BioC 2.12: CHECK report for oligoClasses on george2

Package: oligoClasses

Version: 1.22.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.22.0.tar.gz

StartedAt: 2013-10-09 03:43:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:50:09 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 394.2 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 3.0.1 (2013-05-16)
* 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 ‘1.22.0’
* 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/27s] 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 ... [51s/64s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              9.929  0.196  11.381
makeFeatureGRanges             6.029  0.104   6.343
GenomeAnnotatedDataFrame-class 1.404  0.276  12.117
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [59s/63s]
 [59s/64s] 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	0.628	0.016	0.648
AssayData-methods	9.929	0.196	11.381
AssayDataList	0.892	0.004	0.896
BeadStudioSet-class	0.124	0.004	0.126
CNSet-class	0.128	0.008	0.136
CopyNumberSet-class	0.092	0.000	0.092
CopyNumberSet-methods	0.360	0.056	0.425
FeatureSetExtensions-class	0.344	0.020	0.455
GRanges-methods	0.572	0.012	0.590
GenomeAnnotatedDataFrame-class	1.404	0.276	12.117
GenomeAnnotatedDataFrameFrom-methods	4.641	0.032	4.945
SnpSet-methods	0.268	0.012	0.279
SnpSet2-class	0.156	0.000	0.157
SnpSuperSet-class	0.232	0.000	0.233
affyPlatforms	0.012	0.000	0.015
batch	0.184	0.000	0.185
celfileDate	0.152	0.012	0.164
celfileName	0.088	0.000	0.085
checkExists	0.176	0.004	0.179
checkOrder	0.444	0.000	0.444
chromosome-methods	0.088	0.000	0.088
chromosome2integer	0.092	0.000	0.093
clusterOpts	0.096	0.004	0.101
data-efsExample	0.012	0.000	0.009
data-scqsExample	0.084	0.004	0.086
data-sfsExample	0.108	0.000	0.107
data-sqsExample	0.08	0.00	0.08
db	0.08	0.00	0.08
ff_matrix	0.084	0.000	0.085
ff_or_matrix-class	0.012	0.000	0.012
fileConnections	0.112	0.000	0.112
flags	0.324	0.004	0.359
gSet-class	0.116	0.000	0.118
gSetList-class	0.104	0.000	0.106
genomeBuild	0.096	0.000	0.101
geometry-methods	0.224	0.020	0.245
getBar	0.104	0.000	0.101
getSequenceLengths	0.536	0.012	0.551
i2p_p2i	0.096	0.004	0.098
integerMatrix	0.108	0.000	0.108
is.ffmatrix	0.092	0.000	0.092
isPackageLoaded	0.100	0.000	0.102
kind	0.336	0.032	0.366
largeObjects	0.096	0.000	0.096
ldOpts	0.008	0.000	0.010
library2	0.148	0.004	0.150
list.celfiles	0.232	0.000	0.237
locusLevelData	0.236	0.004	0.242
makeFeatureGRanges	6.029	0.104	6.343
oligoSetExample	0.260	0.016	0.279
pdPkgFromBioC	0.076	0.004	0.080
requireAnnotation	0.072	0.004	0.078
splitVec	0.008	0.000	0.011