Hello,

I try to install SingleR on Debian Release 10.13 but I have the error message below

Is it a gcc-8.3 problem ? Update to Debian 11 ?

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

> BiocManager::install("SingleR")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31)
Installing package(s) 'SingleR'
essai de l'URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SingleR_2.0.0.tar.gz'
Content type 'application/x-gzip' length 728090 bytes (711 KB)
==================================================
downloaded 711 KB

* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/beachmat/include' -I'/usr/local/lib/R/site-library/BiocNeighbors/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/beachmat/include' -I'/usr/local/lib/R/site-library/BiocNeighbors/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c find_classic_markers.cpp -o find_classic_markers.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/beachmat/include' -I'/usr/local/lib/R/site-library/BiocNeighbors/include'    -fpic  -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/buster/r-base-4.2.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c integrate_build.cpp -o integrate_build.o
integrate_build.cpp: In function ‘SEXPREC* integrate_build(Rcpp::IntegerVector, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, int)’:
integrate_build.cpp:29:42: error: call of overloaded ‘XPtr(Rcpp::Vector<19>::Proxy)’ is ambiguous
         PrebuiltXPtr curbuilt(prebuilt[r]);
                                          ^
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:46,
                 from integrate_build.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:113:5: note: candidate: ‘Rcpp::XPtr<T, StoragePolicy, Finalizer, finalizeOnExit>::XPtr(const Rcpp::XPtr<T, StoragePolicy, Finalizer, finalizeOnExit>&) [with T = singlepp::BasicBuilder::Prebuilt; StoragePolicy = Rcpp::PreserveStorage; void (* Finalizer)(T*) = Rcpp::standard_delete_finalizer<singlepp::BasicBuilder::Prebuilt>; bool finalizeOnExit = false]’
     XPtr(const XPtr& other) {
     ^~~~
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:46,
                 from integrate_build.cpp:1:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:104:14: note: candidate: ‘Rcpp::XPtr<T, StoragePolicy, Finalizer, finalizeOnExit>::XPtr(T*, bool, SEXP, SEXP) [with T = singlepp::BasicBuilder::Prebuilt; StoragePolicy = Rcpp::PreserveStorage; void (* Finalizer)(T*) = Rcpp::standard_delete_finalizer<singlepp::BasicBuilder::Prebuilt>; bool finalizeOnExit = false; SEXP = SEXPREC*]’
     explicit XPtr(T* p, bool set_delete_finalizer = true,
              ^~~~
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:78:14: note: candidate: ‘Rcpp::XPtr<T, StoragePolicy, Finalizer, finalizeOnExit>::XPtr(SEXP) [with T = singlepp::BasicBuilder::Prebuilt; StoragePolicy = Rcpp::PreserveStorage; void (* Finalizer)(T*) = Rcpp::standard_delete_finalizer<singlepp::BasicBuilder::Prebuilt>; bool finalizeOnExit = false; SEXP = SEXPREC*]’
     explicit XPtr(SEXP x) { checked_set(x); };
              ^~~~
make: *** [/usr/lib/R/etc/Makeconf:178: integrate_build.o] Error 1
ERROR: compilation failed for package ‘SingleR’
* removing ‘/usr/local/lib/R/site-library/SingleR’

Les packages source téléchargés sont dans
    ‘/tmp/Rtmp3AGMZ8/downloaded_packages’
Message d'avis :
Dans install.packages(...) :
  l'installation du package ‘SingleR’ a eu un statut de sortie non nul



sessionInfo( )
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.20 compiler_4.2.2      tools_4.2.2

Problem solved : upgrade Debian 10 to Debian 11

Debain 10 : gcc-8.3.0

Debian 11 : gcc-10.2.1

I don't see this problem but perhaps you could try installing an attempted patch from the latest master on the GitHub repository.