BioC 2.14: CHECK report for oligoClasses on morelia

Package: oligoClasses

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.24.0.tar.gz

StartedAt: 2014-10-08 00:26:15 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:29:56 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 221.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/oligoClasses.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doMPI’ ‘doRedis’
* 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 ‘oligoClasses’ can be installed ... [15s/16s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
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
Unexported objects imported by ':::' calls:
  ‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘GenomeAnnotatedDataFrameFromMatrix’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 ... NOTE
prepare_Rd: SummarizedExperiment-methods.Rd:42-44: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY'
  generic '[' and siglist 'gSetList,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/38s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
GenomeAnnotatedDataFrame-class 1.672  0.206  16.524
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [27s/28s]
 [27s/28s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘oligoClasses’
Creating a generic function for ‘close’ from package ‘base’ in package ‘oligoClasses’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.327	0.001	0.330
AssayData-methods	4.593	0.112	4.749
AssayDataList	0.001	0.000	0.002
BeadStudioSet-class	0.100	0.007	0.108
CNSet-class	0.078	0.001	0.081
CopyNumberSet-class	0.072	0.000	0.073
CopyNumberSet-methods	0.465	0.055	0.524
FeatureSetExtensions-class	0.219	0.007	0.228
GRanges-methods	0.418	0.008	0.426
GenomeAnnotatedDataFrame-class	1.672	0.206	16.524
GenomeAnnotatedDataFrameFrom-methods	1.528	0.030	1.705
SnpSet-methods	0.100	0.001	0.102
SnpSet2-class	0.067	0.000	0.067
SnpSuperSet-class	0.131	0.003	0.133
affyPlatforms	0.001	0.000	0.002
batch	0.384	0.006	0.393
celfileDate	0.041	0.003	0.101
celfileName	0.001	0.000	0.001
checkExists	0.012	0.001	0.013
checkOrder	0.229	0.011	0.242
chromosome-methods	0.001	0.000	0.001
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.004	0.001	0.004
data-efsExample	0.003	0.001	0.003
data-scqsExample	0.003	0.000	0.002
data-sfsExample	0.003	0.000	0.004
data-sqsExample	0.002	0.001	0.004
db	0.001	0.000	0.000
ff_matrix	0.001	0.000	0.002
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.001
flags	0.101	0.002	0.104
gSet-class	0.002	0.000	0.001
gSetList-class	0.002	0.000	0.002
genomeBuild	0.005	0.001	0.005
geometry-methods	0.329	0.019	0.354
getBar	0.001	0.000	0.002
getSequenceLengths	0.238	0.009	0.252
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.002	0.000	0.001
isPackageLoaded	0.002	0.000	0.001
kind	0.318	0.017	0.339
largeObjects	0.004	0.000	0.004
ldOpts	0.002	0.000	0.002
library2	0.036	0.002	0.037
list.celfiles	0.032	0.003	0.035
locusLevelData	0.076	0.006	0.082
makeFeatureGRanges	4.144	0.068	4.264
oligoSetExample	0.196	0.009	0.207
pdPkgFromBioC	0.001	0.000	0.000
requireAnnotation	0.001	0.000	0.001
splitVec	0.004	0.001	0.004