Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Balamuta, James Joseph
Simon,

I sent a PR that updates the Travis CI to use the R 4.0.0 branch as R-devel and 
new gfortran binaries.

https://github.com/travis-ci/travis-build/pull/1885

I'm waiting to hear back from the community maintainers if they are interested 
in pulling in binaries from 

http://mac.r-project.org/libs-4/

Best,

JJB

On 4/1/20, 5:01 PM, "R-SIG-Mac on behalf of Balamuta, James Joseph" 
 wrote:

Simon,

Thank you for the quick response! 

>  1. correct, there was too much trouble in this. But please feel free to 
start a new thread about this here if you have strong opinions.

Best news leading into R 4.0.0.

> 2.  we're talking about the oldest system that our binaries will run on, 
so 10.13 is actually very aggressive.

Okay.  

> There is still a very significant portion of users that have older 
versions of macOS and cannot upgrade. Apple is interested in selling new 
products, we are interested in supporting people that need a statistical 
software regardless of their income.

Agreed. When I asked this question, I was worried about the backwards 
compatibility issues arising from the new security model enacted on 10.14/10.15 
that caused installer signing problems in R 3.6.3.

>3. not at all. As I said, 10.13 is already way too high, in fact we 
picked it precisely so we don't need to change it for several years.

Great to hear 10.13 will be the default for several years to come! As an 
added benefit, it is the last version with support for NVIDIA eGPUs.

Regarding Travis, I'll update the build script here with the new changes.


https://github.com/travis-ci/travis-build/blob/ab196aed5b227288a2f4dcb5c7822868b430b110/lib/travis/build/script/r.rb
 

Best,

JJB

On 4/1/20, 4:03 PM, "Simon Urbanek"  wrote:

JJB,

1. correct, there was too much trouble in this. But please feel free to 
start a new thread about this here if you have strong opinions.

2. we're talking about the oldest system that our binaries will run on, 
so 10.13 is actually very aggressive. There is still a very significant portion 
of users that have older versions of macOS and cannot upgrade. Apple is 
interested in selling new products, we are interested in supporting people that 
need a statistical software regardless of their income.

3. not at all. As I said, 10.13 is already way too high, in fact we 
picked it precisely so we don't need to change it for several years.

Just to make sure we're clear - it's ok to use Catalina to build 
binaries for let's say macOS 10.11, so it's not about what system you use to 
build. It is about who is able to use the resulting software. The current R 
builds are actually running on Catalina.

Thanks for your offer, it would be very helpful. Travis would be a good 
start - it needs command line tools, GNU fortran from

https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
the binaries from
http://mac.r-project.org/libs-4/
and there is actually a machine-readable list in
http://mac.r-project.org/libs-4/INDEX
and R from
http://mac.r-project.org/high-sierra/R-4.0-branch/R-4.0-branch.pkg

Thanks,
Simon


> On 2/04/2020, at 2:30 AM, Balamuta, James Joseph 
 wrote:
> 
> Simon,
> 
> Thanks for the overview! A few quick questions:
> 
> 1. Compiler-wise, the external clang compiler requirement was removed 
and, so, there is no guarantee of OpenMP on macOS again? 
> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given 
the new push for increased security by Apple?
> 3. How likely is the oldest system requirement to be bumped in a 
patch release? 
> 
> Also, if you need help with mac-builder, Travis, or GitHub Actions, 
I'm more than happy to help! 
> 
> Best,
> 
> JJB
> 
> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
 
wrote:
> 
>Dear Mac users,
> 
>R 4.0.0 will be using an entirely new toolchain, entirely new 
build system on entirely new macOS version and hardware. Therefore I would like 
to ask you kindly to test the binaries from
> 
>https://mac.R-project.org
> 
>before the release as much as you can. Raising any issues after 
the release is too late! So please, please, test the pre-releases. Report any 
issues either directly to me or this mailing list.
> 
>The nightly builds are signed, but not necessarily notarized. 
However, the build fulfils Apple's conditions and is known to pass notarization 
(in fact the the package available for download today is actually notarized) so 
it should be a 

Re: [R-SIG-Mac] Transitioning from Mac to LInux?

2020-04-01 Thread Duncan Murdoch

On 01/04/2020 2:48 p.m., Carl Witthoft wrote:


   If I should ask over at r-sig-debian instead of here, please tell me.
I don't wish to clog r-sig-mac with off-topic stuff.


I've been watching the massive headaches people are dealing with trying
to keep R fully compatible with each MacOS X upgrade,  I'm wondering
whether replacing my iMac (2009) with a new Mac really makes sense from
an R - user point of view, as opposed to getting some inexpensive
desktop and installing Linux.  I know I can run R and RStudio under
Linux, for example,  but don't know what limitations, if any there are
when it comes to building packages from source, getting compatible
compilers,  and so on.

What have some of you 'power R users' discovered when/if you tried to
build , or incorporate Bioconductor or other repository's packages under
Linux?




If your iMac is still working, try installing Ubuntu or some other Linux 
on it.  I think at that age Apple is no longer providing upgrades, but I 
just put Ubuntu on a 2008 iMac, and it works well.  (I needed to upgrade 
the memory, but that just cost $40 for 4 GB.)


So I got a $40 desktop, with a nice screen.

Duncan Murdoch

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Re: [R-SIG-Mac] Transitioning from Mac to LInux?

2020-04-01 Thread Eberhard W Lisse
Actually, you can easily run Linux in Virtual Box.

But I agree, with Homebrew there is tons of unix tools available from the 
command line, and then some.

el

—
Sent from Dr Lisse’s iPad Mini 5
On 1 Apr 2020, 23:42 +0200, Simon Urbanek , wrote:
> Carl,
>
> I would argue that you won't really gain anything - if you use R the 
> Linux-way (build R from sources), it would be the same on macOS and Linux - 
> and some people do that. So for R I don't think there is a difference. I'm 
> using Linux for everything other than my desktop/laptop and the main reason 
> I'm sticking with macOS at the edge is the availability of software for 
> dealing with the rest of the world (MS Office, Adobe, Apple Mail etc.). If 
> you don't need any of it, then you may be happy with Linux. The biggest issue 
> there tends to be setting up your machine as the hardware support is far less 
> streamlined than on macOS. Some of my friends are running Linux on Mac 
> hardware - but you need the be real expert for that.
>
> Cheers,
> Simon
>
>
> > On 2/04/2020, at 7:48 AM, Carl Witthoft  wrote:
> >
> >
> > If I should ask over at r-sig-debian instead of here, please tell me. I 
> > don't wish to clog r-sig-mac with off-topic stuff.
> >
> >
> > I've been watching the massive headaches people are dealing with trying to 
> > keep R fully compatible with each MacOS X upgrade, I'm wondering whether 
> > replacing my iMac (2009) with a new Mac really makes sense from an R - user 
> > point of view, as opposed to getting some inexpensive desktop and 
> > installing Linux. I know I can run R and RStudio under Linux, for example, 
> > but don't know what limitations, if any there are when it comes to building 
> > packages from source, getting compatible compilers, and so on.
> >
> > What have some of you 'power R users' discovered when/if you tried to build 
> > , or incorporate Bioconductor or other repository's packages under Linux?
> >
> >
> > --
> > Carl Witthoft
> > c...@witthoft.com
> > resume: https://app.box.com/file/498153801347
> >
> > ___
> > 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] PCRE JIT compilation error

2020-04-01 Thread Göran Broström

No problem at all with 10.13.6.

G,

Den 2020-04-01 kl. 15:20, skrev Bryan Hanson:

Having played with things a bit more, this message appears all over the place 
as people are beginning to report.

Another simple way to trigger it is to do:

?dist

Bryan


On Apr 1, 2020, at 8:36 AM, Matthias Krawutschke  
wrote:

Hello together,
i´ve got this message too, but my systems show me first the list of all 
installed libraries on my MAC.

Best regards and take care….



Matthias Krawutschke, Dipl. Inf.

Universität Potsdam
ZIM - Zentrum für Informationstechnologie und Medienmanagement
Team Infrastruktur Server und Storage
Spezialized: High-Performance-Computing and Kubernetes


Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam
Tel: +49 331 977-153065, Fax: +49 331 977-1750

Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html


-Ursprüngliche Nachricht-
Von: R-SIG-Mac  Im Auftrag von Bryan Hanson
Gesendet: Mittwoch, 1. April 2020 13:30
An: r-sig-mac R 
Betreff: [R-SIG-Mac] PCRE JIT compilation error

On a fresh install of the binary from mac.r-project.org, if I simply do:

library()

I see:

R > library()
There were 30 warnings (use warnings() to see them) R > warnings() Warning 
messages:
1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
'no more memory'
2: In FUN(X[[i]], ...) : PCRE JIT compilation error
'no more memory'

etc.  The usual window with installed packages does open.

