R SIG Debian - Jan 2019 - Still hitting odd problems trying to install R 3.5.2 on Debian amd64 machine

My Emails a week or so back were about installing Rstudio and the R shiny server
on Debian. I was using an old Toshiba laptop as a sandbox for that and it would
only install i386 (same for Ubuntu). Using the information at
https://cran.r-project.org/bin/linux/debian/ I did get to the point where I had
R 3.5.2, Rstudio and the server on there (with some help from Dirk that is in
the list archives).  However, the server wouldn't start and I knew that the
hardware I will need to run it from is amd64 so I stopped there and managed to
find another old laptop (an advent) that would install amd64 Debian.

So I downloaded a new clean iso of stretch amd64 and it installed OK but my
first time through I seemed to hit a total mess of refusals to load from
repositories because of missing release files and/or missing png keys.  I lost
track of where I'd gone wrong with /etc/apt/choices.list, wiped the
installation and started again! I installed a few packages through synaptic: no
warnings, fine, I added contrib through synaptic settings: no problems.  I
installed emacs, no problems!

But now I'm stuck and I am hoping to sort things with the help of the list
so here's where I am:

root at DebianAdvent:/etc/apt# apt-get update 
Hit:1 [ http://security.debian.org/debian-security |
http://security.debian.org/debian-security ] stretch/updates InRelease
Ign:2 [ http://mirror.mythic-beasts.com/debian |
http://mirror.mythic-beasts.com/debian ] stretch InRelease
Hit:3 [ http://mirror.mythic-beasts.com/debian |
http://mirror.mythic-beasts.com/debian ] stretch-updates InRelease
Hit:4 [ http://mirror.mythic-beasts.com/debian |
http://mirror.mythic-beasts.com/debian ] stretch Release
Get:5 [ http://cran.ma.imperial.ac.uk/bin/linux/debian |
http://cran.ma.imperial.ac.uk/bin/linux/debian ] jessie-cran35/ InRelease [4,369
B]
Ign:5 [ http://cran.ma.imperial.ac.uk/bin/linux/debian |
http://cran.ma.imperial.ac.uk/bin/linux/debian ] jessie-cran35/ InRelease
Get:7 [ http://cran.ma.imperial.ac.uk/bin/linux/debian |
http://cran.ma.imperial.ac.uk/bin/linux/debian ] jessie-cran35/ Packages [17.8
kB]
Fetched 22.2 kB in 0s (27.5 kB/s) 
Reading package lists... Done 
W: GPG error: [ http://cran.ma.imperial.ac.uk/bin/linux/debian |
http://cran.ma.imperial.ac.uk/bin/linux/debian ] jessie-cran35/ InRelease: The
following signatures couldn't be verified because the public key is not
available: NO_PUBKEY FCAE2A0E115C3D8A
W: The repository ' [ http://cran.ma.imperial.ac.uk/bin/linux/debian |
http://cran.ma.imperial.ac.uk/bin/linux/debian ] jessie-cran35/ InRelease'
is not signed.
N: Data from such a repository can't be authenticated and is therefore
potentially dangerous to use.
N: See apt-secure(8) manpage for repository creation and user configuration
details.

OK, that fits the advice about secure apt in Johannes's page so:

root at DebianAdvent:/etc/apt# apt-key adv --keyserver keys.gnupg.net --recv-key
'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
Executing: /tmp/apt-key-gpghome.qC3CUffAEm/gpg.1.sh --keyserver keys.gnupg.net
--recv-key E19F5F87128899B192B1A2C2AD5F960A256A04AF
gpg: failed to start the dirmngr '/usr/bin/dirmngr': No such file or
directory
gpg: connecting dirmngr at '/tmp/apt-key-gpghome.qC3CUffAEm/S.dirmngr'
failed: No such file or directory
gpg: keyserver receive failed: No dirmngr 

Might be worth adding a warning about this to that page but I think I can manage
this (!) and I installed it using synaptic after this:

root at DebianAdvent:/etc/apt# apt-get install drmngr 
Reading package lists... Done 
Building dependency tree 
Reading state information... Done 
E: Unable to locate package drmngr 

Synaptic installed it fine.  So now I can do this:

root at DebianAdvent:/etc/apt# apt-key adv --keyserver keys.gnupg.net --recv-key
'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
Executing: /tmp/apt-key-gpghome.qnQrK8dgus/gpg.1.sh --keyserver keys.gnupg.net
--recv-key E19F5F87128899B192B1A2C2AD5F960A256A04AF
key AD5F960A256A04AF: 
4 signatures not checked due to missing keys 
gpg: key AD5F960A256A04AF: public key "Johannes Ranke (Wissenschaftlicher
Berater) < johannes.ranke at jrwb.de >" imported
gpg: Total number processed: 1 
gpg: imported: 1 
root at DebianAdvent:/etc/apt# 

So now I try to install R base using synaptic and I get a message like
"Warning: you are about to install software that cannot be ..."
(paraphrasing)

