BioC 3.5: CHECK report for clusterExperiment on oaxaca

Package: clusterExperiment

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterExperiment_1.1.1.tar.gz

StartedAt: 2017-03-04 00:44:15 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:53:08 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 532.3 seconds

RetCode: 0

Status:  OK

CheckDir: clusterExperiment.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 clusterExperiment_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘1.1.1’
* 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 ... OK
* 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 ... 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 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 36.766  0.620  42.415
plotHeatmap         24.888  0.240  29.813
plotClusters         5.187  0.222   5.882
* 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: OK

* 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’
Creating a new generic function for ‘transform’ in package ‘clusterExperiment’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clusterExperiment)

name	user	system	elapsed
ClusterExperiment-class	0.730	0.004	0.815
addClusters	1.015	0.027	1.198
clusterContrasts	1.669	0.068	2.090
clusterD	2.766	0.084	3.245
clusterMany	3.823	0.183	4.861
clusterSingle	0.117	0.014	0.133
combineMany	2.718	0.119	4.013
getBestFeatures	3.032	0.078	3.562
makeDendrogram	1.860	0.035	2.245
mergeClusters	3.036	0.066	3.453
plotClusters	5.187	0.222	5.882
plotHeatmap	24.888	0.240	29.813
plottingFunctions	0.233	0.018	0.304
seqCluster	0.001	0.000	0.001
simData	0.021	0.002	0.023
subsampleClustering	36.766	0.620	42.415
transform	0.04	0.00	0.04
workflowClusters	2.120	0.118	2.241