diff --git a/.gitignore b/.gitignore
index 94d5fa0b15a2b38bebbba4fcc67efafc9fa10080..51c293e4bc2a9ef5d1fb9f55837fcbab31b2295f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,6 @@ renv/staging/
renv/cache/
# Data files
-r_objects/
+data/
R/performance_analysis_files
R/performance_analysis.html
\ No newline at end of file
diff --git a/R/assign_functional_groups.R b/R/assign_functional_groups.R
new file mode 100644
index 0000000000000000000000000000000000000000..ee2a06f6390e6ea98475cf654867a026a385e644
--- /dev/null
+++ b/R/assign_functional_groups.R
@@ -0,0 +1,34 @@
+load("data/r_objects/range_maps.RData")
+
+# Get taxonomic information for target species
+names_unique = unique(range_maps$name_matched[!is.na(range_maps$name_matched)])
+
+species_matched = lapply(names_unique, function(name){
+ match_result = Symobio::gbif_match_name(name = name)
+ if(match_result$status != "ACCEPTED"){
+ match_result = gbif_match_name(usageKey = match_result$acceptedUsageKey)
+ }
+ match_result$name_orig = name
+ return(match_result)
+}) %>%
+ bind_rows()
+
+# Assign functional groups
+functional_groups = species_matched %>%
+ mutate(
+ functional_group = case_when(
+ order %in% c("Carnivora", "Artiodactyla", "Cingulata", "Perissodactyla") ~ 1,
+ order %in% c("Rodentia", "Didelphimorphia", "Soricomorpha", "Paucituberculata", "Lagomorpha") ~ 2,
+ order %in% c("Primates", "Pilosa") ~ 3,
+ order %in% c("Chiroptera") ~ 4
+ ),
+ functional_group = factor(functional_group, labels = c("large ground-dwelling", "small ground-dwelling", "arboreal", "flying"))
+ ) %>%
+ dplyr::select(
+ name_orig,
+ name_matched = species,
+ functional_group
+ ) %>%
+ distinct()
+
+save(functional_groups, file = "data/r_objects/functional_groups.RData")
diff --git a/R/install_torch.R b/R/install_torch.R
new file mode 100644
index 0000000000000000000000000000000000000000..597d7de0d9a4afb2fbd775e9fe2fd9b4fa9c68bf
--- /dev/null
+++ b/R/install_torch.R
@@ -0,0 +1,88 @@
+# Installation
+
+options(timeout = 600) # increasing timeout is recommended since we will be downloading a 2GB file.
+# For Windows and Linux: "cpu", "cu117" are the only currently supported
+# For MacOS the supported are: "cpu-intel" or "cpu-m1"
+kind <- "cu117"
+version <- available.packages()["torch","Version"]
+options(repos = c(
+ torch = sprintf("https://torch-cdn.mlverse.org/packages/%s/%s/", kind, version),
+ CRAN = "https://cloud.r-project.org" # or any other from which you want to install the other R dependencies.
+))
+install.packages("torch", type = "binary")
+
+
+install.packages("torchvision")
+install.packages("luz")
+
+# Load packages
+library(torch)
+library(torchvision)
+library(luz)
+
+
+# Get dataset
+
+dir <- "../playground/dataset/mnist"
+
+train_ds <- mnist_dataset(
+ dir,
+ download = TRUE,
+ transform = transform_to_tensor
+)
+
+test_ds <- mnist_dataset(
+ dir,
+ train = FALSE,
+ transform = transform_to_tensor
+)
+
+train_dl <- dataloader(train_ds, batch_size = 128, shuffle = TRUE)
+test_dl <- dataloader(test_ds, batch_size = 128)
+
+# Plot example character
+image <- train_ds$data[1,1:28,1:28]
+image_df <- data.table::melt(image)
+ggplot(image_df, aes(x=Var2, y=Var1, fill=value))+
+ geom_tile(show.legend = FALSE) +
+ xlab("") + ylab("") +
+ scale_fill_gradient(low="white", high="black")
+
+
+# Build network
+net <- nn_module(
+ "Net",
+ initialize = function() {
+ self$conv1 <- nn_conv2d(1, 32, 3, 1)
+ self$conv2 <- nn_conv2d(32, 64, 3, 1)
+ self$dropout1 <- nn_dropout2d(0.25)
+ self$dropout2 <- nn_dropout2d(0.5)
+ self$fc1 <- nn_linear(9216, 128)
+ self$fc2 <- nn_linear(128, 10)
+ },
+ forward = function(x) {
+ x %>% # N * 1 * 28 * 28
+ self$conv1() %>% # N * 32 * 26 * 26
+ nnf_relu() %>%
+ self$conv2() %>% # N * 64 * 24 * 24
+ nnf_relu() %>%
+ nnf_max_pool2d(2) %>% # N * 64 * 12 * 12
+ self$dropout1() %>%
+ torch_flatten(start_dim = 2) %>% # N * 9216
+ self$fc1() %>% # N * 128
+ nnf_relu() %>%
+ self$dropout2() %>%
+ self$fc2() # N * 10
+ }
+)
+
+# Train
+fitted <- net %>%
+ setup(
+ loss = nn_cross_entropy_loss(),
+ optimizer = optim_adam,
+ metrics = list(
+ luz_metric_accuracy()
+ )
+ ) %>%
+ fit(train_dl, epochs = 10, valid_data = test_dl)
diff --git a/R/model_target_species.R b/R/model_target_species.R
index c56475806988f417752c2370ebe227fb9f2edc9a..420d219c9224028a45e8a9c3a6e9e78a8542edee 100644
--- a/R/model_target_species.R
+++ b/R/model_target_species.R
@@ -19,13 +19,13 @@ library(pROC)
library(cito)
source("R/utils.R")
+
con = db_connect()
sf::sf_use_s2(use_s2 = FALSE)
# ---------------------------------------------------------------------------#
# Prepare Geodata ####
# ---------------------------------------------------------------------------#
-
raster_info = tbl(con, "datasets") %>%
dplyr::filter(stringr::str_detect(name, "CHELSA")) %>%
collect()
@@ -40,11 +40,11 @@ sa_polygon = rnaturalearth::ne_countries() %>%
# ---------------------------------------------------------------------------#
# Prepare Occurrence Data ####
# ---------------------------------------------------------------------------#
-load("r_objects/test_species.RData")
-test_species = unique(test_species$name_matched)
+load("data/r_objects/range_maps.RData")
+target_species = unique(range_maps$name_matched[!is.na(range_maps$name_matched)])
occs = tbl(con, "species_occurrences") %>%
- dplyr::filter(species %in% test_species) %>%
+ dplyr::filter(species %in% target_species) %>%
dplyr::select(-year) %>%
dplyr::distinct() %>%
collect() %>%
@@ -81,10 +81,13 @@ occs_final = occs %>%
inner_join(env_vars, by = "coordinate_id") %>%
dplyr::select(-coordinate_id)
-save(occs_final, file = "r_objects/occs_final.RData")
+save(occs_final, file = "data/r_objects/occs_final.RData")
# ---------------------------------------------------------------------------#
# Main loop ####
# ---------------------------------------------------------------------------#
+load("data/r_objects/occs_final.RData")
+load("data/r_objects/sa_polygon.RData")
+
occs_split = split(occs_final, occs_final$species)
future::plan("multisession", workers = 16)
@@ -130,7 +133,7 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
terra::extract(sample_points) %>%
dplyr::select(-ID) %>%
dplyr::mutate(
- presence = "absent",
+ presence = 0,
geometry = sample_points$x
) %>%
tibble()
@@ -139,9 +142,11 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
# Create modeling dataset ####
# ------------------------------- #
model_data = occs_spec %>%
- dplyr::mutate(presence = "present") %>%
+ dplyr::mutate(presence = 1) %>%
bind_rows(abs_spec) %>%
- dplyr::mutate(presence = as.factor(presence))
+ dplyr::mutate(
+ presence_fct = as.factor(ifelse(presence == 0, "absent", "present"))
+ )
# Define cross-validation folds
spatial_folds = blockCV::cv_spatial(
@@ -162,10 +167,7 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
# Define predictor columns
predictors = paste0("layer_", 1:19)
- # ------------------------------- #
- # Train models ####
- # ------------------------------- #
- # Preparation
+ # Define empty performance summary
na_performance = list(
AUC = NA,
Accuracy = NA,
@@ -175,18 +177,42 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
F1 = NA
)
- # Feature selection
- # --> Very time consuming!
-
- # feature_selection = rfe(
- # x = dplyr::select(model_data, contains("layer")),
- # y = model_data$presence,
- # rfeControl = rfeControl(functions = caretFuncs,
- # method = "cv",
- # number = 3, # Number of folds
- # verbose = T)
+ # ------------------------------- #
+ # Train models ####
+ # ------------------------------- #
+ ## cito ####
+ # model_data_nn = model_data %>%
+ # dplyr::mutate(across(all_of(predictors), scale)) %>%
+ # select(-species, -longitude, -latitude)
+ #
+ # train_data_nn = model_data_nn[train_index, ]
+ # test_data_nn = model_data_nn[-train_index, ]
+ #
+ # nn_fit = dnn(
+ # Y = train_data_nn$presence,
+ # X = as.matrix(train_data_nn[, predictors]),
+ # hidden = c(500L, 500L),
+ # loss = "binomial",
+ # activation = "leaky_relu",
+ # epochs = 2000L,
+ # lr = 0.02,
+ # dropout = 0.2, # Regularization
+ # burnin = Inf,
+ # optimizer = config_optimizer("adam", weight_decay = 0.001),
+ # lr_scheduler = config_lr_scheduler("reduce_on_plateau", patience = 10, factor = 0.7),
+ # early_stopping = 500L, # stop training when validation loss does not decrease anymore
+ # validation = 0.2, # used for early stopping and lr_scheduler
+ # device = "cpu",
+ # bootstrap = 50L
# )
+ #
+ # nn_fit$successfull
+ # preds = predict(nn_fit, type = "response") # --> Strange discrete steps of size 1/bootstrap_value
+ # plot(preds)
+ # Metrics::auc(train_data_nn$presence, round(preds[,1]))
+ ## caret ####
+ # Define training routine
index_train = lapply(unique(sort(train_data$fold)), function(x){
return(which(train_data$fold != x))
})
@@ -207,7 +233,7 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
rf_fit = caret::train(
x = train_data[, predictors],
- y = train_data$presence,
+ y = train_data$presence_fct,
method = "rf",
metric = "ROC",
tuneGrid = rf_grid,
@@ -226,10 +252,10 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
shrinkage = c(0.01, 0.005, 0.001), # Lower learning rates
n.minobsinnode = c(10, 20) # Minimum number of observations in nodes
)
-
+
gbm_fit = train(
x = train_data[, predictors],
- y = train_data$presence,
+ y = train_data$presence_fct,
method = "gbm",
metric = "ROC",
verbose = F,
@@ -245,7 +271,7 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
glm_performance = tryCatch({
glm_fit = train(
x = train_data[, predictors],
- y = train_data$presence,
+ y = train_data$presence_fct,
method = "glm",
family=binomial,
metric = "ROC",
@@ -273,4 +299,4 @@ model_results = furrr::future_map(occs_split, .options = furrr::furrr_options(se
return(performance_summary)
})
-save(model_results, file = "r_objects/model_results.RData")
+save(model_results, file = "data/r_objects/model_results.RData")
diff --git a/R/performance_analysis.qmd b/R/performance_analysis.qmd
index 30fc4d5d5ff87d47285f3a1e26b3c930f87a434f..252c7bb3344e6e850f1c4321e4749bb31de829aa 100644
--- a/R/performance_analysis.qmd
+++ b/R/performance_analysis.qmd
@@ -11,35 +11,36 @@ library(sf)
library(plotly)
library(DT)
-load("../r_objects/model_results.RData")
-load("../r_objects/test_species.RData")
-load("../r_objects/range_maps.RData")
-load("../r_objects/range_maps_gridded.RData")
-load("../r_objects/occs_final.RData")
+load("../data/r_objects/model_results.RData")
+load("../data/r_objects/range_maps.RData")
+load("../data/r_objects/range_maps_gridded.RData")
+load("../data/r_objects/occs_final.RData")
+load("../data/r_objects/functional_groups.RData")
sf::sf_use_s2(use_s2 = FALSE)
```
## Summary
-This document summarizes the performance of three SDM algorithms (Random Forest, Gradient Boosting Machine, Generalized Linear Model) for 96 South American terrestrial mammal species. We use six metrics (AUC, F1, kappa, accuracy, precision, and recall) to evaluate model performance and look at how performance varies with five factors (number of records, range size, range occupancy, spatial dispersion, and functional group).
