From fbbdc16010cda4665926758f1fef3edcbb7b390a Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Tue, 1 Oct 2024 09:56:05 +0200
Subject: [PATCH 01/11] fix gitalb CI
---
.gitlab-ci.yml | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cbd3dd4..a0961de 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -35,7 +35,6 @@ variables:
REPO_NAME: "{repo_name}"
R_LIBS: "ci/lib"
R_LIBS_USER: "ci/lib"
- postgres_version: "14"
#key for caching per branch
@@ -81,8 +80,10 @@ buildpackage:
#- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled RODBC
- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled stacomirtools RPostgres xtable magrittr intervals RColorBrewer
# these are for code coverage
- - install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled covr DT
- - install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled reshape2 graphics utils stats lattice grDevices Hmisc lubridate mgcv withr XML
+ - install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled covr DT &> install.log
+ - Rscript -e 'if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak")}'
+ - Rscript -e 'pak::pkg_install(pkg = c("reshape2", "graphics", "utils", "stats", "lattice", "grDevices", "Hmisc", "lubridate", "mgcv", "withr", "XML"), upgrade = TRUE)'
+ #- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled reshape2 graphics utils stats lattice grDevices Hmisc lubridate mgcv withr XML
- rm -rf /tmp/downloaded_packages
#- r -e 'install.packages(c("stacomirtools","RPostgres","xtable","magrittr","intervals","RColorBrewer"), lib= "ci/lib", dependencies = TRUE, repos =)'> public/logr
#- r -e 'install.packages(c(), lib= "ci/lib", repos= "https://pbil.univ-lyon1.fr/CRAN/", dependencies = TRUE)'>> public/logr
--
GitLab
From fdaa2967ef0d9b333ed1934092ce0bb0c4463bc1 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Tue, 1 Oct 2024 10:17:39 +0200
Subject: [PATCH 02/11] fix: gitlab-ci using pak
---
.gitlab-ci.yml | 11 +++++------
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a0961de..cd1bf1b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -78,12 +78,11 @@ buildpackage:
- apt-get install -y libpq-dev
- apt-get install -y r-cran-rodbc
#- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled RODBC
- - install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled stacomirtools RPostgres xtable magrittr intervals RColorBrewer
- # these are for code coverage
- - install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled covr DT &> install.log
- Rscript -e 'if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak")}'
- - Rscript -e 'pak::pkg_install(pkg = c("reshape2", "graphics", "utils", "stats", "lattice", "grDevices", "Hmisc", "lubridate", "mgcv", "withr", "XML"), upgrade = TRUE)'
- #- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled reshape2 graphics utils stats lattice grDevices Hmisc lubridate mgcv withr XML
+ - Rscript -e 'pak::pkg_install(pkg = c("stacomirtools", "RPostgres", "xtable", "magrittr", "intervals", "RColorBrewer"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
+ # these are for code coverage
+ - Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
+ - Rscript -e 'pak::pkg_install(pkg = c("reshape2", "graphics", "utils", "stats", "lattice", "grDevices", "Hmisc", "lubridate", "mgcv", "withr", "XML"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
- rm -rf /tmp/downloaded_packages
#- r -e 'install.packages(c("stacomirtools","RPostgres","xtable","magrittr","intervals","RColorBrewer"), lib= "ci/lib", dependencies = TRUE, repos =)'> public/logr
#- r -e 'install.packages(c(), lib= "ci/lib", repos= "https://pbil.univ-lyon1.fr/CRAN/", dependencies = TRUE)'>> public/logr
@@ -95,7 +94,7 @@ buildpackage:
when: always
paths:
- public
- - ci/lib
+ - ${R_LIBS_USER}
- "$(ls -rt *.zip |tail -1)"
- "$(ls -rt *.tar.gz |tail -1)"
--
GitLab
From 1889f13c5cc27354fa937f74a6798b6c8f154d39 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Tue, 1 Oct 2024 14:42:10 +0200
Subject: [PATCH 03/11] Merge branch 'renv'
---
.Rbuildignore | 4 +-
renv.lock | 1155 +++++++++++++++++++++++++++++++++++++++++
renv/.gitignore | 7 +
renv/activate.R | 1220 ++++++++++++++++++++++++++++++++++++++++++++
renv/settings.json | 19 +
5 files changed, 2404 insertions(+), 1 deletion(-)
