Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:39 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 MultiBaC on nebbiolo2


To the developers/maintainers of the MultiBaC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MultiBaC.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1239/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiBaC 1.4.0  (landing page)
Manuel Ugidos
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MultiBaC
git_branch: RELEASE_3_14
git_last_commit: cfad776
git_last_commit_date: 2021-10-26 13:01:04 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MultiBaC
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MultiBaC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MultiBaC_1.4.0.tar.gz
StartedAt: 2022-04-12 08:23:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:25:35 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 126.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MultiBaC.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MultiBaC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MultiBaC_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MultiBaC.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiBaC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiBaC’ version ‘1.4.0’
* 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 ‘MultiBaC’ 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 ... NOTE
Q2_plot: no visible global function definition for ‘rgb’
explained_varPlot: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  rgb
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'ARSyNbac':
ARSyNbac
  Code: function(mbac, batchEstimation = TRUE, filterNoise = TRUE,
                 Interaction = FALSE, Variability = 0.9, beta = 2,
                 modelName = "Model 1", showplot = TRUE)
  Docs: function(mbac, batchEstimation = TRUE, Interaction = FALSE,
                 Variability = 0.9, beta = 2, modelName = "Model 1",
                 showplot = TRUE)
  Argument names in code not in docs:
    filterNoise
  Mismatches in argument names (first 3):
    Position: 3 Code: filterNoise Docs: Interaction
    Position: 4 Code: Interaction Docs: Variability
    Position: 5 Code: Variability Docs: beta

* 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
MultiBaC          11.948  0.176  12.124
Q2_plot           11.279  0.151  11.431
explained_varPlot 11.046  0.096  11.142
batchCorrection   11.054  0.087  11.142
inner_relPlot     10.865  0.060  10.925
plot              10.627  0.056  10.684
plot_pca          10.654  0.016  10.671
ARSyNbac           8.781  0.395   9.177
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/MultiBaC.Rcheck/00check.log’
for details.



Installation output

MultiBaC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL MultiBaC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘MultiBaC’ ...
** using staged installation
** R
** data
** 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 (MultiBaC)

Tests output


Example timings

MultiBaC.Rcheck/MultiBaC-Ex.timings

nameusersystemelapsed
ARSyNbac8.7810.3959.177
MultiBaC11.948 0.17612.124
Q2_plot11.279 0.15111.431
batchCorrection11.054 0.08711.142
batchEstPlot0.7300.0160.745
createMbac0.370.000.37
explained_varPlot11.046 0.09611.142
genMissingOmics0.9650.0040.969
genModelList0.5840.0000.584
inner_relPlot10.865 0.06010.925
multiyeast0.0020.0000.002
plot10.627 0.05610.684
plot_pca10.654 0.01610.671
summary0.3590.0040.364