date:20200429

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

2020-04-29 Thread Eric K

Kevin,

which clang gives /usr/bin/clang, and xcode-select -p and xcrun
--show-sdk-path give same output as yours.

I am sure it is something I messed up along the way, and/or is related to
having homebrew also installed.

Someday soon I will upgrade to Catalina and see if that resolves the issue
(or makes it worse).

Best regards,
Eric


On Wed, Apr 29, 2020 at 1:31 PM Kevin Ushey  wrote:

> Normally, you shouldn't need to set -isysroot or SDKROOT when using
> Apple Clang -- it will automatically find and use system headers for
> you.
>
> Per Hervé's original point, I wonder if you have a different compiler
> on the PATH? What is the output of:
>
> which clang
>
> My suspicion is that you might have an alternate compiler on the PATH
> that is being used instead of the default Apple Clang.
>
> You might also check e.g.
>
> xcode-select -p
> xcrun --show-sdk-path
>
> just to make sure those are pointing in the right place -- e.g. I have:
>
> kevinushey@Kevins-MBP:~
> $ xcode-select -p
> /Library/Developer/CommandLineTools
> kevinushey@Kevins-MBP:~
> $ xcrun --show-sdk-path
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>
> You could also set CC=/usr/bin/clang just to force the use of the
> system compiler (and avoid looking up whatever is first on the PATH).
>
> Best,
> Kevin
>
> On Wed, Apr 29, 2020 at 10:24 AM Eric K  wrote:
> >
> > One more update. I had to add the -isysroot flag to avoid collisions
> > between incompatible headers when building some packages. Thinking about
> it
> > more I remembered that I have also used Homebrew in the past for some
> > installations of unrelated software (so my installation is not as
> "Vanilla"
> > as I previously asserted). I wonder then if the source of my woes here is
> > collisions between homebrew and Xcode? Regardless, this ~/.R/Makevars is
> > working for me to allow building source packages with the official R 4.0
> > binary on macOs 10.14.6 with XCode 11.3.1 :
> >
> > CFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> > CXXFLAGS =
> > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> > CPPFLAGS =
> > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> >
> > Thanks again!
> > -Eric
> >
> >
> > On Wed, Apr 29, 2020 at 1:01 PM Eric K  wrote:
> >
> > > Thank you Hervé.
> > >
> > > So yes, with this ~/.R/Makevars everything works fine again (with a
> couple
> > > extra flags to keep things quiet):
> > >
> > > CFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > > -Wno-nullability-completeness -Wno-expansion-to-defined
> > > CXXFLAGS =
> > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > > -Wno-nullability-completeness -Wno-expansion-to-defined
> > > CPPFLAGS =
> > > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > > -Wno-nullability-completeness -Wno-expansion-to-defined
> > >
> > > I am curious why I need this Makevars with what I believe to be a
> vanilla
> > > MacOS / XCode / R installation? But since things are working, my
> > > curiosity will not keep me up at night.
> > >
> > > Thanks again for pointing me in the right direction.
> > >
> > > -Eric
> > >
> > >
> > > On Wed, Apr 29, 2020 at 12:42 PM Hervé Pagès 
> wrote:
> > >
> > >> Hi Eric,
> > >>
> > >> FWIW, here is what I see on my system (Mojave):
> > >>
> > >>machv2:~ biocbuild$ which clang
> > >>/usr/bin/clang
> > >>
> > >>machv2:~ biocbuild$ clang -v
> > >>Apple LLVM version 10.0.1 (clang-1001.0.46.4)
> > >>Target: x86_64-apple-darwin18.7.0
> > >>Thread model: posix
> > >>InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> > >>
> > >>machv2:~ biocbuild$ ls -l
> > >>
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
> > >>-r--r--r--  1 root  wheel  16319 Feb 22  2019
> > >>
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
> > >>
> > >> I'm not a Mac expert but I believe these locations for Apple clang and
> > >> associated standard C header files have not changed for years.
> > >>
> > >> Hope this helps,
> > >> H.
> > >>
> > >>
> > >> On 4/29/20 07:05, Eric K wrote:
> > >> > Running R 3.6 has been working fine. I just upgraded to R 4.0 and I
> > >> cannot
> > >> > build packages from source. I have tried the following:
> > >> >
> > >> > 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation
> went
> > >> > fine, but when I try to build packages from source I get errors like
> > >> this:
> > >> >
> > >> > * installing *source* package ‘MASS’ ...
> > >> >

Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread Fox, John

Dear JB,

> On Apr 29, 2020, at 1:44 PM, jean benoit TANIS  wrote:
> 
> This actually works well on the terminal session !! Very strange that the App 
> GUI does not work well. I do not know if it is a general Mac problem or due 
> to my computer settings…. 

I don't think that it could be a general Mac problem, because R.app works with 
the Rcmdr for me and others. At least you now have a couple of solutions.

