diff --git a/content/blog/mori-0-1-0/.Rprofile b/content/blog/mori-0-1-0/.Rprofile new file mode 100644 index 000000000..81b960f5c --- /dev/null +++ b/content/blog/mori-0-1-0/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/content/blog/mori-0-1-0/featured.jpg b/content/blog/mori-0-1-0/featured.jpg new file mode 100644 index 000000000..a994ce179 Binary files /dev/null and b/content/blog/mori-0-1-0/featured.jpg differ diff --git a/content/blog/mori-0-1-0/index.md b/content/blog/mori-0-1-0/index.md new file mode 100644 index 000000000..bd4e4ac1a --- /dev/null +++ b/content/blog/mori-0-1-0/index.md @@ -0,0 +1,198 @@ +--- +title: 'mori: Shared memory for R objects' +date: 2026-04-23T00:00:00.000Z +people: + - Charlie Gao +description: > + mori is a new R package for sharing R objects across processes via OS-level + shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same + physical pages — share once, read anywhere. +image: featured.jpg +image-alt: > + Macro close-up of a computer RAM module, showing the blue circuit board and + metallic connectors in sharp detail with a shallow depth-of-field blur. +topics: + - Best Practices +software: + - mori +languages: + - R +tags: + - Parallelism +photo: + url: https://unsplash.com/photos/macro-shot-photo-of-a-computer-ram-lYxQ5F9xBDM + author: Liam Briese +nohero: false +hidesubscription: false +--- + + +We're pleased to announce the first CRAN release of [mori](https://shikokuchuo.net/mori/). + +Until now, parallel R has meant serializing your data to every worker and duplicating it in each worker's RAM. Eight workers × 1 GB is 8 GB, plus the serialization, transfer, and deserialization cost to get it there. R processes don't share memory --- each has its own heap, so data crosses between them through a serialization pipe. + +mori changes that. It places an R object once into OS-level shared memory and lets every process on the machine read the same physical pages directly --- with no data copying between processes. + +``` r +install.packages("mori") +``` + +mori is built on R's [ALTREP](https://svn.r-project.org/R/branches/ALTREP/ALTREP.html) (Alternative Representation) framework, which lets a package expose a custom vector backend that reads its data from somewhere other than ordinary R memory --- a memory map, a database, a compressed store, or in this case, OS shared memory. + +## How it looks + +The entry point is `share()`. You pass it an R object, you get back a shared version that you can use in the same way as the original: + +``` r +library(mori) + +set.seed(42) +x <- share(rnorm(1e6)) +mean(x) +``` + + [1] 0.0005737398 + +`share()` works on atomic vector types, lists, and data frames --- it writes them directly into shared memory with attributes preserved. In practice that also covers tibbles, data.tables, factors, dates, and matrices, since they're built on those types. Environments, functions, S4 objects, and external pointers are returned unchanged, since their state can't be meaningfully exposed as raw bytes in shared memory. + +The returned object is an ALTREP view into shared memory --- it costs no additional RAM beyond the original region. It also serializes compactly: instead of sending the full 8 MB payload, mori's ALTREP hooks serialize shared objects as their shared-memory name, just over 100 bytes on the wire. + +``` r +x |> serialize(NULL) |> length() +``` + + [1] 125 + +That compact serialization is what makes the rest of the picture work. + +## Parallel workers, one copy + + + +mori pairs naturally with [mirai](https://mirai.r-lib.org/). When you send a shared object to a local daemon, only the shared-memory name crosses the wire; the daemon maps the same physical pages and sees the full data with no deserialization cost. The same is true for any other parallel backend that uses R serialization. + +Here's the motivating case --- a bootstrap across eight workers on a 200 MB data frame: + +``` r +library(mirai) +library(purrr) + +daemons(8) + +df <- as.data.frame(matrix(rnorm(25e6), ncol = 5)) +shared_df <- share(df) + +boot <- \(i) colMeans(data[sample(nrow(data), replace = TRUE), ]) + +# Without mori — each daemon deserializes its own copy +system.time( + map(1:8, in_parallel(\(i) boot(i), boot = boot, data = df)) +) +``` + + user system elapsed + 0.445 3.338 10.454 + +``` r +# With mori — each daemon maps the same shared memory +system.time( + map(1:8, in_parallel(\(i) boot(i), boot = boot, data = shared_df)) +) +``` + + user system elapsed + 0.001 0.000 4.959 + +``` r +daemons(0) +``` + +The payload each daemon receives is ~300 bytes instead of 200 MB --- roughly 700,000× smaller. There's a ~2× wall-clock saving on this run, and eight workers now share a single 200 MB copy in memory instead of materializing one each. The function call is the same; the savings come from not copying data that's already in RAM. + +`share()` itself is paid once upfront --- roughly the cost of one serialization to write into shared memory. Daemons don't pay a deserialize cost on the other end, since they read the same physical memory directly --- so even a single send is a net win, and the savings compound with every additional daemon. + +The wall-clock gap depends on how much of the run is data transfer versus compute. On cheap per-task work --- bootstrap, cross-validation, parameter sweeps --- serialization dominates and the wall-clock win is largest; the ratio shrinks as each task starts to involve more substantial compute, although we always get the memory saving. + +Lists and data frames travel element-wise too: sending a single column of a shared data frame transmits only that element's reference, not the whole data frame. + +``` r +daemons(3) + +x <- share(list(a = rnorm(1e6), b = rnorm(1e6), c = rnorm(1e6))) + +mirai_map(x, \(v) lobstr::obj_size(v) |> format())[.flat] +``` + + a b c + "840 B" "840 B" "840 B" + +``` r +daemons(0) +``` + +## What this unlocks + +Anywhere parallel R workers process the same large dataset, `share()` removes the per-worker copy: + +- A [Shiny](https://shiny.posit.co/) dashboard where every worker process reads from one shared reference dataset instead of loading its own. +- A [tidymodels](https://www.tidymodels.org/) `tune_grid()` sweep --- or a [targets](https://docs.ropensci.org/targets/) pipeline branching over model variants --- where every fit reads the same training data without copying it. +- Bootstrap, Monte Carlo, or permutation work dispatched across [mirai](https://mirai.r-lib.org/) or [crew](https://wlandau.github.io/crew/), where thousands of iterations all read from one shared dataset. + +The pattern is the same in each case: call `share()` on your dataset once, then pass the result wherever you'd normally pass the data. Parallel dispatches that hit the serialization path transmit only the reference, not the data. + +## Access and lifetime + +A shared data frame lives in a single shared region, but ALTREP columns are only materialized when touched. A task that reads three columns out of one hundred pays for three --- character vectors are lazier still, with per-element access. Workers only pay for the data they actually touch. + +Shared memory is tied to R's garbage collector. As long as the shared object (or anything extracted from it) is live in R, the data stays available; when the last reference is dropped, it's freed automatically with no manual cleanup. The process that called `share()` needs to hold its reference until a consumer has mapped a view --- from that point on, the view itself keeps the shared memory alive. + +Mutations go through R's normal copy-on-write: editing a value inside a shared vector produces a private copy of that one vector, leaving the rest of the shared region untouched. + +``` r +x <- share(rnorm(1e6)) +lobstr::obj_size(x) +``` + + 960 B + +``` r +x[1] <- 0 # local mutation materializes a private copy +lobstr::obj_size(x) +``` + + 8.00 MB + +## Sharing by name + +If you want to access a shared region from another process without going through serialization at all, you can pass its name directly: + +``` r +x <- share(1:1e6) + +nm <- shared_name(x) +nm +``` + + [1] "/mori_113fe_4" + +``` r +# Works from another process; same session here to demonstrate +y <- map_shared(nm) +identical(x[], y[]) +``` + + [1] TRUE + +Handy when the consumer needs to attach by name rather than receive the shared object through R's serialization path. + +## How mori fits + +R has had partial answers to cross-process data sharing before. [bigmemory](https://CRAN.R-project.org/package=bigmemory) offers shared `big.matrix` objects --- effective, but limited to numeric matrices. [SharedObject](https://bioconductor.org/packages/SharedObject/) on Bioconductor targets a similar goal with its own memory-sharing machinery, oriented around BiocParallel workflows. [Arrow](https://arrow.apache.org/docs/r/)'s memory-mapped Parquet gives zero-copy columnar reads across processes, though the data lives on disk. On Unix, `parallel::mclapply` gets shared memory via fork copy-on-write (until a worker writes to a page), with the usual fork caveats (unsafe in GUI sessions, with open DB connections, or alongside multithreaded libraries), and with no equivalent on Windows. + +mori is usable across any backend that plugs into R's standard serialization --- mirai, future, parallel, foreach, callr --- with no special cooperation required. Atomic vectors, lists, and character vectors are all supported, with lazy per-element access preserved in every process. Lifetimes are managed by R's garbage collector: shared regions are freed automatically when the last reference drops. And mori itself is pure C --- POSIX shared memory on Linux and macOS, Win32 file mapping on Windows, nothing beyond the package to install. + +## Try it + +mori is [available from CRAN](https://CRAN.R-project.org/package=mori). The [package website](https://shikokuchuo.net/mori/) has a walkthrough of the mirai integration and full reference documentation. mori is designed to slot quietly into existing parallel-R workflows --- anywhere a worker currently receives a big dataset, `share()` it first and you're done. It complements [mirai](https://mirai.r-lib.org/): mirai handles async evaluation and daemon coordination, mori handles shared access to the data those daemons work on. + +The package is in the experimental lifecycle stage while the API settles, so feedback and issue reports on [GitHub](https://github.com/shikokuchuo/mori/issues) are very welcome. diff --git a/content/blog/mori-0-1-0/index.qmd b/content/blog/mori-0-1-0/index.qmd new file mode 100644 index 000000000..816bd3d9c --- /dev/null +++ b/content/blog/mori-0-1-0/index.qmd @@ -0,0 +1,167 @@ +--- +title: "mori: Shared memory for R objects" +date: 2026-04-23 +people: + - Charlie Gao +description: > + mori is a new R package for sharing R objects across processes via OS-level + shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same + physical pages — share once, read anywhere. +image: featured.jpg +image-alt: > + Macro close-up of a computer RAM module, showing the blue circuit board and + metallic connectors in sharp detail with a shallow depth-of-field blur. +topics: + - Best Practices +software: + - mori +languages: + - R +tags: + - Parallelism +photo: + url: https://unsplash.com/photos/macro-shot-photo-of-a-computer-ram-lYxQ5F9xBDM + author: Liam Briese +nohero: false +hidesubscription: false +--- + +We're pleased to announce the first CRAN release of [mori](https://shikokuchuo.net/mori/). + +Until now, parallel R has meant serializing your data to every worker and duplicating it in each worker's RAM. Eight workers × 1 GB is 8 GB, plus the serialization, transfer, and deserialization cost to get it there. R processes don't share memory — each has its own heap, so data crosses between them through a serialization pipe. + +mori changes that. It places an R object once into OS-level shared memory and lets every process on the machine read the same physical pages directly — with no data copying between processes. + +```{r} +#| eval: false +install.packages("mori") +``` + +mori is built on R's [ALTREP](https://svn.r-project.org/R/branches/ALTREP/ALTREP.html) (Alternative Representation) framework, which lets a package expose a custom vector backend that reads its data from somewhere other than ordinary R memory — a memory map, a database, a compressed store, or in this case, OS shared memory. + +## How it looks + +The entry point is `share()`. You pass it an R object, you get back a shared version that you can use in the same way as the original: + +```{r} +library(mori) + +set.seed(42) +x <- share(rnorm(1e6)) +mean(x) +``` + +`share()` works on atomic vector types, lists, and data frames — it writes them directly into shared memory with attributes preserved. In practice that also covers tibbles, data.tables, factors, dates, and matrices, since they're built on those types. Environments, functions, S4 objects, and external pointers are returned unchanged, since their state can't be meaningfully exposed as raw bytes in shared memory. + +The returned object is an ALTREP view into shared memory — it costs no additional RAM beyond the original region. It also serializes compactly: instead of sending the full 8 MB payload, mori's ALTREP hooks serialize shared objects as their shared-memory name, just over 100 bytes on the wire. + +```{r} +x |> serialize(NULL) |> length() +``` + +That compact serialization is what makes the rest of the picture work. + +## Parallel workers, one copy + +![](mori-diagram.svg){fig-alt="Diagram: share() writes an R object once into OS-level shared memory; multiple worker processes each memory-map the same region via zero-copy ALTREP wrappers, so every worker sees the same physical pages with no deserialization."} + +mori pairs naturally with [mirai](https://mirai.r-lib.org/). When you send a shared object to a local daemon, only the shared-memory name crosses the wire; the daemon maps the same physical pages and sees the full data with no deserialization cost. The same is true for any other parallel backend that uses R serialization. + +Here's the motivating case — a bootstrap across eight workers on a 200 MB data frame: + +```{r} +library(mirai) +library(purrr) + +daemons(8) + +df <- as.data.frame(matrix(rnorm(25e6), ncol = 5)) +shared_df <- share(df) + +boot <- \(i) colMeans(data[sample(nrow(data), replace = TRUE), ]) + +# Without mori — each daemon deserializes its own copy +system.time( + map(1:8, in_parallel(\(i) boot(i), boot = boot, data = df)) +) + +# With mori — each daemon maps the same shared memory +system.time( + map(1:8, in_parallel(\(i) boot(i), boot = boot, data = shared_df)) +) + +daemons(0) +``` + +The payload each daemon receives is ~300 bytes instead of 200 MB — roughly 700,000× smaller. There's a ~2× wall-clock saving on this run, and eight workers now share a single 200 MB copy in memory instead of materializing one each. The function call is the same; the savings come from not copying data that's already in RAM. + +`share()` itself is paid once upfront — roughly the cost of one serialization to write into shared memory. Daemons don't pay a deserialize cost on the other end, since they read the same physical memory directly — so even a single send is a net win, and the savings compound with every additional daemon. + +The wall-clock gap depends on how much of the run is data transfer versus compute. On cheap per-task work — bootstrap, cross-validation, parameter sweeps — serialization dominates and the wall-clock win is largest; the ratio shrinks as each task starts to involve more substantial compute, although we always get the memory saving. + +Lists and data frames travel element-wise too: sending a single column of a shared data frame transmits only that element's reference, not the whole data frame. + +```{r} +daemons(3) + +x <- share(list(a = rnorm(1e6), b = rnorm(1e6), c = rnorm(1e6))) + +mirai_map(x, \(v) lobstr::obj_size(v) |> format())[.flat] + +daemons(0) +``` + +## What this unlocks + +Anywhere parallel R workers process the same large dataset, `share()` removes the per-worker copy: + +- A [Shiny](https://shiny.posit.co/) dashboard where every worker process reads from one shared reference dataset instead of loading its own. +- A [tidymodels](https://www.tidymodels.org/) `tune_grid()` sweep — or a [targets](https://docs.ropensci.org/targets/) pipeline branching over model variants — where every fit reads the same training data without copying it. +- Bootstrap, Monte Carlo, or permutation work dispatched across [mirai](https://mirai.r-lib.org/) or [crew](https://wlandau.github.io/crew/), where thousands of iterations all read from one shared dataset. + +The pattern is the same in each case: call `share()` on your dataset once, then pass the result wherever you'd normally pass the data. Parallel dispatches that hit the serialization path transmit only the reference, not the data. + +## Access and lifetime + +A shared data frame lives in a single shared region, but ALTREP columns are only materialized when touched. A task that reads three columns out of one hundred pays for three — character vectors are lazier still, with per-element access. Workers only pay for the data they actually touch. + +Shared memory is tied to R's garbage collector. As long as the shared object (or anything extracted from it) is live in R, the data stays available; when the last reference is dropped, it's freed automatically with no manual cleanup. The process that called `share()` needs to hold its reference until a consumer has mapped a view — from that point on, the view itself keeps the shared memory alive. + +Mutations go through R's normal copy-on-write: editing a value inside a shared vector produces a private copy of that one vector, leaving the rest of the shared region untouched. + +```{r} +x <- share(rnorm(1e6)) +lobstr::obj_size(x) + +x[1] <- 0 # local mutation materializes a private copy +lobstr::obj_size(x) +``` + +## Sharing by name + +If you want to access a shared region from another process without going through serialization at all, you can pass its name directly: + +```{r} +x <- share(1:1e6) + +nm <- shared_name(x) +nm + +# Works from another process; same session here to demonstrate +y <- map_shared(nm) +identical(x[], y[]) +``` + +Handy when the consumer needs to attach by name rather than receive the shared object through R's serialization path. + +## How mori fits + +R has had partial answers to cross-process data sharing before. [bigmemory](https://CRAN.R-project.org/package=bigmemory) offers shared `big.matrix` objects — effective, but limited to numeric matrices. [SharedObject](https://bioconductor.org/packages/SharedObject/) on Bioconductor targets a similar goal with its own memory-sharing machinery, oriented around BiocParallel workflows. [Arrow](https://arrow.apache.org/docs/r/)'s memory-mapped Parquet gives zero-copy columnar reads across processes, though the data lives on disk. On Unix, `parallel::mclapply` gets shared memory via fork copy-on-write (until a worker writes to a page), with the usual fork caveats (unsafe in GUI sessions, with open DB connections, or alongside multithreaded libraries), and with no equivalent on Windows. + +mori is usable across any backend that plugs into R's standard serialization — mirai, future, parallel, foreach, callr — with no special cooperation required. Atomic vectors, lists, and character vectors are all supported, with lazy per-element access preserved in every process. Lifetimes are managed by R's garbage collector: shared regions are freed automatically when the last reference drops. And mori itself is pure C — POSIX shared memory on Linux and macOS, Win32 file mapping on Windows, nothing beyond the package to install. + +## Try it + +mori is [available from CRAN](https://CRAN.R-project.org/package=mori). The [package website](https://shikokuchuo.net/mori/) has a walkthrough of the mirai integration and full reference documentation. mori is designed to slot quietly into existing parallel-R workflows — anywhere a worker currently receives a big dataset, `share()` it first and you're done. It complements [mirai](https://mirai.r-lib.org/): mirai handles async evaluation and daemon coordination, mori handles shared access to the data those daemons work