+This document summarizes the performance of three SDM algorithms (Random Forest, Gradient Boosting Machine, Generalized Linear Model) for `{r} length(model_results)` South American mammal species. We use six metrics (AUC, F1, kappa, accuracy, precision, and recall) to evaluate model performance and look at how performance varies with five factors (number of records, range size, range coverage, range coverage bias, and functional group).
Modeling decisions:
-- Randomly sampled pseudo-absences from expanded area of extent of occurrence records (×1.25)
-- Balanced presences and absences for each species
-- Predictors: all 19 CHELSA bioclim variables
-- Spatial block cross-validation
-- 70/30 Split of training vs. test data
-- Grid search hyperparameter tuning for RF and GBM
+- Randomly sampled pseudo-absences from expanded area of extent of occurrence records (×1.25)
+- Balanced presences and absences for each species
+- Predictors: all 19 CHELSA bioclim variables
+- Spatial block cross-validation
+- 70/30 Split of training vs. test data
+- Grid search hyperparameter tuning for RF and GBM
Key findings:
-- RF and GBM models generally performed better than GLM across metrics
-- More occurrence records and larger range sizes tended to improve model accuracy
-- Higher range occupancy correlated with better performance.
-- Spatial dispersion and functional group showed some impact but were less consistent
+- RF performed best, GBM slightly worse, GLM worst
+- More occurrence records and larger range sizes tended to improve model performance
+- Higher range coverage correlated with better performance.
+- Range coverage bias and functional group showed some impact but were less consistent <!-- TODO: check after rerun -->
## Analysis
+
The table below shows the analysed modeling results.
```{r performance, echo = FALSE, message=FALSE, warnings=FALSE}
@@ -50,7 +51,7 @@ performance = model_results %>%
dplyr::filter(!is.na(value)) %>%
dplyr::mutate(
metric = factor(metric, levels = c("auc", "kappa", "f1", "accuracy", "precision", "recall")),
- value = pmax(value, 0, na.rm = T) # Fix one weird instance of f1 < 0
+ value = round(pmax(value, 0, na.rm = T), 3) # Fix one weird instance of f1 < 0
)
DT::datatable(performance)
@@ -59,7 +60,7 @@ DT::datatable(performance)
### Number of records
- Model performance was generally better for species with more observations
-- No major improvements in model performance beyond \~500 observations
+- Very poor performance below 50-100 observations
```{r number_of_records, echo = FALSE, message=FALSE, warnings=FALSE}
df_plot = performance
@@ -89,7 +90,7 @@ plot <- plot_ly(
plot <- plot %>%
layout(
title = "Model Performance vs. Number of observations",
- xaxis = list(title = "Number of observations"),
+ xaxis = list(title = "Number of observations", type = "log"),
yaxis = list(title = "Value"),
legend = list(x = 1.1, y = 0.5), # Move legend to the right of the plot
margin = list(r = 150), # Add right margin to accommodate legend
@@ -115,12 +116,12 @@ bslib::card(plot, full_screen = T)
### Range characteristics
-The spatial coverage of species occurrences was evaluated using a systematic hexagonal grid system, with each cell spanning 1 degree in both latitudinal and longitudinal dimensions. Two complementary metrics were used to assess range coverage: First, sampling completeness was quantified by determining the number of grid cells containing at least one occurrence record (*occupancy*). Second, we calculated the theoretical maximum number of occupied hexagons possible given the total number of observations (*spatial dispersion*).
-
#### Range size
-- Model performance was lower for small ranged species
-- No major improvements in model performance beyond range size of \~3M km²
+Range size was calculated based on polygon layers from the IUCN Red List of Threatened Species (2016).
+
+- Model performance tended to be slightly higher for species with larger range size
+- Only RF shows continuous performance improvements beyond range sizes of \~5M km²
```{r range_size, echo = FALSE, message=FALSE, warnings=FALSE}
df_join = range_maps %>%
@@ -179,11 +180,17 @@ plot <- plot %>%
bslib::card(plot, full_screen = T)
```
-#### Occupancy
+#### Range coverage
+
+Species ranges were split into continuous hexagonal grid cells of 1 degree diameter. Range coverage was then calculated as the number of grid cells containing at least one occurrence record divided by the number of total grid cells.
+
+$$
+RangeCoverage = \frac{N_{cells\_occ}}{N_{cells\_total}}
+$$
-- Models for species with higher range occupancy showed slightly better performance
+- Models for species with higher range coverage showed slightly better performance
-```{r range_occupancy, echo = FALSE, message=FALSE, warnings=FALSE}
+```{r range_coverage, echo = FALSE, message=FALSE, warnings=FALSE}
df_cells_total = range_maps_gridded %>%
dplyr::rename("species" = name_matched) %>%
group_by(species) %>%
@@ -199,8 +206,8 @@ df_cells_occ <- range_maps_gridded %>%
df_join = df_cells_total %>%
dplyr::inner_join(df_cells_occ, by = "species") %>%
- dplyr::mutate(occupancy = cells_occupied / cells_total) %>%
- dplyr::select(species, occupancy)
+ dplyr::mutate(range_cov = cells_occupied / cells_total) %>%
+ dplyr::select(species, range_cov)
df_plot = performance %>%
inner_join(df_join, by = "species")
@@ -208,14 +215,14 @@ df_plot = performance %>%
# Create base plot
plot <- plot_ly(
data = df_plot,
- x = ~occupancy,
+ x = ~range_cov,
y = ~value,
color = ~model,
type = 'scatter',
mode = 'markers',
name = ~model,
hoverinfo = 'text',
- text = ~paste("Species:", species, "<br>Range occupancy:", round(occupancy, 3), "<br>Value:", round(value, 3)),
+ text = ~paste("Species:", species, "<br>Range coverage:", round(range_cov, 3), "<br>Value:", round(value, 3)),
transforms = list(
list(
type = 'filter',
@@ -229,8 +236,8 @@ plot <- plot_ly(
# Add dropdown for selecting metric
plot <- plot %>%
layout(
- title = "Model Performance vs. Range occupancy",
- xaxis = list(title = "Range occupancy"),
+ title = "Model Performance vs. Range coverage",
+ xaxis = list(title = "Range coverage"),
yaxis = list(title = "Value"),
legend = list(x = 1.1, y = 0.5), # Move legend to the right of the plot
margin = list(r = 150), # Add right margin to accommodate legend
@@ -254,13 +261,19 @@ plot <- plot %>%
bslib::card(plot, full_screen = T)
```
-#### Spatial dispersion
+#### Range coverage bias
-- Models for species with higher spatial dispersion tended to exhibit lower performance
+Range coverage bias was calculated as the as the minimum of total grid cells and total occurrences divided by the number of occupied cells.
-- Large spread, weak relationship
+$$
+RangeCoverageBias = \frac{min(N_{cells\_total}, N_{obs\_total})}{N_{cells\_occupied}}
+$$
-```{r spatial_dispersion, echo = FALSE, message=FALSE, warnings=FALSE}
+Higher bias values indicate that occurrence records are spatially more clustered within the range of the species.
+
+- There was no strong relationship between range coverage bias and model performance
+
+```{r range_coverage_bias, echo = FALSE, message=FALSE, warnings=FALSE}
df_occs_total = occs_final %>%
st_drop_geometry() %>%
group_by(species) %>%
@@ -269,7 +282,7 @@ df_occs_total = occs_final %>%
df_join = df_occs_total %>%
dplyr::inner_join(df_cells_total, by = "species") %>%
dplyr::inner_join(df_cells_occ, by = "species") %>%
- dplyr::mutate(dispersion = cells_occupied / pmin(cells_total, occs_total))
+ dplyr::mutate(range_bias = pmin(cells_total, occs_total) / cells_occupied)
df_plot = performance %>%
inner_join(df_join, by = "species")
@@ -277,14 +290,14 @@ df_plot = performance %>%
# Create base plot
plot <- plot_ly(
data = df_plot,
- x = ~dispersion,
+ x = ~range_bias,
y = ~value,
color = ~model,
type = 'scatter',
mode = 'markers',
name = ~model,
hoverinfo = 'text',
- text = ~paste("Species:", species, "<br>Dispersion:", round(dispersion, 3), "<br>Value:", round(value, 3)),
+ text = ~paste("Species:", species, "<br>Range coverage bias:", round(range_bias, 3), "<br>Value:", round(value, 3)),
transforms = list(
list(
type = 'filter',
@@ -298,8 +311,8 @@ plot <- plot_ly(
# Add dropdown for selecting metric
plot <- plot %>%
layout(
- title = "Model Performance vs. Dispersion",
- xaxis = list(title = "Dispersion"),
+ title = "Model Performance vs. Range coverage bias",
+ xaxis = list(title = "Range coverage bias", type = "log"),
yaxis = list(title = "Value"),
legend = list(x = 1.1, y = 0.5), # Move legend to the right of the plot
margin = list(r = 150), # Add right margin to accommodate legend
@@ -325,15 +338,20 @@ bslib::card(plot, full_screen = T)
### Functional group
-- No major difference in model performance among functional groups
+Functional groups were assigned based on taxonomic order. The following groupings were used:
-```{r functional_groups, echo = FALSE, message=FALSE, warnings=FALSE}
-df_join = test_species %>%
- dplyr::distinct(name_matched, functional_group) %>%
- dplyr::mutate(functional_group = factor(functional_group, labels = c("arboreal", "large ground-dwelling", "small ground-dwelling")))
+| Functional group | Taxomic orders |
+|-----------------------|-----------------------------------------------------------------------|
+| large ground-dwelling | Carnivora, Artiodactyla, Cingulata, Perissodactyla |
+| small ground-dwelling | Rodentia, Didelphimorphia, Soricomorpha, Paucituberculata, Lagomorpha |
+| arboreal | Primates, Pilosa |
+| flying | Chiroptera |
+- Models for bats tended to perform slightly worse than for other groups.
