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This page was generated on 2025-09-13 12:04 -0400 (Sat, 13 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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

Package 1192/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBECS 1.13.0  (landing page)
Michael Olbrich
Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 Sep 2025)
git_url: https://git.bioconductor.org/packages/MBECS
git_branch: devel
git_last_commit: b8d89b6
git_last_commit_date: 2025-04-15 12:46:50 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MBECS on lconway

To the developers/maintainers of the MBECS package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MBECS
Version: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-09-12 21:50:09 -0400 (Fri, 12 Sep 2025)
EndedAt: 2025-09-12 21:55:32 -0400 (Fri, 12 Sep 2025)
EllapsedTime: 323.5 seconds
RetCode: 0
Status:   OK  
CheckDir: MBECS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MBECS.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.13.0’
* 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 code 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dummy.ps.Rd: phyloseq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
mbecModelVariance     6.633  0.041   6.700
mbecCorrection        6.372  0.132   6.527
mbecVarianceStatsPlot 5.890  0.039   5.957
mbecBox               5.261  0.060   5.344
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/MBECS.Rcheck/00check.log’
for details.


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/4.5-x86_64/Resources/library’
* installing *source* package ‘MBECS’ ...
** this is package ‘MBECS’ version ‘1.13.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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")
Ignoring unknown labels:
* shape : "NA"
Ignoring unknown labels:
* shape : "NA"
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'
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.
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 110 | SKIP 0 | PASS 282 ]

[ FAIL 0 | WARN 110 | SKIP 0 | PASS 282 ]
> 
> proc.time()
   user  system elapsed 
 93.429   1.865  96.144 

Example timings

MBECS.Rcheck/MBECS-Ex.timings

nameusersystemelapsed
MbecData0.1110.0140.126
colinScore0.3750.0550.433
dot-mbecGetData0.0330.0040.038
dot-mbecGetPhyloseq0.0430.0050.049
dot-mbecSetData0.0720.0060.079
dummy.list0.0040.0010.005
dummy.mbec0.0260.0030.029
dummy.ps0.0050.0020.007
mbecBox5.2610.0605.344
mbecBoxPlot4.5590.0444.624
mbecCorrection6.3720.1326.527
mbecDummy0.1320.0020.136
mbecGetData-MbecData-method0.0340.0040.038
mbecGetData0.0320.0040.036
mbecGetPhyloseq-MbecData-method0.0500.0030.054
mbecGetPhyloseq0.0430.0030.047
mbecHeat0.2150.0100.227
mbecHeatPlot0.1480.0050.154
mbecHelpFactor0.0050.0020.008
mbecLM0.9260.0120.943
mbecMixedVariance0.0450.0030.048
mbecModelVariance6.6330.0416.700
mbecMosaic1.5180.0101.536
mbecMosaicPlot1.3980.0121.416
mbecPCA-MbecData-method1.6530.0181.678
mbecPCA1.5240.0121.541
mbecPCAPlot1.4650.0131.485
mbecPVCAStatsPlot1.2090.0151.227
mbecProcessInput-MbecData-method0.0280.0020.030
mbecProcessInput-list-method0.0270.0030.031
mbecProcessInput-phyloseq-method0.0360.0020.038
mbecProcessInput0.0250.0020.028
mbecRDAStatsPlot0.1750.0040.179
mbecRLE0.3910.0120.404
mbecRLEPlot0.2050.0050.211
mbecReportPost3.8380.0253.876
mbecReportPrelim1.9910.0162.019
mbecRunCorrections2.0210.0392.071
mbecSCOEFStatsPlot0.1900.0050.196
mbecSetData-MbecData-method0.0450.0040.050
mbecSetData0.0480.0050.055
mbecTestModel0.0330.0030.037
mbecTransform0.1510.0030.156
mbecValidateModel0.0310.0020.034
mbecVarianceStats0.0140.0010.016
mbecVarianceStatsPlot5.8900.0395.957
percentileNorm2.0550.0202.083
poscore000