Best,
 John

> 
> JB
> 
>> On 29 Apr 2020, at 18:18, Fox, John  wrote:
>> 
>> Dear JB,
>> 
>> If you use the Rcmdr with RStudio, by default it will direct output to the 
>> RStudio console. You can change that, if you wish -- look at the Rcmdr 
>> options in ?Commander.
>> 
>> Also, have you tried running R and the Rcmdr in a Terminal window, as I 
>> suggested? If the problem is with R.app, then that might work too.
>> 
>> Peter: Thanks for chiming in.
>> 
>> Best,
>> John
>> 
>>> -Original Message-
>>> From: jean benoit TANIS 
>>> Sent: Wednesday, April 29, 2020 1:04 PM
>>> To: peter dalgaard 
>>> Cc: Fox, John ; R-Sig-Mac 
>>> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
>>> 
>>> I have just tried with R studio and it works … I do not know why it does
>>> not work with Rapp but at least I can use it now.
>>> 
>>> Thank you very much for your precious help !!
>>> 
>>> JB
>>> 
 On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
 
 Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
>>> bothered to upgrade at this point). Works both from R.app and Terminal,
>>> and even from RStudio.
 
 One thought is a missing font, but same font is used elsewhere is it
>>> not?
 
 You could try playing with generic Tcl/Tk via the tcltk package and
 see if you can reproduce the problem in a simpler setting (perhaps try
 the package demos?)
 
 -pd
 
> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
> 
> Dear JB,
> 
> We corresponded privately about this problem, and I suggested that you
>>> post a message to the R-SIG-Mac list when I was unable to help you solve
>>> it. I don't experience the problem on a Mac similar to yours, but running
>>> macOS Catalina, and no one else to my knowledge has reported a similar
>>> problem (with blank menus).
> 
> I do have one additional suggestion: I assume that you're running the
>>> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
>>> That is open the Mac Terminal, type R  at the % command prompt and then
>>> library(Rcmdr) at the R > prompt.
> 
> Perhaps others will think of additional suggestions.
> 
> Best,
> John
> 
>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS 
>>> wrote:
>> 
>> Hi,
>> 
>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
>>> used to work on R2.6 on Windows).
>> 
>> When I load the Rcmdr package, this is what I obtain - see picture
>> (the drop down menu does not display). 
>> 
>> I manage to have access to the drop-down menu only once despite 20 or
>>> so attempts of closing and reopening R.
>> 
>> I have tried to:
>> - turn-off nap-app => same issue
>> - uninstall R and rebook and start again => same issue
>> - uninstall XQuartz and reboot and start again => same issue
>> 
>> For more information about my system, please find the pictures below
>> 
>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
>> 
>> Did you encounter this problem before ? Is there any way you could
>>> help me solving it ?
>> 
>> 
>> Thank you very much for your help,
>> 
>> Best wishes,
>> 
>> 
>> JB
>> 
>> 
>> ___
>> 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
 
 --
 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
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Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread jean benoit TANIS

This actually works well on the terminal session !! Very strange that the App 
GUI does not work well. I do not know if it is a general Mac problem or due to 
my computer settings…. 

JB

> On 29 Apr 2020, at 18:18, Fox, John  wrote:
> 
> Dear JB,
> 
> If you use the Rcmdr with RStudio, by default it will direct output to the 
> RStudio console. You can change that, if you wish -- look at the Rcmdr 
> options in ?Commander.
> 
> Also, have you tried running R and the Rcmdr in a Terminal window, as I 
> suggested? If the problem is with R.app, then that might work too.
> 
> Peter: Thanks for chiming in.
> 
> Best,
> John
> 
>> -Original Message-
>> From: jean benoit TANIS 
>> Sent: Wednesday, April 29, 2020 1:04 PM
>> To: peter dalgaard 
>> Cc: Fox, John ; R-Sig-Mac 
>> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
>> 
>> I have just tried with R studio and it works … I do not know why it does
>> not work with Rapp but at least I can use it now.
>> 
>> Thank you very much for your precious help !!
>> 
>> JB
>> 
>>> On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
>>> 
>>> Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
>> bothered to upgrade at this point). Works both from R.app and Terminal,
>> and even from RStudio.
>>> 
>>> One thought is a missing font, but same font is used elsewhere is it
>> not?
>>> 
>>> You could try playing with generic Tcl/Tk via the tcltk package and
>>> see if you can reproduce the problem in a simpler setting (perhaps try
>>> the package demos?)
>>> 
>>> -pd
>>> 
 On 29 Apr 2020, at 15:07 , Fox, John  wrote:
 
 Dear JB,
 
 We corresponded privately about this problem, and I suggested that you
>> post a message to the R-SIG-Mac list when I was unable to help you solve
>> it. I don't experience the problem on a Mac similar to yours, but running
>> macOS Catalina, and no one else to my knowledge has reported a similar
>> problem (with blank menus).
 
 I do have one additional suggestion: I assume that you're running the
>> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
>> That is open the Mac Terminal, type R  at the % command prompt and then
>> library(Rcmdr) at the R > prompt.
 
 Perhaps others will think of additional suggestions.
 
