|
| 1 | +# Derived from a combination of |
| 2 | +# |
| 3 | +# 1) The bootstrap.R files in the arrow-adbc suite of R packages, |
| 4 | +# https://github.com/apache/arrow-adbc/tree/main/r, all of which are Apache |
| 5 | +# licensed with the following copyright: |
| 6 | +# Copyright 2022 The Apache Software Foundation |
| 7 | +# |
| 8 | +# 2) LightGBM's build-cran-package.sh script, |
| 9 | +# https://github.com/microsoft/LightGBM/blob/master/build-cran-package.sh, |
| 10 | +# which is MIT licensed with the following copyright: |
| 11 | +# Copyright (c) Microsoft Corporation |
| 12 | + |
| 13 | +# Use xfun for find and replace in files / directories |
| 14 | +# require(xfun) |
| 15 | +# if (!require(xfun)) { |
| 16 | +# install.packages("xfun") |
| 17 | +# } |
| 18 | + |
| 19 | +# Create the stochtree_cran folder |
| 20 | +cran_dir <- "stochtree_cran" |
| 21 | +if (!dir.exists(cran_dir)) { |
| 22 | + dir.create(cran_dir, recursive = TRUE) |
| 23 | +} |
| 24 | + |
| 25 | +# Copy the "core" package files to CRAN folder |
| 26 | +src_files <- list.files("src", recursive = TRUE, full.names = TRUE) |
| 27 | +pybind_src_files <- list.files("src", pattern = "^(py_)", recursive = TRUE, full.names = TRUE) |
| 28 | +r_src_files <- src_files[!(src_files %in% pybind_src_files)] |
| 29 | +pkg_core_files <- c( |
| 30 | + ".Rbuildignore", |
| 31 | + "DESCRIPTION", |
| 32 | + "LICENSE", |
| 33 | + "LICENSE.md", |
| 34 | + list.files("man", recursive = TRUE, full.names = TRUE), |
| 35 | + "NAMESPACE", |
| 36 | + list.files("R", recursive = TRUE, full.names = TRUE), |
| 37 | + r_src_files, |
| 38 | + list.files("test/r", recursive = TRUE, full.names = TRUE), |
| 39 | + list.files("vignettes", recursive = TRUE, full.names = TRUE) |
| 40 | +) |
| 41 | +pkg_core_files_dst <- file.path(cran_dir, pkg_core_files) |
| 42 | +if (all(file.exists(pkg_core_files))) { |
| 43 | + n_removed <- suppressWarnings(sum(file.remove(pkg_core_files_dst))) |
| 44 | + if (n_removed > 0) { |
| 45 | + cat(sprintf("Removed %d previously vendored files from temporary CRAN directory (%s)\n", n_removed, cran_dir)) |
| 46 | + } |
| 47 | + |
| 48 | + cat( |
| 49 | + sprintf( |
| 50 | + "Copying core package files to CRAN subdirectory\n" |
| 51 | + ) |
| 52 | + ) |
| 53 | + |
| 54 | + # Recreate the directory structure |
| 55 | + dst_dirs <- unique(dirname(pkg_core_files_dst)) |
| 56 | + for (dst_dir in dst_dirs) { |
| 57 | + if (!dir.exists(dst_dir)) { |
| 58 | + dir.create(dst_dir, recursive = TRUE) |
| 59 | + } |
| 60 | + } |
| 61 | + |
| 62 | + if (all(file.copy(pkg_core_files, pkg_core_files_dst))) { |
| 63 | + cat("All core package files successfully copied to CRAN subdirectory\n") |
| 64 | + } else { |
| 65 | + stop("Failed to copy all core package files") |
| 66 | + } |
| 67 | +} |
| 68 | + |
| 69 | +# Overwrite PKG_CPPFLAGS in src/Makevars |
| 70 | +cran_makevars <- file.path(cran_dir, "src/Makevars") |
| 71 | +makevars_lines <- readLines(cran_makevars) |
