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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:dreamlet.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings dreamlet_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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 ... 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      64.696  1.852  66.550
plotVarPart-methods     16.752  0.117  16.869
fitVarPart              16.482  0.189  16.673
plotPercentBars-methods 15.773  0.089  15.862
sortCols-method         15.807  0.035  15.842
meta_analysis           13.049  0.094  13.143
run_mash                 8.995  0.050   9.039
stackAssays              8.870  0.048   8.919
compositePosteriorTest   7.906  0.126   8.033
* 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

Quitting from cell_covs.Rmd:56-79 [preprocess.data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─ExperimentHub::ExperimentHub()
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cell_covs.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘cell_covs.Rmd’

--- re-building ‘dreamlet.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/dreamlet.contrasts-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/heatmap-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/heatmap2-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/cellTypeSpecificity-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/plotPercentBars-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/vign_test/dreamlet/vignettes/dreamlet_files/figure-html/plotPercentBars-2.png" but not available.
--- finished 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:
  ‘cell_covs.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/dreamlet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL dreamlet
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘dreamlet’ ...
** this is package ‘dreamlet’ version ‘1.8.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from colsum_beachmat.cpp:1:
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<M> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.22-bioc/R/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.22-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++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o dreamlet.so RcppExports.o colsum_beachmat.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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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")
  B cells...0.27 secs
  B cells...0.23 secs

Processing block [[1/1, 1/1]] ... OK
  B cells...0.23 secs
  CD14+ Monocytes...0.31 secs
  CD4 T cells...0.28 secs
  CD8 T cells...0.16 secs
  FCGR3A+ Monocytes...0.27 secs
  B cells...2.7 secs
  CD14+ Monocytes...3.6 secs
  CD4 T cells...2.8 secs
  CD8 T cells...1.7 secs
  FCGR3A+ Monocytes...3.4 secs


  B cells...0.17 secs
  CD14+ Monocytes...0.26 secs
  CD4 T cells...0.17 secs
  CD8 T cells...0.11 secs
  FCGR3A+ Monocytes...0.21 secs


RUNIT TEST PROTOCOL -- Thu Feb 19 00:13:06 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 
Warning messages:
1: the 'findbars' function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainter to do so.
This warning is displayed once per session. 
2: the 'nobars' function has moved to the reformulas package. Please update your imports, or ask an upstream package maintainter to do so.
This warning is displayed once per session. 
> 
> proc.time()
   user  system elapsed 
 45.699   1.818  61.782