on. + +The package is in the experimental lifecycle stage while the API settles, so feedback and issue reports on [GitHub](https://github.com/shikokuchuo/mori/issues) are very welcome. diff --git a/content/blog/mori-0-1-0/mori-diagram.svg b/content/blog/mori-0-1-0/mori-diagram.svg new file mode 100644 index 000000000..8bda26003 --- /dev/null +++ b/content/blog/mori-0-1-0/mori-diagram.svg @@ -0,0 +1,45 @@ + + + + Shared Memory + (OS-backed) + + + share(obj) + write once + + + + + + + + + + + + mmap + + + + Process 1 + + + Process 2 + + + Process 3 + + + Process 4 + + + ALTREP wrappers — zero-copy reads + + + + + + + + diff --git a/content/blog/mori-0-1-0/renv.lock b/content/blog/mori-0-1-0/renv.lock new file mode 100644 index 000000000..0b4cfd29f --- /dev/null +++ b/content/blog/mori-0-1-0/renv.lock @@ -0,0 +1,1383 @@ +{ + "R": { + "Version": "4.5.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://cloud.r-project.org" + } + ] + }, + "Packages": { + "R6": { + "Package": "R6", + "Version": "2.6.1", + "Source": "Repository", + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "c( person(\"Winston\", \"Chang\", , \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. 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It also contains a number of lower level 'CLI' elements: rules, boxes, trees, and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and text styles as well.", + "License": "MIT + file LICENSE", + "URL": "https://cli.r-lib.org, https://github.com/r-lib/cli", + "BugReports": "https://github.com/r-lib/cli/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "utils" + ], + "Suggests": [ + "callr", + "covr", + "crayon", + "digest", + "glue (>= 1.6.0)", + "grDevices", + "htmltools", + "htmlwidgets", + "knitr", + "methods", + "processx", + "ps (>= 1.3.4.9000)", + "rlang (>= 1.0.2.9003)", + "rmarkdown", + "rprojroot", + "rstudioapi", + "testthat (>= 3.2.0)", + "tibble", + "whoami", + "withr" + ], + "Config/Needs/website": "r-lib/asciicast, bench, brio, cpp11, decor, desc, fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, usethis, vctrs", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-04-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Hadley Wickham [ctb], Kirill Müller [ctb], Salim Brüggemann [ctb] (ORCID: ), Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.4", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (ORCID: ), Jim Hester [aut] (ORCID: ), Romain François [aut] (ORCID: ), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "digest": { + "Package": "digest", + "Version": "0.6.39", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\", comment = c(ORCID = \"0000-0002-8059-9767\")), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8552-0029\")), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0492-6647\")), person(\"Ion\", \"Suruceanu\", role=\"ctb\", comment = c(ORCID = \"0009-0005-6446-4909\")), person(\"Bill\", \"Denney\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5759-428X\")), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\", comment = c(ORCID = \"0009-0008-8480-1329\")), person(\"Sergey\", \"Fedorov\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5970-7233\")), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\", comment = c(ORCID = \"0009-0000-5948-4503\")), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Carl\", \"Pearson\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0701-7860\")))", + "Date": "2025-11-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://eddelbuettel.github.io/digest/, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown", + "rbenchmark" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (ORCID: ), Antoine Lucas [ctb] (ORCID: ), Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (ORCID: ), Simon Urbanek [ctb] (ORCID: ), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb] (ORCID: ), Duncan Murdoch [ctb], Jim Hester [ctb] (ORCID: ), Wush Wu [ctb] (ORCID: ), Qiang Kou [ctb] (ORCID: ), Thierry Onkelinx [ctb] (ORCID: ), Michel Lang [ctb] (ORCID: ), Viliam Simko [ctb], Kurt Hornik [ctb] (ORCID: ), Radford Neal [ctb] (ORCID: ), Kendon Bell [ctb] (ORCID: ), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb] (ORCID: ), Ion Suruceanu [ctb] (ORCID: ), Bill Denney [ctb] (ORCID: ), Dirk Schumacher [ctb], András Svraka [ctb] (ORCID: ), Sergey Fedorov [ctb] (ORCID: ), Will Landau [ctb] (ORCID: ), Floris Vanderhaeghe [ctb] (ORCID: ), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (ORCID: ), Mark van der Loo [ctb] (ORCID: ), Chris Muir [ctb] (ORCID: ), Moritz Beller [ctb] (ORCID: ), Sebastian Campbell [ctb] (ORCID: ), Winston Chang [ctb] (ORCID: ), Dean Attali [ctb] (ORCID: ), Michael Chirico [ctb] (ORCID: ), Kevin Ushey [ctb] (ORCID: ), Carl Pearson [ctb] (ORCID: )", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "https://packagemanager.posit.co/cran/latest" + }, + "evaluate": { + "Package": "evaluate", + "Version": "1.0.5", + "Source": "Repository", + "Type": "Package", + "Title": "Parsing and Evaluation Tools that Provide More Details than the Default", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.", + "License": "MIT + file LICENSE", + "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate", + "BugReports": "https://github.com/r-lib/evaluate/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "callr", + "covr", + "ggplot2 (>= 3.3.6)", + "lattice", + "methods", + "pkgload", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.5)", + "knitr", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (ORCID: ), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "fastmap": { + "Package": "fastmap", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (ORCID: ), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (ORCID: ), Devon Ryan [ctb] (ORCID: ), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" + }, + "vctrs": { + "Package": "vctrs", + "Version": "0.7.3", + "Source": "Repository", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , 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"Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + } + } +} diff --git a/content/blog/mori-0-1-0/renv/.gitignore b/content/blog/mori-0-1-0/renv/.gitignore new file mode 100644 index 000000000..0ec0cbba2 --- /dev/null +++ b/content/blog/mori-0-1-0/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/content/blog/mori-0-1-0/renv/activate.R b/content/blog/mori-0-1-0/renv/activate.R new file mode 100644 index 000000000..187592214 --- /dev/null +++ b/content/blog/mori-0-1-0/renv/activate.R @@ -0,0 +1,1438 @@ + +local({ + + # the requested version of renv + version <- "1.2.1" + attr(version, "md5") <- "51fff37c14949274ac148a9a087ab6bd" + 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 + # 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;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-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()) + + # also check for config environment variables that should suppress messages + # https://github.com/rstudio/renv/issues/2214 + enabled <- Sys.getenv("RENV_CONFIG_STARTUP_QUIET", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("true", "1")) + return(invisible()) + + enabled <- Sys.getenv("RENV_CONFIG_SYNCHRONIZED_CHECK", unset = NA) + if (!is.na(enabled) && tolower(enabled) %in% c("false", "0")) + 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) + + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # ensure the target library path exists; required for file.copy(..., recursive = TRUE) + dir.create(library, showWarnings = FALSE, recursive = TRUE) + + # try to install renv from cache + md5 <- attr(version, "md5", exact = TRUE) + if (length(md5)) { + pkgpath <- renv_bootstrap_find(version) + if (length(pkgpath) && file.exists(pkgpath)) { + ok <- file.copy(pkgpath, library, recursive = TRUE) + if (isTRUE(ok)) + return(invisible()) + } + } + + # 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)) { + + # split on ';' if present + parts <- strsplit(repos, ";", fixed = TRUE)[[1L]] + + # split into named repositories if present + idx <- regexpr("=", parts, fixed = TRUE) + keys <- substring(parts, 1L, idx - 1L) + vals <- substring(parts, idx + 1L) + names(vals) <- keys + + # if we have a single unnamed repository, call it CRAN + if (length(vals) == 1L && identical(keys, "")) + names(vals) <- "CRAN" + + return(vals) + + } + + # 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_find <- function(version) { + + path <- renv_bootstrap_find_cache(version) + if (length(path) && file.exists(path)) { + catf("- Using renv %s from global package cache", version) + return(path) + } + + } + + renv_bootstrap_find_cache <- function(version) { + + md5 <- attr(version, "md5", exact = TRUE) + if (is.null(md5)) + return() + + # infer path to renv cache + cache <- Sys.getenv("RENV_PATHS_CACHE", unset = "") + if (!nzchar(cache)) { + root <- Sys.getenv("RENV_PATHS_ROOT", unset = NA) + if (!is.na(root)) + cache <- file.path(root, "cache") + } + + if (!nzchar(cache)) { + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) { + root <- tools$R_user_dir("renv", "cache") + cache <- file.path(root, "cache") + } + } + + # start completing path to cache + file.path( + cache, + renv_bootstrap_cache_version(), + renv_bootstrap_platform_prefix(), + "renv", + version, + md5, + "renv" + ) + + } + + 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 (is.null(token)) + 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_default <- function() { + + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) + + # 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) + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() + + # build list of path components + components <- c(version, 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"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(c(expected), c(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(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + tryCatch( + renv_bootstrap_run_impl(project, libpath, version), + error = function(e) { + msg <- paste( + "failed to bootstrap renv: the project will not be loaded.", + paste("Reason:", conditionMessage(e)), + "Use `renv::activate()` to re-initialize