Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:13 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 MBECS on merida1


To the developers/maintainers of the MBECS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MBECS.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 1091/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBECS 1.0.0  (landing page)
Michael Olbrich
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MBECS
git_branch: RELEASE_3_15
git_last_commit: 748a3fb
git_last_commit_date: 2022-04-26 12:21:40 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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: MBECS
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBECS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBECS_1.0.0.tar.gz
StartedAt: 2022-10-19 04:15:39 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:24:44 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 545.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MBECS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MBECS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MBECS_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MBECS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ 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 ‘MBECS’ 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 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
mbecReportPost        95.820  0.369  96.359
mbecModelVariance     12.392  0.047  12.456
mbecVarianceStatsPlot 10.480  0.029  10.522
mbecCorrection         7.664  0.213   7.907
* 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

MBECS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MBECS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘MBECS’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MBECS)

Tests output

MBECS.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(MBECS)
> 
> test_check("MBECS")
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
No negative control features provided.
                Using pseudo-negative controls.
Applying Remove Unwanted Variantion v3 (RUV-III).
No 'sID' column present, creating from rownames now.
No 'sID' column present, creating from rownames now.
Set tss-transformed counts.
No 'sID' column present, creating from rownames now.
Set tss-transformed counts.
Construct lm-formula from covariates.
Construct lm-formula from covariates.
There is a problem with the estimatibility of your model.
            Check out covariate: 'sIDS40'
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Calculating RLE for group: A
Calculating RLE for group: B
Fitting linear model to every feature and extract proportion of
          variance explained by covariates.
Construct formula from covariates.

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Fitting linear-mixed model to every feature and extract proportion
            of variance explained by covariates.
Construct formula from covariates.

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boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
[1] "batch"
[1] "group"
Set tss-transformed counts.
Found zeros, function will add a small pseudo-count
                (1/#features) for log-ratio transformation.
Applying ComBat (sva) for batch-correction.
Found2batches
Adjusting for1covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding nonparametric adjustments
Adjusting the Data

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 265 ]
> 
> proc.time()
   user  system elapsed 
105.748   1.400 107.365 

Example timings

MBECS.Rcheck/MBECS-Ex.timings

nameusersystemelapsed
MbecData0.2430.0080.251
colinScore1.2130.0141.228
dot-mbecGetData0.0480.0040.052
dot-mbecGetPhyloseq0.0700.0030.073
dot-mbecSetData0.0770.0050.081
dummy.list0.0080.0020.010
dummy.mbec0.0400.0020.041
dummy.ps0.0080.0020.010
mbecBox3.7520.0773.834
mbecBoxPlot3.1600.0173.181
mbecCorrection7.6640.2137.907
mbecDummy0.2520.0260.279
mbecGetData-MbecData-method0.0500.0060.056
mbecGetData0.1560.0050.162
mbecGetPhyloseq-MbecData-method0.0770.0030.081
mbecGetPhyloseq0.0730.0040.077
mbecHeat0.3260.0080.335
mbecHeatPlot0.2660.0070.275
mbecLM1.8950.0511.948
mbecMixedVariance0.0730.0030.077
mbecModelVariance12.392 0.04712.456
mbecMosaic1.5400.0081.550
mbecMosaicPlot1.3640.0081.373
mbecPCA-MbecData-method1.6190.0161.637
mbecPCA1.5980.0121.613
mbecPCAPlot1.3780.0131.392
mbecPVCAStatsPlot2.1580.0132.176
mbecProcessInput-MbecData-method0.0420.0030.045
mbecProcessInput-list-method0.0420.0030.045
mbecProcessInput-phyloseq-method0.0550.0010.057
mbecProcessInput0.0430.0040.047
mbecRDAStatsPlot0.1700.0050.175
mbecRLE0.5230.0070.531
mbecRLEPlot0.2660.0040.271
mbecReportPost95.820 0.36996.359
mbecReportPrelim3.5090.0153.530
mbecRunCorrections3.3960.0443.450
mbecSCOEFStatsPlot0.1010.0040.106
mbecSetData-MbecData-method0.0790.0050.084
mbecSetData0.0790.0050.085
mbecTestModel0.0510.0030.054
mbecTransform0.3920.0050.397
mbecValidateModel0.0610.0030.064
mbecVarianceStats0.0320.0020.034
mbecVarianceStatsPlot10.480 0.02910.522
percentileNorm4.1660.0354.208
poscore0.0000.0000.001