BioC 2.13: CHECK report for oligoClasses on zin1

Package: oligoClasses

Version: 1.24.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.24.0.tar.gz

StartedAt: 2014-04-05 02:47:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:50:19 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 177.6 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/oligoClasses.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.24.0’
* 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 ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Unexported objects imported by ‘:::’ calls:
  ‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘GenomeAnnotatedDataFrameFromMatrix’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... [22s/24s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [24s/25s]
 [24s/25s] OK
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.276	0.004	0.281
AssayData-methods	4.652	0.080	4.746
AssayDataList	0.008	0.000	0.008
BeadStudioSet-class	0.068	0.004	0.071
CNSet-class	0.072	0.000	0.069
CopyNumberSet-class	0.052	0.000	0.051
CopyNumberSet-methods	0.180	0.036	0.219
FeatureSetExtensions-class	0.196	0.000	0.196
GRanges-methods	0.380	0.016	0.397
GenomeAnnotatedDataFrame-class	0.916	0.124	3.335
GenomeAnnotatedDataFrameFrom-methods	1.412	0.028	1.526
SnpSet-methods	0.092	0.000	0.091
SnpSet2-class	0.072	0.000	0.070
SnpSuperSet-class	0.132	0.000	0.133
affyPlatforms	0.004	0.000	0.003
batch	0.088	0.000	0.091
celfileDate	0.068	0.000	0.072
celfileName	0.020	0.000	0.018
checkExists	0.032	0.008	0.044
checkOrder	0.536	0.012	0.549
chromosome-methods	0.016	0.000	0.018
chromosome2integer	0.016	0.000	0.018
clusterOpts	0.016	0.004	0.020
data-efsExample	0.000	0.000	0.002
data-scqsExample	0.016	0.000	0.019
data-sfsExample	0.020	0.000	0.019
data-sqsExample	0.020	0.000	0.019
db	0.012	0.004	0.019
ff_matrix	0.004	0.000	0.002
ff_or_matrix-class	0.016	0.000	0.018
fileConnections	0.016	0.000	0.017
flags	0.104	0.004	0.110
gSet-class	0.000	0.000	0.003
gSetList-class	0.020	0.000	0.022
genomeBuild	0.020	0.004	0.024
geometry-methods	0.240	0.024	0.264
getBar	0.000	0.000	0.002
getSequenceLengths	0.188	0.008	0.199
i2p_p2i	0.004	0.000	0.002
integerMatrix	0.000	0.000	0.002
is.ffmatrix	0.020	0.000	0.021
isPackageLoaded	0.016	0.000	0.020
kind	0.240	0.032	0.273
largeObjects	0.020	0.000	0.022
ldOpts	0.004	0.000	0.003
library2	0.024	0.004	0.029
list.celfiles	0.048	0.000	0.057
locusLevelData	0.088	0.000	0.141
makeFeatureGRanges	3.116	0.048	3.192
oligoSetExample	0.196	0.000	0.194
pdPkgFromBioC	0.020	0.000	0.017
requireAnnotation	0.016	0.000	0.017
splitVec	0.020	0.000	0.021