BioC 3.1: CHECK report for oligoClasses on morelia

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 04:32:08 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:35:07 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 179.0 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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/oligoClasses.Rcheck’
* using R version 3.2.2 (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 ‘1.30.0’
* 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 ... [15s/15s] 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 ... [17s/32s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
GenomeAnnotatedDataFrame-class 1.399  0.288  14.938
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [23s/23s]
 [24s/24s] 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	0.108	0.011	0.120
AssayData-methods	2.712	0.159	3.428
AssayDataList	0.001	0.000	0.001
BeadStudioSet-class	0.066	0.000	0.066
CNSet-class	0.044	0.005	0.050
CopyNumberSet-class	0.035	0.005	0.039
CopyNumberSet-methods	0.216	0.058	0.273
FeatureSetExtensions-class	0.126	0.000	0.125
GRanges-methods	0.407	0.012	0.420
GenomeAnnotatedDataFrame-class	1.399	0.288	14.938
GenomeAnnotatedDataFrameFrom-methods	1.108	0.122	1.300
SnpSet-methods	0.036	0.004	0.041
SnpSet2-class	0.048	0.009	0.057
SnpSuperSet-class	0.097	0.002	0.098
affyPlatforms	0.001	0.000	0.001
batch	0.045	0.010	0.056
celfileDate	0.028	0.004	0.213
celfileName	0.000	0.000	0.001
checkExists	0.008	0.001	0.009
checkOrder	0.234	0.079	0.313
chromosome-methods	0.001	0.000	0.002
chromosome2integer	0.001	0.001	0.002
clusterOpts	0.002	0.001	0.003
data-efsExample	0.003	0.002	0.004
data-scqsExample	0.003	0.001	0.003
data-sfsExample	0.002	0.000	0.002
data-sqsExample	0.002	0.001	0.002
db	0.001	0.000	0.000
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0.000	0.000	0.001
fileConnections	0.001	0.000	0.001
flags	0.413	0.003	0.417
gSet-class	0.003	0.000	0.004
gSetList-class	0.002	0.000	0.002
genomeBuild	0.005	0.000	0.005
geometry-methods	0.259	0.008	0.268
getBar	0.001	0.000	0.002
getSequenceLengths	0.163	0.005	0.168
i2p_p2i	0.000	0.000	0.001
integerMatrix	0.001	0.001	0.001
is.ffmatrix	0.002	0.000	0.001
isPackageLoaded	0.002	0.000	0.002
kind	0.327	0.027	0.354
largeObjects	0.002	0.000	0.003
ldOpts	0.001	0.000	0.002
library2	0.057	0.002	0.059
list.celfiles	0.021	0.002	0.053
locusLevelData	0.055	0.011	0.066
makeFeatureGRanges	2.379	0.114	2.608
oligoSetExample	0.531	0.048	0.579
pdPkgFromBioC	0.001	0.000	0.000
requireAnnotation	0	0	0
splitVec	0.003	0.001	0.004