On Oct 14, 2020, at 2:18 PM, Berend Hasselman <bhh at xs4all.nl> wrote:
Do you by any chance have ~/.R/Makevars ?
If yes does it define CC and CXX and LDFLAGS with clang7?
Try removing them.
Berend
On 14 Oct 2020, at 14:14, Koenker, Roger W <rkoenker at illinois.edu> wrote:
Humm? so I have now removed clang7 from /usr/local and I now see:
/usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/clang7/include/c++/v1 -fPIC -Wall -g -O2 -c mcmb.c -o mcmb.o
/bin/sh: /usr/local/clang7/bin/clang: No such file or directory
But unfortunately I still don?t see where R CMD build is asking for clang7. I tried reinstalling R
after removing clang7 but this didn?t change the result above. Nothing in my environment or
in .Rprofile refers to clang
My ChangeLog reveals that I had a similar problem a couple of years ago, but unhelpfully it doesn?t reveal
how it was fixed, only that the one C source file of the package was removed for a while, and then reinstated
after resolving a problem with header files for clang6.
Roger
On Oct 14, 2020, at 12:36 PM, Ken Beath <ken at kjbeath.com.au> wrote:
clang7 seems to be unnecessary for current R. It isn?t in my system and from memory was one of the things I removed to get everything working. This involved removing the clang and fortran that had been previously installed. I may have needed some other things but my systems will build your package.
Ken
On 14 Oct 2020, at 10:01 pm, Koenker, Roger W <rkoenker at illinois.edu> wrote:
Simon,
Thanks, I still have the same error:
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>
I didn?t do anything beyond upgrading R and installing fortran 8.2.0, and the CLT 12.2.
but I didn?t remove anything, should I have? I now see:
yzzy: which clang
/usr/bin/clang
yzzy: clang --version
Apple clang version 12.0.0 (clang-1200.0.32.2)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
The last time I faced this sort of thing James suggested this:
https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY
but the names and locations are somewhat different now, so I?m reluctant to experiment.
Roger
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