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This page was generated on 2024-03-04 11:39:27 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1155/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBECS 1.7.0  (landing page)
Michael Olbrich
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/MBECS
git_branch: devel
git_last_commit: 04afd60
git_last_commit_date: 2023-10-24 11:40:00 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for MBECS on merida1


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: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2024-03-02 06:15:57 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 06:25:46 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 588.8 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MBECS.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBECS/DESCRIPTION’ ... OK
* this is package ‘MBECS’ version ‘1.7.0’
* 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 R 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mbecModelVariance     12.069  0.129  14.537
mbecVarianceStatsPlot 10.513  0.094  12.172
mbecCorrection        10.037  0.191  12.162
mbecReportPost         7.144  0.061   8.306
mbecBox                5.921  0.233   7.256
percentileNorm         5.520  0.074   6.493
mbecBoxPlot            4.867  0.054   5.798
* 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-x86_64/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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")
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 
131.886   2.915 155.394 

Example timings

MBECS.Rcheck/MBECS-Ex.timings

nameusersystemelapsed
MbecData0.8030.0160.982
colinScore0.6980.0600.907
dot-mbecGetData0.0560.0090.079
dot-mbecGetPhyloseq0.0760.0110.101
dot-mbecSetData0.0870.0140.116
dummy.list0.0080.0030.013
dummy.mbec0.0390.0060.055
dummy.ps0.0070.0040.015
mbecBox5.9210.2337.256
mbecBoxPlot4.8670.0545.798
mbecCorrection10.037 0.19112.162
mbecDummy0.3110.0060.374
mbecGetData-MbecData-method0.0510.0070.070
mbecGetData0.0520.0060.072
mbecGetPhyloseq-MbecData-method0.0800.0050.107
mbecGetPhyloseq0.0750.0050.095
mbecHeat0.4080.0280.510
mbecHeatPlot0.3180.0100.398
mbecHelpFactor0.0080.0040.017
mbecLM2.0760.0292.458
mbecMixedVariance0.0780.0040.107
mbecModelVariance12.069 0.12914.537
mbecMosaic1.8700.0232.178
mbecMosaicPlot1.7170.0222.003
mbecPCA-MbecData-method1.9000.0302.229
mbecPCA1.9290.0272.239
mbecPCAPlot1.6760.0231.950
mbecPVCAStatsPlot2.2670.0262.654
mbecProcessInput-MbecData-method0.0410.0050.053
mbecProcessInput-list-method0.0410.0040.052
mbecProcessInput-phyloseq-method0.0590.0030.072
mbecProcessInput0.0420.0040.050
mbecRDAStatsPlot0.1900.0060.222
mbecRLE0.5300.0120.623
mbecRLEPlot0.2740.0080.321
mbecReportPost7.1440.0618.306
mbecReportPrelim3.5820.0304.108
mbecRunCorrections4.1360.0614.959
mbecSCOEFStatsPlot0.1090.0050.131
mbecSetData-MbecData-method0.0820.0080.110
mbecSetData0.0840.0070.113
mbecTestModel0.1260.0050.151
mbecTransform0.3590.0080.411
mbecValidateModel0.0590.0040.070
mbecVarianceStats0.0260.0030.035
mbecVarianceStatsPlot10.513 0.09412.172
percentileNorm5.5200.0746.493
poscore0.0000.0000.003