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CHECK report for RPA on tokay1

This page was generated on 2021-05-06 12:33:20 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the RPA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1571/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RPA 1.46.0  (landing page)
Leo Lahti
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RPA
Branch: RELEASE_3_12
Last Commit: 2024292
Last Changed Date: 2020-10-27 10:36:05 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RPA
Version: 1.46.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RPA_1.46.0.tar.gz
StartedAt: 2021-05-06 06:25:14 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:29:03 -0400 (Thu, 06 May 2021)
EllapsedTime: 229.0 seconds
RetCode: 0
Status:   OK   
CheckDir: RPA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RPA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RPA_1.46.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RPA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RPA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RPA' version '1.46.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'rpa.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RPA_1.46.0.tar.gz && rm -rf RPA.buildbin-libdir && mkdir RPA.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RPA.buildbin-libdir RPA_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RPA_1.46.0.zip && rm RPA_1.46.0.tar.gz RPA_1.46.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  118k  100  118k    0     0  8317k      0 --:--:-- --:--:-- --:--:-- 9078k

install for i386

* installing *source* package 'RPA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RPA'
    finding HTML links ... done
    RPA-package                             html  
    RPA.iteration                           html  
    RPA.preprocess                          html  
    calculate.rpa                           html  
    collect.hyperparameters                 html  
    d.update.fast                           html  
    estimate.affinities                     html  
    estimate.hyperparameters                html  
    frpa                                    html  
    get.batches                             html  
    get.probe.matrix                        html  
    get.probe.parameters                    html  
    get.probeset                            html  
    hyperparameter.update                   html  
    levelmap                                html  
    n.phylotypes.per.oligo                  html  
    online.quantile                         html  
    probe.parameters.tolist                 html  
    probe.performance                       html  
    probeplot                               html  
    probetable                              html  
    retrieve.probesets                      html  
    rpa                                     html  
    rpa.complete                            html  
    rpa.fit                                 html  
    rpa.online                              html  
    rpa.plot                                html  
    rpa.summarize                           html  
    rpaplot                                 html  
    sample.probeset                         html  
    summarize.batch                         html  
    summarize.batches                       html  
    summarize.rpa                           html  
    summarize.sum                           html  
    summarize_probedata                     html  
    updating.hyperparameters                html  
** 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

install for x64

* installing *source* package 'RPA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RPA' as RPA_1.46.0.zip
* DONE (RPA)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RPA' successfully unpacked and MD5 sums checked

Tests output

RPA.Rcheck/tests_i386/rpa.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "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 
  17.15    1.03   18.31

RPA.Rcheck/tests_x64/rpa.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "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 
  16.34    0.48   16.95

Example timings

RPA.Rcheck/examples_i386/RPA-Ex.timings

nameusersystemelapsed
RPA-package000
RPA.iteration000
RPA.preprocess000
collect.hyperparameters000
d.update.fast000
estimate.affinities000
estimate.hyperparameters000
frpa000
get.batches000
get.probe.matrix000
get.probe.parameters000
get.probeset0.020.000.01
hyperparameter.update000
online.quantile000
probe.parameters.tolist000
probe.performance000
probeplot000
probetable000
retrieve.probesets000
rpa000
rpa.complete000
rpa.fit000
rpa.online000
rpa.plot000
rpa.summarize000
rpaplot000
sample.probeset000
summarize.batch000
summarize.batches000
summarize_probedata000
updating.hyperparameters000

RPA.Rcheck/examples_x64/RPA-Ex.timings

nameusersystemelapsed
RPA-package000
RPA.iteration000
RPA.preprocess000
collect.hyperparameters000
d.update.fast000
estimate.affinities000
estimate.hyperparameters000
frpa000
get.batches000
get.probe.matrix000
get.probe.parameters000
get.probeset000
hyperparameter.update000
online.quantile000
probe.parameters.tolist000
probe.performance000
probeplot000
probetable000
retrieve.probesets000
rpa000
rpa.complete000
rpa.fit000
rpa.online000
rpa.plot000
rpa.summarize000
rpaplot000
sample.probeset000
summarize.batch000
summarize.batches000
summarize_probedata000
updating.hyperparameters000