Re: [R-SIG-Mac] Xcode 9

[Kasper Daniel Hansen]

Thanks. Nice to know it got fixed despite the somewhat pessimistic original
post.

Best,
Kasper

On Wed, Sep 27, 2017 at 4:32 AM, peter dalgaard  wrote:

>
> > On 27 Sep 2017, at 08:43 , Prof Brian Ripley 
> wrote:
> >
> > On 27/09/2017 03:28, Kasper Daniel Hansen wrote:
> >> I don't see this with
> >>   Xcode 9
> >>   OS X Sierra (10.12.6)
> >> and either
> >> R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered
> >> Consequences"
> >> Copyright (C) 2017 The R Foundation for Statistical Computing
> >> Platform: x86_64-apple-darwin16.7.0 (64-bit)
> >> or
> >> R version 3.4.2 RC (2017-09-26 r73351) -- "Short Summer"
> >> Copyright (C) 2017 The R Foundation for Statistical Computing
> >> Platform: x86_64-apple-darwin16.7.0 (64-bit)
> >> Specifically I can compile R and it passes make check.  Perhaps it got
> >> fixed since the post.
> >
> > It did (look at the logs for r73347 and r73351), but also we have
> discovered that not all upgrades to Xcode 9 had the problem.
> >
>
> Yes. My home desktop machine updated command line tools only and didn't
> see the problem. The laptop wants to upgrade the full Xcode (no idea how
> that came to be...) but claims to need another 1.66GB of disk to upgrade,
> so it is probably not in the cards to check a build there just now. The
> work machine had the problem until I downgraded to Xcode 8.3.3, but as this
> is the machine building the actual release, I'm not touching it until some
> weeks after the 3.4.2 release.
>
> Right now, we just override the configure detected utimensat() declaration
> on all Macs, which should be harmless (also on High Sierra, although we
> wouldn't claim to support an OS which was unreleased at the code freeze).
> We'll think of a better fix --- it looks like the Curl developers have
> fixed a similar issue, so we can copy their approach.
>
> > While we are at it, there is a problem with finding the default time
> zone on High Sierra.  This is worked around already in R-devel and will be
> in 3.4.2 patched: until then setting TZ is a good workaround (and that is
> in the R-admin manual for 3.4.2 RC).
> >
> >> On Fri, Sep 22, 2017 at 4:47 AM, peter dalgaard 
> wrote:
> >>> Just a quick note: Xcode 9 will not presently create a working R on
> Sierra
> >>> or earlier.
> >
> > (I don't believe Xcode 9 is available for 'earlier'.)
>
> You're probably right. I wasn't sure when I wrote that (& also not sure
> whether one could cross-compile.)
>
> -pd
>
> >
> >>>
> >>> This is because it ships with an SDK for 10.13 (unreleased) and
> defines an
> >>> entry for utimensat(), which is not actually in the system library for
> >>> earlier versions.
> >>>
> >>> There is no way we can fix this reliably for the upcoming 3.4.2
> release,
> >>> so if you intend to build R from sources, either
> >>>
> >>> - just do not upgrade, stay on Xcode 8.3.3
> >>>
> >>> or
> >>>
> >>> - manually remove the line from config.h saying
> >>>
> >>> #define HAVE_UTIMENSAT 1
> >>>
> >>>
> >>> 
> >>>
> >>> The slightly longer story is that Apple decided to have their include
> >>> files generate a _warning_ that utimensat() is only available in 10.13,
> >>> like this:
> >>>
> >>> gcc -I../../../R/src/extra  -I. -I../../src/include
> >>> -I../../../R/src/include  -I/usr/local/include -I../../../R/src/nmath
> >>> -DHAVE_CONFIG_H -g -O2  -c ../../../R/src/main/platform.c -o
> platform.o
> >>> ../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only
> >>> available on
> >>>   macOS 10.13 or newer [-Wunguarded-availability-new]
> >>> utimensat(AT_FDCWD, to, times, 0);
> >>> ^
> >>> /Applications/Xcode.app/Contents/Developer/Platforms/
> >>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/
> include/sys/stat.h:374:5:
> >>> note:
> >>>   'utimensat' has been explicitly marked partial here
> >>> int utimensat(int __fd, const char *__path, const struct timespec
> __...
> >>> ^
> >>> ../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
> >>>   __builtin_available check to silence this warning
> >>> utimensat(AT_FDCWD, to, times, 0);
> >>> ^
> >>> ../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only
> >>> available
> >>>   on macOS 10.13 or newer [-Wunguarded-availability-new]
> >>> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
> >>>   ^
> >>> /Applications/Xcode.app/Contents/Developer/Platforms/
> >>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/
> include/sys/stat.h:374:5:
> >>> note:
> >>>   'utimensat' has been explicitly marked partial here
> >>> int utimensat(int __fd, const char *__path, const struct timespec
> __...
> >>> ^
> >>> ../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
> >>>   __builtin_available check to silence this warning
> >>> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
> >>>   ^
> >>> 2 warnings 

