From a22bb90bde03b38637da8c11766ac9be205da9bb Mon Sep 17 00:00:00 2001 From: Joris Goosen Date: Tue, 21 Sep 2021 12:41:55 +0200 Subject: [PATCH] Flatpak stuff - make R part more user friendly - update renv version - more user friendly and get rid of forced lowercase - got debug symbols - update README a bit - improve caching slightly + make working directory check more lenient - Also updated appdata from tryFixFlatpak branch --- Tools/flatpak/RPackages.json | 4115 +---------------- Tools/flatpak/org.jaspstats.JASP.appdata.xml | 62 + Tools/flatpak/org.jaspstats.JASP.json | 60 +- Tools/flatpak/setup-rpkgs/R/Rprofile.R | 2 +- .../setup-rpkgs/R/flatpakGeneratePkgsList.R | 87 +- .../R/flatpakRegenerateRenvStructure.R | 13 +- Tools/flatpak/setup-rpkgs/R/functions.R | 222 +- Tools/flatpak/setup-rpkgs/R/validators.R | 80 + Tools/flatpak/setup-rpkgs/README.md | 26 +- Tools/flatpak/setup-rpkgs/renv.lock | 4 +- Tools/flatpak/setup-rpkgs/renv/activate.R | 18 +- 11 files changed, 439 insertions(+), 4250 deletions(-) create mode 100644 Tools/flatpak/setup-rpkgs/R/validators.R diff --git a/Tools/flatpak/RPackages.json b/Tools/flatpak/RPackages.json index 159b06850f..db73b7fb3f 100644 --- a/Tools/flatpak/RPackages.json +++ b/Tools/flatpak/RPackages.json @@ -1,4126 +1,21 @@ { - 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"buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/ggdendro_0.1-20.tar.gz", - "sha256": "125cae904fa5d426cccaf32ebe9c6297e9ef0c6fd3f19f61513834d03a0cf8ff" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "ggExtra", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/ggExtra_0.9.tar.gz", - "sha256": "f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "haven", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/haven_2.2.0.tar.gz", - "sha256": "199ee9b14e1ff70a0b0c3b9ce33dfdec8ed3b5e857a2a36bfb82e78a7b352d3d" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "Hmisc", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/Hmisc_4.3-0.tar.gz", - "sha256": "7ff2f9adcfd67f2e70345e73db3608ed46f8e07e2f696d0d591f533482a96165" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "metaBMA", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/metaBMA_0.6.2.tar.gz", - "sha256": "be225f719a3da4c61d91c3442291b819ea61c4a09cdc867b72c0e19cf2bb563c" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "mitml", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/mitml_0.3-7.tar.gz", - "sha256": "c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "qgraph", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/qgraph_1.6.3.tar.gz", - "sha256": "363791067ae640cf4bd6f7ec4a84de9c4abaa468dfc18f21890e3f3fd1e45355" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "rio", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/rio_0.5.16.tar.gz", - "sha256": "d3eb8d5a11e0a3d26169bb9d08f834a51a6516a349854250629072d59c29d465" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "semPlot", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/semPlot_1.1.2.tar.gz", - "sha256": "b987d3ea1acdd93702de01cb434646becca971828d703b1d8fa9ec1ba24f3b50" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "shinystan", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/shinystan_2.5.0.tar.gz", - "sha256": "45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "car", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/car_3.0-4.tar.gz", - "sha256": "6e503be0632c2849383108cc1456d10b5b08d345c31267c65756796156ee0ed6" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "graphicalVAR", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/graphicalVAR_0.2.2.tar.gz", - "sha256": "681d218db5f4498efe387dbf45462fbddf96221953fc8d4443ec5feadbc2f0cb" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "heplots", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/heplots_1.3-5.tar.gz", - "sha256": "964629cba7feadbf3ac223e417310016e86067da4bbf11ad3c213e63ee74d0ef" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "IsingFit", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/IsingFit_0.3.1.tar.gz", - "sha256": "8741d65b63818c927819155f13a62d21f7d7f4942b9d218e6f93ce12eeff2ddf" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "mgm", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/mgm_1.2-7.tar.gz", - "sha256": "5a415cf32857a1862b78e025bec950bf556c07c2077526d43a063481654f15e8" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "mice", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/mice_3.6.0.tar.gz", - "sha256": "7bc72bdb631bc9f67d8f76ffb48a7bb275228d861075e20c24c09c736bebec5d" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "NetworkComparisonTest", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/NetworkComparisonTest_2.2.1.tar.gz", - "sha256": "1753961e9fb41d3aae6d12392445d7468d312a5e42629d34597ffa1e6e329b28" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "NetworkToolbox", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/NetworkToolbox_1.3.2.tar.gz", - "sha256": "6a8f5bd609b82a838515622b88f7a07f99418483d18fe89eb175bccda3600936" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "onewaytests", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/onewaytests_2.4.tar.gz", - "sha256": "464da1ebac5c