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A collection of docker image of various R implementations on various platform both vanilla and with geospatial R packages.

Makefile 18.30% Dockerfile 25.16% R 54.09% Python 2.28% Shell 0.17%

docker-image r mro renjin docker fastr pqr debian fedora archlinux

dockers's Introduction

dockeRs

A collection of docker image of various R implementations on various platform both vanilla and with geospatial R packages.

This is part of my master thesis.

Docker Images

Vanilla R (18/18)

	GNU-R	MRO	Renjin	FastR	pqR	TERR
Debian	✔️	✔️	✔️	✔️	✔️	✔️
Fedora	✔️	✔️	⛔	✔️	⛔	⛔
Arch Linux	✔️	✔️	⛔	⛔	⛔	⛔

with Geospatial R Packages (18/18)

	GNU-R	MRO	Renjin	FastR	pqR	TERR
Debian	✔️	✔️	❌	❌	❌	❌
Fedora	✔️	✔️	❌	❌	❌	❌
Arch Linux	✔️	❓	❌	❌	❌	❌

Legends:

✔️ : Complete
❌ : Not possible
⛔ : Won't be checked because it is not supported based on other result
❓ : Unknown due to time limit
❔ : Unknown / Not checked yet

SDSR's benchmark status

For more detailed result can be read in my master thesis.

Content

Each docker image directory contains:

(mandatory) README.MD: description of the docker image and how to obtain it
Dockerfile : the dockerfile, if not available on other source
(mandatory) Makefile : Some handy command to run the docker container
Error.txt : error message if not possible to create, or related to it

Naming

The format is : [R-implementation]-[version]-[platform]-[geospatial].

dockers's People

Contributors

Stargazers

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nuest

dockers's Issues

FastR + Arch Linux + Geospatial

The Dockerfiles in this repository should be published under an open license. Please add a LICENSE file and mention the license in the README. Please double check that you have properly attributed when you copied a Dockerfile from somewhere else. If needed you could also use different licenses for specific a specific Dockerfile when you build on someone else's work published under a specific license.

> install.packages('sf')
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 7975k  100 7975k    0     0  83569      0  0:01:37  0:01:37 --:--:--  175k
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.2
checking GDAL version >= 2.0.0... yes
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... no
checking proj_api.h presence... no
checking for proj_api.h... no
configure: error: proj_api.h not found in standard or given locations.
ERROR: configuration failed for package ‘sf’

* installing *source* package ‘polyclip’ ...
** package ‘polyclip’ successfully unpacked and MD5 sums checked
compiling under C++11
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpxuvQGf/R.INSTALL1a21e027aa/polyclip':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘polyclip’
* removing ‘/opt/microsoft/ropen/3.5.3/lib64/R/library/polyclip’

pqR + Arch Linux + Geospatial

Can not install `sf` in Fastr

* installing *source* package ?sf? ...
** package ?sf? successfully unpacked and MD5 sums checked
configure: CC: gcc
configure: CXX: g++
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.3
checking GDAL version >= 2.0.0... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ.4 is available for linking:... yes
checking GDAL: checking whether PROJ.4 is available fur running:... yes
configure: pkg-config proj exists, will use it
checking proj_api.h usability... no
checking proj_api.h presence... no
checking for proj_api.h... no
configure: error: proj_api.h not found in standard or given locations.
ERROR: configuration failed for package ?sf?
* removing ?/fastr/library/sf?


The downloaded source packages are in
	?/tmp/Rtmp1Dcnc6/downloaded_packages?
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("sf") :
  installation of package ?sf? had non-zero exit status

It seems it couldn't find proj_api.h

* installing *source* package ‘dbmss’ ...
** package ‘dbmss’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.3/lib64/R/include -DNDEBUG  -I"/opt/microsoft/ropen/3.5.3/lib64/R/library/Rcpp/include" -I"/opt/microsoft/ropen/3.5.3/lib64/R/library/RcppParallel/include" -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -g -O2 -c CountNbd.cpp -o CountNbd.o
g++ -std=gnu++11 -I/opt/microsoft/ropen/3.5.3/lib64/R/include -DNDEBUG  -I"/opt/microsoft/ropen/3.5.3/lib64/R/library/Rcpp/include" -I"/opt/microsoft/ropen/3.5.3/lib64/R/library/RcppParallel/include" -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/opt/microsoft/ropen/3.5.3/lib64/R/lib -o dbmss.so CountNbd.o RcppExports.o Microsoft R Services MKL End User License Agreement These license terms are an agreement between Microsoft Corporation ("Microsoft" or "us") and you ("User" or "you"). Please read them. By selecting the "I ACCEPT" box, accessing, or otherwise using the R Services MKL software or documentation, you agree to all the terms of this agreement. If you do not agree with all of these terms, do not select the "I ACCEPT" box, access, or otherwise use the R Services MKL software or documentation. User does not become a licensed user of, and is not authorized to use, the R Services MKL software or documentation unless and until it has agreed to be bound by all of these terms. R Services MKL is a software package provided for use with Microsoft R Server, Microsoft R Open, and any successors or other software applications released by us ("Licensed Products") that can be used with the Intel® Math Kernel Libraries ("MKL")(for more information, see https://software.intel.com/en-us/intel-mkl). This software package is referred to herein as the "R Services MKL." Intel Corporation is referred to as "Intel." 1. License. The R Services MKL is licensed for exclusive use with the Licensed Products. Subject to all of the terms and conditions of this Agreement, Microsoft grants User a non-exclusive, non-transferable, non-sublicensable right to use R Services MKL. R Services MKL must be used as a single integrated software application and may not be separated into its constituent parts. 2. Restrictions. User shall not, directly or indirectly: (i) sublicense, resell, rent, lease, distribute, market, commer

label: world (with options) 
List of 4
 $ fig.cap: chr "Earth country boundaries; left: mapping long/lat to x and y; right: as seen from space"
 $ fig    : logi TRUE
 $ echo   : logi FALSE
 $ message: logi FALSE

Quitting from lines 3029-3066 (sds.Rmd) 
Error in geos_op2_geom("intersection", x, y) : 
  st_crs(x) == st_crs(y) is not TRUE
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval

Execution halted

I try to run the code manually, it does give the error message.