Starting the conversation here on the Mac list, though it may be a bigger 
problem.

Thanks, Bryan

Prof. Bryan Hanson (emeritus)
Dept of Chemistry & Biochemistry
DePauw University
Greencastle IN 46135 USA
Web: academic.depauw.edu/~hanson/index.html
Repo: github.com/bryanhanson
Nerdy Blog: ChemoSpec.org
The Twit: @ProfBryanHanson
I’m usually @ -4 GMT/UTC

R > sessionInfo()
R version 4.0.0 alpha (2020-03-29 r78109)
Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.0.0












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Re: [R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread Bryan Hanson
Confirmed (r78130).  Thank you as always Simon.  Bryan

> On Apr 1, 2020, at 4:46 PM, Simon Urbanek  wrote:
> 
> Bryan,
> 
> thanks! There seems to be an issue with PCRE2 JIT on Mojave. I have now 
> disabled JIT in PCRE2 which seems to be the recommended fix 
> 
> I have built the latest version of R 4.0.0 alpha - it is now available from
> 
> http://mac.r-project.org/high-sierra/R-4.0-branch/R-4.0-branch.pkg
> 
> as usual.
> 
> Thanks,
> Simon
> 
> 
>> On 2/04/2020, at 12:30 AM, Bryan Hanson  wrote:
>> 
>> On a fresh install of the binary from mac.r-project.org, if I simply do:
>> 
>> library()
>> 
>> I see:
>> 
>> R > library()
>> There were 30 warnings (use warnings() to see them)
>> R > warnings()
>> Warning messages:
>> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>>  'no more memory'
>> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>>  'no more memory'
>> 
>> etc.  The usual window with installed packages does open.
>> 
>> Starting the conversation here on the Mac list, though it may be a bigger 
>> problem.
>> 
>> Thanks, Bryan
>> 
>> Prof. Bryan Hanson (emeritus)
>> Dept of Chemistry & Biochemistry
>> DePauw University
>> Greencastle IN 46135 USA
>> Web: academic.depauw.edu/~hanson/index.html
>> Repo: github.com/bryanhanson
>> Nerdy Blog: ChemoSpec.org
>> The Twit: @ProfBryanHanson
>> I’m usually @ -4 GMT/UTC
>> 
>> R > sessionInfo()
>> R version 4.0.0 alpha (2020-03-29 r78109)
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> Running under: macOS Mojave 10.14.6
>> 
>> Matrix products: default
>> BLAS:   
>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>> LAPACK: 
>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods  
>> [7] base 
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.0.0
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 

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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Balamuta, James Joseph
Simon,

Thank you for the quick response! 

>  1. correct, there was too much trouble in this. But please feel free to 
> start a new thread about this here if you have strong opinions.

Best news leading into R 4.0.0.

> 2.  we're talking about the oldest system that our binaries will run on, so 
> 10.13 is actually very aggressive.

Okay.  

> There is still a very significant portion of users that have older versions 
> of macOS and cannot upgrade. Apple is interested in selling new products, we 
> are interested in supporting people that need a statistical software 
> regardless of their income.

Agreed. When I asked this question, I was worried about the backwards 
compatibility issues arising from the new security model enacted on 10.14/10.15 
that caused installer signing problems in R 3.6.3.

>3. not at all. As I said, 10.13 is already way too high, in fact we picked 
> it precisely so we don't need to change it for several years.

Great to hear 10.13 will be the default for several years to come! As an added 
benefit, it is the last version with support for NVIDIA eGPUs.

Regarding Travis, I'll update the build script here with the new changes.

https://github.com/travis-ci/travis-build/blob/ab196aed5b227288a2f4dcb5c7822868b430b110/lib/travis/build/script/r.rb
 

Best,

JJB

On 4/1/20, 4:03 PM, "Simon Urbanek"  wrote:

JJB,

1. correct, there was too much trouble in this. But please feel free to 
start a new thread about this here if you have strong opinions.

2. we're talking about the oldest system that our binaries will run on, so 
10.13 is actually very aggressive. There is still a very significant portion of 
users that have older versions of macOS and cannot upgrade. Apple is interested 
in selling new products, we are interested in supporting people that need a 
statistical software regardless of their income.

3. not at all. As I said, 10.13 is already way too high, in fact we picked 
it precisely so we don't need to change it for several years.

Just to make sure we're clear - it's ok to use Catalina to build binaries 
for let's say macOS 10.11, so it's not about what system you use to build. It 
is about who is able to use the resulting software. The current R builds are 
actually running on Catalina.

Thanks for your offer, it would be very helpful. Travis would be a good 
start - it needs command line tools, GNU fortran from

https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
the binaries from
http://mac.r-project.org/libs-4/
and there is actually a machine-readable list in
http://mac.r-project.org/libs-4/INDEX
and R from
http://mac.r-project.org/high-sierra/R-4.0-branch/R-4.0-branch.pkg

Thanks,
Simon


> On 2/04/2020, at 2:30 AM, Balamuta, James Joseph  
wrote:
> 
> Simon,
> 
> Thanks for the overview! A few quick questions:
> 
> 1. Compiler-wise, the external clang compiler requirement was removed 
and, so, there is no guarantee of OpenMP on macOS again? 
> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the 
new push for increased security by Apple?
> 3. How likely is the oldest system requirement to be bumped in a patch 
release? 
> 
> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm 
more than happy to help! 
> 
> Best,
> 
> JJB
> 
> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
 
wrote:
> 
>Dear Mac users,
> 
>R 4.0.0 will be using an entirely new toolchain, entirely new build 
system on entirely new macOS version and hardware. Therefore I would like to 
ask you kindly to test the binaries from
> 
>https://mac.R-project.org
> 
>before the release as much as you can. Raising any issues after the 
release is too late! So please, please, test the pre-releases. Report any 
issues either directly to me or this mailing list.
> 
>The nightly builds are signed, but not necessarily notarized. However, 
the build fulfils Apple's conditions and is known to pass notarization (in fact 
the the package available for download today is actually notarized) so it 
should be a good test for the release which will be notarized and should work 
on Catalina.
> 
>For those that want to replicate our setup - technical details: we are 
now building with macOS 10.13 (High Sierra) as target (i.e. the oldest 
supported system), regular Apple Xcode/command line tools and GNU Fortran 8.2. 
R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 
10.13 target. Packages are built on macOS 10.13 VMs with just Apple command 
line tools (this should make it easy to replicate the setup using Travis, for 
example). All 3rd party libraries that CRAN uses are available in 
http://mac.r-project.org/libs-4/
> 
>The new R build system is in
>

Re: [R-SIG-Mac] Transitioning from Mac to LInux?

2020-04-01 Thread Simon Urbanek
Carl,

I would argue that you won't really gain anything - if you use R the Linux-way 
(build R from sources), it would be the same on macOS and Linux - and some 
people do that. So for R I don't think there is a difference. I'm using Linux 
for everything other than my desktop/laptop and the main reason I'm sticking 
with macOS at the edge is the availability of software for dealing with the 
rest of the world (MS Office, Adobe, Apple Mail etc.). If you don't need any of 
it, then you may be happy with Linux. The biggest issue there tends to be 
setting up your machine as the hardware support is far less streamlined than on 
macOS. Some of my friends are running Linux on Mac hardware - but you need the 
be real expert for that.

