Elizabeth Purdom
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/clusterExperiment |
| Branch: RELEASE_3_9 |
| Last Commit: 7199648 |
| Last Changed Date: 2019-06-07 14:39:55 -0400 (Fri, 07 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:09:14 -0400 (Wed, 16 Oct 2019).
| Package 292/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterExperiment 2.4.4 Elizabeth Purdom
| malbec2 | Linux (Ubuntu 18.04.2 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: 2.4.4 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clusterExperiment_2.4.4.tar.gz |
| StartedAt: 2019-10-16 00:35:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:51:35 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 955.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: 3 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clusterExperiment_2.4.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.4.4’
* 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:
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-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 ... 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 ... WARNING
Undocumented S4 methods:
generic 'defaultNDims' and siglist 'matrixOrHDF5'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 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 25.993 0.040 26.048
plotClusters 7.329 0.004 7.354
assignUnassigned 5.403 0.156 5.575
* 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: 3 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.Rcheck/00check.log’
for details.
clusterExperiment.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL clusterExperiment
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘clusterExperiment’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c search_pairs.cpp -o search_pairs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function ‘Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)’:
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
~~^~~~~~~~~~~~~~~~~~~
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
~~^~~~~~~~~~~~~~~~~~~
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if((it->second).first>0 | (it->second).second==NA_INTEGER){
~~~~~~~~~~~~~~~~~~^~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-clusterExperiment/00new/clusterExperiment/libs
** R
** data
** byte-compile and prepare 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 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> 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: 781 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
251.247 1.338 257.857
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> 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
112.926 0.770 113.726
clusterExperiment.Rcheck/tests/testthat_j-z.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
> 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
141.263 1.200 142.380
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
| name | user | system | elapsed | |
| ClusterExperiment-class | 0.304 | 0.000 | 0.304 | |
| ClusterFunction-class | 0.014 | 0.000 | 0.014 | |
| addClusterings | 1.832 | 0.012 | 1.848 | |
| assignUnassigned | 5.403 | 0.156 | 5.575 | |
| builtInClusteringFunctions | 0.000 | 0.000 | 0.001 | |
| clusterContrasts | 2.691 | 0.008 | 2.713 | |
| clusterMany | 4.691 | 0.008 | 4.700 | |
| clusterSingle | 0.163 | 0.004 | 0.167 | |
| getBestFeatures | 3.688 | 0.004 | 3.693 | |
| getClusterManyParams | 3.803 | 0.008 | 3.812 | |
| mainClustering | 0.808 | 0.012 | 0.820 | |
| makeConsensus | 2.685 | 0.000 | 2.685 | |
| makeDendrogram | 0.917 | 0.004 | 0.920 | |
| mergeClusters | 2.748 | 0.004 | 2.752 | |
| numericalAsCharacter | 0.001 | 0.000 | 0.001 | |
| plotBarplot | 4.327 | 0.000 | 4.339 | |
| plotClusters | 7.329 | 0.004 | 7.354 | |
| plotClustersTable | 3.690 | 0.000 | 3.692 | |
| plotClustersWorkflow | 3.691 | 0.000 | 3.691 | |
| plotContrastHeatmap | 2.176 | 0.000 | 2.176 | |
| plotDendrogram | 1.899 | 0.004 | 1.915 | |
| plotFeatureBoxplot | 1.919 | 0.000 | 1.919 | |
| plotFeatureScatter | 2.042 | 0.004 | 2.046 | |
| plotHeatmap | 25.993 | 0.040 | 26.048 | |
| plotReducedDims | 1.502 | 0.004 | 1.506 | |
| plottingFunctions | 3.154 | 0.000 | 3.153 | |
| reduceFunctions | 0.215 | 0.000 | 0.214 | |
| rsecFluidigm | 0 | 0 | 0 | |
| seqCluster | 0.001 | 0.000 | 0.000 | |
| simData | 0.000 | 0.001 | 0.000 | |
| subsampleClustering | 0 | 0 | 0 | |
| transformData | 0.077 | 0.002 | 0.079 | |
| workflowClusters | 2.239 | 0.008 | 2.248 | |