Elizabeth Purdom
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/clusterExperiment |
| Branch: master |
| Last Commit: 59568a4 |
| Last Changed Date: 2019-10-29 13:41:48 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:45:38 -0500 (Thu, 16 Jan 2020).
| Package 308/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterExperiment 2.7.0 Elizabeth Purdom
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: clusterExperiment |
| Version: 2.7.0 |
| 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_2.7.0.tar.gz |
| StartedAt: 2020-01-16 02:58:54 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 03:34:24 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 2130.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running 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_2.7.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clusterExperiment.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.7.0’
* 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 dependencies in R code ... OK
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Output for data("rsecFluidigm", package = "clusterExperiment"):
Search path was changed
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotHeatmap 39.881 0.881 40.948
plotClusters 16.151 0.342 16.505
assignUnassigned 14.231 0.180 14.412
clusterMany 12.916 0.189 13.108
plotBarplot 11.502 0.240 11.743
plotClustersWorkflow 10.265 0.181 10.447
getClusterManyParams 9.919 0.380 10.301
workflowClusters 9.328 0.160 9.498
mergeClusters 8.537 0.490 9.028
clusterContrasts 8.757 0.200 8.972
makeConsensus 6.877 0.189 7.069
getBestFeatures 6.567 0.209 7.318
plotClustersTable 6.400 0.104 6.506
plotContrastHeatmap 5.796 0.157 5.956
plotDendrogram 5.777 0.092 5.878
plottingFunctions 5.016 0.212 5.252
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat_a-c.R’
Running ‘testthat_d-i.R’
Running ‘testthat_j-z.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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’ * installing *source* package ‘clusterExperiment’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/00LOCK-clusterExperiment/00new/clusterExperiment/libs ** R ** data ** byte-compile and prepare package for lazy loading From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; [where=<environment: 0x7f9e7bc05a10>, where2=<environment: namespace:clusterExperiment>] From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; [where=<environment: 0x7f9e7bc05a10>, where2=<environment: namespace:clusterExperiment>] From .checkSubclasses(): subclass "ReshapedHDF5Matrix" of class "HDF5Matrix" is not local and is not updated for new inheritance information currently; [where=<environment: 0x7f9e7bc05a10>, where2=<environment: namespace:clusterExperiment>] 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 from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clusterExperiment)
clusterExperiment.Rcheck/tests/testthat_a-c.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> test_check("clusterExperiment",filter = "^[A-Ca-c]")
Loading required package: 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 782 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
565.512 34.537 620.466
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> test_check("clusterExperiment",filter = "^[D-Id-i]")
Loading required package: 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 416 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
382.520 6.850 398.329
clusterExperiment.Rcheck/tests/testthat_j-z.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
> test_check("clusterExperiment",filter = "^[J-Zj-z]")
Loading required package: 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, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, 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, rowsum
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 334 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
316.285 16.100 340.791
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
| name | user | system | elapsed | |
| ClusterExperiment-class | 0.572 | 0.043 | 0.616 | |
| ClusterFunction-class | 0.022 | 0.005 | 0.026 | |
| addClusterings | 1.842 | 0.085 | 1.927 | |
| assignUnassigned | 14.231 | 0.180 | 14.412 | |
| builtInClusteringFunctions | 0.002 | 0.001 | 0.002 | |
| clusterContrasts | 8.757 | 0.200 | 8.972 | |
| clusterMany | 12.916 | 0.189 | 13.108 | |
| clusterSingle | 0.408 | 0.015 | 0.423 | |
| getBestFeatures | 6.567 | 0.209 | 7.318 | |
| getClusterManyParams | 9.919 | 0.380 | 10.301 | |
| mainClustering | 1.274 | 0.169 | 1.442 | |
| makeConsensus | 6.877 | 0.189 | 7.069 | |
| makeDendrogram | 3.590 | 0.078 | 3.671 | |
| mergeClusters | 8.537 | 0.490 | 9.028 | |
| numericalAsCharacter | 0.001 | 0.000 | 0.001 | |
| plotBarplot | 11.502 | 0.240 | 11.743 | |
| plotClusters | 16.151 | 0.342 | 16.505 | |
| plotClustersTable | 6.400 | 0.104 | 6.506 | |
| plotClustersWorkflow | 10.265 | 0.181 | 10.447 | |
| plotContrastHeatmap | 5.796 | 0.157 | 5.956 | |
| plotDendrogram | 5.777 | 0.092 | 5.878 | |
| plotFeatureBoxplot | 3.800 | 0.196 | 3.997 | |
| plotFeatureScatter | 3.426 | 0.103 | 3.529 | |
| plotHeatmap | 39.881 | 0.881 | 40.948 | |
| plotReducedDims | 4.337 | 0.087 | 4.433 | |
| plottingFunctions | 5.016 | 0.212 | 5.252 | |
| reduceFunctions | 0.466 | 0.026 | 0.492 | |
| rsecFluidigm | 0.001 | 0.000 | 0.001 | |
| seqCluster | 0.001 | 0.000 | 0.001 | |
| simData | 0.000 | 0.001 | 0.002 | |
| subsampleClustering | 0.000 | 0.001 | 0.001 | |
| transformData | 0.245 | 0.001 | 0.246 | |
| workflowClusters | 9.328 | 0.160 | 9.498 | |