BioC 3.6: CHECK report for clusterExperiment on malbec1

Package: clusterExperiment

Version: 1.3.2

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.3.2.tar.gz

StartedAt: 2017-08-15 22:03:08 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:10:47 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 459.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clusterExperiment.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.3.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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 28.792  0.092  28.907
plotHeatmap         16.672  0.056  16.752
* 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, 1 NOTE
See
  ‘/home/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	0.324	0.012	0.335
ClusterFunction-class	0.012	0.000	0.012
addClusters	0.936	0.012	0.949
builtInClusteringFunctions	0.004	0.000	0.002
clusterContrasts	1.948	0.012	2.033
clusterMany	2.668	0.012	2.681
clusterSingle	0.096	0.008	0.100
combineMany	2.304	0.016	2.327
getBestFeatures	2.284	0.012	2.299
mainClustering	2.040	0.000	2.056
makeDendrogram	1.392	0.000	1.392
mergeClusters	2.936	0.004	2.944
plotBarplot	1.580	0.008	1.592
plotClusters	4.432	0.016	4.455
plotDendrogram	1.484	0.008	1.493
plotHeatmap	16.672	0.056	16.752
plottingFunctions	0.156	0.004	0.161
seqCluster	0.000	0.000	0.001
simData	0.016	0.000	0.017
subsampleClustering	28.792	0.092	28.907
transform	0.028	0.000	0.028
workflowClusters	1.296	0.016	1.312