BioC 3.5: CHECK report for oligoClasses on tokay2

Package: oligoClasses

Version: 1.38.0

Command: rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.38.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.38.0.tar.gz

StartedAt: 2017-08-16 01:41:06 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:46:44 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 337.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 2

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### Running command:
###
###   rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.38.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/oligoClasses.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 1.13   0.24   24.81
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R'
 OK
* checking PDF version of manual ... OK
* DONE

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

install for i386

* 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

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.38.0.zip
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.58	0.00	0.57
AssayData-methods	1.03	0.12	1.19
AssayDataList	0	0	0
BeadStudioSet-class	0.05	0.00	0.04
CNSet-class	0.07	0.00	0.08
CopyNumberSet-class	0.03	0.00	0.03
CopyNumberSet-methods	0.16	0.08	0.24
FeatureSetExtensions-class	0.14	0.00	0.14
GRanges-methods	0.61	0.03	0.64
GenomeAnnotatedDataFrame-class	1.13	0.24	24.81
GenomeAnnotatedDataFrameFrom-methods	1.34	0.03	1.78
SnpSet-methods	0.03	0.00	0.03
SnpSet2-class	0.05	0.00	0.05
SnpSuperSet-class	0.04	0.00	0.05
affyPlatforms	0	0	0
batch	0.06	0.00	0.07
celfileDate	0.11	0.00	0.32
celfileName	0	0	0
checkExists	0.02	0.00	0.02
checkOrder	0.29	0.01	0.31
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0.00	0.02	0.02
data-scqsExample	0	0	0
data-sfsExample	0.00	0.01	0.01
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0	0	0
fileConnections	0	0	0
flags	0.47	0.00	0.47
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.15	0.03	0.17
getBar	0	0	0
getSequenceLengths	0.12	0.04	0.16
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0.02	0.00	0.02
kind	0.21	0.03	0.25
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.05	0.00	0.04
list.celfiles	0.05	0.00	0.14
locusLevelData	0.15	0.00	0.16
makeFeatureGRanges	0.47	0.03	0.50
oligoSetExample	0.2	0.0	0.2
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	1.11	0.00	1.11
AssayData-methods	1.41	0.03	1.44
AssayDataList	0	0	0
BeadStudioSet-class	0.05	0.00	0.04
CNSet-class	0.09	0.00	0.10
CopyNumberSet-class	0.01	0.00	0.02
CopyNumberSet-methods	0.14	0.05	0.19
FeatureSetExtensions-class	0.16	0.00	0.15
GRanges-methods	0.8	0.0	0.8
GenomeAnnotatedDataFrame-class	0.76	0.11	0.87
GenomeAnnotatedDataFrameFrom-methods	1.22	0.01	1.24
SnpSet-methods	0.05	0.00	0.05
SnpSet2-class	0.05	0.00	0.04
SnpSuperSet-class	0.06	0.00	0.06
affyPlatforms	0	0	0
batch	0.11	0.00	0.11
celfileDate	0.01	0.00	0.02
celfileName	0	0	0
checkExists	0	0	0
checkOrder	0.2	0.0	0.2
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0.00	0.02	0.01
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0.02	0.00	0.02
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0.01	0.00	0.02
fileConnections	0	0	0
flags	0.13	0.00	0.12
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.28	0.00	0.28
getBar	0	0	0
getSequenceLengths	0.13	0.00	0.13
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.72	0.01	0.74
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.05	0.00	0.04
list.celfiles	0.01	0.00	0.02
locusLevelData	0.08	0.00	0.08
makeFeatureGRanges	0.3	0.0	0.3
oligoSetExample	0.13	0.02	0.14
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0