4
git_last_commit_date: 2021-10-26 13:13:35 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'phyloseq' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: benchdamic
Version: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2022-01-21 18:18:32 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 18:26:14 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 462.2 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.1.0’
* 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 7.703  0.020   7.723
areaCAT           6.492  0.108   6.601
plotConcordance   5.410  0.024   5.435
* 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-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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=95.20, log10(eps+1)=Inf, stillActive=88
it= 1, nll=95.06, log10(eps+1)=0.04, stillActive=56
it= 2, nll=92.88, log10(eps+1)=0.05, stillActive=48
it= 3, nll=90.98, log10(eps+1)=0.06, stillActive=38
it= 4, nll=89.52, log10(eps+1)=0.08, stillActive=34
it= 5, nll=90.13, log10(eps+1)=0.06, stillActive=26
it= 6, nll=91.79, log10(eps+1)=0.06, stillActive=12
it= 7, nll=91.75, log10(eps+1)=0.06, stillActive=10
it= 8, nll=91.68, log10(eps+1)=0.07, stillActive=9
it= 9, nll=92.13, log10(eps+1)=0.05, stillActive=6
it=10, nll=92.05, log10(eps+1)=0.07, stillActive=5
it=11, nll=91.83, log10(eps+1)=0.08, stillActive=4
it=12, nll=92.88, 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 
 45.554   1.321  46.839 

Example timings

benchdamic.Rcheck/benchdamic-Ex.timings

nameusersystemelapsed
DA_ALDEx23.5520.4644.019
DA_DESeq23.3700.2633.634
DA_MAST0.7850.0190.805
DA_Seurat0.8050.0240.830
DA_corncob1.3150.0201.349
DA_edgeR0.3300.0040.334
DA_limma0.0900.0040.093
DA_metagenomeSeq0.2300.0040.235
RMSE0.0010.0000.001
addKnowledge0.1330.0040.137
areaCAT6.4920.1086.601
checkNormalization000
createColors0.0040.0000.004
createConcordance7.7030.0207.723
createEnrichment0.2110.0000.211
createMocks0.0000.0040.004
createPositives0.7410.0070.749
createSplits0.0360.0000.036
createTIEC1.6400.0041.644
enrichmentTest0.0750.0000.075
extractDA0.1770.0030.180
extractStatistics0.1830.0000.183
fitDM0.0290.0040.033
fitHURDLE0.4130.0360.449
fitModels1.3020.0081.310
fitNB0.0470.0020.048
fitZIG0.0560.0040.059
fitZINB0.5010.0020.503
getDA0.0690.0120.081
getPositives0.0690.0080.078
getStatistics0.0660.0060.072
iterative_ordering0.0080.0010.009
meanDifferences0.0020.0000.002
norm_CSS0.0680.0040.072
norm_DESeq20.4950.0000.495
norm_TSS0.0340.0000.034
norm_edgeR0.0380.0000.037
plotConcordance5.4100.0245.435
plotContingency0.9490.0000.949
plotEnrichment0.8190.0200.838
plotFPR1.3180.0081.325
plotKS1.2560.0041.260
plotMD2.2340.0122.246
plotMutualFindings0.8090.0000.809
plotPositives0.6030.0000.603
plotQQ1.3880.0081.396
plotRMSE1.6260.0001.627
prepareObserved0.0010.0000.002
runDA0.5140.0000.514
runMocks0.6420.0120.654
runNormalizations0.4890.0040.492
runSplits3.0120.0123.023
setNormalizations0.0010.0000.001
set_ALDEx20.0060.0000.006
set_DESeq20.0070.0000.006
set_MAST0.0060.0000.005
set_Seurat0.0060.0000.006
set_corncob0.0060.0000.005
set_edgeR0.0110.0000.011
set_limma0.0080.0000.008
set_metagenomeSeq0.0050.0000.006
weights_ZINB0.4210.0000.420