Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 618/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dreamlet 1.6.0  (landing page)
Gabriel Hoffman
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/dreamlet
git_branch: RELEASE_3_21
git_last_commit: 4c88cb1
git_last_commit_date: 2025-04-15 13:20:27 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for dreamlet on kjohnson1

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.

raw results


Summary

Package: dreamlet
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2025-10-14 20:08:57 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 20:21:24 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 746.7 seconds
RetCode: 0
Status:   OK  
CheckDir: dreamlet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/dreamlet.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 15.0.0 (clang-1500.0.40.1)’
* 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 ... 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 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      86.213  6.723  94.239
plotVarPart-methods     18.309  0.136  18.691
sortCols-method         17.870  0.104  18.196
plotPercentBars-methods 17.856  0.104  18.238
fitVarPart              17.510  0.139  18.114
meta_analysis           16.995  0.364  17.981
run_mash                13.385  0.120  13.666
compositePosteriorTest  12.169  0.157  12.550
stackAssays             10.133  0.120  10.358
aggregateNonCountSignal  7.668  0.400   8.178
plotVolcano-methods      5.263  0.069   5.397
processAssays            5.090  0.050   5.182
coefNames-methods        5.027  0.087   5.157
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/dreamlet.Rcheck/00check.log’
for details.


Installation output

dreamlet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL dreamlet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘dreamlet’ ...
** this is package ‘dreamlet’ version ‘1.6.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/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/4.5-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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 arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)

Tests output

dreamlet.Rcheck/tests/runTests.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 objects are masked from 'package:limma':

    eBayes, 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 check_dep_version(dep_pkg = "TMB") : package version mismatch: 
glmmTMB was built with TMB package version 1.9.17
Current TMB package version is 1.9.18
Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
> library(RUnit)
> 
> BiocGenerics:::testPackage("dreamlet")
  B cells...0.42 secs
  B cells...0.32 secs

Processing block [[1/1, 1/1]] ... OK
  B cells...0.37 secs
  CD14+ Monocytes...0.51 secs
  CD4 T cells...0.48 secs
  CD8 T cells...0.24 secs
  FCGR3A+ Monocytes...0.41 secs
  B cells...2.8 secs
  CD14+ Monocytes...3.9 secs
  CD4 T cells...3.2 secs
  CD8 T cells...1.9 secs
  FCGR3A+ Monocytes...3.7 secs


  B cells...0.2 secs
  CD14+ Monocytes...0.3 secs
  CD4 T cells...0.21 secs
  CD8 T cells...0.13 secs
  FCGR3A+ Monocytes...0.38 secs


RUNIT TEST PROTOCOL -- Tue Oct 14 20:21:11 2025 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
dreamlet RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 59.448   2.412  83.894 

Example timings

dreamlet.Rcheck/dreamlet-Ex.timings

nameusersystemelapsed
aggregateNonCountSignal7.6680.4008.178
aggregateToPseudoBulk0.8090.0330.854
aggregateVar1.0520.0711.136
as.dreamletResult1.3240.0491.389
buildClusterTreeFromPB0.5690.0290.601
cellCounts0.4830.0200.506
cellTypeSpecificity2.2150.0742.314
checkFormula0.0000.0000.001
coefNames-methods5.0270.0875.157
compositePosteriorTest12.169 0.15712.550
computeCellCounts0.2400.0160.264
computeLogCPM1.7410.0631.828
computeNormCounts0.3150.0290.348
details-methods2.5860.0352.648
diffVar-methods4.5520.0524.640
dreamlet3.6020.0403.665
dreamletCompareClusters3.1770.0423.239
dropRedundantTerms0.0050.0000.006
equalFormulas0.0000.0010.000
extractData-methods2.6560.0382.729
fitVarPart17.510 0.13918.114
getTreat-methods3.5370.0643.818
meta_analysis16.995 0.36417.981
outlier0.0030.0000.004
outlierByAssay2.6560.0392.722
plotBeeswarm4.1790.0524.341
plotCellComposition1.3440.0291.404
plotForest-methods4.0000.0384.076
plotGeneHeatmap-methods4.0700.0384.279
plotHeatmap-methods0.8570.0200.884
plotPCA4.6760.0654.779
plotPercentBars-methods17.856 0.10418.238
plotProjection0.7790.0540.817
plotVarPart-methods18.309 0.13618.691
plotViolin-methods1.1160.0341.165
plotVolcano-methods5.2630.0695.397
plotVoom-methods4.0060.0404.072
processAssays5.0900.0505.182
removeConstantTerms0.0050.0000.004
residuals-methods3.5520.0293.605
run_mash13.385 0.12013.666
seeErrors-methods3.6610.0833.789
sortCols-method17.870 0.10418.196
stackAssays10.133 0.12010.358
topTable-methods3.6300.0293.694
zenith_gsa-methods86.213 6.72394.239