Package: BiocGenerics

Version: 0.26.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiocGenerics_0.26.0.tar.gz

StartedAt: 2018-10-15 22:46:19 -0400 (Mon, 15 Oct 2018)

EndedAt: 2018-10-15 22:47:03 -0400 (Mon, 15 Oct 2018)

EllapsedTime: 44.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BiocGenerics_0.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘0.26.0’
* 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

* 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 5.32  0.264   5.634
* 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-3.7-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BiocGenerics
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BiocGenerics’ ...
** 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 ‘lengths’ 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 ‘rowSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘colSums’ in package ‘BiocGenerics’
Creating a new generic function for ‘rowMeans’ in package ‘BiocGenerics’
Creating a new generic function for ‘colMeans’ 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
* DONE (BiocGenerics)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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


RUNIT TEST PROTOCOL -- Mon Oct 15 22:46:58 2018 
*********************************************** 
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 
  0.760   0.016   0.771 

name	user	system	elapsed
BiocGenerics-package	0.000	0.000	0.001
Extremes	0.008	0.000	0.008
IQR	0.000	0.000	0.001
Ontology	1.728	0.052	1.782
annotation	0.008	0.000	0.010
append	0.000	0.000	0.002
as.data.frame	0.000	0.000	0.002
as.vector	0.004	0.000	0.002
boxplot	0.000	0.000	0.001
cbind	0.004	0.000	0.003
clusterApply	0.020	0.004	0.024
combine	0.048	0.004	0.055
dbconn	0.048	0.000	0.049
density	0.000	0.000	0.002
do.call	0.004	0.000	0.001
duplicated	0.004	0.000	0.004
eval	0.000	0.004	0.002
evalq	0.000	0.000	0.001
fileName	2.116	0.048	2.889
funprog	0.008	0.000	0.007
get	0.004	0.000	0.003
grep	0.004	0.000	0.001
image	0.000	0.000	0.002
is.unsorted	0.004	0.000	0.002
lapply	0.004	0.000	0.004
lengths	0.040	0.000	0.039
mad	0.004	0.000	0.002
mapply	0.000	0.000	0.001
match	0.004	0.000	0.002
matrix-summary	0.004	0.000	0.002
mean	0.000	0.000	0.002
normalize	0.02	0.00	0.02
nrow	0.008	0.000	0.006
order	0.004	0.000	0.002
organism_species	0.204	0.000	0.203
paste	0.004	0.000	0.002
path	0.020	0.004	0.024
plotMA	5.320	0.264	5.634
plotPCA	2.312	0.004	2.318
rank	0.000	0.000	0.003
relist	0.000	0.000	0.002
rep	0.004	0.000	0.003
residuals	0.004	0.000	0.001
row_colnames	0.008	0.000	0.009
score	0.068	0.000	0.066
sets	0.008	0.000	0.007
sort	0.004	0.000	0.003
start	0.048	0.000	0.048
strand	0.068	0.000	0.071
subset	0.020	0.000	0.021
t	0.004	0.000	0.005
table	0.004	0.000	0.002
tapply	0.000	0.000	0.002
testPackage	0.460	0.024	0.502
unique	0.004	0.000	0.004
unlist	0.004	0.000	0.004
unsplit	0.004	0.000	0.003
updateObject	0.296	0.016	0.311
var	0.004	0.000	0.004
weights	0.004	0.000	0.004
which	0.012	0.000	0.011
xtabs	0.004	0.000	0.004