It's not what I'd expect because the system headers don't matter in the current
CRAN release as it's not relying on the system headers anymore. That's why I'd
need the actual full output - the command line and the error - so I could tract
why it's failing.
> On Jul 24, 2019, at 11:02 AM, Roy
Ok, mystery solved: you will get the error if you override the provided CRAN
flags with flags that remove the SDK. So the issue doesn't exist in released R
unless you modify the flags yourself. So please don't do that - don't set
CPPFLAGS or if you really have to, make sure you include at least
But is there a difference in where headers are being looked for when building R
as compared to when a package is built from source. As I said, what was
failing was try to do source installs of packages from CRAN.
-Roy
> On Jul 24, 2019, at 8:09 AM, Simon Urbanek
> wrote:
>
> It's not
I want to avoid that "fix" because it is not guaranteed to work in the future.
Can someone who did NOT instal the system-level headers below please report the
actual issue? The whole point of using the SDK was to make sure it's not
necessary.
Thanks,
Simon
> On Jul 24, 2019, at 10:54 AM,
Thanks Bryan. Given my age, I always have to wonder if I am hallucinating or
did something careless. I want to emphasize that I don't think it is an R
issue, it really does look like when installing the new Xcode, the headers
got wiped out. Since both a new Xcode and a new Command Line
HI Simon:
Perhaps if you can find someone who hasn't done the Xcode and Command Line
Update, have them list the directories that you are interested in, and then
list the same after the update to see what it is doing. Also is it possible
you have something in your .Rpofile of the like that
Ah, I think I have an idea - is it possible that you were using an older
version of R? That would explain.
Cheers,
Simon
> On Jul 24, 2019, at 10:46 AM, Roy Mendelssohn - NOAA Federal
> wrote:
>
> Hi Simon:
>
>> ls /Library/Developer/CommandLineTools/SDKs
>> MacOSX.sdk MacOSX10.14.sdk
>
If it helps troubleshoot, I updated more or less on the same timeline as Roy
did and had the same problems Roy had, and Roy’s most recent response below
gives the same response on my Mac. Roy’s fix * fixed things for me. Bryan
* open
Hi Simon:
> ls /Library/Developer/CommandLineTools/SDKs
> MacOSX.sdkMacOSX10.14.sdk
Also when have done:
> sudo xcode-select --install
I often get a message to install through App store (the command line tools). I
am not certain exactly what macOS_SDK_headers_for_macOS_10.14.pkg
Roy,
thanks, I just wanted to clarify which headers have been deleted exactly. The
system location (/usr/includes) is what Apple doesn't like, which is why we are
now using the SDK. Can you check, please, whether you do have
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
I would hope that
Hi Simon:
I am using CRAN release, recommended CRAN compilers. Yesterday morning one
updated package needed to be installed from source, worked. Yesterday
afternoon did the update of Xcode (and OSX). This morning installing a package
update from source failed, couldn't find header files
Roy,
that shouldn't be necessary if you use the CRAN release since it specifically
points to the SDK. If you are compiling your own R you may want to add
CPPFLAGS='-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include'
which is what the CRAN build uses. FWIW you can
If like me you updated to Xcode 10.3, in Apple's infinite wisdom the install
again wipes out the header files. So if you did the update and install from
source remember to re-install the headers:
> open
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
13 matches
Mail list logo