Cheers,
Simon


> On 2/04/2020, at 7:48 AM, Carl Witthoft  wrote:
> 
> 
> If I should ask over at r-sig-debian instead of here, please tell me. I don't 
> wish to clog r-sig-mac with off-topic stuff.
> 
> 
> I've been watching the massive headaches people are dealing with trying to 
> keep R fully compatible with each MacOS X upgrade,  I'm wondering whether 
> replacing my iMac (2009) with a new Mac really makes sense from an R - user 
> point of view, as opposed to getting some inexpensive desktop and installing 
> Linux.  I know I can run R and RStudio under Linux, for example,  but don't 
> know what limitations, if any there are when it comes to building packages 
> from source, getting compatible compilers,  and so on.
> 
> What have some of you 'power R users' discovered when/if you tried to build , 
> or incorporate Bioconductor or other repository's packages under Linux?
> 
> 
> -- 
> Carl Witthoft
> c...@witthoft.com
> resume: https://app.box.com/file/498153801347
> 
> ___
> 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] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Simon Urbanek
Thanks! Now fixed.
Simon


> On 2/04/2020, at 4:08 AM, Bob Rudis  wrote:
> 
> Hey Simon!
> 
> At the bottom of https://mac.r-project.org/libs-4/ is:
> 
>curl -O 
> http://mac.R_project.org/libs-4/pkgconfig-0.28-darwin.17-x86_64.tar.gz
> 
> While most folks will figure it out, it should be:
> 
>curl -O 
> http://mac.R-project.org/libs-4/pkgconfig-0.28-darwin.17-x86_64.tar.gz
> 
> (dash instead of underline).
> 
> -boB
> 
> 
>> On Apr 1, 2020, at 09:30, Balamuta, James Joseph  
>> wrote:
>> 
>> Simon,
>> 
>> Thanks for the overview! A few quick questions:
>> 
>> 1. Compiler-wise, the external clang compiler requirement was removed and, 
>> so, there is no guarantee of OpenMP on macOS again? 
>> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
>> push for increased security by Apple?
>> 3. How likely is the oldest system requirement to be bumped in a patch 
>> release? 
>> 
>> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
>> than happy to help! 
>> 
>> Best,
>> 
>> JJB
>> 
>> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
>>  
>> wrote:
>> 
>>   Dear Mac users,
>> 
>>   R 4.0.0 will be using an entirely new toolchain, entirely new build system 
>> on entirely new macOS version and hardware. Therefore I would like to ask 
>> you kindly to test the binaries from
>> 
>>   https://mac.R-project.org
>> 
>>   before the release as much as you can. Raising any issues after the 
>> release is too late! So please, please, test the pre-releases. Report any 
>> issues either directly to me or this mailing list.
>> 
>>   The nightly builds are signed, but not necessarily notarized. However, the 
>> build fulfils Apple's conditions and is known to pass notarization (in fact 
>> the the package available for download today is actually notarized) so it 
>> should be a good test for the release which will be notarized and should 
>> work on Catalina.
>> 
>>   For those that want to replicate our setup - technical details: we are now 
>> building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
>> system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R 
>> builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 
>> 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command 
>> line tools (this should make it easy to replicate the setup using Travis, 
>> for example). All 3rd party libraries that CRAN uses are available in 
>> http://mac.r-project.org/libs-4/
>> 
>>   The new R build system is in
>>   https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
>>   Packages build system has not changed and is in
>>   https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
>> 
>>   We also plan to have a mac-builder available with similar function as the 
>> win-builder where pre-submission tests can be performed and potentially a 
>> Travis template.
>> 
>>   Please test R pre-releases and provide feedback!
>> 
>>   Thanks,
>>   Simon
>> 
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>> 
>> 
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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Simon Urbanek
Patrick, Bob et al ,

thanks! Please start a new thread here about CI builds - I'm open to whatever 
the best or most popular options are.

Thanks,
Simon


> On 2/04/2020, at 3:07 AM, Patrick Schratz  wrote:
> 
> The same goes here regarding support.
> 
> I am (co-)maintaining a package on ropensci focusing on provider-agnostic CI 
> approaches for R (tic) and have quite some experience with all the little 
> culprits there.
> 
> Since you mentioned Travis: Be aware that the R community is (slowly but 
> actively) moving away from Travis for a few reasons.
> Also on GitHub Actions you can only build on 10.15 (Catalina) right now.
> 
> Best, Patrick
> On 1. Apr 2020, 15:41 +0200, Bob Rudis , wrote:
>> I shall pile on with an additional offer of assistance, Simon and a huge #ty 
>> for this and all the work you do.
>> 
>>> On Apr 1, 2020, at 09:30, Balamuta, James Joseph  
>>> wrote:
>>> 
>>> Simon,
>>> 
>>> Thanks for the overview! A few quick questions:
>>> 
>>> 1. Compiler-wise, the external clang compiler requirement was removed and, 
>>> so, there is no guarantee of OpenMP on macOS again?
>>> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
>>> push for increased security by Apple?
>>> 3. How likely is the oldest system requirement to be bumped in a patch 
>>> release?
>>> 
>>> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm 
>>> more than happy to help!
>>> 
>>> Best,
>>> 
>>> JJB
>>> 
>>> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
>>>  
>>> wrote:
>>> 
>>> Dear Mac users,
>>> 
>>> R 4.0.0 will be using an entirely new toolchain, entirely new build system 
>>> on entirely new macOS version and hardware. Therefore I would like to ask 
>>> you kindly to test the binaries from
>>> 
>>> https://mac.R-project.org
>>> 
>>> before the release as much as you can. Raising any issues after the release 
>>> is too late! So please, please, test the pre-releases. Report any issues 
>>> either directly to me or this mailing list.
>>> 
>>> The nightly builds are signed, but not necessarily notarized. However, the 
>>> build fulfils Apple's conditions and is known to pass notarization (in fact 
>>> the the package available for download today is actually notarized) so it 
>>> should be a good test for the release which will be notarized and should 
>>> work on Catalina.
>>> 
>>> For those that want to replicate our setup - technical details: we are now 
>>> building with macOS 10.13 (High Sierra) as target (i.e. the oldest 
>>> supported system), regular Apple Xcode/command line tools and GNU Fortran 
>>> 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using 
>>> macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple 
>>> command line tools (this should make it easy to replicate the setup using 
>>> Travis, for example). All 3rd party libraries that CRAN uses are available 
>>> in http://mac.r-project.org/libs-4/
>>> 
>>> The new R build system is in
>>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
>>> Packages build system has not changed and is in
>>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
>>> 
>>> We also plan to have a mac-builder available with similar function as the 
>>> win-builder where pre-submission tests can be performed and potentially a 
>>> Travis template.
>>> 
>>> Please test R pre-releases and provide feedback!
>>> 
>>> Thanks,
>>> Simon
>>> 
>>> ___
>>> 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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>   [[alternative HTML version deleted]]
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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Simon Urbanek
JJB,

1. correct, there was too much trouble in this. But please feel free to start a 
new thread about this here if you have strong opinions.

2. we're talking about the oldest system that our binaries will run on, so 
10.13 is actually very aggressive. There is still a very significant portion of 
users that have older versions of macOS and cannot upgrade. Apple is interested 
in selling new products, we are interested in supporting people that need a 
statistical software regardless of their income.

3. not at all. As I said, 10.13 is already way too high, in fact we picked it 
precisely so we don't need to change it for several years.

Just to make sure we're clear - it's ok to use Catalina to build binaries for 
let's say macOS 10.11, so it's not about what system you use to build. It is 
about who is able to use the resulting software. The current R builds are 
actually running on Catalina.

Thanks for your offer, it would be very helpful. Travis would be a good start - 
it needs command line tools, GNU fortran from
https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
the binaries from
http://mac.r-project.org/libs-4/
and there is actually a machine-readable list in
http://mac.r-project.org/libs-4/INDEX
and R from
http://mac.r-project.org/high-sierra/R-4.0-branch/R-4.0-branch.pkg

Thanks,
Simon


> On 2/04/2020, at 2:30 AM, Balamuta, James Joseph  
> wrote:
> 
> Simon,
> 
> Thanks for the overview! A few quick questions:
> 
> 1. Compiler-wise, the external clang compiler requirement was removed and, 
> so, there is no guarantee of OpenMP on macOS again? 
> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
> push for increased security by Apple?
> 3. How likely is the oldest system requirement to be bumped in a patch 
> release? 
> 
> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
> than happy to help! 
> 
> Best,
> 
> JJB
> 
> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
>  
> wrote:
> 
>Dear Mac users,
> 
>R 4.0.0 will be using an entirely new toolchain, entirely new build system 
> on entirely new macOS version and hardware. Therefore I would like to ask you 
> kindly to test the binaries from
> 
>https://mac.R-project.org
> 
>before the release as much as you can. Raising any issues after the 
> release is too late! So please, please, test the pre-releases. Report any 
> issues either directly to me or this mailing list.
> 
>The nightly builds are signed, but not necessarily notarized. However, the 
> build fulfils Apple's conditions and is known to pass notarization (in fact 
> the the package available for download today is actually notarized) so it 
> should be a good test for the release which will be notarized and should work 
> on Catalina.
> 
>For those that want to replicate our setup - technical details: we are now 
> building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
> system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds 
> are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 
> target. Packages are built on macOS 10.13 VMs with just Apple command line 
> tools (this should make it easy to replicate the setup using Travis, for 
> example). All 3rd party libraries that CRAN uses are available in 
> http://mac.r-project.org/libs-4/
> 
>The new R build system is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
>Packages build system has not changed and is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
> 
>We also plan to have a mac-builder available with similar function as the 
> win-builder where pre-submission tests can be performed and potentially a 
> Travis template.
> 
>Please test R pre-releases and provide feedback!
> 
>Thanks,
>Simon
> 
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> 
> 
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Re: [R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread Simon Urbanek
Bryan,

thanks! There seems to be an issue with PCRE2 JIT on Mojave. I have now 
disabled JIT in PCRE2 which seems to be the recommended fix 

I have built the latest version of R 4.0.0 alpha - it is now available from

http://mac.r-project.org/high-sierra/R-4.0-branch/R-4.0-branch.pkg

as usual.

