Multiple platform build/check report for BioC 3.21 - CHECK results for MBECS on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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 nebbiolo1

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: 1.11.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MBECS_1.11.0.tar.gz

StartedAt: 2024-12-23 23:29:18 -0500 (Mon, 23 Dec 2024)

EndedAt: 2024-12-23 23:33:45 -0500 (Mon, 23 Dec 2024)

EllapsedTime: 267.3 seconds

RetCode: 0

Status: OK

CheckDir: MBECS.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MBECS_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MBECS.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.11.0’
* 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 ... 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
mbecCorrection 5.684  0.176    5.86
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/MBECS.Rcheck/00check.log’
for details.

Installation output

MBECS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL MBECS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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 
 58.303   1.031  59.328

Example timings

MBECS.Rcheck/MBECS-Ex.timings

name	user	system	elapsed
MbecData	0.091	0.000	0.092
colinScore	0.242	0.023	0.266
dot-mbecGetData	0.028	0.005	0.032
dot-mbecGetPhyloseq	0.035	0.006	0.042
dot-mbecSetData	0.045	0.001	0.047
dummy.list	0.002	0.002	0.005
dummy.mbec	0.023	0.000	0.024
dummy.ps	0.004	0.001	0.004
mbecBox	2.463	0.074	2.538
mbecBoxPlot	2.044	0.026	2.070
mbecCorrection	5.684	0.176	5.860
mbecDummy	0.105	0.001	0.106
mbecGetData-MbecData-method	0.029	0.001	0.030
mbecGetData	0.026	0.003	0.030
mbecGetPhyloseq-MbecData-method	0.043	0.000	0.043
mbecGetPhyloseq	0.041	0.001	0.041
mbecHeat	0.175	0.002	0.178
mbecHeatPlot	0.125	0.001	0.126
mbecHelpFactor	0.004	0.001	0.005
mbecLM	0.748	0.000	0.748
mbecMixedVariance	0.035	0.000	0.035
mbecModelVariance	4.933	0.036	4.970
mbecMosaic	0.805	0.033	0.839
mbecMosaicPlot	0.704	0.016	0.721
mbecPCA-MbecData-method	0.770	0.001	0.771
mbecPCA	0.782	0.000	0.783
mbecPCAPlot	0.729	0.004	0.733
mbecPVCAStatsPlot	0.993	0.023	1.015
mbecProcessInput-MbecData-method	0.024	0.002	0.026
mbecProcessInput-list-method	0.024	0.001	0.025
mbecProcessInput-phyloseq-method	0.028	0.001	0.030
mbecProcessInput	0.024	0.001	0.026
mbecRDAStatsPlot	0.094	0.002	0.096
mbecRLE	0.189	0.013	0.201
mbecRLEPlot	0.133	0.002	0.134
mbecReportPost	2.890	0.010	2.901
mbecReportPrelim	1.486	0.004	1.491
mbecRunCorrections	1.907	0.008	1.916
mbecSCOEFStatsPlot	0.058	0.000	0.060
mbecSetData-MbecData-method	0.041	0.001	0.043
mbecSetData	0.087	0.000	0.087
mbecTestModel	0.030	0.000	0.031
mbecTransform	0.125	0.000	0.125
mbecValidateModel	0.025	0.000	0.026
mbecVarianceStats	0.012	0.000	0.012
mbecVarianceStatsPlot	4.253	0.040	4.293
percentileNorm	2.104	0.063	2.167
poscore	0	0	0