the project.", + sep = "\n" + ) + warning(msg, call. = FALSE) + } + ) + } + + renv_bootstrap_run_impl <- function(project, libpath, version) { + + # 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 = project)) + } + + # 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_bootstrap_cache_version <- function() { + # NOTE: users should normally not override the cache version; + # this is provided just to make testing easier + Sys.getenv("RENV_CACHE_VERSION", unset = "v5") + } + + renv_bootstrap_cache_version_previous <- function() { + version <- renv_bootstrap_cache_version() + number <- as.integer(substring(version, 2L)) + paste("v", number - 1L, sep = "") + } + + 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_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + + + # 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/content/blog/mori-0-1-0/renv/settings.json b/content/blog/mori-0-1-0/renv/settings.json new file mode 100644 index 000000000..46f2f31cc --- /dev/null +++ b/content/blog/mori-0-1-0/renv/settings.json @@ -0,0 +1,21 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "lockfile.sanitize": true, + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.dev": false, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/content/software/mori/_index.md b/content/software/mori/_index.md new file mode 100644 index 000000000..14c27d747 --- /dev/null +++ b/content/software/mori/_index.md @@ -0,0 +1,35 @@ +--- +topics: +- Best Practices +color: '#4A7C59' +description: Shared Memory for R Objects +github: shikokuchuo/mori +image: logo.svg +languages: +- R +latest_release: '2026-04-22T00:00:00+00:00' +people: +- Charlie Gao +title: mori +website: https://shikokuchuo.net/mori/ + +external: # updated automatically, do not edit + description: Shared Memory for R Objects + first_commit: '2026-04-16T12:27:58+01:00' + forks: 1 + languages: + - R + last_updated: '2026-04-22T00:00:00+00:00' + latest_release: '2026-04-22T00:00:00+00:00' + license: MIT License + people: + - Charlie Gao + repo: shikokuchuo/mori + stars: 19 + title: mori + website: https://shikokuchuo.net/mori/ +--- + +mori shares R objects across processes on the same machine via a single copy in OS-level shared memory — POSIX shared memory on Linux and macOS, Win32 file mapping on Windows. Every process reads from the same physical pages through the R ALTREP framework, giving lazy, zero-copy access. + +`share()` writes an R object into shared memory and returns an ALTREP wrapper that behaves like a regular R vector. Shared objects serialize compactly as their shared-memory name rather than their full contents, so sending a shared data frame to a mirai daemon transmits ~300 bytes instead of the underlying 200 MB. Shared memory is managed by R's garbage collector and freed automatically when the last reference is dropped, and consumer processes see the data as read-only so copy-on-write keeps mutations local. diff --git a/content/software/mori/logo.svg b/content/software/mori/logo.svg new file mode 100644 index 000000000..43f4f7d96 --- /dev/null +++ b/content/software/mori/logo.svg @@ -0,0 +1,3 @@ + + + diff --git a/content/software/mori/readme b/content/software/mori/readme new file mode 100644 index 000000000..81f3f2571 --- /dev/null +++ b/content/software/mori/readme @@ -0,0 +1,223 @@ + + + +# mori + + + +[![Lifecycle: +experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +[![CRAN +status](https://www.r-pkg.org/badges/version/mori)](https://CRAN.R-project.org/package=mori) +[![R-CMD-check](https://github.com/shikokuchuo/mori/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/shikokuchuo/mori/actions/workflows/R-CMD-check.yaml) +[![Codecov test +coverage](https://codecov.io/gh/shikokuchuo/mori/graph/badge.svg)](https://app.codecov.io/gh/shikokuchuo/mori) + + + ________ + /\ mori \ + / \ \ + \ / 森 / + \/_______/ + +Shared Memory for R Objects + +→ `share()` writes an R object into shared memory and returns a shared +version + +→ ALTREP serialization hooks — shared objects serialize compactly and +work transparently with `serialize()` and `mirai()` + +→ ALTREP-backed lazy access — a 100-column data frame is one `mmap`; +columns materialize on first touch + +→ OS-level shared memory (POSIX / Win32) — pure C, no external +dependencies; read-only in other processes, preventing corruption of +shared data + +→ Automatic cleanup — shared memory is freed when the R object is +garbage collected + +
