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CHECK report for clusterExperiment on malbec2

This page was generated on 2018-01-19 07:11:26 -0500 (Fri, 19 Jan 2018).

Package 250/1482HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 1.5.0
Elizabeth Purdom
Snapshot Date: 2018-01-18 17:01:21 -0500 (Thu, 18 Jan 2018)
URL: https://git.bioconductor.org/packages/clusterExperiment
Branch: master
Last Commit: 123e89e
Last Changed Date: 2017-10-30 12:54:21 -0500 (Mon, 30 Oct 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  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 1.5.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.5.0.tar.gz
StartedAt: 2018-01-18 22:07:53 -0500 (Thu, 18 Jan 2018)
EndedAt: 2018-01-18 22:14:29 -0500 (Thu, 18 Jan 2018)
EllapsedTime: 396.2 seconds
RetCode: 0
Status:  OK 
CheckDir: clusterExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --no-vignettes --timings clusterExperiment_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2017-12-05 r73840)
* 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 ‘1.5.0’
* 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 ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc   10.0Mb
* 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 ... 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
plotHeatmap 16.476  0.032  16.523
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.



Installation output

clusterExperiment.Rcheck/00install.out

* installing *source* package ‘clusterExperiment’ ...
** R
** data
** 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)

Tests output

clusterExperiment.Rcheck/tests/testthat.Rout


R Under development (unstable) (2017-12-05 r73840) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(clusterExperiment)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

> 
> test_check("clusterExperiment")
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: Merging will be done on ' combineMany ', with clustering index 1 
Note: If `isCount=TRUE` the data will be transformed with voom() rather than
with the transformation function in the slot `transformation`.
This makes sense only for counts. 
Note: no clusters specified to combine, using results from clusterMany 
Note: Merging will be done on ' combineMany ', with clustering index 1 
Note: If `isCount=TRUE` the data will be transformed with voom() rather than
with the transformation function in the slot `transformation`.
This makes sense only for counts. 
Note: clusters will not be merged because argument 'mergeMethod' was not given (or was equal to 'none') 
Note: no clusters specified to combine, using results from clusterMany 
 [1] -1 -2 1  2  2  2  3  3  3  4  4  4  5  5  5 
Levels: -1 -2 1 2 3 4 5
class: ClusterExperiment 
dim: 20 15 
Primary cluster type: User 
Primary cluster label: Cluster1 
Table of clusters (of primary clustering):
-1 -2  1  2  3  4  5 
 1  1  1  3  3  3  3 
Total number of clusterings: 2 
No dendrogram present
-----------
Workflow progress:
clusterMany run? No 
combineMany run? No 
makeDendrogram run? No 
mergeClusters run? No 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: no clusters specified to combine, using results from clusterMany 
Note: no clusters specified to combine, using results from clusterMany 
Note: no clusters specified to combine, using results from clusterMany 
Note: Merging will be done on ' cluster1 ', with clustering index 21 
Note: Merging will be done on ' Cluster1 ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: no clusters specified to combine, using results from clusterMany 
Note: no clusters specified to combine, using results from clusterMany 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 2 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 2 
Note: Merging will be done on ' clusterSingle ', with clustering index 3 
Note: Merging will be done on ' clusterSingle ', with clustering index 4 
Note: Merging will be done on ' clusterSingle ', with clustering index 4 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' clusterSingle ', with clustering index 1 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: Merging will be done on ' nPCAFeatures=5,k=NA,findBestK=TRUE ', with clustering index 1 
Note: merging with these parameters did not result in any clusters being merged. 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
Note: makeDendrogram encountered following error and therefore clusters were not merged:
 Error in .local(x, ...) : all samples have clusterIds<0
 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 496 SKIPPED: 8 FAILED: 0
> 
> proc.time()
   user  system elapsed 
174.688   0.476 175.267 

Example timings

clusterExperiment.Rcheck/clusterExperiment-Ex.timings

nameusersystemelapsed
ClusterExperiment-class0.2560.0000.254
ClusterFunction-class0.0080.0000.009
addClusters1.0240.0001.024
builtInClusteringFunctions0.0000.0000.002
clusterContrasts1.4440.0121.493
clusterMany2.1280.0002.131
clusterSingle0.1040.0000.103
combineMany2.0080.0082.018
getBestFeatures1.6520.0321.684
getClusterManyParams1.3800.0001.383
mainClustering0.9080.0040.916
makeDendrogram1.0000.0041.007
mergeClusters3.3880.0043.394
plotBarplot1.9200.0121.939
plotClusters3.3640.0083.376
plotClustersWorkflow2.000.022.02
plotContrastHeatmap1.5360.0041.541
plotDendrogram1.0000.0041.003
plotDimReduce1.1680.0041.173
plotHeatmap16.476 0.03216.523
plottingFunctions1.9960.0001.998
rsecFluidigm000
seqCluster0.0040.0000.001
simData0.0000.0000.001
subsampleClustering000
transform0.0480.0000.050
workflowClusters1.1880.0081.196