Error installing FastPG on Mac M1 chip

[dancelestini]

I am having problems installing FastPG using this command :

BiocManager::install("sararselitsky/FastPG")

At first, I got an omp.h problem which I solved by installing libomp.

Now I am facing another problem which seems very strange and gives me a lot of errors I will put a couple ones here :

• installing source package ‘FastPG’ ... using staged installation libs using C compiler: ‘gcc-13 (Homebrew GCC 13.2.0) 13.2.0’ using C++ compiler: ‘g++-13 (Homebrew GCC 13.2.0) 13.2.0’ using C++11 using SDK: ‘’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RngStream.cpp -o RngStream.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c buildNextPhase.cpp -o buildNextPhase.o buildNextPhase.cpp:92:9: warning: variable 'nT' set but not used [-Wunused-but-set-variable] int nT; ^ buildNextPhase.cpp:100:10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^ buildNextPhase.cpp:102:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^ buildNextPhase.cpp:102:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^ buildNextPhase.cpp:105:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^ buildNextPhase.cpp:262:12: warning: unused variable 'time1' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^ buildNextPhase.cpp:262:19: warning: unused variable 'time2' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^ buildNextPhase.cpp:262:26: warning: unused variable 'time3' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^ buildNextPhase.cpp:262:33: warning: unused variable 'time4' [-Wunused-variable] double time1, time2, time3, time4; //For timing purposes ^ buildNextPhase.cpp:263:12: warning: unused variable 'total' [-Wunused-variable] double total = 0, totItr = 0; ^ buildNextPhase.cpp:263:23: warning: unused variable 'totItr' [-Wunused-variable] double total = 0, totItr = 0; ^ buildNextPhase.cpp:264:10: warning: unused variable 'percentange' [-Wunused-variable] long percentange = 80; ^ buildNextPhase.cpp:267:13: warning: unused variable 'NE_in' [-Wunused-variable] long NE_in = Gin->numEdges; ^ buildNextPhase.cpp:398:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^ buildNextPhase.cpp:451:13: warning: unused variable 'NE' [-Wunused-variable] long NE = G->numEdges; ^ 15 warnings generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coloringDistanceOne.cpp -o coloringDistanceOne.o

[dancelestini]

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich
tzcode source: internal

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

[sararselitsky]

I've had these issues and I think they are a C++ compiler issue. Mahantesh, does that sound right?

On Tue, Sep 19, 2023 at 8:44 AM dancelestini @.***> wrote:

sessionInfo() R version 4.3.0 (2023-04-21) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.0

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Zurich tzcode source: internal

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

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[jefferys]

I don't see any errors in what you posted; they are only warnings. Warnings are common in R C++ packages due to varying compilers checking for different potential issues. That said, I have not tried to compile and install anything from the R universe on Apple silicon. From a quick look around the web, doing so is not always trivial when compilation is needed. Many posts involve tweaking the "~/.R/Makevars" file. FastPG does install (and run) under R 4.3.1 on Linux on x86 architecture. It is conceivable that the code could have architecture dependencies, but I am not aware of any.