Problems with gfortran location in installation? (OSX) #24
Comments
|
Hi Keiler:
I have gone through the code, and there is not a place in there when I can change that location. My suggestion would be to create the noted directory and put a copy of gfortran there. I know that is a clunky work-around, but I can't come up with a better one at the moment.
…-Tim
______________________________
Timothy R. Frasier
Coordinator: Forensic Sciences Program
Professor: Biology
Saint Mary's University
923 Robie Street
Halifax, Nova Scotia B3H 3C3
Canada
Tel: (902) 491-6382
E-mail: ***@***.***
frasierlab.ca
________________________________
From: Keiler Collier ***@***.***>
Sent: Tuesday, November 26, 2024 1:49 AM
To: timothyfrasier/related ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [timothyfrasier/related] Problems with gfortran location in installation? (OSX) (Issue #24)
Hello,
I am attempting to compile and load Related on a OSX system (M2 chip, if that makes a difference).
I initially followed the instructions on this Repo's README to the letter, but when I ran the final install command in Rstudio ('install.packages("~/related_1.0.tar.gz", repos = NULL, type = "source")', it failed with the following message:
sh: /opt/gfortran/bin/gfortran: Not a directory
Warning in system(paste(fc, "--version"), intern = TRUE) :
running command '/opt/gfortran/bin/gfortran -arch arm64 --version' had status 126
using Fortran compiler: ‘NA’
using SDK: ‘MacOSX14.0.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c family_sim.c -o family_sim.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c related.f90 -o related.o
make: /opt/gfortran/bin/gfortran: No such file or directory
make: *** [related.o] Error 1
ERROR: compilation failed for package ‘related’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/related’
Looking at the first error, I assumed it was a problem with my gfortran installation. I confirmed that I had a working version at /opt/homebrew/bin/gfortran, and then added that location to my path as well. In both cases, the same error occurs, where the makefile seems to be looking for gfortran at /opt/gfortran/bin/gfortran (where it doesn't exist), causing fatal errors.
Do you have either the whole makefile (so I can use my working fortran to compile the package before installing it), or some suggestions on what's going wrong?
Thanks in advance for your time.
—
Reply to this email directly, view it on GitHub<#24>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA3NYWLSHEFGBH267QARG232CQDVVAVCNFSM6AAAAABSPSWGAOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY4TGMRVGU4TEOA>.
You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
|
|
I appreciate the reply, and actually ended up doing something similar to make it work. related ended up not being a great solution for our SNP datasets anyways, but it was nice to at least try it out. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hello,
I am attempting to compile and load Related on a OSX system (M2 chip, if that makes a difference).
I initially followed the instructions on this Repo's README to the letter, but when I ran the final install command in Rstudio
('install.packages("~/related_1.0.tar.gz", repos = NULL, type = "source")', it failed with the following message:sh: /opt/gfortran/bin/gfortran: Not a directory
Warning in system(paste(fc, "--version"), intern = TRUE) :
running command '/opt/gfortran/bin/gfortran -arch arm64 --version' had status 126
using Fortran compiler: ‘NA’
using SDK: ‘MacOSX14.0.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c family_sim.c -o family_sim.o
/opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c related.f90 -o related.o
make: /opt/gfortran/bin/gfortran: No such file or directory
make: *** [related.o] Error 1
ERROR: compilation failed for package ‘related’
removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/related’
Looking at the first error, I assumed it was a problem with my gfortran installation. I confirmed that I had a working version at
/opt/homebrew/bin/gfortran, and then added that location to my path as well. In both cases, the same error occurs, where the makefile seems to be looking for gfortran at/opt/gfortran/bin/gfortran(where it doesn't exist), causing fatal errors.Do you have either the whole makefile (so I can use my working fortran to compile the package before installing it), or some suggestions on what's going wrong?
Thanks in advance for your time.
The text was updated successfully, but these errors were encountered: