BioC 2.13: CHECK report for oligoClasses on perceval

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: 2014-04-05 03:05:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:10:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 330.5 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/oligoClasses.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [23s/24s] 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 ... OK
* 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 examples ... [43s/57s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              8.355  0.269   8.944
makeFeatureGRanges             5.803  0.181   6.184
GenomeAnnotatedDataFrame-class 2.414  0.458  15.962
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [47s/48s]
 [47s/49s] OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.540	0.024	0.580
AssayData-methods	8.355	0.269	8.944
AssayDataList	0.611	0.006	0.652
BeadStudioSet-class	0.102	0.007	0.113
CNSet-class	0.098	0.008	0.110
CopyNumberSet-class	0.071	0.006	0.080
CopyNumberSet-methods	0.315	0.106	0.452
FeatureSetExtensions-class	0.267	0.033	0.307
GRanges-methods	0.668	0.044	0.742
GenomeAnnotatedDataFrame-class	2.414	0.458	15.962
GenomeAnnotatedDataFrameFrom-methods	3.098	0.081	3.314
SnpSet-methods	0.184	0.009	0.197
SnpSet2-class	0.120	0.005	0.129
SnpSuperSet-class	0.240	0.007	0.256
affyPlatforms	0.073	0.003	0.077
batch	0.147	0.007	0.172
celfileDate	0.179	0.011	0.192
celfileName	0.128	0.005	0.137
checkExists	0.117	0.010	0.128
checkOrder	1.275	0.036	1.345
chromosome-methods	0.054	0.005	0.062
chromosome2integer	0.003	0.003	0.006
clusterOpts	0.059	0.005	0.068
data-efsExample	0.004	0.003	0.007
data-scqsExample	0.064	0.005	0.072
data-sfsExample	0.074	0.007	0.091
data-sqsExample	0.004	0.004	0.009
db	0.054	0.004	0.064
ff_matrix	0.058	0.004	0.063
ff_or_matrix-class	0.089	0.007	0.105
fileConnections	0.063	0.006	0.070
flags	0.267	0.020	0.293
gSet-class	0.059	0.005	0.064
gSetList-class	0.071	0.008	0.078
genomeBuild	0.054	0.004	0.057
geometry-methods	0.609	0.034	0.665
getBar	0.003	0.002	0.006
getSequenceLengths	0.503	0.029	0.548
i2p_p2i	0.059	0.005	0.069
integerMatrix	0.056	0.004	0.061
is.ffmatrix	0.069	0.006	0.077
isPackageLoaded	0.058	0.004	0.063
kind	0.606	0.033	0.644
largeObjects	0.070	0.007	0.077
ldOpts	0.061	0.003	0.064
library2	0.058	0.006	0.065
list.celfiles	0.170	0.012	0.183
locusLevelData	0.086	0.011	0.097
makeFeatureGRanges	5.803	0.181	6.184
oligoSetExample	0.256	0.021	0.284
pdPkgFromBioC	0.002	0.003	0.005
requireAnnotation	0.002	0.004	0.006
splitVec	0.072	0.007	0.079