* using log directory ‘/srv/hornik/tmp/CRAN_pretest/ToolsRTM.Rcheck’ * using R Under development (unstable) (2025-12-11 r89152) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.6 (2) Debian flang version 21.1.6 (2) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘ToolsRTM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ToolsRTM’ version ‘0.65’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/6s] NOTE Maintainer: ‘The package maintainer ’ New submission Non-FOSS package license (`use_gpl3_license()`) Possibly misspelled words in DESCRIPTION: modelsand (11:79) radiative (11:60) Unknown, possibly misspelled, fields in DESCRIPTION: ‘Import’ Found the following (possibly) invalid URLs: URL: http://r.789695.n4.nabble.com/Generating-uniformly-distributed-correlated-data-td3314905.html From: man/runifcor.cor.Rd Status: Error Message: Could not resolve hostname [r.789695.n4.nabble.com]: Could not resolve host: r.789695.n4.nabble.com URL: https://doi.org/10.1016/0034-4257 From: README.md Status: 404 Message: Not Found Found the following (possibly) invalid file URIs: URI: 10.1109/IGARSS53475.2024.10642442 From: README.md URI: 10.1109/IGARSS53475.2024.10641613 From: README.md The Title field should be in title case. Current version is: ‘A package for simulating RT models’ In title case that is: ‘A Package for Simulating RT Models’ DESCRIPTION fields with placeholder content: Maintainer: The package maintainer Size of tarball: 58349796 bytes * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... WARNING Found the following file with a non-portable file name: inst/applications/STAC/www/scenario/bark_beetle outbreak.gpkg These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. Found the following non-portable file path: ToolsRTM/vignettes/SCOPEinR/outs/2024-09-17_14-31-54/Plots/5-Hemispherically_Integrated_upwelling_radiance.png Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘ToolsRTM’ can be installed ... [8s/8s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... WARNING Non-standard license specification: `use_gpl3_license()` Standardizable: FALSE Maintainer field differs from that derived from Authors@R Maintainer: ‘The package maintainer ’ Authors@R: ‘Carlos Camino ’ * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... WARNING Found the following files with non-ASCII characters: R/get.plot.ML.R R/get.plot.plsr.R Portable packages must use only ASCII characters in their R code and NAMESPACE directives, except perhaps in comments. Use \uxxxx escapes for other characters. Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII characters in files. * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING '::' or ':::' imports not declared from: ‘MASS’ ‘MLmetrics’ ‘SCOPEinR’ ‘caret’ ‘caretEnsemble’ ‘corrplot’ ‘data.table’ ‘doParallel’ ‘dplyr’ ‘e1071’ ‘expint’ ‘factoextra’ ‘fmsb’ ‘gdalUtils’ ‘gdalcubes’ ‘ggplot2’ ‘hsdar’ ‘keras’ ‘lubridate’ ‘ncdf4’ ‘nnet’ ‘pls’ ‘plyr’ ‘progress’ ‘randomForest’ ‘raster’ ‘renv’ ‘reshape2’ ‘rlang’ ‘rstac’ ‘scales’ ‘sensitivity’ ‘sf’ ‘shiny’ ‘signal’ ‘stringr’ ‘tidyr’ 'library' or 'require' calls not declared from: ‘dplyr’ ‘foreach’ ‘keras’ ‘lubridate’ ‘parallel’ ‘tensorflow’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘renv’ 'library' or 'require' calls in package code: ‘dplyr’ ‘foreach’ ‘keras’ ‘lubridate’ ‘parallel’ ‘tensorflow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported objects: ‘ToolsRTM::fluspect_B_CX_PSI_PSII_combined’ ‘ToolsRTM::getIndicesSE2a’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [18s/18s] NOTE COST_4Fluspect: no visible global function definition for ‘fluspect_B_CX_PSI_PSII_combined’ COST_4Fluspect: no visible global function definition for ‘approx’ GetMosaics: no visible global function definition for ‘extent’ GetMosaics: no visible global function definition for ‘raster’ GetMosaics: no visible global function definition for ‘projection<-’ GetMosaics: no visible global function definition for ‘writeRaster’ GetSpectralseries: no visible global function definition for ‘txtProgressBar’ GetSpectralseries: no visible global function definition for ‘setTxtProgressBar’ GetSpectralseries: no visible global function definition for ‘as_Spatial’ GetSpectralseries: no visible global function definition for ‘stack’ GetSpectralseries: no visible binding for global variable ‘n_bands.points’ SPART: no visible binding for global variable ‘inputs.SPART’ SPART: no visible binding for global variable ‘inputs’ SPART: no visible binding for global variable ‘optipar2021.Pro.CX’ SPART: no visible binding for global variable ‘dataSpec_PRO’ SPART: no visible global function definition for ‘aes’ SPART: no visible binding for global variable ‘wave’ SPART: no visible global function definition for ‘labs’ SPART: no visible global function definition for ‘xlim’ SPART: no visible global function definition for ‘geom_line’ SPART: no visible binding for global variable ‘Kp’ SPART: no visible binding for global variable ‘Kcbc’ SPART: no visible global function definition for ‘theme_bw’ SPART: no visible global function definition for ‘guides’ SPART: no visible global function definition for ‘guide_legend’ SPART: no visible global function definition for ‘theme’ SPART: no visible binding for global variable ‘Kcab’ SPART: no visible binding for global variable ‘Kca’ SPART: no visible binding for global variable ‘Kant’ SPART: no visible global function definition for ‘getinputLUT’ SPART: no visible binding for global variable ‘SCOPE.LUT.default’ SPART: no visible binding for global variable ‘rfl.soil’ SPART: no visible binding for global variable ‘dataSpec_PDB’ SPART: no visible binding for global variable ‘Extraterrestrial_irradiance’ SPART: no visible binding for global variable ‘irrad’ SPART: no visible binding for global variable ‘rad.toa’ SPART: no visible binding for global variable ‘rfl.toa’ SPART: no visible global function definition for ‘geom_point’ SPART: no visible binding for global variable ‘rfl.toc’ SPART: no visible binding for global variable ‘rfl.toc.brdf’ SPART.simN: no visible binding for global variable ‘inputs.SPART’ SPART.simN: no visible binding for global variable ‘optipar2021.Pro.CX’ SPART.simN: no visible binding for global variable ‘dataSpec_PRO’ SPART.simN: no visible global function definition for ‘getinputLUT’ SPART.simN: no visible binding for global variable ‘SCOPE.LUT.default’ SPART.simN: no visible binding for global variable ‘LUT’ SPART.simN: no visible binding for global variable ‘dataSpec_PDB’ SPART.simN: no visible binding for global variable ‘Extraterrestrial_irradiance’ amerge: no visible global function definition for ‘na.omit’ carspls: no visible global function definition for ‘ceil’ color.gradient: no visible global function definition for ‘colorRampPalette’ correlatedValue: no visible global function definition for ‘rnorm’ exp1_base : : no visible