Installation of SingleR in R/4.2.2 using BiocManager v3.16 fails

[star0044]

I'm trying to re-install SingleR after upgrading to R/4.2.2 and I get the following error message

make: *** [integrate_build.o] Error 1 ERROR: compilation failed for package ‘SingleR’

Any advice on how I can get SingleR installed will be greatly appreciated

I am able to install all the dependencies, but still get the error. Here is the full output of my attempt to install SingleR. At the end is the session info:

BiocManager::install("SingleR") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://mirror.las.iastate.edu/CRAN Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.2 (2022-10-31) Installing package(s) 'SingleR' trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SingleR_2.0.0.tar.gz' Content type 'application/gzip' length 728090 bytes (711 KB)

downloaded 711 KB

• installing source package ‘SingleR’ ... using staged installation libs /common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/gcc-8.2.0-ztp76o3ikzl4yhf3fohot7loczbtkhra/bin/g++ -std=gnu++17 -I"/common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/r-4.2.2-vp7tydeosl55o3d5hp5plulp6evljtbp/rlib/R/include" -DNDEBUG -I../inst/include/ -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/beachmat/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o /common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/gcc-8.2.0-ztp76o3ikzl4yhf3fohot7loczbtkhra/bin/g++ -std=gnu++17 -I"/common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/r-4.2.2-vp7tydeosl55o3d5hp5plulp6evljtbp/rlib/R/include" -DNDEBUG -I../inst/include/ -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/beachmat/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o /common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/gcc-8.2.0-ztp76o3ikzl4yhf3fohot7loczbtkhra/bin/g++ -std=gnu++17 -I"/common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/r-4.2.2-vp7tydeosl55o3d5hp5plulp6evljtbp/rlib/R/include" -DNDEBUG -I../inst/include/ -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/beachmat/include' -I'/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -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 /panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include/Rcpp.h:46, from integrate_build.cpp:1: /panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/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; bool finalizeOnExit = false]' XPtr(const XPtr& other) { ^~~~ In file included from /panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include/Rcpp.h:46, from integrate_build.cpp:1: /panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/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; bool finalizeOnExit = false; SEXP = SEXPREC]' explicit XPtr(T p, bool set_delete_finalizer = true, ^~~~ /panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/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; bool finalizeOnExit = false; SEXP = SEXPREC*]' explicit XPtr(SEXP x) { checked_set(x); }; ^~~~ make: *** [integrate_build.o] Error 1 ERROR: compilation failed for package ‘SingleR’
• removing ‘/panfs/jay/groups/18/starrt2/star0044/R/x86_64-pc-linux-gnu-library/4.2/SingleR’

The downloaded source packages are in ‘/tmp/Rtmp1jg8q6/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘SingleR’ had non-zero exit status

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/r-4.2.2-vp7tydeosl55o3d5hp5plulp6evljtbp/rlib/R/lib/libRblas.so LAPACK: /common/software/install/spack/linux-centos7-ivybridge/gcc-8.2.0/r-4.2.2-vp7tydeosl55o3d5hp5plulp6evljtbp/rlib/R/lib/libRlapack.so

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

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

other attached packages: [1] BiocManager_1.30.22

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

[LTLA]

Looks related to #232, and probably fixed by f3c97e7092417068980876792be88ad3ec3ab229. It seems you'd have to update your installation anyway, given that it says you're running BioC 3.16 (latest is 3.18).