[R-sig-Debian] Still hitting odd problems trying to install R 3.5.2 on Debian amd64 machine

[Chris Evans]

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 using 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 using 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 using 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 using 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 using jrwb.de >" imported 
gpg: Total number processed: 1 
gpg: imported: 1 
root using 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 using 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 using 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 using 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 using DebianAdvent:~$ cd /etc/apt
chris using 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 using DebianAdvent:/etc/apt$

TIA,

Chris

-- 
Chris Evans <chris using psyctc.org> Skype: chris-psyctc
Visiting Professor, University of Sheffield <chris.evans using sheffield.ac.uk>
I do some consultation work for the University of Roehampton <chris.evans using roehampton.ac.uk> and other places but this <chris using 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!