Entering edit mode
The most recent CoGAPS 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?
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’
Thanks for the bug report. I'm one of the CoGAPS developers and I've wrestled with this issue also--one question though first: are your mac OS and Xcode tools both updated to the newest version? There have been some C issues ironed out in recent releases, and in the past updating has fixed this issue for me.
In parallel, I'm looking into this error and trying to reproduce it on my own M1 mac. I will reply to this comment with a link to the fix on github.
Been working on this. Could you install from github, using our master branch? I removed the flag but it won't be reflected in the Bioconductor release yet.
devtools::install_github("FertigLab/CoGAPS")
Let me know how it goes, J
I just installed the package. The compilation did not fail this time!
There appears to be a few minor errors during the installation:
However, these errors do not impede installation, and the tests check out at the end.
Thanks for your help!
Below is the output during installation:
Thanks for the reply! My apologies for the very late response.
MacOS Version: 12.5 Xcode tools version: 14.0.0 (This is the same as clang --version, right?)