Re: [R-sig-Debian] R-4.0.0 and Texlive 2020 installed on EmmabuntusDE4 (Debian Bullseye)

[Johannes Ranke]

Dear Patrice,

thanks for sharing your experience with Debian based distributions. It is 
amazing how many distros you tested!

In your situation I would recommend apt pinning for installing texlive 2020 
from Debian sid on Debian bullseye aka testing or related systems. Simply 
adding sid sources as you did will make your system upgrade to sid. It seems 
you partially upgraded some of your test systems to sid and were left with 
broken systems.

This will also apply to emmabunt� - if you just added the sid repository 
without editing /etc/apt/preferences, you will always pull packages from sid 
which may be ok for your use case, but you should be aware of it.

You would need to edit /etc/apt/preferences in order to tell apt to just use 
texlive from sid and the other packages from bullseye.

Regarding the command to add my key, this is actually there, but I believe it 
was too far down - I just moved the section on secure apt before the section 
on the different distributions. Thanks for the hint!

Regarding your attempt to use the backports for bullseye on CRAN for your 
Emmabunt�s system, chances are it would have worked if you would have used the 
command I am listing there (of course adding sudo):

  sudo apt install -t bullseye-cran40 r-base

instead of simply 

  sudo apt install r-base

However, now you have the newest devel version compiled from sources for 
checking your packages on Linux which is nice as well!

Kind regards,

Johannes


Am Dienstag, 28. April 2020, 20:49:31 CEST schrieb Patrice Kiener:
> Dear all,
> 
> 
> I whish to relate my installation of R-4.0.0 on Debian.
> 
> I am mainly a Windows user and occasionnaly verify the CRAN checks of my
> packages on a second laptop equipped with Linux Mint Debian Edition 3
> (LMDE3) based on Debian Stretch. On Friday, April 24, it took me a few
> hours to have R-4.0.0 installed on Windows and the sources compiled,
> thanks to the instructions provided by Jeroen Ooms:
>  https://cloud.r-project.org/bin/windows/Rtools/ + links
> 
> I decided to repeat the exercise on Debian with a clean SSD disk, a
> recent Debian distribution, Texlive 2020 and R-4.0.0 to replace the
> obsolete LMDE3. The main difficulty was to find the appropriate
> distribution that accepts Texlive 2020. I downloaded and tested:
> 
> - Debian Buster 10.3 (the current stable version with a few desktops:
> Gnome, KDE-Plasma, XFCE, LXDE, LXQt, Mosaic),
> - Netrunner (Debian Buster 10.3 + KDE),
> - Linux Mint LMDE4 (Debian Buster 10.3 + Cinnamon),
> - Emmabunt�s DE3 (Debian Buster 10.3 + XFCE),
> - Xubuntu (Ubuntu + XFCE),
> - Debian Bullseye (the testing version + LXQt),
> - Emmabunt�s DE4 alpha (Debian Bullseye + XFCE + LXQt) published on
> April 27 (yesterday),
> - Debian sid (the unstable version).
> 
> - Once again in four years, I had many difficulties with the independant
> install-tl-unix.tar.gz (*.sh) program provided by Texlive and the final
> steps with the PATH update. The program was not found and tlmgr --gui
> did not reconnect to the CTAN repository. Once again, I gave up.
> - All distributions based on Buster 10.3 have Texlive 2018 in their
> repositories. In a few distributions, it is possible to write the sid
> (unstable) repository in the sources.list file:
>  deb http://deb.debian.org/debian/ sid main contrib
> 
> Then, a sudo apt-get update and apt search Texlive gives access to
> Texlive 2020. Unfortunately, installing Texlive 2020 this way will
> suppress Libre Office and numerous libraries, a few of them being used
> by the display manager. This is a sure way to break the distribution at
> the next startup.
> - Debian Bullseye offers Texlive 2019 in its repository. Writing the sid
>   line in sources.list is again easy. But accessing it is much more
> difficult as Debian considers it unsecure, throws a warning message and
> requests some parameter change in another file (which is not clearly
> designated) to accept this repository. I kept it as a potential solution.
> - The installation of Debian sid follows other paths. It is a
> distribution meant for testing and chasing bugs, not for a permanent
> use. I did not insist.
> 
> The great winner is Emmabunt�s DE4, which can be downloaded from here:
>  https://emmabuntus.org/emmabuntus-de4/
>  http://dl.emma-de4x64.emmabuntus.org/
> 
> https://emmabuntus.org/on-april-27-2020-emmade4-debian-11-bullseye-is-rollin
> g-out-early/
> 
> (Disclaimer: I do not have any ties with the development team. I
> discovered the distribution 10 days ago when searching for alternatives
> to Ubuntu and Mint. I tested first DE3 and discovered yesterday by
> surprise that DE4 was released.)
> 
> With its predecessor DE3, they are very surprising distributions with a
> completely different philosophy than the most well-known distributions,
> like Ubuntu and Mint, on the number of preinstalled packages. They are
> meant for people who have recent 64 bits or old computers, including 32
> bits, a poor internet 

[R-sig-Debian] R-4.0.0 and Texlive 2020 installed on EmmabuntusDE4 (Debian Bullseye)

[Patrice Kiener]

Dear all,


I whish to relate my installation of R-4.0.0 on Debian.

