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
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
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
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
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
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
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
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:
>
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
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
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.
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
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.
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
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
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
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
>
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