 Best,
 John
 
> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS 
>> wrote:
> 
> Hi,
> 
> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
>> used to work on R2.6 on Windows).
> 
> When I load the Rcmdr package, this is what I obtain - see picture
> (the drop down menu does not display). 
> 
> I manage to have access to the drop-down menu only once despite 20 or
>> so attempts of closing and reopening R.
> 
> I have tried to:
> - turn-off nap-app => same issue
> - uninstall R and rebook and start again => same issue
> - uninstall XQuartz and reboot and start again => same issue
> 
> For more information about my system, please find the pictures below
> 
> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
> 
> Did you encounter this problem before ? Is there any way you could
>> help me solving it ?
> 
> 
> Thank you very much for your help,
> 
> Best wishes,
> 
> 
> JB
> 
> 
> ___
> 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
>>> 
>>> --
>>> 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@r-project.org
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Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

2020-04-29 Thread Kevin Ushey

Normally, you shouldn't need to set -isysroot or SDKROOT when using
Apple Clang -- it will automatically find and use system headers for
you.

Per Hervé's original point, I wonder if you have a different compiler
on the PATH? What is the output of:

which clang

My suspicion is that you might have an alternate compiler on the PATH
that is being used instead of the default Apple Clang.

You might also check e.g.

xcode-select -p
xcrun --show-sdk-path

just to make sure those are pointing in the right place -- e.g. I have:

kevinushey@Kevins-MBP:~
$ xcode-select -p
/Library/Developer/CommandLineTools
kevinushey@Kevins-MBP:~
$ xcrun --show-sdk-path
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

You could also set CC=/usr/bin/clang just to force the use of the
system compiler (and avoid looking up whatever is first on the PATH).

Best,
Kevin

On Wed, Apr 29, 2020 at 10:24 AM Eric K  wrote:
>
> One more update. I had to add the -isysroot flag to avoid collisions
> between incompatible headers when building some packages. Thinking about it
> more I remembered that I have also used Homebrew in the past for some
> installations of unrelated software (so my installation is not as "Vanilla"
> as I previously asserted). I wonder then if the source of my woes here is
> collisions between homebrew and Xcode? Regardless, this ~/.R/Makevars is
> working for me to allow building source packages with the official R 4.0
> binary on macOs 10.14.6 with XCode 11.3.1 :
>
> CFLAGS = -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> CXXFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> CPPFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
>
> Thanks again!
> -Eric
>
>
> On Wed, Apr 29, 2020 at 1:01 PM Eric K  wrote:
>
> > Thank you Hervé.
> >
> > So yes, with this ~/.R/Makevars everything works fine again (with a couple
> > extra flags to keep things quiet):
> >
> > CFLAGS = -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined
> > CXXFLAGS =
> > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined
> > CPPFLAGS =
> > -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> > -Wno-nullability-completeness -Wno-expansion-to-defined
> >
> > I am curious why I need this Makevars with what I believe to be a vanilla
> > MacOS / XCode / R installation? But since things are working, my
> > curiosity will not keep me up at night.
> >
> > Thanks again for pointing me in the right direction.
> >
> > -Eric
> >
> >
> > On Wed, Apr 29, 2020 at 12:42 PM Hervé Pagès  wrote:
> >
> >> Hi Eric,
> >>
> >> FWIW, here is what I see on my system (Mojave):
> >>
> >>machv2:~ biocbuild$ which clang
> >>/usr/bin/clang
> >>
> >>machv2:~ biocbuild$ clang -v
> >>Apple LLVM version 10.0.1 (clang-1001.0.46.4)
> >>Target: x86_64-apple-darwin18.7.0
> >>Thread model: posix
> >>InstalledDir: /Library/Developer/CommandLineTools/usr/bin
> >>
> >>machv2:~ biocbuild$ ls -l
> >> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
> >>-r--r--r--  1 root  wheel  16319 Feb 22  2019
> >> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
> >>
> >> I'm not a Mac expert but I believe these locations for Apple clang and
> >> associated standard C header files have not changed for years.
> >>
> >> Hope this helps,
> >> H.
> >>
> >>
> >> On 4/29/20 07:05, Eric K wrote:
> >> > Running R 3.6 has been working fine. I just upgraded to R 4.0 and I
> >> cannot
> >> > build packages from source. I have tried the following:
> >> >
> >> > 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
> >> > fine, but when I try to build packages from source I get errors like
> >> this:
> >> >
> >> > * installing *source* package ‘MASS’ ...
> >> > ** package ‘MASS’ successfully unpacked and MD5 sums checked
> >> > ** using staged installation
> >> > ** libs
> >> > clang -mmacosx-version-min=10.13
> >> > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> >> > -I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
> >> > MASS.c:18:10: fatal error: 'stdlib.h' file not found
> >> > #include 
> >> >
> >> > Indeed, stdlib.h is not in /usr/local/include.
> >> >
> >> > 2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that did
> >> not
> >> > fix the problem
> >> >
> >> > 3. So I installed Xcode 11.3.1 itself. That did not fix the problem.
> >> >
> >> >

