BioC 3.4: CHECK report for clusterExperiment on morelia

Package: clusterExperiment

Version: 0.99.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterExperiment_0.99.3.tar.gz

StartedAt: 2016-09-20 04:37:39 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:43:41 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 362.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clusterExperiment.Rcheck

Warnings: 2

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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_0.99.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.3’
* 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 ... WARNING
---- unloading
Error in .getClassFromCache(what, resolve.confl = "all") : 
  argument "where" is missing, with no default
Calls: unloadNamespace ... <Anonymous> -> .removeSuperclassBackRefs -> .getClassFromCache
Execution halted
* 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 ... WARNING
Missing link or links in documentation object 'seqCluster.Rd':
  ‘tightClust’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 22.634  0.393  23.030
plotHeatmap         15.322  0.211  15.603
* 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: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.4-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'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
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	0.064	0.002	0.066
addClusters	0.241	0.016	0.258
clusterContrasts	1.059	0.038	1.097
clusterD	1.867	0.064	1.965
clusterMany	2.896	0.118	3.014
clusterSingle	0.076	0.007	0.083
combineMany	1.353	0.069	1.423
getBestFeatures	0.707	0.032	0.739
makeDendrogram	0.263	0.013	0.276
mergeClusters	0.974	0.042	1.017
plotClusters	3.901	0.169	4.077
plotHeatmap	15.322	0.211	15.603
plottingFunctions	0.151	0.013	0.173
seqCluster	0.001	0.000	0.000
simData	0.017	0.003	0.019
subsampleClustering	22.634	0.393	23.030
transform	0.023	0.000	0.023
workflowClusters	1.598	0.102	1.703