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nelsopet / lecospec

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remove rgdal use #118

Open nelsopet opened 2 years ago

nelsopet commented 2 years ago

Loading required package: rgdal Please note that rgdal will be retired by the end of 2023, plan transition to sf/stars/terra functions using GDAL and PROJ at your earliest convenience.

krbundy commented 3 months ago

This is all the places that rgdal is mentioned: 55 results - 16 files

README.Rmd: 13 require(sf) 14: library(rgdal) 15 library(tidyverse)

Scripts/manual_validation.ipynb: 44 "\n", 45: "Loading required package: rgdal\n", 46 "\n", 47: "Please note that rgdal will be retired during October 2023,\n", 48 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

50 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n", 51: "rgdal: version: 1.6-7, (SVN revision 1203)\n", 52 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

60 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 61: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 62 "\n",

Scripts/split_bonanza.ipynb: 63 "\n", 64: "Loading required package: rgdal\n", 65 "\n", 66: "Please note that rgdal will be retired during October 2023,\n", 67 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

69 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n", 70: "rgdal: version: 1.6-7, (SVN revision 1203)\n", 71 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

79 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 80: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 81 "\n",

Scripts/Archive/7C_Visualizations_ReadKML_plot_map.R: 1: library(rgdal) 2 library(tidyverse)

Scripts/Archive/gs_revised_RF.ipynb: 66 "\"package 'hsdar' was built under R version 4.2.2\"\n", 67: "Loading required package: rgdal\n", 68 "\n", 69 "Warning message:\n", 70: "\"package 'rgdal' was built under R version 4.2.2\"\n", 71: "Please note that rgdal will be retired during 2023,\n", 72 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

74 "See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution\n", 75: "rgdal: version: 1.6-2, (SVN revision 1183)\n", 76 "Geospatial Data Abstraction Library extensions to R successfully loaded\n", 77 "Loaded GDAL runtime: GDAL 3.5.2, released 2022/09/02\n", 78: "Path to GDAL shared files: C:/Users/Nelson Lab/AppData/Local/R/win-library/4.2/rgdal/gdal\n", 79 "GDAL binary built with GEOS: TRUE \n", 80 "Loaded PROJ runtime: Rel. 8.2.1, January 1st, 2022, [PJ_VERSION: 821]\n", 81: "Path to PROJ shared files: C:/Users/Nelson Lab/AppData/Local/R/win-library/4.2/rgdal/proj\n", 82 "PROJ CDN enabled: FALSE\n",

84 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 85: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 86 "\n",

Scripts/Archive/gs_xgboost.ipynb: 44 "\n", 45: "Loading required package: rgdal\n", 46 "\n", 47: "Please note that rgdal will be retired during 2023,\n", 48 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

50 "See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution\n", 51: "rgdal: version: 1.6-6, (SVN revision 1201)\n", 52 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

60 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 61: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 62 "\n",

Scripts/Archive/site_specific_model_experiments.ipynb: 42 "\n", 43: "Loading required package: rgdal\n", 44 "\n", 45: "Please note that rgdal will be retired by the end of 2023,\n", 46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n", 49: "rgdal: version: 1.5-32, (SVN revision 1176)\n", 50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 59: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 60 "\n",

Scripts/Archive/tree_visualization.ipynb: 42 "\n", 43: "Loading required package: rgdal\n", 44 "\n", 45: "Please note that rgdal will be retired by the end of 2023,\n", 46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n", 49: "rgdal: version: 1.5-32, (SVN revision 1176)\n", 50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 59: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 60 "\n",

Scripts/ExploratoryDataAnalysis/7_Visualizations_Ground_and_UAS_Spectra_locations.R: 2 require(sf) 3: library(rgdal) 4 library(tidyverse)

Scripts/ExploratoryDataAnalysis/model_building.ipynb: 42 "\n", 43: "Loading required package: rgdal\n", 44 "\n", 45: "Please note that rgdal will be retired by the end of 2023,\n", 46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n", 49: "rgdal: version: 1.5-32, (SVN revision 1176)\n", 50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 59: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 60 "\n",

Scripts/TrainingDataCreation/merge_data.ipynb: 42 "\n", 43: "Loading required package: rgdal\n", 44 "\n", 45: "Please note that rgdal will be retired by the end of 2023,\n", 46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n", 49: "rgdal: version: 1.5-32, (SVN revision 1176)\n", 50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 59: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 60 "\n",

Scripts/TrainingDataCreation/speclib_processing.ipynb: 76 "\n", 77: "Loading required package: rgdal\n", 78 "\n", 79: "Please note that rgdal will be retired during October 2023,\n", 80 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

82 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n", 83: "rgdal: version: 1.6-7, (SVN revision 1203)\n", 84 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

92 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n", 93: "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading sp or rgdal.\n", 94 "\n",

Scripts/TrainingDataCreation/Image/101_Crop_TarpWhiteRefs.R: 3 require(raster) 4: require(rgdal) 5

Scripts/TrainingDataCreation/Image/101_Crop_Training_PFT_vector.R: 3 require(raster) 4: require(rgdal) 5

Scripts/TrainingDataCreation/Image/101_Crop_Training_Quads.R: 3 require(raster) 4: require(rgdal) 5

Scripts/Utilities/install_dependenies.R: 1 lecospec_depenencies <- c( 2: "rgdal", 3 "gdalUtils",

krbundy commented 3 months ago

So far, all are holdovers from before rgdal was removed from Functions/lecospectR.R. The notebooks simply maintain a reference to the package from before since they have not been run in a long time.

krbundy commented 3 months ago

These are the remaining mentions that actually need to be addressed:

Note that since I removed it from install_dependencies, the package will no longer be installed automatically.

Do you want to see if these are things that should be addressed @nelsopet ?