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

2020-04-29 Thread Eric K

One more update. I had to add the -isysroot flag to avoid collisions
between incompatible headers when building some packages. Thinking about it
more I remembered that I have also used Homebrew in the past for some
installations of unrelated software (so my installation is not as "Vanilla"
as I previously asserted). I wonder then if the source of my woes here is
collisions between homebrew and Xcode? Regardless, this ~/.R/Makevars is
working for me to allow building source packages with the official R 4.0
binary on macOs 10.14.6 with XCode 11.3.1 :

CFLAGS = -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS =
-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS =
-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined -isysroot
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

Thanks again!
-Eric


On Wed, Apr 29, 2020 at 1:01 PM Eric K  wrote:

> Thank you Hervé.
>
> So yes, with this ~/.R/Makevars everything works fine again (with a couple
> extra flags to keep things quiet):
>
> CFLAGS = -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined
> CXXFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined
> CPPFLAGS =
> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
> -Wno-nullability-completeness -Wno-expansion-to-defined
>
> I am curious why I need this Makevars with what I believe to be a vanilla
> MacOS / XCode / R installation? But since things are working, my
> curiosity will not keep me up at night.
>
> Thanks again for pointing me in the right direction.
>
> -Eric
>
>
> On Wed, Apr 29, 2020 at 12:42 PM Hervé Pagès  wrote:
>
>> Hi Eric,
>>
>> FWIW, here is what I see on my system (Mojave):
>>
>>machv2:~ biocbuild$ which clang
>>/usr/bin/clang
>>
>>machv2:~ biocbuild$ clang -v
>>Apple LLVM version 10.0.1 (clang-1001.0.46.4)
>>Target: x86_64-apple-darwin18.7.0
>>Thread model: posix
>>InstalledDir: /Library/Developer/CommandLineTools/usr/bin
>>
>>machv2:~ biocbuild$ ls -l
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
>>-r--r--r--  1 root  wheel  16319 Feb 22  2019
>> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
>>
>> I'm not a Mac expert but I believe these locations for Apple clang and
>> associated standard C header files have not changed for years.
>>
>> Hope this helps,
>> H.
>>
>>
>> On 4/29/20 07:05, Eric K wrote:
>> > Running R 3.6 has been working fine. I just upgraded to R 4.0 and I
>> cannot
>> > build packages from source. I have tried the following:
>> >
>> > 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
>> > fine, but when I try to build packages from source I get errors like
>> this:
>> >
>> > * installing *source* package ‘MASS’ ...
>> > ** package ‘MASS’ successfully unpacked and MD5 sums checked
>> > ** using staged installation
>> > ** libs
>> > clang -mmacosx-version-min=10.13
>> > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>> > -I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
>> > MASS.c:18:10: fatal error: 'stdlib.h' file not found
>> > #include 
>> >
>> > Indeed, stdlib.h is not in /usr/local/include.
>> >
>> > 2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that did
>> not
>> > fix the problem
>> >
>> > 3. So I installed Xcode 11.3.1 itself. That did not fix the problem.
>> >
>> > 4. For good measure, I re-ran xcode-select --install
>> >
>> > 5. Googling suggested installing /Library/Developer/CommandLineTools/
>> > Packages/macOS_SDK_headers_for_macOS_10.14.pkg, but that package is not
>> on
>> > my computer.
>> >
>> > 6. I tried building R 4.0 from source with this config.site:
>> >
>> > CC=clang
>> > OBJC=$CC
>> > FC=/usr/local/gfortran/bin/gfortran
>> > CXX=clang++
>> >
>> > configure went ok, but then the build failed with:
>> >
>> > trying to compile and link a JNI program
>> > detected JNI cpp flags: -I$(JAVA_HOME)/include
>> > -I$(JAVA_HOME)/include/darwin
>> > detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>> > clang -I"/Users/Eric.Kort/build/R-4.0.0/include" -DNDEBUG
>> > -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include
>> >
>> -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin
>> >   -I/usr/local/include   -fPIC  -g -O2  -c conftest.c -o conftest.o
>> > In file included from conftest.c:1:
>> >
>> /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/jni.h:39:10:
>> > fatal error: 'stdio.h' file not found
>> >

Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread Fox, John

Dear JB,

If you use the Rcmdr with RStudio, by default it will direct output to the 
RStudio console. You can change that, if you wish -- look at the Rcmdr options 
in ?Commander.

Also, have you tried running R and the Rcmdr in a Terminal window, as I 
suggested? If the problem is with R.app, then that might work too.

Peter: Thanks for chiming in.

