BioC 2.12: CHECK report for oligoClasses on petty

Package: oligoClasses

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.22.0.tar.gz

StartedAt: 2013-10-08 23:19:04 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:25:12 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 368.3 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/oligoClasses.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.22.0'
* 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 ... [28s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated dependencies in R code ... OK
* 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 ... [40s/49s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              8.059  0.230   8.377
makeFeatureGRanges             5.454  0.171   5.916
GenomeAnnotatedDataFrame-class 1.742  0.320   9.641
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [47s/50s]
 [48s/50s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-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	0.549	0.012	0.566
AssayData-methods	8.059	0.230	8.377
AssayDataList	0.483	0.004	0.501
BeadStudioSet-class	0.155	0.005	0.161
CNSet-class	0.151	0.008	0.159
CopyNumberSet-class	0.107	0.006	0.113
CopyNumberSet-methods	0.403	0.114	0.520
FeatureSetExtensions-class	0.332	0.024	0.357
GRanges-methods	0.604	0.019	0.625
GenomeAnnotatedDataFrame-class	1.742	0.320	9.641
GenomeAnnotatedDataFrameFrom-methods	3.930	0.068	4.047
SnpSet-methods	0.204	0.011	0.217
SnpSet2-class	0.144	0.005	0.149
SnpSuperSet-class	0.238	0.006	0.245
affyPlatforms	0.047	0.003	0.050
batch	0.195	0.006	0.217
celfileDate	0.152	0.015	0.217
celfileName	0.095	0.006	0.107
checkExists	0.140	0.008	0.312
checkOrder	0.463	0.024	0.504
chromosome-methods	0.045	0.004	0.052
chromosome2integer	0.049	0.004	0.060
clusterOpts	0.006	0.004	0.010
data-efsExample	0.047	0.004	0.055
data-scqsExample	0.052	0.003	0.063
data-sfsExample	0.045	0.005	0.052
data-sqsExample	0.051	0.004	0.059
db	0.046	0.003	0.048
ff_matrix	0.045	0.003	0.050
ff_or_matrix-class	0.003	0.003	0.006
fileConnections	0.046	0.004	0.054
flags	0.260	0.014	0.296
gSet-class	0.043	0.005	0.050
gSetList-class	0.609	0.007	0.629
genomeBuild	0.008	0.003	0.011
geometry-methods	0.246	0.023	0.289
getBar	0.004	0.003	0.006
getSequenceLengths	0.353	0.024	0.379
i2p_p2i	0.047	0.005	0.057
integerMatrix	0.046	0.006	0.056
is.ffmatrix	0.049	0.006	0.056
isPackageLoaded	0.006	0.005	0.012
kind	0.250	0.028	0.281
largeObjects	0.050	0.008	0.059
ldOpts	0.056	0.005	0.061
library2	0.090	0.007	0.100
list.celfiles	0.088	0.014	0.103
locusLevelData	0.183	0.014	0.198
makeFeatureGRanges	5.454	0.171	5.916
oligoSetExample	0.365	0.022	0.411
pdPkgFromBioC	0.002	0.002	0.005
requireAnnotation	0.045	0.004	0.053
splitVec	0.049	0.006	0.062