[R-sig-Debian] Default CXXFLAGS

[Jeroen Ooms]

Compiling packages with C++ code using the default r-base-dev
configuration on debian:sid shows a lot of:

   cc1plus: warning: '-Werror=' argument
'-Werror=implicit-function-declaration' is not valid for C++

Can this flag be removed from R CMD config CXXFLAGS?

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[R-sig-Debian] Documentation for installing on Ubuntu outdated

[Jeroen Ooms]

Users searching for how to install R on Ubuntu probably end up on
either of these pages:

 - https://cran.r-project.org/bin/linux/ubuntu/
 - https://cran.r-project.org/bin/linux/ubuntu/fullREADME.html

Which talk about the "current" R 4.2 release, and the latter document
also goes on talking about 4.1 packages, and even an example of
setting R_LIBS_USER for R-3.5.

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Re: [R-sig-Debian] Ubuntu packages on s390x

[Jeroen Ooms]

On Thu, Aug 3, 2023 at 9:16 PM Vivian Kong  wrote:
>
> Hello,
>
> Are there any plans to add R packages for Ubuntu on other architectures in 
> addition to amd64?  We are looking for s390x packages as the version from the 
> distro's package manger is 4.2.2.  I'm happy to help in any way I can.

You can easily do this for free using launchpad:

Create a launchpad repository (PPA), then go to "change settings", and
there you can select which architectures to build. By default only
amd64 is enabled, but you can enable any from the following:

 AMD x86-64 (amd64)
 ARM ARMv8 (arm64)
 ARM ARMv7 Hard Float (armhf)
 Intel x86 (i386)
 PowerPC (powerpc)
 PowerPC64 Little-Endian (ppc64el)
 IBM System z (s390x)

Now you just upload the r-base source packages to the PPA and they get
built for all these architectures. You can do this from the command
line, but you can even simply copy them from Michael Rutter's
backports ppa:

Go to https://launchpad.net/~marutter/+archive/ubuntu/rrutter4.0/ then
click "view package details" and then "copy packages". Select the
distro (e.g. jammy), then the r-base package and select "Rebuild the
copied sources" to r-base to your own PPA. That's it, it will
automatically build and publish the binaries.

I tested that this actually works here:
https://launchpad.net/~jeroen/+archive/ubuntu/r-backports . You can
see the repo has s390x binaries for r-4.3.1 and the page lists
installation instructions using apt.

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[R-sig-Debian] Enabling arm64 in launchpad PPA's

[Jeroen Ooms]

I was wondering if it would be possible to enable arm64 in some of the
PPA's, such as rrutter4.0. As far as I can tell, currently only i686
and amd64 are provided. It would be great to have arm64 builds for the
ubuntu-lts backports of r-base.

You can enable other platforms in the PPA settings. Go to "Change
details" on your PPA and look under "Processors".

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[R-sig-Debian] c2d4u: missing dependency for r-cran-gert and r-cran-v8 on bionic

[Jeroen Ooms]

A user has reported, and I have confirmed, that r-cran-gert from c2d4u
is uninstallable on bionic because it is compiled against a version of
libgit2 that is not included with c2d4u:

 # apt-get install r-cran-gert
 The following packages have unmet dependencies:
   r-cran-gert : Depends: libgit2-27 (>= 0.26.0) but it is not installable
  E: Unable to correct problems, you have held broken packages.

>From the c2d4u buildlog I can see that it is compiling r-cran-gert
against the libgit2 backports from ppa:cran/libgit2. So I think the
easiest solution is to put a copy of that libgit2 into c2d4u.

The same seems to hold for r-cran-v8.

The problem does not exist for ubuntu:focal because here the stock
versions of libgit2 and libv8 are sufficient and we do not provide ppa
backports.

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Re: [R-sig-Debian] Timezone conversion on Ubuntu 20.04

[Jeroen Ooms]

On Sat, Apr 25, 2020 at 10:41 AM Johannes Ranke  wrote:
>
> Am Samstag, 25. April 2020, 01:02:38 CEST schrieb Jeroen Ooms:
> > Hi all,
> >
> > I am testing R 4.0 and ran into an issue with timezones on Ubuntu
> > Focal: converting a timestamp to another timezone results in NA:
> >
> >   as.POSIXct(as.POSIXlt(Sys.time(), tz = "CET"), tz = "EST")
> >
> > This only happens on Ubuntu Focal, it seems to work fine on Ubuntu
> > Bionic. I am the standard ubuntu docker image icw/ r-base from Dirk's
> > ppa:edd/r-4.0 on both systems.
>
> works fine using the backported R 4.0.0 on Debian buster:
>
> R> as.POSIXct(as.POSIXlt(Sys.time(), tz = "CET"), tz = "EST")
> [1] "2020-04-25 10:05:29 EST"

Perhaps the root cause of the change in behavior is that on the
focal/bullseye docker images, /usr/bin/timedatectl exists, but it does
not work:

   root@focal:/# timedatectl
   System has not been booted with systemd as init system (PID 1).
Can't operate.
   Failed to create bus connection: Host is down

R assumes that if it timedatectl exists, it can be used. On the docker
image of bionic and buster, timedatectl simply is not installed so R
does not call it.