Best,
 John

> -Original Message-
> From: jean benoit TANIS 
> Sent: Wednesday, April 29, 2020 1:04 PM
> To: peter dalgaard 
> Cc: Fox, John ; R-Sig-Mac 
> Subject: Re: [R-SIG-Mac] Graphic problem Rcmdr
> 
> I have just tried with R studio and it works … I do not know why it does
> not work with Rapp but at least I can use it now.
> 
> Thank you very much for your precious help !!
> 
> JB
> 
> > On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
> >
> > Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be
> bothered to upgrade at this point). Works both from R.app and Terminal,
> and even from RStudio.
> >
> > One thought is a missing font, but same font is used elsewhere is it
> not?
> >
> > You could try playing with generic Tcl/Tk via the tcltk package and
> > see if you can reproduce the problem in a simpler setting (perhaps try
> > the package demos?)
> >
> > -pd
> >
> >> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
> >>
> >> Dear JB,
> >>
> >> We corresponded privately about this problem, and I suggested that you
> post a message to the R-SIG-Mac list when I was unable to help you solve
> it. I don't experience the problem on a Mac similar to yours, but running
> macOS Catalina, and no one else to my knowledge has reported a similar
> problem (with blank menus).
> >>
> >> I do have one additional suggestion: I assume that you're running the
> Rcmdr under the standard R.app GUI. Try running R in a Terminal session.
> That is open the Mac Terminal, type R  at the % command prompt and then
> library(Rcmdr) at the R > prompt.
> >>
> >> Perhaps others will think of additional suggestions.
> >>
> >> Best,
> >> John
> >>
> >>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
> used to work on R2.6 on Windows).
> >>>
> >>> When I load the Rcmdr package, this is what I obtain - see picture
> >>> (the drop down menu does not display). 
> >>>
> >>> I manage to have access to the drop-down menu only once despite 20 or
> so attempts of closing and reopening R.
> >>>
> >>> I have tried to:
> >>> - turn-off nap-app => same issue
> >>> - uninstall R and rebook and start again => same issue
> >>> - uninstall XQuartz and reboot and start again => same issue
> >>>
> >>> For more information about my system, please find the pictures below
> >>>
> >>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
> >>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
> >>>
> >>> Did you encounter this problem before ? Is there any way you could
> help me solving it ?
> >>>
> >>>
> >>> Thank you very much for your help,
> >>>
> >>> Best wishes,
> >>>
> >>>
> >>> JB
> >>>
> >>>
> >>> ___
> >>> 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
> >
> > --
> > 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] Linking R 4.0 to an alternative BLAS

2020-04-29 Thread Braun, Michael

Under R 3.6.3 and earlier, I would link R to an alternative BLAS. Following R 
for Mac FAQ, Sec. 10.5, I would redirect the symbolic link 
$R_HOME/lib/libRblas.dylib to point to whichever BLAS  I wanted to use, (either 
vecLib or Intel MKL) instead of the reference BLAS at libRblas.0.dylib.

With the R 4.0.0 precompiled binaries from CRAN, under $R_HOME/lib,  
libRblas.dylib is the reference BLAS itself, and there is no libRblas.0.dylib 
file.  Is this by design?  Is there an officially recommended alternative?

Thanks,

MB

--
Michael Braun
Associate Professor of Marketing, and
  Corrigan Research Professor
Cox School of Business
Southern Methodist University
Dallas, TX 75275
braunm _at_ smu.edu








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Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread jean benoit TANIS

I have just tried with R studio and it works … I do not know why it does not 
work with Rapp but at least I can use it now. 

Thank you very much for your precious help !! 

JB 

> On 29 Apr 2020, at 16:14, peter dalgaard  wrote:
> 
> Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be 
> bothered to upgrade at this point). Works both from R.app and Terminal, and 
> even from RStudio.
> 
> One thought is a missing font, but same font is used elsewhere is it not?
> 
> You could try playing with generic Tcl/Tk via the tcltk package and see if 
> you can reproduce the problem in a simpler setting (perhaps try the package 
> demos?)
> 
> -pd
> 
>> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
>> 
>> Dear JB,
>> 
>> We corresponded privately about this problem, and I suggested that you post 
>> a message to the R-SIG-Mac list when I was unable to help you solve it. I 
>> don't experience the problem on a Mac similar to yours, but running macOS 
>> Catalina, and no one else to my knowledge has reported a similar problem 
>> (with blank menus).
>> 
>> I do have one additional suggestion: I assume that you're running the Rcmdr 
>> under the standard R.app GUI. Try running R in a Terminal session. That is 
>> open the Mac Terminal, type R  at the % command prompt and then 
>> library(Rcmdr) at the R > prompt.
>> 
>> Perhaps others will think of additional suggestions.
>> 
>> Best,
>> John
>> 
>>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS  wrote:
>>> 
>>> Hi,
>>> 
>>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I used 
>>> to work on R2.6 on Windows). 
>>> 
>>> When I load the Rcmdr package, this is what I obtain - see picture (the 
>>> drop down menu does not display). 
>>> 
>>> I manage to have access to the drop-down menu only once despite 20 or so 
>>> attempts of closing and reopening R. 
>>> 
>>> I have tried to:
>>> - turn-off nap-app => same issue 
>>> - uninstall R and rebook and start again => same issue 
>>> - uninstall XQuartz and reboot and start again => same issue 
>>> 
>>> For more information about my system, please find the pictures below 
>>> 
>>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
>>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
>>> 
>>> Did you encounter this problem before ? Is there any way you could help me 
>>> solving it ? 
>>> 
>>> 
>>> Thank you very much for your help,
>>> 
>>> Best wishes,
>>> 
>>> 
>>> JB 
>>> 
>>> 
>>> ___
>>> 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
> 
> -- 
> 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] fatal error: 'stdio.h' file not found

2020-04-29 Thread Eric K

Thank you Hervé.

