BioC 3.1: CHECK report for oligoClasses on petty

Package: oligoClasses

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings oligoClasses_1.30.0.tar.gz

StartedAt: 2015-10-09 00:53:22 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:57:53 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 271.4 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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/oligoClasses.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘oligoClasses’ can be installed ... [21s/22s] 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 ... [29s/48s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
makeFeatureGRanges             4.797  0.098   5.045
AssayData-methods              4.613  0.179   5.238
GenomeAnnotatedDataFrame-class 2.789  0.414  21.506
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [36s/37s]
 [36s/38s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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 ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.158	0.012	0.170
AssayData-methods	4.613	0.179	5.238
AssayDataList	0.001	0.000	0.002
BeadStudioSet-class	0.076	0.000	0.077
CNSet-class	0.084	0.002	0.086
CopyNumberSet-class	0.076	0.007	0.083
CopyNumberSet-methods	0.405	0.110	0.545
FeatureSetExtensions-class	0.219	0.000	0.219
GRanges-methods	0.786	0.007	0.796
GenomeAnnotatedDataFrame-class	2.789	0.414	21.506
GenomeAnnotatedDataFrameFrom-methods	1.815	0.035	1.950
SnpSet-methods	0.047	0.000	0.048
SnpSet2-class	0.046	0.001	0.047
SnpSuperSet-class	0.121	0.001	0.122
affyPlatforms	0.002	0.000	0.003
batch	0.065	0.001	0.065
celfileDate	0.063	0.004	0.166
celfileName	0.001	0.000	0.002
checkExists	0.010	0.001	0.011
checkOrder	0.383	0.013	0.396
chromosome-methods	0.002	0.000	0.002
chromosome2integer	0.002	0.001	0.002
clusterOpts	0.003	0.000	0.004
data-efsExample	0.004	0.001	0.004
data-scqsExample	0.003	0.000	0.004
data-sfsExample	0.003	0.000	0.004
data-sqsExample	0.003	0.000	0.004
db	0.001	0.001	0.000
ff_matrix	0.002	0.000	0.002
ff_or_matrix-class	0.002	0.000	0.002
fileConnections	0.001	0.000	0.002
flags	0.610	0.004	0.616
gSet-class	0.002	0.000	0.003
gSetList-class	0.002	0.000	0.002
genomeBuild	0.006	0.001	0.006
geometry-methods	0.868	0.010	0.881
getBar	0.001	0.000	0.001
getSequenceLengths	0.464	0.007	0.474
i2p_p2i	0.001	0.000	0.001
integerMatrix	0.001	0.000	0.001
is.ffmatrix	0.003	0.000	0.002
isPackageLoaded	0.003	0.000	0.003
kind	0.769	0.017	0.788
largeObjects	0.004	0.001	0.005
ldOpts	0.002	0.000	0.003
library2	0.176	0.006	0.183
list.celfiles	0.054	0.004	0.088
locusLevelData	0.108	0.015	0.130
makeFeatureGRanges	4.797	0.098	5.045
oligoSetExample	0.275	0.013	0.289
pdPkgFromBioC	0.001	0.000	0.000
requireAnnotation	0.001	0.000	0.000
splitVec	0.005	0.002	0.007