Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[Timothy Bates]

Thanks Marc!

I didn't think the `xcode-select --install` was needed any longer.
Did that and all worked well with the `macOS_SDK_headers_for_macOS_10.14.pkg`
install.

Many thanks again!
tim



On Tue, Sep 25, 2018 at 5:36 PM Marc Schwartz  wrote:

> Hi Tim,
>
> Be sure that you are running the latest version of Xcode:
>
>   https://itunes.apple.com/us/app/xcode/id497799835?mt=12
>
> and that you also install/re-install the command line tools afterwards:
>
>   xcode-select --install
>
> With a major macOS version upgrade like this, you should do a fully clean
> install of R and afterwards, of XQuartz:
>
>   https://www.xquartz.org
>
> Regards,
>
> Marc
>
>
> > On Sep 25, 2018, at 11:59 AM, Tim Bates 
> wrote:
> >
> > fyi
> >
> > home$ sudo installer -pkg \
> >>
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> \
> >> -target /
> > Password:
> > installer: Error - the package path specified was invalid:
> '/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg'.
> > spearman:OpenMx tim$
> >
> >
> >> On 25 Sep 2018, at 1:04 pm, Marc Schwartz via R-SIG-Mac <
> r-sig-mac@r-project.org> wrote:
> >>
> >> Thanks to both of you for the pointers on this.
> >>
> >> I have not used a dark theme since my Fedora days. Still getting used
> to it... :-)
> >>
> >> Regards,
> >>
> >> Marc Schwartz
> >>
> >>
> >>> On Sep 25, 2018, at 5:55 AM, peter dalgaard  wrote:
> >>>
> >>> [Oops. Forgot to copy this back to R-sig-mac, it seems...]
> >>>
> >>> Thanks, Brian,
> >>>
> >>> Yes, we have previously learned the hard way that timing R releases
> too close to MacOS updates is a bad idea...
> >>>
> >>> The manual updates haven't made it to CRAN yet, you need to look in
> the sources.
> >>>
> >>> For those who might be curious, but lazy:
> >>>
> >>>
> >>> As from macOS 10.14 (‘Mojave’) an additional step is needed to install
> the headers to /usr/include: from a Terminal run
> >>>
> >>> sudo installer -pkg \
> >>>
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> \
> >>> -target /
> >>>
> >>> Alternatively, change the include path via
> >>>
> >>> CPPFLAGS="-isystem
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
> >>> 
> >>>
> >>>
> >>> Incidentally, probably unrelated, I discovered that the R-patched
> snapshots had stalled since Sep 13 due to an SVN database error. This
> should be cleared up now.
> >>>
> >>> -pd
> >>>
>  On 25 Sep 2018, at 08:59 , Prof Brian Ripley 
> wrote:
> 
>  A heads up:
> 
>  The Mojave update removes /usr/include and (re)installing the Command
> Line Tools does not put the standard system headers there.  Workarounds are
> now described in the R-admin manual for R-devel and R-patched.
> 
>  --
>  Brian D. Ripley,  rip...@stats.ox.ac.uk
>  Emeritus Professor of Applied Statistics, University of Oxford
> 
>  ___
> 
> 
>  R-SIG-Mac mailing list
>  R-SIG-Mac@r-project.org
>  https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>>
> >>> --
> >>> Peter Dalgaard, Professor,
> >>> Center for Statistics, Copenhagen Business School
> >>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> >>> Phone: (+45)38153501 <+45%2038%2015%2035%2001>
> >>> Office: A 4.23
> >>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>
>

[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[Marc Schwartz via R-SIG-Mac]

Hi Tim,

Be sure that you are running the latest version of Xcode:

  https://itunes.apple.com/us/app/xcode/id497799835?mt=12

and that you also install/re-install the command line tools afterwards:

  xcode-select --install

With a major macOS version upgrade like this, you should do a fully clean 
install of R and afterwards, of XQuartz:

  https://www.xquartz.org

Regards,

Marc


> On Sep 25, 2018, at 11:59 AM, Tim Bates  wrote:
> 
> fyi
> 
> home$ sudo installer -pkg \
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>  \
>> -target /
> Password:
> installer: Error - the package path specified was invalid: 
> '/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg'.
> spearman:OpenMx tim$ 
> 
> 
>> On 25 Sep 2018, at 1:04 pm, Marc Schwartz via R-SIG-Mac 
>>  wrote:
>> 
>> Thanks to both of you for the pointers on this.
>> 
>> I have not used a dark theme since my Fedora days. Still getting used to 
>> it... :-)
>> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>> 
>>> On Sep 25, 2018, at 5:55 AM, peter dalgaard  wrote:
>>> 
>>> [Oops. Forgot to copy this back to R-sig-mac, it seems...]
>>> 
>>> Thanks, Brian,
>>> 
>>> Yes, we have previously learned the hard way that timing R releases too 
>>> close to MacOS updates is a bad idea...
>>> 
>>> The manual updates haven't made it to CRAN yet, you need to look in the 
>>> sources. 
>>> 
>>> For those who might be curious, but lazy:
>>> 
>>> 
>>> As from macOS 10.14 (‘Mojave’) an additional step is needed to install the 
>>> headers to /usr/include: from a Terminal run
>>> 
>>> sudo installer -pkg \
>>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>  \
>>> -target /
>>> 
>>> Alternatively, change the include path via
>>> 
>>> CPPFLAGS="-isystem 
>>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
>>> 
>>> 
>>> 
>>> Incidentally, probably unrelated, I discovered that the R-patched snapshots 
>>> had stalled since Sep 13 due to an SVN database error. This should be 
>>> cleared up now.
>>> 
>>> -pd 
>>> 
 On 25 Sep 2018, at 08:59 , Prof Brian Ripley  wrote:
 
 A heads up:
 
 The Mojave update removes /usr/include and (re)installing the Command Line 
 Tools does not put the standard system headers there.  Workarounds are now 
 described in the R-admin manual for R-devel and R-patched.
 
