BioC 3.0: CHECK report for oligoClasses on moscato1

Package: oligoClasses

Version: 1.28.0

Command: rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.28.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.28.0.tar.gz

StartedAt: 2015-04-10 03:46:17 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:53:04 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 407.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 4

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### Running command:
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###   rm -rf oligoClasses.buildbin-libdir oligoClasses.Rcheck && mkdir oligoClasses.buildbin-libdir oligoClasses.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.28.0.tar.gz >oligoClasses.Rcheck\00install.out 2>&1 && cp oligoClasses.Rcheck\00install.out oligoClasses-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.28.0.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/oligoClasses.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.28.0'
* 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
addFeatureAnnotation.pd2: no visible global function definition for
  'dbGetQuery'
addFeatureAnnotation.pd2: no visible global function definition for
  'dbListTables'
getSequenceLengths: no visible binding for global variable 'seqlengths'
allele,SnpFeatureSet: no visible global function definition for
  'dbGetQuery'
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'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'clone2'
Undocumented S4 methods:
  generic 'clone2' and siglist 'BafLrrSetList'
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 ... WARNING
'library' or 'require' calls not declared from:
  'SNPchip' 'VanillaICE' 'crlmm'
'data(package=)' call not declared from: 'crlmm'
* 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' ... [106s] WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                               user system elapsed
AssayData-methods              4.58   0.17    5.43
GenomeAnnotatedDataFrame-class 1.92   0.20   80.69
** running examples for arch 'x64' ... [28s] WARNING
Found the following significant warnings:

  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
  Warning: 'isIdCurrent' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                   user system elapsed
makeFeatureGRanges 5.87   0.02    5.88
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [33s]
 [34s] OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [32s]
 [32s] OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 4 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-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_1.28.0.zip
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.25	0.00	0.25
AssayData-methods	4.58	0.17	5.43
AssayDataList	0	0	0
BeadStudioSet-class	0.09	0.00	0.09
CNSet-class	0.1	0.0	0.1
CopyNumberSet-class	0.04	0.00	0.04
CopyNumberSet-methods	0.38	0.08	0.45
FeatureSetExtensions-class	0.48	0.00	0.48
GRanges-methods	0.41	0.03	0.44
GenomeAnnotatedDataFrame-class	1.92	0.20	80.69
GenomeAnnotatedDataFrameFrom-methods	1.5	0.0	2.0
SnpSet-methods	0.04	0.00	0.04
SnpSet2-class	0.05	0.00	0.05
SnpSuperSet-class	0.34	0.00	0.34
affyPlatforms	0	0	0
batch	0.05	0.00	0.05
celfileDate	0.04	0.00	1.10
celfileName	0	0	0
checkExists	0.01	0.00	0.02
checkOrder	0.22	0.00	0.22
chromosome-methods	0	0	0
chromosome2integer	0.02	0.00	0.01
clusterOpts	0	0	0
data-efsExample	0	0	0
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0.00	0.02	0.01
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0	0	0
fileConnections	0	0	0
flags	0.11	0.00	0.11
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0.02	0.00	0.02
geometry-methods	0.45	0.03	0.48
getBar	0	0	0
getSequenceLengths	0.19	0.03	0.22
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0.02	0.00	0.01
kind	0.57	0.05	0.63
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.06	0.00	0.06
list.celfiles	0.03	0.00	0.97
locusLevelData	0.06	0.00	0.06
makeFeatureGRanges	3.82	0.12	3.95
oligoSetExample	0.24	0.02	0.25
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0

name	user	system	elapsed
AlleleSet-class	0.30	0.00	0.29
AssayData-methods	4.66	0.11	4.78
AssayDataList	0	0	0
BeadStudioSet-class	0.06	0.00	0.07
CNSet-class	0.08	0.00	0.07
CopyNumberSet-class	0.32	0.00	0.33
CopyNumberSet-methods	0.22	0.03	0.25
FeatureSetExtensions-class	0.19	0.00	0.18
GRanges-methods	0.43	0.02	0.46
GenomeAnnotatedDataFrame-class	2.17	0.15	2.33
GenomeAnnotatedDataFrameFrom-methods	1.53	0.00	1.53
SnpSet-methods	0.08	0.00	0.08
SnpSet2-class	0.05	0.00	0.04
SnpSuperSet-class	0.10	0.00	0.11
affyPlatforms	0	0	0
batch	0.07	0.00	0.07
celfileDate	0.04	0.00	0.04
celfileName	0	0	0
checkExists	0.00	0.02	0.02
checkOrder	0.64	0.00	0.64
chromosome-methods	0	0	0
chromosome2integer	0	0	0
clusterOpts	0	0	0
data-efsExample	0	0	0
data-scqsExample	0.02	0.00	0.01
data-sfsExample	0	0	0
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0	0	0
ff_or_matrix-class	0.01	0.00	0.02
fileConnections	0	0	0
flags	0.08	0.00	0.08
gSet-class	0	0	0
gSetList-class	0	0	0
genomeBuild	0.02	0.00	0.01
geometry-methods	0.68	0.08	0.77
getBar	0	0	0
getSequenceLengths	0.22	0.03	0.47
i2p_p2i	0	0	0
integerMatrix	0	0	0
is.ffmatrix	0	0	0
isPackageLoaded	0	0	0
kind	0.33	0.07	0.41
largeObjects	0	0	0
ldOpts	0	0	0
library2	0.08	0.00	0.08
list.celfiles	0.03	0.00	0.03
locusLevelData	0.11	0.00	0.11
makeFeatureGRanges	5.87	0.02	5.88
oligoSetExample	0.33	0.00	0.33
pdPkgFromBioC	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0