Package: oligoClasses

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.20.0.tar.gz

StartedAt: 2013-03-25 00:39:03 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:43:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 256.2 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/oligoClasses.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'oligoClasses' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* 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              6.626  0.345   7.134
GenomeAnnotatedDataFrame-class 1.052  0.425   8.082
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-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	0.142	0.006	0.150
AssayData-methods	6.626	0.345	7.134
AssayDataList	0.001	0.000	0.001
BeadStudioSet-class	0.092	0.002	0.098
CNSet-class	0.107	0.012	0.136
CopyNumberSet-class	0.067	0.001	0.068
CopyNumberSet-methods	0.603	0.087	0.696
FeatureSetExtensions-class	0.244	0.013	0.260
GRanges-methods	0.385	0.014	0.400
GenomeAnnotatedDataFrame-class	1.052	0.425	8.082
GenomeAnnotatedDataFrameFrom-methods	2.493	0.070	2.618
RangedDataCNV-classes	0.001	0.000	0.001
RangedDataCNV-utils	0.642	0.027	0.677
SnpSet-methods	0.515	0.002	0.523
SnpSet2-class	0.059	0.001	0.060
SnpSuperSet-class	0.105	0.001	0.107
affyPlatforms	0.002	0.000	0.002
batch	0.071	0.001	0.072
celfileDate	0.042	0.011	0.099
celfileName	0	0	0
checkExists	0.008	0.003	0.015
checkOrder	0.319	0.032	0.363
chromosome-methods	0.001	0.000	0.000
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.112	0.015	0.127
data-efsExample	0.002	0.000	0.003
data-scqsExample	0.001	0.000	0.002
data-sfsExample	0.001	0.001	0.003
data-sqsExample	0.001	0.001	0.002
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0	0	0
findOverlaps	1.521	0.061	1.604
flags	1.110	0.022	1.137
gSet-class	0.001	0.000	0.002
gSetList-class	0.000	0.000	0.001
genomeBuild	0.005	0.000	0.005
geometry-methods	0.190	0.030	0.222
getBar	0.001	0.001	0.001
getSequenceLengths	0.167	0.016	0.183
i2p_p2i	0.001	0.000	0.000
integerMatrix	0.001	0.000	0.000
is.ffmatrix	0.001	0.000	0.001
isPackageLoaded	0.001	0.000	0.001
kind	0.193	0.034	0.228
largeObjects	0.002	0.001	0.004
ldOpts	0.002	0.001	0.002
library2	0.036	0.007	0.045
list.celfiles	0.035	0.009	0.044
locusLevelData	0.149	0.015	0.166
makeFeatureGRanges	3.835	0.355	4.257
oligoSetExample	0.231	0.016	0.250
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0.006	0.025	0.030