Problem Installing Version 3.18.0 - clang: error: the clang compiler does not support '-march=native'

[MedSciMay]

The most recent Version 3.18.0 fails to install on my computer. Version 3.15.2 installs correctly.

I think this may be due to a C++ compiling error on Mac with M1 Pro chip. See: https://stackoverflow.com/questions/65966969/why-does-march-native-not-work-on-apple-m1

Is there any way to change the clang version used when compiling CoGAPS?

My apologies in advance if I'm not using computing terms correctly! I'm new to CompBio.

Thanks!

Old packages: 'CoGAPS'
Update all/some/none? [a/s/n]: 
a
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘CoGAPS’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘CoGAPS’

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/CoGAPS_3.18.0.tar.gz'
Content type 'application/x-gzip' length 20839969 bytes (19.9 MB)
==================================================
downloaded 19.9 MB

* installing *source* package ‘CoGAPS’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -arch arm64 -std=gnu++14 accepts -g... (cached) yes
./configure: line 2752: AX_COMPILER_VENDOR: command not found
./configure: line 2753: AX_COMPILER_VERSION: command not found
./configure: line 2764: AX_OPENMP: command not found
building on  compiler version 
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include  -march=native  -fPIC  -falign-functions=64 -Wall -g -O2  -c Cogaps.cpp -o Cogaps.o
clang: error: the clang compiler does not support '-march=native'
make: *** [Cogaps.o] Error 1
ERROR: compilation failed for package ‘CoGAPS’

[jeanettejohnson]

Hello, thanks for this report and looking into it now. I think I need to regenerate the config script used to compile the C.

[jeanettejohnson]

pushed a fix-- should be able to install now using devtools::install_github("FertigLab/CoGAPS", force=TRUE)