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This page was generated on 2022-12-07 11:06:27 -0500 (Wed, 07 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4506
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4283
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4312
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 stageR on nebbiolo2


To the developers/maintainers of the stageR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/stageR.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 1969/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
stageR 1.20.0  (landing page)
Koen Van den Berge
Snapshot Date: 2022-12-06 14:00:04 -0500 (Tue, 06 Dec 2022)
git_url: https://git.bioconductor.org/packages/stageR
git_branch: RELEASE_3_16
git_last_commit: 1bb57ec
git_last_commit_date: 2022-11-01 11:16:38 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: stageR
Version: 1.20.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:stageR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings stageR_1.20.0.tar.gz
StartedAt: 2022-12-07 00:06:26 -0500 (Wed, 07 Dec 2022)
EndedAt: 2022-12-07 00:09:47 -0500 (Wed, 07 Dec 2022)
EllapsedTime: 200.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: stageR.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:stageR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings stageR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/stageR.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘stageR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stageR’ version ‘1.20.0’
* 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 : <anonymous>: 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}’

Documented arguments not in \usage in documentation object 'stageR':
  ‘...’

Documented arguments not in \usage in documentation object 'stageRTx':
  ‘...’

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 LazyData ... 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 ...
  ‘stageRVignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/stageR.Rcheck/00check.log’
for details.



Installation output

stageR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL stageR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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)

Tests output

stageR.Rcheck/tests/testthat.Rout


R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
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, aperm, 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: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'stageR'

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

    getMethod

> 
> test_check("stageR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  6.119   0.372   6.475 

Example timings

stageR.Rcheck/stageR-Ex.timings

nameusersystemelapsed
adjustedAlphaLevel0.0210.0030.025
getAdjustedPValues0.0200.0130.034
getAlpha0.0190.0040.023
getMethod0.0230.0000.023
getPConfirmation0.0000.0030.004
getPScreen0.0020.0010.002
getResults0.0200.0040.024
getSignificantGenes0.0400.0040.044
getSignificantTx0.0420.0040.047
getTx2gene0.0070.0120.019
isAdjusted0.0190.0040.023
isPScreenAdjusted0.0010.0000.001
stageR0.0020.0000.002
stageRTx0.0010.0000.001
stageWiseAdjustment0.0170.0080.025