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: 2013-03-24 08:17:23 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 08:22:43 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 319.6 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 3.0.0 beta (2013-03-21 r62346)
* 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 '1.21.16'
* 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/26s] 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 ... [37s/41s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              6.911  0.223   7.251
makeFeatureGRanges             4.973  0.186   5.406
GenomeAnnotatedDataFrame-class 1.894  0.289   5.912
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [45s/46s]
 [45s/47s] 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	0.468	0.026	0.494
AssayData-methods	6.911	0.223	7.251
AssayDataList	0.485	0.004	0.490
BeadStudioSet-class	0.122	0.007	0.130
CNSet-class	0.104	0.008	0.112
CopyNumberSet-class	0.095	0.008	0.104
CopyNumberSet-methods	0.344	0.125	0.468
FeatureSetExtensions-class	0.280	0.029	0.309
GRanges-methods	0.511	0.023	0.534
GenomeAnnotatedDataFrame-class	1.894	0.289	5.912
GenomeAnnotatedDataFrameFrom-methods	3.177	0.080	3.319
SnpSet-methods	0.162	0.013	0.175
SnpSet2-class	0.118	0.006	0.125
SnpSuperSet-class	0.194	0.007	0.204
affyPlatforms	0.047	0.006	0.053
batch	0.130	0.006	0.135
celfileDate	0.105	0.014	0.152
celfileName	0.051	0.005	0.055
checkExists	0.104	0.012	0.115
checkOrder	0.456	0.033	0.489
chromosome-methods	0.053	0.006	0.059
chromosome2integer	0.047	0.004	0.051
clusterOpts	0.638	0.005	0.644
data-efsExample	0.051	0.005	0.056
data-scqsExample	0.004	0.004	0.008
data-sfsExample	0.052	0.007	0.059
data-sqsExample	0.048	0.005	0.053
db	0.045	0.003	0.048
ff_matrix	0.003	0.003	0.007
ff_or_matrix-class	0.045	0.005	0.049
fileConnections	0.046	0.005	0.051
flags	0.186	0.024	0.210
gSet-class	0.005	0.006	0.011
gSetList-class	0.053	0.008	0.060
genomeBuild	0.008	0.004	0.012
geometry-methods	0.209	0.022	0.232
getBar	0.046	0.006	0.052
getSequenceLengths	0.311	0.023	0.335
i2p_p2i	0.004	0.004	0.009
integerMatrix	0.048	0.007	0.056
is.ffmatrix	0.048	0.007	0.055
isPackageLoaded	0.005	0.005	0.010
kind	0.249	0.025	0.275
largeObjects	0.054	0.008	0.065
ldOpts	0.051	0.004	0.056
library2	0.088	0.007	0.096
list.celfiles	0.096	0.012	0.108
locusLevelData	0.160	0.027	0.188
makeFeatureGRanges	4.973	0.186	5.406
oligoSetExample	0.372	0.040	0.421
pdPkgFromBioC	0.053	0.004	0.056
requireAnnotation	0.003	0.007	0.010
splitVec	0.059	0.010	0.069