Thanks,
Simon


> On 2/04/2020, at 12:30 AM, Bryan Hanson  wrote:
> 
> On a fresh install of the binary from mac.r-project.org, if I simply do:
> 
> library()
> 
> I see:
> 
> R > library()
> There were 30 warnings (use warnings() to see them)
> R > warnings()
> Warning messages:
> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>   'no more memory'
> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>   'no more memory'
> 
> etc.  The usual window with installed packages does open.
> 
> Starting the conversation here on the Mac list, though it may be a bigger 
> problem.
> 
> Thanks, Bryan
> 
> Prof. Bryan Hanson (emeritus)
> Dept of Chemistry & Biochemistry
> DePauw University
> Greencastle IN 46135 USA
> Web: academic.depauw.edu/~hanson/index.html
> Repo: github.com/bryanhanson
> Nerdy Blog: ChemoSpec.org
> The Twit: @ProfBryanHanson
> I’m usually @ -4 GMT/UTC
> 
> R > sessionInfo()
> R version 4.0.0 alpha (2020-03-29 r78109)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Mojave 10.14.6
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Simon Urbanek
Patrick,

firstly, please don't post such things - they are often wrong (as are parts of 
what you included it this e-mail) and it's impossible for us to track all blogs 
that have incorrect advice. Unfortunately, a lot of the issues we see out there 
are due to people finding bad advice and using it. Ideally, it should be 
sufficient to point to the official R documentation since that is the canonical 
source. If you post a blog, it should point to the official documentation. If 
that documentation is missing or not covering a need, please post here so we 
can fix it. It is more important that the official source is complete and much 
better for the community than to have random tidbits that may or may not be 
correct floating around.

As for the script, please do not use R tar balls - first, you're picking the 
wrong one (there is no R-devel for el-capitan. R 4.0.0 pre-releases are in 
R-4-0-branch and they are built for high sierra). Second, the tar ball doesn't 
have the entitlements enabled so it doesn't match the release. Please use the 
signed R package. This may change, but with the complications of the Apple 
notarization process that's what it is today.

Then there is the question of the SDK. What are you trying to setup here? What 
you posted here has nothing to do with the CRAN setup. You don't need 10.13 SDK 
to compile igraph, it compiles just fine using stock command line tools on High 
Sierra which is what we use on CRAN. You can, of course, pick any SDK you like, 
but please don't tell people that's what they should do. One of the most 
annoying issues is that people are recommending messing with Makevars which is 
incredibly fragile and will cause things to break left and right with any 
update. It's ok to do that for a very special purpose, but no regular user 
should have Makevars in their home.

So if you really want to serve the community, please suggest improvements to 
the official documentation and post them here. If you have special needs, ask 
about them here.

Thanks,
Simon



> On 1/04/2020, at 9:47 PM, Patrick Schratz  wrote:
> 
> Thanks Simon,
> 
> This simplifies things a lot and clears up the process. While the 
> instructions on https://mac.r-project.org/ are more clear now I think there 
> is still simplification needed for the install process and custom 
> modifications that are needed.
> This not only applies to the dev page but finally also to production end 
> users if the SDK 10.15 issues (see below) persists.
> 
> I’ve scripted all installation steps (R-devel, gfortran, SDK 10.13) and will 
> probably write a blog post about it to make the R community more aware about 
> it. Let me know if anything is wrong about it - otherwise I’ll use the code 
> below in the blog post.
> 
> # install R-devel
> wget 
> https://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz
> sudo tar fvxz R*.tar.gz -C /
> rm R-devel-el-capitan-sa-x86_64.tar.gz
> 
> # install gfortran
> wget 
> https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
> sudo hdiutil attach gfortran*.dmg
> sudo installer -package /Volumes/gfortran*/gfortran*/gfortran*.pkg -target /
> sudo hdiutil detach /Volumes/gfortran-8.2-Mojave
> 
> # install SDK10.13
> wget 
> https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz
> tar fvxz MacOSX10.13.sdk.tar.xz
> sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/
> rm -rf MacOSX10.13*
> 
> In addition people need to set custom CFLAGS in ~/.R/Makevars to actually use 
> it:
> 
> CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
> CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
> CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
> CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
> 
> In addition there really seem to be major problems regarding the 10.15 SDK. 
> For example, {igraph} which is a package on which lots of other packages 
> depend, cannot be installed from source with SDK 10.15 but works with SDK 
> 10.13.
> 
> Patrick
> On 1. Apr 2020, 09:38 +0200, Simon Urbanek , 
> wrote:
>> Hervé,
>> 
>> 
>>> On 1/04/2020, at 6:19 PM, Hervé Pagès  wrote:
>>> 
>>> Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha 
>>> build from https://mac.r-project.org/ for the Bioconductor build system. 
>>> Bioconductor packages depend on thousands of CRAN packages and one thing 
>>> that makes it hard for us and for our users to build/check Bioconductor 
>>> packages at the moment is the absence of Mac binary packages for R 4.0.0 on 
>>> CRAN. Do you have an estimate of when they will become available?
>>> 
>> 
>> Both the packages and R are now available. I always recommend using the 
>> Mac-master https://mac.R-project.org as "mirror" since that one is most 
>> up-to-date.
>> 
>> 
>>> Another question is where they are going to be hosted on CRAN. We need 

Re: [R-SIG-Mac] Transitioning from Mac to LInux?

2020-04-01 Thread Hervé Pagès
My 2 cents: Just go for the inexpensive desktop + Linux. Debian-based or 
RedHat-based distros are great for developing R/Bioconductor packages. 
I've been maintaining/troubleshooting package builds on 
Linux/Windows/Mac for 15 years and Linux is **by far** the easiest 
platform to deal with. Still a mystery to me why one would choose macOS 
for developing R/Bioconductor packages.


H.

On 4/1/20 11:48, Carl Witthoft wrote:


  If I should ask over at r-sig-debian instead of here, please tell me. 
I don't wish to clog r-sig-mac with off-topic stuff.



I've been watching the massive headaches people are dealing with trying 
to keep R fully compatible with each MacOS X upgrade,  I'm wondering 
whether replacing my iMac (2009) with a new Mac really makes sense from 
an R - user point of view, as opposed to getting some inexpensive 
desktop and installing Linux.  I know I can run R and RStudio under 
Linux, for example,  but don't know what limitations, if any there are 
when it comes to building packages from source, getting compatible 
compilers,  and so on.


What have some of you 'power R users' discovered when/if you tried to 
build , or incorporate Bioconductor or other repository's packages under 
Linux?





--
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] Transitioning from Mac to LInux?

2020-04-01 Thread Bert Gunter
As you are asking about R experience from Unix-alike OS users, I think
you would clearly do better to ask on the - debian and/or -fedora
sigs.

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Wed, Apr 1, 2020 at 11:49 AM Carl Witthoft  wrote:
>
>
>   If I should ask over at r-sig-debian instead of here, please tell me.
> I don't wish to clog r-sig-mac with off-topic stuff.
>
>
> I've been watching the massive headaches people are dealing with trying
> to keep R fully compatible with each MacOS X upgrade,  I'm wondering
> whether replacing my iMac (2009) with a new Mac really makes sense from
> an R - user point of view, as opposed to getting some inexpensive
> desktop and installing Linux.  I know I can run R and RStudio under
> Linux, for example,  but don't know what limitations, if any there are
> when it comes to building packages from source, getting compatible
> compilers,  and so on.
>
> What have some of you 'power R users' discovered when/if you tried to
> build , or incorporate Bioconductor or other repository's packages under
> Linux?
>
>
> --
> Carl Witthoft
> c...@witthoft.com
> resume: https://app.box.com/file/498153801347
>
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[R-SIG-Mac] Transitioning from Mac to LInux?

2020-04-01 Thread Carl Witthoft



 If I should ask over at r-sig-debian instead of here, please tell me. 
I don't wish to clog r-sig-mac with off-topic stuff.



I've been watching the massive headaches people are dealing with trying 
to keep R fully compatible with each MacOS X upgrade,  I'm wondering 
whether replacing my iMac (2009) with a new Mac really makes sense from 
an R - user point of view, as opposed to getting some inexpensive 
desktop and installing Linux.  I know I can run R and RStudio under 
Linux, for example,  but don't know what limitations, if any there are 
when it comes to building packages from source, getting compatible 
compilers,  and so on.


What have some of you 'power R users' discovered when/if you tried to 
build , or incorporate Bioconductor or other repository's packages under 
Linux?



--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Hervé Pagès
I see bin/macosx/contrib/4.0/ now (e.g. 
https://cran.r-project.org/bin/macosx/contrib/4.0/). Thanks!


H.

On 4/1/20 00:37, Simon Urbanek wrote:

Hervé,



On 1/04/2020, at 6:19 PM, Hervé Pagès  wrote:

Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha build from 
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.r-2Dproject.org_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=SgN9XTf8oSzk28ZilVDsjOU2Fpf0lRzDmF8QEBnwJno=n2gZ5tfjXIG7SNEmqQd8-QMsUj5t6y0-r1r-qaCgd7I=
  for the Bioconductor build system. Bioconductor packages depend on thousands of CRAN packages and one 
thing that makes it hard for us and for our users to build/check Bioconductor packages at the moment is 
the absence of Mac binary packages for R 4.0.0 on CRAN. Do you have an estimate of when they will 
become available?



Both the packages and R are now available. I always recommend using the Mac-master 
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=SgN9XTf8oSzk28ZilVDsjOU2Fpf0lRzDmF8QEBnwJno=-zAfQSmtuRs4uqHBVFcX5ssEWKX2vsSrEqVTwxI_WuM=
  as "mirror" since that one is most up-to-date.



Another question is where they are going to be hosted on CRAN. We need to 
follow CRAN's layout for Bioconductor package repositories.




We have removed the extra layer, the package type is back to "mac.binary", so 
bin/macosx/contrib is the location.

Cheers,
Simon




Thanks!
H.


On 3/31/20 21:27, Simon Urbanek wrote:

Dear Mac users,
R 4.0.0 will be using an entirely new toolchain, entirely new build system on 
entirely new macOS version and hardware. Therefore I would like to ask you 
kindly to test the binaries from
https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=FJYxweW9WiMXbNMPpMM0bHXy020Gx9P-dHMrWmt7YzE=
before the release as much as you can. Raising any issues after the release is 
too late! So please, please, test the pre-releases. Report any issues either 
directly to me or this mailing list.
The nightly builds are signed, but not necessarily notarized. However, the 
build fulfils Apple's conditions and is known to pass notarization (in fact the 
the package available for download today is actually notarized) so it should be 
a good test for the release which will be notarized and should work on Catalina.
For those that want to replicate our setup - technical details: we are now building with macOS 10.13 
(High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and 
GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 
target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it 
easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are 
available in 
https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_libs-2D4_=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=3ZbcXBticg_8MfXltGKdQ9SFNqqeLqqwK_pUhEet7QY=
The new R build system is in
https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_R4=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=Mmt7_pVM5aUDR3hz93-e-PtadG7wSYpaZe8Ayi5Pv4I=
Packages build system has not changed and is in
https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_packages=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=eId6n08LVeIAMhMXe3jvLFKn9QGi4_by8owFreDDc84=
We also plan to have a mac-builder available with similar function as the 
win-builder where pre-submission tests can be performed and potentially a 
Travis template.
Please test R pre-releases and provide feedback!
Thanks,
Simon
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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Bob Rudis
Hey Simon!

At the bottom of https://mac.r-project.org/libs-4/ is:

curl -O 
http://mac.R_project.org/libs-4/pkgconfig-0.28-darwin.17-x86_64.tar.gz

While most folks will figure it out, it should be:

curl -O 
http://mac.R-project.org/libs-4/pkgconfig-0.28-darwin.17-x86_64.tar.gz

(dash instead of underline).

-boB


> On Apr 1, 2020, at 09:30, Balamuta, James Joseph  
> wrote:
> 
> Simon,
> 
> Thanks for the overview! A few quick questions:
> 
> 1. Compiler-wise, the external clang compiler requirement was removed and, 
> so, there is no guarantee of OpenMP on macOS again? 
> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
> push for increased security by Apple?
> 3. How likely is the oldest system requirement to be bumped in a patch 
> release? 
> 
> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
> than happy to help! 
> 
> Best,
> 
> JJB
> 
> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
>  
> wrote:
> 
>Dear Mac users,
> 
>R 4.0.0 will be using an entirely new toolchain, entirely new build system 
> on entirely new macOS version and hardware. Therefore I would like to ask you 
> kindly to test the binaries from
> 
>https://mac.R-project.org
> 
>before the release as much as you can. Raising any issues after the 
> release is too late! So please, please, test the pre-releases. Report any 
> issues either directly to me or this mailing list.
> 
>The nightly builds are signed, but not necessarily notarized. However, the 
> build fulfils Apple's conditions and is known to pass notarization (in fact 
> the the package available for download today is actually notarized) so it 
> should be a good test for the release which will be notarized and should work 
> on Catalina.
> 
>For those that want to replicate our setup - technical details: we are now 
> building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
> system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds 
> are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 
> target. Packages are built on macOS 10.13 VMs with just Apple command line 
> tools (this should make it easy to replicate the setup using Travis, for 
> example). All 3rd party libraries that CRAN uses are available in 
> http://mac.r-project.org/libs-4/
> 
>The new R build system is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
>Packages build system has not changed and is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
> 
>We also plan to have a mac-builder available with similar function as the 
> win-builder where pre-submission tests can be performed and potentially a 
> Travis template.
> 
>Please test R pre-releases and provide feedback!
> 
>Thanks,
>Simon
> 
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> 
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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Göran Broström

Hello JJB,

Den 2020-04-01 kl. 15:30, skrev Balamuta, James Joseph:

Simon,

Thanks for the overview! A few quick questions:

1. Compiler-wise, the external clang compiler requirement was removed and, so, 
there is no guarantee of OpenMP on macOS again?
2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
push for increased security by Apple?


One reason is that I am on 10.13(.6) without possibility to upgrade to 
10.14 (MacBook Pro & Air, 2010).



3. How likely is the oldest system requirement to be bumped in a patch release?


Hopefully very unlikely;)

Best, Göran

PS. I have installed and run the 4.0.0 binary without any problem (so far).



Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
than happy to help!

Best,

JJB

On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
 wrote:

 Dear Mac users,
 
 R 4.0.0 will be using an entirely new toolchain, entirely new build system on entirely new macOS version and hardware. Therefore I would like to ask you kindly to test the binaries from
 
 https://mac.R-project.org
 
 before the release as much as you can. Raising any issues after the release is too late! So please, please, test the pre-releases. Report any issues either directly to me or this mailing list.
 
 The nightly builds are signed, but not necessarily notarized. However, the build fulfils Apple's conditions and is known to pass notarization (in fact the the package available for download today is actually notarized) so it should be a good test for the release which will be notarized and should work on Catalina.
 
 For those that want to replicate our setup - technical details: we are now building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are available in http://mac.r-project.org/libs-4/
 
 The new R build system is in

 https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
 Packages build system has not changed and is in
 https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
 
 We also plan to have a mac-builder available with similar function as the win-builder where pre-submission tests can be performed and potentially a Travis template.
 
 Please test R pre-releases and provide feedback!
 
