Package: stageR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:stageR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings stageR_1.6.0.tar.gz

StartedAt: 2019-10-16 07:09:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:13:27 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 211.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: stageR.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:stageR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings stageR_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/stageR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stageR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stageR’ version ‘1.6.0’
* 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 ‘stageR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stageWiseTest : : warning in gsub(x = paste(namesList[ii],
  namesListElements[[ii]]), pattern = " ", replace = ":"): partial
  argument match of 'replace' to 'replacement'
.stageWiseTest: no visible global function definition for ‘p.adjust’
stageR: no visible global function definition for ‘new’
stageRTx: no visible global function definition for ‘new’
Undefined global functions or variables:
  new p.adjust
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "p.adjust")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'getAdjustedPValues.Rd':
  ‘stageWiseAdjustment,stageR,character,numeric-method’

Missing link or links in documentation object 'stageRClass.Rd':
  ‘getAdjustedPValues,stageR,logical,logical-method’
  ‘getResults,stageR-method’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘stageR’ ‘stageRTx’
Undocumented S4 methods:
  generic 'adjustedAlphaLevel' and siglist 'stageR'
  generic 'getAdjustedPValues' and siglist 'stageR,logical,logical'
  generic 'getAlpha' and siglist 'stageR'
  generic 'getMethod' and siglist 'stageR'
  generic 'getPConfirmation' and siglist 'stageR'
  generic 'getPScreen' and siglist 'stageR'
  generic 'getResults' and siglist 'stageR'
  generic 'getSignificantGenes' and siglist 'stageRTx'
  generic 'getSignificantTx' and siglist 'stageRTx'
  generic 'getTx2gene' and siglist 'stageRTx'
  generic 'isAdjusted' and siglist 'stageR'
  generic 'isPScreenAdjusted' and siglist 'stageR'
  generic 'stageWiseAdjustment' and siglist 'stageR,character,numeric'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'adjustedAlphaLevel'
  ‘...’
Objects in \usage without \alias in documentation object 'adjustedAlphaLevel':
  ‘\S4method{adjustedAlphaLevel}{stageR}’

Objects in \usage without \alias in documentation object 'getAdjustedPValues':
  ‘\S4method{getAdjustedPValues}{stageR,logical,logical}’

Objects in \usage without \alias in documentation object 'getAlpha':
  ‘\S4method{getAlpha}{stageR}’

Objects in \usage without \alias in documentation object 'getMethod':
  ‘\S4method{getMethod}{stageR}’

Undocumented arguments in documentation object 'getPConfirmation'
  ‘...’
Objects in \usage without \alias in documentation object 'getPConfirmation':
  ‘\S4method{getPConfirmation}{stageR}’

Objects in \usage without \alias in documentation object 'getPScreen':
  ‘\S4method{getPScreen}{stageR}’

Undocumented arguments in documentation object 'getResults'
  ‘...’
Objects in \usage without \alias in documentation object 'getResults':
  ‘\S4method{getResults}{stageR}’

Undocumented arguments in documentation object 'getSignificantGenes'
  ‘...’
Objects in \usage without \alias in documentation object 'getSignificantGenes':
  ‘\S4method{getSignificantGenes}{stageRTx}’

Undocumented arguments in documentation object 'getSignificantTx'
  ‘...’
Objects in \usage without \alias in documentation object 'getSignificantTx':
  ‘\S4method{getSignificantTx}{stageRTx}’

Objects in \usage without \alias in documentation object 'getTx2gene':
  ‘\S4method{getTx2gene}{stageRTx}’

Objects in \usage without \alias in documentation object 'isAdjusted':
  ‘\S4method{isAdjusted}{stageR}’

Objects in \usage without \alias in documentation object 'isPScreenAdjusted':
  ‘\S4method{isPScreenAdjusted}{stageR}’

Objects in \usage without \alias in documentation object 'stageWiseAdjustment':
  ‘\S4method{stageWiseAdjustment}{stageR,character,numeric}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/stageR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL stageR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘stageR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (stageR)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(testthat)
> library(stageR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum


Attaching package: 'stageR'

The following object is masked from 'package:methods':

    getMethod

> 
> test_check("stageR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.149   0.904  11.675 

name	user	system	elapsed
adjustedAlphaLevel	0.064	0.001	0.065
getAdjustedPValues	0.084	0.001	0.089
getAlpha	0.056	0.003	0.067
getMethod	0.062	0.006	0.069
getPConfirmation	0.011	0.009	0.022
getPScreen	0.009	0.007	0.016
getResults	0.060	0.005	0.069
getSignificantGenes	0.120	0.009	0.134
getSignificantTx	0.108	0.004	0.114
getTx2gene	0.053	0.025	0.078
isAdjusted	0.050	0.002	0.054
isPScreenAdjusted	0.002	0.001	0.003
stageR	0.004	0.001	0.005
stageRTx	0.003	0.001	0.003
stageWiseAdjustment	0.063	0.006	0.069