Michael Olbrich
| Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1204/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MBECS 1.13.0 (landing page) Michael Olbrich
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: MBECS |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MBECS_1.13.0.tar.gz |
| StartedAt: 2025-10-17 10:42:18 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 10:48:17 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 358.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MBECS.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:MBECS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MBECS_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MBECS.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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
mbecModelVariance 7.541 0.064 7.633
mbecBox 6.471 0.829 7.325
mbecCorrection 6.939 0.259 7.221
mbecVarianceStatsPlot 6.604 0.068 6.696
mbecBoxPlot 5.456 0.171 5.648
* 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
‘/home/biocbuild/bbs-3.22-bioc/meat/MBECS.Rcheck/00check.log’
for details.
MBECS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MBECS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-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)
MBECS.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
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')
[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
107.335 1.283 108.959
MBECS.Rcheck/MBECS-Ex.timings
| name | user | system | elapsed | |
| MbecData | 0.107 | 0.032 | 0.141 | |
| colinScore | 0.405 | 0.068 | 0.475 | |
| dot-mbecGetData | 0.033 | 0.004 | 0.037 | |
| dot-mbecGetPhyloseq | 0.051 | 0.000 | 0.051 | |
| dot-mbecSetData | 0.083 | 0.032 | 0.115 | |
| dummy.list | 0.005 | 0.000 | 0.006 | |
| dummy.mbec | 0.025 | 0.000 | 0.025 | |
| dummy.ps | 0.005 | 0.000 | 0.005 | |
| mbecBox | 6.471 | 0.829 | 7.325 | |
| mbecBoxPlot | 5.456 | 0.171 | 5.648 | |
| mbecCorrection | 6.939 | 0.259 | 7.221 | |
| mbecDummy | 0.171 | 0.012 | 0.183 | |
| mbecGetData-MbecData-method | 0.030 | 0.004 | 0.035 | |
| mbecGetData | 0.034 | 0.000 | 0.035 | |
| mbecGetPhyloseq-MbecData-method | 0.046 | 0.008 | 0.054 | |
| mbecGetPhyloseq | 0.048 | 0.000 | 0.048 | |
| mbecHeat | 0.277 | 0.008 | 0.285 | |
| mbecHeatPlot | 0.194 | 0.004 | 0.199 | |
| mbecHelpFactor | 0.002 | 0.004 | 0.006 | |
| mbecLM | 1.198 | 0.000 | 1.203 | |
| mbecMixedVariance | 0.049 | 0.000 | 0.048 | |
| mbecModelVariance | 7.541 | 0.064 | 7.633 | |
| mbecMosaic | 1.758 | 0.004 | 1.768 | |
| mbecMosaicPlot | 1.691 | 0.004 | 1.701 | |
| mbecPCA-MbecData-method | 1.925 | 0.004 | 1.937 | |
| mbecPCA | 1.880 | 0.000 | 1.887 | |
| mbecPCAPlot | 1.751 | 0.020 | 1.777 | |
| mbecPVCAStatsPlot | 1.493 | 0.016 | 1.515 | |
| mbecProcessInput-MbecData-method | 0.027 | 0.000 | 0.028 | |
| mbecProcessInput-list-method | 0.027 | 0.000 | 0.027 | |
| mbecProcessInput-phyloseq-method | 0.030 | 0.008 | 0.038 | |
| mbecProcessInput | 0.024 | 0.004 | 0.027 | |
| mbecRDAStatsPlot | 0.194 | 0.008 | 0.202 | |
| mbecRLE | 0.487 | 0.004 | 0.492 | |
| mbecRLEPlot | 0.253 | 0.000 | 0.254 | |
| mbecReportPost | 4.518 | 0.091 | 4.627 | |
| mbecReportPrelim | 2.274 | 0.000 | 2.282 | |
| mbecRunCorrections | 2.500 | 0.052 | 2.561 | |
| mbecSCOEFStatsPlot | 0.223 | 0.000 | 0.225 | |
| mbecSetData-MbecData-method | 0.052 | 0.000 | 0.052 | |
| mbecSetData | 0.052 | 0.000 | 0.052 | |
| mbecTestModel | 0.035 | 0.000 | 0.036 | |
| mbecTransform | 0.188 | 0.000 | 0.190 | |
| mbecValidateModel | 0.038 | 0.000 | 0.038 | |
| mbecVarianceStats | 0.016 | 0.000 | 0.016 | |
| mbecVarianceStatsPlot | 6.604 | 0.068 | 6.696 | |
| percentileNorm | 3.440 | 0.072 | 3.524 | |
| poscore | 0 | 0 | 0 | |