So yes, with this ~/.R/Makevars everything works fine again (with a couple
extra flags to keep things quiet):

CFLAGS = -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined
CXXFLAGS =
-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined
CPPFLAGS =
-I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
-Wno-nullability-completeness -Wno-expansion-to-defined

I am curious why I need this Makevars with what I believe to be a vanilla
MacOS / XCode / R installation? But since things are working, my
curiosity will not keep me up at night.

Thanks again for pointing me in the right direction.

-Eric


On Wed, Apr 29, 2020 at 12:42 PM Hervé Pagès  wrote:

> Hi Eric,
>
> FWIW, here is what I see on my system (Mojave):
>
>machv2:~ biocbuild$ which clang
>/usr/bin/clang
>
>machv2:~ biocbuild$ clang -v
>Apple LLVM version 10.0.1 (clang-1001.0.46.4)
>Target: x86_64-apple-darwin18.7.0
>Thread model: posix
>InstalledDir: /Library/Developer/CommandLineTools/usr/bin
>
>machv2:~ biocbuild$ ls -l
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
>-r--r--r--  1 root  wheel  16319 Feb 22  2019
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
>
> I'm not a Mac expert but I believe these locations for Apple clang and
> associated standard C header files have not changed for years.
>
> Hope this helps,
> H.
>
>
> On 4/29/20 07:05, Eric K wrote:
> > Running R 3.6 has been working fine. I just upgraded to R 4.0 and I
> cannot
> > build packages from source. I have tried the following:
> >
> > 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
> > fine, but when I try to build packages from source I get errors like
> this:
> >
> > * installing *source* package ‘MASS’ ...
> > ** package ‘MASS’ successfully unpacked and MD5 sums checked
> > ** using staged installation
> > ** libs
> > clang -mmacosx-version-min=10.13
> > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> > -I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
> > MASS.c:18:10: fatal error: 'stdlib.h' file not found
> > #include 
> >
> > Indeed, stdlib.h is not in /usr/local/include.
> >
> > 2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that did
> not
> > fix the problem
> >
> > 3. So I installed Xcode 11.3.1 itself. That did not fix the problem.
> >
> > 4. For good measure, I re-ran xcode-select --install
> >
> > 5. Googling suggested installing /Library/Developer/CommandLineTools/
> > Packages/macOS_SDK_headers_for_macOS_10.14.pkg, but that package is not
> on
> > my computer.
> >
> > 6. I tried building R 4.0 from source with this config.site:
> >
> > CC=clang
> > OBJC=$CC
> > FC=/usr/local/gfortran/bin/gfortran
> > CXX=clang++
> >
> > configure went ok, but then the build failed with:
> >
> > trying to compile and link a JNI program
> > detected JNI cpp flags: -I$(JAVA_HOME)/include
> > -I$(JAVA_HOME)/include/darwin
> > detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
> > clang -I"/Users/Eric.Kort/build/R-4.0.0/include" -DNDEBUG
> > -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include
> >
> -I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin
> >   -I/usr/local/include   -fPIC  -g -O2  -c conftest.c -o conftest.o
> > In file included from conftest.c:1:
> >
> /Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/jni.h:39:10:
> > fatal error: 'stdio.h' file not found
> > #include 
> >
> > Can anyone spot what I am doing wrong? Thank you!
> >
> > -Eric
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=MF1GsseSwZpmjo7qspeJtAlyY9nDQ_XZnJGweoVjCfE=oFtPJDZ3gSkizBSLFUqqZ2SGa402cZZHDFxpHmk5rNM=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

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Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

2020-04-29 Thread Hervé Pagès


Hi Eric,

FWIW, here is what I see on my system (Mojave):

  machv2:~ biocbuild$ which clang
  /usr/bin/clang

  machv2:~ biocbuild$ clang -v
  Apple LLVM version 10.0.1 (clang-1001.0.46.4)
  Target: x86_64-apple-darwin18.7.0
  Thread model: posix
  InstalledDir: /Library/Developer/CommandLineTools/usr/bin

  machv2:~ biocbuild$ ls -l 
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h
  -r--r--r--  1 root  wheel  16319 Feb 22  2019 
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h


I'm not a Mac expert but I believe these locations for Apple clang and 
associated standard C header files have not changed for years.


Hope this helps,
H.


