Re: [R-sig-Debian] signing key of repo expired -- tangential question

[J C Nash]

I've seen several issues like this with "private" repositories or
sections thereof. Is there a reasonable way to set things up so keys
or access is shared across several people or held in an organizational
escrow? I think there is general good will on the part of most people
contributing, but things happen in life, and the collective can be
inconvenienced.

Best,

JN


On 2021-11-16 8:28 a.m., Johannes Ranke wrote:

Hi all,

sorry to all users of the CRAN Debian backports for the inconvenience caused
by the expiration of my signing key.

I have created a new key and uploaded it to keyserver.ubuntu.com, and signed
the buster40 and bullseye40 repositories with it. The repos signed with the
new key will be available to all users of the CRAN Debian archive as soon as
the synchronisation has taken place.

Kind regards,

Johannes

P.S.: Unfortunately I could not change the key expiration of the old key, as I
have lost the passphrase of the corresponding master key. For the same reason,
the new key is not signed with the old one.

Am Dienstag, 16. November 2021, 14:18:06 CET schrieb Dirk Eddelbuettel:

On 16 November 2021 at 12:08, bodo riediger-klaus wrote:
| Hello,
|
| i get a key-expired message when i try to update my repository
|
| root@merlot:/etc/apt/sources.list.d# cat rbase-stable.list
| deb http://ftp.gwdg.de/pub/misc/cran/bin/linux/debian buster-cran40/
|
|
| W: GPG-Fehler: http://ftp.gwdg.de/pub/misc/cran/bin/linux/debian
| buster-cran40/ InRelease: Die folgenden Signaturen waren ungültig:
| EXPKEYSIG FCAE2A0E115C3D8A Johannes Ranke (Wissenschaftlicher Berater)
| 

As it is the personal key of Johannes, only Johannes (CC'ed) can fix it.
It is my understanding that he has been contacted, but as we had not said so
on the list it is good to have it here too.

Dirk

| As you can see on
|
| https://keyserver.ubuntu.com/pks/lookup?search=0xE19F5F87128899B192B1A2C2A
| D5F960A256A04AF=on=index
|
| there are two Expired Sub-Keys:
|
| sub rsa3072/5bc121cfdc61bdae03062260af83ce117fbb4c22
| 2016-11-15T20:12:04Z
| sig sbind ad5f960a256a04af 2016-11-15T20:12:04Z 
| 2021-11-14T18:17:46Z []
|
| sub rsa3072/ad7b5162ba456be3526f8d92fcae2a0e115c3d8a
| 2016-11-15T19:58:24Z
| sig sbind ad5f960a256a04af 2016-11-15T19:58:24Z 
| 2021-11-14T18:17:46Z []
|
|
| greetings, bodo
|
| --
| R.-Bodo Riediger-Klaus IT-Dienst FB MI Freie Universität Berlin
| bodo.riediger-kl...@fu-berlin.de Takustr.9 R.038 Fon: 030 838 75175
|
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Re: [R-sig-Debian] Bootable USB for R / was 32 bit 64 bit question, ELFCLASS32 error

[J C Nash]

A message from Harvey Friedman put an idea in my mind.

Linux-Ottawa has had a rather back-burner project to build a "club" distro.
Based on Antix (I think 17.??) we built a small test iso, since Antix has
a neat tool to convert running distro to an iso either for backup or
distribution.

In Virtualbox I added R to this using the debian repo for that version of
Antix -- unfortunately R 3.3.3, so mightily out of date. Then built the
iso. And then set it as the "cd" and booted it on Virtualbox and checked
R would run.

This took a half hour or so, though only about 5 minutes of my time. So there's
a pathway to build an R live-USB fairly painlessly. I suspect the largest part
of the effort will be to get current R (i.e., do the Secure Apt etc. to get
appropriate repository links) if that is needed. I'm sure fancier stuff can
be done, like adding RStudio and lots of packages, etc.