The consequence though, is very subtle changes in behavior of time
conversion edge cases that I cannot explain. For example we get
differences between "UTC" and "Etc/UTC":

> Sys.timezone()
[1] "Etc/UTC"
# System has not been booted with systemd as init system (PID 1). Can't operate.
# Failed to create bus connection: Host is down
Warning message:
In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1

as.POSIXct(strptime("24.04.2020 01:00", format = "%d.%m.%Y %H:%M", tz
= "CET"), tz = "")
[1] NA

as.POSIXct(strptime("24.04.2020 01:00", format = "%d.%m.%Y %H:%M", tz
= "CEST"), tz = "")
[1] "2020-04-24 01:00:00 UTC"

> as.POSIXct(strptime("24.04.2020 01:00", format = "%d.%m.%Y %H:%M", tz = 
> "CET"), tz = "Etc/UTC")
[1] NA

> as.POSIXct(strptime("24.04.2020 01:00", format = "%d.%m.%Y %H:%M", tz = 
> "CET"), tz = "UTC")
[1] "2020-04-24 01:00:00 UTC"

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[R-sig-Debian] Timezone conversion on Ubuntu 20.04

[Jeroen Ooms]

Hi all,

I am testing R 4.0 and ran into an issue with timezones on Ubuntu
Focal: converting a timestamp to another timezone results in NA:

  as.POSIXct(as.POSIXlt(Sys.time(), tz = "CET"), tz = "EST")

This only happens on Ubuntu Focal, it seems to work fine on Ubuntu
Bionic. I am the standard ubuntu docker image icw/ r-base from Dirk's
ppa:edd/r-4.0 on both systems.

Am I missing a system dependency for tzone data?

Jeroen

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[R-sig-Debian] c2d4u3.5 packages not working in R 3.5 anymore

[Jeroen Ooms]

Travis users are reporting a lot of these errors when testing packages on R 3.5:

  Error: package or namespace load failed for ‘’ in rbind(info,
getNamespaceInfo(env, "S3methods")):

This problem seems to happen when a c2d4u package was compiled with R
3.6 and is loaded in R 3.5. The problem does not appear when using the
same r-cran-xyz package on R 3.6. I'm not entirely sure what the root
cause is but I think it has to do with a new feature in R 3.6 (from
the NEWS file):

  S3method() directives in ‘NAMESPACE’ can now also be used to perform
delayed S3 method registration.

Maybe c2d4u3.5 packages should be compiled with R 3.5 instead of R
3.6? I think backward compatibility not a problem.

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[R-sig-Debian] bug in r-cran-curl from c2d4u

[Jeroen Ooms]

On Bionic with c2d4u I see:

The following packages have been kept back:
  r-cran-curl

The problem is that r-cran-curl from 2d4du has a runtime dependency on
libcurl4-openssl-dev. This dev package cannot be installed in
conjunction with libcurl4-gnutls-dev (which again is required by some
other packages).

This is a bug because libcurl4-openssl-dev should be a build-depends
only, the runtime depends is 'libcurl4'. The debian r-cran-curl
package has got this correct, perhaps we can just upload the debian
package to 2cd4u? https://packages.debian.org/buster/r-cran-curl

Thanks!

Jeroen

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Re: [R-sig-Debian] Announcing cran2deb4ubuntu for R 3.5.0

[Jeroen Ooms]

On Sun, May 27, 2018 at 2:20 PM, Michael Rutter <ma...@psu.edu> wrote:
>
>
> On 05/27/2018 08:08 AM, Dirk Eddelbuettel wrote:
>>
>>
>> On 27 May 2018 at 12:56, Jeroen Ooms wrote:
>> | Thanks Michael!
>>
>> Seconded!
>
>
> You're welcome.
>
>> | One more issue I ran into:
>> |
>> | apt-get install r-cran-rgdal
>> |
>> | The following packages have unmet dependencies:
>> |  r-cran-rgdal : Depends: gdal-abi-2-1-0 but it is not installable
>> | Depends: libgdal20 (>= 2.0.1) but it is not installable
>> | E: Unable to correct problems, you have held broken packages.
>>
>> Which flavour / distribution is that on?
>
>
> Likely Trusty.  You need to add the ubuntugis-stable PPA as well
> (https://launchpad.net/~ubuntugis/+archive/ubuntu/ppa).  Nothing related to
> gdal builds based on stock Trusty.  Many packages requires
> gdal >= 2.1.  This solves a bunch of issues.