 Thanks,

 Simon
 
 ___

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Re: [R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread peter dalgaard
Yes, sorry:

> osVersion
[1] "macOS Mojave 10.14.6"


> On 1 Apr 2020, at 16:14 , Prof Brian Ripley  wrote:
> 
> It seems to depend on the OS version: there are known issues with PCRE JIT 
> and macOS 10.15 not just with R, but not for everyone.
> 
> Similarly, installation issues of some Rcpp-using packages is only known to 
> occur under 10.15 and not with 10.13 (which is what will be used for building 
> binary packages and has been extensively tested there).  These should go away 
> with the next Rcpp update, available pro tem via
> 
> install.packages("Rcpp", repos="https://rcppcore.github.io/drat;)
> 
> So it really is necessary to remind people to follow the posting guide and 
> include the output from sessionInfo() or at the very least
> 
> > osVersion
> [1] "macOS Catalina 10.15.4"
> 
> 
> On 01/04/2020 14:37, peter dalgaard wrote:
>> Yes, this has been happening to a number of people, including Simon 
>> Urbanek...
>> Oddly enough, I'm seeing nothing of the sort on my slightly different build 
>> setup:
>> clang8 + gfortran6.1 as per https://cran.r-project.org/bin/macosx/tools
>> PCRE2 from http://mac.r-project.org/libs/
>> $ cat config.site
>> prefix=$HOME/tmp
>> CC=clang
>> CXX=clang++
>> with_blas="-framework vecLib"
>> with_lapack=yes
>> x_includes=/opt/X11/include
>> x_libraries=/opt/X11/lib
>> CURL_CONFIG=/usr/bin/curl-config
>> (And no, it is not because JIT is off:
>>> options("PCRE_use_JIT")
>> $PCRE_use_JIT
>> [1] TRUE
>> )
>> -pd
>>> On 1 Apr 2020, at 13:30 , Bryan Hanson  wrote:
>>> 
>>> On a fresh install of the binary from mac.r-project.org, if I simply do:
>>> 
>>> library()
>>> 
>>> I see:
>>> 
>>> R > library()
>>> There were 30 warnings (use warnings() to see them)
>>> R > warnings()
>>> Warning messages:
>>> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>>> 'no more memory'
>>> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>>> 'no more memory'
>>> 
>>> etc.  The usual window with installed packages does open.
>>> 
>>> Starting the conversation here on the Mac list, though it may be a bigger 
>>> problem.
>>> 
>>> Thanks, Bryan
>>> 
>>> Prof. Bryan Hanson (emeritus)
>>> Dept of Chemistry & Biochemistry
>>> DePauw University
>>> Greencastle IN 46135 USA
>>> Web: academic.depauw.edu/~hanson/index.html
>>> Repo: github.com/bryanhanson
>>> Nerdy Blog: ChemoSpec.org
>>> The Twit: @ProfBryanHanson
>>> I’m usually @ -4 GMT/UTC
>>> 
>>> R > sessionInfo()
>>> R version 4.0.0 alpha (2020-03-29 r78109)
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>>> 
>>> Matrix products: default
>>> BLAS:   
>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>>> LAPACK: 
>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats graphics  grDevices utils datasets  methods
>>> [7] base
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] compiler_4.0.0
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
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> 
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford

-- 
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] PCRE JIT compilation error

2020-04-01 Thread Prof Brian Ripley
It seems to depend on the OS version: there are known issues with PCRE 
JIT and macOS 10.15 not just with R, but not for everyone.


Similarly, installation issues of some Rcpp-using packages is only known 
to occur under 10.15 and not with 10.13 (which is what will be used for 
building binary packages and has been extensively tested there).  These 
should go away with the next Rcpp update, available pro tem via


install.packages("Rcpp", repos="https://rcppcore.github.io/drat;)

So it really is necessary to remind people to follow the posting guide 
and include the output from sessionInfo() or at the very least


> osVersion
[1] "macOS Catalina 10.15.4"


On 01/04/2020 14:37, peter dalgaard wrote:

Yes, this has been happening to a number of people, including Simon Urbanek...

Oddly enough, I'm seeing nothing of the sort on my slightly different build 
setup:

clang8 + gfortran6.1 as per https://cran.r-project.org/bin/macosx/tools
PCRE2 from http://mac.r-project.org/libs/

$ cat config.site
prefix=$HOME/tmp
CC=clang
CXX=clang++
with_blas="-framework vecLib"
with_lapack=yes
x_includes=/opt/X11/include
x_libraries=/opt/X11/lib
CURL_CONFIG=/usr/bin/curl-config

(And no, it is not because JIT is off:


options("PCRE_use_JIT")

$PCRE_use_JIT
[1] TRUE

)


-pd


On 1 Apr 2020, at 13:30 , Bryan Hanson  wrote:

On a fresh install of the binary from mac.r-project.org, if I simply do:

library()

I see:

R > library()
There were 30 warnings (use warnings() to see them)
R > warnings()
Warning messages:
1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
'no more memory'
2: In FUN(X[[i]], ...) : PCRE JIT compilation error
'no more memory'

etc.  The usual window with installed packages does open.

Starting the conversation here on the Mac list, though it may be a bigger 
problem.

Thanks, Bryan

Prof. Bryan Hanson (emeritus)
Dept of Chemistry & Biochemistry
DePauw University
Greencastle IN 46135 USA
Web: academic.depauw.edu/~hanson/index.html
Repo: github.com/bryanhanson
Nerdy Blog: ChemoSpec.org
The Twit: @ProfBryanHanson
I’m usually @ -4 GMT/UTC

R > sessionInfo()
R version 4.0.0 alpha (2020-03-29 r78109)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.0.0












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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Patrick Schratz
The same goes here regarding support.

I am (co-)maintaining a package on ropensci focusing on provider-agnostic CI 
approaches for R (tic) and have quite some experience with all the little 
culprits there.

Since you mentioned Travis: Be aware that the R community is (slowly but 
actively) moving away from Travis for a few reasons.
Also on GitHub Actions you can only build on 10.15 (Catalina) right now.

Best, Patrick
On 1. Apr 2020, 15:41 +0200, Bob Rudis , wrote:
> I shall pile on with an additional offer of assistance, Simon and a huge #ty 
> for this and all the work you do.
>
> > On Apr 1, 2020, at 09:30, Balamuta, James Joseph  
> > wrote:
> >
> > Simon,
> >
> > Thanks for the overview! A few quick questions:
> >
> > 1. Compiler-wise, the external clang compiler requirement was removed and, 
> > so, there is no guarantee of OpenMP on macOS again?
> > 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
> > push for increased security by Apple?
> > 3. How likely is the oldest system requirement to be bumped in a patch 
> > release?
> >
> > Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm 
> > more than happy to help!
> >
> > Best,
> >
> > JJB
> >
> > On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
> >  
> > wrote:
> >
> > Dear Mac users,
> >
> > R 4.0.0 will be using an entirely new toolchain, entirely new build system 
> > on entirely new macOS version and hardware. Therefore I would like to ask 
> > you kindly to test the binaries from
> >
> > https://mac.R-project.org
> >
> > before the release as much as you can. Raising any issues after the release 
> > is too late! So please, please, test the pre-releases. Report any issues 
> > either directly to me or this mailing list.
> >
> > The nightly builds are signed, but not necessarily notarized. However, the 
> > build fulfils Apple's conditions and is known to pass notarization (in fact 
> > the the package available for download today is actually notarized) so it 
> > should be a good test for the release which will be notarized and should 
> > work on Catalina.
> >
> > For those that want to replicate our setup - technical details: we are now 
> > building with macOS 10.13 (High Sierra) as target (i.e. the oldest 
> > supported system), regular Apple Xcode/command line tools and GNU Fortran 
> > 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using 
> > macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple 
> > command line tools (this should make it easy to replicate the setup using 
> > Travis, for example). All 3rd party libraries that CRAN uses are available 
> > in http://mac.r-project.org/libs-4/
> >
> > The new R build system is in
> > https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
> > Packages build system has not changed and is in
> > https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
> >
> > We also plan to have a mac-builder available with similar function as the 
> > win-builder where pre-submission tests can be performed and potentially a 
> > Travis template.
> >
> > Please test R pre-releases and provide feedback!
> >
> > Thanks,
> > Simon
> >
> > ___
> > 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] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Bob Rudis
I shall pile on with an additional offer of assistance, Simon and a huge #ty 
for this and all the work you do.

> On Apr 1, 2020, at 09:30, Balamuta, James Joseph  
> wrote:
> 
> Simon,
> 
> Thanks for the overview! A few quick questions:
> 
> 1. Compiler-wise, the external clang compiler requirement was removed and, 
> so, there is no guarantee of OpenMP on macOS again? 
> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
> push for increased security by Apple?
> 3. How likely is the oldest system requirement to be bumped in a patch 
> release? 
> 
> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
> than happy to help! 
> 
> Best,
> 
> JJB
> 
> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
>  
> wrote:
> 
>Dear Mac users,
> 
>R 4.0.0 will be using an entirely new toolchain, entirely new build system 
> on entirely new macOS version and hardware. Therefore I would like to ask you 
> kindly to test the binaries from
> 
>https://mac.R-project.org
> 
>before the release as much as you can. Raising any issues after the 
> release is too late! So please, please, test the pre-releases. Report any 
> issues either directly to me or this mailing list.
> 
>The nightly builds are signed, but not necessarily notarized. However, the 
> build fulfils Apple's conditions and is known to pass notarization (in fact 
> the the package available for download today is actually notarized) so it 
> should be a good test for the release which will be notarized and should work 
> on Catalina.
> 
>For those that want to replicate our setup - technical details: we are now 
> building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
> system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds 
> are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 
> target. Packages are built on macOS 10.13 VMs with just Apple command line 
> tools (this should make it easy to replicate the setup using Travis, for 
> example). All 3rd party libraries that CRAN uses are available in 
> http://mac.r-project.org/libs-4/
> 
>The new R build system is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
>Packages build system has not changed and is in
>https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages
> 
>We also plan to have a mac-builder available with similar function as the 
> win-builder where pre-submission tests can be performed and potentially a 
> Travis template.
> 
>Please test R pre-releases and provide feedback!
> 
>Thanks,
>Simon
> 
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> 
> 
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Re: [R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread peter dalgaard
Yes, this has been happening to a number of people, including Simon Urbanek...