+
+```{r functional_groups, echo = FALSE, message=FALSE, warnings=FALSE}
df_plot = performance %>%
- dplyr::left_join(df_join, by = c("species" = "name_matched"))
+ dplyr::left_join(functional_groups, by = c("species" = "name_matched"))
plot <- plot_ly(
data = df_plot,
@@ -359,7 +377,7 @@ plot <- plot_ly(
plot <- plot %>%
layout(
title = "Model Performance vs. Functional Group",
- xaxis = list(title = "Range occupancy"),
+ xaxis = list(title = "Functional group"),
yaxis = list(title = "Value"),
legend = list(x = 1.1, y = 0.5), # Move legend to the right of the plot
margin = list(r = 150), # Add right margin to accommodate legend
diff --git a/R/process_range_maps.R b/R/process_range_maps.R
index bcb030afa087cd4876c1d36b6d497a0d53f20b0e..120b28652047f17948af4367f09f98287914de03 100644
--- a/R/process_range_maps.R
+++ b/R/process_range_maps.R
@@ -3,8 +3,6 @@ library(Symobio)
library(sf)
library(rnaturalearth)
-load("r_objects/test_species.RData")
-
sf::sf_use_s2(use_s2 = FALSE)
# Load range maps
@@ -15,13 +13,16 @@ range_maps = st_read(
) %>%
dplyr::filter(!legend %in% c("Extinct", "Not Mapped"))
-# Load South America polygon
-sa_polygon = rnaturalearth::ne_countries() %>%
- dplyr::filter(continent == "South America") %>%
- sf::st_union()
+# Find species that intersect with Amazon
+amazon = st_read(
+ "data/geospatial/amazonia_polygons/amazonia_polygons.shp",
+ geometry_column = "geometry",
+ promote_to_multi = T
+)
+range_maps = st_filter(range_maps, amazon)
# Match names against GBIF backbone
-maps_names_matched = lapply(unique(range_maps$binomial), function(name){
+range_maps_names_matched = lapply(unique(range_maps$binomial), function(name){
tryCatch({
match_result = Symobio::gbif_match_name(name = name)
if(match_result$status != "ACCEPTED"){
@@ -34,25 +35,25 @@ maps_names_matched = lapply(unique(range_maps$binomial), function(name){
return(NULL)
})
})
-
-save(range_maps_names_matched, file = "r_objects/range_maps_names_matched.RData")
+save(range_maps_names_matched, file = "data/r_objects/range_maps_names_matched.RData")
# Subset range maps to target species and focal region
-names_subset = Filter(is.data.frame, range_maps_names_matched) %>%
- bind_rows() %>%
- dplyr::filter(name_matched %in% test_species$name_matched)
+names_matched = Filter(is.data.frame, range_maps_names_matched) %>%
+ bind_rows()
range_maps = range_maps %>%
- inner_join(names_subset, by = c("binomial" = "name_orig")) %>%
+ inner_join(names_matched, by = c("binomial" = "name_orig")) %>%
group_by(name_matched) %>%
- summarize(geometry = suppressMessages(st_union(geometry))) %>%
- st_intersection(sa_polygon)
+ summarize(geometry = suppressMessages(st_union(geometry)))
-save(range_maps, file = "r_objects/range_maps.RData")
+save(range_maps, file = "data/r_objects/range_maps.RData")
# Gridded range maps
-range_maps_gridded = st_make_grid(sa_polygon, square = FALSE, cellsize = 1) %>%
+range_maps_gridded = rnaturalearth::ne_countries() %>%
+ dplyr::filter(continent == "South America") %>%
+ sf::st_union() %>%
+ st_make_grid(square = FALSE, cellsize = 1) %>%
st_sf() %>%
st_join(range_maps, st_intersects, left = F)
-save(range_maps_gridded, file = "r_objects/range_maps_gridded.RData")
+save(range_maps_gridded, file = "data/r_objects/range_maps_gridded.RData")
diff --git a/R/utils.R b/R/utils.R
index fcf30f0839e93ed63388fc7d827cf09940d862ee..cafad510ff031b21a380dc4b47163e9484744e3a 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -28,7 +28,7 @@ evaluate_model <- function(model, test_data, threshold = 0.5) {
# Predict probabilities
probs <- predict(model, test_data, type = "prob")$present
preds <- predict(model, test_data, type = "raw")
- actual <- test_data$presence
+ actual <- test_data$presence_fct
# Calculate AUC
auc <- pROC::roc(actual, probs, levels = c("present", "absent"), direction = ">")$auc
diff --git a/renv.lock b/renv.lock
index 4c08d37a3fb085d14424f9691a61ca0bf4feead5..a7338f5c9c8ef7950d1dff8034e976480a3a7baf 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,2518 +1,2518 @@
-{
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- "Hash": "0d8472dc938498e75c5110649f569bd1"
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+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "bslib",
+ "evaluate",
+ "fontawesome",
+ "htmltools",
+ "jquerylib",
+ "jsonlite",
+ "knitr",
+ "methods",
+ "tinytex",
+ "tools",
+ "utils",
+ "xfun",
+ "yaml"
+ ],
+ "Hash": "062470668513dcda416927085ee9bdc7"
+ },
+ "rnaturalearth": {
+ "Package": "rnaturalearth",
+ "Version": "1.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "httr",
+ "jsonlite",
+ "sf",
+ "terra",
+ "utils"
+ ],
+ "Hash": "741166cab0fe76d8a5670d3ee459a2a4"
+ },
+ "rpart": {
+ "Package": "rpart",
+ "Version": "4.1.19",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "b3c892a81783376cc2204af0f5805a80"
+ },
+ "rstudioapi": {
+ "Package": "rstudioapi",
+ "Version": "0.16.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "96710351d642b70e8f02ddeb237c46a7"
+ },
+ "rvest": {
+ "Package": "rvest",
+ "Version": "1.0.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "httr",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "selectr",
+ "tibble",
+ "xml2"
+ ],
+ "Hash": "0bcf0c6f274e90ea314b812a6d19a519"
+ },
+ "s2": {
+ "Package": "s2",
+ "Version": "1.1.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "wk"
+ ],
+ "Hash": "3c8013cdd7f1d20de5762e3f97e5e274"
+ },
+ "safetensors": {
+ "Package": "safetensors",
+ "Version": "0.1.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R6",
+ "cli",
+ "jsonlite",
+ "rlang"
+ ],
+ "Hash": "3afaf7fb96750bf1375c7b0485a3f1d5"
+ },
+ "sass": {
+ "Package": "sass",
+ "Version": "0.4.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R6",
+ "fs",
+ "htmltools",
+ "rappdirs",
+ "rlang"
+ ],
+ "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+ },
+ "scales": {
+ "Package": "scales",
+ "Version": "1.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "RColorBrewer",
+ "cli",
+ "farver",
+ "glue",
+ "labeling",
+ "lifecycle",
+ "munsell",
+ "rlang",
+ "viridisLite"
+ ],
+ "Hash": "c19df082ba346b0ffa6f833e92de34d1"
+ },
+ "selectr": {
+ "Package": "selectr",
+ "Version": "0.4-2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "methods",
+ "stringr"
+ ],
+ "Hash": "3838071b66e0c566d55cc26bd6e27bf4"
+ },
+ "sf": {
+ "Package": "sf",
+ "Version": "1.0-17",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DBI",
+ "R",
+ "Rcpp",
+ "classInt",
+ "grDevices",
+ "graphics",
+ "grid",
+ "magrittr",
+ "methods",
+ "s2",
+ "stats",
+ "tools",
+ "units",
+ "utils"
+ ],
+ "Hash": "453a7d0263eae87a7831242a74fe9b60"
+ },
+ "shape": {
+ "Package": "shape",
+ "Version": "1.4.6.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "5c47e84dc0a3ca761ae1d307889e796d"
+ },
+ "sp": {
+ "Package": "sp",
+ "Version": "2.1-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "grid",
+ "lattice",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "75940133cca2e339afce15a586f85b11"
+ },
+ "stringi": {
+ "Package": "stringi",
+ "Version": "1.8.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "tools",
+ "utils"
+ ],
+ "Hash": "39e1144fd75428983dc3f63aa53dfa91"
+ },
+ "stringr": {
+ "Package": "stringr",
+ "Version": "1.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "stringi",
+ "vctrs"
+ ],
+ "Hash": "960e2ae9e09656611e0b8214ad543207"
+ },
+ "survival": {
+ "Package": "survival",
+ "Version": "3.5-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "R",
+ "graphics",
+ "methods",
+ "splines",
+ "stats",
+ "utils"
+ ],
+ "Hash": "d683341b1fa2e8d817efde27d6e6d35b"
+ },
+ "sys": {
+ "Package": "sys",
+ "Version": "3.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
+ },
+ "systemfonts": {
+ "Package": "systemfonts",
+ "Version": "1.1.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11",
+ "lifecycle"
+ ],
+ "Hash": "213b6b8ed5afbf934843e6c3b090d418"
+ },
+ "terra": {
+ "Package": "terra",
+ "Version": "1.7-78",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "methods"
+ ],
+ "Hash": "8f020def0792119cb98bd8f696dab22d"
+ },
+ "textshaping": {
+ "Package": "textshaping",
+ "Version": "0.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11",
+ "lifecycle",
+ "systemfonts"
+ ],
+ "Hash": "5142f8bc78ed3d819d26461b641627ce"
+ },
+ "tibble": {
+ "Package": "tibble",
+ "Version": "3.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "fansi",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pillar",
+ "pkgconfig",
+ "rlang",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+ },
+ "tidyr": {
+ "Package": "tidyr",
+ "Version": "1.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "cpp11",
+ "dplyr",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "purrr",
+ "rlang",
+ "stringr",
+ "tibble",
+ "tidyselect",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
+ },
+ "tidyselect": {
+ "Package": "tidyselect",
+ "Version": "1.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "829f27b9c4919c16b593794a6344d6c0"
+ },
+ "tidyverse": {
+ "Package": "tidyverse",
+ "Version": "2.0.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "broom",
+ "cli",
+ "conflicted",
+ "dbplyr",
+ "dplyr",
+ "dtplyr",
+ "forcats",
+ "ggplot2",
+ "googledrive",
+ "googlesheets4",
+ "haven",
+ "hms",
+ "httr",
+ "jsonlite",
+ "lubridate",
+ "magrittr",
+ "modelr",
+ "pillar",
+ "purrr",
+ "ragg",
+ "readr",
+ "readxl",
+ "reprex",
+ "rlang",
+ "rstudioapi",
+ "rvest",
+ "stringr",
+ "tibble",
+ "tidyr",
+ "xml2"
+ ],
+ "Hash": "c328568cd14ea89a83bd4ca7f54ae07e"
+ },
+ "timeDate": {
+ "Package": "timeDate",
+ "Version": "4041.110",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "c5e48e8ac24d4472ddb122bcdeb011ad"
+ },
+ "timechange": {
+ "Package": "timechange",
+ "Version": "0.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11"
+ ],
+ "Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
+ },
+ "tinytex": {
+ "Package": "tinytex",
+ "Version": "0.53",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "xfun"
+ ],
+ "Hash": "9db859e8aabbb474293dde3097839420"
+ },
+ "torch": {
+ "Package": "torch",
+ "Version": "0.13.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R6",
+ "Rcpp",
+ "bit64",
+ "callr",
+ "cli",
+ "coro",
+ "desc",
+ "ellipsis",
+ "glue",
+ "jsonlite",
+ "magrittr",
+ "methods",
+ "rlang",
+ "safetensors",
+ "stats",
+ "tools",
+ "utils",
+ "withr"
+ ],
+ "Hash": "bfa11273fe711c8640a95b09ba51492e"
+ },
+ "torchvision": {
+ "Package": "torchvision",
+ "Version": "0.6.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "abind",
+ "fs",
+ "jpeg",
+ "magrittr",
+ "png",
+ "rappdirs",
+ "rlang",
+ "torch",
+ "utils",
+ "withr"
+ ],
+ "Hash": "b2a96f59385ceb8633c447b69b019402"
+ },
+ "triebeard": {
+ "Package": "triebeard",
+ "Version": "0.4.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Rcpp"
+ ],
+ "Hash": "642507a148b0dd9b5620177e0a044413"
+ },
+ "tzdb": {
+ "Package": "tzdb",
+ "Version": "0.4.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11"
+ ],
+ "Hash": "f561504ec2897f4d46f0c7657e488ae1"
+ },
+ "units": {
+ "Package": "units",
+ "Version": "0.8-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp"
+ ],
+ "Hash": "119d19da480e873f72241ff6962ffd83"
+ },
+ "urltools": {
+ "Package": "urltools",
+ "Version": "1.7.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "methods",
+ "triebeard"
+ ],
+ "Hash": "e86a704261a105f4703f653e05defa3e"
+ },
+ "utf8": {
+ "Package": "utf8",
+ "Version": "1.2.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "62b65c52671e6665f803ff02954446e9"
+ },
+ "uuid": {
+ "Package": "uuid",
+ "Version": "1.2-1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "34e965e62a41fcafb1ca60e9b142085b"
+ },
+ "vctrs": {
+ "Package": "vctrs",
+ "Version": "0.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang"
+ ],
+ "Hash": "c03fa420630029418f7e6da3667aac4a"
+ },
+ "viridisLite": {
+ "Package": "viridisLite",
+ "Version": "0.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+ },
+ "vroom": {
+ "Package": "vroom",
+ "Version": "1.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "bit64",
+ "cli",
+ "cpp11",
+ "crayon",
+ "glue",
+ "hms",
+ "lifecycle",
+ "methods",
+ "progress",
+ "rlang",
+ "stats",
+ "tibble",
+ "tidyselect",
+ "tzdb",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "390f9315bc0025be03012054103d227c"
+ },
+ "whisker": {
+ "Package": "whisker",
+ "Version": "0.4.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "c6abfa47a46d281a7d5159d0a8891e88"
+ },
+ "withr": {
+ "Package": "withr",
+ "Version": "3.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics"
+ ],
+ "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
+ },
+ "wk": {
+ "Package": "wk",
+ "Version": "0.9.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "9ca478d7cb1450b42dcb8af2ea5681cc"
+ },
+ "xfun": {
+ "Package": "xfun",
+ "Version": "0.47",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "stats",
+ "tools"
+ ],
+ "Hash": "36ab21660e2d095fef0d83f689e0477c"
+ },
+ "xml2": {
+ "Package": "xml2",
+ "Version": "1.3.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "methods",
+ "rlang"
+ ],
+ "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
+ },
+ "yaml": {
+ "Package": "yaml",
+ "Version": "2.3.10",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
+ }
+ }
+}
diff --git a/renv/activate.R b/renv/activate.R
index 9b2e7f18413ee15a187684439a02cc65308d336e..b182ee3a9dd851331cbec564b6a83b1c1229e516 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -1,1201 +1,1305 @@
-
-local({
-
- # the requested version of renv
- version <- "1.0.5"
- attr(version, "sha") <- NULL
-
- # the project directory
- project <- getwd()
-
- # use start-up diagnostics if enabled
- diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
- if (diagnostics) {
- start <- Sys.time()
- profile <- tempfile("renv-startup-", fileext = ".Rprof")
- utils::Rprof(profile)
- on.exit({
- utils::Rprof(NULL)
- elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
- writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
- writeLines(sprintf("- Profile: %s", profile))
- print(utils::summaryRprof(profile))
- }, add = TRUE)
- }
-
- # figure out whether the autoloader is enabled
- enabled <- local({
-
- # first, check config option
- override <- getOption("renv.config.autoloader.enabled")
- if (!is.null(override))
- return(override)
-
- # if we're being run in a context where R_LIBS is already set,
- # don't load -- presumably we're being run as a sub-process and
- # the parent process has already set up library paths for us
- rcmd <- Sys.getenv("R_CMD", unset = NA)
- rlibs <- Sys.getenv("R_LIBS", unset = NA)
- if (!is.na(rlibs) && !is.na(rcmd))
- return(FALSE)
-
- # next, check environment variables
- # TODO: prefer using the configuration one in the future
- envvars <- c(
- "RENV_CONFIG_AUTOLOADER_ENABLED",
- "RENV_AUTOLOADER_ENABLED",
- "RENV_ACTIVATE_PROJECT"
- )
-
- for (envvar in envvars) {
- envval <- Sys.getenv(envvar, unset = NA)
- if (!is.na(envval))
- return(tolower(envval) %in% c("true", "t", "1"))
- }
-
- # enable by default
- TRUE
-
- })
-
- # bail if we're not enabled
- if (!enabled) {
-
- # if we're not enabled, we might still need to manually load
- # the user profile here
- profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
- if (file.exists(profile)) {
- cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
- if (tolower(cfg) %in% c("true", "t", "1"))
- sys.source(profile, envir = globalenv())
- }
-
- return(FALSE)
-
- }
-
- # avoid recursion
- if (identical(getOption("renv.autoloader.running"), TRUE)) {
- warning("ignoring recursive attempt to run renv autoloader")
- return(invisible(TRUE))
- }
-
- # signal that we're loading renv during R startup
- options(renv.autoloader.running = TRUE)
- on.exit(options(renv.autoloader.running = NULL), add = TRUE)
-
- # signal that we've consented to use renv
- options(renv.consent = TRUE)
-
- # load the 'utils' package eagerly -- this ensures that renv shims, which
- # mask 'utils' packages, will come first on the search path
- library(utils, lib.loc = .Library)
-
- # unload renv if it's already been loaded
- if ("renv" %in% loadedNamespaces())
- unloadNamespace("renv")
-
- # load bootstrap tools
- `%||%` <- function(x, y) {
- if (is.null(x)) y else x
- }
-
- catf <- function(fmt, ..., appendLF = TRUE) {
-
- quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
- if (quiet)
- return(invisible())
-
- msg <- sprintf(fmt, ...)
- cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
-
- invisible(msg)
-
- }
-
- header <- function(label,
- ...,
- prefix = "#",
- suffix = "-",
- n = min(getOption("width"), 78))
- {
- label <- sprintf(label, ...)
- n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
- if (n <= 0)
- return(paste(prefix, label))
-
- tail <- paste(rep.int(suffix, n), collapse = "")
- paste0(prefix, " ", label, " ", tail)
-
- }
-
- startswith <- function(string, prefix) {
- substring(string, 1, nchar(prefix)) == prefix
- }
-
- bootstrap <- function(version, library) {
-
- friendly <- renv_bootstrap_version_friendly(version)
- section <- header(sprintf("Bootstrapping renv %s", friendly))
- catf(section)
-
- # attempt to download renv
- catf("- Downloading renv ... ", appendLF = FALSE)
- withCallingHandlers(
- tarball <- renv_bootstrap_download(version),
- error = function(err) {
- catf("FAILED")
- stop("failed to download:\n", conditionMessage(err))
- }
- )
- catf("OK")
- on.exit(unlink(tarball), add = TRUE)
-
- # now attempt to install
- catf("- Installing renv ... ", appendLF = FALSE)
- withCallingHandlers(
- status <- renv_bootstrap_install(version, tarball, library),
- error = function(err) {
- catf("FAILED")
- stop("failed to install:\n", conditionMessage(err))
- }
- )
- catf("OK")
-
- # add empty line to break up bootstrapping from normal output
- catf("")
-
- return(invisible())
- }
-
- renv_bootstrap_tests_running <- function() {
- getOption("renv.tests.running", default = FALSE)
- }
-
- renv_bootstrap_repos <- function() {
-
- # get CRAN repository
- cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
-
- # check for repos override
- repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
- if (!is.na(repos)) {
-
- # check for RSPM; if set, use a fallback repository for renv
- rspm <- Sys.getenv("RSPM", unset = NA)
- if (identical(rspm, repos))
- repos <- c(RSPM = rspm, CRAN = cran)
-
- return(repos)
-
- }
-
- # check for lockfile repositories
- repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
- if (!inherits(repos, "error") && length(repos))
- return(repos)
-
- # retrieve current repos
- repos <- getOption("repos")
-
- # ensure @CRAN@ entries are resolved
- repos[repos == "@CRAN@"] <- cran
-
- # add in renv.bootstrap.repos if set
- default <- c(FALLBACK = "https://cloud.r-project.org")
- extra <- getOption("renv.bootstrap.repos", default = default)
- repos <- c(repos, extra)
-
- # remove duplicates that might've snuck in
- dupes <- duplicated(repos) | duplicated(names(repos))
- repos[!dupes]
-
- }
-
- renv_bootstrap_repos_lockfile <- function() {
-
- lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
- if (!file.exists(lockpath))
- return(NULL)
-
- lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
- if (inherits(lockfile, "error")) {
- warning(lockfile)
- return(NULL)
- }
-
- repos <- lockfile$R$Repositories
- if (length(repos) == 0)
- return(NULL)
-
- keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
- vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
- names(vals) <- keys
-
- return(vals)
-
- }
-
- renv_bootstrap_download <- function(version) {
-
- sha <- attr(version, "sha", exact = TRUE)
-
- methods <- if (!is.null(sha)) {
-
- # attempting to bootstrap a development version of renv
- c(
- function() renv_bootstrap_download_tarball(sha),
- function() renv_bootstrap_download_github(sha)
- )
-
- } else {
-
- # attempting to bootstrap a release version of renv
- c(
- function() renv_bootstrap_download_tarball(version),
- function() renv_bootstrap_download_cran_latest(version),
- function() renv_bootstrap_download_cran_archive(version)
- )
-
- }
-
- for (method in methods) {
- path <- tryCatch(method(), error = identity)
- if (is.character(path) && file.exists(path))
- return(path)
- }
-
- stop("All download methods failed")
-
- }
-
- renv_bootstrap_download_impl <- function(url, destfile) {
-
- mode <- "wb"
-
- # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
- fixup <-
- Sys.info()[["sysname"]] == "Windows" &&
- substring(url, 1L, 5L) == "file:"
-
- if (fixup)
- mode <- "w+b"
-
- args <- list(
- url = url,
- destfile = destfile,
- mode = mode,
- quiet = TRUE
- )
-
- if ("headers" %in% names(formals(utils::download.file)))
- args$headers <- renv_bootstrap_download_custom_headers(url)
-
- do.call(utils::download.file, args)
-
- }
-
- renv_bootstrap_download_custom_headers <- function(url) {
-
- headers <- getOption("renv.download.headers")
- if (is.null(headers))
- return(character())
-
- if (!is.function(headers))
- stopf("'renv.download.headers' is not a function")
-
- headers <- headers(url)
- if (length(headers) == 0L)
- return(character())
-
- if (is.list(headers))
- headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
-
- ok <-
- is.character(headers) &&
- is.character(names(headers)) &&
- all(nzchar(names(headers)))
-
- if (!ok)
- stop("invocation of 'renv.download.headers' did not return a named character vector")
-
- headers
-
- }
-
- renv_bootstrap_download_cran_latest <- function(version) {
-
- spec <- renv_bootstrap_download_cran_latest_find(version)
- type <- spec$type
- repos <- spec$repos
-
- baseurl <- utils::contrib.url(repos = repos, type = type)
- ext <- if (identical(type, "source"))
- ".tar.gz"
- else if (Sys.info()[["sysname"]] == "Windows")
- ".zip"
- else
- ".tgz"
- name <- sprintf("renv_%s%s", version, ext)
- url <- paste(baseurl, name, sep = "/")
-
- destfile <- file.path(tempdir(), name)
- status <- tryCatch(
- renv_bootstrap_download_impl(url, destfile),
- condition = identity
- )
-
- if (inherits(status, "condition"))
- return(FALSE)
-
- # report success and return
- destfile
-
- }
-
- renv_bootstrap_download_cran_latest_find <- function(version) {
-
- # check whether binaries are supported on this system
- binary <-
- getOption("renv.bootstrap.binary", default = TRUE) &&
- !identical(.Platform$pkgType, "source") &&
- !identical(getOption("pkgType"), "source") &&
- Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
-
- types <- c(if (binary) "binary", "source")
-
- # iterate over types + repositories
- for (type in types) {
- for (repos in renv_bootstrap_repos()) {
-
- # retrieve package database
- db <- tryCatch(
- as.data.frame(
- utils::available.packages(type = type, repos = repos),
- stringsAsFactors = FALSE
- ),
- error = identity
- )
-
- if (inherits(db, "error"))
- next
-
- # check for compatible entry
- entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
- if (nrow(entry) == 0)
- next
-
- # found it; return spec to caller
- spec <- list(entry = entry, type = type, repos = repos)
- return(spec)
-
- }
- }
-
- # if we got here, we failed to find renv
- fmt <- "renv %s is not available from your declared package repositories"
- stop(sprintf(fmt, version))
-
- }
-
- renv_bootstrap_download_cran_archive <- function(version) {
-
- name <- sprintf("renv_%s.tar.gz", version)
- repos <- renv_bootstrap_repos()
- urls <- file.path(repos, "src/contrib/Archive/renv", name)
- destfile <- file.path(tempdir(), name)
-
- for (url in urls) {
-
- status <- tryCatch(
- renv_bootstrap_download_impl(url, destfile),
- condition = identity
- )
-
- if (identical(status, 0L))
- return(destfile)
-
- }
-
- return(FALSE)
-
- }
-
- renv_bootstrap_download_tarball <- function(version) {
-
- # if the user has provided the path to a tarball via
- # an environment variable, then use it
- tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
- if (is.na(tarball))
- return()
-
- # allow directories
- if (dir.exists(tarball)) {
- name <- sprintf("renv_%s.tar.gz", version)
- tarball <- file.path(tarball, name)
- }
-
- # bail if it doesn't exist
- if (!file.exists(tarball)) {
-
- # let the user know we weren't able to honour their request
- fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
- msg <- sprintf(fmt, tarball)
- warning(msg)
-
- # bail
- return()
-
- }
-
- catf("- Using local tarball '%s'.", tarball)
- tarball
-
- }
-
- renv_bootstrap_download_github <- function(version) {
-
- enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
- if (!identical(enabled, "TRUE"))
- return(FALSE)
-
- # prepare download options
- pat <- Sys.getenv("GITHUB_PAT")
- if (nzchar(Sys.which("curl")) && nzchar(pat)) {
- fmt <- "--location --fail --header \"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
- saved <- options("download.file.method", "download.file.extra")
- options(download.file.method = "curl", download.file.extra = extra)
- on.exit(do.call(base::options, saved), add = TRUE)
- } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
- fmt <- "--header=\"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
- saved <- options("download.file.method", "download.file.extra")
- options(download.file.method = "wget", download.file.extra = extra)
- on.exit(do.call(base::options, saved), add = TRUE)
- }
-
- url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
- name <- sprintf("renv_%s.tar.gz", version)
- destfile <- file.path(tempdir(), name)
-
- status <- tryCatch(
- renv_bootstrap_download_impl(url, destfile),
- condition = identity
- )
-
- if (!identical(status, 0L))
- return(FALSE)
-
- renv_bootstrap_download_augment(destfile)
-
- return(destfile)
-
- }
-
- # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
- # can use renv::install() to fully capture metadata.
