BioC 3.2: CHECK report for oligoClasses on oaxaca

Package: oligoClasses

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.32.0.tar.gz

StartedAt: 2016-04-23 02:43:56 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:47:20 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 204.5 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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/oligoClasses.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘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 ... [16s/16s] 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’
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 ... [20s/40s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
GenomeAnnotatedDataFrame-class 1.656   0.27  20.782
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [25s/25s]
 [25s/25s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.133	0.001	0.134
AssayData-methods	3.464	0.099	3.846
AssayDataList	0.002	0.000	0.002
BeadStudioSet-class	0.083	0.001	0.084
CNSet-class	0.068	0.003	0.071
CopyNumberSet-class	0.053	0.006	0.058
CopyNumberSet-methods	0.251	0.067	0.319
FeatureSetExtensions-class	0.177	0.000	0.178
GRanges-methods	0.388	0.006	0.394
GenomeAnnotatedDataFrame-class	1.656	0.270	20.782
GenomeAnnotatedDataFrameFrom-methods	1.138	0.025	1.238
SnpSet-methods	0.057	0.001	0.057
SnpSet2-class	0.040	0.000	0.041
SnpSuperSet-class	0.092	0.000	0.094
affyPlatforms	0.002	0.001	0.002
batch	0.050	0.000	0.051
celfileDate	0.072	0.005	0.252
celfileName	0.000	0.000	0.001
checkExists	0.008	0.001	0.009
checkOrder	0.231	0.009	0.240
chromosome-methods	0.001	0.000	0.001
chromosome2integer	0.001	0.000	0.002
clusterOpts	0.451	0.003	0.509
data-efsExample	0.001	0.000	0.002
data-scqsExample	0.002	0.001	0.002
data-sfsExample	0.003	0.001	0.003
data-sqsExample	0.002	0.001	0.003
db	0.001	0.000	0.001
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.001	0.001	0.001
fileConnections	0.001	0.000	0.001
flags	0.063	0.002	0.064
gSet-class	0.003	0.001	0.003
gSetList-class	0.002	0.000	0.003
genomeBuild	0.004	0.000	0.005
geometry-methods	0.311	0.007	0.319
getBar	0.001	0.000	0.001
getSequenceLengths	0.195	0.005	0.201
i2p_p2i	0.001	0.001	0.000
integerMatrix	0.001	0.000	0.000
is.ffmatrix	0.001	0.000	0.002
isPackageLoaded	0.002	0.000	0.002
kind	0.324	0.010	0.334
largeObjects	0.002	0.000	0.003
ldOpts	0.002	0.001	0.003
library2	0.087	0.005	0.093
list.celfiles	0.020	0.001	0.072
locusLevelData	0.075	0.005	0.080
makeFeatureGRanges	2.959	0.074	3.118
oligoSetExample	0.573	0.009	0.582
pdPkgFromBioC	0.000	0.000	0.001
requireAnnotation	0	0	0
splitVec	0.003	0.001	0.005