Failure to install on macOS 10.14 Mojave with R 3.5.1

[mojaveazure]

Hello, I'm having issues installing fs on macOS 10.14 under R 3.5.1; it says it cannot find AE/AE.h and no amount of Googling has lead me anywhere. Do you have any ideas what I'm missing and how I can get it?

Thanks,
Paul

> install.packages('fs')
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/fs_1.2.6.tar.gz'
Content type 'application/x-gzip' length 799325 bytes (780 KB)
==================================================
downloaded 780 KB

* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** libs
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c dir.cc -o dir.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c error.cc -o error.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c file.cc -o file.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c fs.cc -o fs.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c id.cc -o id.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c link.cc -o link.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c path.cc -o path.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c utils.cc -o utils.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c unix/getmode.cc -o unix/getmode.o
clang++  -I"/usr/local/Cellar/r/3.5.1/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -c RcppExports.cpp -o RcppExports.o
cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4
(cd libuv \
		&& touch aclocal.m4 \
		&& touch -r aclocal.m4 configure Makefile.in \
	&& CC="clang" CFLAGS="-I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/include/darwin  -fPIC " AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib" ./configure --quiet)
make --directory=libuv \
		HAVE_DTRACE=0
  CC       src/libuv_la-fs-poll.lo
  CC       src/libuv_la-inet.lo
  CC       src/libuv_la-threadpool.lo
  CC       src/libuv_la-uv-common.lo
  CC       src/libuv_la-version.lo
  CC       src/unix/libuv_la-async.lo
  CC       src/unix/libuv_la-core.lo
  CC       src/unix/libuv_la-dl.lo
  CC       src/unix/libuv_la-fs.lo
  CC       src/unix/libuv_la-getaddrinfo.lo
  CC       src/unix/libuv_la-getnameinfo.lo
  CC       src/unix/libuv_la-loop-watcher.lo
  CC       src/unix/libuv_la-loop.lo
  CC       src/unix/libuv_la-pipe.lo
  CC       src/unix/libuv_la-poll.lo
  CC       src/unix/libuv_la-process.lo
  CC       src/unix/libuv_la-signal.lo
  CC       src/unix/libuv_la-stream.lo
  CC       src/unix/libuv_la-tcp.lo
  CC       src/unix/libuv_la-thread.lo
  CC       src/unix/libuv_la-timer.lo
  CC       src/unix/libuv_la-tty.lo
  CC       src/unix/libuv_la-udp.lo
  CC       src/unix/libuv_la-bsd-ifaddrs.lo
  CC       src/unix/libuv_la-darwin.lo
  CC       src/unix/libuv_la-darwin-proctitle.lo
In file included from src/unix/darwin-proctitle.c:30:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/ApplicationServices.framework/Headers/ApplicationServices.h:23:
/usr/local/include/CoreServices/CoreServices.h:24:10: fatal error: 'AE/AE.h'
      file not found
#include <AE/AE.h>
         ^~~~~~~~~
1 error generated.
make[1]: *** [src/unix/libuv_la-darwin-proctitle.lo] Error 1
make: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘fs’
* removing ‘/usr/local/lib/R/3.5/site-library/fs’

The downloaded source packages are in
	‘/private/var/folders/g1/4jstv96n7tl947f0pvlybb_80000gn/T/RtmpMOHkIC/downloaded_packages’
Warning message:
In install.packages("fs") :
  installation of package ‘fs’ had non-zero exit status
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin17.4.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] colorout_1.2-0

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1   

[jimhester]

Make sure you have installed the command line tools for Mojave, you may need to run xcode-select --reset. https://stackoverflow.com/a/53089500/2055486

I am running Mojave myself and have no issues installing fs, so this is likely a configuration issue.

[mojaveazure]

I ended up needing to reinstall Xcode and the command line tools (needed from Apple's website) to get fs to compile. Thanks!

[serbinsh]

I am dealing with some similar issues (perhaps)

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/CoreGraphics.framework/Headers/CGPDFDictionary.h:116:15: error: expected identifier or '(' before '^' token
 typedef bool (^CGPDFDictionaryApplierBlock)(const char * key,
               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/CoreGraphics.framework/Headers/CGPDFDictionary.h:126:5: error: unknown type name 'CGPDFDictionaryApplierBlock'; did you mean 'CGPDFDictionaryApplierFunction'?
     CGPDFDictionaryApplierBlock cg_nullable block, void * __nullable info)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
     CGPDFDictionaryApplierFunction
make[2]: *** [src/unix/libuv_la-darwin-proctitle.lo] Error 1
make[1]: *** [libuv/.libs/libuv.a] Error 2
ERROR: compilation failed for package ‘fs’
* removing ‘/Users/sserbin/R/library/fs’
* restoring previous ‘/Users/sserbin/R/library/fs’
Error in i.p(...) :
  (converted from warning) installation of package ‘fs’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted

real	1m47.607s
user	1m5.040s
sys	0m17.456s
make: *** [.doc/base/db] Error 1

I have updated to the latest command line tools (march 25 2019), xcode (10.2) etc

[zibo-wang]

Same problem here, same output with R 3.5.2, Xcode 10.2.1 on Mojave.