Oddly enough, I'm seeing nothing of the sort on my slightly different build 
setup: 

clang8 + gfortran6.1 as per https://cran.r-project.org/bin/macosx/tools
PCRE2 from http://mac.r-project.org/libs/ 

$ cat config.site 
prefix=$HOME/tmp
CC=clang
CXX=clang++
with_blas="-framework vecLib"
with_lapack=yes
x_includes=/opt/X11/include
x_libraries=/opt/X11/lib
CURL_CONFIG=/usr/bin/curl-config

(And no, it is not because JIT is off:

> options("PCRE_use_JIT")
$PCRE_use_JIT
[1] TRUE

)


-pd

> On 1 Apr 2020, at 13:30 , Bryan Hanson  wrote:
> 
> On a fresh install of the binary from mac.r-project.org, if I simply do:
> 
> library()
> 
> I see:
> 
> R > library()
> There were 30 warnings (use warnings() to see them)
> R > warnings()
> Warning messages:
> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>   'no more memory'
> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>   'no more memory'
> 
> etc.  The usual window with installed packages does open.
> 
> Starting the conversation here on the Mac list, though it may be a bigger 
> problem.
> 
> Thanks, Bryan
> 
> Prof. Bryan Hanson (emeritus)
> Dept of Chemistry & Biochemistry
> DePauw University
> Greencastle IN 46135 USA
> Web: academic.depauw.edu/~hanson/index.html
> Repo: github.com/bryanhanson
> Nerdy Blog: ChemoSpec.org
> The Twit: @ProfBryanHanson
> I’m usually @ -4 GMT/UTC
> 
> R > sessionInfo()
> R version 4.0.0 alpha (2020-03-29 r78109)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Mojave 10.14.6
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Balamuta, James Joseph
Simon,

Thanks for the overview! A few quick questions:

1. Compiler-wise, the external clang compiler requirement was removed and, so, 
there is no guarantee of OpenMP on macOS again? 
2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new 
push for increased security by Apple?
3. How likely is the oldest system requirement to be bumped in a patch release? 

Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm more 
than happy to help! 

Best,

JJB

On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" 
 
wrote:

Dear Mac users,

R 4.0.0 will be using an entirely new toolchain, entirely new build system 
on entirely new macOS version and hardware. Therefore I would like to ask you 
kindly to test the binaries from

https://mac.R-project.org

before the release as much as you can. Raising any issues after the release 
is too late! So please, please, test the pre-releases. Report any issues either 
directly to me or this mailing list.

The nightly builds are signed, but not necessarily notarized. However, the 
build fulfils Apple's conditions and is known to pass notarization (in fact the 
the package available for download today is actually notarized) so it should be 
a good test for the release which will be notarized and should work on Catalina.

For those that want to replicate our setup - technical details: we are now 
building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds 
are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 target. 
Packages are built on macOS 10.13 VMs with just Apple command line tools (this 
should make it easy to replicate the setup using Travis, for example). All 3rd 
party libraries that CRAN uses are available in http://mac.r-project.org/libs-4/

The new R build system is in
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4
Packages build system has not changed and is in
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages

We also plan to have a mac-builder available with similar function as the 
win-builder where pre-submission tests can be performed and potentially a 
Travis template.

Please test R pre-releases and provide feedback!

Thanks,
Simon

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Re: [R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread Bryan Hanson
Having played with things a bit more, this message appears all over the place 
as people are beginning to report.

Another simple way to trigger it is to do:

?dist

Bryan

> On Apr 1, 2020, at 8:36 AM, Matthias Krawutschke  
> wrote:
> 
> Hello together,
> i´ve got this message too, but my systems show me first the list of all 
> installed libraries on my MAC.
> 
> Best regards and take care….
> 
> 
> 
> Matthias Krawutschke, Dipl. Inf.
> 
> Universität Potsdam
> ZIM - Zentrum für Informationstechnologie und Medienmanagement
> Team Infrastruktur Server und Storage 
> Spezialized: High-Performance-Computing and Kubernetes
> 
> 
> Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam
> Tel: +49 331 977-153065, Fax: +49 331 977-1750
> 
> Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html
> 
> 
> -Ursprüngliche Nachricht-
> Von: R-SIG-Mac  Im Auftrag von Bryan Hanson
> Gesendet: Mittwoch, 1. April 2020 13:30
> An: r-sig-mac R 
> Betreff: [R-SIG-Mac] PCRE JIT compilation error
> 
> On a fresh install of the binary from mac.r-project.org, if I simply do:
> 
> library()
> 
> I see:
> 
> R > library()
> There were 30 warnings (use warnings() to see them) R > warnings() Warning 
> messages:
> 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
>   'no more memory'
> 2: In FUN(X[[i]], ...) : PCRE JIT compilation error
>   'no more memory'
> 
> etc.  The usual window with installed packages does open.
> 
> Starting the conversation here on the Mac list, though it may be a bigger 
> problem.
> 
> Thanks, Bryan
> 
> Prof. Bryan Hanson (emeritus)
> Dept of Chemistry & Biochemistry
> DePauw University
> Greencastle IN 46135 USA
> Web: academic.depauw.edu/~hanson/index.html
> Repo: github.com/bryanhanson
> Nerdy Blog: ChemoSpec.org
> The Twit: @ProfBryanHanson
> I’m usually @ -4 GMT/UTC
> 
> R > sessionInfo()
> R version 4.0.0 alpha (2020-03-29 r78109)
> Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6
> 
> Matrix products: default
> BLAS:   
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods  
> [7] base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>   [[alternative HTML version deleted]]
> 
> ___
> 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] PCRE JIT compilation error

2020-04-01 Thread Matthias Krawutschke
Hello together,
i´ve got this message too, but my systems show me first the list of all 
installed libraries on my MAC.

Best regards and take care….



Matthias Krawutschke, Dipl. Inf.

Universität Potsdam
ZIM - Zentrum für Informationstechnologie und Medienmanagement
Team Infrastruktur Server und Storage 
Spezialized: High-Performance-Computing and Kubernetes


Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam
Tel: +49 331 977-153065, Fax: +49 331 977-1750

Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html


-Ursprüngliche Nachricht-
Von: R-SIG-Mac  Im Auftrag von Bryan Hanson
Gesendet: Mittwoch, 1. April 2020 13:30
An: r-sig-mac R 
Betreff: [R-SIG-Mac] PCRE JIT compilation error

On a fresh install of the binary from mac.r-project.org, if I simply do:

library()

I see:

R > library()
There were 30 warnings (use warnings() to see them) R > warnings() Warning 
messages:
1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
'no more memory'
2: In FUN(X[[i]], ...) : PCRE JIT compilation error
'no more memory'

etc.  The usual window with installed packages does open.

Starting the conversation here on the Mac list, though it may be a bigger 
problem.

Thanks, Bryan

Prof. Bryan Hanson (emeritus)
Dept of Chemistry & Biochemistry
DePauw University
Greencastle IN 46135 USA
Web: academic.depauw.edu/~hanson/index.html
Repo: github.com/bryanhanson
Nerdy Blog: ChemoSpec.org
The Twit: @ProfBryanHanson
I’m usually @ -4 GMT/UTC

R > sessionInfo()
R version 4.0.0 alpha (2020-03-29 r78109)
Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods  
[7] base 

loaded via a namespace (and not attached):
[1] compiler_4.0.0












[[alternative HTML version deleted]]

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[R-SIG-Mac] R 4.0: many PCRE JIT compilation errors

2020-04-01 Thread Daniel Kelley
I am  trying to build the "oce" package, and I get many (tens of thousands) of 
warnings of form similar to

```R
Warning in gsub("\n \\.([^\n])", "\n  .\\1", gsub("\n[ \t]*\n", "\n .\n ",  :
  PCRE JIT compilation error
'no more memory'
```

I am working through the build/check/install in stages, and documenting things 
at

https://github.com/dankelley/oce/issues/1674

in case that's of any help to anyone else.  Perhaps my grep() and gsub() calls 
are poorly framed, but I've never seen this warning before, and I suspect the 
warnings (or some of them) may be coming from he "R CMD" stage itself, so my 
guess is that this is an indication of a problem with R-4.0/macos.