On 4/29/20 07:05, Eric K wrote:

Running R 3.6 has been working fine. I just upgraded to R 4.0 and I cannot
build packages from source. I have tried the following:

1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
fine, but when I try to build packages from source I get errors like this:

* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
MASS.c:18:10: fatal error: 'stdlib.h' file not found
#include 

Indeed, stdlib.h is not in /usr/local/include.

2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that did not
fix the problem

3. So I installed Xcode 11.3.1 itself. That did not fix the problem.

4. For good measure, I re-ran xcode-select --install

5. Googling suggested installing /Library/Developer/CommandLineTools/
Packages/macOS_SDK_headers_for_macOS_10.14.pkg, but that package is not on
my computer.

6. I tried building R 4.0 from source with this config.site:

CC=clang
OBJC=$CC
FC=/usr/local/gfortran/bin/gfortran
CXX=clang++

configure went ok, but then the build failed with:

trying to compile and link a JNI program
detected JNI cpp flags: -I$(JAVA_HOME)/include
-I$(JAVA_HOME)/include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I"/Users/Eric.Kort/build/R-4.0.0/include" -DNDEBUG
-I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include
-I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin
  -I/usr/local/include   -fPIC  -g -O2  -c conftest.c -o conftest.o
In file included from conftest.c:1:
/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/jni.h:39:10:
fatal error: 'stdio.h' file not found
#include 

Can anyone spot what I am doing wrong? Thank you!

-Eric

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread peter dalgaard

Also not seen by me on Mojave (admittedly 4.0.0 beta, which I can't be bothered 
to upgrade at this point). Works both from R.app and Terminal, and even from 
RStudio.

One thought is a missing font, but same font is used elsewhere is it not?

You could try playing with generic Tcl/Tk via the tcltk package and see if you 
can reproduce the problem in a simpler setting (perhaps try the package demos?)

-pd

> On 29 Apr 2020, at 15:07 , Fox, John  wrote:
> 
> Dear JB,
> 
> We corresponded privately about this problem, and I suggested that you post a 
> message to the R-SIG-Mac list when I was unable to help you solve it. I don't 
> experience the problem on a Mac similar to yours, but running macOS Catalina, 
> and no one else to my knowledge has reported a similar problem (with blank 
> menus).
> 
> I do have one additional suggestion: I assume that you're running the Rcmdr 
> under the standard R.app GUI. Try running R in a Terminal session. That is 
> open the Mac Terminal, type R  at the % command prompt and then 
> library(Rcmdr) at the R > prompt.
> 
> Perhaps others will think of additional suggestions.
> 
> Best,
> John
> 
>> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS  wrote:
>> 
>> Hi,
>> 
>> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I used 
>> to work on R2.6 on Windows). 
>> 
>> When I load the Rcmdr package, this is what I obtain - see picture (the drop 
>> down menu does not display). 
>> 
>> I manage to have access to the drop-down menu only once despite 20 or so 
>> attempts of closing and reopening R. 
>> 
>> I have tried to:
>> - turn-off nap-app => same issue 
>> - uninstall R and rebook and start again => same issue 
>> - uninstall XQuartz and reboot and start again => same issue 
>> 
>> For more information about my system, please find the pictures below 
>> 
>> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
>> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
>> 
>> Did you encounter this problem before ? Is there any way you could help me 
>> solving it ? 
>> 
>> 
>> Thank you very much for your help,
>> 
>> Best wishes,
>> 
>> 
>> JB 
>> 
>> 
>> ___
>> 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@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] 4.0.0

2020-04-29 Thread Dr Eberhard W Lisse

For all it is worth,

homebrew upgraded R to 4.0.0 on Catalina and I did notice that homebrew
asked for an XCode Command Line Tools upgrade

I then sourced as usual my package.R which installs the ones I use, and
it did install a number of packages from source (which I assusme is
becasue they haven't yet loaded as binary packages).

No drama whatsoever. In particular a complicated :yX report with knitR 
produces the expected result :-)-O

el

On 29/04/2020 16:05, Eric K wrote:
> Running R 3.6 has been working fine. I just upgraded to R 4.0 and I cannot
> build packages from source. I have tried the following:
> 
> 1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
> fine, but when I try to build packages from source I get errors like this:
[...]

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[R-SIG-Mac] fatal error: 'stdio.h' file not found

2020-04-29 Thread Eric K

Running R 3.6 has been working fine. I just upgraded to R 4.0 and I cannot
build packages from source. I have tried the following:

1. Installed R 4.0 binary on my mac (macOS 10.14.6). Installation went
fine, but when I try to build packages from source I get errors like this:

* installing *source* package ‘MASS’ ...
** package ‘MASS’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -mmacosx-version-min=10.13
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I/usr/local/include   -fPIC  -Wall -g -O2  -c MASS.c -o MASS.o
MASS.c:18:10: fatal error: 'stdlib.h' file not found
#include 

Indeed, stdlib.h is not in /usr/local/include.