| 72 | +makevars_lines[grep("^(PKG_CPPFLAGS)", makevars_lines)] <- "PKG_CPPFLAGS= -I$(PKGROOT)/src/include" |
| 73 | +writeLines(makevars_lines, cran_makevars) |
| 74 | + |
| 75 | +# Copy fast_double_parser header to an include/ subdirectory of src/ |
| 76 | +header_folders <- c("nlohmann", "stochtree") |
| 77 | +header_files_to_vendor_src <- c() |
| 78 | +header_files_to_vendor_dst <- c() |
| 79 | +for (header_folder in header_folders) { |
| 80 | + # Existing source files |
| 81 | + header_subfolder_src <- paste0("include/", header_folder) |
| 82 | + header_filenames_src <- list.files(header_subfolder_src, recursive = TRUE) |
| 83 | + header_src <- file.path(header_subfolder_src, header_filenames_src) |
| 84 | + header_files_to_vendor_src <- c(header_files_to_vendor_src, header_src) |
| 85 | + |
| 86 | + # Destination files |
| 87 | + header_subfolder_dst <- paste0(cran_dir, "/src/include/", header_folder) |
| 88 | + header_dst <- file.path(header_subfolder_dst, basename(header_src)) |
| 89 | + header_files_to_vendor_dst <- c(header_files_to_vendor_dst, header_dst) |
| 90 | +} |
| 91 | + |
| 92 | +fast_double_parser_src <- file.path("deps/fast_double_parser/include/fast_double_parser.h") |
| 93 | +fast_double_parser_dst <- file.path(cran_dir, "src/include/fast_double_parser.h") |
| 94 | +if (file.exists(fast_double_parser_src)) { |
| 95 | + file_removed <- suppressWarnings(sum(file.remove(fast_double_parser_dst)) > 0) |
| 96 | + if (file_removed) { |
| 97 | + cat(sprintf("Removed previously vendored fast_double_parser.h file from src/include\n")) |
| 98 | + } |
| 99 | + |
| 100 | + cat( |
| 101 | + sprintf( |
| 102 | + "Vendoring fast_double_parser.h file from deps/fast_double_parser/include to src/include\n" |
| 103 | + ) |
| 104 | + ) |
| 105 | + |
| 106 | + # Recreate the directory structure |
| 107 | + dst_dir <- dirname(fast_double_parser_dst) |
| 108 | + if (!dir.exists(dst_dir)) { |
| 109 | + dir.create(dst_dir, recursive = TRUE) |
| 110 | + } |
| 111 | + |
| 112 | + if (file.copy(fast_double_parser_src, fast_double_parser_dst)) { |
| 113 | + cat("fast_double_parser.h header file successfully copied to src/include\n") |
| 114 | + } else { |
| 115 | + stop("Failed to vendor fast_double_parser.h header file") |
| 116 | + } |
| 117 | +} |
| 118 | + |
| 119 | +# Copy include/ headers to an include/ subdirectory of src/ |
| 120 | +header_folders <- c("nlohmann", "stochtree") |
| 121 | +header_files_to_vendor_src <- c() |
| 122 | +header_files_to_vendor_dst <- c() |
| 123 | +for (header_folder in header_folders) { |
| 124 | + # Existing source files |
| 125 | + header_subfolder_src <- paste0("include/", header_folder) |
| 126 | + header_filenames_src <- list.files(header_subfolder_src, recursive = TRUE) |
| 127 | + header_src <- file.path(header_subfolder_src, header_filenames_src) |
| 128 | + header_files_to_vendor_src <- c(header_files_to_vendor_src, header_src) |
| 129 | + |
| 130 | + # Destination files |
| 131 | + header_subfolder_dst <- paste0(cran_dir, "/src/include/", header_folder) |
