Multiple platform build/check report for BioC 3.9 - CHECK report for BiocGenerics on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocGenerics_0.30.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.30.0’
* 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’ ‘parallel’
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 ... WARNING
Codoc mismatches from documentation object 'clusterApply':
parLapply
  Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, fun, ...)
  Argument names in code not in docs:
    chunk.size
parSapply
  Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE, chunk.size = NULL)
  Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE)
  Argument names in code not in docs:
    chunk.size
parApply
  Code: function(cl = NULL, X, MARGIN, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, MARGIN, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parRapply
  Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, x, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parCapply
  Code: function(cl = NULL, x, FUN, ..., chunk.size = NULL)
  Docs: function(cl = NULL, x, FUN, ...)
  Argument names in code not in docs:
    chunk.size
parLapplyLB
  Code: function(cl = NULL, X, fun, ..., chunk.size = NULL)
  Docs: function(cl = NULL, X, fun, ...)
  Argument names in code not in docs:
    chunk.size
parSapplyLB
  Code: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE, chunk.size = NULL)
  Docs: function(cl = NULL, X, FUN, ..., simplify = TRUE, USE.NAMES =
                 TRUE)
  Argument names in code not in docs:
    chunk.size

Codoc mismatches from documentation object 'matrix-summary':
colSums
  Code: function(x, na.rm = FALSE, dims = 1, ...)
  Docs: function(x, na.rm = FALSE, dims = 1)
  Argument names in code not in docs:
    ...
rowSums
  Code: function(x, na.rm = FALSE, dims = 1, ...)
  Docs: function(x, na.rm = FALSE, dims = 1)
  Argument names in code not in docs:
    ...
colMeans
  Code: function(x, na.rm = FALSE, dims = 1, ...)
  Docs: function(x, na.rm = FALSE, dims = 1)
  Argument names in code not in docs:
    ...
rowMeans
  Code: function(x, na.rm = FALSE, dims = 1, ...)
  Docs: function(x, na.rm = FALSE, dims = 1)
  Argument names in code not in docs:
    ...

* 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 or elapsed time > 5s
       user system elapsed
plotMA 8.73  0.321   9.099
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocGenerics
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ 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 ‘clusterCall’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapplyLB’ 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


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.

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

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


RUNIT TEST PROTOCOL -- Wed Oct 16 00:05:38 2019 
*********************************************** 
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 
  1.107   0.037   1.130

Example timings

name	user	system	elapsed
BiocGenerics-package	0.001	0.000	0.001
Extremes	0.01	0.00	0.01
IQR	0.002	0.000	0.002
Ontology	3.001	0.119	3.165
annotation	0.014	0.001	0.015
append	0.003	0.000	0.003
as.data.frame	0.003	0.000	0.004
as.vector	0.002	0.000	0.003
boxplot	0.001	0.000	0.001
cbind	0.006	0.000	0.005
clusterApply	0.098	0.004	0.103
combine	0.078	0.003	0.083
dbconn	0.068	0.000	0.068
density	0.002	0.000	0.002
dims	0.014	0.000	0.014
do.call	0.001	0.001	0.002
duplicated	0.199	0.006	0.207
eval	0.003	0.000	0.002
evalq	0.001	0.000	0.000
fileName	2.791	0.088	2.891
funprog	0.008	0.000	0.008
get	0.003	0.000	0.003
grep	0.001	0.000	0.001
image	0.002	0.000	0.002
is.unsorted	0.002	0.000	0.002
lapply	0.004	0.000	0.004
mad	0.002	0.000	0.002
mapply	0.002	0.000	0.002
match	0.002	0.000	0.003
matrix-summary	0.002	0.000	0.002
mean	0.002	0.000	0.002
normalize	0.025	0.000	0.025
nrow	0.008	0.000	0.008
order	0.003	0.000	0.003
organism_species	0.353	0.008	0.361
paste	0.003	0.000	0.003
path	0.054	0.000	0.054
plotMA	8.730	0.321	9.099
plotPCA	3.643	0.017	3.660
rank	0.012	0.000	0.013
relist	0.002	0.001	0.002
rep	0.002	0.000	0.002
residuals	0.002	0.000	0.002
row_colnames	0.009	0.000	0.009
score	0.065	0.000	0.065
sets	0.008	0.000	0.009
sort	0.002	0.000	0.002
start	0.06	0.00	0.06
strand	0.074	0.003	0.078
subset	0.025	0.000	0.025
t	0.005	0.000	0.005
table	0.001	0.000	0.001
tapply	0.002	0.000	0.002
testPackage	0.427	0.000	0.472
toTable	0.058	0.000	0.057
unique	0.002	0.000	0.003
unlist	0.003	0.000	0.003
unsplit	0.001	0.000	0.002
updateObject	0.273	0.000	0.274
var	0.003	0.000	0.003
weights	0.002	0.000	0.001
which	0.008	0.000	0.009
xtabs	0.002	0.000	0.002

CHECK report for BiocGenerics on malbec2

Summary

Command output

Installation output

Tests output

Example timings