BioC 3.3: CHECK report for oligoClasses on zin2

Package: oligoClasses

Version: 1.34.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.34.0.tar.gz

StartedAt: 2016-10-13 04:52:48 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:55:05 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 137.1 seconds

RetCode: 0

Status:  OK

CheckDir: oligoClasses.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/oligoClasses.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.34.0’
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/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	0.090	0.000	0.091
AssayData-methods	2.245	0.032	2.292
AssayDataList	0.001	0.000	0.002
BeadStudioSet-class	0.045	0.000	0.045
CNSet-class	0.042	0.000	0.042
CopyNumberSet-class	0.030	0.004	0.034
CopyNumberSet-methods	0.140	0.048	0.189
FeatureSetExtensions-class	0.113	0.000	0.112
GRanges-methods	0.242	0.004	0.246
GenomeAnnotatedDataFrame-class	1.126	0.098	4.108
GenomeAnnotatedDataFrameFrom-methods	0.884	0.008	0.919
SnpSet-methods	0.028	0.000	0.027
SnpSet2-class	0.028	0.000	0.029
SnpSuperSet-class	0.363	0.004	0.365
affyPlatforms	0.001	0.000	0.002
batch	0.036	0.000	0.036
celfileDate	0.016	0.004	0.074
celfileName	0.000	0.000	0.001
checkExists	0.006	0.000	0.006
checkOrder	0.170	0.008	0.177
chromosome-methods	0.001	0.000	0.000
chromosome2integer	0.001	0.000	0.001
clusterOpts	0.001	0.000	0.002
data-efsExample	0.002	0.000	0.001
data-scqsExample	0.002	0.000	0.002
data-sfsExample	0.001	0.000	0.002
data-sqsExample	0.002	0.000	0.002
db	0	0	0
ff_matrix	0.001	0.000	0.001
ff_or_matrix-class	0	0	0
fileConnections	0.000	0.000	0.001
flags	0.041	0.000	0.041
gSet-class	0.001	0.000	0.002
gSetList-class	0.001	0.000	0.001
genomeBuild	0.004	0.000	0.003
geometry-methods	0.175	0.012	0.188
getBar	0.000	0.000	0.001
getSequenceLengths	0.099	0.000	0.099
i2p_p2i	0.000	0.000	0.001
integerMatrix	0	0	0
is.ffmatrix	0.000	0.000	0.001
isPackageLoaded	0.001	0.000	0.001
kind	0.155	0.004	0.159
largeObjects	0.002	0.000	0.003
ldOpts	0.002	0.000	0.001
library2	0.033	0.000	0.033
list.celfiles	0.012	0.000	0.054
locusLevelData	0.056	0.000	0.056
makeFeatureGRanges	2.429	0.028	2.454
oligoSetExample	0.130	0.004	0.134
pdPkgFromBioC	0.001	0.000	0.000
requireAnnotation	0	0	0
splitVec	0.003	0.000	0.003