I recently upgraded my R version to 4.1.1 using HomeBrew. After straightening out some path problems in R, I tried re-installing my old packages, but I get a very long series of errors which seem to have to do with C compilation. Here's what happens when I try to install a package:
> install.packages("utf8")
trying URL 'http://cran.r-project.org/src/contrib/utf8_1.2.2.tar.gz'
Content type 'application/x-gzip' length 240327 bytes (234 KB)
==================================================
downloaded 234 KB
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/local/opt/llvm/bin/clang -fopenmp -I"/usr/local/Cellar/r/4.1.1/lib/R/include" -DNDEBUG
-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer
/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Iutf8lite/src -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c as_utf8.c -o as_utf8.o
In file included from as_utf8.c:21:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:64:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:137:9: warning:
type nullability specifier '_Nullable' is a Clang
extension [-Wnullability-extension]
int (* _Nullable _close)(void *);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:93:16: warning:
pointer is missing a nullability type specifier
(_Nonnull, _Nullable, or _Null_unspecified)
[-Wnullability-completeness]
unsigned char *_base;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/_stdio.h:93:16: note:
insert '_Nullable' if the pointer may be null
unsigned char *_base;
^
_Nullable
[many similar errors omitted here]
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:220:5: error:
'TARGET_OS_IPHONE' is not defined, evaluates to 0
[-Werror,-Wundef-prefix=TARGET_OS_]
#if TARGET_OS_IPHONE
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:385:25: warning:
type nullability specifier '_Nullable' is a Clang
extension [-Wnullability-extension]
int (* _Nullable)(void *, cha...
^
[Many similar messages omitted here]
21 warnings and 1 error generated.
make: *** [as_utf8.o] Error 1
ERROR: compilation failed for package ‘utf8’
* removing ‘/usr/local/Cellar/r/4.1.1/lib/R/library/utf8’
The downloaded source packages are in
‘/private/var/folders/9n/dw965k251pv8jzk_n62djdl80000gn/T/RtmpoZ1OqU/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("utf8") :
installation of package ‘utf8’ had non-zero exit status
The most I can figure out is that this has something to do with a failure to compile and link C code.
I'm running Mac OS 10.15.7 Catalina (the latest that my Mid-2012 MacBook Pro can run). However, I somehow seem to have the SDK for a newer version of Mac OS:
/Library/Developer/CommandLineTools/SDKs % ls
MacOSX.sdk MacOSX10.15.sdk MacOSX11.1.sdk
and the default SDK (MacOSX.sdk) seems to link to the newer version (newer than my OS):
/Library/Developer/CommandLineTools/SDKs % ls -ltr .
total 0
lrwxr-xr-x 1 root wheel 14 Oct 2 17:32 MacOSX.sdk -> MacOSX11.1.sdk
drwxr-xr-x 7 root wheel 224 Oct 2 17:33 MacOSX11.1.sdk
drwxr-xr-x 8 root wheel 256 Oct 2 17:34 MacOSX10.15.sdk
My R paths are the standard ones for Homebrew:
.libPaths()
[1] "/usr/local/Cellar/r/4.1.1/lib/R/library"
R.home()
[1] "/usr/local/Cellar/r/4.1.1/lib/R"
and I don't see anything obviously wrong with my path, which seems to contain gcc
echo $PATH
/usr/local/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:
/sbin:/Applications/VMware Fusion.app/Contents/Public:
/Library/TeX/texbin:/usr/local/share/dotnet:/opt/X11/bin:
~/.dotnet/tools:/Library/Apple/usr/bin
ls /usr/local/bin/gcc*
/usr/local/bin/gcc-11 /usr/local/bin/gcc-nm-11
/usr/local/bin/gcc-ar-11 /usr/local/bin/gcc-ranlib-11
Oddly, gcc seems to be set to compile using the 10.15 version of SDK, not the current 11.1 version:
gcc --version
Configured with: --prefix=/Library/Developer/CommandLineTools/usr
--with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
For what it's worth, I also have this going on:
xcrun --show-sdk-path
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
So I'm a bit confused about which version of the SDK is actually being used, etc.
My plan at the moment is to uninstall Xcode and reinstall version 12.4, which is the latest version you can run on 10.15 Catalina. I'm not sure if this will help.
Does anyone have any idea what the problem might be or how I might fix it? As of right now I basically can't use R, which is preventing me from doing virtually all of my work! Any help would be greatly appreciated.
