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 @@
{
- "name": "RPackages",
+ "name": "RPackages2",
"buildsystem": "simple",
"build-commands": [],
"modules":
[
{
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+ "name": "Rpackages",
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+ "url": "http://static.jasp-stats.org/flatpak_archive.tar.gz",
+ "sha256": "63400dc87d1e3fa0179cb01a18e75b67b2de46d598e6a51e83f3b4a35b200118"
}
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- "url": "http://static.jasp-stats.org/RPkgs/conting_1.7.tar.gz",
- "sha256": "efa3242c24bc4a68ac76f4b1d77753caabb4c19e1301d5a02697f5376438c221"
- }
- ],
- "build-commands": [ "R CMD INSTALL ." ]
- },
- {
- "name": "cowplot",
- "buildsystem": "simple",
- "sources": [
- {
- "type": "archive",
- "url": "http://static.jasp-stats.org/RPkgs/cowplot_1.0.0.tar.gz",
- "sha256": "70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5"
- }
- ],
- "build-commands": [ "R CMD INSTALL ." ]
- },
- {
- "name": "flexplot",
- "buildsystem": "simple",
- "sources": [
- {
- "type": "git",
- "url": "https://github.com/dustinfife/flexplot",
- "commit": "163137fe30d9541234eb0053d6d86e1f96cd3dc5"
- }
- ],
- "build-commands": [ "R CMD INSTALL ." ]
- },
- {
- "name": "ggbeeswarm",
- "buildsystem": "simple",
- "sources": [
- {
- "type": "archive",
- "url": "http://static.jasp-stats.org/RPkgs/ggbeeswarm_0.6.0.tar.gz",
- "sha256": "bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333"
- }
- ],
- "build-commands": [ "R CMD INSTALL ." ]
- },
- {
- "name": "ggdendro",
- "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