So I try this:

root at DebianAdvent:/etc/apt# 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 (>= 3.5.2-1~jessiecran.0) but it is not going
to be installed
Depends: r-recommended (= 3.5.2-1~jessiecran.0) 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. 
root at DebianAdvent:/etc/apt# apt-get install r-base-core 
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-core : Depends: libicu52 (>= 52~m1-1~) but it is not installable 
Depends: libpng12-0 (>= 1.2.13-4) but it is not installable 
Depends: libreadline6 (>= 6.0) but it is not installable 
Recommends: r-recommended but it is not going to be installed 
Recommends: r-base-dev but it is not going to be installed 
Recommends: r-doc-html but it is not going to be installed 
E: Unable to correct problems, you have held broken packages. 
root at DebianAdvent:/etc/apt# 

r-base-core: 
Depends: libicu52 (>=52~m1-1~) but it is not installable 
Depends: libpng12-0 (>=1.2.13-4) but it is not installable 
Depends: libreadline6 (>=6.0) but it is not installable 
Recommends: r-recommended but it is not going to be installed 
Recommends: r-base-dev but it is not going to be installed

At this point, before trying anything more under my own, perhaps inept, steam, I
decided to stop and ask the list if someone can see from those messages what
I'm doing wrong.

Here is my current sources.list:

chris at DebianAdvent:~$ cd /etc/apt
chris at DebianAdvent:/etc/apt$ cat sources.list


# deb cdrom:[Debian GNU/Linux 9.6.0 _Stretch_ - Official amd64 NETINST
20181110-11:34]/ stretch main

# deb cdrom:[Debian GNU/Linux 9.6.0 _Stretch_ - Official amd64 NETINST
20181110-11:34]/ stretch main

deb http://mirror.mythic-beasts.com/debian/ stretch main contrib non-free
deb-src http://mirror.mythic-beasts.com/debian/ stretch contrib main non-free

deb http://security.debian.org/debian-security/ stretch/updates main
deb-src http://security.debian.org/debian-security/ stretch/updates main

# stretch-updates, previously known as 'volatile'
deb http://mirror.mythic-beasts.com/debian/ stretch-updates main
deb-src http://mirror.mythic-beasts.com/debian/ stretch-updates main

### that was where I'd gotten to with synaptic
### this is for CRAN for Debian


deb http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/
deb-src http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/

chris at DebianAdvent:/etc/apt$

TIA,

Chris

-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Visiting Professor, University of Sheffield <chris.evans at
sheffield.ac.uk>
I do some consultation work for the University of Roehampton <chris.evans at
roehampton.ac.uk> and other places but this <chris at psyctc.org>
remains my main Email address.
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book
to talk, I am trying to keep that to Thursdays and my diary is now available at:
https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/
Beware: French time, generally an hour ahead of UK.  That page will also take
you to my blog which started with earlier joys in France and Spain!

Hi Chris,

Am Sonntag, 20. Januar 2019, 19:30:16 CET schrieb Chris Evans:
...
> root at DebianAdvent:/etc/apt# apt-get install drmngr
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Unable to locate package drmngr
That was just a typo.
 
...
> deb http://mirror.mythic-beasts.com/debian/ stretch main contrib non-free
> deb-src http://mirror.mythic-beasts.com/debian/ stretch contrib main
> non-free
Obviously you are running Debian stretch.

...
> deb http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/
> deb-src http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/
jessie-cran35 is for Debian jessie, please use stretch-cran35 for stretch.

Good luck!

Johannes

Oh dear.  Both stupid errors.  I had noticed the typo and meant to cut that bit.
I was suggesting that it was worth adding a line to the
https://cran.r-project.org/bin/linux/debian/#debian-stretch-stable page in that
secure apt bit warning people that they'll need to install dirmngr.

I've now got a question that probably should be a new post but many thanks,
both for the swift answer and all your work on the Debian repository.

Chris

----- Original Message -----
> From: "Johannes Ranke" <johannes.ranke at jrwb.de>
> To: "r-sig-debian" <r-sig-debian at r-project.org>,
"Chris Evans" <chrishold at psyctc.org>
> Sent: Monday, 21 January, 2019 02:12:57
> Subject: Re: [R-sig-Debian] Still hitting odd problems trying to install R
3.5.2 on Debian amd64 machine
> Hi Chris,
> 
> Am Sonntag, 20. Januar 2019, 19:30:16 CET schrieb Chris Evans:
> ...
> 
>> root at DebianAdvent:/etc/apt# apt-get install drmngr
>> Reading package lists... Done
>> Building dependency tree
>> Reading state information... Done
>> E: Unable to locate package drmngr
> 
> That was just a typo.
> 
> ...
> 
>> deb http://mirror.mythic-beasts.com/debian/ stretch main contrib
non-free
>> deb-src http://mirror.mythic-beasts.com/debian/ stretch contrib main
>> non-free
> 
> Obviously you are running Debian stretch.
> 
> ...
> 
>> deb http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/
>> deb-src http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/
> 
> jessie-cran35 is for Debian jessie, please use stretch-cran35 for stretch.
> 
> Good luck!
> 
> Johannes
-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Visiting Professor, University of Sheffield <chris.evans at
sheffield.ac.uk>
I do some consultation work for the University of Roehampton <chris.evans at
roehampton.ac.uk> and other places but this <chris at psyctc.org>
remains my main Email address.
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book
to talk, I am trying to keep that to Thursdays and my diary is now available at:
https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/
Beware: French time, generally an hour ahead of UK.  That page will also take
you to my blog which started with earlier joys in France and Spain!