Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-18 12:03:59 -0400 (Mon, 18 Oct 2021).

CHECK results for BiocGenerics on riesling1

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.
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raw results

Package 158/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.39.2  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BiocGenerics
git_branch: master
git_last_commit: fbd9dbf
git_last_commit_date: 2021-08-18 02:27:52 -0400 (Wed, 18 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BiocGenerics
Version: 0.39.2
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocGenerics_0.39.2.tar.gz
StartedAt: 2021-10-18 00:00:25 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 00:02:16 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 111.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocGenerics.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings BiocGenerics_0.39.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '0.39.2'
* 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 5.92   0.16    6.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
plotMA 6.08   0.24    6.31
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.



Installation output

BiocGenerics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BiocGenerics_0.39.2.tar.gz && rm -rf BiocGenerics.buildbin-libdir && mkdir BiocGenerics.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocGenerics.buildbin-libdir BiocGenerics_0.39.2.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BiocGenerics_0.39.2.zip && rm BiocGenerics_0.39.2.tar.gz BiocGenerics_0.39.2.zip
###
##############################################################################
##############################################################################


  % 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 47454  100 47454    0     0   302k      0 --:--:-- --:--:-- --:--:--  302k

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: D:/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: D:/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_0.39.2.zip
* DONE (BiocGenerics)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BiocGenerics' successfully unpacked and MD5 sums checked

Tests output

BiocGenerics.Rcheck/tests_i386/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> 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 -- Mon Oct 18 00:01:21 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 
   0.56    0.01    0.57 

BiocGenerics.Rcheck/tests_x64/run_unitTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
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.

> 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 -- Mon Oct 18 00:01:21 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 
   0.53    0.04    0.56 

Example timings

BiocGenerics.Rcheck/examples_i386/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes000
IQR000
Ontology2.700.112.81
annotation0.020.000.02
append000
as.data.frame000
as.list0.030.000.03
as.vector000
boxplot0.140.000.14
cbind0.010.020.03
colSums000
combine0.050.000.05
dbconn0.060.000.06
density000
dims0.050.000.05
do.call000
duplicated000
eval000
evalq000
fileName2.500.152.66
funprog000
get0.010.000.01
grep000
image0.030.000.04
is.unsorted000
lapply0.020.000.01
mad000
mapply000
match000
mean000
normalize0.030.000.03
nrow000
order000
organism_species0.180.020.20
paste000
path0.030.000.03
plotMA5.920.166.08
plotPCA2.790.002.80
rank0.020.000.01
relist000
rep000
residuals000
row_colnames000
score0.080.010.10
sets000
sort0.010.000.01
start0.070.000.07
strand0.110.000.11
subset0.030.000.03
t000
table0.010.000.01
tapply000
testPackage0.310.020.33
toTable0.080.000.08
type0.100.030.12
unique000
unlist000
unsplit000
updateObject0.130.000.12
var000
weights000
which0.080.000.08
which.min0.030.000.03
xtabs0.010.000.02

BiocGenerics.Rcheck/examples_x64/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package000
Extremes000
IQR000
Ontology2.340.102.44
annotation0.020.000.01
append000
as.data.frame000
as.list0.010.000.02
as.vector0.020.000.02
boxplot0.080.010.09
cbind0.000.020.01
colSums000
combine0.040.000.05
dbconn0.000.030.03
density000
dims0.020.000.01
do.call000
duplicated0.010.000.02
eval000
evalq000
fileName2.020.112.12
funprog000
get0.010.000.02
grep000
image0.020.000.02
is.unsorted000
lapply000
mad000
mapply000
match000
mean000
normalize0.020.000.02
nrow0.020.000.01
order000
organism_species0.090.030.13
paste000
path0.010.000.02
plotMA6.080.246.31
plotPCA2.280.032.33
rank0.020.000.02
relist000
rep000
residuals000
row_colnames0.020.000.01
score0.030.020.05
sets0.010.000.01
sort000
start0.020.010.03
strand0.040.020.07
subset0.020.000.01
t0.020.000.02
table000
tapply000
testPackage0.170.000.17
toTable0.030.020.04
type0.060.030.10
unique000
unlist000
unsplit000
updateObject0.110.020.13
var000
weights000
which0.060.000.07
which.min0.050.000.04
xtabs0.020.000.02