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BioDT / uc-CWR

The code base for the Crop-Wild-Relative (CWR) use-case led by UiO
MIT License
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Container Image not building due to missing intSDM from CRAN #15

Open dnlbauer opened 3 months ago

dnlbauer commented 3 months ago

Hi,

Raising this issue because my last PR got closed without any feedback; so I am not sure if you are accepting PRs..

Building the container image fails for me at Line 203. Apparently, intSDM is not available from CRAN as expected during this step https://github.com/BioDT/uc-CWR/blob/ece6f10b088126e9c7d8ee1ade002df9d5b60321/container/Dockerfile#L203-L209

13.96 * DONE (PointedSDMs)
14.58 Warning message:
14.58 package 'intSDM' is not available for this version of R
14.58 
14.58 A version of this package for your version of R might be available elsewhere,
14.58 see the ideas at
14.58 https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
15.36 Error: Failed to install 'unknown package' from GitHub:
15.36   Line starting 'Vi ...' is malformed!
15.36 Execution halted
------
Dockerfile:203
--------------------
 202 |     # Install intSDM etc
 203 | >>> RUN . /conda/etc/profile.d/conda.sh && \
 204 | >>>     conda activate /conda/env && \
 205 | >>>     Rscript -e 'devtools::install_github("PhilipMostert/PointedSDMs", dependencies=FALSE)' && \
 206 | >>>     # Bugfix: Installing intSDM directly from github doesn't work so we install it first from cran
 207 | >>>     Rscript -e 'install.packages("intSDM")' && \
 208 | >>>     Rscript -e 'devtools::install_github("PhilipMostert/intSDM", dependencies=FALSE)' && \
 209 | >>>     /conda/bin/conda clean -afy
 210 |

Also, building HEAD of PhilipMostert/intSDM throws errors for me. I was able to get the container to build by using the latest release version of "intSDM" from github: https://github.com/PhilipMostert/intSDM/releases/tag/V2.0.1:

RUN . /conda/etc/profile.d/conda.sh && \
    conda activate /conda/env && \
    Rscript -e 'devtools::install_github("PhilipMostert/PointedSDMs", dependencies=FALSE)' && \
    Rscript -e 'devtools::install_url("https://github.com/PhilipMostert/intSDM/archive/refs/tags/V2.0.1.zip", dependencies=FALSE)' && \
    /conda/bin/conda clean -afy

Are there any concerns with using this version, or does MoDGP also work with intSDM 2.0.1?