BioC 3.0: CHECK report for oligoClasses on perceval

Package: oligoClasses

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.28.0.tar.gz

StartedAt: 2015-04-10 04:27:02 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:32:29 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 326.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 3

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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_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/oligoClasses.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.28.0’
* 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 ... [23s/38s] 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addFeatureAnnotation.pd2: no visible global function definition for
  ‘dbGetQuery’
addFeatureAnnotation.pd2: no visible global function definition for
  ‘dbListTables’
getSequenceLengths: no visible binding for global variable ‘seqlengths’
allele,SnpFeatureSet: no visible global function definition for
  ‘dbGetQuery’
coerce,CNSet-CopyNumberSet: no visible global function definition for
  ‘totalCopynumber’
geometry,FeatureSet: no visible global function definition for ‘getPD’
initialize,DBPDInfo: no visible global function definition for
  ‘dbGetQuery’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘clone2’
Undocumented S4 methods:
  generic 'clone2' and siglist 'BafLrrSetList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 ... WARNING
'library' or 'require' calls not declared from:
  ‘SNPchip’ ‘VanillaICE’ ‘crlmm’
'data(package=)' call not declared from: ‘crlmm’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/43s] WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              7.139  0.235   7.541
makeFeatureGRanges             6.488  0.144   6.714
GenomeAnnotatedDataFrame-class 2.418  0.485   8.050
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [47s/51s]
 [48s/52s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 3 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.498	0.002	0.500
AssayData-methods	7.139	0.235	7.541
AssayDataList	0.001	0.000	0.002
BeadStudioSet-class	0.080	0.001	0.080
CNSet-class	0.070	0.005	0.075
CopyNumberSet-class	0.062	0.016	0.079
CopyNumberSet-methods	0.338	0.093	0.431
FeatureSetExtensions-class	0.194	0.001	0.194
GRanges-methods	0.671	0.027	0.699
GenomeAnnotatedDataFrame-class	2.418	0.485	8.050
GenomeAnnotatedDataFrameFrom-methods	2.508	0.052	2.638
SnpSet-methods	0.115	0.002	0.117
SnpSet2-class	0.061	0.001	0.061
SnpSuperSet-class	0.108	0.001	0.108
affyPlatforms	0.002	0.000	0.002
batch	0.062	0.000	0.062
celfileDate	0.063	0.009	0.223
celfileName	0.000	0.001	0.000
checkExists	0.008	0.001	0.018
checkOrder	0.928	0.022	0.951
chromosome-methods	0.001	0.000	0.002
chromosome2integer	0.002	0.000	0.002
clusterOpts	0.004	0.001	0.005
data-efsExample	0.002	0.001	0.003
data-scqsExample	0.004	0.001	0.005
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.001	0.003
db	0.000	0.000	0.001
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.001
flags	0.114	0.004	0.118
gSet-class	0.002	0.000	0.002
gSetList-class	0.002	0.001	0.002
genomeBuild	0.006	0.000	0.006
geometry-methods	1.476	0.040	1.517
getBar	0.001	0.001	0.001
getSequenceLengths	0.392	0.017	0.410
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.002	0.000	0.002
isPackageLoaded	0.002	0.000	0.002
kind	0.734	0.040	0.774
largeObjects	0.003	0.001	0.004
ldOpts	0.003	0.000	0.003
library2	0.159	0.011	0.170
list.celfiles	0.053	0.009	0.077
locusLevelData	0.137	0.015	0.151
makeFeatureGRanges	6.488	0.144	6.714
oligoSetExample	0.231	0.015	0.245
pdPkgFromBioC	0.001	0.001	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.003	0.002	0.004