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R configurations for Docker
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bspm behaviour for installing R-package {tmap} #422

Closed Maddocent closed 3 years ago

Maddocent commented 3 years ago

Dear collegue,

Thank you on this amazing work!

Working with /https://github.com/rocker-org/rocker/tree/master/r-bspm/bionic Dockerfile, I build a container by cloning this repo, copying the ppa file and than ran: docker build --tag bspm_testing .

Attaching the shell of the running container provides me with a Bash terminal loged in as root. I then run sudo R to get into the R kernel:

I see bpsm is actively tracing install.packages() function when it tells me:

...[Loading required package: utils Tracing function "install.packages" in package "utils"]...

Than, to test the functionality of bspm, I tried to install the package {tmap} which I know has a number of Linux system dependencies that it needs to succesfully install.

First I ran: install.packages("tmap") which failed on a number of system dependencies not being installed and consequently a number of R-packages failling to install. This was unexpected to me.

Then I looked at the 'Imports' field in the dev repo of {tmap), the packages needed by tmap are:

tmaptools (>= 3.1), sf (>= 0.9-3), stars (>= 0.4-2), units (>= 0.6-1), grid, RColorBrewer, viridisLite, classInt (>= 0.4-3), htmltools, htmlwidgets, widgetframe, leaflet (>= 2.0.2), leafsync, leafem (>= 0.1), stats, rlang, utils

The ERROR from installing tmap with install.packages("tmap") tells me {sf}, {stars} and {XML} failed to install successfully. after running bspm::enable() I ran, in order: install.packages("XML") install.packages("sf") install.packages("stars")

These three installed succesfully. Subsequent installation of {tmap} with install.packages("tmap") resulted in successfull installation of the {tmap} package, beacause obviously all sytem requirements were already met.

Is there a work-around to this situation?

Do I understand correctly that having system dependencies listed in the SystemRequirements field in {tmap}, like mentioned in e.g. {sf} like below, would solve this issue?

SystemRequirements: | C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0)

Just experimenting with bpsm to wrap my head around the intended use-cae, I am also exploring this to be able to use it in deploying RStudio Server workspaces for users that intend to install additional R-packages and if all works out, do not need to worry about system dependencies.

Hope to hear if a solution is available, or if it is something I did wrong here.

Kind regards, Marc

eddelbuettel commented 3 years ago

(It is written 'bspm', not 'bpsm' -- 'bridge to system package manageer'. I fixed your title:)

It can install a binary where a binary is available. When I do apt update followed by apt-cache search r-cran-tmap I see it being available (on the 20.04 container I usually try) and it installs just fine. For 18.04 it seems to run into an Ubuntu package dependency issue. That can happen with complicated packages, Your best bet here would be to document it and to contact the maintainer, Michael Rutter, maybe via the r-sig-debian list he reads.

For the record, the successful 20.04 run log (apologies for the double lines from commands and weird symbols, copy and paste from Emacs buffer to more easily get all output lines):

edd@rob:~$ docker run --rm -ti rocker/r-bspm:20.04
]0;root@86670eec15ef: /root@86670eec15ef:/# apt update -qq  # important to update apt index
apt update -qq
24 packages can be upgraded. Run 'apt list --upgradable' to see them.
]0;root@86670eec15ef: /root@86670eec15ef:/# install.r tmap  # wrapper to install.packages
install.r tmap  # wrapper to install.packages
(loaded the methods namespace)
Loading required package: utils
Tracing function "install.packages" in package "utils"
Install system packages as root...
Reading package lists... Done
Building dependency tree        
Reading state information... Done
Hit http://archive.ubuntu.com/ubuntu focal InRelease
Hit http://security.ubuntu.com/ubuntu focal-security InRelease
Hit http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease
Hit http://archive.ubuntu.com/ubuntu focal-updates InRelease
Hit http://archive.ubuntu.com/ubuntu focal-backports InRelease
Hit http://ppa.launchpad.net/edd/r-4.0/ubuntu focal InRelease
Hit http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease
Fetched 0 B in 0s (0 B/s)
Reading package lists... Done    
Building dependency tree          
Reading state information... Done
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]0;root@86670eec15ef: /root@86670eec15ef:/# R
R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: utils
Tracing function "install.packages" in package "utils"
> library(tmap)
library(tmap)
> q()
q()
Save workspace image? [y/n/c]: n
n
]0;root@86670eec15ef: /root@86670eec15ef:/# exit
edd@rob:~$

Our containers can only use what it is in the repos, so that 18.04 failed for you here is unfortunate but outside our scope. So I am closing this report.

Thanks for your early interest in BSPM! I plan to promote it more (and just did some work on Travis CI with it...).

Maddocent commented 3 years ago

Dear Dr. Eddelbuettel,

Thank you for your comment and solution. This will solve my issue. Thank you! Kind regards, Marc

eddelbuettel commented 3 years ago

Marc,

Sounds good -- BSPM can definitely help you here on 20.04 (and it is in fact a great example, I'll check if this works out of the box with RSPM and it may not given the complexity. I'll also CC Michael now (hi @marutter) which I should have done earlier.

Michael: It's not fully logged but if you use a 18.04 container with the PPAs as my rocker/r-bspm:18.04 then install,packages("tmap") launches and dispatches to apt as one would hope but it ends in some inter-package dependency errors on 18.04 oas Marc found and documented. Any chance you can take a peek and maybe to partial rebuilds there?

BSPM on top of the PPAs is like magic. I should have something more to say "soon" for the Travis CI or GitHub Actions use case.

Maddocent commented 3 years ago

Dear Erik, Michael, Thank's for your efforts to document this and for the solutions provided.

Kind regards, Marc

Outlook voor Android downloadenhttps://aka.ms/ghei36

From: Dirk Eddelbuettel notifications@github.com Sent: Wednesday, September 16, 2020 7:30:19 PM To: rocker-org/rocker rocker@noreply.github.com Cc: Marc Teunis marc.teunis@hu.nl; Author author@noreply.github.com Subject: Re: [rocker-org/rocker] bspm behaviour for installing R-package {tmap} (#422)

Marc,

Sounds good -- BSPM can definitely help you here on 20.04 (and it is in fact a great example, I'll check if this works out of the box with RSPM and it may not given the complexity. I'll also CC Michael now (hi @marutterhttps://github.com/marutter) which I should have done earlier.

Michael: It's not fully logged but if you use a 18.04 container with the PPAs as my rocker/r-bspm:18.04 then install,packages("tmap") launches and dispatches to apt as one would hope but it ends in some inter-package dependency errors on 18.04 oas Marc found and documented. Any chance you can take a peek and maybe to partial rebuilds there?

BSPM on top of the PPAs is like magic. I should have something more to say "soon" for the Travis CI or GitHub Actions use case.

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