8909d2d694830118d84aa913ac0647eccbbf00505d5e8dab4ae7" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "rstanarm", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/rstanarm_2.19.2.tar.gz", - "sha256": "3f1a625d435ff97cf729439acc7439b813d0e6b1a683992c58cefb7a09559acc" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "weights", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/weights_1.0.tar.gz", - "sha256": "8cb0e72edce061886ab67190c621a7da5caace787719a6a0cecf7638af5b0605" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "afex", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/afex_0.28-0.tar.gz", - "sha256": "9191ec35e670059b389f8247a96582f28b1a5c85be4fb81559827f4a055e8730" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "candisc", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/candisc_0.8-0.tar.gz", - "sha256": "b1821c11b2fe2a1758015e2f1a626cdeb3b9966c3d09269c8339a483375f0543" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "smacof", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/smacof_2.0-0.tar.gz", - "sha256": "de1f4b76f7b64828422757f18e8f6efbf62d085ef404a9b718ad869d1511fd19" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "networktools", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/networktools_1.2.1.tar.gz", - "sha256": "efc50135c06dd760e7cb42f15111eab438615a60a64a914dccf74f0cac62fd68" - } - ], - "build-commands": [ "R CMD INSTALL ." ] - }, - { - "name": "bootnet", - "buildsystem": "simple", - "sources": [ - { - "type": "archive", - "url": "http://static.jasp-stats.org/RPkgs/bootnet_1.2.4.tar.gz", - "sha256": "e2da980c55be4b5dec957d1869ecf1cd6d0a89146b619bf5960c707ae67c5f94" - } - ], - "build-commands": [ "R CMD INSTALL ." ] + "build-commands": [ "R --vanilla --file=flatpak-helper/r-helpers/flatpakRegenerateRenvStructure.R" ] } - ] } diff --git a/Tools/flatpak/org.jaspstats.JASP.appdata.xml b/Tools/flatpak/org.jaspstats.JASP.appdata.xml index 28b2835532..948882d522 100644 --- a/Tools/flatpak/org.jaspstats.JASP.appdata.xml +++ b/Tools/flatpak/org.jaspstats.JASP.appdata.xml @@ -35,6 +35,68 @@ https://github.com/jasp-stats/jasp-issues/issues https://jasp-stats.org/donate/ + + + New release 0.15 + + New features and improvements + + - Plot editing + -- Allow custom fonts in plots + -- Resized plots are kept after refreshing + - Supports more languages, English, German, Dutch, Galician, Japanese, Portuguese and rudimentary Chinese and Spanish + - Windows workarounds: + -- Support reading "native" locale encoded csvs and utf-8 both, dependent on BOM. (Aka save as csv vs csv with utf-8 in excel) + -- Support installing jasp for user with username in native locale characters + - New module “Prophet” for time series prediction + - Descriptives: + -- Dot plots + -- Stem-and-leaf tables + -- Descriptives table can now be transposed + - SEM: + -- Possibility to define several models + -- MIMIC model analysis + -- Latent Growth analysis + -- Improved labels in tables + -- Footnote fit-table listwise deletion + - T-Tests and ANOVAs: Raincloud plots + - Distributions: Major update including 23 new continuous and 5 discrete distributions + - Learn Bayes: + -- Binary classification + -- Game of chance + -- Game of skill + -- Buffon’s needle + -- Some edge case scenario and esthetical fixes for binomial estimation + - Regression: + -- Bootstrapping in correlation + -- Categorical variables can be used as predictors in linear regression + -- Adjusted lower limit for wls weights + -- Relaxed error check on the covariance matrix of predictors + - Frequencies: + - Show more informative footnote when phi cannot be calculated + -- Choose odds ratio for contingency table + -- Guttman and Kruskal’s lambda for contingency tables + - Factor analysis: Factor loadings can now be sorted in EFA and CFA + - Mixed Models + -- Fixing plotting themes + -- Improving warning messages + -- Changing default links for gamma and negative binomial family + - Meta-Analyses - Complete update of the RoBMA module + - Reliability + -- Classical intraclass correlation coefficients + -- Adding options for mean and SD + -- Restructuring of R-code to improve computational time and reduce error-proneness + -- Manage huge .jasp file sizes produced by sampling in reliability analysis + - Audit - Added mean and median to descriptive output of prior and posterior distribution + + Bug fixes + - Several fixes to sav loading (spss files) + - Loading data repeated measures ANOVA + - Cohen’s d was incorrectly calculated + - Fixed error in density graph Bayesian meta-analysis + - Fixed error in computing the total number of edges in Network analysis + + New release 0.14 diff --git a/Tools/flatpak/org.jaspstats.JASP.json b/Tools/flatpak/org.jaspstats.JASP.json index 102e09def4..80d76a591f 100644 --- a/Tools/flatpak/org.jaspstats.JASP.json +++ b/Tools/flatpak/org.jaspstats.JASP.json @@ -1,8 +1,10 @@ { "app-id": "org.jaspstats.JASP", "runtime": "org.kde.Platform", - "runtime-version": "5.12", + "runtime-version": "5.15", "sdk": "org.kde.Sdk", + "base": "io.qt.qtwebengine.BaseApp", + "base-version": "5.15", "command": "org.jaspstats.JASP", "finish-args": [ "--socket=x11", @@ -13,38 +15,45 @@ "--device=dri" ], "build-options": { - "env": { - "CXX11": "g++", - "CXX14": "g++", - "CXX11FLAGS": "-std=gnu++11", - "CXX14FLAGS": "-std=gnu++14" - }, "cxxflags": "-O2 -g -Wno-error", "cflags": "-Wno-error", "ldflags": "-lgfortran", "append-ld-library-path": "/app/lib64/R/lib", "env": { - "GIT_DISCOVERY_ACROSS_FILESYSTEM": "true", - "R_HOME": "/app/lib64/R/", - "PREFIX": "/app" + + "CXX11": "g++", + "CXX14": "g++", + "CXX11FLAGS": "-std=gnu++11", + "CXX14FLAGS": "-std=gnu++14", + + "JASP_R_REPOSITORY": "file:///app/lib64/local-cran", + "GITHUB_PAT_DEF": "Z2hwX0M3YnZhaEJIYjF5QVVxN0p5NmtjTXhpcWRveXIyOTEwOXc4Rwo", + "GITHUB_PAT": "Z2hwX1FVQmt2dWk0WFV5SWJrN0VKc2JUWWVnTzFaVnQxbzROWmxwdwo", + + "GIT_DISCOVERY_ACROSS_FILESYSTEM": "true", + + "PREFIX": "/app", + "R_HOME": "/app/lib64/R/", + + "QMAKEPATH": "/app/lib" } }, "cleanup": [ "/include" ], - "modules":[ - { - "name": "boost", - "buildsystem": "simple", + "modules":[ + { + "name": "boost", + "buildsystem": "simple", "build-commands":[ "./bootstrap.sh --with-libraries=filesystem,system", "./b2 -j${FLATPAK_BUILDER_N_JOBS} install --prefix=/app" ], "sources":[ { - "type": "archive", - "url": "https://dl.bintray.com/boostorg/release/1.71.0/source/boost_1_71_0.tar.gz", - "sha256": "96b34f7468f26a141f6020efb813f1a2f3dfb9797ecf76a7d7cbd843cc95f5bd" + "type": "archive", + "url": "https://boostorg.jfrog.io/artifactory/main/release/1.71.0/source/boost_1_71_0.tar.gz", + "sha256": "96b34f7468f26a141f6020efb813f1a2f3dfb9797ecf76a7d7cbd843cc95f5bd" } ] }, @@ -62,11 +71,11 @@ "sources": [ { "type": "archive", - "url": "http://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz", - "sha256": "5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389" + "url": "http://cran.r-project.org/src/base/R-4/R-4.1.0.tar.gz", + "sha256": "e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781" } ] - }, + }, { "name": "LAPACK", "buildsystem": "cmake", @@ -85,8 +94,8 @@ "type": "archive", "sha256": "8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc", "url": "https://static.jasp-stats.org/RPkgs/JAGS-4.3.0.tar.gz" - } ] - }, + } ] + }, "RPackages.json", { "name": "readstat", @@ -100,12 +109,15 @@ { "name": "jasp", "buildsystem": "qmake", + "config-opts": [ + "QMAKE_INCDIR+=/app/include/QtWebEngine" + ], "sources": [ { "type": "git", - "tag": "v0.13.0.0_rc0_flathub_fix0", - "url": "https://github.com/jasp-stats/jasp-desktop" + "commit": "0046fa53f209a50577f25b439be74994844f2bff", + "url": "https://github.com/vandenman/jasp-desktop" } ] } diff --git a/Tools/flatpak/setup-rpkgs/R/Rprofile.R b/Tools/flatpak/setup-rpkgs/R/Rprofile.R index 929406d532..c38f390628 100644 --- a/Tools/flatpak/setup-rpkgs/R/Rprofile.R +++ b/Tools/flatpak/setup-rpkgs/R/Rprofile.R @@ -10,7 +10,7 @@ } stripUrl <- function(url) { - tolower(gsub("/+", "_", strsplit(url, "repos/", fixed = TRUE)[[1L]][2])) + gsub("/+", "_", strsplit(url, "repos/", fixed = TRUE)[[1L]][2]) } download_override_flatpak <- function(url, destfile, mode = "wb", quiet = FALSE, headers = NULL) { diff --git a/Tools/flatpak/setup-rpkgs/R/flatpakGeneratePkgsList.R b/Tools/flatpak/setup-rpkgs/R/flatpakGeneratePkgsList.R index bf9d4e1efa..809f0ea2fc 100644 --- a/Tools/flatpak/setup-rpkgs/R/flatpakGeneratePkgsList.R +++ b/Tools/flatpak/setup-rpkgs/R/flatpakGeneratePkgsList.R @@ -1,45 +1,70 @@ -# This file needs internet! - -# TODO: look at https://github.com/andrie/miniCRAN/issues/50#issuecomment-374624319 -# it would be nice to be able to outsource this to miniCRAN which has a method for adding local pkgs to a repository -# the only downside is that it looks like miniCRAN is not actively maintained anymore. - -# when running this file on a new computer, adjust these paths -jaspDir <- "~/github/jasp-desktop" # local clone of https://github.com/jasp-stats/jasp-desktop -flatpakDir <- "~/github/flatpak/org.jaspstats.JASP" # local clone of https://github.com/flathub/org.jaspstats.JASP - -source("R/functions.R") - -# you probably want to set a GITHUB_PAT because otherwise you WILL get rate-limited by GitHub. -# Sys.setenv("GITHUB_PAT" = ...) +# Since everybody has a different setup, it might be that you need to adjust some (minor) things +# when running this on a new PC. The things you may need to adjust can be found by searching for +# the comment `| HERE |`. +# +# Some other remarks: +# +# - you MUST set a GITHUB_PAT, otherwise you'll get an error. Do not commit that to this file because then GitHub will invalidate it. +# - you can call this from cmd via Rscript R/flatpakGeneratePkgsList.R. (in Tools/flatpak/setup-rpkgs) + +# TODO: +# +# - look at https://github.com/andrie/miniCRAN/issues/50#issuecomment-374624319 +# it would be nice to be able to outsource this to miniCRAN which has a method for adding local pkgs to a repository +# the only downside is that it looks like miniCRAN is not actively maintained anymore. +# +# - there is some rudimentary support for caching downloaded CRAN pkgs. +# this should be extended to GitHub packages as well, but it doesn't work because I delete all old files related to a particular +# github pkg if renv alreadyd downloaded it. So now we're downloading jaspBase 20 times. + +expectedDirs <- c("R", "renv") +if (!all(expectedDirs %in% list.dirs(getwd(), recursive = FALSE, full.names = FALSE))) + stop("Incorrect working directory! Expected these directories at the top level: ", paste(expectedDirs, collapse = ", ")) + +# | HERE | you may want to adjust the paths when running this file on a new computer +jaspDir <- normalizePath(file.path(getwd(), "..", "..", "..")) # local clone of https://github.com/jasp-stats/jasp-desktop +flatpakDir <- normalizePath(file.path(jaspDir, "..", "org.jaspstats.JASP")) # local clone of https://github.com/flathub/org.jaspstats.JASP + +renvProject <- file.path(jaspDir, "Tools", "flatpak", "setup-rpkgs") +if (!identical(renv::project(), renvProject)) + renv::activate(renvProject) + +if (!identical(renv::project(), renvProject)) + stop("Failed to set renv project") + +source(file.path("R", "functions.R")) +source(file.path("R", "validators.R")) + +validateSetup(jaspDir, flatpakDir) options(repos = list(repos = c(CRAN = "https://cran.rstudio.com"))) -dirs <- setupJaspDirs("flatpak_folder") # NOTE: if you change the flatpak_dir anywhere you must also change it in the flatpak builder script! +dirs <- setupJaspDirs("flatpak_folder") Sys.setenv("RENV_PATHS_CACHE" = dirs["renv-cache"]) Sys.setenv("RENV_PATHS_ROOT" = dirs["renv-root"]) -# use the default branch of all modules -- always the latest version -jaspModules <- paste0("jasp-stats/", Filter(function(x) startsWith(x, "jasp"), dir(file.path(jaspDir, "Modules")))) - -# this uses the local versions -- but modules that are dependencies are still retrieved from github -# isJaspModule <- function(path) file.exists(file.path(path, "DESCRIPTION")) && file.exists(file.path(path, "inst", "Description.qml")) -# jaspModules <- Filter(isJaspModule, list.dirs("~/github/jasp-desktop/Modules", recursive = FALSE)) +# this version uses the default branch of all modules -- always the latest version +# jaspModules <- paste0("jasp-stats/", Filter(function(x) startsWith(x, "jasp"), dir(file.path(jaspDir, "Modules")))) +# this version uses the local checked-out versions -- but modules that are dependencies are still retrieved from github +isJaspModule <- function(path) file.exists(file.path(path, "DESCRIPTION")) && file.exists(file.path(path, "inst", "Description.qml")) +jaspModules <- Filter(isJaspModule, list.dirs(file.path(jaspDir, "Modules"), recursive = FALSE)) names(jaspModules) <- basename(jaspModules) -moduleEnvironments <- getModuleEnvironments(jaspModules) -saveRDS(moduleEnvironments, file = file.path(dirs["module-environments"], "module-environments.rds")) -# moduleEnvironments <- readRDS(file.path(dirs["module-environments"], "module-environments.rds")) -# names(moduleEnvironments[[1]]$records)[1:5] +# | HERE | you can add modules to exclude +jaspModules <- jaspModules[setdiff(names(jaspModules), c("jaspCircular"))] + +getModuleEnvironments(jaspModules) +# system("beep_finished.sh") + +moveMissingTarBalls(dirs) installRecommendedPackages(dirs) cleanupBigPackages(dirs) -# downloadFakeV8(dirs) updateV8Rpackage(dirs) createLocalPackageRepository(dirs) @@ -50,15 +75,17 @@ createLocalPackageRepository(dirs) # all(tb == 1) # tb[tb != 1] # these packages appear more than once -# downloadV8(dirs) +downloadV8ifneeded() copyV8Lib(dirs) copyRfiles(dirs) +validateFlatpakFolder(dirs) + # debugonce(createTarArchive) info <- createTarArchive(dirs, jaspDir, verbose = FALSE, compression = "best") -# update Rpackages.json & install build flatpak -writeRpkgsJson(file.path(flatpakDir, "RPackages.json"), info) +# | HERE | you may wish to flip the local flag to adjust the script so it uses the local archive +writeRpkgsJson(file.path(flatpakDir, "RPackages.json"), info, local = TRUE) # IF you have ssh setup this will upload the tar.gz to static-jasp. It's nicer to do this via a terminal because there you see a progress bar -uploadTarArchive(info["tar-file"]) +# uploadTarArchive(info["tar-file"]) diff --git a/Tools/flatpak/setup-rpkgs/R/flatpakRegenerateRenvStructure.R b/Tools/flatpak/setup-rpkgs/R/flatpakRegenerateRenvStructure.R index c28de29a55..e611169ea5 100644 --- a/Tools/flatpak/setup-rpkgs/R/flatpakRegenerateRenvStructure.R +++ b/Tools/flatpak/setup-rpkgs/R/flatpakRegenerateRenvStructure.R @@ -46,8 +46,13 @@ dirV8 <- file.path(dirLib64, "v8") # This must be an absolute path, since installation is staged if (runningLocally) dirV8 <- normalizePath(dirV8) +prettyCat(dir()) +prettyCat(dir(dirApp)) + +dirLibGit2 <- file.path(dirApp, "libgit2") configureVars <- c( - V8 = sprintf("INCLUDE_DIR=%1$s/include LIB_DIR=%1$s/lib", dirV8) + V8 = sprintf("INCLUDE_DIR=%1$s/include LIB_DIR=%1$s/lib", dirV8), + gert = sprintf("INCLUDE_DIR=%1$s/include LIB_DIR=%1$s", dirLibGit2) ) options(configure.vars = configureVars) prettyCat(configureVars) @@ -57,8 +62,10 @@ libArch <- system("uname -m", intern = TRUE) Sys.setenv("LIB_ARCH" = if (identical(libArch, "x86_64")) "x64" else "aarch64") prettyCat(Sys.getenv("LIB_ARCH")) -# install V8 here so later it only needs to be retrieved from the cache -renv::install("V8") +# install V8 and gert here so later they only need to be retrieved from the cache +availablePkgs <- available.packages() +toInstall <- intersect(c("V8", "gert"), availablePkgs[, "Package"]) +renv::install(toInstall) installJaspStats(c("jaspBase", "jaspGraphs"), dirs) diff --git a/Tools/flatpak/setup-rpkgs/R/functions.R b/Tools/flatpak/setup-rpkgs/R/functions.R index a2669eafe7..00cd1f1bfe 100644 --- a/Tools/flatpak/setup-rpkgs/R/functions.R +++ b/Tools/flatpak/setup-rpkgs/R/functions.R @@ -30,6 +30,11 @@ stopEarlyExit <- function(message = "expected error: early exit", call = NULL, . download_override <- function(url, destfile, mode = "wb", quiet = FALSE, headers = NULL) { + # TODO: + # tweak this so that previously downloaded packages are not downloaded again + # just make an environment with recorded urls + local file locations + # right now, jaspBase + jaspGraphs are redownloaded for every module... + # this allows us to just use the standard renv construction for installing stuff tryCatch({ options("renv.download.override" = NULL) @@ -38,15 +43,60 @@ download_override <- function(url, destfile, mode = "wb", quiet = FALSE, headers # a little bit hacky, but without the correct type the GITHUB_PAT is not used (and we really want that to be used) type <- get("type", parent.frame(1)) + dirs <- getDirs() + + if (!is.null(type)) { + if (type == "repository") { + + # check if this pkg has been downloaded before + pkg <- basename(url) + if (pkg != "PACKAGES.rds") { + pkgName <- gsub("_.*", "", pkg) + localFile0 <- file.path(dirs["local-cran"], "src", "contrib", pkg) + localFile1 <- file.path(dirs["renv-root"], "source", "repository", pkgName, pkg) + if (file.exists(localFile1)) { + ws <- strrep(" ", 35 - nchar(pkg)) # NetworkComparisonTest is the longest package name I encountered + maybecat(sprintf("Already downloaded %s%sreusing %s\n", pkg, ws, makePathRelative(localFile1, dirs["jasp-subdir"]))) + if (!file.exists(localFile0)) + file.copy(from = localFile1, to = localFile0) + return(localFile1) + } + } + } else if (type == "github") { + + if (grepl("/tarball/.+$", url)) { + + pieces <- strsplit(url, "/", TRUE)[[1]] + pkgName <- pieces[6] + SHA <- pieces[8] + + localFile0 <- file.path(dirs["local-github"], stripUrl(url)) + localFile1 <- file.path(dirs["renv-root"], "source", "github", pkgName, paste0(pkgName, "_", SHA, ".tar.gz")) + if (file.exists(localFile1)) { + ws <- strrep(" ", 35 - nchar(pkgName)) # NetworkComparisonTest is the longest package name I encountered + maybecat(sprintf("Already downloaded %s%sreusing %s\n", pkgName, ws, makePathRelative(localFile1, dirs["jasp-subdir"]))) + if (!file.exists(localFile0)) + file.copy(from = localFile1, to = localFile0) + return(localFile1) + } + } + } + } + file <- renv:::download(url, destfile, type = type, quiet = quiet, headers = headers) if (!identical(type, "github")) { maybecat(sprintf("skipping url: %s\n", url)) } else { to <- file.path(dirs["local-github"], stripUrl(url)) - maybecat(sprintf("recording github url: %s to %s\n", url, to)) - if (file.exists(to)) - maybecat(sprintf("%s already exists!", to)) + maybecat(sprintf("recording github url: %s to %s\n", makeGitHubUrlRelative(url), makePathRelative(to))) + if (file.exists(to)) { + maybecat(sprintf("%s already exists, deleting older versions!\n", makePathRelative(to))) + existingFiles <- list.files(path = dirname(to), pattern = paste(basename(to), "*"), full.names = TRUE) + res <- file.remove(existingFiles) + if (!all(res)) + stop("Failed to remove previously downloaded GitHub packages: ", paste(existingFiles[!res], collapse = ", "), domain = NA) + } file.copy(from = destfile, to = to, overwrite = TRUE) } @@ -55,36 +105,11 @@ download_override <- function(url, destfile, mode = "wb", quiet = FALSE, headers if (endsWith(url, "PACKAGES.rds") || endsWith(destfile, ".json") || startsWith(basename(destfile), "renv-")) { return(file) } - # browser() - # maybecat(sprintf("recording url: %s, destfile: %s\n", url, destfile)) maybecat(sprintf("recording package url: %s\n", url)) - # resultsEnv <- getResultsEnv() - storeUrl(url, destfile) return(file) -# -# # here we optionally download the package to a temporary directory (useful for testing a local CRAN repo) -# if (resultsEnv$downloadPkgs) { -# # renv expects this function to return where a package was downloaded -# path <- renv:::download(url, destfile, type = type, quiet = quiet, headers = headers) -# -# maybe_copy(path) -# -# if (resultsEnv$fromLockFile) -# stopEarlyExit() -# -# return(path) -# } else { -# -# if (resultsEnv$fromLockFile) -# stopEarlyExit() -# -# file.copy(from = resultsEnv$fakepkgtar, to = destfile, overwrite = TRUE) -# -# return(destfile) -# } }, error = function(e) { browser() @@ -150,11 +175,10 @@ storeUrl <- function(url, destfile) { stripUrl <- function(url) { # since repos is hardcoded in renv:::renv_remotes_resolve_github_ref_impl and we modify host, # this ooks like the safest approach - tolower(gsub("/+", "_", strsplit(url, "repos/", fixed = TRUE)[[1L]][2])) + gsub("/+", "_", strsplit(url, "repos/", fixed = TRUE)[[1L]][2]) } mkdir <- function(x, deleteIfExists = FALSE) { - if (deleteIfExists) { if (dir.exists(x)) unlink(x, recursive = TRUE) @@ -162,7 +186,6 @@ mkdir <- function(x, deleteIfExists = FALSE) { } else if (!dir.exists(x)) { dir.create(x, recursive = TRUE) } - } hasRenvLockFile <- function(modulePkg) { @@ -175,18 +198,20 @@ postProcessResults <- function() { resultsEnv$packages <- character(length(resultsEnv$url)) resultsEnv$version <- character(length(resultsEnv$url)) - idx_cran <- grep("src/contrib/", resultsEnv$url) - temp <- strsplit(basename(resultsEnv$url[idx_cran]), "_", fixed = TRUE) + idx_cran <- grep("src/contrib/", resultsEnv$url) + if (length(resultsEnv$url) > 0L) { + temp <- strsplit(basename(resultsEnv$url[idx_cran]), "_", fixed = TRUE) - resultsEnv$packages[idx_cran] <- vapply(temp, `[`, character(1L), 1L) - resultsEnv$version [idx_cran] <- sub(".tar.gz$", "", vapply(temp, `[`, character(1L), 2L)) - resultsEnv$source [idx_cran] <- "repository" + resultsEnv$packages[idx_cran] <- vapply(temp, `[`, character(1L), 1L) + resultsEnv$version [idx_cran] <- sub(".tar.gz$", "", vapply(temp, `[`, character(1L), 2L)) + resultsEnv$source [idx_cran] <- "repository" - idx_github <- grep("api.github.com/", resultsEnv$url) + idx_github <- grep("api.github.com/", resultsEnv$url) - resultsEnv$packages[idx_github] <- gsub(".*/(.+)/tarball/.*", "\\1", resultsEnv$url[idx_github]) - resultsEnv$version [idx_github] <- basename(resultsEnv$url[idx_github]) # actually just the commit - resultsEnv$source [idx_github] <- "github" + resultsEnv$packages[idx_github] <- gsub(".*/(.+)/tarball/.*", "\\1", resultsEnv$url[idx_github]) + resultsEnv$version [idx_github] <- basename(resultsEnv$url[idx_github]) # actually just the commit + resultsEnv$source [idx_github] <- "github" + } for (i in seq_along(resultsEnv$records)) if (isGitHubRecord(resultsEnv$records[[i]])) @@ -195,8 +220,13 @@ postProcessResults <- function() { return(resultsEnv) } -makePathRelative <- function(path, base = getwd()) { - gsub(pattern = paste0(base, .Platform$file.sep), replacement = "", x = path, fixed = TRUE) +makePathRelative <- function(path, base = getwd(), prepend = TRUE) { + if (prepend) base <- paste0(base, .Platform$file.sep) + gsub(pattern = base, replacement = "", x = path, fixed = TRUE) +} + +makeGitHubUrlRelative <- function(url) { + makePathRelative(url, "https://api.github.com/", FALSE) } getFlatpakJSONFromDESCRIPTION <- function(pathToModule, dirForPkgs = tempdir(), downloadPkgs = FALSE) { @@ -204,31 +234,6 @@ getFlatpakJSONFromDESCRIPTION <- function(pathToModule, dirForPkgs = tempdir(), if (!downloadPkgs) warning("with downloadPkgs = FALSE dependencies of DEPENDENCIES won't show up in the results!", immediate. = TRUE) - # options("renv.download.override" = download_override) - # on.exit(options("renv.download.override" = NULL)) - - # oldinstall.opts <- options("install.opts") - # on.exit(options(install.opts = oldinstall.opts), add = TRUE) - # options(install.opts = "--no-byte-compile --no-test-load --fake --no-R --no-libs --no-data --no-help --no-demo --no-exec --no-inst") - - # oldCache <- Sys.getenv("RENV_PATHS_CACHE") - # tempCache <- tempdir() - # if (dir.exists(file.path(tempCache, "v5"))) - # unlink(file.path(tempCache, "v5"), recursive = TRUE) - # Sys.setenv("RENV_PATHS_CACHE" = tempCache) - # on.exit(Sys.setenv("RENV_PATHS_CACHE" = oldCache), add = TRUE) - - # old_renv_install <- renv:::renv_install - # on.exit(assignFunctionInPackage(old_renv_install, "renv_install", "renv"), add = TRUE) - # assignFunctionInPackage(identity, "renv_install", "renv") - # - # library <- file.path(dirForPkgs, "library") - # mkdir(library) - # - # resultsEnv <- createResultsEnv(dirForPkgs, downloadPkgs) - # records <- renv::install(packages = pathToModule, library = library, rebuild = TRUE, sources = "") - # resultsEnv$records <- records - library <- file.path(dirForPkgs, "library") mkdir(library) resultsEnv <- createResultsEnv(dirForPkgs, downloadPkgs) @@ -243,9 +248,9 @@ customRenvInstall <- function(packages, library = NULL, rebuild = TRUE, customDo on.exit(options("renv.download.override" = NULL)) } - old_renv_install <- renv:::renv_install - on.exit(assignFunctionInPackage(old_renv_install, "renv_install", "renv"), add = TRUE) - assignFunctionInPackage(identity, "renv_install", "renv") + old_renv_impl_install <- renv:::renv_install_impl + on.exit(assignFunctionInPackage(old_renv_impl_install, "renv_install_impl", "renv"), add = TRUE) + assignFunctionInPackage(identity, "renv_install_impl", "renv") renv::install(packages = packages, library = library, rebuild = rebuild) @@ -413,13 +418,14 @@ setupJaspDirs <- function(root = getwd(), jaspSubdir = "jasp-build", flatpakSubd } getModuleEnvironments <- function(jaspModules) { + # moduleEnvironments contains all meta data for the packages (versions, url, etc.) moduleEnvironments <- setNames(vector("list", length(jaspModules)), names(jaspModules)) for (url in jaspModules) { nm <- basename(url) moduleEnvironments[[nm]] <- getFlatpakJSONFromModule(url, downloadPkgs = TRUE) } - return(moduleEnvironments) + return(invisible(moduleEnvironments)) } installGitHubRecords <- function(githubRecords, tempLib) { @@ -511,16 +517,19 @@ downloadFile <- function(url, destdir) { downloadRenv <- function(destdir) { # TODO: don't hardcode the renv version? maybe use 1 older than the current release so the url always