BioC 3.6: CHECK report for clusterExperiment on veracruz1

Package: clusterExperiment

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterExperiment_1.3.2.tar.gz

StartedAt: 2017-08-16 01:17:45 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:27:24 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 579.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clusterExperiment.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterExperiment_1.3.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘1.3.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘clusterExperiment’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
':::' call which should be '::': ‘ape:::.PlotPhyloEnv’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘ape:::.matchDataPhylo’
  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 ... OK
* checking Rd files ... WARNING
mergeClusters.Rd: non-ASCII input and no declared encoding
plotClusters.Rd: non-ASCII input and no declared encoding
problems found in ‘mergeClusters.Rd’, ‘plotClusters.Rd’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
subsampleClustering 34.834  0.868  43.381
plotHeatmap         21.659  0.287  29.204
plotClusters         4.169  0.095   5.491
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.

* installing *source* package ‘clusterExperiment’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘RNeXML’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clusterExperiment)

name	user	system	elapsed
ClusterExperiment-class	0.437	0.003	0.559
ClusterFunction-class	0.013	0.000	0.016
addClusters	0.799	0.014	1.032
builtInClusteringFunctions	0.002	0.001	0.002
clusterContrasts	1.807	0.048	2.357
clusterMany	3.035	0.073	3.984
clusterSingle	0.119	0.005	0.155
combineMany	2.217	0.070	2.876
getBestFeatures	2.780	0.047	3.521
mainClustering	1.156	0.061	1.579
makeDendrogram	1.511	0.016	1.988
mergeClusters	3.122	0.055	4.288
plotBarplot	2.037	0.073	2.954
plotClusters	4.169	0.095	5.491
plotDendrogram	1.359	0.036	1.793
plotHeatmap	21.659	0.287	29.204
plottingFunctions	0.198	0.014	0.271
seqCluster	0.001	0.000	0.001
simData	0.019	0.001	0.023
subsampleClustering	34.834	0.868	43.381
transform	0.030	0.000	0.031
workflowClusters	1.485	0.118	1.656