- renv_bootstrap_download_augment <- function(destfile) {
- sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
- if (is.null(sha)) {
- return()
- }
-
- # Untar
- tempdir <- tempfile("renv-github-")
- on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
- untar(destfile, exdir = tempdir)
- pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
-
- # Modify description
- desc_path <- file.path(pkgdir, "DESCRIPTION")
- desc_lines <- readLines(desc_path)
- remotes_fields <- c(
- "RemoteType: github",
- "RemoteHost: api.github.com",
- "RemoteRepo: renv",
- "RemoteUsername: rstudio",
- "RemotePkgRef: rstudio/renv",
- paste("RemoteRef: ", sha),
- paste("RemoteSha: ", sha)
- )
- writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
-
- # Re-tar
- local({
- old <- setwd(tempdir)
- on.exit(setwd(old), add = TRUE)
-
- tar(destfile, compression = "gzip")
- })
- invisible()
- }
-
- # Extract the commit hash from a git archive. Git archives include the SHA1
- # hash as the comment field of the tarball pax extended header
- # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
- # For GitHub archives this should be the first header after the default one
- # (512 byte) header.
- renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
-
- # open the bundle for reading
- # We use gzcon for everything because (from ?gzcon)
- # > Reading from a connection which does not supply a 'gzip' magic
- # > header is equivalent to reading from the original connection
- conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
- on.exit(close(conn))
-
- # The default pax header is 512 bytes long and the first pax extended header
- # with the comment should be 51 bytes long
- # `52 comment=` (11 chars) + 40 byte SHA1 hash
- len <- 0x200 + 0x33
- res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
-
- if (grepl("^52 comment=", res)) {
- sub("52 comment=", "", res)
- } else {
- NULL
- }
- }
-
- renv_bootstrap_install <- function(version, tarball, library) {
-
- # attempt to install it into project library
- dir.create(library, showWarnings = FALSE, recursive = TRUE)
- output <- renv_bootstrap_install_impl(library, tarball)
-
- # check for successful install
- status <- attr(output, "status")
- if (is.null(status) || identical(status, 0L))
- return(status)
-
- # an error occurred; report it
- header <- "installation of renv failed"
- lines <- paste(rep.int("=", nchar(header)), collapse = "")
- text <- paste(c(header, lines, output), collapse = "\n")
- stop(text)
-
- }
-
- renv_bootstrap_install_impl <- function(library, tarball) {
-
- # invoke using system2 so we can capture and report output
- bin <- R.home("bin")
- exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
- R <- file.path(bin, exe)
-
- args <- c(
- "--vanilla", "CMD", "INSTALL", "--no-multiarch",
- "-l", shQuote(path.expand(library)),
- shQuote(path.expand(tarball))
- )
-
- system2(R, args, stdout = TRUE, stderr = TRUE)
-
- }
-
- renv_bootstrap_platform_prefix <- function() {
-
- # construct version prefix
- version <- paste(R.version$major, R.version$minor, sep = ".")
- prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
-
- # include SVN revision for development versions of R
- # (to avoid sharing platform-specific artefacts with released versions of R)
- devel <-
- identical(R.version[["status"]], "Under development (unstable)") ||
- identical(R.version[["nickname"]], "Unsuffered Consequences")
-
- if (devel)
- prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
-
- # build list of path components
- components <- c(prefix, R.version$platform)
-
- # include prefix if provided by user
- prefix <- renv_bootstrap_platform_prefix_impl()
- if (!is.na(prefix) && nzchar(prefix))
- components <- c(prefix, components)
-
- # build prefix
- paste(components, collapse = "/")
-
- }
-
- renv_bootstrap_platform_prefix_impl <- function() {
-
- # if an explicit prefix has been supplied, use it
- prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
- if (!is.na(prefix))
- return(prefix)
-
- # if the user has requested an automatic prefix, generate it
- auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
- if (auto %in% c("TRUE", "True", "true", "1"))
- return(renv_bootstrap_platform_prefix_auto())
-
- # empty string on failure
- ""
-
- }
-
- renv_bootstrap_platform_prefix_auto <- function() {
-
- prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
- if (inherits(prefix, "error") || prefix %in% "unknown") {
-
- msg <- paste(
- "failed to infer current operating system",
- "please file a bug report at https://github.com/rstudio/renv/issues",
- sep = "; "
- )
-
- warning(msg)
-
- }
-
- prefix
-
- }
-
- renv_bootstrap_platform_os <- function() {
-
- sysinfo <- Sys.info()
- sysname <- sysinfo[["sysname"]]
-
- # handle Windows + macOS up front
- if (sysname == "Windows")
- return("windows")
- else if (sysname == "Darwin")
- return("macos")
-
- # check for os-release files
- for (file in c("/etc/os-release", "/usr/lib/os-release"))
- if (file.exists(file))
- return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
-
- # check for redhat-release files
- if (file.exists("/etc/redhat-release"))
- return(renv_bootstrap_platform_os_via_redhat_release())
-
- "unknown"
-
- }
-
- renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
-
- # read /etc/os-release
- release <- utils::read.table(
- file = file,
- sep = "=",
- quote = c("\"", "'"),
- col.names = c("Key", "Value"),
- comment.char = "#",
- stringsAsFactors = FALSE
- )
-
- vars <- as.list(release$Value)
- names(vars) <- release$Key
-
- # get os name
- os <- tolower(sysinfo[["sysname"]])
-
- # read id
- id <- "unknown"
- for (field in c("ID", "ID_LIKE")) {
- if (field %in% names(vars) && nzchar(vars[[field]])) {
- id <- vars[[field]]
- break
- }
- }
-
- # read version
- version <- "unknown"
- for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
- if (field %in% names(vars) && nzchar(vars[[field]])) {
- version <- vars[[field]]
- break
- }
- }
-
- # join together
- paste(c(os, id, version), collapse = "-")
-
- }
-
- renv_bootstrap_platform_os_via_redhat_release <- function() {
-
- # read /etc/redhat-release
- contents <- readLines("/etc/redhat-release", warn = FALSE)
-
- # infer id
- id <- if (grepl("centos", contents, ignore.case = TRUE))
- "centos"
- else if (grepl("redhat", contents, ignore.case = TRUE))
- "redhat"
- else
- "unknown"
-
- # try to find a version component (very hacky)
- version <- "unknown"
-
- parts <- strsplit(contents, "[[:space:]]")[[1L]]
- for (part in parts) {
-
- nv <- tryCatch(numeric_version(part), error = identity)
- if (inherits(nv, "error"))
- next
-
- version <- nv[1, 1]
- break
-
- }
-
- paste(c("linux", id, version), collapse = "-")
-
- }
-
- renv_bootstrap_library_root_name <- function(project) {
-
- # use project name as-is if requested
- asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
- if (asis)
- return(basename(project))
-
- # otherwise, disambiguate based on project's path
- id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
- paste(basename(project), id, sep = "-")
-
- }
-
- renv_bootstrap_library_root <- function(project) {
-
- prefix <- renv_bootstrap_profile_prefix()
-
- path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
- if (!is.na(path))
- return(paste(c(path, prefix), collapse = "/"))
-
- path <- renv_bootstrap_library_root_impl(project)
- if (!is.null(path)) {
- name <- renv_bootstrap_library_root_name(project)
- return(paste(c(path, prefix, name), collapse = "/"))
- }
-
- renv_bootstrap_paths_renv("library", project = project)
-
- }
-
- renv_bootstrap_library_root_impl <- function(project) {
-
- root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
- if (!is.na(root))
- return(root)
-
- type <- renv_bootstrap_project_type(project)
- if (identical(type, "package")) {
- userdir <- renv_bootstrap_user_dir()
- return(file.path(userdir, "library"))
- }
-
- }
-
- renv_bootstrap_validate_version <- function(version, description = NULL) {
-
- # resolve description file
- #
- # avoid passing lib.loc to `packageDescription()` below, since R will
- # use the loaded version of the package by default anyhow. note that
- # this function should only be called after 'renv' is loaded
- # https://github.com/rstudio/renv/issues/1625
- description <- description %||% packageDescription("renv")
-
- # check whether requested version 'version' matches loaded version of renv
- sha <- attr(version, "sha", exact = TRUE)
- valid <- if (!is.null(sha))
- renv_bootstrap_validate_version_dev(sha, description)
- else
- renv_bootstrap_validate_version_release(version, description)
-
- if (valid)
- return(TRUE)
-
- # the loaded version of renv doesn't match the requested version;
- # give the user instructions on how to proceed
- remote <- if (!is.null(description[["RemoteSha"]])) {
- paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
- } else {
- paste("renv", description[["Version"]], sep = "@")
- }
-
- # display both loaded version + sha if available
- friendly <- renv_bootstrap_version_friendly(
- version = description[["Version"]],
- sha = description[["RemoteSha"]]
- )
-
- fmt <- paste(
- "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
- "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
- "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
- sep = "\n"
- )
- catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
-
- FALSE
-
- }
-
- renv_bootstrap_validate_version_dev <- function(version, description) {
- expected <- description[["RemoteSha"]]
- is.character(expected) && startswith(expected, version)
- }
-
- renv_bootstrap_validate_version_release <- function(version, description) {
- expected <- description[["Version"]]
- is.character(expected) && identical(expected, version)
- }
-
- renv_bootstrap_hash_text <- function(text) {
-
- hashfile <- tempfile("renv-hash-")
- on.exit(unlink(hashfile), add = TRUE)
-
- writeLines(text, con = hashfile)
- tools::md5sum(hashfile)
-
- }
-
- renv_bootstrap_load <- function(project, libpath, version) {
-
- # try to load renv from the project library
- if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
- return(FALSE)
-
- # warn if the version of renv loaded does not match
- renv_bootstrap_validate_version(version)
-
- # execute renv load hooks, if any
- hooks <- getHook("renv::autoload")
- for (hook in hooks)
- if (is.function(hook))
- tryCatch(hook(), error = warnify)
-
- # load the project
- renv::load(project)
-
- TRUE
-
- }
-
- renv_bootstrap_profile_load <- function(project) {
-
- # if RENV_PROFILE is already set, just use that
- profile <- Sys.getenv("RENV_PROFILE", unset = NA)
- if (!is.na(profile) && nzchar(profile))
- return(profile)
-
- # check for a profile file (nothing to do if it doesn't exist)
- path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
- if (!file.exists(path))
- return(NULL)
-
- # read the profile, and set it if it exists
- contents <- readLines(path, warn = FALSE)
- if (length(contents) == 0L)
- return(NULL)
-
- # set RENV_PROFILE
- profile <- contents[[1L]]
- if (!profile %in% c("", "default"))
- Sys.setenv(RENV_PROFILE = profile)
-
- profile
-
- }
-
- renv_bootstrap_profile_prefix <- function() {
- profile <- renv_bootstrap_profile_get()
- if (!is.null(profile))
- return(file.path("profiles", profile, "renv"))
- }
-
- renv_bootstrap_profile_get <- function() {
- profile <- Sys.getenv("RENV_PROFILE", unset = "")
- renv_bootstrap_profile_normalize(profile)
- }
-
- renv_bootstrap_profile_set <- function(profile) {
- profile <- renv_bootstrap_profile_normalize(profile)
- if (is.null(profile))
- Sys.unsetenv("RENV_PROFILE")
- else
- Sys.setenv(RENV_PROFILE = profile)
- }
-
- renv_bootstrap_profile_normalize <- function(profile) {
-
- if (is.null(profile) || profile %in% c("", "default"))
- return(NULL)
-
- profile
-
- }
-
- renv_bootstrap_path_absolute <- function(path) {
-
- substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
- substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
- substr(path, 2L, 3L) %in% c(":/", ":\\")
- )
-
- }
-
- renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
- renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
- root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
- prefix <- if (profile) renv_bootstrap_profile_prefix()
- components <- c(root, renv, prefix, ...)
