Multiple platform build/check report for BioC 3.20 - CHECK results for MBECS on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4685
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4400
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4349
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 nebbiolo2

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: 1.9.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MBECS_1.9.0.tar.gz

StartedAt: 2024-06-15 00:30:49 -0400 (Sat, 15 Jun 2024)

EndedAt: 2024-06-15 00:35:20 -0400 (Sat, 15 Jun 2024)

EllapsedTime: 270.5 seconds

RetCode: 0

Status: OK

CheckDir: MBECS.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MBECS_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MBECS.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.9.0’
* 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 loading without being on the library search path ... 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
mbecCorrection 5.642  0.148   5.791
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

MBECS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MBECS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

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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 101 | SKIP 0 | PASS 282 ]

[ FAIL 0 | WARN 101 | SKIP 0 | PASS 282 ]
> 
> proc.time()
   user  system elapsed 
 56.543   1.085  57.625

Example timings

MBECS.Rcheck/MBECS-Ex.timings

name	user	system	elapsed
MbecData	0.100	0.001	0.100
colinScore	0.263	0.009	0.271
dot-mbecGetData	0.028	0.005	0.033
dot-mbecGetPhyloseq	0.041	0.000	0.042
dot-mbecSetData	0.042	0.003	0.046
dummy.list	0.005	0.001	0.005
dummy.mbec	0.025	0.003	0.028
dummy.ps	0.005	0.000	0.005
mbecBox	2.361	0.105	2.464
mbecBoxPlot	1.888	0.051	1.941
mbecCorrection	5.642	0.148	5.791
mbecDummy	0.1	0.0	0.1
mbecGetData-MbecData-method	0.028	0.009	0.036
mbecGetData	0.03	0.00	0.03
mbecGetPhyloseq-MbecData-method	0.045	0.000	0.045
mbecGetPhyloseq	0.04	0.00	0.04
mbecHeat	0.190	0.007	0.198
mbecHeatPlot	0.114	0.012	0.126
mbecHelpFactor	0.005	0.000	0.005
mbecLM	0.746	0.012	0.758
mbecMixedVariance	0.036	0.000	0.036
mbecModelVariance	4.568	0.096	4.665
mbecMosaic	0.752	0.008	0.761
mbecMosaicPlot	0.686	0.020	0.705
mbecPCA-MbecData-method	0.768	0.044	0.811
mbecPCA	0.770	0.004	0.774
mbecPCAPlot	0.726	0.016	0.742
mbecPVCAStatsPlot	0.863	0.000	0.863
mbecProcessInput-MbecData-method	0.025	0.000	0.025
mbecProcessInput-list-method	0.025	0.000	0.025
mbecProcessInput-phyloseq-method	0.023	0.004	0.028
mbecProcessInput	0.025	0.000	0.025
mbecRDAStatsPlot	0.177	0.000	0.177
mbecRLE	0.192	0.004	0.195
mbecRLEPlot	0.144	0.004	0.148
mbecReportPost	2.991	0.044	3.035
mbecReportPrelim	1.490	0.016	1.506
mbecRunCorrections	2.031	0.004	2.035
mbecSCOEFStatsPlot	0.062	0.000	0.062
mbecSetData-MbecData-method	0.039	0.004	0.042
mbecSetData	0.080	0.012	0.092
mbecTestModel	0.033	0.000	0.032
mbecTransform	0.124	0.000	0.123
mbecValidateModel	0.023	0.004	0.027
mbecVarianceStats	0.010	0.004	0.014
mbecVarianceStatsPlot	4.288	0.036	4.325
percentileNorm	2.017	0.112	2.128
poscore	0	0	0