Best, John Nash


On 2021-02-01 9:53 a.m., profjohn wrote:
> On 2021-02-01 9:32 a.m., Dirk Eddelbuettel wrote:
>>
>>
>> Wow. Blast from the past.
>>
>> As what may be your real question: where do I in 2021 get a current bootable
>> usb with R: no idea, sorry.
> 
> I've remastered a few bootable usb iso's over the past 15 years. Not
> trivial, but if there is interest in a "bootable R" I'd be willing to
> collaborate, but don't want to work alone, so get in touch off-list.
> 
> Partly off topic: 32 bit also still of curiosity interest as I've still
> got a working Asus EEE 901 netbook (2008). Has 2GB RAM (I couldn't
> resist upgrading) and about 20 GB of flash disk. Currently run it in
> Bunsenlabs linux (I think I've got the Helium distro on it).
> 
> JN
> 
> 
>>
>> Another related answer is that 32 and 64 bit _can_ coexist (as they do on
>> other OSs) but that never really took off in common use. So there may still
>> be way to use what you have but you may need to consult the specific
>> documentation.
>>
>> Dirk
>>

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[R-sig-Debian] Xenial repository for R 4.0.0

[J C Nash]

Over a week ago (on r-help, my bad!) I raised a question of why the
ubuntu install instructions

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

instruct users with a xenial-based system to use

deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/

Looking at https://cloud.r-project.org/bin/linux/ubuntu/
there is no xenial-cran40 directory. However,
https://cran.r-project.org/bin/linux/ubuntu/
does have this directory, and I managed to update a machine
still running Linux Mint 18.3 by putting in
deb https://cran.r-project.org/bin/linux/ubuntu xenial-cran40/

I suspect novice users might not have found this work-around, and
it was only by chance I found it.

My query: Is it intended that xenial support will not be available
for R 4.0? Or is this this just an oversight? Or some quirk that affects
just my environment? I've tried to ensure caches are updated.

Side-bar: I would update the example machine, but it runs some software needed
for another use-case that is not working at all on more modern systems.
Where possible, I try to keep up to date, and am migrating the use-case over
time to a different software environment.

Best, JN

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[R-sig-Debian] Corrected msg about Linux Mint 19.1 install

[J C Nash]

Apologies for some errors inserted by overly-helpful input filters on 
Thunderbird.

Here's the corrected version.

Just in case others hit the same glitch. It's not directly an R issue, but if 
folk can't get
an install to work, they are not going to use R.

While I've always had a straightforward experience before, this install gave 
some troubles.

I added the repository
   deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/

When I "saved" in Software Sources to add the additional repository, I got a 
malformed repository error.
So I took out the "deb" bit of the line, and it was accepted.

I added the key for Michael Rutter and checked it is not the second key as per
http://rubuntu.netlify.com/post/changes-to-cran-ubuntu-webpage-regarding-apt-secure-key/

Then I got
  "The repository 'https://cloud.r-project.org/bin/linux/ubuntu bionic Release' 
does not have a Release file."

Note no "-cran35". Turns out that Software Sources added a "bionic" so the 
repository line read
  deb https://cloud.r-project.org/bin/linux/ubuntu bionic bionic-cran35/

Took out the bionic and things worked fine.

JN

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[R-sig-Debian] Linux Mint Tessa 19.1 R install glitch

[J C Nash]

Just in case others hit the same glitch. It's not directly an R issue, but if 
folk can't get
an install to work, they are not going to use R.

While I've always had a straightforward experience before, this install gave 
some troubles.

I added the repository
   https://deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/

When I "saved" in Software Sources to add the additional repository, I got a 
malformed repository error.
So I took out the "deb" bit of the line, and it was accepted.

I added the key for Michael Rutter and checked it is not the second key as per
http://rubuntu.netlify.com/post/changes-to-cran-ubuntu-webpage-regarding-apt-secure-key/

Then I got
  "The repository 'https://cloud.r-project.org/bin/linux/ubuntu bionic Release' 
does not have a Release file."

Note no "-cran35". Turns out that Software Sources added a "bionic" so the 
repository line read
  deb https://deb https://cloud.r-project.org/bin/linux/ubuntu bionic 
bionic-cran35/

Took out the bionic and things worked fine.

JN

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Re: [R-sig-Debian] rJava Broken on Linux + R 3.4

[J C Nash]

For those going to UseR! in Brussels, maybe a short meeting over coffee
to make some notes about the issues. I know I've had troubles before with
rJava over the years, and I won't pretend to be much more than a recipe
follower. However, if it's possible to have a few notes on "where to
look" for diagnostics and fixes, or even explaining what is going wrong,
I'll be happy to write them up and post somewhere. I've been doing such
short how-to items on our oclug.on.ca wiki for other software, and feedback
has been positive.