create mode 100644 renv.lock
create mode 100644 renv/.gitignore
create mode 100644 renv/activate.R
create mode 100644 renv/settings.json
diff --git a/.Rbuildignore b/.Rbuildignore
index aae23e1..74e08d2 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
^README\.Rmd$
^README-.*\.png$
^README\.md$
@@ -26,4 +28,4 @@ tests/testhat/\~import_coe20092015\.csv
^CRAN-RELEASE$
^public
^ci
-^Scripts
\ No newline at end of file
+^Scripts
diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000..53554c0
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,1155 @@
+{
+ "R": {
+ "Version": "4.4.1",
+ "Repositories": [
+ {
+ "Name": "CRAN",
+ "URL": "https://cloud.r-project.org"
+ }
+ ]
+ },
+ "Packages": {
+ "DBI": {
+ "Package": "DBI",
+ "Version": "1.2.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "065ae649b05f1ff66bb0c793107508f5"
+ },
+ "Formula": {
+ "Package": "Formula",
+ "Version": "1.2-5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "7a29697b75e027767a53fde6c903eca7"
+ },
+ "Hmisc": {
+ "Package": "Hmisc",
+ "Version": "5.1-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Formula",
+ "R",
+ "base64enc",
+ "cluster",
+ "colorspace",
+ "data.table",
+ "foreign",
+ "ggplot2",
+ "grid",
+ "gridExtra",
+ "gtable",
+ "htmlTable",
+ "htmltools",
+ "knitr",
+ "methods",
+ "nnet",
+ "rmarkdown",
+ "rpart",
+ "viridis"
+ ],
+ "Hash": "9a446aea30bff7e8ee20f4c0973e8851"
+ },
+ "MASS": {
+ "Package": "MASS",
+ "Version": "7.3-61",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "0cafd6f0500e5deba33be22c46bf6055"
+ },
+ "Matrix": {
+ "Package": "Matrix",
+ "Version": "1.7-0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "grid",
+ "lattice",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "1920b2f11133b12350024297d8a4ff4a"
+ },
+ "R6": {
+ "Package": "R6",
+ "Version": "2.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+ },
+ "RColorBrewer": {
+ "Package": "RColorBrewer",
+ "Version": "1.1-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "45f0398006e83a5b10b72a90663d8d8c"
+ },
+ "RODBC": {
+ "Package": "RODBC",
+ "Version": "1.3-23",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats"
+ ],
+ "Hash": "544fd4ca5c8fa534604c3c0336f1a9e4"
+ },
+ "RPostgres": {
+ "Package": "RPostgres",
+ "Version": "1.4.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DBI",
+ "R",
+ "bit64",
+ "blob",
+ "cpp11",
+ "hms",
+ "lubridate",
+ "methods",
+ "plogr",
+ "withr"
+ ],
+ "Hash": "beb7e18bf3f9e096f716a52a77ec793c"
+ },
+ "Rcpp": {
+ "Package": "Rcpp",
+ "Version": "1.0.12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods",
+ "utils"
+ ],
+ "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+ },
+ "backports": {
+ "Package": "backports",
+ "Version": "1.4.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c39fbec8a30d23e721980b8afb31984c"
+ },
+ "base64enc": {
+ "Package": "base64enc",
+ "Version": "0.1-3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "543776ae6848fde2f48ff3816d0628bc"
+ },
+ "bit": {
+ "Package": "bit",
+ "Version": "4.5.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
+ },
+ "bit64": {
+ "Package": "bit64",
+ "Version": "4.5.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "bit",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "e84984bf5f12a18628d9a02322128dfd"
+ },
+ "blob": {
+ "Package": "blob",
+ "Version": "1.2.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods",
+ "rlang",
+ "vctrs"
+ ],
+ "Hash": "40415719b5a479b87949f3aa0aee737c"
+ },
+ "bslib": {
+ "Package": "bslib",
+ "Version": "0.7.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "base64enc",
+ "cachem",
+ "fastmap",
+ "grDevices",
+ "htmltools",
+ "jquerylib",
+ "jsonlite",
+ "lifecycle",
+ "memoise",
+ "mime",
+ "rlang",
+ "sass"
+ ],
+ "Hash": "8644cc53f43828f19133548195d7e59e"
+ },
+ "cachem": {
+ "Package": "cachem",
+ "Version": "1.1.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "fastmap",
+ "rlang"
+ ],
+ "Hash": "cd9a672193789068eb5a2aad65a0dedf"
+ },
+ "checkmate": {
+ "Package": "checkmate",
+ "Version": "2.3.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "backports",
+ "utils"
+ ],
+ "Hash": "c01cab1cb0f9125211a6fc99d540e315"
+ },
+ "cli": {
+ "Package": "cli",