Re: [R-SIG-Mac] Xcode 9

[peter dalgaard]

> On 27 Sep 2017, at 08:43 , Prof Brian Ripley  wrote:
> 
> On 27/09/2017 03:28, Kasper Daniel Hansen wrote:
>> I don't see this with
>>   Xcode 9
>>   OS X Sierra (10.12.6)
>> and either
>> R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered
>> Consequences"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin16.7.0 (64-bit)
>> or
>> R version 3.4.2 RC (2017-09-26 r73351) -- "Short Summer"
>> Copyright (C) 2017 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin16.7.0 (64-bit)
>> Specifically I can compile R and it passes make check.  Perhaps it got
>> fixed since the post.
> 
> It did (look at the logs for r73347 and r73351), but also we have discovered 
> that not all upgrades to Xcode 9 had the problem.
> 

Yes. My home desktop machine updated command line tools only and didn't see the 
problem. The laptop wants to upgrade the full Xcode (no idea how that came to 
be...) but claims to need another 1.66GB of disk to upgrade, so it is probably 
not in the cards to check a build there just now. The work machine had the 
problem until I downgraded to Xcode 8.3.3, but as this is the machine building 
the actual release, I'm not touching it until some weeks after the 3.4.2 
release.

Right now, we just override the configure detected utimensat() declaration on 
all Macs, which should be harmless (also on High Sierra, although we wouldn't 
claim to support an OS which was unreleased at the code freeze). We'll think of 
a better fix --- it looks like the Curl developers have fixed a similar issue, 
so we can copy their approach.

> While we are at it, there is a problem with finding the default time zone on 
> High Sierra.  This is worked around already in R-devel and will be in 3.4.2 
> patched: until then setting TZ is a good workaround (and that is in the 
> R-admin manual for 3.4.2 RC).
> 
>> On Fri, Sep 22, 2017 at 4:47 AM, peter dalgaard  wrote:
>>> Just a quick note: Xcode 9 will not presently create a working R on Sierra
>>> or earlier.
> 
> (I don't believe Xcode 9 is available for 'earlier'.)

You're probably right. I wasn't sure when I wrote that (& also not sure whether 
one could cross-compile.)

-pd

> 
>>> 
>>> This is because it ships with an SDK for 10.13 (unreleased) and defines an
>>> entry for utimensat(), which is not actually in the system library for
>>> earlier versions.
>>> 
>>> There is no way we can fix this reliably for the upcoming 3.4.2 release,
>>> so if you intend to build R from sources, either
>>> 
>>> - just do not upgrade, stay on Xcode 8.3.3
>>> 
>>> or
>>> 
>>> - manually remove the line from config.h saying
>>> 
>>> #define HAVE_UTIMENSAT 1
>>> 
>>> 
>>> 
>>> 
>>> The slightly longer story is that Apple decided to have their include
>>> files generate a _warning_ that utimensat() is only available in 10.13,
>>> like this:
>>> 
>>> gcc -I../../../R/src/extra  -I. -I../../src/include
>>> -I../../../R/src/include  -I/usr/local/include -I../../../R/src/nmath
>>> -DHAVE_CONFIG_H -g -O2  -c ../../../R/src/main/platform.c -o platform.o
>>> ../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only
>>> available on
>>>   macOS 10.13 or newer [-Wunguarded-availability-new]
>>> utimensat(AT_FDCWD, to, times, 0);
>>> ^
>>> /Applications/Xcode.app/Contents/Developer/Platforms/
>>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
>>> note:
>>>   'utimensat' has been explicitly marked partial here
>>> int utimensat(int __fd, const char *__path, const struct timespec __...
>>> ^
>>> ../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
>>>   __builtin_available check to silence this warning
>>> utimensat(AT_FDCWD, to, times, 0);
>>> ^
>>> ../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only
>>> available
>>>   on macOS 10.13 or newer [-Wunguarded-availability-new]
>>> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
>>>   ^
>>> /Applications/Xcode.app/Contents/Developer/Platforms/
>>> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
>>> note:
>>>   'utimensat' has been explicitly marked partial here
>>> int utimensat(int __fd, const char *__path, const struct timespec __...
>>> ^
>>> ../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
>>>   __builtin_available check to silence this warning
>>> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
>>>   ^
>>> 2 warnings generated.
>>> 
>>> Because of dynamic linking, we do not see the effect of this until we
>>> actually try running the binary:
>>> 
>>> begin installing recommended package MASS
>>> dyld: lazy symbol binding failed: Symbol not found: _utimensat
>>>   Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
>>>   Expected in: /usr/lib/libSystem.B.dylib

Re: [R-SIG-Mac] Xcode 9

[Prof Brian Ripley]

On 27/09/2017 03:28, Kasper Daniel Hansen wrote:

I don't see this with
   Xcode 9
   OS X Sierra (10.12.6)

and either

R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered
Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

or

R version 3.4.2 RC (2017-09-26 r73351) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

Specifically I can compile R and it passes make check.  Perhaps it got
fixed since the post.


