BioC 3.6: CHECK report for oligoClasses on tokay1

Package: oligoClasses

Version: 1.39.1

Command: rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.39.1.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.39.1.tar.gz

StartedAt: 2017-08-16 01:17:32 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:22:32 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 299.9 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-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.39.1.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.39.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-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 '1.39.1'
* 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
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
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
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'
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'
Undefined global functions or variables:
  available.packages chromosomeList contrib.url 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 1.07   0.22   21.67
** 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-3.6-bioc/meat/oligoClasses.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'oligoClasses' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.39.1.zip
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.24	0.00	0.24
AssayData-methods	1.24	0.05	1.63
AssayDataList	0.01	0.00	0.02
BeadStudioSet-class	0.03	0.00	0.03
CNSet-class	0.07	0.00	0.06
CopyNumberSet-class	0.03	0.00	0.03
CopyNumberSet-methods	0.20	0.03	0.23
FeatureSetExtensions-class	0.13	0.00	0.13
GRanges-methods	0.61	0.00	0.61
GenomeAnnotatedDataFrame-class	1.07	0.22	21.67
GenomeAnnotatedDataFrameFrom-methods	1.25	0.08	1.66
SnpSet-methods	0.02	0.00	0.02
SnpSet2-class	0.03	0.00	0.04
SnpSuperSet-class	0.06	0.00	0.06
affyPlatforms	0	0	0
batch	0.09	0.00	0.09
celfileDate	0.03	0.02	0.05
celfileName	0	0	0
checkExists	0.00	0.01	0.01
checkOrder	0.33	0.10	0.43
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0	0	0
data-scqsExample	0.01	0.00	0.02
data-sfsExample	0	0	0
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	0.43	0.00	0.42
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.19	0.00	0.19
getBar	0	0	0
getSequenceLengths	0.08	0.01	0.10
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.16	0.05	0.20
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.02	0.02	0.03
list.celfiles	0.03	0.00	0.17
locusLevelData	0.14	0.01	0.16
makeFeatureGRanges	0.52	0.05	0.56
oligoSetExample	0.19	0.00	0.19
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	0.37	0.00	0.37
AssayData-methods	1.45	0.06	1.52
AssayDataList	0	0	0
BeadStudioSet-class	0.03	0.02	0.05
CNSet-class	0.13	0.00	0.12
CopyNumberSet-class	0.01	0.00	0.02
CopyNumberSet-methods	0.17	0.02	0.19
FeatureSetExtensions-class	0.14	0.00	0.14
GRanges-methods	0.72	0.00	0.72
GenomeAnnotatedDataFrame-class	0.95	0.06	1.02
GenomeAnnotatedDataFrameFrom-methods	1.26	0.00	1.27
SnpSet-methods	0.03	0.00	0.03
SnpSet2-class	0.03	0.00	0.03
SnpSuperSet-class	0.07	0.00	0.06
affyPlatforms	0.01	0.00	0.02
batch	0.08	0.00	0.08
celfileDate	0.06	0.00	0.06
celfileName	0	0	0
checkExists	0.02	0.00	0.02
checkOrder	0.16	0.00	0.15
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0.00	0.00	0.03
data-efsExample	0	0	0
data-scqsExample	0.00	0.01	0.02
data-sfsExample	0	0	0
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	0.02	0.02	0.03
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.76	0.03	0.79
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	0.22	0.00	0.22
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.03	0.00	0.03
list.celfiles	0.02	0.00	0.01
locusLevelData	0.08	0.00	0.08
makeFeatureGRanges	0.37	0.05	0.42
oligoSetExample	0.19	0.00	0.19
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0