Elizabeth Purdom
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/clusterExperiment |
| Branch: RELEASE_3_12 |
| Last Commit: 499be02 |
| Last Changed Date: 2021-02-05 16:08:37 -0400 (Fri, 05 Feb 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:19 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the clusterExperiment package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 321/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clusterExperiment 2.10.1 (landing page) Elizabeth Purdom
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: clusterExperiment |
| Version: 2.10.1 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clusterExperiment_2.10.1.tar.gz |
| StartedAt: 2021-05-06 01:31:28 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:10:24 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 2336.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: clusterExperiment.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clusterExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings clusterExperiment_2.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clusterExperiment/DESCRIPTION' ... OK
* this is package 'clusterExperiment' version '2.10.1'
* package encoding: UTF-8
* 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 whether package 'clusterExperiment' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:206: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:210: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:252: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:190: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:111: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:217: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:68: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:167: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:45: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:62: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/fluidigmData.Rd:30: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:78: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:79: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:87: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:135: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:248: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mainClustering.Rd:44: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/makeDendrogram.Rd:66: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mergeClusters.Rd:174: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:66: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:152: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:229: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotDendrogram.Rd:124: file link 'tiplabels' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureBoxplot.Rd:45: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:45: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:56: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:74: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:145: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:121: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:205: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:316: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/rsecFluidigm.Rd:51: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/seqCluster.Rd:25: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/subsampleClustering.Rd:37: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/transformData.Rd:37: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:55: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:61: file link 'nodeLabels' in package 'phylobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
R 1.3Mb
data 3.6Mb
libs 2.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/clusterExperiment/libs/i386/clusterExperiment.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/clusterExperiment/libs/x64/clusterExperiment.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotHeatmap 24.25 0.13 24.38
plotClusters 10.11 0.25 10.36
clusterMany 9.37 0.07 9.44
assignUnassigned 8.01 0.17 8.20
plotClustersWorkflow 8.10 0.05 8.14
plotBarplot 8.12 0.03 8.16
workflowClusters 7.59 0.04 7.64
getClusterManyParams 6.61 0.02 6.63
ClusterExperiment-methods 4.92 0.85 5.77
mergeClusters 5.69 0.00 5.69
clusterContrasts 5.27 0.26 6.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotHeatmap 30.25 0.16 30.43
plotClusters 16.76 0.03 16.80
clusterMany 13.24 0.14 13.37
plotBarplot 12.77 0.07 12.95
assignUnassigned 12.06 0.06 12.14
plotClustersWorkflow 11.31 0.06 11.38
workflowClusters 9.31 0.05 9.37
clusterContrasts 9.21 0.06 9.26
mergeClusters 7.94 0.03 9.25
getClusterManyParams 7.56 0.13 7.69
plotClustersTable 6.75 0.03 6.92
plotReducedDims 6.10 0.06 6.16
makeConsensus 6.11 0.03 6.25
ClusterExperiment-methods 5.80 0.16 5.95
getBestFeatures 5.61 0.01 5.64
plotDendrogram 5.26 0.00 5.27
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat_a-c.R'
Running 'testthat_d-i.R'
Running 'testthat_j-z.R'
OK
** running tests for arch 'x64' ...
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: 2 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.Rcheck/00check.log'
for details.
clusterExperiment.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/clusterExperiment_2.10.1.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.10.1.zip && rm clusterExperiment_2.10.1.tar.gz clusterExperiment_2.10.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4099k 100 4099k 0 0 70.7M 0 --:--:-- --:--:-- --:--:-- 72.7M
install for i386
* installing *source* package 'clusterExperiment' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs/i386
** 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
converting help for package 'clusterExperiment'
finding HTML links ... done
ClusterExperiment-class html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:206: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:210: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:252: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
ClusterExperiment-methods html
ClusterFunction-class html
ClusterFunction-methods html
RSEC html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:190: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
addClusterings html
assignUnassigned html
builtInClusteringFunctions html
clusterContrasts html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic
clusterDendrogram html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:111: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:217: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
clusterExperiment-deprecated html
clusterMany html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:68: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:167: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
clusterSingle html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:45: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:62: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
fluidigmData html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/fluidigmData.Rd:30: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
getBestFeatures html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:78: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:79: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:87: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:135: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:248: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
getClusterIndex html
getClusterManyParams html
mainClustering html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mainClustering.Rd:44: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
makeConsensus html
makeDendrogram html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/makeDendrogram.Rd:66: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
mergeClusters html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mergeClusters.Rd:174: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
numericalAsCharacter html
plotBarplot html
plotClusters html
plotClustersTable html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:66: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:152: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:229: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
plotClustersWorkflow html
plotContrastHeatmap html
plotDendrogram html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotDendrogram.Rd:124: file link 'tiplabels' in package 'ape' does not exist and so has been treated as a topic
plotFeatureBoxplot html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureBoxplot.Rd:45: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
plotFeatureScatter html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:45: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:56: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotHeatmap html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:74: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:145: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
plotReducedDims html
plottingFunctions html
reduceFunctions html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:121: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:205: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:316: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
renameClusters html
rsecFluidigm html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/rsecFluidigm.Rd:51: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
search_pairs html
seqCluster html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/seqCluster.Rd:25: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
simData html
subsampleClustering html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/subsampleClustering.Rd:37: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
subset html
transformData html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/transformData.Rd:37: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
updateObject html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:55: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:61: file link 'nodeLabels' in package 'phylobase' does not exist and so has been treated as a topic
workflowClusters html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'clusterExperiment' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_2.10.1.zip
* DONE (clusterExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'clusterExperiment' successfully unpacked and MD5 sums checked
|
clusterExperiment.Rcheck/tests_i386/testthat_a-c.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
== Skipped tests ===============================================================
* On Windows (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 831 ]
>
> proc.time()
user system elapsed
337.23 6.12 346.51
|
clusterExperiment.Rcheck/tests_x64/testthat_a-c.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
3 parameter combinations, 0 use sequential method, 0 use subsampling method
Running Clustering on Parameter Combinations...
done.
== Skipped tests ===============================================================
* On Windows (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 831 ]
>
> proc.time()
user system elapsed
316.95 2.92 321.93
|
|
clusterExperiment.Rcheck/tests_i386/testthat_d-i.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 416 ]
>
> proc.time()
user system elapsed
232.00 3.32 235.34
|
clusterExperiment.Rcheck/tests_x64/testthat_d-i.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 416 ]
>
> proc.time()
user system elapsed
228.23 1.06 229.37
|
|
clusterExperiment.Rcheck/tests_i386/testthat_j-z.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
== Skipped tests ===============================================================
* On Bioconductor (1)
* On Windows (4)
[ FAIL 0 | WARN 0 | SKIP 5 | PASS 338 ]
>
> proc.time()
user system elapsed
182.89 3.95 187.06
|
clusterExperiment.Rcheck/tests_x64/testthat_j-z.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
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.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
== Skipped tests ===============================================================
* On Bioconductor (1)
* On Windows (4)
[ FAIL 0 | WARN 0 | SKIP 5 | PASS 338 ]
>
> proc.time()
user system elapsed
188.26 1.73 190.92
|
|
clusterExperiment.Rcheck/examples_i386/clusterExperiment-Ex.timings
|
clusterExperiment.Rcheck/examples_x64/clusterExperiment-Ex.timings
|