BioC 3.3: CHECK report for oligoClasses on oaxaca

Package: oligoClasses

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.34.0.tar.gz

StartedAt: 2016-10-13 04:16:50 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:29:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 776.0 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/oligoClasses.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
AssayData-methods              2.403  0.073   6.469
GenomeAnnotatedDataFrame-class 1.309  0.241  57.195
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/oligoClasses.Rcheck/00check.log’
for details.

* 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
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.075	0.002	0.076
AssayData-methods	2.403	0.073	6.469
AssayDataList	0.002	0.000	0.006
BeadStudioSet-class	0.039	0.001	0.039
CNSet-class	0.045	0.000	0.046
CopyNumberSet-class	0.042	0.002	0.045
CopyNumberSet-methods	0.205	0.070	0.373
FeatureSetExtensions-class	0.158	0.001	0.159
GRanges-methods	0.284	0.009	0.317
GenomeAnnotatedDataFrame-class	1.309	0.241	57.195
GenomeAnnotatedDataFrameFrom-methods	0.883	0.020	1.207
SnpSet-methods	0.023	0.001	0.023
SnpSet2-class	0.044	0.000	0.044
SnpSuperSet-class	0.399	0.002	0.403
affyPlatforms	0.002	0.000	0.003
batch	0.041	0.000	0.041
celfileDate	0.021	0.003	0.291
celfileName	0.000	0.000	0.001
checkExists	0.007	0.001	0.012
checkOrder	0.212	0.008	0.226
chromosome-methods	0.000	0.000	0.002
chromosome2integer	0.001	0.001	0.002
clusterOpts	0.002	0.000	0.002
data-efsExample	0.003	0.001	0.003
data-scqsExample	0.002	0.001	0.002
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.002	0.000	0.007
db	0.001	0.000	0.001
ff_matrix	0.000	0.000	0.001
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.000	0.001	0.001
flags	0.047	0.001	0.049
gSet-class	0.002	0.001	0.003
gSetList-class	0.001	0.000	0.002
genomeBuild	0.004	0.001	0.005
geometry-methods	0.221	0.008	0.260
getBar	0.001	0.000	0.001
getSequenceLengths	0.130	0.005	0.169
i2p_p2i	0.000	0.001	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.002	0.000	0.002
isPackageLoaded	0.002	0.000	0.002
kind	0.219	0.008	0.900
largeObjects	0.001	0.000	0.002
ldOpts	0.002	0.000	0.003
library2	0.044	0.001	0.050
list.celfiles	0.018	0.003	0.283
locusLevelData	0.075	0.005	0.080
makeFeatureGRanges	2.652	0.070	3.012
oligoSetExample	0.201	0.009	0.221
pdPkgFromBioC	0.001	0.000	0.001
requireAnnotation	0.001	0.000	0.000
splitVec	0.003	0.001	0.004