Best, JN

On 2017-06-26 08:40 AM, Lorenzo Isella wrote:

Hi Dirk,
It was unclear to me to which extent it is a
kernel/security patch vs (r)Java issue.

In any case, this is really problematic for me as it prevents me de
facto from running some key R packages for my daily work.
I'll post again if I see some solution (other than downgrading the
kernel) somewhere.
Meanwhile, any suggestions for a fix is welcome.
Cheers

Lorenzo


On Mon, Jun 26, 2017 at 06:19:11AM -0500, Dirk Eddelbuettel wrote:


On 26 June 2017 at 10:43, Lorenzo Isella wrote:
| Dear All,
| I think there is something wrong with rJava on any Debian based
| distribution.

It is a Java issue related to a security fix many (most? all?) distros
applied.

| I may be wrong, but I experiencing exactly the problems mentioned at
|
| https://github.com/amattioc/SDMX/issues/130
|
| and at
|
| https://github.com/s-u/rJava/issues/110
|
| A couple of packages (RJSDMX and xlsx) are now impossible to install
| on my debian stretch platform running R 3.4.
|
| It seems I am not the only one experiencing this and it may be due to
| some security patches just released.
| However, if I run on my machine
|
| > library(rJava)
| > .jinit()
|
| I get a segmentation fault, though I was able to install rJava, it
| does not seem to work properly.
| Does anyone have a fix for that?

Reading the links you providing it also becomes clear that this is not an
issue with rJava, or Debian -- it is Java, interacting with the kernel.

For now, I would suggest following those discussions.

Dirk

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


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Re: [R-sig-Debian] R installation problems on Linux Mint 18.1 via jessie-cran3

[J C Nash]

Is there a reason for jessie-cran3 rather than xenial? For Linux Mint 18 
(admittedly
not 18.1) I have

deb https://cloud.r-project.org/bin/linux/ubuntu xenial/

as one of the apt entries.

JN

On 2017-04-27 02:57 PM, Clive Nicholas wrote:

Okay folks, I give up and - frankly - I'm fed up! I thought I'd sorted all
this last week, but clearly not. I've tried using mirrors from here in the
UK, Ireland, France and the USA and whichever mirror I use, all I get is
this:

clive@climate ~ $ sudo apt-get update
Hit:1 http://ubuntu.mirrors.uk2.net/ubuntu xenial InRelease
Ign:2 http://dl.google.com/linux/chrome/deb stable InRelease

Ign:3 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages
serena InRelease
Ign:4 http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran3/
InRelease
Hit:5 http://ubuntu.mirrors.uk2.net/ubuntu xenial-updates InRelease

Hit:6 http://archive.canonical.com/ubuntu xenial InRelease

Hit:7 http://dl.google.com/linux/chrome/deb stable Release

Hit:8 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages
serena Release
Hit:9 http://ubuntu.mirrors.uk2.net/ubuntu xenial-backports InRelease

Hit:10 http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran3/ Release

Get:11 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Hit:14 https://repo.skype.com/deb stable InRelease
Fetched 102 kB in 2s (37.7 kB/s)
Reading package lists... Done
W: http://cran.ma.imperial.ac.uk/bin/linux/debian/jessie-cran3/Release.gpg:
Signature by key 6212B7B7931C4BB16280BA1306F90DE5381BA480 uses weak digest
algorithm (SHA1)

To fix this SHA1 problem, I followed this page
 *to the letter* and
implemented this in a file on my Linux machine called ~/.gnupg/gpg.conf
(apologies for the length, but included for completeness; the key detail is
contained right at the bottom):