It did (look at the logs for r73347 and r73351), but also we have 
discovered that not all upgrades to Xcode 9 had the problem.


While we are at it, there is a problem with finding the default time 
zone on High Sierra.  This is worked around already in R-devel and will 
be in 3.4.2 patched: until then setting TZ is a good workaround (and 
that is in the R-admin manual for 3.4.2 RC).




On Fri, Sep 22, 2017 at 4:47 AM, peter dalgaard  wrote:


Just a quick note: Xcode 9 will not presently create a working R on Sierra
or earlier.


(I don't believe Xcode 9 is available for 'earlier'.)



This is because it ships with an SDK for 10.13 (unreleased) and defines an
entry for utimensat(), which is not actually in the system library for
earlier versions.

There is no way we can fix this reliably for the upcoming 3.4.2 release,
so if you intend to build R from sources, either

- just do not upgrade, stay on Xcode 8.3.3

or

- manually remove the line from config.h saying

#define HAVE_UTIMENSAT 1




The slightly longer story is that Apple decided to have their include
files generate a _warning_ that utimensat() is only available in 10.13,
like this:

gcc -I../../../R/src/extra  -I. -I../../src/include
-I../../../R/src/include  -I/usr/local/include -I../../../R/src/nmath
-DHAVE_CONFIG_H -g -O2  -c ../../../R/src/main/platform.c -o platform.o
../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only
available on
   macOS 10.13 or newer [-Wunguarded-availability-new]
 utimensat(AT_FDCWD, to, times, 0);
 ^
/Applications/Xcode.app/Contents/Developer/Platforms/
MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
note:
   'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
 ^
../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
   __builtin_available check to silence this warning
 utimensat(AT_FDCWD, to, times, 0);
 ^
../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only
available
   on macOS 10.13 or newer [-Wunguarded-availability-new]
 res = utimensat(AT_FDCWD, fn, times, 0) == 0;
   ^
/Applications/Xcode.app/Contents/Developer/Platforms/
MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
note:
   'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
 ^
../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
   __builtin_available check to silence this warning
 res = utimensat(AT_FDCWD, fn, times, 0) == 0;
   ^
2 warnings generated.

Because of dynamic linking, we do not see the effect of this until we
actually try running the binary:

begin installing recommended package MASS
dyld: lazy symbol binding failed: Symbol not found: _utimensat
   Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
   Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
   Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
   Expected in: /usr/lib/libSystem.B.dylib

/Users/pd/r-release-branch/BUILD-dist/bin/INSTALL: line 34: 59149 Done
 echo 'tools:::.install_packages()'
  59150 Abort trap: 6   | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}


Same warning also happens during the configure checks, but as it is not an
error the test program compiles and links OK (but is never run), and we get

checking whether utimensat exists and is declared... yes

Ugh!...


- Peter D.


--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

Re: [R-SIG-Mac] Xcode 9

[Kasper Daniel Hansen]

I don't see this with
  Xcode 9
  OS X Sierra (10.12.6)

and either

R Under development (unstable) (2017-09-26 r73351) -- "Unsuffered
Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

or

R version 3.4.2 RC (2017-09-26 r73351) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin16.7.0 (64-bit)

Specifically I can compile R and it passes make check.  Perhaps it got
fixed since the post.

On Fri, Sep 22, 2017 at 4:47 AM, peter dalgaard  wrote:

> Just a quick note: Xcode 9 will not presently create a working R on Sierra
> or earlier.
>
> This is because it ships with an SDK for 10.13 (unreleased) and defines an
> entry for utimensat(), which is not actually in the system library for
> earlier versions.
>
> There is no way we can fix this reliably for the upcoming 3.4.2 release,
> so if you intend to build R from sources, either
>
> - just do not upgrade, stay on Xcode 8.3.3
>
> or
>
> - manually remove the line from config.h saying
>
> #define HAVE_UTIMENSAT 1
>
>
> 
>
> The slightly longer story is that Apple decided to have their include
> files generate a _warning_ that utimensat() is only available in 10.13,
> like this:
>
> gcc -I../../../R/src/extra  -I. -I../../src/include
> -I../../../R/src/include  -I/usr/local/include -I../../../R/src/nmath
> -DHAVE_CONFIG_H -g -O2  -c ../../../R/src/main/platform.c -o platform.o
> ../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only
> available on
>   macOS 10.13 or newer [-Wunguarded-availability-new]
> utimensat(AT_FDCWD, to, times, 0);
> ^
> /Applications/Xcode.app/Contents/Developer/Platforms/
> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
> note:
>   'utimensat' has been explicitly marked partial here
> int utimensat(int __fd, const char *__path, const struct timespec __...
> ^
> ../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
>   __builtin_available check to silence this warning
> utimensat(AT_FDCWD, to, times, 0);
> ^
> ../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only
> available
>   on macOS 10.13 or newer [-Wunguarded-availability-new]
> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
>   ^
> /Applications/Xcode.app/Contents/Developer/Platforms/
> MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
> note:
>   'utimensat' has been explicitly marked partial here
> int utimensat(int __fd, const char *__path, const struct timespec __...
> ^
> ../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
>   __builtin_available check to silence this warning
> res = utimensat(AT_FDCWD, fn, times, 0) == 0;
>   ^
> 2 warnings generated.
>
> Because of dynamic linking, we do not see the effect of this until we
> actually try running the binary:
>
> begin installing recommended package MASS
> dyld: lazy symbol binding failed: Symbol not found: _utimensat
>   Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: _utimensat
>   Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
>   Expected in: /usr/lib/libSystem.B.dylib
>
> /Users/pd/r-release-branch/BUILD-dist/bin/INSTALL: line 34: 59149 Done
> echo 'tools:::.install_packages()'
>  59150 Abort trap: 6   | R_DEFAULT_PACKAGES= LC_COLLATE=C
> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
>
>
> Same warning also happens during the configure checks, but as it is not an
> error the test program compiles and links OK (but is never run), and we get
>
> checking whether utimensat exists and is declared... yes
>
> Ugh!...
>
>
> - Peter D.
>
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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[R-SIG-Mac] Xcode 9

[peter dalgaard]

Just a quick note: Xcode 9 will not presently create a working R on Sierra or 
earlier.

This is because it ships with an SDK for 10.13 (unreleased) and defines an 
entry for utimensat(), which is not actually in the system library for earlier 
versions. 

There is no way we can fix this reliably for the upcoming 3.4.2 release, so if 
you intend to build R from sources, either 

- just do not upgrade, stay on Xcode 8.3.3 

or 

- manually remove the line from config.h saying

#define HAVE_UTIMENSAT 1




The slightly longer story is that Apple decided to have their include files 
generate a _warning_ that utimensat() is only available in 10.13, like this: 

gcc -I../../../R/src/extra  -I. -I../../src/include -I../../../R/src/include  
-I/usr/local/include -I../../../R/src/nmath -DHAVE_CONFIG_H -g -O2  -c 
../../../R/src/main/platform.c -o platform.o
../../../R/src/main/platform.c:2474:5: warning: 'utimensat' is only available on
  macOS 10.13 or newer [-Wunguarded-availability-new]
utimensat(AT_FDCWD, to, times, 0);
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
 note: 
  'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
^
../../../R/src/main/platform.c:2474:5: note: enclose 'utimensat' in a
  __builtin_available check to silence this warning
utimensat(AT_FDCWD, to, times, 0);
^
../../../R/src/main/platform.c:2890:11: warning: 'utimensat' is only available
  on macOS 10.13 or newer [-Wunguarded-availability-new]
res = utimensat(AT_FDCWD, fn, times, 0) == 0;
  ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/sys/stat.h:374:5:
 note: 
  'utimensat' has been explicitly marked partial here
int utimensat(int __fd, const char *__path, const struct timespec __...
^
../../../R/src/main/platform.c:2890:11: note: enclose 'utimensat' in a
  __builtin_available check to silence this warning
res = utimensat(AT_FDCWD, fn, times, 0) == 0;
  ^
2 warnings generated.

Because of dynamic linking, we do not see the effect of this until we actually 
try running the binary:

begin installing recommended package MASS
dyld: lazy symbol binding failed: Symbol not found: _utimensat
  Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _utimensat
  Referenced from: /Users/pd/r-release-branch/BUILD-dist/bin/exec/x86_64/R
  Expected in: /usr/lib/libSystem.B.dylib

/Users/pd/r-release-branch/BUILD-dist/bin/INSTALL: line 34: 59149 Done  
  echo 'tools:::.install_packages()'
 59150 Abort trap: 6   | R_DEFAULT_PACKAGES= LC_COLLATE=C 
"${R_HOME}/bin/R" $myArgs --slave --args ${args}


Same warning also happens during the configure checks, but as it is not an 
error the test program compiles and links OK (but is never run), and we get

checking whether utimensat exists and is declared... yes

Ugh!...


- Peter D.


-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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