Hi, I'm new to R Studio and I'm intimidated with the package installation.
I can't install "vegan".
I already did the following:
- temrinal: xcode-select --install
- installed the latest version (intel) of gfortan 12.1(Releases · fxcoudert/gfortran-for-macOS · GitHub)
This is the last error I get:
> install.packages("vegan")
There is a binary version available but the source version is later:
binary source needs_compilation
vegan 2.6-2 2.6-4 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘vegan’
trying URL 'https://cran.rstudio.com/src/contrib/vegan_2.6-4.tar.gz'
Content type 'application/x-gzip' length 1496110 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
* installing *source* package ‘vegan’ ...
** package ‘vegan’ 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 data2hill.c -o data2hill.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c decorana.f -o decorana.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c getF.c -o getF.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c goffactor.c -o goffactor.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
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c monoMDS.f -o monoMDS.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nestedness.c -o nestedness.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls -fPIC -Wall -g -O2 -c ordering.f -o ordering.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pnpoly.c -o pnpoly.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c stepacross.c -o stepacross.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c vegdist.c -o vegdist.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 vegan.so data2hill.o decorana.o getF.o goffactor.o init.o monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.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 -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/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (12.3) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-vegan/00new/vegan/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘vegan’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-vegan/00new/vegan/libs/vegan.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-vegan/00new/vegan/libs/vegan.so, 0x0006): symbol not found in flat namespace (__gfortran_os_error_at)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/vegan’
Warning in install.packages :
installation of package ‘vegan’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/n3/hytr03qx30v_r4kr_g2z6n840000gn/T/RtmpXq3VHL/downloaded_packages’
I appreaciate your help with this issue!There are some packages I have been able to download, but I got stuck with vegan...
Thanks in advance!
Malena