Package: clusterExperiment

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clusterExperiment_1.4.0.tar.gz

StartedAt: 2018-04-12 01:50:59 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:00:43 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 583.9 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clusterExperiment/DESCRIPTION’ ... OK
* this is package ‘clusterExperiment’ version ‘1.4.0’
* 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 15.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc   13.2Mb
* 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       25.959  0.273  32.222
mergeClusters      4.408  0.042   5.771
plotClusters       4.090  0.097   5.862
plottingFunctions  3.756  0.032   5.110
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.

* 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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, cbind, colMeans, colSums, colnames, 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


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    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 
211.377   7.589 223.280 

name	user	system	elapsed
ClusterExperiment-class	0.309	0.030	0.424
ClusterFunction-class	0.014	0.000	0.021
addClusters	1.296	0.012	1.666
builtInClusteringFunctions	0.002	0.000	0.007
clusterContrasts	1.400	0.049	1.800
clusterMany	2.737	0.075	3.575
clusterSingle	0.124	0.007	0.168
combineMany	2.172	0.065	2.868
getBestFeatures	2.629	0.069	3.420
getClusterManyParams	1.865	0.070	2.497
mainClustering	1.305	0.057	1.675
makeDendrogram	1.640	0.018	2.131
mergeClusters	4.408	0.042	5.771
plotBarplot	1.664	0.064	2.385
plotClusters	4.090	0.097	5.862
plotClustersWorkflow	2.129	0.075	3.089
plotContrastHeatmap	2.687	0.037	3.715
plotDendrogram	1.898	0.019	2.677
plotDimReduce	1.437	0.065	1.903
plotHeatmap	25.959	0.273	32.222
plottingFunctions	3.756	0.032	5.110
rsecFluidigm	0.001	0.000	0.002
seqCluster	0.000	0.000	0.001
simData	0.002	0.000	0.006
subsampleClustering	0.001	0.000	0.000
transform	0.032	0.000	0.049
workflowClusters	1.455	0.063	1.978