BioC 3.5: CHECK report for oligoClasses on veracruz2

Package: oligoClasses

Version: 1.38.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.38.0.tar.gz

StartedAt: 2017-08-16 06:05:02 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:08:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 223.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/oligoClasses.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘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 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’
getSequenceLengths: no visible binding for global variable ‘seqlengths’
pdPkgFromBioC: no visible binding for global variable ‘contrib.url’
pdPkgFromBioC: no visible global function definition for
  ‘available.packages’
pdPkgFromBioC: no visible global function definition for
  ‘install.packages’
allele,SnpFeatureSet: no visible global function definition for
  ‘dbGetQuery’
chromosome,gSetList: no visible global function definition for
  ‘chromosomeList’
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’
Undefined global functions or variables:
  available.packages chromosomeList contrib.url dbGetQuery getPD
  install.packages seqlengths totalCopynumber
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "install.packages")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'CNSet,ANY,ANY,ANY'
  generic '[' and siglist 'gSetList,ANY,ANY,ANY'
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 ... OK
* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘scriptsForExampleData/CreateExampleData.R’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
No methods found in "RSQLite" for requests: dbGetQuery
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.706	0.004	0.725
AssayData-methods	1.012	0.056	1.136
AssayDataList	0.006	0.000	0.006
BeadStudioSet-class	0.046	0.001	0.050
CNSet-class	0.101	0.001	0.105
CopyNumberSet-class	0.025	0.001	0.031
CopyNumberSet-methods	0.170	0.054	0.235
FeatureSetExtensions-class	0.168	0.001	0.169
GRanges-methods	0.837	0.007	0.871
GenomeAnnotatedDataFrame-class	0.825	0.110	1.190
GenomeAnnotatedDataFrameFrom-methods	1.037	0.018	1.076
SnpSet-methods	0.025	0.000	0.026
SnpSet2-class	0.033	0.000	0.033
SnpSuperSet-class	0.062	0.001	0.063
affyPlatforms	0.002	0.000	0.002
batch	0.076	0.001	0.076
celfileDate	0.018	0.002	0.021
celfileName	0.001	0.000	0.001
checkExists	0.005	0.000	0.006
checkOrder	0.185	0.008	0.195
chromosome-methods	0.001	0.001	0.000
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.001	0.000	0.002
data-efsExample	0.002	0.000	0.003
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.001	0.001	0.002
data-sqsExample	0.001	0.000	0.002
db	0	0	0
ff_matrix	0.001	0.000	0.000
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.001
flags	0.036	0.001	0.038
gSet-class	0.001	0.001	0.002
gSetList-class	0.001	0.000	0.002
genomeBuild	0.004	0.001	0.004
geometry-methods	0.222	0.007	0.232
getBar	0.001	0.000	0.001
getSequenceLengths	0.127	0.006	0.134
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.002	0.000	0.002
kind	0.218	0.009	0.236
largeObjects	0.003	0.001	0.003
ldOpts	0.002	0.000	0.002
library2	0.046	0.001	0.047
list.celfiles	0.015	0.002	0.017
locusLevelData	0.063	0.006	0.070
makeFeatureGRanges	0.388	0.015	0.412
oligoSetExample	0.157	0.006	0.166
pdPkgFromBioC	0.000	0.000	0.001
requireAnnotation	0.001	0.000	0.001
splitVec	0.002	0.000	0.004