Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:05 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 RPA on merida1


To the developers/maintainers of the RPA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RPA.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 1695/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.52.0  (landing page)
Leo Lahti
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/RPA
git_branch: RELEASE_3_15
git_last_commit: feedfed
git_last_commit_date: 2022-04-26 11:03:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: RPA
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RPA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RPA_1.52.0.tar.gz
StartedAt: 2022-06-24 07:57:15 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 08:02:43 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 328.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RPA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RPA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RPA_1.52.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RPA.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RPA’ version ‘1.52.0’
* 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 ‘RPA’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘rpa.R’
 OK
* 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: OK


Installation output

RPA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RPA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘RPA’ ...
** using staged installation
** R
** 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 (RPA)

Tests output

RPA.Rcheck/tests/rpa.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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(affy)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> library(affydata)
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/4.2/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
> library(RPA)
Loading required package: BiocStyle
Loading required package: rmarkdown

Attaching package: 'rmarkdown'

The following objects are masked from 'package:BiocStyle':

    html_document, md_document, pdf_document


RPA Copyright (C) 2008-2021 Leo Lahti. See http://microbiome.github.io/

> data(Dilution)
> eset <- rpa(Dilution)
Preprocessing affybatch...
Background correcting...

Normalizing...
Logging PM values...
Retrieving probe positions..
...
Preprocessing completed.
Setting quantile basis
Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> 
> proc.time()
   user  system elapsed 
 33.495   0.999  46.545 

Example timings

RPA.Rcheck/RPA-Ex.timings

nameusersystemelapsed
RPA-package000
RPA.iteration000
RPA.preprocess0.0010.0000.001
collect.hyperparameters000
d.update.fast0.0000.0010.000
estimate.affinities000
estimate.hyperparameters000
frpa0.0000.0000.001
get.batches000
get.probe.matrix000
get.probe.parameters000
get.probeset0.0010.0010.001
hyperparameter.update0.0010.0000.000
online.quantile0.0010.0000.000
probe.parameters.tolist000
probe.performance0.0000.0000.001
probeplot000
probetable0.0000.0000.001
retrieve.probesets000
rpa0.0000.0000.001
rpa.complete000
rpa.fit000
rpa.online0.0000.0010.000
rpa.plot000
rpa.summarize000
rpaplot000
sample.probeset000
summarize.batch0.0000.0000.006
summarize.batches000
summarize_probedata000
updating.hyperparameters000