BioC 3.3: CHECK report for oligoClasses on moscato2

Package: oligoClasses

Version: 1.34.0

Command: rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.34.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.34.0.tar.gz

StartedAt: 2016-10-13 06:53:58 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:00:18 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 379.1 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.34.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.34.0.tar.gz
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/oligoClasses.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.34.0'
* 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
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 ... OK
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 1.36   0.16   49.24
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
GenomeAnnotatedDataFrame-class 1.28   0.05    8.27
* 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: 3 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/oligoClasses.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.34.0.zip
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.08	0.00	0.08
AssayData-methods	2.51	0.07	3.22
AssayDataList	0	0	0
BeadStudioSet-class	0.05	0.00	0.04
CNSet-class	0.04	0.00	0.05
CopyNumberSet-class	0.05	0.00	0.05
CopyNumberSet-methods	0.19	0.06	0.32
FeatureSetExtensions-class	0.33	0.00	0.33
GRanges-methods	0.29	0.01	0.31
GenomeAnnotatedDataFrame-class	1.36	0.16	49.24
GenomeAnnotatedDataFrameFrom-methods	1.40	0.00	2.54
SnpSet-methods	0.05	0.00	0.05
SnpSet2-class	0.06	0.00	0.06
SnpSuperSet-class	0.11	0.00	0.11
affyPlatforms	0	0	0
batch	0.04	0.00	0.04
celfileDate	0.32	0.00	1.47
celfileName	0	0	0
checkExists	0.01	0.00	0.01
checkOrder	0.27	0.00	0.27
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0	0	0
data-scqsExample	0	0	0
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	0.05	0.00	0.04
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.23	0.02	0.25
getBar	0	0	0
getSequenceLengths	0.12	0.01	0.14
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.20	0.02	0.22
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.03	0.00	0.03
list.celfiles	0.03	0.00	0.51
locusLevelData	0.14	0.00	0.14
makeFeatureGRanges	2.84	0.09	2.97
oligoSetExample	0.19	0.02	0.20
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	0.13	0.00	0.12
AssayData-methods	3.29	0.09	3.39
AssayDataList	0	0	0
BeadStudioSet-class	0.08	0.00	0.08
CNSet-class	0.06	0.00	0.06
CopyNumberSet-class	0.03	0.00	0.03
CopyNumberSet-methods	0.20	0.01	0.22
FeatureSetExtensions-class	0.17	0.00	0.17
GRanges-methods	0.30	0.02	0.31
GenomeAnnotatedDataFrame-class	1.28	0.05	8.27
GenomeAnnotatedDataFrameFrom-methods	1.19	0.00	1.19
SnpSet-methods	0.05	0.00	0.05
SnpSet2-class	0.05	0.00	0.05
SnpSuperSet-class	0.53	0.00	0.53
affyPlatforms	0	0	0
batch	0.07	0.00	0.08
celfileDate	0.02	0.00	0.54
celfileName	0.02	0.00	0.02
checkExists	0	0	0
checkOrder	0.20	0.00	0.21
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0.00	0.01	0.01
data-efsExample	0	0	0
data-scqsExample	0	0	0
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	0.05	0.00	0.05
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.24	0.05	0.29
getBar	0	0	0
getSequenceLengths	0.19	0.00	0.18
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0.01	0.00	0.02
isPackageLoaded	0	0	0
kind	0.30	0.01	0.31
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.06	0.00	0.06
list.celfiles	0.01	0.00	0.02
locusLevelData	0.08	0.00	0.07
makeFeatureGRanges	2.88	0.05	3.23
oligoSetExample	0.18	0.00	0.17
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0