From c7d1ca0ee8e5b45101fae53b299891a77a732c35 Mon Sep 17 00:00:00 2001 From: c1au6i0 Date: Thu, 7 Nov 2024 23:00:05 -0500 Subject: [PATCH] feat: readme with some examples --- .Rbuildignore | 2 + .Rprofile | 1 + README.Rmd | 198 +++++++ README.md | 257 ++++++--- condathis.Rproj | 1 - renv.lock | 703 ++++++++++++++++++++++++ renv/.gitignore | 7 + renv/activate.R | 1305 ++++++++++++++++++++++++++++++++++++++++++++ renv/settings.json | 19 + 9 files changed, 2412 insertions(+), 81 deletions(-) create mode 100644 .Rprofile create mode 100644 README.Rmd create mode 100644 renv.lock create mode 100644 renv/.gitignore create mode 100644 renv/activate.R create mode 100644 renv/settings.json diff --git a/.Rbuildignore b/.Rbuildignore index 13a8f6d..5fb21ea 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^condathis\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ 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/README.Rmd b/README.Rmd new file mode 100644 index 0000000..281c459 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,198 @@ +--- +output: github_document +--- + + + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + fig.path = "man/figures/README-", + out.width = "100%" +) +``` + +# condathis + + +[![R-CMD-check](https://github.com/luciorq/condathis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/luciorq/condathis/actions/workflows/R-CMD-check.yaml) + + +Run system command line interface (CLI) tools in a **reproducible** and **isolated** environment **within R**. + +## Get started + +Install package from [R-Universe](https://luciorq.r-universe.dev/condathis): + +```r +install.packages("condathis", repos = c("https://luciorq.r-universe.dev", getOption("repos"))) +``` + +### Installing the development version + +``` r +remotes::install_github("luciorq/condathis") +``` + +## Motivation + +One of the main disadvantages of calling CLI tools within `R` is that they are system-specific. This affects the replicability of your code, making it dependent on the system it’s run on. Additionally, using multiple CLI tools increases the likelihood of encountering version conflicts, where different tools require different versions of the same library. Therefore, relying on system-specific tools within `R` is generally not recommended. + +The package `{condathis}` lets you call CLI tools within R while keeping things reproducible and isolated. + +This means you can use `R` alongside other tools without the drawback of having system-specific code. It opens up the possibility of creating code and pipelines in `R` that integrate multiple CLI tools. This is especially useful for bioinformatics and other fields that rely on many software tools for conducting complex analysis. + +## Reproducibility: An Example + +### The issue with `system` + +Suppose you're writing a pipeline or just a script for some analysis, and you want to use [`fastqc`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) — a program to check the quality of FASTQ files. You've installed `fastqc` and use `system2` to run it. + +The `fastqc` command synopsis is `fastqc -o `. The output directory is where `fastqc` saves its quality control reports. + + + +```{r eval=FALSE} +fastq_file <- system.file("extdata", "sample1_L001_R1_001.fastq.gz", package = "condathis") +temp_out_dir <- tempdir() + +system2(command = "fastqc", args = c(fastq_file, "-o", temp_out_dir)) +``` + + +The `fastqc` program generates several output files, including a zip file that is 424KB in size. To get information about one of the output files, we can use: + +```{r eval=FALSE} +library(fs) +library(dplyr) + +file_info(fs::dir_ls(temp_out_dir, glob = "*zip")) |> + mutate(file_name = path_file(path) ) |> + select(file_name, size) +``` + + +```{r echo=FALSE, message=FALSE} +fastq_file <- system.file("extdata", "sample1_L001_R1_001.fastq.gz", package = "condathis") +temp_out_dir <- tempdir() +condathis::create_env(packages = "fastqc==0.11.2", env_name = "fastqc-0.11.2") +condathis::run("fastqc", fastq_file, "-o", temp_out_dir, env_name = "fastqc-0.11.2") + +library(fs) +library(dplyr) + +file_info(fs::dir_ls(temp_out_dir, glob = "*zip")) |> + mutate(file_name = path_file(path) ) |> + select(file_name, size) +``` + +Now, let's consider the scenario where you share your code with someone else or revisit it yourself after a year. There's no guarantee the code will run because it relies on a specific CLI tool installed on the system. In the worst case, it might run without throwing any errors but produce different results, so you