- paste(components, collapse = "/")
- }
-
- renv_bootstrap_project_type <- function(path) {
-
- descpath <- file.path(path, "DESCRIPTION")
- if (!file.exists(descpath))
- return("unknown")
-
- desc <- tryCatch(
- read.dcf(descpath, all = TRUE),
- error = identity
- )
-
- if (inherits(desc, "error"))
- return("unknown")
-
- type <- desc$Type
- if (!is.null(type))
- return(tolower(type))
-
- package <- desc$Package
- if (!is.null(package))
- return("package")
-
- "unknown"
-
- }
-
- renv_bootstrap_user_dir <- function() {
- dir <- renv_bootstrap_user_dir_impl()
- path.expand(chartr("\\", "/", dir))
- }
-
- renv_bootstrap_user_dir_impl <- function() {
-
- # use local override if set
- override <- getOption("renv.userdir.override")
- if (!is.null(override))
- return(override)
-
- # use R_user_dir if available
- tools <- asNamespace("tools")
- if (is.function(tools$R_user_dir))
- return(tools$R_user_dir("renv", "cache"))
-
- # try using our own backfill for older versions of R
- envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
- for (envvar in envvars) {
- root <- Sys.getenv(envvar, unset = NA)
- if (!is.na(root))
- return(file.path(root, "R/renv"))
- }
-
- # use platform-specific default fallbacks
- if (Sys.info()[["sysname"]] == "Windows")
- file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
- else if (Sys.info()[["sysname"]] == "Darwin")
- "~/Library/Caches/org.R-project.R/R/renv"
- else
- "~/.cache/R/renv"
-
- }
-
- renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
- sha <- sha %||% attr(version, "sha", exact = TRUE)
- parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
- paste(parts, collapse = "")
- }
-
- renv_bootstrap_exec <- function(project, libpath, version) {
- if (!renv_bootstrap_load(project, libpath, version))
- renv_bootstrap_run(version, libpath)
- }
-
- renv_bootstrap_run <- function(version, libpath) {
-
- # perform bootstrap
- bootstrap(version, libpath)
-
- # exit early if we're just testing bootstrap
- if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
- return(TRUE)
-
- # try again to load
- if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
- return(renv::load(project = getwd()))
- }
-
- # failed to download or load renv; warn the user
- msg <- c(
- "Failed to find an renv installation: the project will not be loaded.",
- "Use `renv::activate()` to re-initialize the project."
- )
-
- warning(paste(msg, collapse = "\n"), call. = FALSE)
-
- }
-
- renv_json_read <- function(file = NULL, text = NULL) {
-
- jlerr <- NULL
-
- # if jsonlite is loaded, use that instead
- if ("jsonlite" %in% loadedNamespaces()) {
-
- json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
- if (!inherits(json, "error"))
- return(json)
-
- jlerr <- json
-
- }
-
- # otherwise, fall back to the default JSON reader
- json <- tryCatch(renv_json_read_default(file, text), error = identity)
- if (!inherits(json, "error"))
- return(json)
-
- # report an error
- if (!is.null(jlerr))
- stop(jlerr)
- else
- stop(json)
-
- }
-
- renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
- text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
- jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
- }
-
- renv_json_read_default <- function(file = NULL, text = NULL) {
-
- # find strings in the JSON
- text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
- pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
- locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
-
- # if any are found, replace them with placeholders
- replaced <- text
- strings <- character()
- replacements <- character()
-
- if (!identical(c(locs), -1L)) {
-
- # get the string values
- starts <- locs
- ends <- locs + attr(locs, "match.length") - 1L
- strings <- substring(text, starts, ends)
-
- # only keep those requiring escaping
- strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
-
- # compute replacements
- replacements <- sprintf('"\032%i\032"', seq_along(strings))
-
- # replace the strings
- mapply(function(string, replacement) {
- replaced <<- sub(string, replacement, replaced, fixed = TRUE)
- }, strings, replacements)
-
- }
-
- # transform the JSON into something the R parser understands
- transformed <- replaced
- transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
- transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
- transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
- transformed <- gsub(":", "=", transformed, fixed = TRUE)
- text <- paste(transformed, collapse = "\n")
-
- # parse it
- json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
-
- # construct map between source strings, replaced strings
- map <- as.character(parse(text = strings))
- names(map) <- as.character(parse(text = replacements))
-
- # convert to list
- map <- as.list(map)
-
- # remap strings in object
- remapped <- renv_json_read_remap(json, map)
-
- # evaluate
- eval(remapped, envir = baseenv())
-
- }
-
- renv_json_read_remap <- function(json, map) {
-
- # fix names
- if (!is.null(names(json))) {
- lhs <- match(names(json), names(map), nomatch = 0L)
- rhs <- match(names(map), names(json), nomatch = 0L)
- names(json)[rhs] <- map[lhs]
- }
-
- # fix values
- if (is.character(json))
- return(map[[json]] %||% json)
-
- # handle true, false, null
- if (is.name(json)) {
- text <- as.character(json)
- if (text == "true")
- return(TRUE)
- else if (text == "false")
- return(FALSE)
- else if (text == "null")
- return(NULL)
- }
-
- # recurse
- if (is.recursive(json)) {
- for (i in seq_along(json)) {
- json[i] <- list(renv_json_read_remap(json[[i]], map))
- }
- }
-
- json
-
- }
-
- # load the renv profile, if any
- renv_bootstrap_profile_load(project)
-
- # construct path to library root
- root <- renv_bootstrap_library_root(project)
-
- # construct library prefix for platform
- prefix <- renv_bootstrap_platform_prefix()
-
- # construct full libpath
- libpath <- file.path(root, prefix)
-
- # run bootstrap code
- renv_bootstrap_exec(project, libpath, version)
-
- invisible()
-
-})
+
+local({
+
+ # the requested version of renv
+ version <- "1.0.11"
+ attr(version, "sha") <- NULL
+
+ # the project directory
+ project <- Sys.getenv("RENV_PROJECT")
+ if (!nzchar(project))
+ project <- getwd()
+
+ # use start-up diagnostics if enabled
+ diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+ if (diagnostics) {
+ start <- Sys.time()
+ profile <- tempfile("renv-startup-", fileext = ".Rprof")
+ utils::Rprof(profile)
+ on.exit({
+ utils::Rprof(NULL)
+ elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+ writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+ writeLines(sprintf("- Profile: %s", profile))
+ print(utils::summaryRprof(profile))
+ }, add = TRUE)
+ }
+
+ # figure out whether the autoloader is enabled
+ enabled <- local({
+
+ # first, check config option
+ override <- getOption("renv.config.autoloader.enabled")
+ if (!is.null(override))
+ return(override)
+
+ # if we're being run in a context where R_LIBS is already set,
+ # don't load -- presumably we're being run as a sub-process and
+ # the parent process has already set up library paths for us
+ rcmd <- Sys.getenv("R_CMD", unset = NA)
+ rlibs <- Sys.getenv("R_LIBS", unset = NA)
+ if (!is.na(rlibs) && !is.na(rcmd))
+ return(FALSE)
+
+ # next, check environment variables
+ # TODO: prefer using the configuration one in the future
+ envvars <- c(
+ "RENV_CONFIG_AUTOLOADER_ENABLED",
+ "RENV_AUTOLOADER_ENABLED",
+ "RENV_ACTIVATE_PROJECT"
+ )
+
+ for (envvar in envvars) {
+ envval <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(envval))
+ return(tolower(envval) %in% c("true", "t", "1"))
+ }
+
+ # enable by default
+ TRUE
+
+ })
+
+ # bail if we're not enabled
+ if (!enabled) {
+
+ # if we're not enabled, we might still need to manually load
+ # the user profile here
+ profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+ if (file.exists(profile)) {
+ cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+ if (tolower(cfg) %in% c("true", "t", "1"))
+ sys.source(profile, envir = globalenv())
+ }
+
+ return(FALSE)
+
+ }
+
+ # avoid recursion
+ if (identical(getOption("renv.autoloader.running"), TRUE)) {
+ warning("ignoring recursive attempt to run renv autoloader")
+ return(invisible(TRUE))
+ }
+
+ # signal that we're loading renv during R startup
+ options(renv.autoloader.running = TRUE)
+ on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+ # signal that we've consented to use renv
+ options(renv.consent = TRUE)
+
+ # load the 'utils' package eagerly -- this ensures that renv shims, which
+ # mask 'utils' packages, will come first on the search path
+ library(utils, lib.loc = .Library)
+
+ # unload renv if it's already been loaded
+ if ("renv" %in% loadedNamespaces())
+ unloadNamespace("renv")
+
+ # load bootstrap tools
+ ansify <- function(text) {
+ if (renv_ansify_enabled())
+ renv_ansify_enhanced(text)
+ else
+ renv_ansify_default(text)
+ }
+
+ renv_ansify_enabled <- function() {
+
+ override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+ if (!is.na(override))
+ return(as.logical(override))
+
+ pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+ if (identical(pane, "build"))
+ return(FALSE)
+
+ testthat <- Sys.getenv("TESTTHAT", unset = "false")
+ if (tolower(testthat) %in% "true")
+ return(FALSE)
+
+ iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+ if (tolower(iderun) %in% "false")
+ return(FALSE)
+
+ TRUE
+
+ }
+
+ renv_ansify_default <- function(text) {
+ text
+ }
+
+ renv_ansify_enhanced <- function(text) {
+
+ # R help links
+ pattern <- "`\\?(renv::(?:[^`])+)`"
+ replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+ text <- gsub(pattern, replacement, text, perl = TRUE)
+
+ # runnable code
+ pattern <- "`(renv::(?:[^`])+)`"
+ replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+ text <- gsub(pattern, replacement, text, perl = TRUE)
+
+ # return ansified text
+ text
+
+ }
+
+ renv_ansify_init <- function() {
+
+ envir <- renv_envir_self()
+ if (renv_ansify_enabled())
+ assign("ansify", renv_ansify_enhanced, envir = envir)
+ else
+ assign("ansify", renv_ansify_default, envir = envir)
+
+ }
+
+ `%||%` <- function(x, y) {
+ if (is.null(x)) y else x
+ }
+
+ catf <- function(fmt, ..., appendLF = TRUE) {
+
+ quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+ if (quiet)
+ return(invisible())
+
+ msg <- sprintf(fmt, ...)
+ cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+
+ invisible(msg)
+
+ }
+
+ header <- function(label,
+ ...,
+ prefix = "#",
+ suffix = "-",
+ n = min(getOption("width"), 78))
+ {
+ label <- sprintf(label, ...)
