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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:48:14 -0400 (Wed, 17 Oct 2018).
| Package 1272/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RPA 1.36.0 Leo Lahti
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
############################################################################## ############################################################################## ### ### Running 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 ### ############################################################################## ############################################################################## * 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
RPA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RPA ### ############################################################################## ############################################################################## * 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)
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
RPA.Rcheck/RPA-Ex.timings
| name | user | system | elapsed | |
| RPA-package | 0.000 | 0.000 | 0.001 | |
| RPA.iteration | 0.001 | 0.000 | 0.001 | |
| RPA.preprocess | 0.001 | 0.000 | 0.001 | |
| collect.hyperparameters | 0.001 | 0.000 | 0.001 | |
| d.update.fast | 0.000 | 0.000 | 0.001 | |
| estimate.affinities | 0.001 | 0.000 | 0.000 | |
| estimate.hyperparameters | 0.001 | 0.000 | 0.001 | |
| frpa | 0.001 | 0.000 | 0.000 | |
| get.batches | 0.001 | 0.000 | 0.001 | |
| get.probe.matrix | 0.001 | 0.000 | 0.001 | |
| get.probe.parameters | 0.001 | 0.000 | 0.001 | |
| get.probeset | 0.001 | 0.000 | 0.001 | |
| hyperparameter.update | 0.002 | 0.000 | 0.002 | |
| online.quantile | 0.001 | 0.000 | 0.001 | |
| probe.parameters.tolist | 0.001 | 0.000 | 0.001 | |
| probe.performance | 0.001 | 0.000 | 0.001 | |
| probeplot | 0.001 | 0.000 | 0.001 | |
| probetable | 0.001 | 0.000 | 0.001 | |
| retrieve.probesets | 0 | 0 | 0 | |
| rpa | 0.001 | 0.000 | 0.001 | |
| rpa.complete | 0.001 | 0.000 | 0.001 | |
| rpa.fit | 0 | 0 | 0 | |
| rpa.online | 0.000 | 0.000 | 0.001 | |
| rpa.plot | 0.001 | 0.000 | 0.000 | |
| rpa.summarize | 0.001 | 0.000 | 0.001 | |
| rpaplot | 0.001 | 0.000 | 0.001 | |
| sample.probeset | 0.000 | 0.000 | 0.001 | |
| summarize.batch | 0.001 | 0.000 | 0.001 | |
| summarize.batches | 0.001 | 0.000 | 0.000 | |
| summarize_probedata | 0.001 | 0.000 | 0.002 | |
| updating.hyperparameters | 0.001 | 0.000 | 0.001 | |