adakteen
commented
9 months ago Hi there. Different problem but same outcome. I'm running R v. 4.3 on a Monterey MacOS v12.7.3. Running BiocManager::install("glmGamPoi") progresses until it gets to the point of looking for the math.h file. Now I've checked the file path and confirmed that math.h is in the correct directory. I've also re-installed Xcode (twice) and gfortran. I've even explicitly defined the file path when trying to install with bash in the mac terminal.
I've noticed this problem was previously reported here, but the solutions outlined in that thread don't seem to work anymore. Does anybody know what is happening and how I can fix it?
> BiocManager::install("glmGamPoi")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'glmGamPoi'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘glmGamPoi’
Do you want to attempt to install these from sources? (Yes/no/cancel) y
installing the source package ‘glmGamPoi’
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/glmGamPoi_1.14.3.tar.gz'
Content type 'application/x-gzip' length 2104554 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
* installing *source* package ‘glmGamPoi’ ...
** using staged installation
** libs
using C++ compiler: ‘clang version 5.0.1 (tags/RELEASE_501/final)’
using C++11
using SDK: ‘MacOSX13.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang-5.0: warning: optimization flag '-falign-functions=64' is not supported [-Wignored-optimization-argument]
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/RcppCommon.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/Rcpp/r/headers.h:62:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
In file included from /usr/local/include/c++/v1/cmath:305:
/usr/local/include/c++/v1/math.h:301:15: fatal error: 'math.h' file not found
#include_next <math.h>
^~~~~~~~
1 error generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘glmGamPoi’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/glmGamPoi’
The downloaded source packages are in
‘/private/var/folders/dy/95pjl7vs75l8b8wdvx4mqsg00000gn/T/RtmpRkzfHM/downloaded_packages’
Old packages: 'HDF5Array'
Update all/some/none? [a/s/n]:
n
Warning message:
In install.packages(...) :
installation of package ‘glmGamPoi’ had non-zero exit statusHere is my R session
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.7.3
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-x86_64/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: ********/********
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] macrtools_0.0.3.01 BiocManager_1.30.22
loaded via a namespace (and not attached):
[1] compiler_4.3.2 tools_4.3.2 sys_3.4.2 askpass_1.2.0 
const-ae
Hello,
I am unable to install glmGamPoi on my intel mac locally on R.
`if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("glmGamPoi")`
I get the error message after installing from source:
ld: warning: search path '/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0' not found ld: warning: search path '/opt/gfortran/lib' not found ld: library 'gfortran' not found clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [glmGamPoi.so] Error 1 ERROR: compilation failed for package ‘glmGamPoi’
In install.packages(...) : installation of package ‘glmGamPoi’ had non-zero exit status
Any advice would be appreciated.
R version 4.3.3 RC (2024-02-22 r85993) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.6.3