works? - downloadFile("https://cran.r-project.org/src/contrib/renv_0.13.2.tar.gz", destdir) + downloadFile("https://cran.r-project.org/src/contrib/renv_0.14.0.tar.gz", destdir) } downloadRemotes <- function(destdir) { downloadFile("https://cran.r-project.org/src/contrib/remotes_2.4.0.tar.gz", destdir) } - copyRfiles <- function(dirs) { - file.copy(from = list.files("R", pattern = "*\\.R$", full.names = TRUE), to = dirs["r-helpers"], overwrite = TRUE) + rfiles <- list.files("R", pattern = "*\\.R$", full.names = TRUE) + successes <- file.copy(from = rfiles, to = dirs["r-helpers"], overwrite = TRUE) + if (!all(successes)) + stop("failed to copy these R files: ", paste(rfiles[!successes], collapse = ", "), " to ", dirs["r-helpers"]) + } createTarArchive <- function(dirs, jaspDir, outputPath = "archives/flatpak_archive_%s.tar.gz", compression = c("fast", "none", "best"), @@ -559,7 +568,7 @@ createTarArchive <- function(dirs, jaspDir, outputPath = "archives/flatpak_archi mkdir(dirname(outputPath)) creatArchive <- sprintf( - "tar %s -%s%sf %s %s", + "tar --mode=a+rw %s -%s%sf %s %s", compression, if (verbose) "v" else "", if (update) "u" else "c", @@ -648,7 +657,7 @@ installJaspStats <- function(pkgs, dirs) { paths <- character(length(pkgs)) for (i in seq_along(pkgs)) { - pathsFound <- list.files(path = dirs["local-github"], pattern = sprintf("^jasp-stats_%s_tarball_", tolower(pkgs[i])), full.names = TRUE) + pathsFound <- list.files(path = dirs["local-github"], pattern = sprintf("^jasp-stats_%s_tarball_", pkgs[i]), full.names = TRUE) if (length(pathsFound) != 1L) stop("There are ", if (length(pathsFound) < 1L) "zero" else "multiple", " ", pkgs[i], "_*.tar.gz present!") paths[i] <- pathsFound @@ -756,12 +765,17 @@ downloadV8 <- function(dirs) { } copyV8Lib <- function(dirs, source = "other_deps/v8") { - file.copy(source, to = dirs["other-dependencies"], recursive = TRUE) + if (!file.copy(source, to = dirs["other-dependencies"], recursive = TRUE)) + stop("Failed to copy from ", source, " to ", dirs["other-dependencies"], domain = NA) } updateV8Rpackage <- function(dirs) { pathV8 <- list.files(file.path(dirs["renv-root"], "source", "repository", "V8"), pattern = "^V8_*", full.names = TRUE) + if (length(pathV8) == 0L) { + warning("No V8 package found. This is fine if you adjusted some things and are not building everything.", domain = NA) + return() + } dirTemp <- file.path(tempdir(), "V8_fix") mkdir(dirTemp, deleteIfExists = TRUE) untar(tarfile = pathV8, exdir = dirTemp) @@ -780,3 +794,57 @@ updateV8Rpackage <- function(dirs) { file.copy(from = newPathV8, to = pathV8, overwrite = TRUE) } + +moveMissingTarBalls <- function(dirs) { + # sometimes renv realizes that it does not need to redownload a github package because it already has the source in + # flatpak_folder/jasp-build/renv-root/source/github. + # this function locates any missing tarballs and copies them to flatpak_folder/flatpak-helper/local-github/ + + allFiles <- list.files(dirs["local-github"]) + + r <- "^(.*)_contents_DESCRIPTION\\?ref=(.+)$" + matches <- regmatches(allFiles, regexec(r, allFiles)) + matches <- matches[lengths(matches) > 0L] + + SHAs <- unlist(lapply(matches, `[[`, 3L), use.names = FALSE) + names(SHAs) <- unlist(lapply(matches, `[[`, 2L), use.names = FALSE) + tarballs <- file.path(dirs["local-github"], paste0(names(SHAs), "_tarball_", SHAs)) + missing <- which(!file.exists(tarballs)) + + if (length(missing) > 0L) { + repoNames <- vapply(strsplit(names(SHAs[missing]), "_", fixed = TRUE), `[[`, character(1L), 2L) + backupTarballNames <- paste0(repoNames, "_", SHAs[missing], ".tar.gz") + backupTarballs <- file.path(dirs["renv-root"], "source", "github", repoNames, backupTarballNames) + + found <- file.exists(backupTarballs) + file.copy(from = backupTarballs[found], to = tarballs[missing][found]) + + cat("Moved these tarballs:\n", paste(basename(tarballs[missing][found]), collapse = ", "), "\n") + + if (any(!found)) { + warning("Did not find these tarballs: ", paste(backupTarballs[!found], collapse = ","), + " check if these tarballs are ok: ", paste(tarballs[missing][!found], collapse = ","), domain = NA) + } + } else { + cat("No missing tarballs.\n") + } +} + +downloadV8ifneeded <- function(destination = "other_deps") { + + if (!dir.exists(file.path(destination, "v8"))) { + # ensure parent folder exists + mkdir(destination) + downloadFile(url = "http://static.jasp-stats.org/v8.tar.gz", destination) + + oldwd <- getwd() + setwd(destination) + on.exit(setwd(oldwd)) + untar(tarfile = normalizePath("v8.tar.gz")) + } + +} + +getDirs <- function() { + get("dirs", envir = .GlobalEnv) +} diff --git a/Tools/flatpak/setup-rpkgs/R/validators.R b/Tools/flatpak/setup-rpkgs/R/validators.R new file mode 100644 index 0000000000..f8176271cd --- /dev/null +++ b/Tools/flatpak/setup-rpkgs/R/validators.R @@ -0,0 +1,80 @@ +assertDirExists <- function(x) { + if (!dir.exists(x)) + stop("Directory ", x, " does not exist", domain = NA) +} + +validateJaspDir <- function(dir) { + assertDirExists(dir) + expectedDirs <- c("Common", "Desktop", "Engine", "Modules", "R-Interface", "Resources", "Tools") + if (!all(expectedDirs %in% list.dirs(dir, full.names = FALSE, recursive = FALSE))) + stop("Invalid jaspDir. Expected these folders: ", paste(expectedDirs, collapse = ", "), domain = NA) +} + +validateFlatpakDir <- function(dir) { + assertDirExists(dir) + expectedFiles <- c("flathub.json", "org.jaspstats.JASP.json", "RPackages.json") + if (!all(expectedFiles %in% list.files(dir))) + stop("Invalid flatpakDir. Expected these files", domain = NA) +} + +validateGithubPath <- function() { + if (Sys.getenv("GITHUB_PAT") == "") + stop("GITHUB_PAT is not set!", domain = NA) +} + +validateSetup <- function(jaspDir, flatpakDir) { + # call this before downloading pkgs + validateJaspDir(jaspDir) + validateFlatpakDir(flatpakDir) + validateGithubPath() +} + +validateGithubPkgs <- function(dirs) { + + errorMessages <- character() + allFiles <- list.files(dirs["local-github"]) + + r <- "^(.