*# Options for GnuPG*
*# Copyright 1998, 1999, 2000, 2001, 2002, 2003,*
*#   2010 Free Software Foundation, Inc.*
*# *
*# This file is free software; as a special exception the author gives*
*# unlimited permission to copy and/or distribute it, with or without*
*# modifications, as long as this notice is preserved.*
*# *
*# This file is distributed in the hope that it will be useful, but*
*# WITHOUT ANY WARRANTY, to the extent permitted by law; without even the*
*# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.*
*#*
*# Unless you specify which option file to use (with the command line*
*# option "--options filename"), GnuPG uses the file ~/.gnupg/gpg.conf*
*# by default.*
*#*
*# An options file can contain any long options which are available in*
*# GnuPG. If the first non white space character of a line is a '#',*
*# this line is ignored.  Empty lines are also ignored.*
*#*
*# See the man page for a list of options.*

*# Uncomment the following option to get rid of the copyright notice*

*#no-greeting*

*# If you have more than 1 secret key in your keyring, you may want to*
*# uncomment the following option and set your preferred keyid.*

*#default-key 621CC013*

*# If you do not pass a recipient to gpg, it will ask for one.  Using*
*# this option you can encrypt to a default key.  Key validation will*
*# not be done in this case.  The second form uses the default key as*
*# default recipient.*

*#default-recipient some-user-id*
*#default-recipient-self*

*# Use --encrypt-to to add the specified key as a recipient to all*
*# messages.  This is useful, for example, when sending mail through a*
*# mail client that does not automatically encrypt mail to your key.*
*# In the example, this option allows you to read your local copy of*
*# encrypted mail that you've sent to others.*

*#encrypt-to some-key-id*

*# By default GnuPG creates version 4 signatures for data files as*
*# specified by OpenPGP.  Some earlier (PGP 6, PGP 7) versions of PGP*
*# require the older version 3 signatures.  Setting this option forces*
*# GnuPG to create version 3 signatures.*

*#force-v3-sigs*

*# Because some mailers change lines starting with "From " to ">From "*
*# it is good to handle such lines in a special way when creating*
*# cleartext signatures; all other PGP versions do it this way too.*

*#no-escape-from-lines*

*# If you do not use the Latin-1 (ISO-8859-1) charset, you should tell*
*# GnuPG which is the native character set.  Please check the man page*
*# for supported character sets.  This character set is only used for*
*# metadata and not for the actual message which does not undergo any*
*# translation.  Note that future version of GnuPG will change to UTF-8*
*# as default character set.  In most cases this option is not required*
*# as GnuPG is able to figure out the correct charset at runtime.*

*#charset utf-8*

*# Group names may be defined like this:*
*#   group mynames = paige 0x12345678 joe patti*
*#*
*# Any time "mynames" is a recipient (-r or --recipient), it will be*
*# expanded to the names "paige", "joe", and "patti", and the 

Re: [R-sig-Debian] Cannot install R on Ubuntu 14.04 LTS

[Prof J C Nash (U30A)]

A possibly silly thought -- Did you sudo apt-get update after doing 
the sudo apt-add repository ... statement? In other installs (non-R) 
I've managed to shoot myself that way.


JN

On 15-06-13 04:17 PM, Austin Putz wrote:

Hello everyone,

I've spent the last 2 days trying to install base R on my Ubuntu 14.04 LTS
machine. I even just wiped my entire computer and reinstalled the operating
system thinking that was the problem (since some people have problems
updating R).

So far I've tried to follow this link exactly that has instructions:

http://mirror.las.iastate.edu/CRAN/

Since I just reinstalled Ubuntu I figured I would have no problems. I was
just wondering if anyone else has had this happen to them. I was getting an
error while doing sudo apt-get update that said:

public key not available iastate... NO_PUBKEY 51716619E084DAB9

So I followed that link above and installed the keys (as far as I know).

The current error while trying sudo apt-get install r-base (not installed
previously, fresh OS) is:


Sat Jun 13 : ~ $ sudo apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
  r-base : Depends: r-base-core (= 3.2.0-4precise0) but it is not going to
be installed
   Depends: r-recommended (= 3.2.0-4precise0) but it is not going to
be installed
   Recommends: r-base-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.



I've tried countless other things and I'm just frustrated now from 2 days
of trying something that should be fairly straightforward (so I
thought...). I have tried installing the Depends packages, but no dice. I
tried going to Ubuntu Software Center thinking it may do something
differnet but no help either. Can't install dependencies. I don't even know
what else I've tried. I'm out of ideas.

Any help or solution would be greatly appreciated.