might not even realize that. + +The exact same code run on the same system but with an updated version of `fastqc` (0.12.1 instead of 0.11.2) generates a different file, and its size is different as well: *446k instead of 424k*. + + +```{r echo=FALSE} +temp_out_dir_2 <- tempdir() + +condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc-0.12.1") +condathis::run("fastqc", fastq_file, "-o", temp_out_dir, env_name = "fastqc-0.12.1") + +condathis::remove_env("fastqc-0.12.1") + +file_info(fs::dir_ls(temp_out_dir_2, glob = "*zip")) |> + mutate(file_name = path_file(path) ) |> + select(file_name, size) +``` + +This discrepancy limits the workflow, pipelines, and scripts to using only `R` packages! + +What can we do about it? We can use `{condathis}`! + +The package **`{condathis}`** ensures that the code you share and the results from running `fastqc` will be **consistent across different systems and over time**! + + +### The solution with `{condathis}` + +We would first create an isolated environment containing a specific version of the package `fastqc` (0.12.1). The command automatically manages all the library dependencies of `fastqc`, making sure that they are compatible with the specific operating system. + + +```{r echo=FALSE} +rm(temp_out_dir_2) +``` + + +```{r} +condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env") +``` + +Then we run the command inside the environment just created which contains a version 0.12.1 of `fastqc`. + +```{r echo=FALSE} +# dir of output files +temp_out_dir_2 <- tempdir() +out <- condathis::run("fastqc", fastq_file, "-o", temp_out_dir_2, # command + env_name = "fastqc_env" # environment + ) +``` + +In our temp directory, `fastqc` generated the output files as expected. + +```{r} +out +``` + +In the our temp dir, `fastqc`generated the output files as expected. + +```{r} +fs::dir_ls(temp_out_dir_2) +``` + +The code that we created with `{condathis}` **uses a system CLI tool but is reproducible**. + +## Isolation: an example + +Another key feature of `{condathis}` is the ability to run CLI tools in **independent, isolated environments**. This allows you to run packages within R that would have conflicting dependencies. This makes it possible for `{condathis}` to run two versions of the same CLI tool simultaneously! + +For example, the system's `curl` is of a specific version: + +```{r} +libcurlVersion() +``` + +However, we can choose to use a different version of `curl` run in a different environment. Here, for example, we are installing a different version of `curl` in a separate environment, and checking the version of the newly installed `curl`. + +```{r} +condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env") + +out <- condathis::run("curl", "--version", + env_name = "curl_env" # environment + ) + +cat(out$stdout) + +``` + +This isolation feature of `{condathis}` allows not only running different versions of the same CLI tools but also different tools that have **incompatible dependencies**. One common example is CLI tools that rely on different versions of Python. + +## Details + +The package `{condathis}` relies on [**`micromamba`**](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) to bring **reproducibility and isolation**. `micromamba` is a lightweight, fast, and efficient package manager that "does not need a base environment and does not come with a default version of Python". + +The integration of `micromamba` into `R` is handled using the `processx` and `withr` packages. The package `processx` runs external processes and manages their input and output, ensuring that commands to `micromamba` are executed correctly from within R. The package `withr` temporarily modifies environment variables and settings, allowing `micromamba` to run smoothly without permanently altering your `R` environment. + +## Known limitations + +Special characters in CLI commands are interpreted as literals and not expanded. + +- It is not supported the use of output redirections in commands, e.g. "|" or ">". + - Instead of redirects (e.g. ">"), use the argument `stdout = ".txt"`. + Instead of Pipes ("|"), simple run multiple calls to `condathis::run()`, + using `stdout` argument to control the output and input of each command. +- File paths should not use special characters for relative paths, e.g. "~", ".", "..". + - Expand file paths directly in R, using `base` functions + or functions from the `fs` package. + + + + diff --git a/README.md b/README.md index 99000ee..3dc1b9b 100644 --- a/README.md +++ b/README.md @@ -1,136 +1,233 @@ + + + # condathis + [![R-CMD-check](https://github.com/luciorq/condathis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/luciorq/condathis/actions/workflows/R-CMD-check.yaml) -## `condathis` R package - -Run any CLI tool that is available through Conda environments. +Run system command line interface (CLI) tools in a **reproducible** and +**isolated** environment **within R**. -### Get started +## Get started -Install package from [R-Universe](https://luciorq.r-universe.dev/condathis): +Install package from +[R-Universe](https://luciorq.r-universe.dev/condathis): -```r +``` r install.packages("condathis", repos = c("https://luciorq.r-universe.dev", getOption("repos"))) ``` -#### Installing the development version +### Installing the development version ``` r remotes::install_github("luciorq/condathis") ``` -### Try it +## Motivation -#### General Command line tool +One of the main disadvantages of calling CLI tools within `R` is that +they are system-specific. This affects the replicability of your code, +making it dependent on the system it’s run on. Additionally, using +multiple CLI tools increases the likelihood of encountering version +conflicts, where different tools require different versions of the same +library. Therefore, relying on system-specific tools within `R` is +generally not recommended. -``` r -library(condathis) -create_env("python=3.8") -run("python", "-c", "import os; print(os.getcwd())") -``` +The package `{condathis}` lets you call CLI tools within R while keeping +things reproducible and isolated. -Create Conda environment from a environment description YAML file. +This means you can use `R` alongside other tools without the drawback of +having system-specific code. It opens up the possibility of creating +code and pipelines in `R` that integrate multiple CLI tools. This is +especially useful for bioinformatics and other fields that rely on many +software tools for conducting complex analysis. + +## Reproducibility: An Example + +### The issue with `system` + +Suppose you’re writing a pipeline or just a script for some analysis, +and you want to use +[`fastqc`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) — +a program to check the quality of FASTQ files. You’ve installed `fastqc` +and use `system2` to run it. + +The `fastqc` command synopsis is +`fastqc -o `. The output directory is +where `fastqc` saves its quality control reports. ``` r -create_env(env_file = env_yaml_file, env_name = "condathis-yaml-env") -run("python", "-c", "import os; print(os.getcwd())", env_name = "condathis-yaml-env") +fastq_file <- system.file("extdata", "sample1_L001_R1_001.fastq.gz", package = "condathis") +temp_out_dir <- tempdir() + +system2(command = "fastqc", args = c(fastq_file, "-o", temp_out_dir)) ``` -#### Bioinformatics example +The `fastqc` program generates several output files, including a zip +file that is 424KB in size. To get information about one of the output +files, we can use: ``` r -create_env("samtools", env_name = "samtools-env") -run("samtools", "view", "--help", env_name = "samtools-env") +library(fs) +library(dplyr) + +file_info(fs::dir_ls(temp_out_dir, glob = "*zip")) |> + mutate(file_name = path_file(path) ) |> + select(file_name, size) ``` - +What can we do about it? We can use `{condathis}`! +The package **`{condathis}`** ensures that the code you share and the +results from running `fastqc` will be **consistent across different +systems and over time**! ---- +### The solution with `{condathis}` -`condathis` is a powerful R package designed to simplify the execution of command line tools within isolated Conda environments. Built with efficiency and flexibility in mind, `condathis` seamlessly integrates the world of Conda environments with the versatility of R programming. +We would first create an isolated environment containing a specific +version of the package `fastqc` (0.12.1). The command automatically +manages all the library dependencies of `fastqc`, making sure that they +are compatible with the specific operating system. + +``` r +condathis::create_env(packages = "fastqc==0.12.1", env_name = "fastqc_env") +``` -With `condathis`, you can effortlessly create and manage isolated Conda environments directly from your R scripts. These environments provide a controlled and reproducible setting where you can install and run various command line tools without worrying about conflicts or dependencies. Whether you need to execute bioinformatics pipelines, data processing tasks, or any other command line operation, `condathis` ensures