BioC 3.3: CHECK report for oligoClasses on morelia

Package: oligoClasses

Version: 1.33.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.33.2.tar.gz

StartedAt: 2016-04-21 05:39:46 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:42:29 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 162.8 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_1.33.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/oligoClasses.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.33.2’
* 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 ... [13s/13s] 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 ... [15s/27s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
GenomeAnnotatedDataFrame-class 1.063  0.241  12.128
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [22s/22s]
 [22s/23s] 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	0.100	0.003	0.103
AssayData-methods	2.597	0.092	2.939
AssayDataList	0.002	0.000	0.002
BeadStudioSet-class	0.064	0.001	0.065
CNSet-class	0.054	0.005	0.060
CopyNumberSet-class	0.047	0.005	0.051
CopyNumberSet-methods	0.213	0.053	0.266
FeatureSetExtensions-class	0.121	0.000	0.120
GRanges-methods	0.312	0.004	0.316
GenomeAnnotatedDataFrame-class	1.063	0.241	12.128
GenomeAnnotatedDataFrameFrom-methods	1.026	0.022	1.123
SnpSet-methods	0.043	0.000	0.043
SnpSet2-class	0.095	0.001	0.096
SnpSuperSet-class	0.082	0.001	0.083
affyPlatforms	0.001	0.000	0.001
batch	0.048	0.000	0.048
celfileDate	0.024	0.003	0.087
celfileName	0.001	0.000	0.001
checkExists	0.008	0.001	0.009
checkOrder	0.490	0.007	0.498
chromosome-methods	0.001	0.000	0.001
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.001	0.000	0.001
data-efsExample	0.002	0.001	0.003
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.002	0.000	0.002
data-sqsExample	0.002	0.000	0.003
db	0.000	0.000	0.001
ff_matrix	0.001	0.000	0.000
ff_or_matrix-class	0.000	0.000	0.001
fileConnections	0.000	0.000	0.001
flags	0.044	0.002	0.046
gSet-class	0.002	0.000	0.002
gSetList-class	0.002	0.000	0.001
genomeBuild	0.004	0.000	0.005
geometry-methods	0.244	0.010	0.256
getBar	0.002	0.000	0.001
getSequenceLengths	0.138	0.006	0.144
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.001	0.000	0.001
isPackageLoaded	0.001	0.001	0.002
kind	0.216	0.009	0.224
largeObjects	0.002	0.001	0.003
ldOpts	0.003	0.000	0.003
library2	0.046	0.002	0.047
list.celfiles	0.017	0.002	0.116
locusLevelData	0.082	0.006	0.089
makeFeatureGRanges	2.775	0.061	2.914
oligoSetExample	0.183	0.007	0.190
pdPkgFromBioC	0.001	0.000	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.002	0.000	0.002