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cran4linux / bspm

R Bridge to System Package Manager
https://cran4linux.github.io/bspm
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Some Packages Don't Indicate Failure #22

Closed thomascjohnson closed 3 years ago

thomascjohnson commented 3 years ago

Hi! This is a fantastic piece of work. I noticed that if I run the following, however, I don't get any indication that the installation wasn't successful. I'd be happy to contribute to fixing it, but I'd like to get your input on the problem. Here's the series of commands (maybe I'm doing something wrong?):

docker run --rm -it rocker/r-ver bash
apt update
apt install -y python3-apt
R
install.packages("bspm")
bspm::enable()
install.packages("rgdal")
library(rgdal)

In the end I get this output:

> bspm::enable()
Tracing function "install.packages" in package "utils"
> install.packages("rgdal")
Hit http://archive.ubuntu.com/ubuntu focal InRelease                           
Hit http://security.ubuntu.com/ubuntu focal-security InRelease                 
Hit http://archive.ubuntu.com/ubuntu focal-updates InRelease                   
Hit http://archive.ubuntu.com/ubuntu focal-backports InRelease                 
Fetched 0 B in 0s (0 B/s)                                                      
Install system packages as root...
Reading package lists... Done
Building dependency tree        
Reading state information... Done
Reading package lists... Done    
Building dependency tree          
Reading state information... Done
Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9build1 [2737 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 libgdbm6 amd64 1.18.1-5 [27.4 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libgdbm-compat4 amd64 1.18.1-5 [6244 B]
...
Setting up liblwp-protocol-https-perl (6.07-2ubuntu2) ...
Setting up odbcinst (2.3.6-0.1build1) ...
Setting up libwww-perl (6.43-1) ...
Setting up libgdal26 (3.0.4+dfsg-1build3) ...
Setting up r-cran-rgdal (1.4-8-1build2) ...
Setting up libxml-parser-perl (2.46-1) ...
Setting up libxml-twig-perl (1:3.50-2) ...
Setting up libnet-dbus-perl (1.2.0-1) ...
Processing triggers for fontconfig (2.13.1-2ubuntu3) ...
Processing triggers for mime-support (3.64ubuntu1) ...
Processing triggers for libc-bin (2.31-0ubuntu9) ...
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
>

Thoughts?

thomascjohnson commented 3 years ago

Looks like it sets everything up but doesn't actually finish the job and install rgdal:

> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
> bspm::disable()
Untracing function "install.packages" in package "utils"
> install.packages("rgdal")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependency ‘sp’

trying URL 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/sp_1.4-4.tar.gz'
Content type 'binary/octet-stream' length 1948772 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/rgdal_1.5-17.tar.gz'
Content type 'binary/octet-stream' length 5046787 bytes (4.8 MB)
==================================================
downloaded 4.8 MB

* installing *binary* package ‘sp’ ...
* DONE (sp)
* installing *binary* package ‘rgdal’ ...
* DONE (rgdal)

The downloaded source packages are in
    ‘/tmp/RtmpP51ZLi/downloaded_packages’
>
Enchufa2 commented 3 years ago

The installation is successful, but the installation path is not in the libpaths in that container, because it's meant for other purposes. In short: you should use other images. You have one specifically built for bspm: rocker/r-bspm. cc/ @eddelbuettel

eddelbuettel commented 3 years ago

@Enchufa2 is spot on. The rocker/r-ver containers are very nice but explicitly built for RSPM as a successor to MRAN. That also means no system dependencies -- a choice made by Carl and Noam.

You appear to prefer BSPM. So you can just start from rocker/r-bspm which comes in three tags 18.04, 20.04 and testing. Chances are that install rgdal may work (but as we all know rgdal is tricky, and there are extra spatial PPAs that this is NOT wired up for. If memory serves I used rgdal as a spot-check and it passed on 20.04 but failed with 18.04 as the Rutter binary was not in line with other changes that happend in spatial land -- BSPM just passes your install request on so that particular issue is one for the Rutter PPA).