+ +## Installation + +``` r +install.packages("mori") +``` + +## Quick Start + +`share()` writes an R object once into shared memory and returns a +zero-copy ALTREP view. Shared objects serialize compactly via ALTREP +serialization hooks, working transparently with mirai and any R +serialization path. Shared memory is automatically freed when the object +is garbage collected. + +``` r +library(mori) + +# Share a vector — returns an ALTREP-backed object +x <- share(rnorm(1e6)) +mean(x) +#> [1] 0.0005982035 + +# Serialized form is ~100 bytes, not ~8 MB +x |> serialize(NULL) |> length() +#> [1] 124 +``` + +## Sharing by Name + +`shared_name()` extracts the SHM name from a shared object. +`map_shared()` opens a shared region by name — useful for accessing the +same data from another process without serialization: + +``` r +x <- share(1:1e6) + +# Extract the SHM name +nm <- shared_name(x) +nm +#> [1] "/mori_4c0f_1" + +# Another process can map the same region by name +y <- map_shared(nm) +identical(x[], y[]) +#> [1] TRUE +``` + +## Use with mirai + +Shared objects can be sent to local daemons — the ALTREP serialization +hooks ensure only the SHM name crosses the wire, and the daemon maps the +same physical memory. + +``` r +library(lobstr) +library(mirai) + +daemons(1) + +x <- share(rnorm(1e6)) + +# Worker maps the same shared memory — 0 bytes copied +m <- mirai(list(mean = mean(x), size = lobstr::obj_size(x)), x = x) +m[] +#> $mean +#> [1] 0.0008675476 +#> +#> $size +#> 840 B + +daemons(0) +``` + +Elements of a shared list also serialize compactly — each element +travels as a reference to its position in the parent shared region, not +as the full data: + +``` r +daemons(3) + +# Share a list — all 3 vectors in a single shared region +x <- list(a = rnorm(1e6), b = rnorm(1e6), c = rnorm(1e6)) |> share() + +# Each element is sent as (parent_name, index) — zero-copy on the worker +mirai_map(x, \(v) lobstr::obj_size(v) |> format())[.flat] +#> a b c +#> "840 B" "840 B" "840 B" + +daemons(0) +``` + +## Why mori + +Parallel computing multiplies memory. When 8 workers each need the same +210 MB dataset, that is 1.7 GB of serialization, transfer, and +deserialization — with 8 separate copies consuming RAM. + +mori eliminates all of it. `share()` writes data into shared memory +once. Each worker maps the same physical pages, receiving a reference of +~300 bytes instead of the full dataset — a payload ~700,000 times +smaller, which translates into a significant saving in memory usage as +well as total runtime: + +``` r +daemons(8) + +# 200 MB data frame — 5 columns × 5M rows +df <- as.data.frame(matrix(rnorm(25e6), ncol = 5)) +shared_df <- share(df) + +boot_mean <- \(i, data) colMeans(data[sample(nrow(data), replace = TRUE), ]) + +# Without mori — each daemon deserializes a full copy +mirai_map(1:8, boot_mean, data = df)[] |> system.time() +#> user system elapsed +#> 2.135 38.222 5.823 + +# With mori — each daemon maps the same shared memory +mirai_map(1:8, boot_mean, data = shared_df)[] |> system.time() +#> user system elapsed +#> 1.377 27.121 3.949 + +daemons(0) +``` + +## How It Works + +### What gets shared + +All atomic vector types and lists / data frames are written directly +into shared memory, with attributes preserved end-to-end. Pairlists are +coerced to lists. `share()` returns ALTREP wrappers that point into the +shared pages — no deserialization, no per-process memory allocation. + +All other R objects (environments, closures, language objects) are +returned unchanged by `share()` — no shared memory region is created. + +
+ + +
+ +### Lazy access + +A data frame with 10 columns lives in a single shared region. A task +that touches 3 columns pays for 3. Character strings are accessed lazily +per element. + +### Lifetime + +Shared memory is managed by R’s garbage collector. The SHM region stays +alive as long as the shared object (or any element extracted from it) is +referenced in R. When no references remain, the garbage collector frees +the shared memory automatically. + +**Important:** Always assign the result of `share()` to a variable. The +shared memory is kept alive by the R object reference — if the result is +used temporarily (not assigned), the garbage collector may free the +shared memory before a consumer process has mapped it. + +### Copy-on-write + +Shared data is mapped read-only. Mutations are always local — R’s +copy-on-write mechanism ensures other processes continue reading the +original shared data: + +- **Structural changes** to a list or data frame (adding, removing, or + reordering elements) produce a regular R list. The shared region is + unaffected. +- **Modifying values** within a shared vector (e.g., `X[1] <- 0`) + materializes just that vector into a private copy. Other vectors in + the same shared region stay zero-copy. + +– + +Please note that the mori project is released with a [Contributor Code +of Conduct](https://shikokuchuo.net/mori/CODE_OF_CONDUCT.html). By +contributing to this project, you agree to abide by its terms. diff --git a/data/github-repos.toml b/data/github-repos.toml index 130dfce4e..4e9371800 100644 --- a/data/github-repos.toml +++ b/data/github-repos.toml @@ -25339,3 +25339,20 @@ forks = 0 language = "HTML" first_commit = "2026-03-20T03:48:34+00:00" last_updated = "2026-03-20T10:27:38.525786+00:00" + +[[repos]] +repo = "shikokuchuo/mori" +name = "mori" +description = "Shared Memory for R Objects" +website = "https://shikokuchuo.net/mori/" +stars = 19 +forks = 1 +latest_release = "2026-04-22T00:00:00+00:00" +first_commit = "2026-04-16T12:27:58+01:00" +license = "MIT License" +contributors = [ + "shikokuchuo", +] +last_updated = "2026-04-22T00:00:00+00:00" +releases = 1 +language = "R"