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: 2013-05-01 08:45:48 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 08:51:04 -0700 (Wed, 01 May 2013)

EllapsedTime: 316.4 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 Patched (2013-04-08 r62531)
* 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 ... [25s/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/49s] OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
AssayData-methods                    7.351  0.238   8.587
makeFeatureGRanges                   4.217  0.171   5.329
GenomeAnnotatedDataFrameFrom-methods 3.779  0.082   5.395
GenomeAnnotatedDataFrame-class       1.565  0.357   9.128
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [44s/45s]
 [44s/46s] 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	0.496	0.017	0.520
AssayData-methods	7.351	0.238	8.587
AssayDataList	0.462	0.006	0.687
BeadStudioSet-class	0.116	0.008	0.170
CNSet-class	0.113	0.009	0.135
CopyNumberSet-class	0.094	0.008	0.110
CopyNumberSet-methods	0.338	0.122	0.553
FeatureSetExtensions-class	0.287	0.030	0.354
GRanges-methods	0.495	0.022	0.562
GenomeAnnotatedDataFrame-class	1.565	0.357	9.128
GenomeAnnotatedDataFrameFrom-methods	3.779	0.082	5.395
SnpSet-methods	0.162	0.011	0.206
SnpSet2-class	0.072	0.005	0.080
SnpSuperSet-class	0.194	0.006	0.325
affyPlatforms	0.048	0.005	0.052
batch	0.127	0.006	0.149
celfileDate	0.098	0.013	0.157
celfileName	0.045	0.006	0.050
checkExists	0.058	0.010	0.078
checkOrder	0.433	0.024	0.508
chromosome-methods	0.047	0.005	0.052
chromosome2integer	0.047	0.003	0.055
clusterOpts	0.047	0.005	0.053
data-efsExample	0.047	0.004	0.051
data-scqsExample	0.046	0.005	0.054
data-sfsExample	0.047	0.004	0.050
data-sqsExample	0.048	0.004	0.052
db	0.044	0.003	0.048
ff_matrix	0.046	0.003	0.048
ff_or_matrix-class	0.004	0.003	0.006
fileConnections	0.051	0.005	0.063
flags	0.222	0.018	0.251
gSet-class	0.048	0.004	0.056
gSetList-class	0.050	0.005	0.057
genomeBuild	0.056	0.004	0.060
geometry-methods	0.269	0.020	0.297
getBar	0.046	0.003	0.048
getSequenceLengths	0.353	0.020	0.381
i2p_p2i	0.599	0.010	0.635
integerMatrix	0.047	0.006	0.053
is.ffmatrix	0.004	0.005	0.009
isPackageLoaded	0.048	0.005	0.054
kind	0.274	0.027	0.325
largeObjects	0.050	0.008	0.064
ldOpts	0.006	0.005	0.010
library2	0.089	0.007	0.108
list.celfiles	0.095	0.014	0.149
locusLevelData	0.152	0.013	0.165
makeFeatureGRanges	4.217	0.171	5.329
oligoSetExample	0.938	0.035	1.050
pdPkgFromBioC	0.002	0.003	0.005
requireAnnotation	0.045	0.005	0.050
splitVec	0.051	0.008	0.059