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This page was generated on 2021-10-15 15:06:31 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the clusterExperiment package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clusterExperiment.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 330/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clusterExperiment 2.12.0 (landing page) Elizabeth Purdom
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | TIMEOUT | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
Package: clusterExperiment |
Version: 2.12.0 |
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_2.12.0.tar.gz |
StartedAt: 2021-10-14 17:32:09 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 18:12:11 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 2402.3 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: clusterExperiment.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/clusterExperiment.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘clusterExperiment/DESCRIPTION’ ... OK * this is package ‘clusterExperiment’ version ‘2.12.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 2.0Mb data 3.6Mb * 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 plotClusters 34.117 0.135 34.285 plotHeatmap 30.578 0.274 30.874 clusterMany 30.115 0.099 30.234 plotClustersWorkflow 28.810 0.112 28.947 plotBarplot 28.362 0.075 28.457 getClusterManyParams 17.993 0.073 18.079 clusterContrasts 15.882 0.092 15.985 workflowClusters 15.722 0.068 15.807 assignUnassigned 13.859 0.116 13.985 makeConsensus 12.445 0.055 12.515 plotClustersTable 12.149 0.043 12.202 plotReducedDims 8.776 0.028 8.810 plotFeatureBoxplot 8.446 0.030 8.485 ClusterExperiment-methods 8.229 0.206 8.445 mergeClusters 8.101 0.109 8.214 plotFeatureScatter 7.772 0.025 7.808 getBestFeatures 6.745 0.065 6.816 plotDendrogram 6.671 0.029 6.705 plotContrastHeatmap 6.549 0.054 6.611 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat_a-c.R’ Running ‘testthat_d-i.R’
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/4.1/Resources/library’ * installing *source* package ‘clusterExperiment’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c search_pairs.cpp -o search_pairs.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c subsampleLoop.cpp -o subsampleLoop.o clang++ -mmacosx-version-min=10.13 -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-darwin18/8.2.0 -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/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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: 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 objects are masked from 'package:base': I, expand.grid, unname 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by 'RNeXML' Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): PCA. Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by 'RNeXML' Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): PCA. Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by 'RNeXML' Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var. Note: Not all of the methods requested in 'reduceMethod' have been calculated. Will calculate all the methods requested (any pre-existing values -- filtering statistics or dimensionality reductions -- with these names will be recalculated and overwritten): var. 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. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 836 ] > > proc.time() user system elapsed 1265.858 10.852 1277.612
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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: 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 objects are masked from 'package:base': I, expand.grid, unname 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' Also defined by 'RNeXML'
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
name | user | system | elapsed | |
ClusterExperiment-class | 0.725 | 0.046 | 0.777 | |
ClusterExperiment-methods | 8.229 | 0.206 | 8.445 | |
ClusterFunction-class | 0.018 | 0.001 | 0.019 | |
addClusterings | 2.614 | 0.012 | 2.629 | |
assignUnassigned | 13.859 | 0.116 | 13.985 | |
builtInClusteringFunctions | 0.001 | 0.000 | 0.002 | |
clusterContrasts | 15.882 | 0.092 | 15.985 | |
clusterDendrogram | 1.055 | 0.017 | 1.073 | |
clusterMany | 30.115 | 0.099 | 30.234 | |
clusterSingle | 0.811 | 0.005 | 0.816 | |
fluidigmData | 0.000 | 0.001 | 0.000 | |
getBestFeatures | 6.745 | 0.065 | 6.816 | |
getClusterIndex | 0.958 | 0.011 | 0.971 | |
getClusterManyParams | 17.993 | 0.073 | 18.079 | |
mainClustering | 2.954 | 0.036 | 2.994 | |
makeConsensus | 12.445 | 0.055 | 12.515 | |
makeDendrogram | 4.688 | 0.032 | 4.724 | |
mergeClusters | 8.101 | 0.109 | 8.214 | |
numericalAsCharacter | 0.000 | 0.000 | 0.001 | |
plotBarplot | 28.362 | 0.075 | 28.457 | |
plotClusters | 34.117 | 0.135 | 34.285 | |
plotClustersTable | 12.149 | 0.043 | 12.202 | |
plotClustersWorkflow | 28.810 | 0.112 | 28.947 | |
plotContrastHeatmap | 6.549 | 0.054 | 6.611 | |
plotDendrogram | 6.671 | 0.029 | 6.705 | |
plotFeatureBoxplot | 8.446 | 0.030 | 8.485 | |
plotFeatureScatter | 7.772 | 0.025 | 7.808 | |
plotHeatmap | 30.578 | 0.274 | 30.874 | |
plotReducedDims | 8.776 | 0.028 | 8.810 | |
plottingFunctions | 3.158 | 0.037 | 3.199 | |
reduceFunctions | 1.190 | 0.020 | 1.212 | |
renameClusters | 0.978 | 0.008 | 0.987 | |
rsecFluidigm | 0.001 | 0.001 | 0.001 | |
seqCluster | 0.000 | 0.000 | 0.001 | |
simData | 0.000 | 0.001 | 0.001 | |
subsampleClustering | 0.001 | 0.001 | 0.000 | |
subset | 1.414 | 0.012 | 1.427 | |
transformData | 0.399 | 0.002 | 0.402 | |
workflowClusters | 15.722 | 0.068 | 15.807 | |