ecole package dependencies break on a Mac

[nelsopet]

When trying to run the NMS_Clean.R , I can't update the needed packages. I think this may stem from the Rtools issues.

install.packages("mgcv")

There is a binary version available but the source version is later: binary source needs_compilation mgcv 1.8-36 1.8-37 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes installing the source package ‘mgcv’

trying URL 'https://cran.rstudio.com/src/contrib/mgcv_1.8-37.tar.gz' Content type 'application/x-gzip' length 1175506 bytes (1.1 MB)

downloaded 1.1 MB

• installing source package ‘mgcv’ ... package ‘mgcv’ successfully unpacked and MD5 sums checked using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c coxph.c -o coxph.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c davies.c -o davies.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c discrete.c -o discrete.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gdi.c -o gdi.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c magic.c -o magic.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mat.c -o mat.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mgcv.c -o mgcv.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c misc.c -o misc.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c mvn.c -o mvn.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c qp.c -o qp.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c soap.c -o soap.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sparse-smooth.c -o sparse-smooth.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c sparse.c -o sparse.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c tprs.c -o tprs.o clang -mmacosx-version-min=10.13 -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 mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o sparse.o tprs.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: *** [mgcv.so] Error 1 ERROR: compilation failed for package ‘mgcv’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/mgcv’ Warning in install.packages : installation of package ‘mgcv’ had non-zero exit status

The downloaded source packages are in ‘/private/var/folders/4s/7zn1sydd5p531v8qcyn_rsfc0000gq/T/RtmphQiIhb/downloaded_packages’

[phytomosaic]

Package mgcv appears to already exist on the machine; this is testable by running require(mgcv).

[nelsopet]

Yes but the package is v 1.8.1 and ecole requires a newer version hence the need to install a new version.

[nelsopet]

devtools::install_github("https://github.com/phytomosaic/ecole") Downloading GitHub repo phytomosaic/ecole@HEAD ✓ checking for file ‘/private/var/folders/4s/7zn1sydd5p531v8qcyn_rsfc0000gq/T/RtmphQiIhb/remotes77e13d87ab7/phytomosaic-ecole-78e9969/DESCRIPTION’ ... ─ preparing ‘ecole’: ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘ecole_0.8-2021.tar.gz’

• installing source package ‘ecole’ ... using staged installation R ** data * moving datasets to lazyload DB byte-compile and prepare package for lazy loading Error: package ‘mgcv’ 1.8.31 was found, but >= 1.8.34 is required by ‘ecole’ Execution halted ERROR: lazy loading failed for package ‘ecole’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ecole’ Warning message: In i.p(...) : installation of package ‘/var/folders/4s/7zn1sydd5p531v8qcyn_rsfc0000gq/T//RtmphQiIhb/file77e69608e8e/ecole_0.8-2021.tar.gz’ had non-zero exit status