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CHECK report for RPA on merida2

This page was generated on 2018-10-17 08:48:14 -0400 (Wed, 17 Oct 2018).

Package 1272/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.36.0
Leo Lahti
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RPA
Branch: RELEASE_3_7
Last Commit: 77777cd
Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RPA
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RPA_1.36.0.tar.gz
StartedAt: 2018-10-16 23:48:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:50:45 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 163.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RPA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RPA_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RPA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.36.0’
* 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/Versions/Current/Resources/bin/R CMD INSTALL RPA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RPA’ ...
** 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
* DONE (RPA)

Tests output

RPA.Rcheck/tests/rpa.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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/3.5/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
> library(RPA)

RPA Copyright (C) 2008-2017 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 
 19.058   0.695  20.626 

Example timings

RPA.Rcheck/RPA-Ex.timings

nameusersystemelapsed
RPA-package0.0000.0000.001
RPA.iteration0.0010.0000.001
RPA.preprocess0.0010.0000.001
collect.hyperparameters0.0010.0000.001
d.update.fast0.0000.0000.001
estimate.affinities0.0010.0000.000
estimate.hyperparameters0.0010.0000.001
frpa0.0010.0000.000
get.batches0.0010.0000.001
get.probe.matrix0.0010.0000.001
get.probe.parameters0.0010.0000.001
get.probeset0.0010.0000.001
hyperparameter.update0.0020.0000.002
online.quantile0.0010.0000.001
probe.parameters.tolist0.0010.0000.001
probe.performance0.0010.0000.001
probeplot0.0010.0000.001
probetable0.0010.0000.001
retrieve.probesets000
rpa0.0010.0000.001
rpa.complete0.0010.0000.001
rpa.fit000
rpa.online0.0000.0000.001
rpa.plot0.0010.0000.000
rpa.summarize0.0010.0000.001
rpaplot0.0010.0000.001
sample.probeset0.0000.0000.001
summarize.batch0.0010.0000.001
summarize.batches0.0010.0000.000
summarize_probedata0.0010.0000.002
updating.hyperparameters0.0010.0000.001