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      {
        "title": "Debugging R Environment and Dependencies",
        "body": "This skill focuses on resolving problems related to R environments rather than analysis logic. It helps restore a working setup so that R scripts and projects can run successfully.\n\nUse this skill when the user encounters:\n\nPackage installation failures\nVersion conflicts between packages\nrenv or packrat environment issues\nBioconductor version mismatches\nSystem dependency errors (e.g., missing compilers or libraries)\nR failing to start or load packages"
      },
      {
        "title": "What This Skill Does",
        "body": "When activated, this skill will:\n\nDiagnose the environment\n\nCheck R version\nCheck installed packages and versions\nInspect renv.lock or project library\nIdentify Bioconductor version compatibility\n\n\n\nResolve package installation issues\n\nSuggest correct CRAN/Bioconductor repositories\nInstall missing system dependencies (e.g., libxml2, curl, openssl)\nHandle compilation failures on Linux/macOS/Windows\n\n\n\nFix dependency conflicts\n\nAlign package versions\nReinstall broken packages\nClean corrupted package libraries\n\n\n\nRepair project environments\n\nRestore with renv::restore()\nRebuild renv.lock\nReinitialize project library if needed\n\n\n\nBioconductor troubleshooting\n\nMatch Bioconductor version to R version\nUse BiocManager::install() correctly\nResolve common bioinformatics package errors\n\n\n\nSystem-level troubleshooting\n\nInstall missing compilers (e.g., gcc, gfortran)\nInstall development libraries required for R packages\nFix PATH or permission issues"
      },
      {
        "title": "Example User Requests That Should Trigger This Skill",
        "body": "\"I can't install tidyverse\"\n\"This package fails with a compilation error\"\n\"renv restore is broken\"\n\"Bioconductor says my version is incompatible\"\n\"library() fails even though the package is installed\"\n\"R says shared object cannot be loaded\""
      },
      {
        "title": "Example Workflow",
        "body": "User: I get an error when installing sf.\n\nSkill actions:\n\nDetect missing system libraries (GEOS, GDAL, PROJ)\nProvide OS-specific install commands\nRetry R package installation\nConfirm successful library loading"
      },
      {
        "title": "Common Problem Categories",
        "body": "CategoryExamplesMissing system libsxml2, curl, openssl, sf, rJavaCompiler issuesgfortran missing, Xcode tools missingVersion mismatchold R vs new packageBioconductor mismatchwrong Bioc version for Rrenv problemscorrupted cache, lockfile mismatchPermission issuescannot write to library path"
      },
      {
        "title": "Notes",
        "body": "Do not modify analysis code unless necessary\nPrefer fixing the environment over rewriting scripts\nAlways aim to make the project reproducible\nRecommend renv for future environment stability"
      }
    ],
    "body": "Debugging R Environment and Dependencies\n\nThis skill focuses on resolving problems related to R environments rather than analysis logic. It helps restore a working setup so that R scripts and projects can run successfully.\n\nUse this skill when the user encounters:\n\nPackage installation failures\nVersion conflicts between packages\nrenv or packrat environment issues\nBioconductor version mismatches\nSystem dependency errors (e.g., missing compilers or libraries)\nR failing to start or load packages\nWhat This Skill Does\n\nWhen activated, this skill will:\n\nDiagnose the environment\n\nCheck R version\nCheck installed packages and versions\nInspect renv.lock or project library\nIdentify Bioconductor version compatibility\n\nResolve package installation issues\n\nSuggest correct CRAN/Bioconductor repositories\nInstall missing system dependencies (e.g., libxml2, curl, openssl)\nHandle compilation failures on Linux/macOS/Windows\n\nFix dependency conflicts\n\nAlign package versions\nReinstall broken packages\nClean corrupted package libraries\n\nRepair project environments\n\nRestore with renv::restore()\nRebuild renv.lock\nReinitialize project library if needed\n\nBioconductor troubleshooting\n\nMatch Bioconductor version to R version\nUse BiocManager::install() correctly\nResolve common bioinformatics package errors\n\nSystem-level troubleshooting\n\nInstall missing compilers (e.g., gcc, gfortran)\nInstall development libraries required for R packages\nFix PATH or permission issues\nExample User Requests That Should Trigger This Skill\n\"I can't install tidyverse\"\n\"This package fails with a compilation error\"\n\"renv restore is broken\"\n\"Bioconductor says my version is incompatible\"\n\"library() fails even though the package is installed\"\n\"R says shared object cannot be loaded\"\nExample Workflow\n\nUser: I get an error when installing sf.\n\nSkill actions:\n\nDetect missing system libraries (GEOS, GDAL, PROJ)\nProvide OS-specific install commands\nRetry R package installation\nConfirm successful library loading\nCommon Problem Categories\nCategory\tExamples\nMissing system libs\txml2, curl, openssl, sf, rJava\nCompiler issues\tgfortran missing, Xcode tools missing\nVersion mismatch\told R vs new package\nBioconductor mismatch\twrong Bioc version for R\nrenv problems\tcorrupted cache, lockfile mismatch\nPermission issues\tcannot write to library path\nNotes\nDo not modify analysis code unless necessary\nPrefer fixing the environment over rewriting scripts\nAlways aim to make the project reproducible\nRecommend renv for future environment stability"
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