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This page was generated on 2024-03-27 11:39:21 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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Package 601/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dreamlet 1.1.18  (landing page)
Gabriel Hoffman
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/dreamlet
git_branch: devel
git_last_commit: 836366e
git_last_commit_date: 2024-02-14 12:30:42 -0400 (Wed, 14 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for dreamlet on lconway


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: 1.1.18
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_1.1.18.tar.gz
StartedAt: 2024-03-26 20:18:44 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 20:31:54 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 789.7 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_1.1.18.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/dreamlet.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.1.18’
* 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      100.182  5.756 107.064
fitVarPart               22.978  0.256  23.422
plotVarPart-methods      22.194  0.270  22.681
sortCols-method          21.799  0.206  22.161
plotPercentBars-methods  21.364  0.220  21.751
meta_analysis            20.066  0.465  20.734
stackAssays              12.223  0.131  12.430
run_mash                 10.504  0.225  10.811
compositePosteriorTest    9.492  0.165   9.758
aggregateNonCountSignal   7.650  0.488   8.345
plotVolcano-methods       5.888  0.118   6.072
diffVar-methods           5.785  0.105   5.959
plotPCA                   4.960  0.105   5.104
* 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.


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/4.4-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 -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 -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 -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)

Tests output

dreamlet.Rcheck/tests/runTests.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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 checkMatrixPackageVersion(getOption("TMB.check.Matrix", TRUE)) :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.5
Current Matrix version is 1.7.0
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
> 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...0.4 secs
  CD14+ Monocytes...0.42 secs
  CD4 T cells...0.32 secs
  CD8 T cells...0.2 secs
  FCGR3A+ Monocytes...0.5 secs
  B cells...0.28 secs
  CD14+ Monocytes...0.45 secs
  CD4 T cells...0.34 secs
  CD8 T cells...0.2 secs
  FCGR3A+ Monocytes...0.43 secs
  B cells...0.26 secs
  CD14+ Monocytes...0.41 secs
  CD4 T cells...0.29 secs
  CD8 T cells...0.19 secs
  FCGR3A+ Monocytes...0.39 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...0.27 secs
  CD14+ Monocytes...0.39 secs
  CD4 T cells...0.32 secs
  CD8 T cells...0.2 secs
  FCGR3A+ Monocytes...0.47 secs
  B cells...0.24 secs
  CD14+ Monocytes...0.47 secs
  CD4 T cells...0.32 secs
  CD8 T cells...0.19 secs
  FCGR3A+ Monocytes...0.4 secs
  B cells...0.3 secs
  B cells...0.24 secs

Processing block [[1/1, 1/1]] ... OK
  B cells...0.27 secs
  CD14+ Monocytes...0.35 secs
  CD4 T cells...0.32 secs
  CD8 T cells...0.22 secs
  FCGR3A+ Monocytes...0.31 secs
  B cells...3.8 secs
  CD14+ Monocytes...5 secs
  CD4 T cells...3.9 secs
  CD8 T cells...2.5 secs
  FCGR3A+ Monocytes...4.8 secs


  B cells...0.22 secs
  CD14+ Monocytes...0.31 secs
  CD4 T cells...0.22 secs
  CD8 T cells...0.16 secs
  FCGR3A+ Monocytes...0.28 secs


RUNIT TEST PROTOCOL -- Tue Mar 26 20:31:40 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 
 73.828   2.873  94.444 

Example timings

dreamlet.Rcheck/dreamlet-Ex.timings

nameusersystemelapsed
aggregateNonCountSignal7.6500.4888.345
aggregateToPseudoBulk1.2140.0301.256
aggregateVar1.3040.0281.344
as.dreamletResult2.4230.0582.504
buildClusterTreeFromPB0.7040.0210.733
cellCounts0.6810.0360.724
cellTypeSpecificity1.9670.0572.043
checkFormula0.0000.0000.001
coefNames-methods4.3910.0784.514
compositePosteriorTest9.4920.1659.758
computeCellCounts0.1840.0080.197
computeLogCPM0.3930.0450.444
computeNormCounts0.2800.0280.312
details-methods2.3640.0532.439
diffVar-methods5.7850.1055.959
dreamlet3.8110.0663.929
dreamletCompareClusters3.1240.0643.225
dropRedundantTerms0.0050.0010.006
equalFormulas000
extractData-methods2.5550.0512.632
fitVarPart22.978 0.25623.422
getExprGeneNames4.6030.0974.733
getTreat-methods3.4390.0463.510
meta_analysis20.066 0.46520.734
outlier0.0030.0010.004
outlierByAssay3.5410.0683.655
pbWeights3.2740.0783.380
plotBeeswarm3.8110.0863.928
plotCellComposition1.1080.0161.131
plotForest-methods3.5610.0473.630
plotGeneHeatmap-methods3.6570.0523.740
plotHeatmap-methods0.8550.0160.877
plotPCA4.9600.1055.104
plotPercentBars-methods21.364 0.22021.751
plotProjection1.7590.0701.804
plotVarPart-methods22.194 0.27022.681
plotViolin-methods1.1920.0281.233
plotVolcano-methods5.8880.1186.072
plotVoom-methods3.3030.0663.403
processAssays3.3010.0543.395
removeConstantTerms0.0050.0000.005
residuals-methods3.4740.0503.553
run_mash10.504 0.22510.811
seeErrors-methods3.4150.0453.482
sortCols-method21.799 0.20622.161
stackAssays12.223 0.13112.430
topTable-methods3.7180.0653.806
zenith_gsa-methods100.182 5.756107.064