BioC 2.14: CHECK report for oligoClasses on petty

Package: oligoClasses

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.24.0.tar.gz

StartedAt: 2014-10-07 23:17:36 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:23:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 375.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/oligoClasses.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [28s/32s] 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY'
  generic '[' and siglist 'gSetList,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [41s/50s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              8.225  0.231   8.617
makeFeatureGRanges             7.411  0.102   7.577
GenomeAnnotatedDataFrame-class 3.202  0.334  12.402
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [47s/49s]
 [48s/50s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.519	0.003	0.534
AssayData-methods	8.225	0.231	8.617
AssayDataList	0.003	0.000	0.003
BeadStudioSet-class	0.163	0.001	0.166
CNSet-class	0.144	0.001	0.148
CopyNumberSet-class	0.562	0.003	0.573
CopyNumberSet-methods	0.380	0.107	0.494
FeatureSetExtensions-class	0.392	0.014	0.414
GRanges-methods	0.935	0.013	0.962
GenomeAnnotatedDataFrame-class	3.202	0.334	12.402
GenomeAnnotatedDataFrameFrom-methods	2.580	0.055	2.751
SnpSet-methods	0.152	0.003	0.155
SnpSet2-class	0.101	0.001	0.102
SnpSuperSet-class	0.205	0.006	0.228
affyPlatforms	0.004	0.001	0.005
batch	0.713	0.016	0.743
celfileDate	0.081	0.008	0.141
celfileName	0.001	0.000	0.001
checkExists	0.013	0.001	0.015
checkOrder	0.366	0.021	0.390
chromosome-methods	0.002	0.001	0.002
chromosome2integer	0.002	0.000	0.003
clusterOpts	0.005	0.001	0.006
data-efsExample	0.004	0.001	0.005
data-scqsExample	0.004	0.001	0.004
data-sfsExample	0.004	0.001	0.004
data-sqsExample	0.004	0.001	0.005
db	0.001	0.000	0.001
ff_matrix	0.002	0.000	0.002
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.002
flags	0.164	0.004	0.168
gSet-class	0.003	0.000	0.004
gSetList-class	0.003	0.000	0.004
genomeBuild	0.006	0.001	0.007
geometry-methods	0.673	0.032	0.708
getBar	0.002	0.000	0.003
getSequenceLengths	0.491	0.017	0.512
i2p_p2i	0.002	0.000	0.002
integerMatrix	0.002	0.000	0.002
is.ffmatrix	0.004	0.001	0.004
isPackageLoaded	0.004	0.000	0.003
kind	0.656	0.032	0.703
largeObjects	0.006	0.001	0.008
ldOpts	0.005	0.000	0.006
library2	0.071	0.003	0.083
list.celfiles	0.068	0.006	0.080
locusLevelData	0.125	0.009	0.135
makeFeatureGRanges	7.411	0.102	7.577
oligoSetExample	0.315	0.015	0.330
pdPkgFromBioC	0.001	0.000	0.002
requireAnnotation	0.001	0.000	0.001
splitVec	0.005	0.002	0.007