 -- 
 Brian D. Ripley,  rip...@stats.ox.ac.uk
 Emeritus Professor of Applied Statistics, University of Oxford
 
 ___
 R-SIG-Mac mailing list
 R-SIG-Mac@r-project.org
 https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> -- 
>>> 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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Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[Tim Bates]

fyi

home$ sudo installer -pkg \
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>  \
> -target /
Password:
installer: Error - the package path specified was invalid: 
'/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg'.
spearman:OpenMx tim$ 


> On 25 Sep 2018, at 1:04 pm, Marc Schwartz via R-SIG-Mac 
>  wrote:
> 
> Thanks to both of you for the pointers on this.
> 
> I have not used a dark theme since my Fedora days. Still getting used to 
> it... :-)
> 
> Regards,
> 
> Marc Schwartz
> 
> 
>> On Sep 25, 2018, at 5:55 AM, peter dalgaard  wrote:
>> 
>> [Oops. Forgot to copy this back to R-sig-mac, it seems...]
>> 
>> Thanks, Brian,
>> 
>> Yes, we have previously learned the hard way that timing R releases too 
>> close to MacOS updates is a bad idea...
>> 
>> The manual updates haven't made it to CRAN yet, you need to look in the 
>> sources. 
>> 
>> For those who might be curious, but lazy:
>> 
>> 
>> As from macOS 10.14 (‘Mojave’) an additional step is needed to install the 
>> headers to /usr/include: from a Terminal run
>> 
>> sudo installer -pkg \
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>  \
>> -target /
>> 
>> Alternatively, change the include path via
>> 
>> CPPFLAGS="-isystem 
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
>> 
>> 
>> 
>> Incidentally, probably unrelated, I discovered that the R-patched snapshots 
>> had stalled since Sep 13 due to an SVN database error. This should be 
>> cleared up now.
>> 
>> -pd 
>> 
>>> On 25 Sep 2018, at 08:59 , Prof Brian Ripley  wrote:
>>> 
>>> A heads up:
>>> 
>>> The Mojave update removes /usr/include and (re)installing the Command Line 
>>> Tools does not put the standard system headers there.  Workarounds are now 
>>> described in the R-admin manual for R-devel and R-patched.
>>> 
>>> -- 
>>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>>> Emeritus Professor of Applied Statistics, University of Oxford
>>> 
>>> ___
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> -- 
>> 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
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[Marc Schwartz via R-SIG-Mac]

Thanks to both of you for the pointers on this.

I have not used a dark theme since my Fedora days. Still getting used to it... 
:-)

Regards,

Marc Schwartz


> On Sep 25, 2018, at 5:55 AM, peter dalgaard  wrote:
> 
> [Oops. Forgot to copy this back to R-sig-mac, it seems...]
> 
> Thanks, Brian,
> 
> Yes, we have previously learned the hard way that timing R releases too close 
> to MacOS updates is a bad idea...
> 
> The manual updates haven't made it to CRAN yet, you need to look in the 
> sources. 
> 
> For those who might be curious, but lazy:
> 
> 
> As from macOS 10.14 (‘Mojave’) an additional step is needed to install the 
> headers to /usr/include: from a Terminal run
> 
> sudo installer -pkg \
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>  \
> -target /
> 
> Alternatively, change the include path via
> 
> CPPFLAGS="-isystem 
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
> 
> 
> 
> Incidentally, probably unrelated, I discovered that the R-patched snapshots 
> had stalled since Sep 13 due to an SVN database error. This should be cleared 
> up now.
> 
> -pd 
> 
>> On 25 Sep 2018, at 08:59 , Prof Brian Ripley  wrote:
>> 
>> A heads up:
>> 
>> The Mojave update removes /usr/include and (re)installing the Command Line 
>> Tools does not put the standard system headers there.  Workarounds are now 
>> described in the R-admin manual for R-devel and R-patched.
>> 
>> -- 
>> Brian D. Ripley,  rip...@stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
>> 
>> ___
>> R-SIG-Mac mailing list
>> R-SIG-Mac@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> -- 
> 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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Re: [R-SIG-Mac] Installing R on 10.14 (Mojave)

[peter dalgaard]

[Oops. Forgot to copy this back to R-sig-mac, it seems...]

Thanks, Brian,

Yes, we have previously learned the hard way that timing R releases too close 
to MacOS updates is a bad idea...

The manual updates haven't made it to CRAN yet, you need to look in the 
sources. 

For those who might be curious, but lazy:

 
As from macOS 10.14 (‘Mojave’) an additional step is needed to install the 
headers to /usr/include: from a Terminal run

sudo installer -pkg \
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
 \
-target /

Alternatively, change the include path via

CPPFLAGS="-isystem 
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"



Incidentally, probably unrelated, I discovered that the R-patched snapshots had 
stalled since Sep 13 due to an SVN database error. This should be cleared up 
now.

-pd 

> On 25 Sep 2018, at 08:59 , Prof Brian Ripley  wrote:
> 
> A heads up:
> 
> The Mojave update removes /usr/include and (re)installing the Command Line 
> Tools does not put the standard system headers there.  Workarounds are now 
> described in the R-admin manual for R-devel and R-patched.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

-- 
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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[R-SIG-Mac] Installing R on 10.14 (Mojave)

[Prof Brian Ripley]

A heads up:

The Mojave update removes /usr/include and (re)installing the Command 
Line Tools does not put the standard system headers there.  Workarounds 
are now described in the R-admin manual for R-devel and R-patched.


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

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