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This page was generated on 2024-07-18 11:38 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 1151/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBECS 1.9.0  (landing page)
Michael Olbrich
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/MBECS
git_branch: devel
git_last_commit: 7d5cdaa
git_last_commit_date: 2024-04-30 11:40:46 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2024-07-18 00:58:06 -0400 (Thu, 18 Jul 2024)
EndedAt: 2024-07-18 01:02:49 -0400 (Thu, 18 Jul 2024)
EllapsedTime: 282.5 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 4.4.1 (2024-06-14)
* 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 6.347   0.16   6.508
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 62.746   1.216  63.977 

Example timings

MBECS.Rcheck/MBECS-Ex.timings

nameusersystemelapsed
MbecData0.0950.0000.094
colinScore0.2670.0130.278
dot-mbecGetData0.0290.0040.034
dot-mbecGetPhyloseq0.0410.0000.041
dot-mbecSetData0.0390.0080.046
dummy.list0.0010.0030.005
dummy.mbec0.0250.0000.025
dummy.ps0.0050.0000.004
mbecBox2.410.102.51
mbecBoxPlot2.0200.0202.041
mbecCorrection6.3470.1606.508
mbecDummy0.0990.0000.099
mbecGetData-MbecData-method0.0260.0040.030
mbecGetData0.0290.0000.029
mbecGetPhyloseq-MbecData-method0.0420.0000.042
mbecGetPhyloseq0.0390.0000.038
mbecHeat0.1710.0200.191
mbecHeatPlot0.1270.0000.127
mbecHelpFactor0.0050.0000.005
mbecLM0.7710.0120.783
mbecMixedVariance0.0360.0000.037
mbecModelVariance4.6690.0324.701
mbecMosaic0.7940.0000.793
mbecMosaicPlot0.6800.0230.704
mbecPCA-MbecData-method0.7730.0120.785
mbecPCA0.7640.0000.765
mbecPCAPlot0.7160.0000.715
mbecPVCAStatsPlot0.8420.0080.850
mbecProcessInput-MbecData-method0.0250.0000.025
mbecProcessInput-list-method0.0250.0000.024
mbecProcessInput-phyloseq-method0.0350.0040.040
mbecProcessInput0.0250.0000.026
mbecRDAStatsPlot0.1540.0360.190
mbecRLE0.1860.0080.194
mbecRLEPlot0.1350.0080.144
mbecReportPost2.8670.0082.876
mbecReportPrelim1.4510.0121.463
mbecRunCorrections2.1040.0002.104
mbecSCOEFStatsPlot0.0560.0000.056
mbecSetData-MbecData-method0.0410.0000.041
mbecSetData0.0420.0000.041
mbecTestModel0.0310.0000.031
mbecTransform0.1640.0000.164
mbecValidateModel0.0260.0000.025
mbecVarianceStats0.0090.0040.012
mbecVarianceStatsPlot4.2050.0524.256
percentileNorm2.2810.0722.353
poscore0.0000.0000.001