On Oct 14, 2020, at 11:48 AM, Simon Urbanek <simon.urbanek at R-project.org> wrote:
Roger,
the error points to an old local clang - did you remove (or move aside) that one? Check your /usr/local - you seem to have some old stuff there that is breaking. That would solve the original issue. You seem to have done a lot after that error, but didn't tell us what happened then? you can't have the same error if you removed it ;)
Cheers,
Simon
On Oct 14, 2020, at 10:28 PM, Koenker, Roger W <rkoenker at illinois.edu> wrote:
I?ve recently ?upgraded? to catalina, and compilation of my quantreg package failed with:
In file included from mcmb.c:11:
/usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found
#include_next <stdio.h>
So I?ve tried the following:
1. Upgraded R to 4.0.3
2. Upgraded the fortran compiler to 8.2.0 as suggested.
3. Attempted to reinstall command line tools with Xcode-select ?install. This fails with
a popup that says:
Can?t install the software because it is not currently available from the Software Update server.
4. Tried again to reinstall Command line tools 12.2 beta 3 from https://developer.apple.com/download/more/
which successfully installed, but my stdio.h error persisted.
5. Following thread: http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html
I looked at:
yzzy: which clang /usr/bin/clang
yzzy: xcode-select -p /Applications/Xcode.app/Contents/Developer
yzzy: xcrun --show-sdk-path /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
but that didn?t speak to me so further googling led me to:
https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files
so lurking in: /Library/Developer/CommandLineTools/usr/include/c++/v1
is stdio.h, but I?m feeling a bit queasy at this point and would appreciate some expert advice.
Roger