| 132 | + header_dst <- file.path(header_subfolder_dst, basename(header_src)) |
| 133 | + header_files_to_vendor_dst <- c(header_files_to_vendor_dst, header_dst) |
| 134 | +} |
| 135 | + |
| 136 | +if (all(file.exists(header_files_to_vendor_src))) { |
| 137 | + n_removed <- suppressWarnings(sum(file.remove(header_files_to_vendor_dst))) |
| 138 | + if (n_removed > 0) { |
| 139 | + cat(sprintf("Removed %d previously vendored files from src/include\n", n_removed)) |
| 140 | + } |
| 141 | + |
| 142 | + cat( |
| 143 | + sprintf( |
| 144 | + "Vendoring files from include/ to src/include\n" |
| 145 | + ) |
| 146 | + ) |
| 147 | + |
| 148 | + # Recreate the directory structure |
| 149 | + dst_dirs <- unique(dirname(header_files_to_vendor_dst)) |
| 150 | + for (dst_dir in dst_dirs) { |
| 151 | + if (!dir.exists(dst_dir)) { |
| 152 | + dir.create(dst_dir, recursive = TRUE) |
| 153 | + } |
| 154 | + } |
| 155 | + |
| 156 | + if (all(file.copy(header_files_to_vendor_src, header_files_to_vendor_dst))) { |
| 157 | + cat("All include/ header files successfully copied to src/include\n") |
| 158 | + } else { |
| 159 | + stop("Failed to vendor all include/ header files") |
| 160 | + } |
| 161 | +} |
| 162 | + |
| 163 | +# Copy fmt headers to an include/ subdirectory of src/ |
| 164 | +fmt_header_files_to_vendor_src <- c() |
| 165 | +fmt_header_files_to_vendor_dst <- c() |
| 166 | +# Existing source files |
| 167 | +fmt_header_subfolder_src <- "deps/fmt/include/fmt" |
| 168 | +fmt_header_filenames_src <- list.files(fmt_header_subfolder_src, pattern = "\\.(h)$", recursive = TRUE) |
| 169 | +fmt_header_files_to_vendor_src <- file.path(fmt_header_subfolder_src, fmt_header_filenames_src) |
| 170 | +# Destination files |
| 171 | +fmt_header_subfolder_dst <- "src/include/fmt" |
| 172 | +fmt_header_files_to_vendor_dst <- file.path(cran_dir, fmt_header_subfolder_dst, basename(fmt_header_filenames_src)) |
| 173 | + |
| 174 | +if (all(file.exists(fmt_header_files_to_vendor_src))) { |
| 175 | + n_removed <- suppressWarnings(sum(file.remove(fmt_header_files_to_vendor_dst))) |
| 176 | + if (n_removed > 0) { |
| 177 | + cat(sprintf("Removed %d previously vendored files from src/include/fmt\n", n_removed)) |
| 178 | + } |
| 179 | + |
| 180 | + cat( |
| 181 | + sprintf( |
| 182 | + "Vendoring files from deps/fmt/include/ to src/include/fmt\n" |
| 183 | + ) |
| 184 | + ) |
| 185 | + |
| 186 | + # Recreate the directory structure |
| 187 | + dst_dirs <- unique(dirname(fmt_header_files_to_vendor_dst)) |
| 188 | + for (dst_dir in dst_dirs) { |
| 189 | + if (!dir.exists(dst_dir)) { |
| 190 | + dir.create(dst_dir, recursive = TRUE) |
| 191 | + } |
| 192 | + } |
| 193 | + |
| 194 | + if (all(file.copy(fmt_header_files_to_vendor_src, fmt_header_files_to_vendor_dst))) { |
| 195 | + cat("All deps/fmt/include/ header files successfully copied to src/include/fmt\n") |
| 196 | + } else { |
| 197 | + stop("Failed to vendor all deps/fmt/include/ header files") |