a hassle-free experience. +Then we run the command inside the environment just created which +contains a version 0.12.1 of `fastqc`. -## Key Features of `condathis` +In our temp directory, `fastqc` generated the output files as expected. -Conda Environment Management: `condathis` allows you to easily create Conda environments, empowering you to work with different tool configurations for each step of analysis or project. -This ensures that your workflows remain isolated and reproducible. +``` r +out +#> $status +#> [1] 0 +#> +#> $stdout +#> [1] "application/gzip\nAnalysis complete for sample1_L001_R1_001.fastq.gz\n" +#> +#> $stderr +#> [1] "Started analysis of sample1_L001_R1_001.fastq.gz\nApprox 90% complete for sample1_L001_R1_001.fastq.gz\n" +#> +#> $timeout +#> [1] FALSE +``` -Command Line Tool Execution: The package offers a seamless interface for executing command line tools directly from your R code. -With a simple function call, you can run any command line tool installed within any conda environment, enabling you to leverage the vast ecosystem of command line tools in your R workflows. +In the our temp dir, `fastqc`generated the output files as expected. -Dependency Resolution: `condathis` automatically handles the resolution of dependencies required by the command line tools you want to execute. It ensures that the necessary libraries, packages, and binaries are properly installed within the isolated conda environment, eliminating the need for manual setup and ensuring smooth execution. +``` r +fs::dir_ls(temp_out_dir_2) +#> /var/folders/bp/fpwcfq1563l21rz5gdcsfcsw0000gn/T/RtmpCGI9Kp/libloc_220_e600d766ecff9728.rds +#> /var/folders/bp/fpwcfq1563l21rz5gdcsfcsw0000gn/T/RtmpCGI9Kp/libloc_253_f6724fe3a7174438.rds +#> /var/folders/bp/fpwcfq1563l21rz5gdcsfcsw0000gn/T/RtmpCGI9Kp/libloc_263_425eb536d80dd010.rds +#> /var/folders/bp/fpwcfq1563l21rz5gdcsfcsw0000gn/T/RtmpCGI9Kp/sample1_L001_R1_001_fastqc.html +#> /var/folders/bp/fpwcfq1563l21rz5gdcsfcsw0000gn/T/RtmpCGI9Kp/sample1_L001_R1_001_fastqc.zip +``` -`condathis` brings intuitive API and efficient conda environment management, you can streamline your data analysis workflows, enhance reproducibility, and explore a vast range of command line tools — all within the familiar R environment. +The code that we created with `{condathis}` **uses a system CLI tool but +is reproducible**. -## Motivation +## Isolation: an example -Traditionally, [Conda Environments][conda-env-ref] have been designed to solve a problem related to Python Programming and specially tailored for interactive usage. +Another key feature of `{condathis}` is the ability to run CLI tools in +**independent, isolated environments**. This allows you to run packages +within R that would have conflicting dependencies. This makes it +possible for `{condathis}` to run two versions of the same CLI tool +simultaneously! -With `condathis` we want to leverage another great functionality of Conda environments that is running CLI software in isolated environments, without affecting (and also not being affected by) the main R environment. +For example, the system’s `curl` is of a specific version: -This is especially relevant to the Bioinformatics and Computational Biology fields where most of the preprocessing of raw data files is made using Linux/Unix command line tools that benefit from running on isolation. -Where in the later step data is imported into R for interactive analysis. +``` r +libcurlVersion() +#> [1] "8.4.0" +#> attr(,"ssl_version") +#> [1] "SecureTransport (LibreSSL/3.3.6)" +#> attr(,"libssh_version") +#> [1] "" +#> attr(,"protocols") +#> [1] "dict" "file" "ftp" "ftps" "gopher" "gophers" "http" +#> [8] "https" "imap" "imaps" "ldap" "ldaps" "mqtt" "pop3" +#> [15] "pop3s" "rtsp" "smb" "smbs" "smtp" "smtps" "telnet" +#> [22] "tftp" +``` -The focus of this package is to support CLI tools installed inside Conda environments. +However, we can choose to use a different version of `curl` run in a +different environment. Here, for example, we are installing a different +version of `curl` in a separate environment, and checking the version of +the newly installed `curl`. -Providing an API to call those tools in isolation from the main R process. +``` r +condathis::create_env(packages = "curl==8.10.1", env_name = "curl_env") -Despite the name, the main interface we use to access software installed in Conda environments is actually [micromamba][micromamba-ref], a lightweight and open-source reimplementation of the Conda package manager. +out <- condathis::run("curl", "--version", + env_name = "curl_env" # environment + ) -Since this package **is not intended to solve the problem of running Python code**, -`micromamba` has a huge advantage, since it is lighter and does not come with a default version of Python. -If you intend to run Python code chunks or scripts side by side with R code in activate Conda environments, -check [reticulate][reticulate-ref] or [basilisk][basilisk-ref], as they were built to provide this exact solution. +cat(out$stdout) +#> curl 8.10.1 (x86_64-apple-darwin13.4.0) libcurl/8.10.1 OpenSSL/3.3.2 (SecureTransport) zlib/1.3.1 zstd/1.5.6 libssh2/1.11.0 nghttp2/1.64.0 +#> Release-Date: 2024-09-18 +#> Protocols: dict file ftp ftps gopher gophers http https imap imaps ipfs ipns mqtt pop3 pop3s rtsp scp sftp smb smbs smtp smtps telnet tftp ws wss +#> Features: alt-svc AsynchDNS GSS-API HSTS HTTP2 HTTPS-proxy IPv6 Kerberos Largefile libz MultiSSL NTLM SPNEGO SSL threadsafe TLS-SRP UnixSockets zstd +``` -This tool can even be used for running R scripts in separate environments. +This isolation feature of `{condathis}` allows not only running +different versions of the same CLI tools but also different tools that +have **incompatible dependencies**. One common example is CLI tools that +rely on different versions of Python. -## Known limitations +## Details -Special characters in CLI commands are interpreted as literals and not expanded. +The package `{condathis}` relies on +[**`micromamba`**](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html) +to bring **reproducibility and isolation**. `micromamba` is a +lightweight, fast, and efficient package manager that “does not need a +base environment and does not come with a default version of Python”. -- It is not supported the use of output redirections in commands, e.g. "|" or ">". - - Instead of redirects (e.g. ">"), use the argument `stdout = ".txt"`. - Instead of Pipes ("|"), simple run multiple calls to `condathis::run()`, - using `stdout` argument to control the output and input of each command. -- File paths should not use special characters for relative paths, e.g. "~", ".", "..". - - Expand file paths directly in R, using `base` functions - or functions from the `fs` package. +The integration of `micromamba` into `R` is handled using the `processx` +and `withr` packages. The package `processx` runs external processes and +manages their input and output, ensuring that commands to `micromamba` +are executed correctly from within R. The package `withr` temporarily +modifies environment variables and settings, allowing `micromamba` to +run smoothly without permanently altering your `R` environment. ---- +## Known limitations -[conda-env-ref]: https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html -[micromamba-ref]: https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html -[reticulate-ref]: https://rstudio.github.io/reticulate/ -[basilisk-ref]: https://www.bioconductor.org/packages/release/bioc/html/basilisk.html +Special characters in CLI commands are interpreted as literals and not +expanded. + +- It is not supported the use of output redirections in commands, + e.g. “\|” or “\>”. + - Instead of redirects (e.g. “\>”), use the argument + `stdout = ".txt"`. Instead of Pipes (“\|”), simple run + multiple calls to `condathis::run()`, using `stdout` argument to + control the output and input of each command. +- File paths should not use special characters for relative paths, + e.g. “~”, “.”, “..”. + - Expand file paths directly in R, using `base` functions or functions + from the `fs` package. diff --git a/condathis.Rproj b/condathis.Rproj index 80cc645..766b3b2 100644 --- a/condathis.Rproj +++ b/condathis.Rproj @@ -1,5 +1,4 @@ Version: 1.0 -ProjectId: 161cd240-c5f1-43cf-bc0e-d3d23ecd109b RestoreWorkspace: No SaveWorkspace: No diff --git a/renv.lock b/renv.lock new file mode 100644 index 0000000..542b78e --- /dev/null +++ b/renv.lock @@ -0,0 +1,703 @@ +{ + "R": { + "Version": "4.4.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "R6": { + "Package": "R6", + "Version": "2.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": 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mode 100644 index 0000000..0ec0cbb --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 0000000..0eb5108 --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1305 @@ + +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() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..ffdbb32 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +}