diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..77fd53d --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^\.pbattributes$ +^manifest\.json$ diff --git a/.Rprofile b/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/.gitignore b/.gitignore index fae8299..8bd547b 100644 --- a/.gitignore +++ b/.gitignore @@ -37,3 +37,9 @@ vignettes/*.pdf # R Environment Variables .Renviron +manifest.json +Datasets/Raw/*.txt +Datasets/Raw/*.dat +Datasets/Raw/*.zip +Datasets/Raw/*.csv +Datasets/Raw/*.RData diff --git a/.pbattributes b/.pbattributes new file mode 100644 index 0000000..bf2573e --- /dev/null +++ b/.pbattributes @@ -0,0 +1,5 @@ +Datasets/Raw/*.txt +Datasets/Raw/*.dat +Datasets/Raw/*.zip +Datasets/Raw/*.csv +Datasets/Raw/*.RData diff --git a/Codes/00_Dir_Setup.R b/Codes/00_Dir_Setup.R new file mode 100644 index 0000000..b5884ea --- /dev/null +++ b/Codes/00_Dir_Setup.R @@ -0,0 +1,30 @@ +#Settting up directory +##Settting up directory +options(repos = getOption("repos")["CRAN"]) +install.packages("PTXQC") +install.packages("pacman") +pacman::p_load(piggyback, renv, here, tidyverse, targets, + visNetwork) +install.packages('piggyback') +install.packages('renv') +install.packages('here') +install.packages('tidyverse') +install.packages('targets') +install.packages('visNetwork') +#testthat::use_test() + +## Created a first release directly on Github +#pb_new_release("Skourtis/Project_Template") +piggyback::pb_track(c("Datasets/Raw/*.txt", + "Datasets/Raw/*.dat", + "Datasets/Raw/*.zip", + "Datasets/Raw/*.csv", + "Datasets/Raw/*.RData")) + +piggyback::pb_track() %>% + pb_upload(repo = "Skourtis/Project_Template") + +##end +renv::snapshot() + + diff --git a/Codes/01_Downloading_Files.R b/Codes/01_Downloading_Files.R new file mode 100644 index 0000000..f1ee988 --- /dev/null +++ b/Codes/01_Downloading_Files.R @@ -0,0 +1,10 @@ +#Downloading from Git template +#Cachem install error bc 'make' was not installed, Rtools installed +#Manually created .Renv and paste the path from Rtools webpage. +renv::restore() +install.packages('devtools') + +options(repos = getOption("repos")["CRAN"]) +devtools::install_github("bartongroup/Proteus", build_opts= c("--no-resave-data", "--no-manual"), build_vignettes=FALSE) +pacman::p_load(piggyback, renv, here, tidyverse) +pb_download() diff --git a/Codes/functions.R b/Codes/functions.R new file mode 100644 index 0000000..7bca5af --- /dev/null +++ b/Codes/functions.R @@ -0,0 +1,244 @@ +Quality_Control <- function(x){ + ### takes as input the txt output folder of MaxQuant + ### in the form of the here::here function + ### and produces a QC report + pacman::p_temp("PTXQC") + require(methods) + r = createReport(x) +} + +load_MaxQuant <- function(txt_folder){ + ### This function takes the txt folder, + ### the name of the measure_col,number of samples and + ### names of the conditions and output the peptides per condition and + ### reads the Maxquant proteinGroups file + #txt_folder <- here::here("Datasets", "Raw", + # "2020MQ044txt", + # "txt") + + condition_names <- c(rep("control",3), + rep("sh_1",3), + rep("sh_2",3)) + samples_ids <- 1:9 + measure_col <- "Intensity" + + measCols <- list( + HL = measure_col + ) + + eviCols <- list( + sequence = 'Sequence', + modified_sequence = 'Modified sequence', + modifications = 'Modifications', + protein_group = 'Proteins', + protein = 'Leading razor protein', + experiment = 'Experiment', + charge = 'Charge', + reverse = 'Reverse', + contaminant = 'Potential contaminant' + ) + evi <- proteus::readEvidenceFile(paste0(txt_folder, + "/evidence.txt"), + measure.cols=measCols, + data.cols=eviCols, + zeroes.are.missing=FALSE) + + + + meta <- data.frame(experiment = sort(evi$experiment %>% unique()), + measure = measure_col, + condition = condition_names, + sample = sort(evi$experiment %>% unique()), + replicate = c(rep(1,3),rep(2,3),rep(3,3))) + + pepdat <- proteus::makePeptideTable(evi, + meta, + measure.cols=measCols, + experiment.type="label-free") + + measure_columns <- list(paste(measure_col,samples_ids, sep = " " )) %>% unlist %>% + setNames(paste("Sample", samples_ids, sep = "_")) + + list(proteins = proteus::readProteinGroups(paste0(txt_folder, + "/proteinGroups.txt"), + meta, + measure.cols = measure_columns), + peptides = pepdat, meta, measure.cols = measure_columns + ) +} +load_MaxQuanttest <- function(txt_folder){ + ### This function takes the txt folder, + ### the name of the measure_col,number of samples and + ### names of the conditions and output the peptides per condition and + ### reads the Maxquant proteinGroups file + #txt_folder <- here::here("Datasets", "Raw", + # "2020MQ044txt", + # "txt") + + condition_names <- c(1:9) + samples_ids <- 1:9 + measure_col <- "Intensity" + + measCols <- list( + HL = measure_col + ) + + eviCols <- list( + sequence = 'Sequence', + modified_sequence = 'Modified sequence', + modifications = 'Modifications', + protein_group = 'Proteins', + protein = 'Leading razor protein', + experiment = 'Experiment', + charge = 'Charge', + reverse = 'Reverse', + contaminant = 'Potential contaminant' + ) + evi <- proteus::readEvidenceFile(paste0(txt_folder, + "/evidence.txt"), + measure.cols=measCols, + data.cols=eviCols, + zeroes.are.missing=FALSE) + + + + meta <- data.frame(experiment = sort(evi$experiment %>% unique()), + measure = measure_col, + condition = condition_names, + sample = sort(evi$experiment %>% unique()), + replicate = 1,1,1,2,2,2,3,3,3) + + pepdat <- proteus::makePeptideTable(evi, + meta, + measure.cols=measCols, + experiment.type="label-free") + + measure_columns <- list(paste(measure_col,samples_ids, sep = " " )) %>% unlist %>% + setNames(paste("Sample", samples_ids, sep = "_")) + + list(proteins = proteus::readProteinGroups(paste0(txt_folder, + "/proteinGroups.txt"), + meta, + measure.cols = measure_columns), + peptides = pepdat, meta, measure.cols = measure_columns + ) +} + + +is_function = function (expr) { + if (! is_assign(expr)) + return(FALSE) + value = expr[[3]] + is.call(value) && as.character(value[[1]]) == 'function' +} + +function_name = function (expr){ + as.character(expr[[2]])} + +is_assign = function (expr){ + is.call(expr) && as.character(expr[[1]]) %in% c('=', '<-', 'assign')} + + +produce_ipath_map <- function(df, + column_name = NULL){ + ### takes as input a dataframe produced which converts ratios to colours + ### and the columns to map and produces iPath3 images + #df = For_ipath_comparisons + #column_name = columns_for_mapping[1] + + Filtered_proteins <- df %>% + dplyr::select(all_of(c("V1","Width",column_name))) %>% + na.omit() + + #Filtered_proteins$Width <- paste("W",as.character(ntile(Filtered_proteins[,i], 30)),sep="") + Filtered_proteins$Ipath <- paste(Filtered_proteins$V1, + Filtered_proteins %>% pull(column_name), + Filtered_proteins$Width) + + file_name <- here::here("Project_Output", + paste0(column_name, + "_ipath_all_enzymes_bins.tsv")) + + selections <- paste('selection=', + paste(paste(Filtered_proteins$Ipath, + "%0A ",sep = ""), + collapse = " "), + collapse = " ") + + export_type <- "export_type=svg" + + file_ipath <- paste("./../Project_Output/", + column_name,"_ipath_all_enzymes_bins.svg", + sep="") + + ipath_command <- paste(paste("curl -d ", + selections, " -d ", + export_type, + " https://pathways.embl.de/mapping.cgi -o ", + sep = '\"'), + file_ipath, + sep="") + system(ipath_command) + print(column_name) + write_tsv(Filtered_proteins,file_name,col_names = FALSE) + #pacman::p_load("rsvg") + bitmap <- rsvg::rsvg_raw( here::here("Project_Output", + paste0(column_name,"_ipath_all_enzymes_bins.svg")), + width = 3600) + + cowplot::ggdraw()+cowplot::draw_image(bitmap)+ cowplot::draw_figure_label(column_name,"top", size = 65) + + +} + +calculateCoveredProtein_sav <- function (sample_id,proteinIDs, markerproteins) +{ + compartments <- c("S1", "S2", "S3", "S4", "N1", "N2", "N3", + "N4", "C1", "C2", "C3", "C4", "C5", "M1", "M2") + color.code <- c("gold", "orange", "salmon", "tomato2", "grey90", + "grey70", "grey50", "grey30", "lightblue", "aquamarine", + "cyan", "deepskyblue2", "turquoise3", "burlywood4", + "tan4") + compartment.size <- c(358, 351, 252, 174, 192, 121, 231, + 198, 242, 132, 220, 215, 341, 69, 269) + covered.proteins <- intersect(proteinIDs, markerproteins) + if (length(covered.proteins) < 1) + warning("There is no overlap between marker proteins and data!") + c.marker.df <- SubCellBarCode::markerProteins[covered.proteins, + ] + coverageCompWise <- lapply(seq_len(length(compartments)), + function(x) { + temp.df <- c.marker.df[c.marker.df$Compartments == + compartments[x], ] + values <- list(Compartments = compartments[x], ColorCode = color.code[x], + ProteinCoverage = 100 * ((dim(temp.df)[1])/compartment.size[x])) + }) + coverage.df <- as.data.frame(do.call("rbind", coverageCompWise)) + non.enriched.loc <- coverage.df[coverage.df$ProteinCoverage < + 20, ] + if (nrow(non.enriched.loc) == 1) { + warning("There is not enough enrichment at: ", as.character(non.enriched.loc$Compartments), + "\nWe recommend you to perform the fractionation, again.") + } + else if (nrow(non.enriched.loc) > 1) { + comp <- paste(as.character(non.enriched.loc$Compartments), + collapse = ",") + warning("There are not enough enrichments at: ", comp, + "\nWe recommend you to perform the fractionation!") + } + coverage.df$ProteinCoverage <- as.numeric(coverage.df$ProteinCoverage) + coverage.df$Compartments <- as.character(coverage.df$Compartments) + coverage.df$ColorCode <- as.character(coverage.df$ColorCode) + ggplot(data = coverage.df, aes(x = coverage.df$Compartments, + y = coverage.df$ProteinCoverage)) + geom_bar(stat = "identity", + fill = coverage.df$ColorCode) + + scale_x_discrete(limits = c(compartments)) + + theme_bw() + theme(text = element_text(size = 5), plot.title = element_text(hjust = 0.5), + axis.text.x = element_text(face = "bold", color = "black"), + axis.text.y = element_text(face = "bold", color = "black")) + + ylim(0, 100)+ + + labs(title = paste("Marker Protein Coverage Sample",sample_id), + y = "% Protein Coverage", x = "Compartment") + +} diff --git a/Codes/functions_minimal.R b/Codes/functions_minimal.R new file mode 100644 index 0000000..3c2272d --- /dev/null +++ b/Codes/functions_minimal.R @@ -0,0 +1,27 @@ +pacman::p_load("biglm", + "readxl", + "rmarkdown", + "tarchetypes", + "targets", + "tidyverse") + +#' @title Plot ozone from the preprocessed air quality data. +#' @description Plot a histogram of ozone concentration. +#' @return A ggplot histogram showing ozone content. +#' @param data Data frame, preprocessed air quality dataset. +#' @examples +#' library(ggplot2) +#' library(tidyverse) +#' data <- airquality %>% +#' mutate(Ozone = replace_na(Ozone, mean(Ozone, na.rm = TRUE))) +#' create_plot(data) +create_plot <- function(data) { + ggplot(data) + + geom_histogram(aes(x = Ozone), bins = 12) + + theme_gray(24)+ + ggtitle("Hist_1") +} + +#### + + diff --git a/Codes/tests/testthat/test_functions.R b/Codes/tests/testthat/test_functions.R new file mode 100644 index 0000000..e88c103 --- /dev/null +++ b/Codes/tests/testthat/test_functions.R @@ -0,0 +1,11 @@ +source_file_name <- here::here("Codes", + "functions.R") +source(source_file_name) +library(testthat) + + +test_that("addition results is correct",{ + expect_true(is.data.frame(addition(5,6) %>% as.data.frame())) + testthat::expect_error(addition("ab","cd")) +}) + diff --git a/Output/report.Rmd b/Output/report.Rmd new file mode 100644 index 0000000..82faf7d --- /dev/null +++ b/Output/report.Rmd @@ -0,0 +1,17 @@ +--- +title: report +output: html_document +--- + +```{r} +library(targets) +tar_read(dataset) +tar_read(dataset) +tar_read(hist) +``` +I have seen the hist, and it shows.... + +```{r} + +``` + diff --git a/Output/report.html b/Output/report.html new file mode 100644 index 0000000..e3c06da --- /dev/null +++ b/Output/report.html @@ -0,0 +1,485 @@ + + + + + + + + + + + + + +report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + +
library(targets)
+tar_read(dataset)
+
##    x
+## 1  a
+## 2  b
+## 3  c
+## 4  d
+## 5  e
+## 6  f
+## 7  g
+## 8  h
+## 9  i
+## 10 j
+## 11 k
+## 12 l
+## 13 m
+## 14 n
+## 15 o
+## 16 p
+## 17 q
+## 18 r
+## 19 s
+## 20 t
+## 21 u
+## 22 v
+## 23 w
+## 24 x
+## 25 y
+## 26 z
+
tar_read(dataset)
+
##    x
+## 1  a
+## 2  b
+## 3  c
+## 4  d
+## 5  e
+## 6  f
+## 7  g
+## 8  h
+## 9  i
+## 10 j
+## 11 k
+## 12 l
+## 13 m
+## 14 n
+## 15 o
+## 16 p
+## 17 q
+## 18 r
+## 19 s
+## 20 t
+## 21 u
+## 22 v
+## 23 w
+## 24 x
+## 25 y
+## 26 z
+
tar_read(hist)
+

+ + + + +
+ + + + + + + + + + + + + + + diff --git a/Translation.Rproj b/Translation.Rproj new file mode 100644 index 0000000..066341e --- /dev/null +++ b/Translation.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 4 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/_targets.R b/_targets.R new file mode 100644 index 0000000..3b08f1e --- /dev/null +++ b/_targets.R @@ -0,0 +1,27 @@ +library(targets) +library(tarchetypes) +source(here::here("Codes","functions_minimal.R")) +options(tidyverse.quiet = TRUE) +tar_option_set(packages = c("biglm", "tidyverse")) +#in the console run targets::tar_visnetwork() +#and targets::tar_make() +list( + tar_target( + raw_data_file, + here::here("Datasets","Raw","raw_data.csv"), + format = "file" + ), + tar_target( + raw_data, + read_csv(raw_data_file, col_types = cols()) + ), + tar_target( + data, + raw_data %>% + mutate(Ozone = replace_na(Ozone, mean(Ozone, na.rm = TRUE))) + ), + tar_target(hist, create_plot(data)), + tar_render(report, here::here("Output","report.Rmd")), + tar_target(fit, biglm(Ozone ~ Wind + Temp, data)), + tar_target(dataset, data.frame(x = letters)) + ) diff --git a/_targets/meta/meta b/_targets/meta/meta new file mode 100644 index 0000000..d07a9d9 --- /dev/null +++ b/_targets/meta/meta @@ -0,0 +1,17 @@ +name|type|data|command|depend|seed|path|time|size|bytes|format|iteration|parent|children|seconds|warnings|error +create_plot|function|e61c6a8da66f7057|||||||||||||| +raw_data_file|stem|eac4be650daf552d|cbbcdc99e6139936|c3b5fc02cdc369c1|2110307107|C:/Users/skourtis/OneDrive - CRG - Centre de Regulacio Genomica/Bioinformatics Projects/Project_Templates/Datasets/Raw/raw_data.csv|47c963b779fb1145|20920dbb1a6fc21c|3044|file|vector|||0|| +dataset|stem|f13566c79b81ce59|a8d01d6f5107071f|3231d3eb2c5eb031|914614260|_targets/objects/dataset|47ab10173825b87d|9b0159aade793684|179|rds|vector|||0.02|| +raw_data|stem|61d8681b3b24210f|000ed0cc054f0d35|30735c814d24b25d|-979620141|_targets/objects/raw_data|442cf825092ac5ee|a97d6e8847e768fe|1506|rds|vector|||0.09|| +data|stem|f48ef8b55643e0ae|df3101ce91c63e21|84389287dd8d2ca2|1588979285|_targets/objects/data|deafcece7dfda748|0379c188128bbe87|1505|rds|vector|||0.01|| +hist|stem|ed61f2dbfa66f5d8|68877181ab74e51e|4706135c2164f0f2|-1026346201|_targets/objects/hist|ca555af228141179|139c7eb6bf23fe1c|44875|rds|vector|||0.01|| +fit|stem|465fe038b645ff82|aa0df6c5dbd10537|7d53713f6a5cf419|1780184594|_targets/objects/fit|b7662c915418c14c|5f048c881922f08c|1966|rds|vector|||0|| +report|stem|660e1ac050b33815|9d217c579c37125f|3bc84b0a13b07e0f|-237041703|Output/report.html*Output/report.Rmd|f6ce6bf5b9e6944e||630612|file|vector|||0.95||need finite xlim values +create_plot|function|e61c6a8da66f7057 +raw_data_file|stem|eac4be650daf552d|cbbcdc99e6139936|c3b5fc02cdc369c1|2110307107|C:/Users/skourtis/OneDrive - CRG - Centre de Regulacio Genomica/Bioinformatics