Yes this is trusty (Travis). Which other PPA's does c2d4u3.5 depend
on? Then we'll add those to travis as well when we add c2d4u3.5.

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Re: [R-sig-Debian] Announcing cran2deb4ubuntu for R 3.5.0

[Jeroen Ooms]

Thanks Michael! One more issue I ran into:

apt-get install r-cran-rgdal

The following packages have unmet dependencies:
 r-cran-rgdal : Depends: gdal-abi-2-1-0 but it is not installable
Depends: libgdal20 (>= 2.0.1) but it is not installable
E: Unable to correct problems, you have held broken packages.



On Sun, May 27, 2018 at 4:26 AM, Michael Rutter  wrote:
>
> I would like to announce that c2d4u3.5 is now available for public use. You
> can see a blog post here with all the details:
> http://rubuntu.netlify.com/post/2018-05-25-announcing-c2d4u3-5/
>
> There still might be one to two issues.  Please let me know if you have any
> problems.
>
> Michael
>
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[R-sig-Debian] New libpng in c2d4u3.5 breaks many other packages

[Jeroen Ooms]

As of today many Travis users are seeing this error:

The following packages have unmet dependencies:
 libmagick++-dev : Depends: libmagickcore-dev (=
8:6.7.7.10-6ubuntu3.9) but it is not going to be installed
   Depends: libmagickwand-dev (=
8:6.7.7.10-6ubuntu3.9) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.


The problem is that a few hours ago a version of libpng1.6 was
published to c2d4u3.5 which is not compatible with the version of
imagemagick in trusty. Becuase libmagick++ is installed by default on
Travis, this breaks almost all installations.

I think it's best to only publish R packages in c2d4u, not system libs.

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Re: [R-sig-Debian] Advice on upgrading to 3.5.0

[Jeroen Ooms]

On Wed, May 2, 2018 at 10:35 AM, Robin Lovelace  wrote:
> I'd be interested to hear views on how and when Ubuntu users should upgrade
> to R 3.5.0.
> I made the upgrade a few days ago but reverted because of issues installing
> packages such as rJava, which I installed on the system with r-cran-rjava.

My strategy will be to jump to R 3.5 when I upgrade my servers to
Ubuntu Bionic in a few weeks (will probably do a clean install).
Currently c2d4u has pretty great coverage of CRAN binaries for Xenial
(and Trusty) so I will stick with Xenial + R 3.4 for now.

>From activity on launchpad it looks like c2d4u-3.5 is currently
focussing on Ubuntu Bionic, which is great because that will give us a
clean path forward. Hopefully in a few weeks from now, most r-cran
packages will be there so we can upgrade to Bionic and R3.5 at the
same time.

> Also any advice on how to do a clean uninstall of the previous version
> before making the leap greatly appreciated.

Due to the missing api tags, I think it will be very difficult to
automatically determine which r-cran packages you can keep. If you
really need to upgrade you probably want to purge r-cran-* and
r-base-* and reinstall from the new ppa.

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Re: [R-sig-Debian] R 3.5.0 Binaries for Ubuntu now available

[Jeroen Ooms]

On Sun, Apr 29, 2018 at 3:49 PM, Dirk Eddelbuettel <e...@debian.org> wrote:
>
> On 29 April 2018 at 15:30, Jeroen Ooms wrote:
> | On Sat, Apr 28, 2018 at 10:00 PM, Michael Rutter <marut...@gmail.com> wrote:
> | > These have not been mirrored to CRAN as I want to have the other r-cran
> | > packages built against R 3.5 before adding to CRAN.  Worried about 
> breaking
> | > working systems currently on R 3.4.4.
> |
> | Thanks, Michael. I did some simple tests, upgrading existing r-base
> | installations to R 3.5. on Xenial and Bionic, and initially apt did
> | the correct thing of removing the incompatible r-cran-xyz packages.
> |
> | However then I tried installing the (knowingly incompatible)
> | r-cran-rcpp from c2d4u and apt didn't stop me. Do the r-cran-xyz
> | packages from c2d4u not have the same r-api-nn dependency
> | restrictions?
>
> Does it have a r-api-3.4 tag like the official packages?  Michael and I may
> at some have made an executive decision to _not_ impose those on c2d4u 
> packages.
> So blame us.

