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This page was generated on 2021-12-03 13:05:40 -0500 (Fri, 03 Dec 2021).

CHECK results for BiocGenerics on machv2

To the developers/maintainers of the BiocGenerics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocGenerics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 159/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.40.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/BiocGenerics
git_branch: RELEASE_3_14
git_last_commit: 0bc1e0e
git_last_commit_date: 2021-10-26 12:01:29 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BiocGenerics
Version: 0.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.40.0.tar.gz
StartedAt: 2021-12-02 12:07:21 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 12:08:39 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 78.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.40.0’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘graphics’ ‘stats’
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
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... WARNING
Missing link or links in documentation object 'as.data.frame.Rd':
  ‘[IRanges]{as.data.frame,IntegerRanges-method}’

Missing link or links in documentation object 'order.Rd':
  ‘[IRanges]{order,IntegerRanges-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'rep':
  ‘rep.int’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
plotMA  11.987  0.457  12.495
plotPCA  5.872  0.045   6.050
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.



Installation output

BiocGenerics.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocGenerics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BiocGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘union’ in package ‘BiocGenerics’
Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
Creating a new generic function for ‘basename’ in package ‘BiocGenerics’
Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’
** help
*** installing help indices
** building package indices
** 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 (BiocGenerics)

Tests output

BiocGenerics.Rcheck/tests/run_unitTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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.

> require("BiocGenerics") || stop("unable to load BiocGenerics package")
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, 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

[1] TRUE
> BiocGenerics:::.test()


RUNIT TEST PROTOCOL -- Thu Dec  2 12:08:22 2021 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocGenerics RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.099   0.090   1.166 

Example timings

BiocGenerics.Rcheck/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package0.0010.0020.003
Extremes0.0190.0040.022
IQR0.0020.0010.002
Ontology4.5700.1994.771
annotation0.0180.0020.020
append0.0030.0000.004
as.data.frame0.0040.0010.006
as.list0.0300.0040.033
as.vector0.0040.0010.005
boxplot0.1830.0160.199
cbind0.0280.0040.031
colSums0.0010.0010.002
combine0.0620.0260.147
dbconn0.0860.0090.096
density0.0020.0010.003
dims0.0550.0070.062
do.call0.0030.0010.004
duplicated0.0060.0020.009
eval0.0040.0020.005
evalq0.0000.0000.001
fileName4.0430.1194.173
funprog0.0070.0020.010
get0.0030.0010.004
grep0.0020.0000.002
image0.0340.0020.037
is.unsorted0.0030.0000.003
lapply0.0060.0010.007
mad0.0020.0010.003
mapply0.0020.0010.003
match0.0070.0020.009
mean0.0030.0010.004
normalize0.0390.0030.041
nrow0.0110.0020.013
order0.0030.0010.003
organism_species0.2620.0130.276
paste0.0040.0000.004
path0.0420.0070.050
plotMA11.987 0.45712.495
plotPCA5.8720.0456.050
rank0.0430.0010.044
relist0.0040.0010.005
rep0.0040.0010.005
residuals0.0010.0000.002
row_colnames0.0150.0030.019
score0.1410.0090.150
sets0.0130.0020.015
sort0.0040.0010.005
start0.0910.0090.099
strand0.1230.0080.131
subset0.0540.0040.058
t0.0100.0020.011
table0.0040.0020.006
tapply0.0020.0010.003
testPackage0.4360.0050.443
toTable0.1100.0050.115
type0.2250.0140.239
unique0.0030.0010.004
unlist0.0050.0010.006
unsplit0.0020.0000.003
updateObject0.3940.0080.403
var0.0020.0010.003
weights0.0020.0010.004
which0.1740.0090.183
which.min0.0730.0050.079
xtabs0.0460.0040.050