I am mainly a Windows user and occasionnaly verify the CRAN checks of my 
packages on a second laptop equipped with Linux Mint Debian Edition 3 
(LMDE3) based on Debian Stretch. On Friday, April 24, it took me a few 
hours to have R-4.0.0 installed on Windows and the sources compiled, 
thanks to the instructions provided by Jeroen Ooms:

https://cloud.r-project.org/bin/windows/Rtools/ + links

I decided to repeat the exercise on Debian with a clean SSD disk, a 
recent Debian distribution, Texlive 2020 and R-4.0.0 to replace the 
obsolete LMDE3. The main difficulty was to find the appropriate 
distribution that accepts Texlive 2020. I downloaded and tested:


- Debian Buster 10.3 (the current stable version with a few desktops: 
Gnome, KDE-Plasma, XFCE, LXDE, LXQt, Mosaic),

- Netrunner (Debian Buster 10.3 + KDE),
- Linux Mint LMDE4 (Debian Buster 10.3 + Cinnamon),
- Emmabuntüs DE3 (Debian Buster 10.3 + XFCE),
- Xubuntu (Ubuntu + XFCE),
- Debian Bullseye (the testing version + LXQt),
- Emmabuntüs DE4 alpha (Debian Bullseye + XFCE + LXQt) published on 
April 27 (yesterday),

- Debian sid (the unstable version).

- Once again in four years, I had many difficulties with the independant 
install-tl-unix.tar.gz (*.sh) program provided by Texlive and the final 
steps with the PATH update. The program was not found and tlmgr --gui 
did not reconnect to the CTAN repository. Once again, I gave up.
- All distributions based on Buster 10.3 have Texlive 2018 in their 
repositories. In a few distributions, it is possible to write the sid 
(unstable) repository in the sources.list file:

deb http://deb.debian.org/debian/ sid main contrib

Then, a sudo apt-get update and apt search Texlive gives access to 
Texlive 2020. Unfortunately, installing Texlive 2020 this way will 
suppress Libre Office and numerous libraries, a few of them being used 
by the display manager. This is a sure way to break the distribution at 
the next startup.
- Debian Bullseye offers Texlive 2019 in its repository. Writing the sid 
 line in sources.list is again easy. But accessing it is much more 
difficult as Debian considers it unsecure, throws a warning message and 
requests some parameter change in another file (which is not clearly 
designated) to accept this repository. I kept it as a potential solution.
- The installation of Debian sid follows other paths. It is a 
distribution meant for testing and chasing bugs, not for a permanent 
use. I did not insist.


The great winner is Emmabuntüs DE4, which can be downloaded from here:
https://emmabuntus.org/emmabuntus-de4/
http://dl.emma-de4x64.emmabuntus.org/

https://emmabuntus.org/on-april-27-2020-emmade4-debian-11-bullseye-is-rolling-out-early/

(Disclaimer: I do not have any ties with the development team. I 
discovered the distribution 10 days ago when searching for alternatives 
to Ubuntu and Mint. I tested first DE3 and discovered yesterday by 
surprise that DE4 was released.)


With its predecessor DE3, they are very surprising distributions with a 
completely different philosophy than the most well-known distributions, 
like Ubuntu and Mint, on the number of preinstalled packages. They are 
meant for people who have recent 64 bits or old computers, including 32 
bits, a poor internet connection but a large usb key. A large audience 
is people in Africa, for instance Togo. When Ubuntu, Netrunner and Mint 
take 1.6 Go and offer limited software like Libre Office or Thunderbird, 
Emmabuntüs takes 3.3 Go and comes with more than 60 software for all 
usage, most of them being free and a few of them being non-free but 
ready to install like Adobe Flash for Firefox, Skype or TeamViewer 14 
(Jitsi is the recommended free solution). The menus are very long and 
ressemble a bazar in a colored environment.


To ease the configuration, the security has been relaxed and adding the 
sid repository to the sources.list file does not generate any complain, 
as did the pure Debian distribution. I was then able to access and 
download the full Texlive 2020. Due to the short period between the 
releases of Texlive and DE4, no package needs update or removal. This is 
a much better situation than the one with Buster 10.3 (see above). The 
full Texlive 2020 is 3.3 Go when compressed during the transfer and 6.2 
Go after decompression on the disk. The download from the Debian 
repository is also much faster than from the CTAN repository: 15 minutes 
against 40' with my ADSL line. I completed the installation with 
Texworks, TexStudio and Texmaker, then commented the sid line in the 
sources.list file to revert to the standard Bullseye repositories.


