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BioC 3.4: CHECK report for clusterExperiment on zin1

This page was generated on 2016-09-21 03:40:57 -0700 (Wed, 21 Sep 2016).

Package 213/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 0.99.3
Elizabeth Purdom
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clusterExperiment
Last Changed Rev: 119751 / Revision: 121152
Last Changed Date: 2016-07-29 14:24:30 -0700 (Fri, 29 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 0.99.3
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_0.99.3.tar.gz
StartedAt: 2016-09-20 04:39:10 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:44:40 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 329.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clusterExperiment.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_0.99.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/clusterExperiment.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 ‘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 24.228  0.000  24.226
plotHeatmap         13.632  0.036  13.665
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.


clusterExperiment.Rcheck/00install.out:

* 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)

clusterExperiment.Rcheck/clusterExperiment-Ex.timings:

nameusersystemelapsed
ClusterExperiment-class0.0800.0000.081
addClusters0.2120.0120.223
clusterContrasts1.0160.0081.023
clusterD1.7760.0121.795
clusterMany2.8680.0042.874
clusterSingle0.0920.0000.093
combineMany1.8200.0041.824
getBestFeatures0.7520.0040.757
makeDendrogram0.3000.0000.299
mergeClusters1.6560.0001.657
plotClusters3.6680.0083.690
plotHeatmap13.632 0.03613.665
plottingFunctions0.1600.0000.163
seqCluster0.0000.0000.001
simData0.0240.0000.023
subsampleClustering24.228 0.00024.226
transform0.0320.0040.037
workflowClusters1.5400.0001.541