Multiple platform build/check report for BioC 3.14 - CHECK results for BiocGenerics on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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*

Package: BiocGenerics

Version: 0.40.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocGenerics_0.40.0.tar.gz

StartedAt: 2022-04-12 16:15:56 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 16:17:49 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 113.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocGenerics_0.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
plotMA 8.17   1.22   10.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
plotMA 8.92   0.22    9.14
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocGenerics_0.40.0.tar.gz && rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocGenerics.buildbin-libdir BiocGenerics_0.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocGenerics_0.40.0.zip && rm BiocGenerics_0.40.0.tar.gz BiocGenerics_0.40.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 47390  100 47390    0     0   107k      0 --:--:-- --:--:-- --:--:--  107k

install for i386

* 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
  converting help for package 'BiocGenerics'
    finding HTML links ... done
    BiocGenerics-package                    html  
    Extremes                                html  
    IQR                                     html  
    Ontology                                html  
    S3-classes-as-S4-classes                html  
    annotation                              html  
    append                                  html  
    as.data.frame                           html  
    as.list                                 html  
    as.vector                               html  
    boxplot                                 html  
    cbind                                   html  
    colSums                                 html  
    combine                                 html  
    dbconn                                  html  
    density                                 html  
    dge                                     html  
    dims                                    html  
    do.call                                 html  
    duplicated                              html  
    eval                                    html  
    evalq                                   html  
    fileName                                html  
    funprog                                 html  
    get                                     html  
    grep                                    html  
    image                                   html  
    is.unsorted                             html  
    lapply                                  html  
    mad                                     html  
    mapply                                  html  
    match                                   html  
    mean                                    html  
    normalize                               html  
    nrow                                    html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.buildbin-libdir/00LOCK-BiocGenerics/00new/BiocGenerics/help/NROW.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.buildbin-libdir/00LOCK-BiocGenerics/00new/BiocGenerics/help/NCOL.html
    order                                   html  
    organism_species                        html  
    paste                                   html  
    path                                    html  
    plotMA                                  html  
    plotPCA                                 html  
    rank                                    html  
    relist                                  html  
    rep                                     html  
    residuals                               html  
    row_colnames                            html  
    score                                   html  
    sets                                    html  
    sort                                    html  
    start                                   html  
    strand                                  html  
    subset                                  html  
    t                                       html  
    table                                   html  
    tapply                                  html  
    testPackage                             html  
    toTable                                 html  
    type                                    html  
    unique                                  html  
    unlist                                  html  
    unsplit                                 html  
    updateObject                            html  
    var                                     html  
    weights                                 html  
    which                                   html  
    which.min                               html  
    xtabs                                   html  
** 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

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.40.0.zip
* DONE (BiocGenerics)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocGenerics' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> 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 -- Tue Apr 12 16:17:34 2022 
*********************************************** 
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 
   0.85    0.04    0.89


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> 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 -- Tue Apr 12 16:17:36 2022 
*********************************************** 
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 
   1.06    0.03    1.07

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.01	0.00	0.02
IQR	0	0	0
Ontology	3.18	0.28	3.45
annotation	0	0	0
append	0	0	0
as.data.frame	0.02	0.00	0.02
as.list	0.01	0.00	0.02
as.vector	0	0	0
boxplot	0.10	0.02	0.10
cbind	0.01	0.00	0.02
colSums	0	0	0
combine	0.05	0.00	0.05
dbconn	0.05	0.00	0.04
density	0	0	0
dims	0.03	0.00	0.04
do.call	0	0	0
duplicated	0.01	0.00	0.01
eval	0	0	0
evalq	0	0	0
fileName	2.61	0.12	2.74
funprog	0	0	0
get	0	0	0
grep	0	0	0
image	0.03	0.00	0.03
is.unsorted	0	0	0
lapply	0	0	0
mad	0	0	0
mapply	0	0	0
match	0.02	0.00	0.01
mean	0	0	0
normalize	0.02	0.00	0.02
nrow	0.01	0.00	0.01
order	0	0	0
organism_species	0.28	0.02	0.30
paste	0	0	0
path	0.05	0.00	0.05
plotMA	8.17	1.22	10.92
plotPCA	3.28	0.06	3.34
rank	0.05	0.00	0.05
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0.01	0.00	0.02
score	0.07	0.02	0.07
sets	0.01	0.00	0.02
sort	0	0	0
start	0.05	0.00	0.05
strand	0.05	0.03	0.07
subset	0.03	0.00	0.04
t	0	0	0
table	0.01	0.00	0.01
tapply	0	0	0
testPackage	0.44	0.00	0.50
toTable	0.09	0.01	0.11
type	0.18	0.03	0.20
unique	0.01	0.00	0.02
unlist	0	0	0
unsplit	0	0	0
updateObject	0.22	0.00	0.22
var	0	0	0
weights	0	0	0
which	0.09	0.02	0.11
which.min	0.05	0.00	0.05
xtabs	0.03	0.00	0.03

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.02	0.00	0.01
IQR	0	0	0
Ontology	3.41	0.13	3.53
annotation	0.03	0.00	0.03
append	0	0	0
as.data.frame	0.01	0.00	0.02
as.list	0.05	0.00	0.04
as.vector	0	0	0
boxplot	0.24	0.00	0.24
cbind	0.03	0.00	0.04
colSums	0	0	0
combine	0.08	0.00	0.07
dbconn	0.09	0.00	0.10
density	0	0	0
dims	0.05	0.00	0.04
do.call	0.02	0.00	0.02
duplicated	0	0	0
eval	0	0	0
evalq	0	0	0
fileName	2.78	0.15	2.94
funprog	0.01	0.00	0.01
get	0	0	0
grep	0	0	0
image	0.03	0.00	0.03
is.unsorted	0	0	0
lapply	0	0	0
mad	0	0	0
mapply	0	0	0
match	0	0	0
mean	0	0	0
normalize	0.02	0.00	0.02
nrow	0	0	0
order	0	0	0
organism_species	0.20	0.02	0.22
paste	0.02	0.00	0.02
path	0.06	0.00	0.06
plotMA	8.92	0.22	9.14
plotPCA	3.19	0.03	3.22
rank	0	0	0
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0.02	0.00	0.01
score	0.05	0.00	0.07
sets	0	0	0
sort	0	0	0
start	0.06	0.00	0.06
strand	0.06	0.00	0.06
subset	0.03	0.00	0.03
t	0	0	0
table	0	0	0
tapply	0	0	0
testPackage	0.28	0.02	0.30
toTable	0.05	0.01	0.06
type	0.13	0.00	0.13
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.17	0.00	0.18
var	0	0	0
weights	0	0	0
which	0.10	0.00	0.09
which.min	0.03	0.02	0.05
xtabs	0.01	0.00	0.01

CHECK results for BiocGenerics on tokay2

Summary

Command output

Installation output

Tests output

Example timings