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CHECK report for clusterExperiment on malbec2

This page was generated on 2018-07-19 10:40:14 -0400 (Thu, 19 Jul 2018).

Package 261/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clusterExperiment 2.0.2
Elizabeth Purdom
Snapshot Date: 2018-07-18 16:45:10 -0400 (Wed, 18 Jul 2018)
URL: https://git.bioconductor.org/packages/clusterExperiment
Branch: RELEASE_3_7
Last Commit: fc89949
Last Changed Date: 2018-05-17 05:43:11 -0400 (Thu, 17 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clusterExperiment
Version: 2.0.2
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings clusterExperiment_2.0.2.tar.gz
StartedAt: 2018-07-18 23:12:22 -0400 (Wed, 18 Jul 2018)
EndedAt: 2018-07-18 23:21:14 -0400 (Wed, 18 Jul 2018)
EllapsedTime: 532.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clusterExperiment.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings clusterExperiment_2.0.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.5.1 RC (2018-06-24 r74929)
* 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 ‘2.0.2’
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "DelayedArray1" of class "DelayedArray" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/home/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... NOTE
':::' call which should be '::': ‘ape:::reorder.phylo’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .C(ape::node_depth, ...)
  .C(ape::node_depth_edgelength, ...)
  .C(ape::node_height, ...)
  .C(ape::node_height_clado, ...)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Codoc mismatches from documentation object 'reduceFunctions':
\S4method{makeFilterStats}{SummarizedExperiment}
  Code: function(object, filterStats = listBuiltInFilterStats(),
                 transFun = NULL, isCount = FALSE, filterNames = NULL)
  Docs: function(object, filterStats = listBuiltInFilterStats(),
                 transFun = NULL, isCount = FALSE)
  Argument names in code not in docs:
    filterNames

* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotHeatmap  16.004  0.016  16.029
clusterMany   5.324  0.048   5.392
plotClusters  5.132  0.004   5.138
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.



Installation output

clusterExperiment.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL clusterExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘clusterExperiment’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c search_pairs.cpp -o search_pairs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.7-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/clusterExperiment/libs
** R
** data
** byte-compile and prepare package for lazy loading
Warning: subclass "DelayedArray1" of class "DelayedArray" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "DelayedArray1" of class "DelayedArray" is not local and cannot be updated for new inheritance information; consider setClassUnion()
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 version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 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: SingleCellExperiment
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")
[1] "pam"
[1] "clara"
[1] "kmeans"
[1] "hierarchicalK"
[1] "spectral"
[1] "hierarchical01"
[1] "tight"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1220 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
274.748   1.412 276.390 

Example timings

clusterExperiment.Rcheck/clusterExperiment-Ex.timings

nameusersystemelapsed
ClusterExperiment-class0.5240.0000.524
ClusterFunction-class0.0160.0000.016
addClusterings0.7440.0040.750
builtInClusteringFunctions0.0000.0000.001
clusterContrasts3.3160.0403.390
clusterMany5.3240.0485.392
clusterSingle0.2200.0000.221
combineMany2.6000.0122.612
getBestFeatures1.1960.0001.196
getClusterManyParams3.7360.0123.750
mainClustering0.7720.0160.786
makeDendrogram0.7200.0000.722
mergeClusters3.2480.0003.254
plotBarplot4.7120.0004.719
plotClusters5.1320.0045.138
plotClustersWorkflow3.8400.0003.841
plotContrastHeatmap1.7000.0041.704
plotDendrogram1.4680.0121.480
plotFeatureBoxplot1.4600.0081.469
plotHeatmap16.004 0.01616.029
plotReducedDims1.6360.0081.645
plottingFunctions2.760.002.76
reduceFunctions0.2560.0000.257
rsecFluidigm0.0040.0000.001
seqCluster000
simData0.0040.0000.002
subsampleClustering000
transformData0.0880.0000.086
workflowClusters2.2840.0282.314