Error: package installation failed (MacOS Big Sur 11.5.2)

[JoBBurt]

Hello,

I would like to try out this package, but am having trouble installing it. I was wondering if you'd be able to help me with the install. I've pasted the output of the code below.

Thanks,
Jordan

Code Output:

devtools::install_github("ococrook/bandle")
Downloading GitHub repo ococrook/bandle@HEAD
✓ checking for file ‘/private/var/folders/dc/y4crtbv13x17s1kh7txyxdb80000gn/T/RtmpA2e9PK/remotes2780488c88cd/ococrook-bandle-03e0371/DESCRIPTION’ ...
─ preparing ‘bandle’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to process help pages
-----------------------------------
─ installing source package ‘bandle’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c Bessel2ndKind.cpp -o Bessel2ndKind.o
Bessel2ndKind.cpp:621:55: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
nk, tau, D = D, j + 1, nu).t();
~ ^ ~
Bessel2ndKind.cpp:774:49: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
nk, tau, D = D, j + 1).t();
~ ^ ~
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c dmvtCpp.cpp -o dmvtCpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -Wall -pedantic -fdiagnostics-color=always -c pg_sample.cpp -o pg_sample.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [bandle.so] Error 1
ERROR: compilation failed for package ‘bandle’
─ removing ‘/private/var/folders/dc/y4crtbv13x17s1kh7txyxdb80000gn/T/RtmpydhTTz/Rinst286e233c5a05/bandle’
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'bandle' from GitHub:
System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
E> ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
E> ld: library not found for -lgfortran
E> clang: error: linker command fa

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.5.2

[ococrook]

Hi Jordan,

Thanks for opening the issue! Looks like a MacOS error and it isnt able to find your gfortan library. The key warning part is:

ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran

This shouldn't have been a problem but some reason MacOS have been a bit odd recently. The first thing to check is that xcode is installed. Open your terminal and type:

xcode-select --install

I would then try again at this point, but I give it about 50% probability that is still won't work. I would then follow this guide here to further debug:

https://medium.com/biosyntax/following-up-library-dependency-when-compiling-r-packages-89f191b9f227

Let me know if that is still a problem after that, sorry for inconvenience!

We are also planning an ~major update in the next couple of days so you may want to hold off until later in the week? But you can always reinstall after that.

Thanks!

[JoBBurt]

Hi,

Thank you for your advice, I had xcode installed, but I will wait until you push the update to follow the guide to debug.

Thanks!

[ococrook]

Hi Jordan,

The update has been pushed - sorry I forgot to update you!

[JoBBurt]

Hi Oliver,

Thanks for the update. I tried again to install and did follow the instructions in the link you sent without success. I will have to try to install it on another computer.

Best,
Jordan

[ococrook]

Hi Jordan,

We've got it working on several MacOS locally. I'll see if I can track down any more issues and try to get back to you. Let me know if you have anymore issues

[ococrook]

Hi Jordan,

We had a similar issue locally which was fixed by installing the correct binary for your macos: https://cran.r-project.org/bin/macosx/. I hope that helps!

[oliviaconway]

Hi Olly

I'm also having the same issue on MacOS with the same error messages. I have xcode and the correct binary (Rv4.1.1, intel 64-bit). Could another potential work around be to:

1. Install homebrew
2. Install gcc via homebrew
3. Update my /Library/Frameworks/R.framework/Resources/etc/Makeconf to similar paths as suggested here https://medium.com/biosyntax/following-up-library-dependency-when-compiling-r-packages-89f191b9f227
4. Try to install bandle via devtools::install_github('ococrook/bandle') again

Let me know if this sounds plausible or if there's anything I'm missing.

Many thanks,
Olivia

[JoBBurt]

Hi Jordan,

We had a similar issue locally which was fixed by installing the correct binary for your macos: https://cran.r-project.org/bin/macosx/. I hope that helps!

This broke everything :(

[ococrook]

Hi Jordan,
We had a similar issue locally which was fixed by installing the correct binary for your macos: https://cran.r-project.org/bin/macosx/. I hope that helps!

This broke everything :(

Erg, I'm really sorry. Not sure why Mac is being so difficult. There are no build warnings for the package to suggest there are any issues. I'll go pester some people smarter than me

[ococrook]

Hi Olly

I'm also having the same issue on MacOS with the same error messages. I have xcode and the correct binary (Rv4.1.1, intel 64-bit). Could another potential work around be to:

1. Install homebrew
2. Install gcc via homebrew
3. Update my /Library/Frameworks/R.framework/Resources/etc/Makeconf to similar paths as suggested here https://medium.com/biosyntax/following-up-library-dependency-when-compiling-r-packages-89f191b9f227
4. Try to install bandle via devtools::install_github('ococrook/bandle') again

Let me know if this sounds plausible or if there's anything I'm missing.

Many thanks,
Olivia

Hi Olivia,

This could certainly work, I don't have a Mac to try this on but if it works for you let me know!

Best,
Olly