| 198 | + } |
| 199 | +} |
| 200 | + |
| 201 | +# Copy Eigen module headers to an include/Eigen subdirectory of src/ |
| 202 | +eigen_modules <- c("Cholesky", "Core", "Dense", "Eigenvalues", "Geometry", "Householder", "IterativeLinearSolvers", "Jacobi", "LU", "OrderingMethods", "QR", "SVD", "Sparse", "SparseCholesky", "SparseCore", "SparseLU", "SparseQR", "misc", "plugins") |
| 203 | +eigen_files_to_vendor_src <- c() |
| 204 | +eigen_files_to_vendor_dst <- c() |
| 205 | +for (eigen_mod in eigen_modules) { |
| 206 | + # Existing source files |
| 207 | + eigen_module_subfolder_src <- paste0("deps/eigen/Eigen/src/", eigen_mod) |
| 208 | + # eigen_module_filenames_src <- list.files(eigen_module_subfolder_src, recursive = TRUE) |
| 209 | + # eigen_module_source_src <- file.path(eigen_module_subfolder_src, eigen_module_filenames_src) |
| 210 | + eigen_module_source_src <- list.files(eigen_module_subfolder_src, recursive = TRUE, full.names = TRUE) |
| 211 | + if (eigen_mod %in% c("misc", "plugins")) { |
| 212 | + eigen_files_to_vendor_src <- c(eigen_files_to_vendor_src, eigen_module_source_src) |
| 213 | + } else { |
| 214 | + eigen_module_header_src <- file.path("deps/eigen/Eigen", eigen_mod) |
| 215 | + eigen_files_to_vendor_src <- c(eigen_files_to_vendor_src, eigen_module_header_src, eigen_module_source_src) |
| 216 | + } |
| 217 | + |
| 218 | + # Destination files |
| 219 | + eigen_module_source_dst <- gsub("deps/eigen/Eigen", paste0(cran_dir, "/src/include/Eigen"), eigen_module_source_src) |
| 220 | + if (eigen_mod %in% c("misc", "plugins")) { |
| 221 | + eigen_files_to_vendor_dst <- c(eigen_files_to_vendor_dst, eigen_module_source_dst) |
| 222 | + } else { |
| 223 | + eigen_module_header_dst <- file.path(cran_dir, "src/include/Eigen", eigen_mod) |
| 224 | + eigen_files_to_vendor_dst <- c(eigen_files_to_vendor_dst, eigen_module_header_dst, eigen_module_source_dst) |
| 225 | + } |
| 226 | +} |
| 227 | + |
| 228 | +if (all(file.exists(eigen_files_to_vendor_src))) { |
| 229 | + n_removed <- suppressWarnings(sum(file.remove(eigen_files_to_vendor_dst))) |
| 230 | + if (n_removed > 0) { |
| 231 | + cat(sprintf("Removed %d previously vendored files from src/include/Eigen\n", n_removed)) |
| 232 | + } |
| 233 | + |
| 234 | + cat( |
| 235 | + sprintf( |
| 236 | + "Vendoring files from deps/eigen to src/include/Eigen\n" |
| 237 | + ) |
| 238 | + ) |
| 239 | + |
| 240 | + # Recreate the directory structure |
| 241 | + dst_dirs <- unique(dirname(eigen_files_to_vendor_dst)) |
| 242 | + for (dst_dir in dst_dirs) { |
| 243 | + if (!dir.exists(dst_dir)) { |
| 244 | + dir.create(dst_dir, recursive = TRUE) |
| 245 | + } |
| 246 | + } |
| 247 | + |
| 248 | + if (all(file.copy(eigen_files_to_vendor_src, eigen_files_to_vendor_dst))) { |
| 249 | + cat("All Eigen files successfully copied to src/include/Eigen\n") |
| 250 | + } else { |
| 251 | + stop("Failed to vendor all Eigen files") |
| 252 | + } |
| 253 | +} |
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