OK, understand this is a complex operation, but still unfortunate. The
mixing of c2d4u packages with r-base 3.5 will inevitably happen when
people upgrade their systems to R 3.5.

If there would be a way to start adding the appropriate r-api-nn tag
in c2d4u based on which version of R it was built with, that would
probably be an enormous improvement. Not sure if this is something
that can easily be automated.

Thanks for your efforts on this!

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Re: [R-sig-Debian] R 3.5.0 Binaries for Ubuntu now available

[Jeroen Ooms]

On Sat, Apr 28, 2018 at 10:00 PM, Michael Rutter  wrote:
> These have not been mirrored to CRAN as I want to have the other r-cran
> packages built against R 3.5 before adding to CRAN.  Worried about breaking
> working systems currently on R 3.4.4.

Thanks, Michael. I did some simple tests, upgrading existing r-base
installations to R 3.5. on Xenial and Bionic, and initially apt did
the correct thing of removing the incompatible r-cran-xyz packages.

However then I tried installing the (knowingly incompatible)
r-cran-rcpp from c2d4u and apt didn't stop me. Do the r-cran-xyz
packages from c2d4u not have the same r-api-nn dependency
restrictions?

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Re: [R-sig-Debian] FYI libcurl conflicts in ubuntu 18.04

[Jeroen Ooms]

On Sat, Apr 28, 2018 at 2:38 PM, Dirk Eddelbuettel  wrote:
> That said, thanks for the heads up. We'll see what comes out of it. My Debian
> package also still uses curl3, but I noticed that there is a whole formal
> transition going on -- so 'our' r-base-core package would get rebuilt anyway

If I understand it correctly this is a problem only in Ubuntu
currently. They bumped libcurl3 to libcurl4 but only for the openssl
flavor of libcurl, supposedly because they added support for nghttp2
in this build. I don't think they realized this would create a split
in the ecosystem between software that depends on libcurl3 vs
libcurl4.

I *think* that if you are building debian r-base against
libcurl4-openssl-dev, then it will automatically start depending on
libcurl4 once this makes it into testing:
https://packages.debian.org/experimental/libcurl4

Either way you know this better than me. I was mostly giving users
like myself a heads-up that when they try to upgrade to ubuntu 18.04,
apt may uninstall r-base or other packages trying to resolve the
libcurl3 vs libcurl4 conflicts.

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[R-sig-Debian] FYI libcurl conflicts in ubuntu 18.04

[Jeroen Ooms]

One of the curl maintainers has pointed me to this bug report on
Launchpad that may affect r-base users:
https://bugs.launchpad.net/ubuntu/+source/curl/+bug/1754294

The issue is that ubuntu now ships both libcurl3 (gnutls, nss) as well
as libcurl4 (openssl) which cannot be installed concurrently. Because
r-base-core depends on libcurl4, it will conflict with any other
packages depending on libcurl3.

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[R-sig-Debian] Upgrade to 3.4.2 fails due to r-api version conflict

[Jeroen Ooms]

Upgrade of r-base to 3.4.2 on Ubuntu 16.04 using the marutter/rrutter PPA
terribly failed on my server. One way to reproduce the problem is using the
stable opencpu image which currently ships with R 3.4.1:

   docker run -i -t opencpu/base /bin/bash

This image is currently stable. Now add the rrutter ppa and upgrade:

   add-apt-repository ppa:marutter/rrutter
   apt-get update
   apt-get upgrade

Note that if we try apt-get install r-base or r-base-recommended we get:

   Unable to correct problems, you have held broken packages.

Unfortunately what I did was 'apt-get dist-upgrade -y' which uninstalled
most of the system in order to upgrade r-base-core. That left me here:
https://twitter.com/opencpu/status/913714052542746624

[[alternative HTML version deleted]]

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Re: [R-sig-Debian] Why is rstudio not in Ubuntu repo or PPA?

[Jeroen Ooms]

On Thu, Sep 24, 2015 at 3:49 AM, Xu Wang  wrote:
> rstudio is very easy to install, but it would be great if it were just
> an apt-get away. Is there a reason it is not in Ubuntu main repos or
> in rrutter PPA?

Not sure what you need it for, but I did create a ppa with a repack
which I use to formally depend on rstudio-server. Very hacky but it
works: https://launchpad.net/~opencpu/+archive/ubuntu/rstudio

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