##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings dreamlet_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-05 03:12:29 UTC
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.11.0’
* 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 ... NOTE
Found the following notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* 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 loading without being on the library search path ... 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 ... INFO
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 ... ERROR
Running examples in ‘dreamlet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: zenith_gsa,dreamletResult,GeneSetCollection-method
> ### Title: Perform gene set analysis using zenith
> ### Aliases: zenith_gsa,dreamletResult,GeneSetCollection-method
> ###   zenith_gsa,dreamletResult,GeneSetCollection,ANY-method
> ###   zenith_gsa,dreamlet_mash_result,GeneSetCollection-method
> ###   zenith_gsa,dreamlet_mash_result,GeneSetCollection,ANY-method
> 
> ### ** Examples
> 
> library(muscat)
> library(SingleCellExperiment)
> 
> data(example_sce)
> 
> # create pseudobulk for each sample and cell cluster
> pb <- aggregateToPseudoBulk(example_sce,
+   assay = "counts",
+   cluster_id = "cluster_id",
+   sample_id = "sample_id",
+   verbose = FALSE
+ )
> 
> # voom-style normalization
> res.proc <- processAssays(pb, ~group_id)
  B cells...calcNormFactors has been renamed to normLibSizes
0.24 secs
  CD14+ Monocytes...calcNormFactors has been renamed to normLibSizes
0.38 secs
  CD4 T cells...calcNormFactors has been renamed to normLibSizes
0.26 secs
  CD8 T cells...calcNormFactors has been renamed to normLibSizes
0.14 secs
  FCGR3A+ Monocytes...calcNormFactors has been renamed to normLibSizes
0.35 secs
> 
> # Differential expression analysis within each assay,
> # evaluated on the voom normalized data
> res.dl <- dreamlet(res.proc, ~group_id)
  B cells...0.17 secs
  CD14+ Monocytes...0.22 secs
  CD4 T cells...0.21 secs
  CD8 T cells...0.11 secs
  FCGR3A+ Monocytes...0.21 secs
> 
> # Load Gene Ontology database
> # use gene 'SYMBOL', or 'ENSEMBL' id
> # use get_MSigDB() to load MSigDB
> library(zenith)
> go.gs <- get_GeneOntology("CC", to = "SYMBOL")


Error: unable to open database file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
stackAssays             70.195  0.298  70.496
meta_analysis           17.941  0.234  18.189
fitVarPart              17.866  0.219  18.085
sortCols-method         16.324  0.040  16.365
plotPercentBars-methods 16.098  0.168  16.268
plotVarPart-methods     16.196  0.043  16.241
run_mash                 9.468  0.010   9.472
compositePosteriorTest   8.770  0.106   8.877
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘cell_covs.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/cell_covs_files/figure-html/processAssays-1.png" but not available.
--- finished re-building ‘cell_covs.Rmd’

--- re-building ‘dreamlet.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/voom.plots-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/vp.barplt-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/vp.violin-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/plotVolcano-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/plotGeneHeatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/forrest-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/boxplot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/dreamlet.contrasts-1.png" but not available.

Quitting from dreamlet.Rmd:284-296 [zenith]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to open database file
---
Backtrace:
     ▆
  1. └─zenith::get_GeneOntology("CC", to = "SYMBOL")
  2.   └─base::lapply(...)
  3.     └─zenith (local) FUN(X[[i]], ...)
  4.       └─EnrichmentBrowser::getGenesets(...)
  5.         └─EnrichmentBrowser:::.getGO(...)
  6.           └─EnrichmentBrowser:::.getGOFromGODB(...)
  7.             ├─AnnotationDbi::keys(orgpkg, keytype = "GO")
  8.             └─AnnotationDbi::keys(orgpkg, keytype = "GO")
  9.               └─AnnotationDbi:::smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
 10.                 └─AnnotationDbi:::.keys(x, keytype)
 11.                   └─AnnotationDbi:::.legacyKeys(x, keytype)
 12.                     └─AnnotationDbi:::.queryForKeys(x, keytype)
 13.                       └─AnnotationDbi:::dbQuery(dbconn(x), sql)
 14.                         ├─DBI::dbGetQuery(conn, SQL)
 15.                         └─DBI::dbGetQuery(conn, SQL)
 16.                           └─DBI (local) .local(conn, statement, ...)
 17.                             ├─DBI::dbSendQuery(conn, statement, ...)
 18.                             └─RSQLite::dbSendQuery(conn, statement, ...)
 19.                               └─RSQLite (local) .local(conn, statement, ...)
 20.                                 ├─methods::new(...)
 21.                                 │ ├─methods::initialize(value, ...)
 22.                                 │ └─methods::initialize(value, ...)
 23.                                 └─RSQLite:::result_create(conn@ptr, statement)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'dreamlet.Rmd' failed with diagnostics:
unable to open database file
--- failed re-building ‘dreamlet.Rmd’

--- re-building ‘errors.Rmd’ using rmarkdown
--- finished re-building ‘errors.Rmd’

--- re-building ‘h5ad_on_disk.Rmd’ using rmarkdown
--- finished re-building ‘h5ad_on_disk.Rmd’

--- re-building ‘mashr.Rmd’ using rmarkdown
--- finished re-building ‘mashr.Rmd’

--- re-building ‘non_lin_eff.Rmd’ using rmarkdown
--- finished re-building ‘non_lin_eff.Rmd’

SUMMARY: processing the following file failed:
  ‘dreamlet.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/dreamlet.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL dreamlet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘dreamlet’ ...
** this is package ‘dreamlet’ version ‘1.11.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c colsum_beachmat.cpp -o colsum_beachmat.o
In file included from /home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from colsum_beachmat.cpp:1:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
      |             ~~~~^~~~~~~~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
      |             ~~~~^~~~~~~~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
      |             ~~~~^~~~~~~~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
  250 |             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
      |                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.24-bioc/R/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-dreamlet/00new/dreamlet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** 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)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

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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
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> 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: Seqinfo
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 objects are masked from 'package:SingleCellExperiment':

    cpm, tpm

> library(muscat)
> library(RUnit)
> 
> BiocGenerics:::testPackage("dreamlet")
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
  B cells...calcNormFactors has been renamed to normLibSizes
0.31 secs
  B cells...calcNormFactors has been renamed to normLibSizes
0.23 secs
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes

Processing block [[1/1, 1/1]] ... OK
  B cells...calcNormFactors has been renamed to normLibSizes
0.26 secs
  CD14+ Monocytes...calcNormFactors has been renamed to normLibSizes
0.33 secs
  CD4 T cells...calcNormFactors has been renamed to normLibSizes
0.3 secs
  CD8 T cells...calcNormFactors has been renamed to normLibSizes
0.18 secs
  FCGR3A+ Monocytes...calcNormFactors has been renamed to normLibSizes
0.33 secs
  B cells...3.1 secs
  CD14+ Monocytes...3.9 secs
  CD4 T cells...3.1 secs
  CD8 T cells...1.9 secs
  FCGR3A+ Monocytes...3.6 secs


  B cells...0.22 secs
  CD14+ Monocytes...0.27 secs
  CD4 T cells...0.18 secs
  CD8 T cells...0.12 secs
  FCGR3A+ Monocytes...0.23 secs


RUNIT TEST PROTOCOL -- Mon May  4 23:22:26 2026 
*********************************************** 
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 
 49.840   2.663  67.517