+ n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+ if (n <= 0)
+ return(paste(prefix, label))
+
+ tail <- paste(rep.int(suffix, n), collapse = "")
+ paste0(prefix, " ", label, " ", tail)
+
+ }
+
+ heredoc <- function(text, leave = 0) {
+
+ # remove leading, trailing whitespace
+ trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+
+ # split into lines
+ lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+
+ # compute common indent
+ indent <- regexpr("[^[:space:]]", lines)
+ common <- min(setdiff(indent, -1L)) - leave
+ text <- paste(substring(lines, common), collapse = "\n")
+
+ # substitute in ANSI links for executable renv code
+ ansify(text)
+
+ }
+
+ startswith <- function(string, prefix) {
+ substring(string, 1, nchar(prefix)) == prefix
+ }
+
+ bootstrap <- function(version, library) {
+
+ friendly <- renv_bootstrap_version_friendly(version)
+ section <- header(sprintf("Bootstrapping renv %s", friendly))
+ catf(section)
+
+ # attempt to download renv
+ catf("- Downloading renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ tarball <- renv_bootstrap_download(version),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to download:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+ on.exit(unlink(tarball), add = TRUE)
+
+ # now attempt to install
+ catf("- Installing renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ status <- renv_bootstrap_install(version, tarball, library),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to install:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+
+ # add empty line to break up bootstrapping from normal output
+ catf("")
+
+ return(invisible())
+ }
+
+ renv_bootstrap_tests_running <- function() {
+ getOption("renv.tests.running", default = FALSE)
+ }
+
+ renv_bootstrap_repos <- function() {
+
+ # get CRAN repository
+ cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+
+ # check for repos override
+ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+ if (!is.na(repos)) {
+
+ # check for RSPM; if set, use a fallback repository for renv
+ rspm <- Sys.getenv("RSPM", unset = NA)
+ if (identical(rspm, repos))
+ repos <- c(RSPM = rspm, CRAN = cran)
+
+ return(repos)
+
+ }
+
+ # check for lockfile repositories
+ repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+ if (!inherits(repos, "error") && length(repos))
+ return(repos)
+
+ # retrieve current repos
+ repos <- getOption("repos")
+
+ # ensure @CRAN@ entries are resolved
+ repos[repos == "@CRAN@"] <- cran
+
+ # add in renv.bootstrap.repos if set
+ default <- c(FALLBACK = "https://cloud.r-project.org")
+ extra <- getOption("renv.bootstrap.repos", default = default)
+ repos <- c(repos, extra)
+
+ # remove duplicates that might've snuck in
+ dupes <- duplicated(repos) | duplicated(names(repos))
+ repos[!dupes]
+
+ }
+
+ renv_bootstrap_repos_lockfile <- function() {
+
+ lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+ if (!file.exists(lockpath))
+ return(NULL)
+
+ lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+ if (inherits(lockfile, "error")) {
+ warning(lockfile)
+ return(NULL)
+ }
+
+ repos <- lockfile$R$Repositories
+ if (length(repos) == 0)
+ return(NULL)
+
+ keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+ vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+ names(vals) <- keys
+
+ return(vals)
+
+ }
+
+ renv_bootstrap_download <- function(version) {
+
+ sha <- attr(version, "sha", exact = TRUE)
+
+ methods <- if (!is.null(sha)) {
+
+ # attempting to bootstrap a development version of renv
+ c(
+ function() renv_bootstrap_download_tarball(sha),
+ function() renv_bootstrap_download_github(sha)
+ )
+
+ } else {
+
+ # attempting to bootstrap a release version of renv
+ c(
+ function() renv_bootstrap_download_tarball(version),
+ function() renv_bootstrap_download_cran_latest(version),
+ function() renv_bootstrap_download_cran_archive(version)
+ )
+
+ }
+
+ for (method in methods) {
+ path <- tryCatch(method(), error = identity)
+ if (is.character(path) && file.exists(path))
+ return(path)
+ }
+
+ stop("All download methods failed")
+
+ }
+
+ renv_bootstrap_download_impl <- function(url, destfile) {
+
+ mode <- "wb"
+
+ # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+ fixup <-
+ Sys.info()[["sysname"]] == "Windows" &&
+ substring(url, 1L, 5L) == "file:"
+
+ if (fixup)
+ mode <- "w+b"
+
+ args <- list(
+ url = url,
+ destfile = destfile,
+ mode = mode,
+ quiet = TRUE
+ )
+
+ if ("headers" %in% names(formals(utils::download.file))) {
+ headers <- renv_bootstrap_download_custom_headers(url)
+ if (length(headers) && is.character(headers))
+ args$headers <- headers
+ }
+
+ do.call(utils::download.file, args)
+
+ }
+
+ renv_bootstrap_download_custom_headers <- function(url) {
+
+ headers <- getOption("renv.download.headers")
+ if (is.null(headers))
+ return(character())
+
+ if (!is.function(headers))
+ stopf("'renv.download.headers' is not a function")
+
+ headers <- headers(url)
+ if (length(headers) == 0L)
+ return(character())
+
+ if (is.list(headers))
+ headers <- unlist(headers, recursive = FALSE, use.names = TRUE)
+
+ ok <-
+ is.character(headers) &&
+ is.character(names(headers)) &&
+ all(nzchar(names(headers)))
+
+ if (!ok)
+ stop("invocation of 'renv.download.headers' did not return a named character vector")
+
+ headers
+
+ }
+
+ renv_bootstrap_download_cran_latest <- function(version) {
+
+ spec <- renv_bootstrap_download_cran_latest_find(version)
+ type <- spec$type
+ repos <- spec$repos
+
+ baseurl <- utils::contrib.url(repos = repos, type = type)
+ ext <- if (identical(type, "source"))
+ ".tar.gz"
+ else if (Sys.info()[["sysname"]] == "Windows")
+ ".zip"
+ else
+ ".tgz"
+ name <- sprintf("renv_%s%s", version, ext)
+ url <- paste(baseurl, name, sep = "/")
+
+ destfile <- file.path(tempdir(), name)
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (inherits(status, "condition"))
+ return(FALSE)
+
+ # report success and return
+ destfile
+
+ }
+
+ renv_bootstrap_download_cran_latest_find <- function(version) {
+
+ # check whether binaries are supported on this system
+ binary <-
+ getOption("renv.bootstrap.binary", default = TRUE) &&
+ !identical(.Platform$pkgType, "source") &&
+ !identical(getOption("pkgType"), "source") &&
+ Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+
+ types <- c(if (binary) "binary", "source")
+
+ # iterate over types + repositories
+ for (type in types) {
+ for (repos in renv_bootstrap_repos()) {
+
+ # build arguments for utils::available.packages() call
+ args <- list(type = type, repos = repos)
+
+ # add custom headers if available -- note that
+ # utils::available.packages() will pass this to download.file()
+ if ("headers" %in% names(formals(utils::download.file))) {
+ headers <- renv_bootstrap_download_custom_headers(repos)
+ if (length(headers) && is.character(headers))
+ args$headers <- headers
+ }
+
+ # retrieve package database
+ db <- tryCatch(
+ as.data.frame(
+ do.call(utils::available.packages, args),
+ stringsAsFactors = FALSE
+ ),
+ error = identity
+ )
+
+ if (inherits(db, "error"))
+ next
+
+ # check for compatible entry
+ entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+ if (nrow(entry) == 0)
+ next
+
+ # found it; return spec to caller
+ spec <- list(entry = entry, type = type, repos = repos)
+ return(spec)
+
+ }
+ }
+
+ # if we got here, we failed to find renv
+ fmt <- "renv %s is not available from your declared package repositories"
+ stop(sprintf(fmt, version))
+
+ }
+
+ renv_bootstrap_download_cran_archive <- function(version) {
+
+ name <- sprintf("renv_%s.tar.gz", version)
+ repos <- renv_bootstrap_repos()
+ urls <- file.path(repos, "src/contrib/Archive/renv", name)
+ destfile <- file.path(tempdir(), name)
+
+ for (url in urls) {
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (identical(status, 0L))
+ return(destfile)
+
+ }
+
+ return(FALSE)
+
+ }
+
+ renv_bootstrap_download_tarball <- function(version) {
+
+ # if the user has provided the path to a tarball via
+ # an environment variable, then use it
+ tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+ if (is.na(tarball))
+ return()
+
+ # allow directories
+ if (dir.exists(tarball)) {
+ name <- sprintf("renv_%s.tar.gz", version)
+ tarball <- file.path(tarball, name)
+ }
+
+ # bail if it doesn't exist
+ if (!file.exists(tarball)) {
+
+ # let the user know we weren't able to honour their request
+ fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+ msg <- sprintf(fmt, tarball)
+ warning(msg)
+
+ # bail
+ return()
+
+ }
+
+ catf("- Using local tarball '%s'.", tarball)
+ tarball
+
+ }
+
+ renv_bootstrap_github_token <- function() {
+ for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
+ envval <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(envval))
+ return(envval)
+ }
+ }
+
+ renv_bootstrap_download_github <- function(version) {
+
+ enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+ if (!identical(enabled, "TRUE"))
+ return(FALSE)
+
+ # prepare download options
+ token <- renv_bootstrap_github_token()
+ if (nzchar(Sys.which("curl")) && nzchar(token)) {
+ fmt <- "--location --fail --header \"Authorization: token %s\""
+ extra <- sprintf(fmt, token)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "curl", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
+ fmt <- "--header=\"Authorization: token %s\""
+ extra <- sprintf(fmt, token)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "wget", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ }
+
+ url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+ name <- sprintf("renv_%s.tar.gz", version)
+ destfile <- file.path(tempdir(), name)
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (!identical(status, 0L))
+ return(FALSE)
+
+ renv_bootstrap_download_augment(destfile)
+
+ return(destfile)
+
+ }
+
+ # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+ # can use renv::install() to fully capture metadata.
+ renv_bootstrap_download_augment <- function(destfile) {
+ sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+ if (is.null(sha)) {
+ return()
+ }
+
+ # Untar
+ tempdir <- tempfile("renv-github-")
+ on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+ untar(destfile, exdir = tempdir)
+ pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+
+ # Modify description
+ desc_path <- file.path(pkgdir, "DESCRIPTION")
+ desc_lines <- readLines(desc_path)
+ remotes_fields <- c(
+ "RemoteType: github",
+ "RemoteHost: api.github.com",
+ "RemoteRepo: renv",
+ "RemoteUsername: rstudio",
+ "RemotePkgRef: rstudio/renv",
+ paste("RemoteRef: ", sha),
+ paste("RemoteSha: ", sha)
+ )
+ writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+
+ # Re-tar
+ local({
+ old <- setwd(tempdir)
+ on.exit(setwd(old), add = TRUE)
+
+ tar(destfile, compression = "gzip")
+ })
+ invisible()
+ }
+
+ # Extract the commit hash from a git archive. Git archives include the SHA1
+ # hash as the comment field of the tarball pax extended header
+ # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+ # For GitHub archives this should be the first header after the default one
+ # (512 byte) header.
+ renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+
+ # open the bundle for reading
+ # We use gzcon for everything because (from ?gzcon)
+ # > Reading from a connection which does not supply a 'gzip' magic
+ # > header is equivalent to reading from the original connection
+ conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+ on.exit(close(conn))
+
+ # The default pax header is 512 bytes long and the first pax extended header
+ # with the comment should be 51 bytes long
+ # `52 comment=` (11 chars) + 40 byte SHA1 hash
+ len <- 0x200 + 0x33
+ res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+
+ if (grepl("^52 comment=", res)) {
+ sub("52 comment=", "", res)
+ } else {
+ NULL
+ }
+ }
+
+ renv_bootstrap_install <- function(version, tarball, library) {
+
+ # attempt to install it into project library
+ dir.create(library, showWarnings = FALSE, recursive = TRUE)
+ output <- renv_bootstrap_install_impl(library, tarball)
+
+ # check for successful install
+ status <- attr(output, "status")
+ if (is.null(status) || identical(status, 0L))
+ return(status)
+
+ # an error occurred; report it
+ header <- "installation of renv failed"
+ lines <- paste(rep.int("=", nchar(header)), collapse = "")
+ text <- paste(c(header, lines, output), collapse = "\n")
+ stop(text)
+
+ }
+
+ renv_bootstrap_install_impl <- function(library, tarball) {
+
+ # invoke using system2 so we can capture and report output
+ bin <- R.home("bin")
+ exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+ R <- file.path(bin, exe)
+
+ args <- c(
+ "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+ "-l", shQuote(path.expand(library)),
+ shQuote(path.expand(tarball))
+ )
+
+ system2(R, args, stdout = TRUE, stderr = TRUE)
+
+ }
+
+ renv_bootstrap_platform_prefix <- function() {
+
+ # construct version prefix
+ version <- paste(R.version$major, R.version$minor, sep = ".")
+ prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+
+ # include SVN revision for development versions of R
+ # (to avoid sharing platform-specific artefacts with released versions of R)
+ devel <-
+ identical(R.version[["status"]], "Under development (unstable)") ||
+ identical(R.version[["nickname"]], "Unsuffered Consequences")
+
+ if (devel)
+ prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+
+ # build list of path components
+ components <- c(prefix, R.version$platform)
+
+ # include prefix if provided by user
+ prefix <- renv_bootstrap_platform_prefix_impl()
+ if (!is.na(prefix) && nzchar(prefix))
+ components <- c(prefix, components)
+
+ # build prefix
+ paste(components, collapse = "/")
+
+ }
+
+ renv_bootstrap_platform_prefix_impl <- function() {
+
+ # if an explicit prefix has been supplied, use it
+ prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+ if (!is.na(prefix))
+ return(prefix)
+
+ # if the user has requested an automatic prefix, generate it
+ auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+ if (is.na(auto) && getRversion() >= "4.4.0")
+ auto <- "TRUE"
+
+ if (auto %in% c("TRUE", "True", "true", "1"))
+ return(renv_bootstrap_platform_prefix_auto())
+
+ # empty string on failure
+ ""
+
+ }
+
+ renv_bootstrap_platform_prefix_auto <- function() {
+
+ prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+ if (inherits(prefix, "error") || prefix %in% "unknown") {
+
+ msg <- paste(
+ "failed to infer current operating system",
+ "please file a bug report at https://github.com/rstudio/renv/issues",
+ sep = "; "
+ )
+
+ warning(msg)
+
+ }
+
+ prefix
+
+ }
+
+ renv_bootstrap_platform_os <- function() {
+
+ sysinfo <- Sys.info()
+ sysname <- sysinfo[["sysname"]]
+
+ # handle Windows + macOS up front
+ if (sysname == "Windows")
+ return("windows")
+ else if (sysname == "Darwin")
+ return("macos")
+
+ # check for os-release files
+ for (file in c("/etc/os-release", "/usr/lib/os-release"))
+ if (file.exists(file))
+ return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+
+ # check for redhat-release files
+ if (file.exists("/etc/redhat-release"))
+ return(renv_bootstrap_platform_os_via_redhat_release())
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+
+ # read /etc/os-release
+ release <- utils::read.table(
+ file = file,
+ sep = "=",
+ quote = c("\"", "'"),
+ col.names = c("Key", "Value"),
+ comment.char = "#",
+ stringsAsFactors = FALSE
+ )
+
+ vars <- as.list(release$Value)
+ names(vars) <- release$Key
+
+ # get os name
+ os <- tolower(sysinfo[["sysname"]])
+
+ # read id
+ id <- "unknown"
+ for (field in c("ID", "ID_LIKE")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ id <- vars[[field]]
+ break
+ }
+ }
+
+ # read version
+ version <- "unknown"
+ for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ version <- vars[[field]]
+ break
+ }
+ }
+
+ # join together
+ paste(c(os, id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_platform_os_via_redhat_release <- function() {
+
+ # read /etc/redhat-release
+ contents <- readLines("/etc/redhat-release", warn = FALSE)
+
+ # infer id
+ id <- if (grepl("centos", contents, ignore.case = TRUE))
+ "centos"
+ else if (grepl("redhat", contents, ignore.case = TRUE))
+ "redhat"
+ else
+ "unknown"
+
+ # try to find a version component (very hacky)
+ version <- "unknown"
+
+ parts <- strsplit(contents, "[[:space:]]")[[1L]]
+ for (part in parts) {
+
+ nv <- tryCatch(numeric_version(part), error = identity)
+ if (inherits(nv, "error"))
+ next
+
+ version <- nv[1, 1]
+ break
+
+ }
+
+ paste(c("linux", id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_library_root_name <- function(project) {
+
+ # use project name as-is if requested
+ asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+ if (asis)
+ return(basename(project))
+
+ # otherwise, disambiguate based on project's path
+ id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+ paste(basename(project), id, sep = "-")
+
+ }
+
+ renv_bootstrap_library_root <- function(project) {
+
+ prefix <- renv_bootstrap_profile_prefix()
+
+ path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+ if (!is.na(path))
+ return(paste(c(path, prefix), collapse = "/"))
+
+ path <- renv_bootstrap_library_root_impl(project)
+ if (!is.null(path)) {
+ name <- renv_bootstrap_library_root_name(project)
+ return(paste(c(path, prefix, name), collapse = "/"))
+ }
+
+ renv_bootstrap_paths_renv("library", project = project)
+
+ }
+
+ renv_bootstrap_library_root_impl <- function(project) {
+
+ root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+ if (!is.na(root))
+ return(root)
+
+ type <- renv_bootstrap_project_type(project)
+ if (identical(type, "package")) {
+ userdir <- renv_bootstrap_user_dir()
+ return(file.path(userdir, "library"))
+ }
+
+ }
+
+ renv_bootstrap_validate_version <- function(version, description = NULL) {
+
+ # resolve description file
+ #
+ # avoid passing lib.loc to `packageDescription()` below, since R will
+ # use the loaded version of the package by default anyhow. note that
+ # this function should only be called after 'renv' is loaded
+ # https://github.com/rstudio/renv/issues/1625
+ description <- description %||% packageDescription("renv")
+
+ # check whether requested version 'version' matches loaded version of renv
+ sha <- attr(version, "sha", exact = TRUE)
+ valid <- if (!is.null(sha))
+ renv_bootstrap_validate_version_dev(sha, description)
+ else
+ renv_bootstrap_validate_version_release(version, description)
+
+ if (valid)
+ return(TRUE)
+
+ # the loaded version of renv doesn't match the requested version;
+ # give the user instructions on how to proceed
+ dev <- identical(description[["RemoteType"]], "github")
+ remote <- if (dev)
+ paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+ else
+ paste("renv", description[["Version"]], sep = "@")
+
+ # display both loaded version + sha if available
+ friendly <- renv_bootstrap_version_friendly(
+ version = description[["Version"]],
+ sha = if (dev) description[["RemoteSha"]]
+ )
+
+ fmt <- heredoc("
+ renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+ - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+ - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+ ")
+ catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+
+ FALSE
+
+ }
+
+ renv_bootstrap_validate_version_dev <- function(version, description) {
+ expected <- description[["RemoteSha"]]
+ is.character(expected) && startswith(expected, version)
+ }
+
+ renv_bootstrap_validate_version_release <- function(version, description) {
+ expected <- description[["Version"]]
+ is.character(expected) && identical(expected, version)
+ }
+
+ renv_bootstrap_hash_text <- function(text) {
+
+ hashfile <- tempfile("renv-hash-")
+ on.exit(unlink(hashfile), add = TRUE)
+
+ writeLines(text, con = hashfile)
+ tools::md5sum(hashfile)
+
+ }
+
+ renv_bootstrap_load <- function(project, libpath, version) {
+
+ # try to load renv from the project library
+ if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+ return(FALSE)
+
+ # warn if the version of renv loaded does not match
+ renv_bootstrap_validate_version(version)
+
+ # execute renv load hooks, if any
+ hooks <- getHook("renv::autoload")
+ for (hook in hooks)
+ if (is.function(hook))
+ tryCatch(hook(), error = warnify)
+
+ # load the project
+ renv::load(project)
+
+ TRUE
+
+ }
+
+ renv_bootstrap_profile_load <- function(project) {
+
+ # if RENV_PROFILE is already set, just use that
+ profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+ if (!is.na(profile) && nzchar(profile))
+ return(profile)
+
+ # check for a profile file (nothing to do if it doesn't exist)
+ path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+ if (!file.exists(path))
+ return(NULL)
+
+ # read the profile, and set it if it exists
+ contents <- readLines(path, warn = FALSE)
+ if (length(contents) == 0L)
+ return(NULL)
+
+ # set RENV_PROFILE
+ profile <- contents[[1L]]
+ if (!profile %in% c("", "default"))
+ Sys.setenv(RENV_PROFILE = profile)
+
+ profile
+
+ }
+
+ renv_bootstrap_profile_prefix <- function() {
+ profile <- renv_bootstrap_profile_get()
+ if (!is.null(profile))
+ return(file.path("profiles", profile, "renv"))
+ }
+
+ renv_bootstrap_profile_get <- function() {
+ profile <- Sys.getenv("RENV_PROFILE", unset = "")
+ renv_bootstrap_profile_normalize(profile)
+ }
+
+ renv_bootstrap_profile_set <- function(profile) {
+ profile <- renv_bootstrap_profile_normalize(profile)
+ if (is.null(profile))
+ Sys.unsetenv("RENV_PROFILE")
+ else
+ Sys.setenv(RENV_PROFILE = profile)
+ }
+
+ renv_bootstrap_profile_normalize <- function(profile) {
+
+ if (is.null(profile) || profile %in% c("", "default"))
+ return(NULL)
+
+ profile
+
+ }
+
+ renv_bootstrap_path_absolute <- function(path) {
+
+ substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+ substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+ substr(path, 2L, 3L) %in% c(":/", ":\\")
+ )
+
+ }
+
+ renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+ renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+ root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+ prefix <- if (profile) renv_bootstrap_profile_prefix()
+ components <- c(root, renv, prefix, ...)
+ paste(components, collapse = "/")
+ }
+
+ renv_bootstrap_project_type <- function(path) {
+
+ descpath <- file.path(path, "DESCRIPTION")
+ if (!file.exists(descpath))
+ return("unknown")
+
+ desc <- tryCatch(
+ read.dcf(descpath, all = TRUE),
+ error = identity
+ )
+
+ if (inherits(desc, "error"))
+ return("unknown")
+
+ type <- desc$Type
+ if (!is.null(type))
+ return(tolower(type))
+
+ package <- desc$Package
+ if (!is.null(package))
+ return("package")
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_user_dir <- function() {
+ dir <- renv_bootstrap_user_dir_impl()
+ path.expand(chartr("\\", "/", dir))
+ }
+
+ renv_bootstrap_user_dir_impl <- function() {
+
+ # use local override if set
+ override <- getOption("renv.userdir.override")
+ if (!is.null(override))
+ return(override)
+
+ # use R_user_dir if available
+ tools <- asNamespace("tools")
+ if (is.function(tools$R_user_dir))
+ return(tools$R_user_dir("renv", "cache"))
+
+ # try using our own backfill for older versions of R
+ envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+ for (envvar in envvars) {
+ root <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(root))
+ return(file.path(root, "R/renv"))
+ }
+
+ # use platform-specific default fallbacks
+ if (Sys.info()[["sysname"]] == "Windows")
+ file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+ else if (Sys.info()[["sysname"]] == "Darwin")
+ "~/Library/Caches/org.R-project.R/R/renv"
+ else
+ "~/.cache/R/renv"
+
+ }
+
+ renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+ sha <- sha %||% attr(version, "sha", exact = TRUE)
+ parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+ paste(parts, collapse = "")
+ }
+
+ renv_bootstrap_exec <- function(project, libpath, version) {
+ if (!renv_bootstrap_load(project, libpath, version))
+ renv_bootstrap_run(version, libpath)
+ }
+
+ renv_bootstrap_run <- function(version, libpath) {
+
+ # perform bootstrap
+ bootstrap(version, libpath)
+
+ # exit early if we're just testing bootstrap
+ if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+ return(TRUE)
+
+ # try again to load
+ if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+ return(renv::load(project = getwd()))
+ }
+
+ # failed to download or load renv; warn the user
+ msg <- c(
+ "Failed to find an renv installation: the project will not be loaded.",
+ "Use `renv::activate()` to re-initialize the project."
+ )
+
+ warning(paste(msg, collapse = "\n"), call. = FALSE)
+
+ }
+
+ renv_json_read <- function(file = NULL, text = NULL) {
+
+ jlerr <- NULL
+
+ # if jsonlite is loaded, use that instead
+ if ("jsonlite" %in% loadedNamespaces()) {
+
+ json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ jlerr <- json
+
+ }
+
+ # otherwise, fall back to the default JSON reader
+ json <- tryCatch(renv_json_read_default(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ # report an error
+ if (!is.null(jlerr))
+ stop(jlerr)
+ else
+ stop(json)
+
+ }
+
+ renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+ }
+
+ renv_json_read_default <- function(file = NULL, text = NULL) {
+
+ # find strings in the JSON
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
+ locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
+
+ # if any are found, replace them with placeholders
+ replaced <- text
+ strings <- character()
+ replacements <- character()
+
+ if (!identical(c(locs), -1L)) {
+
+ # get the string values
+ starts <- locs
+ ends <- locs + attr(locs, "match.length") - 1L
+ strings <- substring(text, starts, ends)
+
+ # only keep those requiring escaping
+ strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
+
+ # compute replacements
+ replacements <- sprintf('"\032%i\032"', seq_along(strings))
+
+ # replace the strings
+ mapply(function(string, replacement) {
+ replaced <<- sub(string, replacement, replaced, fixed = TRUE)
+ }, strings, replacements)
+
+ }
+
+ # transform the JSON into something the R parser understands
+ transformed <- replaced
+ transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+ transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+ transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+ transformed <- gsub(":", "=", transformed, fixed = TRUE)
+ text <- paste(transformed, collapse = "\n")
+
+ # parse it
+ json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
+
+ # construct map between source strings, replaced strings
+ map <- as.character(parse(text = strings))
+ names(map) <- as.character(parse(text = replacements))
+
+ # convert to list
+ map <- as.list(map)
+
+ # remap strings in object
+ remapped <- renv_json_read_remap(json, map)
+
+ # evaluate
+ eval(remapped, envir = baseenv())
+
+ }
+
+ renv_json_read_remap <- function(json, map) {
+
+ # fix names
+ if (!is.null(names(json))) {
+ lhs <- match(names(json), names(map), nomatch = 0L)
+ rhs <- match(names(map), names(json), nomatch = 0L)
+ names(json)[rhs] <- map[lhs]
+ }
+
+ # fix values
+ if (is.character(json))
+ return(map[[json]] %||% json)
+
+ # handle true, false, null
+ if (is.name(json)) {
+ text <- as.character(json)
+ if (text == "true")
+ return(TRUE)
+ else if (text == "false")
+ return(FALSE)
+ else if (text == "null")
+ return(NULL)
+ }
+
+ # recurse
+ if (is.recursive(json)) {
+ for (i in seq_along(json)) {
+ json[i] <- list(renv_json_read_remap(json[[i]], map))
+ }
+ }
+
+ json
+
+ }
+
+ # load the renv profile, if any
+ renv_bootstrap_profile_load(project)
+
+ # construct path to library root
+ root <- renv_bootstrap_library_root(project)
+
+ # construct library prefix for platform
+ prefix <- renv_bootstrap_platform_prefix()
+
+ # construct full libpath
+ libpath <- file.path(root, prefix)
+
+ # run bootstrap code
+ renv_bootstrap_exec(project, libpath, version)
+
+ invisible()
+
+})