Multiple platform build/check report for BioC 3.20 - CHECK results for MBECS on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 kjohnson3

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: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2024-11-09 06:21:21 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 06:26:17 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 295.9 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MBECS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... 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
* 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: 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/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
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.

  |                                                                                      
  |                                                                                |   0%
  |                                                                                      
  |====                                                                            |   5%
  |                                                                                      
  |========                                                                        |  10%
  |                                                                                      
  |============                                                                    |  15%
  |                                                                                      
  |================                                                                |  20%
  |                                                                                      
  |====================                                                            |  25%
  |                                                                                      
  |========================                                                        |  30%
  |                                                                                      
  |============================                                                    |  35%
  |                                                                                      
  |================================                                                |  40%
  |                                                                                      
  |====================================                                            |  45%
  |                                                                                      
  |========================================                                        |  50%
  |                                                                                      
  |============================================                                    |  55%
  |                                                                                      
  |================================================                                |  60%
  |                                                                                      
  |====================================================                            |  65%
  |                                                                                      
  |========================================================                        |  70%
  |                                                                                      
  |============================================================                    |  75%
  |                                                                                      
  |================================================================                |  80%
  |                                                                                      
  |====================================================================            |  85%
  |                                                                                      
  |========================================================================        |  90%
  |                                                                                      
  |============================================================================    |  95%
  |                                                                                      
  |================================================================================| 100%
Fitting linear-mixed model to every feature and extract proportion
            of variance explained by covariates.
Construct formula from covariates.

  |                                                                                      
  |                                                                                |   0%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |====                                                                            |   5%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |========                                                                        |  10%
  |                                                                                      
  |============                                                                    |  15%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |================                                                                |  20%
  |                                                                                      
  |====================                                                            |  25%
  |                                                                                      
  |========================                                                        |  30%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |============================                                                    |  35%
  |                                                                                      
  |================================                                                |  40%
  |                                                                                      
  |====================================                                            |  45%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |========================================                                        |  50%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |============================================                                    |  55%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |================================================                                |  60%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |====================================================                            |  65%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |========================================================                        |  70%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |============================================================                    |  75%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |================================================================                |  80%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |====================================================================            |  85%
  |                                                                                      
  |========================================================================        |  90%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |============================================================================    |  95%boundary (singular) fit: see help('isSingular')

  |                                                                                      
  |================================================================================| 100%

  |                                                                                      
  |                                                                                |   0%
  |                                                                                      
  |========================================                                        |  50%
  |                                                                                      
  |================================================================================| 100%
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 101 | SKIP 0 | PASS 282 ]

[ FAIL 0 | WARN 101 | SKIP 0 | PASS 282 ]
> 
> proc.time()
   user  system elapsed 
 17.493   0.356  17.850

Example timings

MBECS.Rcheck/MBECS-Ex.timings

name	user	system	elapsed
MbecData	0.025	0.002	0.027
colinScore	0.083	0.004	0.087
dot-mbecGetData	0.011	0.001	0.013
dot-mbecGetPhyloseq	0.014	0.001	0.014
dot-mbecSetData	0.016	0.001	0.017
dummy.list	0.002	0.001	0.002
dummy.mbec	0.009	0.000	0.010
dummy.ps	0.001	0.001	0.002
mbecBox	0.628	0.013	0.641
mbecBoxPlot	0.496	0.001	0.497
mbecCorrection	2.003	0.023	2.025
mbecDummy	0.031	0.001	0.032
mbecGetData-MbecData-method	0.011	0.000	0.012
mbecGetData	0.011	0.000	0.011
mbecGetPhyloseq-MbecData-method	0.014	0.001	0.015
mbecGetPhyloseq	0.013	0.000	0.014
mbecHeat	0.054	0.002	0.056
mbecHeatPlot	0.038	0.001	0.039
mbecHelpFactor	0.002	0.001	0.003
mbecLM	0.191	0.001	0.192
mbecMixedVariance	0.011	0.001	0.011
mbecModelVariance	1.158	0.004	1.163
mbecMosaic	0.208	0.001	0.210
mbecMosaicPlot	0.181	0.002	0.182
mbecPCA-MbecData-method	0.209	0.003	0.212
mbecPCA	0.216	0.002	0.218
mbecPCAPlot	0.200	0.003	0.204
mbecPVCAStatsPlot	0.247	0.003	0.250
mbecProcessInput-MbecData-method	0.011	0.001	0.012
mbecProcessInput-list-method	0.010	0.001	0.012
mbecProcessInput-phyloseq-method	0.009	0.000	0.009
mbecProcessInput	0.010	0.001	0.011
mbecRDAStatsPlot	0.033	0.002	0.035
mbecRLE	0.069	0.003	0.072
mbecRLEPlot	0.037	0.002	0.039
mbecReportPost	0.793	0.005	0.797
mbecReportPrelim	0.395	0.003	0.397
mbecRunCorrections	0.645	0.036	0.680
mbecSCOEFStatsPlot	0.034	0.001	0.036
mbecSetData-MbecData-method	0.019	0.002	0.020
mbecSetData	0.017	0.001	0.017
mbecTestModel	0.012	0.001	0.013
mbecTransform	0.043	0.002	0.044
mbecValidateModel	0.008	0.001	0.009
mbecVarianceStats	0.004	0.001	0.005
mbecVarianceStatsPlot	1.138	0.008	1.146
percentileNorm	0.755	0.014	0.767
poscore	0	0	0