Comments (7)
A few thoughts:
- Use a versioned image?
- rocker provides scripts install2.r and installGithub.r that simplifies installation of R packages. So an alternative for installing the R packages might be:
FROM rocker/rstudio:3.6.3
MAINTAINER="Chris Schnaufer <[email protected]>"
RUN apt-get update && apt-get install -y --no-install-recommends \
libxml2-dev
zlib1g-dev
libfftw3-dev
gdal-bin
libgdal-dev
libxt-dev
RUN install2.r --error \
sp
raster
rgdal
scales
xml2
git2r
usethis
fftwtools
devtools
RUN installGithub.r filipematias23/FIELDimageR
In addition, If you start from rocker/geospatial you get a lot of these dependencies already built in (including tidyverse and a lot of geospatial utilities - not just those required by FieldImageR but some that could be useful for running downstream analyses, as well as a lot of bloat!!)
- it is quite a stack (not clear if additional size / dependencies are worth it), but
- rocker/geospatial https://github.com/rocker-org/geospatial/blob/master/Dockerfile builds on
- rocker/verse https://github.com/rocker-org/rocker-versioned/blob/master/verse/3.6.3.Dockerfile which builds on
- rocker/tidyverse https://github.com/rocker-org/rocker-versioned/blob/master/tidyverse/3.6.3.Dockerfile which builds on
- rocker/rstudio https://github.com/rocker-org/rocker-versioned/blob/master/rstudio/3.6.3.Dockerfile which builds on
- rocker/r-ver which is the base for the versioned images ...
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Thank you for sharing ..!!!
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I have updated the Dockerfile to take advantage of suggested installation changes.
I am putting the suggested additions for downstream analysis into another issue: #9
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Linking to #10
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this can be closed since #10 has been merged and suggestions for improvement are in #9
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Hi @Chris-Schnaufer and @dlebauer,
Thank you a lot for helping with this project.
I am wondering what is the next step? How can I integrate your suggestions (#9 and #10) to the tutorial?
All the best,
Filipe
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I am wondering what is the next step? How can I integrate your suggestions (#9 and #10) to the tutorial?
I think the next step as described in #9 would be to determine if those are changes that are desired and, if so, update the Dockerfile to use the new base image. I don't know who would be best suited to determine if those changes are desired
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Related Issues (20)
- fieldIndex() function is not available HOT 3
- Add FIELDimageR Plugin to QGIS HOT 1
- EX1.Shape$fieldShapeGIS does not have a CRS HOT 3
- Use a buffer for canopy calculation HOT 2
- Dockerfile missing HOT 2
- Use `withr::local_par` to set graphical parameters HOT 2
- Parallel and loop to evaluate multiple images HOT 2
- Extract individual plots & working with large files HOT 4
- problems installing FIELDimageR in docker
- n.cores option causing fieldRotate error HOT 1
- Convert FieldImageR from R to Python HOT 4
- Could not find function "fieldCrop" HOT 5
- Error while trying to read custom data HOT 4
- Overlap error in plant height code when trying to remove soil from the mask HOT 2
- Selection point is shifted HOT 1
- dependencies error HOT 4
- Problem to install FIELDImageR in costum dockerfile
- Couldn't able to install FIELDimageR pacakage both using zip file format and devtools intsallation method HOT 1
- Upcoming changes to R spatial packages
- error installing, object elide not supported by package HOT 1
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