SingleR and gcc-8.3.0
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Entering edit mode
Fabien ▴ 10
@380ecb58
Last seen 7 days ago
France

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
gcc SingleR • 140 views
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Entering edit mode

I am not part of SingleR but my advise for quick testing would be to explore how compilation goes in different containers, for example Docker for debian:10.13, and for 11, and maybe for some different gcc versions. That way you can quickly test what the problem (if any of OS or compiler) it is without doing all sorts of installs on your machine. GitPod is great for these things. I can say that I can smoothly compile it in the Bioconductor Docker image (bioconductor/bioconductor_docker:RELEASE_3_16). Doing things in containers saves you from this OS-specific mess :)

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Entering edit mode
Fabien ▴ 10
@380ecb58
Last seen 7 days ago
France

Problem solved : upgrade Debian 10 to Debian 11

Debain 10 : gcc-8.3.0

Debian 11 : gcc-10.2.1

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Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 45 minutes ago
The city by the bay

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

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