global function definition for ‘integrate’ filter_outliers: no visible global function definition for ‘quantile’ filter_outliers: no visible global function definition for ‘IQR’ foursail.inf: no visible binding for global variable ‘r_understorey’ foursail.inf: no visible binding for global variable ‘r_leaf’ foursail.inf: no visible binding for global variable ‘t_leaf’ foursail_t_o: no visible binding for global variable ‘r_understorey’ foursail_t_o: no visible binding for global variable ‘r_leaf’ foursail_t_o: no visible binding for global variable ‘t_leaf’ foursail_t_s: no visible binding for global variable ‘r_understorey’ foursail_t_s: no visible binding for global variable ‘r_leaf’ foursail_t_s: no visible binding for global variable ‘t_leaf’ gauss_byMin_Max: no visible global function definition for ‘rnorm’ get.LUTfromRanges: no visible binding for global variable ‘inputs’ get.cars.pls: no visible global function definition for ‘mvr’ get.cars.pls: no visible global function definition for ‘crossval’ get.cars.pls: no visible global function definition for ‘ceil’ get.inversion: no visible global function definition for ‘detectCores’ get.inversion: no visible global function definition for ‘as.formula’ get.inversion: no visible global function definition for ‘makeCluster’ get.inversion: no visible global function definition for ‘createMultiFolds’ get.inversion: no visible global function definition for ‘trainControl’ get.inversion: no visible global function definition for ‘tune.control’ get.inversion: no visible global function definition for ‘svm’ get.inversion: no visible global function definition for ‘createFolds’ get.inversion: no visible binding for global variable ‘na.pass’ get.inversion: no visible global function definition for ‘write.csv’ get.inversionOpt: no visible global function definition for ‘txtProgressBar’ get.inversionOpt: no visible global function definition for ‘setTxtProgressBar’ get.packages: no visible global function definition for ‘install.packages’ get.packages: no visible global function definition for ‘installed.packages’ get.plot.ML: no visible global function definition for ‘predict’ get.plot.ML: no visible global function definition for ‘ggplot’ get.plot.ML: no visible global function definition for ‘aes_string’ get.plot.ML: no visible global function definition for ‘geom_point’ get.plot.ML: no visible global function definition for ‘xlim’ get.plot.ML: no visible global function definition for ‘ylim’ get.plot.ML: no visible global function definition for ‘geom_smooth’ get.plot.ML: no visible global function definition for ‘labs’ get.plot.ML: no visible global function definition for ‘theme’ get.plot.ML: no visible global function definition for ‘element_text’ get.plot.ML: no visible global function definition for ‘element_rect’ get.plot.ML: no visible global function definition for ‘element_blank’ get.plot.ML: no visible global function definition for ‘theme_bw’ get.plot.cars.pls: no visible global function definition for ‘layout’ get.plot.cars.pls: no visible global function definition for ‘lines’ get.plot.cars.pls: no visible global function definition for ‘abline’ get.plot.plsr: no visible global function definition for ‘predict’ get.plot.plsr: no visible global function definition for ‘ggplot’ get.plot.plsr: no visible global function definition for ‘aes_string’ get.plot.plsr: no visible global function definition for ‘geom_point’ get.plot.plsr: no visible global function definition for ‘xlim’ get.plot.plsr: no visible global function definition for ‘ylim’ get.plot.plsr: no visible global function definition for ‘geom_smooth’ get.plot.plsr: no visible global function definition for ‘labs’ get.plot.plsr: no visible global function definition for ‘theme’ get.plot.plsr: no visible global function definition for ‘element_text’ get.plot.plsr: no visible global function definition for ‘element_rect’ get.plot.plsr: no visible global function definition for ‘element_blank’ get.plot.plsr: no visible global function definition for ‘theme_bw’ get.plots: no visible global function definition for ‘%>%’ get.plots: no visible global function definition for ‘group_by’ get.plots: no visible binding for global variable ‘band’ get.plots: no visible global function definition for ‘summarise’ get.plots: no visible binding for global variable ‘value’ get.plots: no visible global function definition for ‘median’ get.plots: no visible global function definition for ‘quantile’ get.plots: no visible global function definition for ‘ggplot’ get.plots: no visible global function definition for ‘aes’ get.plots: no visible global function definition for ‘geom_line’ get.plots: no visible binding for global variable ‘average’ get.plots: no visible binding for global variable ‘median’ get.plots: no visible global function definition for ‘geom_ribbon’ get.plots: no visible binding for global variable ‘percentile_25’ get.plots: no visible binding for global variable ‘percentile_75’ get.plots: no visible global function definition for ‘labs’ get.plots: no visible global function definition for ‘theme_bw’ get.plots: no visible global function definition for ‘theme’ get.plots: no visible global function definition for ‘element_text’ get.satellite_collection: no visible global function definition for ‘items_fetch’ get.satellite_collection: no visible global function definition for ‘post_request’ get.satellite_collection: no visible global function definition for ‘stac_search’ get.satellite_collection: no visible global function definition for ‘items_sign’ get.satellite_collection: no visible global function definition for ‘sign_planetary_computer’ get.satellite_collection: no visible global function definition for ‘stac_image_collection’ get.sentinel2_cube: no visible global function definition for ‘cube_view’ get.sentinel2_cube: no visible global function definition for ‘image_mask’ get.sentinel2_cube: no visible global function definition for ‘raster_cube’ get.sentinel2_cube: no visible global function definition for ‘reduce_time’ get.sentinel2_cube: no visible global function definition for ‘select_bands’ get.sentinel2_cube: no visible global function definition for ‘slice_time’ get.sentinel2_cube: no visible global function definition for ‘rast’ get.sentinel2_cube: no visible global function definition for ‘st_as_stars.cube’ get.simulator: no visible global function definition for ‘installed.packages’ get.smac: no visible binding for global variable ‘LUT’ get.sobol.indices: no visible global function definition for ‘%>%’ get.sobol.indices: no visible global function definition for ‘left_join’ get.sobol.indices: no visible global function definition for ‘mutate’ get.sobol.indices: no visible binding for global variable ‘I.Johnson’ get.sobol.indices: no visible global function definition for ‘quantile’ get.spectra.convolved: no visible global function