Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-05-23 12:05:03 -0400 (Mon, 23 May 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4380 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4155 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4221 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 346/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
clusterExperiment 2.16.0 (landing page) Elizabeth Purdom
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: clusterExperiment |
Version: 2.16.0 |
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings clusterExperiment_2.16.0.tar.gz |
StartedAt: 2022-05-22 18:55:19 -0400 (Sun, 22 May 2022) |
EndedAt: 2022-05-22 19:13:44 -0400 (Sun, 22 May 2022) |
EllapsedTime: 1105.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: clusterExperiment.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:clusterExperiment.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings clusterExperiment_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/clusterExperiment.Rcheck’ * using R version 4.2.0 (2022-04-22) * 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 ‘2.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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: .BBSoptions 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 1.1Mb data 3.6Mb libs 1.1Mb * 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 * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .C(ape::node_depth, ...) .C(ape::node_depth_edgelength, ...) .C(ape::node_height, ...) .C(ape::node_height_clado, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... WARNING Output for data("rsecFluidigm", package = "clusterExperiment"): Search path was changed * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotHeatmap 15.433 0.140 15.575 plotClusters 12.811 0.043 12.855 clusterMany 11.643 0.211 11.855 plotBarplot 10.897 0.104 11.003 plotClustersWorkflow 10.327 0.068 10.395 getClusterManyParams 7.939 0.241 8.179 clusterContrasts 6.551 0.181 6.732 workflowClusters 6.381 0.004 6.385 assignUnassigned 5.143 0.240 5.383 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat_a-c.R’ Running ‘testthat_d-i.R’ Running ‘testthat_j-z.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.15-bioc/meat/clusterExperiment.Rcheck/00check.log’ for details.
clusterExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL clusterExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’ * installing *source* package ‘clusterExperiment’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c subsampleLoop.cpp -o subsampleLoop.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o clusterExperiment.so RcppExports.o search_pairs.o subsampleLoop.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.15-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 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: 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 Attaching package: 'BiocGenerics' 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' 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 817 ] > > proc.time() user system elapsed 332.161 3.792 335.860
clusterExperiment.Rcheck/tests/testthat_d-i.Rout
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 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: 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 Attaching package: 'BiocGenerics' 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' [ FAIL 0 | WARN 2 | SKIP 0 | PASS 415 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 415 ] > > proc.time() user system elapsed 182.091 2.532 184.621
clusterExperiment.Rcheck/tests/testthat_j-z.Rout
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 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: 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 Attaching package: 'BiocGenerics' 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' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 349 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • On Bioconductor (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 349 ] > > proc.time() user system elapsed 148.655 2.513 151.042
clusterExperiment.Rcheck/clusterExperiment-Ex.timings
name | user | system | elapsed | |
ClusterExperiment-class | 0.321 | 0.035 | 0.357 | |
ClusterExperiment-methods | 3.048 | 0.176 | 3.223 | |
ClusterFunction-class | 0.009 | 0.003 | 0.013 | |
addClusterings | 1.065 | 0.033 | 1.097 | |
assignUnassigned | 5.143 | 0.240 | 5.383 | |
builtInClusteringFunctions | 0.000 | 0.001 | 0.001 | |
clusterContrasts | 6.551 | 0.181 | 6.732 | |
clusterDendrogram | 0.561 | 0.008 | 0.569 | |
clusterMany | 11.643 | 0.211 | 11.855 | |
clusterSingle | 0.382 | 0.001 | 0.382 | |
fluidigmData | 0.000 | 0.000 | 0.001 | |
getBestFeatures | 2.737 | 0.023 | 2.762 | |
getClusterIndex | 0.545 | 0.003 | 0.549 | |
getClusterManyParams | 7.939 | 0.241 | 8.179 | |
mainClustering | 1.469 | 0.032 | 1.501 | |
makeConsensus | 4.754 | 0.068 | 4.822 | |
makeDendrogram | 1.874 | 0.016 | 1.889 | |
mergeClusters | 3.616 | 0.028 | 3.643 | |
numericalAsCharacter | 0.001 | 0.000 | 0.000 | |
plotBarplot | 10.897 | 0.104 | 11.003 | |
plotClusters | 12.811 | 0.043 | 12.855 | |
plotClustersTable | 4.075 | 0.059 | 4.136 | |
plotClustersWorkflow | 10.327 | 0.068 | 10.395 | |
plotContrastHeatmap | 2.677 | 0.044 | 2.721 | |
plotDendrogram | 2.543 | 0.008 | 2.550 | |
plotFeatureBoxplot | 3.306 | 0.040 | 3.347 | |
plotFeatureScatter | 3.227 | 0.004 | 3.231 | |
plotHeatmap | 15.433 | 0.140 | 15.575 | |
plotReducedDims | 3.720 | 0.012 | 3.732 | |
plottingFunctions | 2.226 | 0.000 | 2.226 | |
reduceFunctions | 0.534 | 0.012 | 0.545 | |
renameClusters | 0.439 | 0.004 | 0.443 | |
rsecFluidigm | 0.000 | 0.002 | 0.002 | |
seqCluster | 0.000 | 0.001 | 0.001 | |
simData | 0.000 | 0.001 | 0.001 | |
subsampleClustering | 0.001 | 0.000 | 0.001 | |
subset | 0.633 | 0.008 | 0.641 | |
transformData | 0.181 | 0.008 | 0.189 | |
workflowClusters | 6.381 | 0.004 | 6.385 | |