Elizabeth Purdom
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:48 -0400 (Wed, 17 Oct 2018).
| Package 261/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterExperiment 2.0.2 Elizabeth Purdom
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: clusterExperiment |
| Version: 2.0.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterExperiment_2.0.2.tar.gz |
| StartedAt: 2018-10-16 20:32:03 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:45:40 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 816.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clusterExperiment_2.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘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 ‘/Users/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 26.796 0.311 27.321
plotClusters 8.710 0.161 8.964
clusterMany 6.863 0.193 7.121
plotBarplot 5.830 0.124 6.020
plotClustersWorkflow 5.383 0.156 5.577
getClusterManyParams 5.316 0.126 5.499
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.
clusterExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clusterExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘clusterExperiment’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c search_pairs.cpp -o search_pairs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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)
clusterExperiment.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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: 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
404.950 14.829 427.049
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
| name | user | system | elapsed | |
| ClusterExperiment-class | 0.503 | 0.004 | 0.514 | |
| ClusterFunction-class | 0.011 | 0.001 | 0.011 | |
| addClusterings | 1.006 | 0.013 | 1.030 | |
| builtInClusteringFunctions | 0.004 | 0.000 | 0.004 | |
| clusterContrasts | 4.142 | 0.119 | 4.313 | |
| clusterMany | 6.863 | 0.193 | 7.121 | |
| clusterSingle | 0.351 | 0.009 | 0.363 | |
| combineMany | 4.057 | 0.099 | 4.204 | |
| getBestFeatures | 1.981 | 0.053 | 2.067 | |
| getClusterManyParams | 5.316 | 0.126 | 5.499 | |
| mainClustering | 1.369 | 0.085 | 1.468 | |
| makeDendrogram | 1.223 | 0.016 | 1.252 | |
| mergeClusters | 4.003 | 0.084 | 4.147 | |
| plotBarplot | 5.830 | 0.124 | 6.020 | |
| plotClusters | 8.710 | 0.161 | 8.964 | |
| plotClustersWorkflow | 5.383 | 0.156 | 5.577 | |
| plotContrastHeatmap | 2.744 | 0.041 | 2.804 | |
| plotDendrogram | 2.151 | 0.035 | 2.207 | |
| plotFeatureBoxplot | 2.346 | 0.051 | 2.417 | |
| plotHeatmap | 26.796 | 0.311 | 27.321 | |
| plotReducedDims | 2.330 | 0.061 | 2.414 | |
| plottingFunctions | 3.154 | 0.040 | 3.220 | |
| reduceFunctions | 0.366 | 0.011 | 0.378 | |
| rsecFluidigm | 0.003 | 0.001 | 0.003 | |
| seqCluster | 0.002 | 0.000 | 0.002 | |
| simData | 0.004 | 0.001 | 0.005 | |
| subsampleClustering | 0.002 | 0.001 | 0.003 | |
| transformData | 0.107 | 0.000 | 0.107 | |
| workflowClusters | 3.205 | 0.075 | 3.289 | |