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BioC 3.0: CHECK report for BiocGenerics on zin1

This page was generated on 2015-04-10 09:39:42 -0700 (Fri, 10 Apr 2015).

Package 89/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.12.1
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiocGenerics
Last Changed Rev: 96708 / Revision: 102249
Last Changed Date: 2014-11-12 18:24:18 -0800 (Wed, 12 Nov 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: BiocGenerics
Version: 0.12.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BiocGenerics_0.12.1.tar.gz
StartedAt: 2015-04-09 21:57:28 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:58:03 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 35.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiocGenerics.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BiocGenerics_0.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/BiocGenerics.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.12.1’
* 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 ... [2s/2s] 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 ... NOTE
testPackage: no visible global function definition for
  ‘defineTestSuite’
testPackage: no visible global function definition for ‘runTestSuite’
testPackage: no visible global function definition for
  ‘printTextProtocol’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'unsplit':
unsplit
  Code: function(value, f, drop = FALSE)
  Docs: function(x, recursive = TRUE, use.names = TRUE)
  Argument names in code not in docs:
    value f drop
  Argument names in docs not in code:
    x recursive use.names
  Mismatches in argument names:
    Position: 1 Code: value Docs: x
    Position: 2 Code: f Docs: recursive
    Position: 3 Code: drop Docs: use.names

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'unsplit'
  ‘x’ ‘recursive’ ‘use.names’
Documented arguments not in \usage in documentation object 'unsplit':
  ‘value’ ‘f’ ‘drop’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 ... [11s/11s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotMA 8.672  0.244   8.947
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘BiocGenerics_unit_tests.R’ [1s/1s]
 [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.

BiocGenerics.Rcheck/00install.out:

* installing *source* package ‘BiocGenerics’ ...
** R
** inst
** preparing 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 ‘as.vector’ 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 ‘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 ‘rep.int’ 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 ‘unlist’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ 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’
Warning in getPackageName(environment(fdef)) :
  Created a package name, ‘2015-04-09 21:57:29’, when none found
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’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BiocGenerics)

BiocGenerics.Rcheck/BiocGenerics-Ex.timings:

nameusersystemelapsed
BiocGenerics-package0.0000.0000.001
Extremes0.0120.0000.011
annotation0.3560.0080.364
append0.0000.0000.003
as.data.frame0.0000.0000.002
as.vector0.0040.0000.002
boxplot0.0040.0000.001
cbind0.0040.0000.003
clusterApply0.0240.0000.023
combine0.1200.0000.119
density0.0000.0000.002
do.call0.0000.0000.002
duplicated0.0040.0000.003
eval0.0040.0000.002
evalq0.0000.0000.001
funprog0.0080.0000.008
get0.0040.0000.003
image0.0040.0000.001
is.unsorted0.0000.0000.002
lapply0.0000.0000.004
mapply0.0000.0000.002
match0.0000.0000.002
normalize0.1400.0240.164
nrow0.0000.0040.007
order0.0000.0000.002
paste0.0000.0040.002
plotMA8.6720.2448.947
rank0.0040.0000.005
relist0.0040.0000.003
rep0.0040.0000.003
residuals0.0000.0000.002
row_colnames0.0120.0000.012
sets0.0080.0000.009
sort0.0040.0000.002
start0.0760.0080.082
strand0.1120.0000.113
table0.0040.0000.002
tapply0.0040.0000.004
unique0.0000.0040.003
unlist0.0040.0000.003
unsplit0.0040.0000.002
updateObject0.2280.0040.232
weights0.0000.0000.002
xtabs0.0040.0000.003