Package: oligoClasses

Version: 1.21.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.21.6.tar.gz

StartedAt: 2013-01-16 04:51:41 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:56:22 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 281.1 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/oligoClasses.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.21.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘doMPI’ ‘doSNOW’ ‘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 ... 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 ... NOTE
coerce,CNSetLM-CNSet: no visible global function definition for
  ‘physical’
updateObject,BeadStudioSet: no visible binding for global variable
  ‘....’
updateObject,CNSet: no visible binding for global variable ‘....’
updateObject,oligoSnpSet: no visible binding for global variable ‘....’
* checking Rd files ... NOTE
prepare_Rd: BeadStudioSetList-class.Rd:38-42: Dropping empty section ‘Methods’
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              7.728  0.136   7.896
GenomeAnnotatedDataFrame-class 0.904  0.140   6.276
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/loc/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	0.156	0.004	0.162
AssayData-methods	7.728	0.136	7.896
AssayDataList	0.012	0.000	0.013
BeadStudioSet-class	0.120	0.000	0.118
CNSet-class	0.089	0.000	0.087
CopyNumberSet-class	0.068	0.000	0.066
CopyNumberSet-methods	0.240	0.048	0.301
FeatureSetExtensions-class	0.264	0.008	0.273
GRanges-methods	0.416	0.012	0.427
GenomeAnnotatedDataFrame-class	0.904	0.140	6.276
GenomeAnnotatedDataFrameFrom-methods	3.296	0.032	3.384
RangedDataCNV-classes	0.056	0.000	0.057
RangedDataCNV-utils	0.680	0.028	0.708
SnpSet-methods	0.172	0.004	0.177
SnpSet2-class	0.156	0.000	0.156
SnpSuperSet-class	0.204	0.000	0.205
affyPlatforms	0.004	0.000	0.005
batch	0.112	0.000	0.115
celfileDate	0.096	0.004	0.134
celfileName	0.052	0.000	0.054
checkExists	0.168	0.000	0.168
checkOrder	0.880	0.012	0.894
chromosome-methods	0.052	0.004	0.056
chromosome2integer	0.056	0.000	0.055
clusterOpts	0.056	0.004	0.060
data-efsExample	0.004	0.000	0.004
data-scqsExample	0.052	0.004	0.054
data-sfsExample	0.056	0.000	0.054
data-sqsExample	0.004	0.000	0.004
db	0.000	0.004	0.004
ff_matrix	0.056	0.000	0.053
ff_or_matrix-class	0.08	0.00	0.08
fileConnections	0.072	0.000	0.072
findOverlaps	1.792	0.028	1.829
flags	0.260	0.004	0.264
gSet-class	0.084	0.000	0.081
gSetList-class	0.072	0.000	0.073
genomeBuild	0.012	0.000	0.012
geometry-methods	0.260	0.028	0.294
getBar	0.004	0.000	0.004
getSequenceLengths	0.276	0.016	0.295
i2p_p2i	0.068	0.000	0.066
integerMatrix	0.068	0.000	0.069
is.ffmatrix	0.080	0.000	0.078
isPackageLoaded	0.068	0.000	0.069
kind	0.332	0.012	0.345
largeObjects	0.068	0.000	0.070
ldOpts	0.012	0.000	0.010
library2	0.108	0.000	0.109
list.celfiles	0.092	0.004	0.105
locusLevelData	0.125	0.000	0.126
makeFeatureGRanges	2.904	0.016	2.924
oligoSetExample	0.272	0.000	0.273
pdPkgFromBioC	0.004	0.000	0.003
requireAnnotation	0.004	0.000	0.003
splitVec	0.008	0.000	0.007