Package: oligoClasses

Version: 1.21.16

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.21.16.tar.gz

StartedAt: 2013-03-25 03:28:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:35:11 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 387.1 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/oligoClasses.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [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 ... [53s/60s] OK
Examples with CPU or elapsed time > 5s
                                      user system elapsed
AssayData-methods                    9.469  0.184  10.067
makeFeatureGRanges                   7.585  0.108   8.086
GenomeAnnotatedDataFrameFrom-methods 5.728  0.052   5.825
GenomeAnnotatedDataFrame-class       1.448  0.188   6.639
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [58s/60s]
 [58s/61s] OK
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/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	0.652	0.016	0.673
AssayData-methods	9.469	0.184	10.067
AssayDataList	0.928	0.008	0.938
BeadStudioSet-class	0.200	0.004	0.201
CNSet-class	0.148	0.004	0.156
CopyNumberSet-class	0.112	0.000	0.113
CopyNumberSet-methods	0.388	0.056	0.445
FeatureSetExtensions-class	0.368	0.020	0.391
GRanges-methods	0.684	0.024	0.708
GenomeAnnotatedDataFrame-class	1.448	0.188	6.639
GenomeAnnotatedDataFrameFrom-methods	5.728	0.052	5.825
SnpSet-methods	0.164	0.008	0.170
SnpSet2-class	0.176	0.000	0.174
SnpSuperSet-class	0.336	0.004	0.339
affyPlatforms	0.096	0.000	0.093
batch	0.348	0.000	0.351
celfileDate	0.136	0.016	0.154
celfileName	0.072	0.000	0.075
checkExists	0.232	0.000	0.233
checkOrder	0.452	0.008	0.461
chromosome-methods	1.296	0.004	1.305
chromosome2integer	0.116	0.004	0.121
clusterOpts	0.092	0.000	0.092
data-efsExample	0.088	0.000	0.086
data-scqsExample	0.008	0.004	0.012
data-sfsExample	0.088	0.000	0.088
data-sqsExample	0.016	0.000	0.016
db	0.104	0.000	0.105
ff_matrix	0.012	0.000	0.013
ff_or_matrix-class	0.108	0.000	0.106
fileConnections	0.116	0.000	0.116
flags	0.416	0.000	0.418
gSet-class	0.144	0.000	0.143
gSetList-class	0.136	0.000	0.139
genomeBuild	0.100	0.008	0.110
geometry-methods	0.340	0.012	0.349
getBar	0.100	0.000	0.097
getSequenceLengths	0.544	0.008	0.554
i2p_p2i	0.068	0.000	0.068
integerMatrix	0.068	0.000	0.069
is.ffmatrix	0.088	0.000	0.086
isPackageLoaded	0.072	0.004	0.075
kind	0.332	0.012	0.342
largeObjects	0.104	0.004	0.108
ldOpts	0.120	0.004	0.125
library2	0.064	0.004	0.068
list.celfiles	0.252	0.004	0.265
locusLevelData	0.236	0.000	0.238
makeFeatureGRanges	7.585	0.108	8.086
oligoSetExample	0.344	0.004	0.347
pdPkgFromBioC	1.244	0.000	1.253
requireAnnotation	0.124	0.000	0.124
splitVec	0.008	0.000	0.012