+ "Version": "3.6.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "utils"
+ ],
+ "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
+ },
+ "cluster": {
+ "Package": "cluster",
+ "Version": "2.1.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "stats",
+ "utils"
+ ],
+ "Hash": "0aaa05204035dc43ea0004b9c76611dd"
+ },
+ "colorspace": {
+ "Package": "colorspace",
+ "Version": "2.1-0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "methods",
+ "stats"
+ ],
+ "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
+ },
+ "cpp11": {
+ "Package": "cpp11",
+ "Version": "0.4.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
+ },
+ "data.table": {
+ "Package": "data.table",
+ "Version": "1.15.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e"
+ },
+ "digest": {
+ "Package": "digest",
+ "Version": "0.6.35",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "utils"
+ ],
+ "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+ },
+ "dplyr": {
+ "Package": "dplyr",
+ "Version": "1.1.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "cli",
+ "generics",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pillar",
+ "rlang",
+ "tibble",
+ "tidyselect",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
+ },
+ "evaluate": {
+ "Package": "evaluate",
+ "Version": "0.23",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
+ },
+ "fansi": {
+ "Package": "fansi",
+ "Version": "1.0.6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "utils"
+ ],
+ "Hash": "962174cf2aeb5b9eea581522286a911f"
+ },
+ "farver": {
+ "Package": "farver",
+ "Version": "2.1.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "680887028577f3fa2a81e410ed0d6e42"
+ },
+ "fastmap": {
+ "Package": "fastmap",
+ "Version": "1.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
+ },
+ "fontawesome": {
+ "Package": "fontawesome",
+ "Version": "0.5.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "htmltools",
+ "rlang"
+ ],
+ "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
+ },
+ "foreign": {
+ "Package": "foreign",
+ "Version": "0.8-86",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods",
+ "stats",
+ "utils"
+ ],
+ "Hash": "550170303dbb19d07b2bcc288068e7dc"
+ },
+ "fs": {
+ "Package": "fs",
+ "Version": "1.6.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
+ },
+ "generics": {
+ "Package": "generics",
+ "Version": "0.1.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
+ },
+ "ggplot2": {
+ "Package": "ggplot2",
+ "Version": "3.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "R",
+ "cli",
+ "glue",
+ "grDevices",
+ "grid",
+ "gtable",
+ "isoband",
+ "lifecycle",
+ "mgcv",
+ "rlang",
+ "scales",
+ "stats",
+ "tibble",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "44c6a2f8202d5b7e878ea274b1092426"
+ },
+ "glue": {
+ "Package": "glue",
+ "Version": "1.7.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "methods"
+ ],
+ "Hash": "e0b3a53876554bd45879e596cdb10a52"
+ },
+ "gridExtra": {
+ "Package": "gridExtra",
+ "Version": "2.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grDevices",
+ "graphics",
+ "grid",
+ "gtable",
+ "utils"
+ ],
+ "Hash": "7d7f283939f563670a697165b2cf5560"
+ },
+ "gtable": {
+ "Package": "gtable",
+ "Version": "0.3.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "grid",
+ "lifecycle",
+ "rlang"
+ ],
+ "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
+ },
+ "highr": {
+ "Package": "highr",
+ "Version": "0.11",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "xfun"
+ ],
+ "Hash": "d65ba49117ca223614f71b60d85b8ab7"
+ },
+ "hms": {
+ "Package": "hms",
+ "Version": "1.1.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "lifecycle",
+ "methods",
+ "pkgconfig",
+ "rlang",
+ "vctrs"
+ ],
+ "Hash": "b59377caa7ed00fa41808342002138f9"
+ },
+ "htmlTable": {
+ "Package": "htmlTable",
+ "Version": "2.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "checkmate",
+ "htmltools",
+ "htmlwidgets",
+ "knitr",
+ "magrittr",
+ "methods",
+ "rstudioapi",
+ "stringr"
+ ],
+ "Hash": "0164d8cade33fac2190703da7e6e3241"
+ },
+ "htmltools": {
+ "Package": "htmltools",
+ "Version": "0.5.8.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "base64enc",
+ "digest",
+ "fastmap",
+ "grDevices",
+ "rlang",
+ "utils"
+ ],
+ "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
