Package: oligoClasses

Version: 1.21.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.21.16.tar.gz

StartedAt: 2013-03-25 03:50:26 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:54:38 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 251.9 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/oligoClasses.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.21.16'
* 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 ... [24s/24s] 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 ... [30s/38s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
makeFeatureGRanges             5.522  0.319   5.850
GenomeAnnotatedDataFrame-class 1.104  0.343   8.851
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [34s/34s]
 [34s/34s] 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	0.278	0.018	0.298
AssayData-methods	4.473	0.199	4.693
AssayDataList	0.006	0.006	0.012
BeadStudioSet-class	0.095	0.006	0.101
CNSet-class	0.084	0.009	0.091
CopyNumberSet-class	0.061	0.007	0.067
CopyNumberSet-methods	0.254	0.097	0.353
FeatureSetExtensions-class	0.222	0.010	0.233
GRanges-methods	0.396	0.048	0.450
GenomeAnnotatedDataFrame-class	1.104	0.343	8.851
GenomeAnnotatedDataFrameFrom-methods	1.808	0.069	1.922
SnpSet-methods	0.119	0.012	0.130
SnpSet2-class	0.125	0.009	0.136
SnpSuperSet-class	0.164	0.008	0.172
affyPlatforms	0.030	0.005	0.035
batch	0.133	0.009	0.142
celfileDate	0.090	0.018	0.114
celfileName	0.054	0.006	0.061
checkExists	0.066	0.015	0.080
checkOrder	0.368	0.031	0.399
chromosome-methods	0.030	0.007	0.036
chromosome2integer	0.055	0.006	0.061
clusterOpts	0.041	0.009	0.050
data-efsExample	0.047	0.008	0.055
data-scqsExample	0.088	0.009	0.097
data-sfsExample	0.045	0.007	0.054
data-sqsExample	0.090	0.010	0.102
db	0.044	0.007	0.051
ff_matrix	0.044	0.007	0.051
ff_or_matrix-class	0.046	0.007	0.054
fileConnections	0.045	0.009	0.054
flags	0.244	0.030	0.274
gSet-class	0.046	0.007	0.054
gSetList-class	0.047	0.010	0.057
genomeBuild	0.052	0.008	0.060
geometry-methods	0.305	0.063	0.368
getBar	0.044	0.007	0.051
getSequenceLengths	0.390	0.049	0.439
i2p_p2i	0.086	0.010	0.096
integerMatrix	0.045	0.008	0.053
is.ffmatrix	0.089	0.011	0.100
isPackageLoaded	0.048	0.008	0.056
kind	0.341	0.065	0.406
largeObjects	0.092	0.014	0.106
ldOpts	0.048	0.007	0.055
library2	0.090	0.014	0.105
list.celfiles	0.127	0.025	0.154
locusLevelData	0.599	0.046	0.647
makeFeatureGRanges	5.522	0.319	5.850
oligoSetExample	0.469	0.031	0.501
pdPkgFromBioC	0.047	0.008	0.054
requireAnnotation	0.044	0.008	0.051
splitVec	0.093	0.012	0.105