Projects/Project_Templates/Datasets/Raw/raw_data.csv|47c963b779fb1145|20920dbb1a6fc21c|3044|file|vector|||0|| +dataset|stem|f13566c79b81ce59|a8d01d6f5107071f|3231d3eb2c5eb031|914614260|_targets/objects/dataset|47ab10173825b87d|9b0159aade793684|179|rds|vector|||0.02|| +raw_data|stem|61d8681b3b24210f|000ed0cc054f0d35|30735c814d24b25d|-979620141|_targets/objects/raw_data|442cf825092ac5ee|a97d6e8847e768fe|1506|rds|vector|||0.09|| +data|stem|f48ef8b55643e0ae|df3101ce91c63e21|84389287dd8d2ca2|1588979285|_targets/objects/data|deafcece7dfda748|0379c188128bbe87|1505|rds|vector|||0.01|| +hist|stem|ed61f2dbfa66f5d8|68877181ab74e51e|4706135c2164f0f2|-1026346201|_targets/objects/hist|ca555af228141179|139c7eb6bf23fe1c|44875|rds|vector|||0.01|| 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{ + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" + }, + "yaml": { + "Package": "yaml", + "Version": "2.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "2826c5d9efb0a88f657c7a679c7106db" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 0000000..62e60ad --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,4 @@ +library/ +lock/ +python/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..6841a96 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,400 @@ + +local({ + + # the requested version of renv + version <- "0.12.3" + + # the project directory + project <- getwd() + + # avoid recursion + if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA))) + return(invisible(TRUE)) + + # signal that we're loading renv during R startup + Sys.setenv("RENV_R_INITIALIZING" = "true") + on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), 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) + + # check to see if renv has already been loaded + if ("renv" %in% loadedNamespaces()) { + + # if renv has already been loaded, and it's the requested version of renv, + # nothing to do + spec <- .getNamespaceInfo(.getNamespace("renv"), "spec") + if (identical(spec[["version"]], version)) + return(invisible(TRUE)) + + # otherwise, unload and attempt to load the correct version of renv + unloadNamespace("renv") + + } + + # load bootstrap tools + bootstrap <- function(version, library) { + + # read repos (respecting override if set) + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (is.na(repos)) + repos <- getOption("repos") + + # fix up repos + on.exit(options(repos = repos), add = TRUE) + repos[repos == "@CRAN@"] <- "https://cloud.r-project.org" + options(repos = repos) + + # attempt to download renv + tarball <- tryCatch(renv_bootstrap_download(version), error = identity) + if (inherits(tarball, "error")) + stop("failed to download renv ", version) + + # now attempt to install + status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) + if (inherits(status, "error")) + stop("failed to install renv ", version) + + } + + 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" + + download.file( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + } + + renv_bootstrap_download <- function(version) { + + # if the renv version number has 4 components, assume it must + # be retrieved via github + nv <- numeric_version(version) + components <- unclass(nv)[[1]] + + methods <- if (length(components) == 4L) { + list(renv_bootstrap_download_github) + } else { + list( + renv_bootstrap_download_cran_latest, + renv_bootstrap_download_cran_archive + ) + } + + for (method in methods) { + path <- tryCatch(method(version), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("failed to download renv ", version) + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + repos <- renv_bootstrap_download_cran_latest_find(version) + + message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE) + + info <- tryCatch( + download.packages("renv", repos = repos, destdir = tempdir(), quiet = TRUE), + condition = identity + ) + + if (inherits(info, "condition")) { + message("FAILED") + return(FALSE) + } + + message("OK") + info[1, 2] + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check for renv on CRAN matching this version + all <- unique(c( + getOption("repos"), + getOption("renv.bootstrap.repos", default = "https://cloud.r-project.org") + )) + + for (repos in all) { + + db <- tryCatch( + as.data.frame(available.packages(repos = repos), stringsAsFactors = FALSE), + error = identity + ) + + if (inherits(db, "error")) + next + + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + return(repos) + + } + + 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 <- getOption("repos") + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) { + message("OK") + return(destfile) + } + + } + + message("FAILED") + return(FALSE) + + } + + 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) + } + + message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) + + 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)) { + message("FAILED") + return(FALSE) + } + + message("Done!") + return(destfile) + + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + message("* Installing renv ", version, " ... ", appendLF = FALSE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # 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", "-l", shQuote(library), shQuote(tarball)) + output <- system2(r, args, stdout = TRUE, stderr = TRUE) + message("Done!") + + # check for successful install + status <- attr(output, "status") + if (is.numeric(status) && !identical(status, 0L)) { + header <- "Error installing renv:" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- c(header, lines, output) + writeLines(text, con = stderr()) + } + + status + + } + + renv_bootstrap_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$platform) + + # include prefix if provided by user + prefix <- Sys.getenv("RENV_PATHS_PREFIX") + if (nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_library_root <- function(project) { + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(path) + + path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(path)) { + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + name <- paste(basename(project), id, sep = "-") + return(file.path(path, name)) + } + + file.path(project, "renv/library") + + } + + renv_bootstrap_validate_version <- function(version) { + + loadedversion <- utils::packageDescription("renv", fields = "Version") + if (version == loadedversion) + return(TRUE) + + # assume four-component versions are from GitHub; three-component + # versions are from CRAN + components <- strsplit(loadedversion, "[.-]")[[1]] + remote <- if (length(components) == 4L) + paste("rstudio/renv", loadedversion, sep = "@") + else + paste("renv", loadedversion, sep = "@") + + fmt <- paste( + "renv %1$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" + ) + + msg <- sprintf(fmt, loadedversion, version, remote) + warning(msg, call. = FALSE) + + FALSE + + } + + 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) + + # load the project + renv::load(project) + + TRUE + + } + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # attempt to load + if (renv_bootstrap_load(project, libpath, version)) + return(TRUE) + + # load failed; inform user we're about to bootstrap + prefix <- paste("# Bootstrapping renv", version) + postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") + header <- paste(prefix, postfix) + message(header) + + # 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)) { + message("* Successfully installed and loaded renv ", version, ".") + return(renv::load()) + } + + # 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) + +}) diff --git a/renv/settings.dcf b/renv/settings.dcf new file mode 100644 index 0000000..bf722e8 --- /dev/null +++ b/renv/settings.dcf @@ -0,0 +1,7 @@ +external.libraries: +ignored.packages: +package.dependency.fields: Imports, Depends, LinkingTo +r.version: +snapshot.type: implicit +use.cache: TRUE +vcs.ignore.library: TRUE diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..ba8e366 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,4 @@ +library(testthat) +library(Project_Templates) + +test_check("Project_Templates")