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: 2015-10-27 06:13:42 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:17:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 200.8 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_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/oligoClasses.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ... [19s/37s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
GenomeAnnotatedDataFrame-class 1.613  0.277  19.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [24s/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	0.128	0.000	0.129
AssayData-methods	3.114	0.092	3.383
AssayDataList	0.001	0.001	0.001
BeadStudioSet-class	0.057	0.000	0.058
CNSet-class	0.053	0.001	0.054
CopyNumberSet-class	0.048	0.005	0.054
CopyNumberSet-methods	0.196	0.054	0.249
FeatureSetExtensions-class	0.164	0.000	0.164
GRanges-methods	0.435	0.007	0.441
GenomeAnnotatedDataFrame-class	1.613	0.277	19.303
GenomeAnnotatedDataFrameFrom-methods	1.507	0.023	1.643
SnpSet-methods	0.060	0.001	0.062
SnpSet2-class	0.048	0.001	0.049
SnpSuperSet-class	0.100	0.000	0.101
affyPlatforms	0.001	0.001	0.001
batch	0.051	0.000	0.051
celfileDate	0.029	0.003	0.267
celfileName	0.001	0.000	0.001
checkExists	0.008	0.001	0.009
checkOrder	0.230	0.012	0.242
chromosome-methods	0.001	0.000	0.001
chromosome2integer	0.001	0.000	0.000
clusterOpts	0.082	0.003	0.099
data-efsExample	0.002	0.001	0.002
data-scqsExample	0.001	0.000	0.001
data-sfsExample	0.002	0.001	0.002
data-sqsExample	0.002	0.000	0.002
db	0.001	0.000	0.000
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.001	0.000	0.001
flags	0.086	0.002	0.088
gSet-class	0.002	0.000	0.003
gSetList-class	0.001	0.000	0.002
genomeBuild	0.003	0.001	0.003
geometry-methods	0.309	0.008	0.317
getBar	0.001	0.000	0.001
getSequenceLengths	0.186	0.004	0.190
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.002	0.000	0.001
isPackageLoaded	0.002	0.000	0.002
kind	0.384	0.010	0.394
largeObjects	0.003	0.001	0.004
ldOpts	0.003	0.000	0.003
library2	0.067	0.002	0.068
list.celfiles	0.023	0.002	0.097
locusLevelData	0.081	0.011	0.093
makeFeatureGRanges	2.928	0.065	3.141
oligoSetExample	0.244	0.008	0.252
pdPkgFromBioC	0.001	0.000	0.001
requireAnnotation	0.000	0.000	0.001
splitVec	0.003	0.001	0.005