eddelbuettel commented 3 years ago

And yes, rocker/r-bspm:20.04 works as promised. Ignore the weird PS1 prompt as I was running this in shell inside emacs for easier copying:

edd@rob:~$ docker run --rm -ti rocker/r-bspm:20.04 bash
]0;root@2e48a27df3d7: /root@2e48a27df3d7:/# install.r rgdal
install.r rgdal
(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
Get:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease [18.0 kB]                   
Get:2 http://security.ubuntu.com/ubuntu focal-security InRelease [107 kB]                              
Hit http://archive.ubuntu.com/ubuntu focal InRelease                                                   
Get:3 http://archive.ubuntu.com/ubuntu focal-updates InRelease [111 kB]                                
Get:4 http://ppa.launchpad.net/edd/r-4.0/ubuntu focal InRelease [18.0 kB]                              
Get:5 http://archive.ubuntu.com/ubuntu focal-backports InRelease [98.3 kB]                             
Get:6 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [626 kB]                
Get:7 http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease [17.5 kB]                    
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Get:18 http://ppa.launchpad.net/edd/r-4.0/ubuntu focal/main amd64 Packages [6808 B]                    
Get:19 http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal/main Sources [9708 B]                 
Get:20 http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal/main amd64 Packages [9208 B]          
Fetched 5746 kB in 0s (0 B/s)                                                                          
Reading package lists... Done    
Building dependency tree          
Reading state information... Done
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Get:3 http://archive.ubuntu.com/ubuntu focal/universe amd64 libaec0 amd64 1.0.4-1 [19.1 kB]            
Get:4 http://archive.ubuntu.com/ubuntu focal/universe amd64 libarpack2 amd64 3.7.0-3 [92.8 kB]         
Get:5 http://archive.ubuntu.com/ubuntu focal/universe amd64 libsuperlu5 amd64 5.2.1+dfsg1-4 [159 kB]   
Get:6 http://archive.ubuntu.com/ubuntu focal/universe amd64 libarmadillo9 amd64 1:9.800.4+dfsg-1build1 [93.2 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl3-gnutls amd64 7.68.0-1ubuntu2.2 [231 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal/universe amd64 libcfitsio8 amd64 3.470-3 [466 kB]         
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Get:15 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgeos-3.8.0 amd64 3.8.0-1build1 [535 kB]
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Get:17 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main amd64 r-cran-rcpparmadillo amd64 0.9.900.3.0-1cran1.2004.0 [1144 kB]
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Get:36 http://archive.ubuntu.com/ubuntu focal/universe amd64 libogdi4.1 amd64 4.1.0+ds-1build1 [198 kB]
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Get:43 http://archive.ubuntu.com/ubuntu focal/universe amd64 libqhull7 amd64 2015.2-4 [152 kB]         
Get:44 http://archive.ubuntu.com/ubuntu focal/universe amd64 libspatialite7 amd64 4.3.0a-6build1 [1286 kB]
Get:45 http://archive.ubuntu.com/ubuntu focal/universe amd64 libxerces-c3.2 amd64 3.2.2+debian-1build3 [878 kB]
Get:46 http://archive.ubuntu.com/ubuntu focal/main amd64 odbcinst amd64 2.3.6-0.1build1 [14.8 kB]      
Get:47 http://archive.ubuntu.com/ubuntu focal/main amd64 odbcinst1debian2 amd64 2.3.6-0.1build1 [41.1 kB]
Get:48 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgdal26 amd64 3.0.4+dfsg-1build3 [6156 kB]
Get:49 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main amd64 r-cran-rgdal amd64 1.5-17-1cran1.2004.0 [4310 kB]
Get:50 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsqlite3-dev amd64 3.31.1-4ubuntu0.2 [696 kB]
Get:51 http://archive.ubuntu.com/ubuntu focal/universe amd64 libproj-dev amd64 6.3.1-1 [1092 kB]       
Fetched 37.5 MB in 0s (0 B/s)                                                                          
Selecting previously unselected package gdal-data.
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]0;root@2e48a27df3d7: /root@2e48a27df3d7:/# 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(rgdal)
library(rgdal)
Loading required package: sp
rgdal: version: 1.5-17, (SVN revision 1070)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
Path to GDAL shared files: /usr/share/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 6.3.1, February 10th, 2020, [PJ_VERSION: 631]
Path to PROJ shared files: /usr/share/proj
Linking to sp version:1.4-2
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
> cat("Taaadaaa!\n")
cat("Taaadaaa!\n")
Taaadaaa!
> q()
q()
Save workspace image? [y/n/c]: n
n
]0;root@2e48a27df3d7: /root@2e48a27df3d7:/# exit
edd@rob:~$

Took maybe a minute. Nice, eh? ;-)

thomascjohnson commented 3 years ago

You guys are great. Thanks for the help.