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BioC 3.5: CHECK report for clusterExperiment on malbec2

This page was generated on 2017-08-16 13:17:43 -0400 (Wed, 16 Aug 2017).

Package 235/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 1.2.0
Elizabeth Purdom
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/clusterExperiment
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 1.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.2.0.tar.gz
StartedAt: 2017-08-15 22:00:25 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:07:19 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 414.1 seconds
RetCode: 0
Status:  OK 
CheckDir: clusterExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.2.0’
* 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 29.684  0.028  29.770
plotHeatmap         16.296  0.056  16.372
* 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

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'
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)

clusterExperiment.Rcheck/clusterExperiment-Ex.timings:

nameusersystemelapsed
ClusterExperiment-class0.3080.0000.308
addClusters1.0160.0081.025
clusterContrasts1.2040.0121.218
clusterD1.4200.0041.423
clusterMany2.5360.0242.564
clusterSingle0.0720.0000.074
combineMany2.0240.0082.036
getBestFeatures2.6880.0082.716
makeDendrogram0.8520.0040.858
mergeClusters2.3520.0002.354
plotClusters3.6000.0163.629
plotHeatmap16.296 0.05616.372
plottingFunctions0.2400.0080.247
seqCluster0.0000.0000.001
simData0.0280.0000.028
subsampleClustering29.684 0.02829.770
transform0.040.000.04
workflowClusters2.1920.0042.200