Fix Docker image: install NatureDataCubeR package#7
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The image was built from the package layout but never installed the NatureDataCubeR package itself, so the app crash-looped at startup with "there is no package called 'NatureDataCubeR'" (502 at the proxy). - Dockerfile: COPY the package source and R CMD INSTALL it, so library(NatureDataCubeR) and system.file() (Shiny app in inst/shiny, data in inst/extdata) resolve at runtime. Launch via the package's own ndc_shiny() launcher instead of a hardcoded /srv path. Drop the obsolete COPY R/naturedatacube_app, R/retrieval_functions, data lines (those paths no longer exist in the package layout). - .env.example: rename AGRO_DATA_TOKEN to ADC_TOKEN to match app.R, which reads ADC_TOKEN and stop()s without it. - .dockerignore: keep .git/.env/tests out of the build context. Verified: image builds, package installs, container boots past the package load (now only the runtime token check remains). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Problem
The deployed app (e.g. https://lter-life-experience.org/naturedatacube) was crash-looping → 502 at the proxy. The container exits on startup with:
The image was built from the package layout, but the Dockerfile never actually installed the
NatureDataCubeRpackage — and the app doeslibrary(NatureDataCubeR). The oldCOPY R/naturedatacube_app,COPY R/retrieval_functions,COPY datalines also referenced paths that no longer exist in the package layout (app moved toinst/shiny/, data toinst/extdata/).Changes
COPYthe package source andR CMD INSTALLit, solibrary(NatureDataCubeR)andsystem.file()(Shiny app ininst/shiny, data ininst/extdata) resolve at runtime. Launch via the package's ownndc_shiny()launcher instead of a hardcoded/srvpath. Drop the obsoleteCOPYlines.AGRO_DATA_TOKEN→ADC_TOKENto matchapp.R, which readsADC_TOKENandstop()s without it..git/.env/testsout of the build context.Verification
docker buildsucceeds;requireNamespace('NatureDataCubeR')isTRUEin the image andsystem.file(...)resolves the app + gpkg.ADC_TOKENenv check remains, which is host.envconfig.🤖 Generated with Claude Code