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: 2017-10-18 06:53:07 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:56:47 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 219.8 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 3.4.2 (2017-09-28)
* 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	0.666	0.009	0.691
AssayData-methods	1.017	0.063	1.135
AssayDataList	0.005	0.000	0.004
BeadStudioSet-class	0.051	0.000	0.053
CNSet-class	0.098	0.002	0.106
CopyNumberSet-class	0.033	0.001	0.034
CopyNumberSet-methods	0.164	0.064	0.233
FeatureSetExtensions-class	0.174	0.001	0.195
GRanges-methods	0.924	0.012	0.959
GenomeAnnotatedDataFrame-class	1.002	0.115	1.528
GenomeAnnotatedDataFrameFrom-methods	1.182	0.023	1.238
SnpSet-methods	0.032	0.001	0.034
SnpSet2-class	0.037	0.001	0.039
SnpSuperSet-class	0.065	0.001	0.068
affyPlatforms	0.001	0.001	0.002
batch	0.082	0.001	0.087
celfileDate	0.026	0.003	0.035
celfileName	0.000	0.001	0.000
checkExists	0.006	0.001	0.007
checkOrder	0.277	0.012	0.299
chromosome-methods	0.000	0.000	0.001
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.002	0.000	0.001
data-efsExample	0.002	0.001	0.003
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.000	0.003
db	0	0	0
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.000	0.001	0.001
fileConnections	0.001	0.000	0.001
flags	0.041	0.002	0.044
gSet-class	0.002	0.000	0.002
gSetList-class	0.002	0.000	0.002
genomeBuild	0.004	0.000	0.004
geometry-methods	0.701	0.011	0.733
getBar	0.001	0.000	0.001
getSequenceLengths	0.145	0.006	0.155
i2p_p2i	0.000	0.000	0.001
integerMatrix	0.001	0.000	0.002
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.001	0.000	0.002
kind	0.212	0.009	0.227
largeObjects	0.003	0.001	0.003
ldOpts	0.002	0.001	0.002
library2	0.047	0.001	0.050
list.celfiles	0.015	0.001	0.017
locusLevelData	0.077	0.008	0.085
makeFeatureGRanges	0.415	0.021	0.453
oligoSetExample	0.188	0.010	0.204
pdPkgFromBioC	0.001	0.001	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.003	0.001	0.005