I then follow Johannes Ranke's instructions to install the R binaries:
https://cloud.r-project.org/bin/linux/debian/
Johannes, you should add in the instructions the following line for your 
new key:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 

Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Dirk Eddelbuettel]

On 28 April 2020 at 09:55, Michael Rutter wrote:
| When I have tested all the releases to ensure they all work, I will 
| announce it on this list-serv and on twitter.  Hopefully, I will have 
| this finished by the end of the day.

Big big BIG thank you from all of us for all this!

Dirk

-- 
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Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Michael Rutter]

On 4/28/20 7:49 AM, Dirk Eddelbuettel wrote:


On 28 April 2020 at 13:31, Thierry Onkelinx wrote:
| Could there be a typo on
| https://cloud.r-project.org/bin/linux/ubuntu/README.html? The installation
| entries mention cran35 for R 4.0. Should that be cran40?

That's a question for Michael who authors this :)  Maybe you can follow up
with him?  Possibly send him a patch with suggested edits?

Dirk



Responses to many things in this thread:

- Until I fully test the CRAN site, I strongly suggest using the PPAs 
that feed the CRAN site.


https://launchpad.net/~marutter/+archive/ubuntu/rrutter3.5

or

https://launchpad.net/~marutter/+archive/ubuntu/rrutter4.0

I prefer to use the PPAs personally, as one apt-add-repository command 
adds the repository and the gpg key with no chance of typos.  Easy to 
remove,  as well.


- For Xenial (16.04), I failed to build r-cran-nnet, which is why 
r-recommended won't install.  It is trying to use r-cran-nnet built 
against R 3.6, which is why it fails.  That has been fixed, and should 
be available after the next sync.


- I have updated the README, thanks for correction.  Again, change 
should appear on the next sync.


- The process of building the repository on CRAN has a lot of moving 
parts, mostly of my own doing.  When a new major version is released, it 
takes some time to create the repository and test it.  Part of the issue 
that the repository is synced twice a day, so it takes time for changes 
to propagate and to test it.  Different mirrors will have different 
contents, so it may work on cran.r-project.org but not on 
cloud.r-project.org for a couple of hours.


I try not to break things, but sometimes a small bug creeps in.  My 
apologizes for that.


When I have tested all the releases to ensure they all work, I will 
announce it on this list-serv and on twitter.  Hopefully, I will have 
this finished by the end of the day.


Michael

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Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Greg Siemon]

Hi Dirk,

Thankyou for letting me know.  I'm up and running now.

Greg


On Tue, 28 Apr 2020 at 21:06, Dirk Eddelbuettel  wrote:

>
> Greg,
>
> On 28 April 2020 at 13:19, Greg Siemon wrote:
> | Thanks for the suggested workarounds. This was just a VM I had spun up
> so I
> | could test R4.0.0. I'm happy to wait for Michael to fix it when he has
> time.
>
> It is already there now:
>
> https://cloud.r-project.org/bin/linux/ubuntu/bionic-cran40/r-recommended_4.0.0-1.1804.0_all.deb
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Dirk Eddelbuettel]

On 28 April 2020 at 13:31, Thierry Onkelinx wrote:
| Could there be a typo on
| https://cloud.r-project.org/bin/linux/ubuntu/README.html? The installation
| entries mention cran35 for R 4.0. Should that be cran40?

That's a question for Michael who authors this :)  Maybe you can follow up
with him?  Possibly send him a patch with suggested edits?

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Thierry Onkelinx]

Hi Dirk,

Could there be a typo on
https://cloud.r-project.org/bin/linux/ubuntu/README.html? The installation
entries mention cran35 for R 4.0. Should that be cran40?

Best regards,

Thierry


ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op di 28 apr. 2020 om 13:07 schreef Dirk Eddelbuettel :

>
> Greg,
>
> On 28 April 2020 at 13:19, Greg Siemon wrote:
> | Thanks for the suggested workarounds. This was just a VM I had spun up
> so I
> | could test R4.0.0. I'm happy to wait for Michael to fix it when he has
> time.
>
> It is already there now:
>
> https://cloud.r-project.org/bin/linux/ubuntu/bionic-cran40/r-recommended_4.0.0-1.1804.0_all.deb
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
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Re: [R-sig-Debian] CRAN R 4.0.0 for Ubuntu repos missing r-recommend dependency

[Dirk Eddelbuettel]

Greg,

On 28 April 2020 at 13:19, Greg Siemon wrote:
| Thanks for the suggested workarounds. This was just a VM I had spun up so I
| could test R4.0.0. I'm happy to wait for Michael to fix it when he has time.

It is already there now:
https://cloud.r-project.org/bin/linux/ubuntu/bionic-cran40/r-recommended_4.0.0-1.1804.0_all.deb
 

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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