Thanks in advance for any help,

Austin




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Re: [R-sig-Debian] r-cran-rgdal: dependency on libgdal1 unsatisfied in ubuntu 12.04?

[Prof J C Nash (U30A)]

I upgrade too, but with some trepidation. I was an unfortunate victim of 
a bad disk space estimator script in the upgrade software (now some 
years ago on an early Ubuntu). The Ubuntu folk were apologetic, but ...


An upgrade that hits the filesystem limit gives one a very 
unsatisfactory system.


John Nash
-- who seems to be the finder of such bugs.


On 14-09-27 04:31 PM, Matt Dowle wrote:

On 27/09/14 21:14, Dirk Eddelbuettel wrote:

On 27 September 2014 at 21:04, Matt Dowle wrote:
| On 27/09/14 20:30, Dirk Eddelbuettel wrote:
| The fear may be that a fresh install will be needed (a pain) as

But Matt, I never said or implied fresh install. My exact words,
from two
emails ago:

I would upgrade, which I do every six months.

Upgrade, not reinstall.

| might not work.  That's why I switched to a rolling release (LMDE) so

Rolling releases rock. Debian pretty much invented this with testing
which
is a rolling release receiving packages from the top (aka unstable) if
(approximatly) no new upload was made, no critical bugs appeared and
it is
not blocking another packages dependency graph.  So in essence always
ten
days fresh (as eg for my R builds).  That rocks, and it is getting more
recognition now.

| I'll never need to upgrade and reinstall and setup all the software I
| need and config again.  So they tell me.   I'll tell you if it's
true in
| a few years!   My /home is mounted on its own partition, so that's
not a
| pain (but is for users who don't know how to use gparted to do that),
| but even then I fear problems if I point a new release to my single
| /home and then need to roll back (the new release may have changed
files
| in ~).
| Do you do a fresh install every 6 months or do you upgrade your
existing?

For one reason or another the majority of my machines (at home and
work) are
actually running Ubuntu.

And I __always__ updated __all of them__ every six months __whenever a
new
release comes out__.  Some of these may now have had over ten
upgrades. No
issues.  I tend to do the auxiliary machines at home first, then my main
laptop, then the server and then the machines at work.

It. just. works.

And is the least amount of work as far as I can tell.

Dirk


Very interesting. Ok, yep, Matthieu really has no excuse for not
upgrading then.

Matt

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Re: [R-sig-Debian] Update R on a new Linux Mint Maya 13 + rJava and XLConnect

[Prof J C Nash (U30A)]

I use several versions of Mint and have found following the CRAN
instructions for Ubuntu (matching the chosen sources.list entry of my
Mint install to the corresponding Ubuntu version -- that is important)
works to get me the latest R.

John Nash


On 14-08-01 01:34 AM, Johannes Ranke wrote:
 Keith,
 
 As Linux Mint Maya 13 appears to be based on Ubuntu Precise, you may be 
 tempted to follow the corresponding Ubuntu README on CRAN. However, CRAN 
 maintainers do not officially support Mint, so I do not recommend this 
 approach 
 as I have no idea in what ways Linux Mint deviates from Ubuntu Precise.
 
 To be on the safe side, you could compile binaries for your platform from  
 suitable source packages in Debian format. There are some hints in the Debian 
 README on CRAN on how to do this.
 
 This takes a bit of effort, which is why we provide binaries for Debian 
 stable 
 and the most important Ubuntu releases on CRAN.
 
 Maybe somebody else knows more about Mint 13 and its compatibility with 
 Ubuntu 
 Precise?
 
 Kind regards,
 
 Johannes
 
 
 
 Am Donnerstag, 31. Juli 2014, 22:28:04 schrieb Keith S Weintraub:
 Folks,
 I was able to get R installed using:
apt-get install r-base-core


 R version 2.14.1 (2011-12-22)
 Copyright (C) 2011 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: i686-pc-linux-gnu (32-bit)


 * What is the best way to upgrade to the latest version of R.
 * What is the best way to install rJava and XLConnect.

 Thanks for your time,
 Best,
 KW

 PS. I know some of you may have seen these questions before from me on
 r-help. I was told this forum might be a better place to peddle my
 problems.

 --

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