BioC 3.1: CHECK report for oligoClasses on moscato2

Package: oligoClasses

Version: 1.30.0

Command: rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.30.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.30.0.tar.gz

StartedAt: 2015-10-09 04:30:35 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:35:39 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 303.9 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-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.30.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.30.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/oligoClasses.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMC' 'doMPI' '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'
chromosome,gSetList : .local: 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'
* 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' ... [53s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
AssayData-methods              2.93   0.09    5.34
GenomeAnnotatedDataFrame-class 1.45   0.17   33.53
** running examples for arch 'x64' ... [19s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [29s]
 [29s] OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [27s]
 [27s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbld/bbs-3.1-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 'nchar' from package 'base' in package 'S4Vectors'
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'oligoClasses' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.30.0.zip
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.08	0.00	0.08
AssayData-methods	2.93	0.09	5.34
AssayDataList	0	0	0
BeadStudioSet-class	0.06	0.00	0.06
CNSet-class	0.05	0.00	0.04
CopyNumberSet-class	0.04	0.00	0.05
CopyNumberSet-methods	0.22	0.03	0.25
FeatureSetExtensions-class	0.13	0.00	0.13
GRanges-methods	0.59	0.02	0.60
GenomeAnnotatedDataFrame-class	1.45	0.17	33.53
GenomeAnnotatedDataFrameFrom-methods	1.84	0.00	2.23
SnpSet-methods	0.06	0.00	0.06
SnpSet2-class	0.04	0.00	0.03
SnpSuperSet-class	0.07	0.00	0.08
affyPlatforms	0	0	0
batch	0.03	0.00	0.03
celfileDate	0.04	0.00	0.28
celfileName	0	0	0
checkExists	0.01	0.00	0.02
checkOrder	0.24	0.01	0.25
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0.01	0.00	0.01
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	0.06	0.00	0.06
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0	0	0
geometry-methods	0.23	0.03	0.26
getBar	0	0	0
getSequenceLengths	0.15	0.00	0.15
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.31	0.02	0.33
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.06	0.00	0.07
list.celfiles	0.00	0.00	0.17
locusLevelData	0.08	0.00	0.08
makeFeatureGRanges	2.92	0.03	4.08
oligoSetExample	0.31	0.00	0.31
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	0.10	0.02	0.11
AssayData-methods	2.77	0.08	4.57
AssayDataList	0	0	0
BeadStudioSet-class	0.06	0.00	0.06
CNSet-class	0.05	0.00	0.05
CopyNumberSet-class	0.03	0.00	0.04
CopyNumberSet-methods	0.19	0.04	0.23
FeatureSetExtensions-class	0.15	0.00	0.16
GRanges-methods	0.36	0.02	0.37
GenomeAnnotatedDataFrame-class	1.27	0.14	1.96
GenomeAnnotatedDataFrameFrom-methods	1.12	0.00	1.12
SnpSet-methods	0.05	0.00	0.05
SnpSet2-class	0.03	0.00	0.03
SnpSuperSet-class	0.06	0.00	0.07
affyPlatforms	0.02	0.00	0.01
batch	0.03	0.00	0.03
celfileDate	0.04	0.00	0.05
celfileName	0	0	0
checkExists	0	0	0
checkOrder	0.56	0.00	0.56
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0.02	0.00	0.02
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0.02	0.00	0.01
ff_or_matrix-class	0	0	0
fileConnections	0	0	0
flags	0.04	0.00	0.05
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0.02	0.00	0.02
geometry-methods	0.23	0.03	0.26
getBar	0	0	0
getSequenceLengths	0.17	0.00	0.17
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.30	0.00	0.29
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.06	0.00	0.06
list.celfiles	0.02	0.00	0.02
locusLevelData	0.06	0.00	0.06
makeFeatureGRanges	2.73	0.02	2.89
oligoSetExample	0.56	0.01	0.57
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0