definition for ‘txtProgressBar’ get.spectra.convolved: no visible global function definition for ‘setTxtProgressBar’ get.spectra.convolved: no visible binding for global variable ‘Sensor’ get.spectra.convolved: no visible global function definition for ‘%>%’ get.spectra.convolved: no visible global function definition for ‘group_by’ get.spectra.convolved: no visible binding for global variable ‘band’ get.spectra.convolved: no visible global function definition for ‘summarise’ get.spectra.convolved: no visible binding for global variable ‘reflectance’ get.spectra.convolved: no visible global function definition for ‘median’ get.spectra.convolved: no visible global function definition for ‘quantile’ get.spectra.convolved: no visible global function definition for ‘ggplot’ get.spectra.convolved: no visible global function definition for ‘aes’ get.spectra.convolved: no visible global function definition for ‘geom_line’ get.spectra.convolved: no visible binding for global variable ‘average’ get.spectra.convolved: no visible binding for global variable ‘median’ get.spectra.convolved: no visible global function definition for ‘geom_ribbon’ get.spectra.convolved: no visible binding for global variable ‘percentile_10’ get.spectra.convolved: no visible binding for global variable ‘percentile_90’ get.spectra.convolved: no visible global function definition for ‘geom_point’ get.spectra.convolved: no visible global function definition for ‘labs’ get.spectra.convolved: no visible global function definition for ‘theme_bw’ get.spectra.convolved: no visible global function definition for ‘theme’ get.spectra.convolved: no visible global function definition for ‘element_text’ get.spectra.convolved: no visible global function definition for ‘element_rect’ get.spectra.convolved: no visible global function definition for ‘element_blank’ get.spectral: no visible binding for global variable ‘Sensor’ get.spectral.convolution: no visible global function definition for ‘aes’ get.spectral.convolution: no visible binding for global variable ‘wave’ get.spectral.convolution: no visible binding for global variable ‘Eo’ get.spectral.convolution: no visible global function definition for ‘labs’ get.spectral.convolution: no visible global function definition for ‘geom_line’ get.spectral.convolution: no visible global function definition for ‘theme_bw’ get.spectral.convolution.rfl: no visible global function definition for ‘aes’ get.spectral.convolution.rfl: no visible binding for global variable ‘wave’ get.spectral.convolution.rfl: no visible binding for global variable ‘RFL’ get.spectral.convolution.rfl: no visible global function definition for ‘labs’ get.spectral.convolution.rfl: no visible global function definition for ‘geom_line’ get.spectral.convolution.rfl: no visible global function definition for ‘theme_bw’ get.spectral.derivative: no visible global function definition for ‘%>%’ get.spectral.derivative: no visible binding for global variable ‘group’ get.spectral.derivative: no visible binding for global variable ‘band’ get.spectral.derivative: no visible global function definition for ‘ggplot’ get.spectral.derivative: no visible global function definition for ‘aes’ get.spectral.derivative: no visible binding for global variable ‘value’ get.spectral.derivative: no visible global function definition for ‘geom_point’ get.spectral.derivative: no visible global function definition for ‘labs’ get.spectral.derivative: no visible global function definition for ‘theme_bw’ get.spectral.derivative: no visible global function definition for ‘theme’ get.spectral.derivative: no visible global function definition for ‘element_text’ get.spectral.derivative: no visible global function definition for ‘element_rect’ get.spectral.derivative: no visible global function definition for ‘element_blank’ get.srf.from_fwhm: no visible global function definition for ‘dnorm’ get.srf.from_fwhm: no visible global function definition for ‘write.table’ get.srf.from_fwhm: no visible global function definition for ‘ggplot’ get.srf.from_fwhm: no visible global function definition for ‘aes’ get.srf.from_fwhm: no visible binding for global variable ‘wavelength’ get.srf.from_fwhm: no visible binding for global variable ‘Response’ get.srf.from_fwhm: no visible binding for global variable ‘spectra_band’ get.srf.from_fwhm: no visible global function definition for ‘geom_line’ get.srf.from_fwhm: no visible global function definition for ‘scale_colour_viridis_d’ get.srf.from_fwhm: no visible global function definition for ‘labs’ get.srf.from_fwhm: no visible global function definition for ‘theme_bw’ get.srf.from_fwhm: no visible global function definition for ‘theme’ get.srf.from_fwhm: no visible global function definition for ‘element_text’ get.stats: no visible global function definition for ‘predict’ get.stats: no visible global function definition for ‘cor’ get.stats.ind: no visible global function definition for ‘cor’ get.stats.plsr: no visible global function definition for ‘predict’ get.stats.plsr: no visible global function definition for ‘cor’ getAnomalies: no visible global function definition for ‘getZ’ getAnomalies: no visible global function definition for ‘stackApply’ getAnomalies: no visible global function definition for ‘writeRaster’ getAnomalies: no visible global function definition for ‘readOGR’ getAnomalies: no visible binding for global variable ‘stack.image’ getAnomalies: no visible binding for global variable ‘rast.2020’ getCor : : no visible global function definition for ‘rnorm’ getCor : : no visible global function definition for ‘runif’ getCor : : no visible global function definition for ‘qpois’ getCor : : no visible global function definition for ‘qnorm’ getCor: no visible global function definition for ‘runif’ getCor: no visible global function definition for ‘cor’ getFLD2_SE: no visible global function definition for ‘interp1’ getIndices: no visible global function definition for ‘txtProgressBar’ getIndices: no visible global function definition for ‘setTxtProgressBar’ getIndicesSE2: no visible binding for global variable ‘data’ getIndicesSE2: no visible global function definition for ‘txtProgressBar’ getIndicesSE2: no visible global function definition for ‘setTxtProgressBar’ getIndicesSE2.ML: no visible binding for global variable ‘data’ getIndicesSE2.ML: no visible global function definition for ‘txtProgressBar’ getIndicesSE2.ML: no visible global function definition for ‘setTxtProgressBar’ getKmeans: no visible global function definition for ‘complete.cases’ getKmeans: no visible global function definition for ‘kmeans’ getLUT: no visible binding for global variable ‘variable’ getLUT_liberty: no visible binding for global variable ‘variable’ getLUT_time: no visible global function definition for ‘install.packages’ getLUT_time: no visible global function definition for ‘aggregate’ getLUT_time: no visible global function definition for ‘minute<-’ getLUT_time: no visible binding for global variable ‘Date’ getMLmodel: no visible global function definition for ‘callback_early_stopping’ getMLmodel: no visible global function definition for ‘optimizer_adam’ getMLmodel: no visible global function definition for ‘optimizer_adadelta’ getMLmodel: no visible global function definition for ‘optimizer_adagrad’ getMLmodel: no visible global function definition for ‘optimizer_adamax’ getMLmodel: no visible global function definition for ‘optimizer_nadam’ getMLmodel: no visible global function definition for ‘optimizer_rmsprop’ getMLmodel: no visible global function definition for ‘optimizer_sgd’ getMLmodel: no visible global function definition for ‘array_reshape’ getMLmodel: no visible global function definition for ‘%>%’ getMLmodel: no visible global function definition for ‘keras_model_sequential’ getMLmodel: no visible global function definition for ‘layer_dense’ getMLmodel: no visible global function definition for ‘layer_dropout’ getMLmodel: no visible global function definition for ‘compile’ getMLmodel: no visible global function definition for ‘fit’ getMLmodel: no visible global function definition for ‘evaluate’ getMLmodel: no visible global function definition for ‘save_model_hdf5’ getMLmodel: no visible global function definition for ‘layer_conv_1d’ getMLmodel: no visible global function definition for ‘layer_max_pooling_1d’ getMLmodel: no visible global function definition for ‘layer_flatten’ getMLmodel: no visible global function definition for ‘expr’ getMLmodel: no visible global function definition for ‘cor’ getMLmodel: no visible global function definition for ‘ggplot’ getMLmodel: no visible global function definition for ‘aes_string’ getMLmodel: no visible global function definition for ‘geom_point’ getMLmodel: no visible global function definition for ‘aes’ getMLmodel: no visible global function definition for ‘theme_bw’ getMLmodel: no visible global function definition for ‘xlim’ getMLmodel: no visible global function definition for ‘ylim’ getMLmodel: no visible global function definition for ‘ggtitle’ getMLmodel: no visible global function definition for ‘scale_color_gradient’ getMLmodel: no visible global function definition for ‘theme’ getMLmodel: no visible global function definition for ‘element_text’ getMLmodel: no visible global function definition for ‘element_blank’ getMLmodel: no visible global function definition for ‘labs’ getMLmodel: no visible global function definition for ‘stat_smooth’ getMLmodel: no visible global function definition for ‘ggsave’ getMLmodel.withRetrain: no visible global function definition for ‘callback_early_stopping’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_adam’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_adadelta’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_adagrad’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_adamax’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_nadam’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_rmsprop’ getMLmodel.withRetrain: no visible global function definition for ‘optimizer_sgd’ getMLmodel.withRetrain: no visible global function definition for ‘array_reshape’ getMLmodel.withRetrain : create_model: no visible global function definition for ‘keras_model_sequential’ getMLmodel.withRetrain : create_model: no visible global function definition for ‘%>%’ getMLmodel.withRetrain : create_model: no visible global function definition for ‘layer_dense’ getMLmodel.withRetrain: no visible global function definition for ‘%>%’ getMLmodel.withRetrain: no visible global function definition for ‘compile’ getMLmodel.withRetrain: no visible global function definition for ‘fit’ getMLmodel.withRetrain: no visible global function definition for ‘evaluate’ getMLmodel.withRetrain: no visible global function definition for ‘save_model_hdf5’ getMLmodel.withRetrain: no visible global function definition for ‘save_model_weights_hdf5’ getMLmodel.withRetrain: no visible global function definition for ‘write.table’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘keras_model_sequential’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘%>%’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘layer_conv_1d’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘layer_max_pooling_1d’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘layer_flatten’ getMLmodel.withRetrain : create_cnn_model: no visible global function definition for ‘layer_dense’ getMLmodel.withRetrain: no visible global function definition for ‘expr’ getMLmodel.withRetrain: no visible global function definition for ‘cor’ getMLmodel.withRetrain: no visible global function definition for ‘ggplot’ getMLmodel.withRetrain: no visible global function definition for ‘aes_string’ getMLmodel.withRetrain: no visible global function definition for ‘geom_point’ getMLmodel.withRetrain: no visible global function definition for ‘aes’ getMLmodel.withRetrain: no visible global function definition for ‘theme_bw’ getMLmodel.withRetrain: no visible global function definition for ‘xlim’ getMLmodel.withRetrain: no visible global function definition for ‘ylim’ getMLmodel.withRetrain: no visible global function definition for ‘ggtitle’ getMLmodel.withRetrain: no visible global function definition for ‘scale_color_gradient’ getMLmodel.withRetrain: no visible global function definition for ‘theme’ getMLmodel.withRetrain: no visible global function definition for ‘element_text’ getMLmodel.withRetrain: no visible global function definition for ‘element_blank’ getMLmodel.withRetrain: no visible global function definition for ‘labs’ getMLmodel.withRetrain: no visible global function definition for ‘stat_smooth’ getMLmodel.withRetrain: no visible global function definition for ‘ggsave’ getMLmodel.withRetrain_app: no visible global function definition for ‘callback_lambda’ getMLmodel.withRetrain_app : : no visible global function definition for ‘incProgress’ getMLmodel.withRetrain_app: no visible global function definition for ‘array_reshape’ getMLmodel.withRetrain_app : create_model: no visible global function definition for ‘keras_model_sequential’ getMLmodel.withRetrain_app : create_model: no visible global function definition for ‘%>%’ getMLmodel.withRetrain_app : create_model: no visible global function definition for ‘layer_dense’ getMLmodel.withRetrain_app: no visible global function definition for ‘%>%’ getMLmodel.withRetrain_app: no visible global function definition for ‘compile’ getMLmodel.withRetrain_app: no visible global function definition for ‘fit’ getMLmodel.withRetrain_app: no visible global function definition for ‘evaluate’ getMLmodel.withRetrain_app: no visible global function definition for ‘save_model_hdf5’ getMLmodel.withRetrain_app: no visible global function definition for ‘save_model_weights_hdf5’ getMLmodel.withRetrain_app: no visible global function definition for ‘write.table’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘keras_model_sequential’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘%>%’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘layer_conv_1d’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘layer_max_pooling_1d’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘layer_flatten’ getMLmodel.withRetrain_app : create_cnn_model: no visible global function definition for ‘layer_dense’ getMLmodel.withRetrain_app: no visible global function definition for ‘expr’ getMLmodel.withRetrain_app: no visible global function definition for ‘cor’ getMLmodel.withRetrain_app: no visible global function definition for ‘ggplot’ getMLmodel.withRetrain_app: no visible global function definition for ‘aes_string’ getMLmodel.withRetrain_app: no visible global function definition for ‘geom_point’ getMLmodel.withRetrain_app: no visible global function definition for ‘xlim’ getMLmodel.withRetrain_app: no visible global function definition for ‘ylim’ getMLmodel.withRetrain_app: no visible global function definition for ‘geom_smooth’ getMLmodel.withRetrain_app: no visible global function definition for ‘labs’ getMLmodel.withRetrain_app: no visible global function definition for ‘theme_bw’ getMLmodel.withRetrain_app: no visible global function definition for ‘stat_smooth’ getMLmodel.withRetrain_app: no visible global function definition for ‘theme’ getMLmodel.withRetrain_app: no visible global function definition for ‘element_text’ getMLmodel.withRetrain_app: no visible global function definition for ‘element_rect’ getMLmodel.withRetrain_app: no visible global function definition for ‘element_blank’ getMLmodel.withRetrain_app: no visible global function definition for ‘ggsave’ getPredicts: no visible global function definition for ‘predict’ getPredicts: no visible global function definition for ‘array_reshape’ getPredicts: no visible binding for global variable ‘sd’ getSCOPE_outputs: no visible global function definition for ‘read.table’ getSCOPE_outputs: no visible global function definition for ‘txtProgressBar’ getSCOPE_outputs: no visible global function definition for ‘setTxtProgressBar’ getSCOPE_outputs_v1: no visible global function definition for ‘txtProgressBar’ getSCOPE_outputs_v1: no visible global function definition for ‘setTxtProgressBar’ getSeries: no visible global function definition for ‘txtProgressBar’ getSeries: no visible global function definition for ‘setTxtProgressBar’ getSeries: no visible global function definition for ‘brick’ getSim_fromLUT: no visible global function definition for ‘install.packages’ getSim_fromLUT: no visible global function definition for ‘%dopar%’ getSim_fromLUT: no visible global function definition for ‘foreach’ getSim_fromLUT: no visible binding for global variable ‘i’ getSim_fromLUT: no visible global function definition for ‘stack’ getSim_fromLUT: no visible global function definition for ‘ggplot’ getSim_fromLUT: no visible global function definition for ‘aes’ getSim_fromLUT: no visible binding for global variable ‘ind’ getSim_fromLUT: no visible binding for global variable ‘values’ getSim_fromLUT: no visible binding for global variable ‘Trait’ getSim_fromLUT: no visible global function definition for ‘theme_bw’ getSim_fromLUT: no visible global function definition for ‘geom_line’ getSim_fromLUT: no visible global function definition for ‘labs’ getSim_fromLUT: no visible global function definition for ‘ggtitle’ getSim_fromLUT: no visible global function definition for ‘geom_point’ getSim_fromLUT: no visible global function definition for ‘theme’ getSim_fromLUT: no visible global function definition for ‘element_text’ getSim_fromLUT: no visible global function definition for ‘rainbow’ getSim_fromLUT: no visible global function definition for ‘legend’ getSpatialTrait: no visible global function definition for ‘brick’ getSpatialTrait: no visible global function definition for ‘st_crs’ getSpatialTrait: no visible global function definition for ‘na.omit’ getSpatialTrait: no visible global function definition for ‘predict’ getSpatialTrait: no visible global function definition for ‘aggregate’ getSpatialTrait: no visible binding for global variable ‘quantile’ getSpatialTrait: no visible global function definition for ‘as.formula’ getSpatialTrait: no visible global function definition for ‘lm’ getSpatialTrait: no visible global function definition for ‘cor’ getSpatialTrait: no visible global function definition for ‘write.table’ getSpatialTrait: no visible global function definition for ‘ggplot’ getSpatialTrait: no visible global function definition for ‘aes’ getSpatialTrait: no visible binding for global variable ‘y’ getSpatialTrait: no visible global function definition for ‘geom_point’ getSpatialTrait: no visible global function definition for ‘geom_smooth’ getSpatialTrait: no visible binding for global variable ‘lm’ getSpatialTrait: no visible global function definition for ‘theme_bw’ getSpatialTrait: no visible global function definition for ‘geom_abline’ getSpatialTrait: no visible global function definition for ‘xlab’ getSpatialTrait: no visible global function definition for ‘ylab’ getSpatialTrait: no visible global function definition for ‘ggtitle’ getSpatialTrait: no visible global function definition for ‘ggsave’ getSpatialTrait: no visible global function definition for ‘writeRaster’ getSpatial_index: no visible global function definition for ‘brick’ getSpectraIndices: no visible global function definition for ‘brick’ getSpectraIndices: no visible global function definition for ‘writeRaster’ getSpectraIndices: no visible global function definition for ‘stack’ getSplitData: no visible global function definition for ‘na.omit’ getSplitData: no visible global function definition for ‘predict’ getSplitData: no visible global function definition for ‘cor’ getSplitData: no visible global function definition for ‘prcomp’ getSplitData_noMessages: no visible global function definition for ‘na.omit’ getSplitData_noMessages: no visible global function definition for ‘predict’ getSplitData_noMessages: no visible global function definition for ‘cor’ getSplitData_noMessages: no visible global function definition for ‘prcomp’ getStacks: no visible global function definition for ‘txtProgressBar’ getStacks: no visible global function definition for ‘setTxtProgressBar’ getStacks: no visible global function definition for ‘raster’ getStacks: no visible global function definition for ‘stack’ getStacks: no visible global function definition for ‘writeRaster’ getStacks_v0: no visible global function definition for ‘txtProgressBar’ getStacks_v0: no visible global function definition for ‘setTxtProgressBar’ getStacks_v0: no visible global function definition for ‘stack’ getStacks_v0: no visible global function definition for ‘writeRaster’ getTIFFs: no visible global function definition for ‘txtProgressBar’ getTIFFs: no visible global function definition for ‘setTxtProgressBar’ getTIFFs: no visible global function definition for ‘nc_open’ getTIFFs: no visible global function definition for ‘ncvar_get’ getTIFFs: no visible global function definition for ‘ncatt_get’ getTIFFs: no visible global function definition for ‘raster’ getTIFFs: no visible global function definition for ‘CRS’ getTIFFs: no visible global function definition for ‘writeRaster’ getTIFFs: no visible global function definition for ‘nc_close’ getVIF: no visible global function definition for ‘formula’ getVIF: no visible global function definition for ‘lm’ getVIF: no visible global function definition for ‘flush.console’ get_append: no visible global function definition for ‘read.table’ get_data: no visible global function definition for ‘runif’ get_distributionLUT: no visible binding for global variable ‘std_gauss’ get_response.R: no visible global function definition for ‘dnorm’ get_simulations: no visible global function definition for ‘install.packages’ get_simulations: no visible binding for global variable ‘LUT’ get_simulations: no visible global function definition for ‘%dopar%’ get_simulations: no visible global function definition for ‘foreach’ get_simulations: no visible binding for global variable ‘i’ get_simulations: no visible global function definition for ‘stack’ get_simulations: no visible global function definition for ‘%>%’ get_simulations: no visible global function definition for ‘group_by’ get_simulations: no visible binding for global variable ‘ind’ get_simulations: no visible binding for global variable ‘group’ get_simulations: no visible global function definition for ‘summarize’ get_simulations: no visible binding for global variable ‘values’ get_simulations: no visible global function definition for ‘n’ get_simulations: no visible global function definition for ‘quantile’ get_simulations: no visible binding for global variable ‘se’ get_simulations: no visible global function definition for ‘ggplot’ get_simulations: no visible global function definition for ‘aes’ get_simulations: no visible global function definition for ‘theme_bw’ get_simulations: no visible global function definition for ‘geom_line’ get_simulations: no visible binding for global variable ‘quantile.25’ get_simulations: no visible binding for global variable ‘quantile.75’ get_simulations: no visible global function definition for ‘labs’ get_simulations: no visible global function definition for ‘ggtitle’ get_simulations: no visible global function definition for ‘geom_point’ get_simulations: no visible global function definition for ‘theme’ get_simulations: no visible global function definition for ‘element_text’ hybrid_inversion: no visible global function definition for ‘install.packages’ hybrid_inversion: no visible global function definition for ‘as.formula’ hybrid_inversion: no visible global function definition for ‘detectCores’ hybrid_inversion: no visible global function definition for ‘makePSOCKcluster’ hybrid_inversion: no visible global function definition for ‘stopCluster’ hybrid_inversion: no visible global function definition for ‘createFolds’ hybrid_inversion: no visible global function definition for ‘caretModelSpec’ hybrid_inversion: no visible global function definition for ‘trainControl’ hybrid_inversion: no visible global function definition for ‘predict’ hybrid_inversion: no visible global function definition for ‘cor’ hybrid_inversion: no visible global function definition for ‘ggplot’ hybrid_inversion: no visible global function definition for ‘aes’ hybrid_inversion: no visible binding for global variable ‘pred’ hybrid_inversion: no visible global function definition for ‘geom_point’ hybrid_inversion: no visible global function definition for ‘geom_smooth’ hybrid_inversion: no visible binding for global variable ‘lm’ hybrid_inversion: no visible global function definition for ‘theme_bw’ hybrid_inversion: no visible global function definition for ‘geom_abline’ hybrid_inversion: no visible global function definition for ‘coord_fixed’ hybrid_inversion: no visible global function definition for ‘xlab’ hybrid_inversion: no visible global function definition for ‘ylab’ hybrid_inversion: no visible global function definition for ‘ggtitle’ hybrid_inversionE: no visible global function definition for ‘install.packages’ hybrid_inversionE: no visible binding for global variable ‘acron’ hybrid_inversionE: no visible global function definition for ‘as.formula’ hybrid_inversionE: no visible global function definition for ‘detectCores’ hybrid_inversionE: no visible global function definition for ‘makePSOCKcluster’ hybrid_inversionE: no visible global function definition for ‘stopCluster’ hybrid_inversionE: no visible global function definition for ‘createFolds’ hybrid_inversionE: no visible global function definition for ‘txtProgressBar’ hybrid_inversionE: no visible global function definition for ‘setTxtProgressBar’ hybrid_inversionE: no visible global function definition for ‘caretModelSpec’ hybrid_inversionE: no visible global function definition for ‘trainControl’ hybrid_inversionE: no visible global function definition for ‘predict’ hybrid_inversionE: no visible global function definition for ‘cor’ hybrid_inversionE: no visible global function definition for ‘ggplot’ hybrid_inversionE: no visible global function definition for ‘aes’ hybrid_inversionE: no visible binding for global variable ‘pred’ hybrid_inversionE: no visible global function definition for ‘geom_point’ hybrid_inversionE: no visible global function definition for ‘geom_smooth’ hybrid_inversionE: no visible binding for global variable ‘lm’ hybrid_inversionE: no visible global function definition for ‘theme_bw’ hybrid_inversionE: no visible global function definition for ‘geom_abline’ hybrid_inversionE: no visible global function definition for ‘coord_fixed’ hybrid_inversionE: no visible global function definition for ‘xlab’ hybrid_inversionE: no visible global function definition for ‘ylab’ hybrid_inversionE: no visible global function definition for ‘ggtitle’ hybrid_inversionE: no visible binding for global variable ‘IncludeModel’ numjacobian: no visible binding for global variable ‘leafbio’ plotspectra: no visible global function definition for ‘par’ plotspectra: no visible global function definition for ‘rect’ plotspectra: no visible global function definition for ‘grid’ plotspectra : : no visible global function definition for ‘points’ plotspectra_SE: no visible global function definition for ‘par’ plotspectra_SE: no visible global function definition for ‘rect’ plotspectra_SE: no visible global function definition for ‘axis’ plotspectra_SE : : no visible global function definition for ‘points’ plotspectra_SE: no visible global function definition for ‘grid’ plotspectra_image: no visible binding for global variable ‘raster’ plotspectra_image: no visible global function definition for ‘stack’ plotspectra_image: no visible global function definition for ‘ggplot’ plotspectra_image: no visible global function definition for ‘aes’ plotspectra_image: no visible binding for global variable ‘ind’ plotspectra_image: no visible binding for global variable ‘values’ plotspectra_image: no visible binding for global variable ‘ID’ plotspectra_image: no visible global function definition for ‘theme_bw’ plotspectra_image: no visible global function definition for ‘geom_line’ plotspectra_image: no visible global function definition for ‘labs’ plotspectra_image: no visible global function definition for ‘ggtitle’ plotspectra_image: no visible global function definition for ‘geom_point’ plotspectra_image: no visible global function definition for ‘theme’ plotspectra_image: no visible global function definition for ‘element_text’ plotspectra_image: no visible global function definition for ‘rainbow’ plotspectra_image: no visible global function definition for ‘legend’ rchisqcor: no visible global function definition for ‘plnorm’ rchisqcor: no visible global function definition for ‘vecNAsearch’ rchisqcor: no visible global function definition for ‘na.omit’ rchisqcor: no visible global function definition for ‘fitdistr’ rchisqcor: no visible binding for global variable ‘qchisq’ resample_fun: no visible global function definition for ‘dnorm’ rgammacor: no visible global function definition for ‘pnorm’ rgammacor: no visible global function definition for ‘vecNAsearch’ rgammacor: no visible global function definition for ‘na.omit’ rgammacor: no visible global function definition for ‘fitdistr’ rgammacor: no visible binding for global variable ‘qgamma’ rlnormcor: no visible global function definition for ‘rlnorm’ rnegbinomcor: no visible global function definition for ‘pnorm’ rnegbinomcor: no visible global function definition for ‘vecNAsearch’ rnegbinomcor: no visible global function definition for ‘na.omit’ rnegbinomcor: no visible global function definition for ‘fitdistr’ rnegbinomcor: no visible binding for global variable ‘qnbinom’ rnormcor: no visible global function definition for ‘rnorm’ rpoiscor: no visible global function definition for ‘plnorm’ rpoiscor: no visible global function definition for ‘vecNAsearch’ rpoiscor: no visible global function definition for ‘na.omit’ rpoiscor: no visible global function definition for ‘fitdistr’ rpoiscor: no visible binding for global variable ‘qpois’ runifcor.cor: no visible global function definition for ‘runif’ rweibullcor: no visible global function definition for ‘pnorm’ rweibullcor: no visible global function definition for ‘vecNAsearch’ rweibullcor: no visible global function definition for ‘na.omit’ rweibullcor: no visible global function definition for ‘fitdistr’ rweibullcor: no visible binding for global variable ‘qweibull’ sanitizeInf: no visible global function definition for ‘anyInf’ Undefined global functions or variables: %>% %dopar% CRS Date Eo Extraterrestrial_irradiance I.Johnson ID IQR IncludeModel Kant Kca Kcab Kcbc Kp LUT RFL Response SCOPE.LUT.default Sensor Trait abline acron aes aes_string aggregate anyInf approx array_reshape as.formula as_Spatial average axis band brick callback_early_stopping callback_lambda caretModelSpec ceil colorRampPalette compile complete.cases coord_fixed cor createFolds createMultiFolds crossval cube_view data dataSpec_PDB dataSpec_PRO detectCores dnorm element_blank element_rect element_text evaluate expr extent fit fitdistr flush.console fluspect_B_CX_PSI_PSII_combined foreach formula geom_abline geom_line geom_point geom_ribbon geom_smooth getZ getinputLUT ggplot ggsave ggtitle grid group group_by guide_legend guides i image_mask incProgress ind inputs inputs.SPART install.packages installed.packages integrate interp1 irrad items_fetch items_sign keras_model_sequential kmeans labs layer_conv_1d layer_dense layer_dropout layer_flatten layer_max_pooling_1d layout leafbio left_join legend lines lm makeCluster makePSOCKcluster median minute<- mutate mvr n n_bands.points na.omit na.pass nc_close nc_open ncatt_get ncvar_get optimizer_adadelta optimizer_adagrad optimizer_adam optimizer_adamax optimizer_nadam optimizer_rmsprop optimizer_sgd optipar2021.Pro.CX par percentile_10 percentile_25 percentile_75 percentile_90 plnorm pnorm points post_request prcomp pred predict projection<- qchisq qgamma qnbinom qnorm qpois quantile quantile.25 quantile.75 qweibull r_leaf r_understorey rad.toa rainbow rast rast.2020 raster raster_cube read.table readOGR rect reduce_time reflectance rfl.soil rfl.toa rfl.toc rfl.toc.brdf rlnorm rnorm runif save_model_hdf5 save_model_weights_hdf5 scale_color_gradient scale_colour_viridis_d sd se select_bands setTxtProgressBar sign_planetary_computer slice_time spectra_band st_as_stars.cube st_crs stac_image_collection stac_search stack stack.image stackApply stat_smooth std_gauss stopCluster summarise summarize svm t_leaf theme theme_bw trainControl tune.control txtProgressBar value values variable vecNAsearch wave wavelength write.csv write.table writeRaster xlab xlim y ylab ylim Consider adding importFrom("grDevices", "colorRampPalette", "rainbow") importFrom("graphics", "abline", "axis", "grid", "layout", "legend", "lines", "par", "points", "rect") importFrom("stats", "IQR", "aggregate", "approx", "as.formula", "complete.cases", "cor", "dnorm", "formula", "integrate", "kmeans", "lm", "median", "na.omit", "na.pass", "plnorm", "pnorm", "prcomp", "predict", "qchisq", "qgamma", "qnbinom", "qnorm", "qpois", "quantile", "qweibull", "rlnorm", "rnorm", "runif", "sd") importFrom("utils", "data", "flush.console", "install.packages", "installed.packages", "read.table", "setTxtProgressBar", "stack", "txtProgressBar", "write.csv", "write.table") to your NAMESPACE file. Found if() conditions comparing class() to string: File ‘ToolsRTM/R/getPredicts.R’: if (class(data.Y) != "numeric") ... File ‘ToolsRTM/R/getSplitData.R’: if (class(data) != "data.frame" | is.null(data)) ... File ‘ToolsRTM/R/getSplitData_noMessages.R’: if (class(data) != "data.frame" | is.null(data)) ... File ‘ToolsRTM/R/getVIF.r’: if (class(in_frame) != "data.frame") ... Use inherits() (or maybe is()) instead. * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... NOTE Rd file 'get.inversionOpt.Rd': \examples lines wider than 100 characters: result <- get.inversionOpt(sensor_data, rtm_data, lut_table, wavelengths, method='merit-RMSE', nOpt=5) result <- get.inversionOpt(sensor_data, rtm_data, lut_table, wavelengths, method = 'merit-RMSE', nOpt = 5) Rd file 'get.satellite_collection.Rd': \examples lines wider than 100 characters: coleccion.microsoft <- c('sentinel-2-l2a','landsat-c2-l2','modis-17A2HGF-061','modis-09A1-061','modis-09Q1-061','modis-11A2-061','modis ... [TRUNCATED] Rd file 'get.sentinel2_cube.Rd': \examples lines wider than 100 characters: shape <- sf::st_as_sf(data.frame(id = 1, geometry = sf::st_sfc(sf::st_polygon(list(rbind(c(4.8, 52.2), c(4.8, 52.4), c(5.0, 52.4), c(5.0, 52.2), c(4.8, 52.2))))), crs = 4326)) sentinel2_cube <- get.sentinel2_cube(s_collection, shape, date_range, aggregation_method = "mean", get.dataset = TRUE) Rd file 'get.spectra.convolved.Rd': \examples lines wider than 100 characters: #spectral response function downloaded from: https://oceancolor.gsfc.nasa.gov/resources/docs/rsr_tables/ reflectance_values <- ToolsRTM::foursail(inputLUT = df.LUT[1,], rsoil = rsoil, LeafModel = 'PROSPECT-PRO') convolved_spectra <- get.spectra.convolved(rfl = sim.matrix, sensor = "Sentinel2a", plot.spectra = TRUE) Rd file 'get.spectral.convolution.Rd': \examples lines wider than 100 characters: df.irradiance <- data.frame(wavelength = seq(400, 700, 1), irradiance = rnorm(301)) # Example irradiance data sensor.i <- data.frame(wavelength = seq(400, 700, 1), response = runif(301)) # Example sensor response Rd file 'get.spectral.derivative.Rd': \examples lines wider than 100 characters: # Assuming you have a DataFrame named 'spectra_df' with columns representing wavelengths and spectral values These lines will be truncated in the PDF manual. * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘EnMap.characteristics’ ‘Extraterrestrial_irradiance’ ‘LANDSAT4.TM’ ‘LANDSAT5.TM’ ‘LANDSAT7.ETM’ ‘LANDSAT8.OLI’ ‘LeafDB.Angers’ ‘Sentinel2A.MSI’ ‘Sentinel2B.MSI’ ‘Sentinel3A.OLCI’ ‘Sentinel3B.OLCI’ ‘TerraAqua.MODIS’ ‘amerge’ ‘carspls’ ‘dataSpec_PDB’ ‘dataSpec_PRO’ ‘dataspec.liberty’ ‘fix’ ‘fwhm.prisma’ ‘getAnomalies’ ‘inputsFlUSPECT’ ‘inputsINFORM’ ‘inputsLiberty’ ‘inputsPROSAIL’ ‘inputsRTMs’ ‘inputsSPART’ ‘leaf_spectrum’ ‘optipar’ ‘optipar.2015’ ‘sanitizeInf’ ‘sensor.characteristics’ ‘srf.prisma’ ‘srf.sentinel2a’ ‘srf.sentinel2b’ Undocumented data sets: ‘EnMap.characteristics’ ‘Extraterrestrial_irradiance’ ‘LANDSAT4.TM’ ‘LANDSAT5.TM’ ‘LANDSAT7.ETM’ ‘LANDSAT8.OLI’ ‘Sentinel2A.MSI’ ‘Sentinel2B.MSI’ ‘Sentinel3A.OLCI’ ‘Sentinel3B.OLCI’ ‘TerraAqua.MODIS’ ‘dataSpec_PDB’ ‘dataSpec_PRO’ ‘fwhm.prisma’ ‘inputsFlUSPECT’ ‘inputsINFORM’ ‘inputsLiberty’ ‘inputsPROSAIL’ ‘inputsRTMs’ ‘inputsSPART’ ‘LeafDB.Angers’ ‘leaf_spectrum’ ‘dataspec.liberty’ ‘optipar’ ‘optipar.2015’ ‘sensor.characteristics’ ‘srf.prisma’ ‘srf.sentinel2a’ ‘srf.sentinel2b’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'getIndices.Rd': getIndices Code: function(data, pattern.rfl = "R.", factor = NULL, spectral.domain = NULL) Docs: function(data, pattern.rfl = "R.", spectral.domain = NULL) Argument names in code not in docs: factor Mismatches in argument names: Position: 3 Code: factor Docs: spectral.domain * checking Rd \usage sections ... WARNING Documented arguments not in \usage in Rd file 'SPART.simN.Rd': ‘N’ Undocumented arguments in Rd file 'foursail2.Rd' ‘FieldObserv’ Undocumented arguments in Rd file 'get.LUTfromRanges.Rd' ‘setseed’ Documented arguments not in \usage in Rd file 'get.LUTfromRanges.Rd': ‘set.seed’ Undocumented arguments in Rd file 'get.inversion.Rd' ‘method.resampling’ ‘...’ Documented arguments not in \usage in Rd file 'get.inversion.Rd': ‘method.control’ Undocumented arguments in Rd file 'get.satellite_collection.Rd' ‘date_range’ Documented arguments not in \usage in Rd file 'getIndices.Rd': ‘header’ Undocumented arguments in Rd file 'getLUT.Rd' ‘setseed’ Undocumented arguments in Rd file 'getLUT_liberty.Rd' ‘setseed’ Undocumented arguments in Rd file 'getMLmodel.withRetrain_app.Rd' ‘n.neurons’ ‘session’ Undocumented arguments in Rd file 'getSpatialTrait.Rd' ‘factorR’ Undocumented arguments in Rd file 'getStacks_v0.Rd' ‘frequency’ Undocumented arguments in Rd file 'get_data.Rd' ‘random.input’ Documented arguments not in \usage in Rd file 'get_data.Rd': ‘seed’ Undocumented arguments in Rd file 'get_distributionLUT.Rd' ‘nSamples’ ‘DepCab’ Documented arguments not in \usage in Rd file 'get_distributionLUT.Rd': ‘nbSamples’ Undocumented arguments in Rd file 'hybrid_inversion.Rd' ‘collinearity’ Undocumented arguments in Rd file 'hybrid_inversionE.Rd' ‘collinearity’ Documented arguments not in \usage in Rd file 'hybrid_inversionE.Rd': ‘method’ ‘acron’ Undocumented arguments in Rd file 'liberty.Rd' ‘inputLUT’ Undocumented arguments in Rd file 'rlnormcor.Rd' ‘...’ Undocumented arguments in Rd file 'rnormcorV.Rd' ‘...’ Undocumented arguments in Rd file 'rpoiscor.Rd' ‘...’ Documented arguments not in \usage in Rd file 'sigmoid.soil.Rd': ‘phi’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'COST_4Fluspect.Rd': ‘params’ ‘measurement’ ‘input’ Argument items with no description in Rd file 'MAE.Rd': ‘m’ ‘o’ Argument items with no description in Rd file 'RMSE.Rd': ‘m’ ‘o’ Argument items with no description in Rd file 'calc_fluspect_bcar.Rd': ‘params’ ‘spectral’ ‘leafbio’ ‘optipar’ Argument items with no description in Rd file 'color.gradient.Rd': ‘x’ ‘colors’ ‘colsteps’ Argument items with no description in Rd file 'ephoton.Rd': ‘lambda’ Argument items with no description in Rd file 'extract_dates_from_tiff_files.Rd': ‘tiff_files’ Argument items with no description in Rd file 'getIndices.Rd': ‘header’ Argument items with no description in Rd file 'getReverse.trans.Rd': ‘digits’ Argument items with no description in Rd file 'normalize.Rd': ‘x’ ‘low’ ‘high’ Argument items with no description in Rd file 'numjacobian.Rd': ‘x’ ‘spectral’ ‘inputLeaf’ ‘optipar’ Argument items with no description in Rd file 'plotspectra.Rd': ‘df’ ‘x’ ‘y’ ‘cols’ ‘xlim’ ‘ylim’ ‘main’ ‘xlab’ ‘ylab’ ‘...’ Argument items with no description in Rd file 'plotspectra_SE.Rd': ‘df’ ‘x’ ‘y’ ‘cols’ ‘xlim’ ‘ylim’ ‘main’ ‘xlab’ ‘ylab’ ‘...’ Argument items with no description in Rd file 'resample_fun.Rd': ‘center’ ‘wl’ ‘fwhm’ * checking for unstated dependencies in examples ... ERROR Warning: parse error in file 'ToolsRTM-Ex.R': 6: unexpected symbol 19: 20: Here adding ^ ** will not attempt to run examples * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... WARNING LazyData DB of 6.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... WARNING Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress Extraterrestrial_irradiance.rda 20Kb 14Kb xz LANDSAT8.OLI.rda 24Kb 12Kb xz Sentinel2A.MSI.rda 40Kb 14Kb xz Sentinel2B.MSI.rda 47Kb 15Kb xz Sentinel3A.OLCI.rda 80Kb 33Kb xz Sentinel3B.OLCI.rda 81Kb 33Kb xz TerraAqua.MODIS.rda 74Kb 49Kb xz dataSpec_PDB.rda 42Kb 22Kb xz dataSpec_PRO.rda 51Kb 31Kb xz leafDB.Angers.rda 4.7Mb 2.3Mb xz leaf_spectrum.rda 28Kb 19Kb xz optipar.rda 80Kb 49Kb xz optipar2015.rda 59Kb 35Kb xz srf.sentinel2a.rda 13Kb 8Kb xz srf.sentinel2b.rda 13Kb 8Kb xz * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [3s/3s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 9 WARNINGs, 4 NOTEs