rgdal retired, causing issues for ggsegExtra on newer R versions

[serenaverdi]

When installing ggsegExtra:-

ERROR: dependency ‘rgdal’ is not available for package ‘ggsegExtra’, as package ‘rgdal’ is not available for later versions of R (my version is 4.3.2 (2023-10-31))

Is there another way I can use ggsegExtra?

Thanks!

[ramroomh]

Try this:

# Download package tarball from CRAN archive: https://cran.r-project.org/src/contrib/Archive/rgdal/
url <- https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-7.tar.gz
pkgFile <- "rgdal_1.6-7.tar.gz"
download.file(url = url, destfile = pkgFile)

# Install package
install.packages(pkgs=pkgFile, type="source", repos=NULL)

# Delete package tarball
unlink(pkgFile)

from: https://stackoverflow.com/questions/24194409/how-do-i-install-a-package-that-has-been-archived-from-cran

[serenaverdi]

Thanks, although it was unsuccessful (see below). I have downloaded gdal (via brew) too, but still no luck. Is there any other way to install ggsegExtra? Thanks for you help!

Install package

install.packages(pkgs=pkgFile, type="source", repos=NULL)

• installing source package ‘rgdal’ ...
  ** package ‘rgdal’ successfully unpacked and MD5 sums checked
  ** using staged installation
  configure: R_HOME: /Library/Frameworks/R.framework/Resources
  configure: CC: clang -arch arm64
  configure: CXX: clang++ -arch arm64 -std=gnu++17
  configure: CFLAGS: -falign-functions=64 -Wall -g -O2
  configure: CPPFLAGS: -I/opt/R/arm64/include
  configure: CXXFLAGS: -falign-functions=64 -Wall -g -O2
  configure: LDFLAGS: -L/opt/R/arm64/lib
  configure: LDFLAGS: -L/opt/R/arm64/lib
  configure: CXX17 is: clang++ -arch arm64, CXX17STD is: -std=gnu++17
  configure: CXX is: clang++ -arch arm64 -std=gnu++17
  configure: C++17 support available
  configure: rgdal: 1.6-7
  checking for /usr/bin/svnversion... no
  configure: svn revision: 1203
  checking for gdal-config... no
  no
  configure: error: gdal-config not found or not executable.
  ERROR: configuration failed for package ‘rgdal’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rgdal’
  Warning in install.packages :
  installation of package ‘rgdal_1.6-7.tar.gz’ had non-zero exit status

[ramroomh]

Try downloading libgdal-dev via brew.

from: https://stackoverflow.com/questions/12141422/error-gdal-config-not-found-while-installing-r-dependent-packages-whereas-gdal

[drmowinckels]

@ramroomh thank you so much for assisting! I'm very busy with other tasks now, but I am paying attention and noting what is being tried, so I can hopefully fix things later.

[amirhusseinab]

@ramroomh I'm trying to use it on my Windows machine. Any suggestions for that? Searching for "rgdal" leads to this page: https://cran.r-project.org/web/packages/rgdal/index.html in which "sf" or "terra" are suggested as a substitute - which I think changes are required for ggsegExtra to be made.

[drmowinckels]

Info have a dev version of the package where i am trying to sub rgdal with sf, but its not working yet and its trickier than expected. I, unfortunately, don't have lots of time.to dedicate to the worn right now. I hope that changes after march

[ramroomh]

Hello everyone,

For now I've created a work around to the dependency problem, where I've created a docker image of an rstudio server with ggseg and associated packages preloaded (including rgdal).

Here are the steps in terminal, please note this requires installing docker and creating a docker hub account:

1. Download the docker image
   docker pull ramroomh/ggseg-rstudio-server:v0.1

2. run the image and port the image to a webserver
   docker run -d -p 8787:8787 -e PASSWORD=password --name ggseg-instance ramroomh/ggseg-rstudio-server:v0.1

3. access the server on a web browser by pasting:
   http://localhost:8787

4. login with default user and pass
   user: rstudio_user, pass: password

5. start using ggseg

6. export plots with:
   docker cp ggseg-instance:/home/rstudio_user/name_of_image.png /path/to/save/name_of_image.png

Currently it is preloaded with the brodmann atlas but happy to add the other atlases if there is interested.