Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:41 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 |
Package 608/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
dreamlet 1.2.1 (landing page) Gabriel Hoffman
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the dreamlet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/dreamlet.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: dreamlet |
Version: 1.2.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dreamlet_1.2.1.tar.gz |
StartedAt: 2024-06-24 03:46:41 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 04:15:00 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1698.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: dreamlet.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dreamlet_1.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘dreamlet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘dreamlet’ version ‘1.2.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘dreamlet’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) meta_analysis.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) meta_analysis.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) outlierByAssay.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) outlierByAssay.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly * 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 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’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed zenith_gsa-methods 176.680 8.246 215.486 fitVarPart 48.927 0.523 58.736 plotVarPart-methods 46.368 0.302 54.012 sortCols-method 45.877 0.449 51.404 plotPercentBars-methods 45.740 0.342 54.469 meta_analysis 37.282 0.628 46.000 stackAssays 26.480 0.252 31.087 aggregateNonCountSignal 14.912 0.954 20.295 run_mash 14.784 0.221 17.388 compositePosteriorTest 12.780 0.209 16.694 plotVolcano-methods 11.423 0.131 13.469 diffVar-methods 10.515 0.188 11.653 plotPCA 10.109 0.141 12.280 plotBeeswarm 9.662 0.143 11.895 dreamlet 8.757 0.131 10.144 plotGeneHeatmap-methods 8.213 0.089 9.727 plotForest-methods 8.125 0.104 9.877 topTable-methods 7.685 0.061 8.927 getTreat-methods 7.653 0.091 9.350 residuals-methods 7.593 0.072 8.845 processAssays 7.531 0.064 8.778 coefNames-methods 7.435 0.087 8.660 seeErrors-methods 7.321 0.106 7.737 getExprGeneNames 6.702 0.103 8.255 pbWeights 6.673 0.117 7.994 plotVoom-methods 6.503 0.085 7.442 dreamletCompareClusters 6.310 0.088 7.334 cellTypeSpecificity 4.872 0.081 5.570 extractData-methods 4.614 0.072 6.082 outlierByAssay 4.523 0.054 5.471 as.dreamletResult 4.193 0.082 5.799 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck/00check.log’ for details.
dreamlet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dreamlet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘dreamlet’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from colsum_beachmat.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3) virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual] sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-dreamlet/00new/dreamlet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help Loading required namespace: variancePartition Loading required namespace: dreamlet *** installing help indices *** copying figures ** 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 (dreamlet)
dreamlet.Rcheck/tests/runTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(Matrix) > library(dreamlet) Loading required package: variancePartition Loading required package: ggplot2 Loading required package: limma Loading required package: BiocParallel Attaching package: 'variancePartition' The following object is masked from 'package:limma': topTable 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 object is masked from 'package:limma': plotMA 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, aperm, 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, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname The following object is masked from 'package:utils': findMatches 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 > library(DelayedArray) Loading required package: S4Arrays Loading required package: abind Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Loading required package: SparseArray Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep > library(edgeR) Attaching package: 'edgeR' The following object is masked from 'package:SingleCellExperiment': cpm > library(muscat) Warning message: In checkDepPackageVersion(dep_pkg = "TMB") : Package version inconsistency detected. glmmTMB was built with