2. So I installed Command_Line_Tools_for_Xcode_11.3.1.dmg, but that did not
fix the problem

3. So I installed Xcode 11.3.1 itself. That did not fix the problem.

4. For good measure, I re-ran xcode-select --install

5. Googling suggested installing /Library/Developer/CommandLineTools/
Packages/macOS_SDK_headers_for_macOS_10.14.pkg, but that package is not on
my computer.

6. I tried building R 4.0 from source with this config.site:

CC=clang
OBJC=$CC
FC=/usr/local/gfortran/bin/gfortran
CXX=clang++

configure went ok, but then the build failed with:

trying to compile and link a JNI program
detected JNI cpp flags: -I$(JAVA_HOME)/include
-I$(JAVA_HOME)/include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I"/Users/Eric.Kort/build/R-4.0.0/include" -DNDEBUG
-I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include
-I/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/darwin
 -I/usr/local/include   -fPIC  -g -O2  -c conftest.c -o conftest.o
In file included from conftest.c:1:
/Library/Java/JavaVirtualMachines/jdk-13.0.1.jdk/Contents/Home/include/jni.h:39:10:
fatal error: 'stdio.h' file not found
#include 

Can anyone spot what I am doing wrong? Thank you!

-Eric

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Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread Fox, John

Dear JB,

We corresponded privately about this problem, and I suggested that you post a 
message to the R-SIG-Mac list when I was unable to help you solve it. I don't 
experience the problem on a Mac similar to yours, but running macOS Catalina, 
and no one else to my knowledge has reported a similar problem (with blank 
menus).

I do have one additional suggestion: I assume that you're running the Rcmdr 
under the standard R.app GUI. Try running R in a Terminal session. That is open 
the Mac Terminal, type R  at the % command prompt and then library(Rcmdr) at 
the R > prompt.

Perhaps others will think of additional suggestions.

Best,
 John

> On Apr 29, 2020, at 2:18 AM, jean benoit TANIS  wrote:
> 
> Hi,
> 
> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I used 
> to work on R2.6 on Windows). 
> 
> When I load the Rcmdr package, this is what I obtain - see picture (the drop 
> down menu does not display). 
> 
> I manage to have access to the drop-down menu only once despite 20 or so 
> attempts of closing and reopening R. 
> 
> I have tried to:
> - turn-off nap-app => same issue 
> - uninstall R and rebook and start again => same issue 
> - uninstall XQuartz and reboot and start again => same issue 
> 
> For more information about my system, please find the pictures below 
> 
> <7D8214F7-97BD-45F0-A21F-9A5333AF2C94.tiff>
> <28E41AFC-0091-4F73-8A48-D9B8D33D341D.tiff>
> 
> Did you encounter this problem before ? Is there any way you could help me 
> solving it ? 
> 
> 
> Thank you very much for your help,
> 
> Best wishes,
> 
> 
> JB 
> 
> 
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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Re: [R-SIG-Mac] Graphic problem Rcmdr

2020-04-29 Thread Dr Eberhard W Lisse

Use Rstudio.

el

On 29/04/2020 08:18, jean benoit TANIS wrote:
> Hi,
> 
> I recently downloaded 4.0.0 and the Rcmdr package with dependencies (I
> used to work on R2.6 on Windows).
> 
> When I load the Rcmdr package, this is what I obtain - see picture
> (the drop down menu does not display).
> 
> I manage to have access to the drop-down menu only once despite 20 or
> so attempts of closing and reopening R.
> 
> I have tried to:
> - turn-off nap-app => same issue 
> - uninstall R and rebook and start again => same issue 
> - uninstall XQuartz and reboot and start again => same issue 
> 
> For more information about my system, please find the pictures below 
> 
> PastedGraphic-1.tiff
> PastedGraphic-2.tiff
> 
> Did you encounter this problem before ?  Is there any way you could
> help me solving it ?
> 
> 
> Thank you very much for your help,
> 
> Best wishes,
> 
> 
> JB 
> 
> 
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

-- 
Dr. Eberhard W. Lisse   \ /   Obstetrician & Gynaecologist 
e...@lisse.na / *  |  Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht  \  /  If this email is signed with GPG/PGP
10007, Namibia   ;/ Sect 20 of Act No. 4 of 2019 may apply

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[R-SIG-Mac] openmp

2020-04-29 Thread Erich Neuwirth

Since we do not have openmp support in R 4.0
is there (or can I easily produce)
a list of packages which either
depend on openmp or
make use of openmp to improve performance?

Erich



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Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] Graphic problem Rcmdr

Re: [R-SIG-Mac] Graphic problem Rcmdr

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] Graphic problem Rcmdr

[R-SIG-Mac] Linking R 4.0 to an alternative BLAS

Re: [R-SIG-Mac] Graphic problem Rcmdr

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] Graphic problem Rcmdr

Re: [R-SIG-Mac] 4.0.0

[R-SIG-Mac] fatal error: 'stdio.h' file not found

Re: [R-SIG-Mac] Graphic problem Rcmdr

Re: [R-SIG-Mac] Graphic problem Rcmdr

[R-SIG-Mac] openmp

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