I wish to note my deep thanks to the team behind macos development for R.

PS. I'm glad to hear that there may be an upcoming macos equivalent to 
winbuilder, because I have had very uneven success with rhub (working one day, 
failing another, on identical code, etc).

Dan E. Kelley [he/him/his 314ppm]
Professor and Senator
Department of Oceanography
Dalhousie University
PO BOX 15000
Halifax, NS, Canada B3H 4R2
dan.kel...@dal.ca

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[R-SIG-Mac] PCRE JIT compilation error

2020-04-01 Thread Bryan Hanson
On a fresh install of the binary from mac.r-project.org, if I simply do:

library()

I see:

R > library()
There were 30 warnings (use warnings() to see them)
R > warnings()
Warning messages:
1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error
'no more memory'
2: In FUN(X[[i]], ...) : PCRE JIT compilation error
'no more memory'

etc.  The usual window with installed packages does open.

Starting the conversation here on the Mac list, though it may be a bigger 
problem.

Thanks, Bryan

Prof. Bryan Hanson (emeritus)
Dept of Chemistry & Biochemistry
DePauw University
Greencastle IN 46135 USA
Web: academic.depauw.edu/~hanson/index.html
Repo: github.com/bryanhanson
Nerdy Blog: ChemoSpec.org
The Twit: @ProfBryanHanson
I’m usually @ -4 GMT/UTC

R > sessionInfo()
R version 4.0.0 alpha (2020-03-29 r78109)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods  
[7] base 

loaded via a namespace (and not attached):
[1] compiler_4.0.0












[[alternative HTML version deleted]]

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Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Patrick Schratz
Thanks Simon,

This simplifies things a lot and clears up the process. While the instructions 
on https://mac.r-project.org/ are more clear now I think there is still 
simplification needed for the install process and custom modifications that are 
needed.
This not only applies to the dev page but finally also to production end users 
if the SDK 10.15 issues (see below) persists.

I’ve scripted all installation steps (R-devel, gfortran, SDK 10.13) and will 
probably write a blog post about it to make the R community more aware about 
it. Let me know if anything is wrong about it - otherwise I’ll use the code 
below in the blog post.

# install R-devel
wget 
https://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz
sudo tar fvxz R*.tar.gz -C /
rm R-devel-el-capitan-sa-x86_64.tar.gz

# install gfortran
wget 
https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg
sudo hdiutil attach gfortran*.dmg
sudo installer -package /Volumes/gfortran*/gfortran*/gfortran*.pkg -target /
sudo hdiutil detach /Volumes/gfortran-8.2-Mojave

# install SDK10.13
wget 
https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz
tar fvxz MacOSX10.13.sdk.tar.xz
sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/
rm -rf MacOSX10.13*

In addition people need to set custom CFLAGS in ~/.R/Makevars to actually use 
it:

CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk

In addition there really seem to be major problems regarding the 10.15 SDK. For 
example, {igraph} which is a package on which lots of other packages depend, 
cannot be installed from source with SDK 10.15 but works with SDK 10.13.

Patrick
On 1. Apr 2020, 09:38 +0200, Simon Urbanek , wrote:
> Hervé,
>
>
> > On 1/04/2020, at 6:19 PM, Hervé Pagès  wrote:
> >
> > Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha 
> > build from https://mac.r-project.org/ for the Bioconductor build system. 
> > Bioconductor packages depend on thousands of CRAN packages and one thing 
> > that makes it hard for us and for our users to build/check Bioconductor 
> > packages at the moment is the absence of Mac binary packages for R 4.0.0 on 
> > CRAN. Do you have an estimate of when they will become available?
> >
>
> Both the packages and R are now available. I always recommend using the 
> Mac-master https://mac.R-project.org as "mirror" since that one is most 
> up-to-date.
>
>
> > Another question is where they are going to be hosted on CRAN. We need to 
> > follow CRAN's layout for Bioconductor package repositories.
> >
>
>
> We have removed the extra layer, the package type is back to "mac.binary", so 
> bin/macosx/contrib is the location.
>
> Cheers,
> Simon
>
>
>
> > Thanks!
> > H.
> >
> >
> > On 3/31/20 21:27, Simon Urbanek wrote:
> > > Dear Mac users,
> > > R 4.0.0 will be using an entirely new toolchain, entirely new build 
> > > system on entirely new macOS version and hardware. Therefore I would like 
> > > to ask you kindly to test the binaries from
> > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=FJYxweW9WiMXbNMPpMM0bHXy020Gx9P-dHMrWmt7YzE=
> > > before the release as much as you can. Raising any issues after the 
> > > release is too late! So please, please, test the pre-releases. Report any 
> > > issues either directly to me or this mailing list.
> > > The nightly builds are signed, but not necessarily notarized. However, 
> > > the build fulfils Apple's conditions and is known to pass notarization 
> > > (in fact the the package available for download today is actually 
> > > notarized) so it should be a good test for the release which will be 
> > > notarized and should work on Catalina.
> > > For those that want to replicate our setup - technical details: we are 
> > > now building with macOS 10.13 (High Sierra) as target (i.e. the oldest 
> > > supported system), regular Apple Xcode/command line tools and GNU Fortran 
> > > 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using 
> > > macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple 
> > > command line tools (this should make it easy to replicate the setup using 
> > > Travis, for example). All 3rd party libraries that CRAN uses are 
> > > available in 
> > > https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_libs-2D4_=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=3ZbcXBticg_8MfXltGKdQ9SFNqqeLqqwK_pUhEet7QY=
> > > The new R build system is in
> > > 

Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!

2020-04-01 Thread Simon Urbanek
Hervé,


> On 1/04/2020, at 6:19 PM, Hervé Pagès  wrote:
> 
> Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha 
> build from https://mac.r-project.org/ for the Bioconductor build system. 
> Bioconductor packages depend on thousands of CRAN packages and one thing that 
> makes it hard for us and for our users to build/check Bioconductor packages 
> at the moment is the absence of Mac binary packages for R 4.0.0 on CRAN. Do 
> you have an estimate of when they will become available?
> 

Both the packages and R are now available. I always recommend using the 
Mac-master https://mac.R-project.org as "mirror" since that one is most 
up-to-date.


> Another question is where they are going to be hosted on CRAN. We need to 
> follow CRAN's layout for Bioconductor package repositories.
> 


We have removed the extra layer, the package type is back to "mac.binary", so 
bin/macosx/contrib is the location.

Cheers,
Simon



> Thanks!
> H.
> 
> 
> On 3/31/20 21:27, Simon Urbanek wrote:
>> Dear Mac users,
>> R 4.0.0 will be using an entirely new toolchain, entirely new build system 
>> on entirely new macOS version and hardware. Therefore I would like to ask 
>> you kindly to test the binaries from
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=FJYxweW9WiMXbNMPpMM0bHXy020Gx9P-dHMrWmt7YzE=
>> before the release as much as you can. Raising any issues after the release 
>> is too late! So please, please, test the pre-releases. Report any issues 
>> either directly to me or this mailing list.
>> The nightly builds are signed, but not necessarily notarized. However, the 
>> build fulfils Apple's conditions and is known to pass notarization (in fact 
>> the the package available for download today is actually notarized) so it 
>> should be a good test for the release which will be notarized and should 
>> work on Catalina.
>> For those that want to replicate our setup - technical details: we are now 
>> building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported 
>> system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R 
>> builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 
>> 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command 
>> line tools (this should make it easy to replicate the setup using Travis, 
>> for example). All 3rd party libraries that CRAN uses are available in 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_libs-2D4_=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=3ZbcXBticg_8MfXltGKdQ9SFNqqeLqqwK_pUhEet7QY=
>> The new R build system is in
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_R4=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=Mmt7_pVM5aUDR3hz93-e-PtadG7wSYpaZe8Ayi5Pv4I=
>> Packages build system has not changed and is in
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_packages=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=eId6n08LVeIAMhMXe3jvLFKn9QGi4_by8owFreDDc84=
>> We also plan to have a mac-builder available with similar function as the 
>> win-builder where pre-submission tests can be performed and potentially a 
>> Travis template.
>> Please test R pre-releases and provide feedback!
>> Thanks,
>> Simon
>> ___
>> 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=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI=ubqivtpb1OZ2I0MEbVvGlGDK-tfti3DPtIv4LQ-Ks6A=
> 
> -- 
> 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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