TMB version 1.9.11 Current TMB version is 1.9.12 Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information) > library(RUnit) > > BiocGenerics:::testPackage("dreamlet") Processing: B cells Computing library sizes... Processing samples... Processing: CD14+ Monocytes Computing library sizes... Processing samples... Processing: CD4 T cells Computing library sizes... Processing samples... Processing: CD8 T cells Computing library sizes... Processing samples... Processing: FCGR3A+ Monocytes Computing library sizes... Processing samples... B cells...0.72 secs CD14+ Monocytes...0.88 secs CD4 T cells...0.71 secs CD8 T cells...0.53 secs FCGR3A+ Monocytes...1.1 secs B cells...0.67 secs CD14+ Monocytes...0.89 secs CD4 T cells...0.68 secs CD8 T cells...0.41 secs FCGR3A+ Monocytes...0.86 secs B cells...0.61 secs CD14+ Monocytes...0.92 secs CD4 T cells...0.65 secs CD8 T cells...0.42 secs FCGR3A+ Monocytes...0.86 secs Processing: B cells Computing library sizes... Processing samples... Processing: CD14+ Monocytes Computing library sizes... Processing samples... Processing: CD4 T cells Computing library sizes... Processing samples... Processing: CD8 T cells Computing library sizes... Processing samples... Processing: FCGR3A+ Monocytes Computing library sizes... Processing samples... B cells...0.62 secs CD14+ Monocytes...0.82 secs CD4 T cells...0.65 secs CD8 T cells...0.41 secs FCGR3A+ Monocytes...0.95 secs B cells...0.58 secs CD14+ Monocytes...0.89 secs CD4 T cells...0.7 secs CD8 T cells...0.47 secs FCGR3A+ Monocytes...0.81 secs B cells...0.59 secs B cells...0.54 secs Processing block [[1/1, 1/1]] ... OK B cells...0.61 secs CD14+ Monocytes...0.77 secs CD4 T cells...0.7 secs CD8 T cells...0.49 secs FCGR3A+ Monocytes...0.68 secs B cells...9.3 secs CD14+ Monocytes...12 secs CD4 T cells...9.6 secs CD8 T cells...5.3 secs FCGR3A+ Monocytes...10 secs B cells...0.6 secs CD14+ Monocytes...0.87 secs CD4 T cells...0.58 secs CD8 T cells...0.35 secs FCGR3A+ Monocytes...0.72 secs RUNIT TEST PROTOCOL -- Mon Jun 24 04:14:20 2024 *********************************************** Number of test functions: 12 Number of errors: 0 Number of failures: 0 1 Test Suite : dreamlet RUnit Tests - 12 test functions, 0 errors, 0 failures Number of test functions: 12 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 144.875 4.299 202.356
dreamlet.Rcheck/dreamlet-Ex.timings
name | user | system | elapsed | |
aggregateNonCountSignal | 14.912 | 0.954 | 20.295 | |
aggregateToPseudoBulk | 2.425 | 0.059 | 3.229 | |
aggregateVar | 2.670 | 0.040 | 3.388 | |
as.dreamletResult | 4.193 | 0.082 | 5.799 | |
buildClusterTreeFromPB | 1.372 | 0.040 | 2.030 | |
cellCounts | 1.257 | 0.058 | 1.676 | |
cellTypeSpecificity | 4.872 | 0.081 | 5.570 | |
checkFormula | 0.000 | 0.002 | 0.002 | |
coefNames-methods | 7.435 | 0.087 | 8.660 | |
compositePosteriorTest | 12.780 | 0.209 | 16.694 | |
computeCellCounts | 0.281 | 0.017 | 0.328 | |
computeLogCPM | 0.640 | 0.076 | 0.740 | |
computeNormCounts | 0.425 | 0.040 | 0.478 | |
details-methods | 4.231 | 0.099 | 4.508 | |
diffVar-methods | 10.515 | 0.188 | 11.653 | |
dreamlet | 8.757 | 0.131 | 10.144 | |
dreamletCompareClusters | 6.310 | 0.088 | 7.334 | |
dropRedundantTerms | 0.011 | 0.001 | 0.022 | |
equalFormulas | 0.001 | 0.001 | 0.001 | |
extractData-methods | 4.614 | 0.072 | 6.082 | |
fitVarPart | 48.927 | 0.523 | 58.736 | |
getExprGeneNames | 6.702 | 0.103 | 8.255 | |
getTreat-methods | 7.653 | 0.091 | 9.350 | |
meta_analysis | 37.282 | 0.628 | 46.000 | |
outlier | 0.005 | 0.002 | 0.008 | |
outlierByAssay | 4.523 | 0.054 | 5.471 | |
pbWeights | 6.673 | 0.117 | 7.994 | |
plotBeeswarm | 9.662 | 0.143 | 11.895 | |
plotCellComposition | 2.298 | 0.038 | 2.825 | |
plotForest-methods | 8.125 | 0.104 | 9.877 | |
plotGeneHeatmap-methods | 8.213 | 0.089 | 9.727 | |
plotHeatmap-methods | 1.767 | 0.029 | 2.113 | |
plotPCA | 10.109 | 0.141 | 12.280 | |
plotPercentBars-methods | 45.740 | 0.342 | 54.469 | |
plotProjection | 2.290 | 0.061 | 2.831 | |
plotVarPart-methods | 46.368 | 0.302 | 54.012 | |
plotViolin-methods | 2.385 | 0.033 | 2.803 | |
plotVolcano-methods | 11.423 | 0.131 | 13.469 | |
plotVoom-methods | 6.503 | 0.085 | 7.442 | |
processAssays | 7.531 | 0.064 | 8.778 | |
removeConstantTerms | 0.011 | 0.001 | 0.013 | |
residuals-methods | 7.593 | 0.072 | 8.845 | |
run_mash | 14.784 | 0.221 | 17.388 | |
seeErrors-methods | 7.321 | 0.106 | 7.737 | |
sortCols-method | 45.877 | 0.449 | 51.404 | |
stackAssays | 26.480 | 0.252 | 31.087 | |
topTable-methods | 7.685 | 0.061 | 8.927 | |
zenith_gsa-methods | 176.680 | 8.246 | 215.486 | |