*)_contents_DESCRIPTION\\?ref=(.+)$" + matches <- regmatches(allFiles, regexec(r, allFiles)) + matches <- matches[lengths(matches) > 0L] + + SHAs <- unlist(lapply(matches, `[[`, 3L), use.names = FALSE) + names(SHAs) <- unlist(lapply(matches, `[[`, 2L), use.names = FALSE) + + # check 1: verify that all the index files match the names - this check is no good if people explicitly specify a commit in the DESCRIPTION + # indexFiles <- allFiles[grep("^([^_]*_){1}[^_]*$", allFiles)] + # diff <- setdiff(names(SHAs), indexFiles) + # if (length(diff) > 0L) + # errorMessages <- c(errorMessages, paste0("These _contents_DESCRIPTION are missing an index file: ", paste0(diff, collapse = ","))) + + # check 2: verify that every "*_contents_description*" has an associated tarball + tarballs <- file.path(dirs["local-github"], paste0(names(SHAs), "_tarball_", SHAs)) + missing <- which(!file.exists(tarballs)) + if (length(missing) > 0L) + errorMessages <- c(errorMessages, paste0("These github packages are missing a tarball: ", paste(names(SHAs)[missing], collapse = ", "))) + + if (length(errorMessages) > 0L) + stop("These error message occurred:\n\n", paste(errorMessages, collapse = "\n")) + + return(invisible(TRUE)) + +} + +validateV8folder <- function(dirs) { + + v8Dir <- file.path(dirs["other-dependencies"], "v8") + if (!dir.exists(v8Dir)) + stop("V8 dir does not exist at ", v8Dir, domain = NA) + + subdirs <- file.path(v8Dir, c("include", "lib", "lic")) + if (!all(dir.exists(subdirs))) + stop("V8 dir does not contain the following subdirectories: ", paste(subdirs, collapse = ", "), domain = NA) + + +} + +validateFlatpakFolder <- function(dirs) { + # call this before creating one tar.gz + validateGithubPkgs(dirs) + validateV8folder(dirs) +} diff --git a/Tools/flatpak/setup-rpkgs/README.md b/Tools/flatpak/setup-rpkgs/README.md index ee75d0a632..72b134928d 100644 --- a/Tools/flatpak/setup-rpkgs/README.md +++ b/Tools/flatpak/setup-rpkgs/README.md @@ -1 +1,25 @@ -Helper functions to JASP work on flatpak +# Helper functions to JASP work on flatpak + +#### Building the flatpak locally. + +From a terminal, run `Rscript R/flatpakGeneratePkgsList.R` to generate a tar.gz under archives that contains all packages. +Alternatively, open the project file in RStudio and source `flatpakGeneratePkgsList.R`. +To build JASP locally, clone https://github.com/flathub/org.jaspstats.JASP and then run `flatpak-builder --user --install --force-clean build org.jaspstats.JASP.json` where `build` is your build folder. + +#### Debugging the flatpak build + +First build the flatpak version locally. +Next, in your clone of flathub/org.jaspstats.JASP do +``` +flatpak run -d --command=sh org.jaspstats.JASP +``` +This starts shell instead of directly starting JASP. +The remainder of the commans should be run from that shell. +To start JASP with a debugger, do +``` +gdb /app/bin/org.jaspstats.JASP +``` +If you get a message about debugsymbols not found, you can hopefully locate these using: +``` +find /app/ -type f -name "*.debug" +``` diff --git a/Tools/flatpak/setup-rpkgs/renv.lock b/Tools/flatpak/setup-rpkgs/renv.lock index 5263abce2e..bf706d3761 100644 --- a/Tools/flatpak/setup-rpkgs/renv.lock +++ b/Tools/flatpak/setup-rpkgs/renv.lock @@ -11,10 +11,10 @@ "Packages": { "renv": { "Package": "renv", - "Version": "0.13.2", + "Version": "0.14.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "079cb1f03ff972b30401ed05623cbe92" + "Hash": "30e5eba91b67f7f4d75d31de14bbfbdc" } } } diff --git a/Tools/flatpak/setup-rpkgs/renv/activate.R b/Tools/flatpak/setup-rpkgs/renv/activate.R index b852628d0d..304fd900a5 100644 --- a/Tools/flatpak/setup-rpkgs/renv/activate.R +++ b/Tools/flatpak/setup-rpkgs/renv/activate.R @@ -2,13 +2,27 @@ local({ # the requested version of renv - version <- "0.13.2" + version <- "0.14.0" # the project directory project <- getwd() + # allow environment variable to control activation + activate <- Sys.getenv("RENV_ACTIVATE_PROJECT") + if (!nzchar(activate)) { + + # don't auto-activate when R CMD INSTALL is running + if (nzchar(Sys.getenv("R_INSTALL_PKG"))) + return(FALSE) + + } + + # bail if activation was explicitly disabled + if (tolower(activate) %in% c("false", "f", "0")) + return(FALSE) + # avoid recursion - if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA))) + if (nzchar(Sys.getenv("RENV_R_INITIALIZING"))) return(invisible(TRUE)) # signal that we're loading renv during R startup