problem installation

[simeonqs]

Hi,

I have never reported an issue on GitHub, so excuses in advance if I'm doing something wrong.

I'm trying to install phylomice as suggested in the README, but get the attached error. Is there any advice on how to make this work? Running with this:

R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Regards,

Simeon

* installing *source* package ‘phylomice’ ...
** 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/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning 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/usr/local/include   -fPIC  -Wall -g -O2  -c testcpp.cpp -o testcpp.o
In file included from testcpp.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:34:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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 phylomice.so RcppExports.o testcpp.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: *** [phylomice.so] Error 1
ERROR: compilation failed for package ‘phylomice’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/phylomice’
Error: Failed to install 'phylomice' from GitHub:
  (converted from warning) installation of package ‘/var/folders/2y/dcr_mfg942x47sf4yl1msdmr0000gn/T//RtmpDF2tuM/filea2cf65dab4fb/phylomice_0.0.0.9000.tar.gz’ had non-zero exit status

[pdrhlik]

Hi @simeonqs,

That's a good first issue, no need to worry :-)

The problem is that I built the package a few years ago and it's obviously not compatible with R v4+. I don't know if you have any experience with package development. You could try changing the target yourself and sending a PR. I don't know when I'll be able to look at this, since I'm quite busy and I'm not really actively maintaining the package anymore.

Cheers, Patrik

[simeonqs]

Hi @pdrhlik,

Thanks a lot for the reply. Unfortunately I know almost nothing about packages in R. I'm trying to reproduce some results from a paper that used your package, but maybe I can run it in an older version of R.

Regards,

Simeon