Installation of SingleR fails with GCC 8.2.0, Centos 7 - XPtr(Rcpp::Vector<19>::Proxy)
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cisbio • 0
@4929405d
Last seen 21 months ago
United Kingdom

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Code should be placed in three backticks as shown below

g++ -std=gnu++17 -I"/project/soft/linux64/R/R-4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/  -I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/Rcpp/include' -I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/beachmat/include' -I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/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]);

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Oracle Linux Server 7.9

Matrix products: default
BLAS:   /project/soft/linux64/R/R-4.2.2/lib64/R/lib/libRblas.so
LAPACK: /project/soft/linux64/R/R-4.2.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.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_1.30.19 compiler_4.2.2      tools_4.2.2        



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

sessionInfo( )
SimpleR • 756 views
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I had a similar issue that was fixed by using gcc 9.1.0 instead of our system default 8.2.0.

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