+ },
+ "htmlwidgets": {
+ "Package": "htmlwidgets",
+ "Version": "1.6.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grDevices",
+ "htmltools",
+ "jsonlite",
+ "knitr",
+ "rmarkdown",
+ "yaml"
+ ],
+ "Hash": "04291cc45198225444a397606810ac37"
+ },
+ "intervals": {
+ "Package": "intervals",
+ "Version": "0.15.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "methods",
+ "utils"
+ ],
+ "Hash": "da1fd6a5634e370ad0ef99a1aa2b17cb"
+ },
+ "isoband": {
+ "Package": "isoband",
+ "Version": "0.2.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grid",
+ "utils"
+ ],
+ "Hash": "0080607b4a1a7b28979aecef976d8bc2"
+ },
+ "jquerylib": {
+ "Package": "jquerylib",
+ "Version": "0.1.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "htmltools"
+ ],
+ "Hash": "5aab57a3bd297eee1c1d862735972182"
+ },
+ "jsonlite": {
+ "Package": "jsonlite",
+ "Version": "1.8.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods"
+ ],
+ "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+ },
+ "knitr": {
+ "Package": "knitr",
+ "Version": "1.48",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "evaluate",
+ "highr",
+ "methods",
+ "tools",
+ "xfun",
+ "yaml"
+ ],
+ "Hash": "acf380f300c721da9fde7df115a5f86f"
+ },
+ "labeling": {
+ "Package": "labeling",
+ "Version": "0.4.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "graphics",
+ "stats"
+ ],
+ "Hash": "b64ec208ac5bc1852b285f665d6368b3"
+ },
+ "later": {
+ "Package": "later",
+ "Version": "1.3.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Rcpp",
+ "rlang"
+ ],
+ "Hash": "a3e051d405326b8b0012377434c62b37"
+ },
+ "lattice": {
+ "Package": "lattice",
+ "Version": "0.22-6",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "grid",
+ "stats",
+ "utils"
+ ],
+ "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
+ },
+ "lifecycle": {
+ "Package": "lifecycle",
+ "Version": "1.0.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "rlang"
+ ],
+ "Hash": "b8552d117e1b808b09a832f589b79035"
+ },
+ "lubridate": {
+ "Package": "lubridate",
+ "Version": "1.9.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "generics",
+ "methods",
+ "timechange"
+ ],
+ "Hash": "680ad542fbcf801442c83a6ac5a2126c"
+ },
+ "magrittr": {
+ "Package": "magrittr",
+ "Version": "2.0.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "7ce2733a9826b3aeb1775d56fd305472"
+ },
+ "memoise": {
+ "Package": "memoise",
+ "Version": "2.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "cachem",
+ "rlang"
+ ],
+ "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
+ },
+ "mgcv": {
+ "Package": "mgcv",
+ "Version": "1.9-1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "R",
+ "graphics",
+ "methods",
+ "nlme",
+ "splines",
+ "stats",
+ "utils"
+ ],
+ "Hash": "110ee9d83b496279960e162ac97764ce"
+ },
+ "mime": {
+ "Package": "mime",
+ "Version": "0.12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "tools"
+ ],
+ "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+ },
+ "munsell": {
+ "Package": "munsell",
+ "Version": "0.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "colorspace",
+ "methods"
+ ],
+ "Hash": "4fd8900853b746af55b81fda99da7695"
+ },
+ "nlme": {
+ "Package": "nlme",
+ "Version": "3.1-165",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "lattice",
+ "stats",
+ "utils"
+ ],
+ "Hash": "2769a88be217841b1f33ed469675c3cc"
+ },
+ "nnet": {
+ "Package": "nnet",
+ "Version": "7.3-19",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "utils"
+ ],
+ "Hash": "2c797b46eea7fb58ede195bc0b1f1138"
+ },
+ "pillar": {
+ "Package": "pillar",
+ "Version": "1.9.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "cli",
+ "fansi",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "utf8",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+ },
+ "pkgconfig": {
+ "Package": "pkgconfig",
+ "Version": "2.0.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "utils"
+ ],
+ "Hash": "01f28d4278f15c76cddbea05899c5d6f"
+ },
+ "plogr": {
+ "Package": "plogr",
+ "Version": "0.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "09eb987710984fc2905c7129c7d85e65"
+ },
+ "plyr": {
+ "Package": "plyr",
+ "Version": "1.8.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp"
+ ],
+ "Hash": "6b8177fd19982f0020743fadbfdbd933"
+ },
+ "pool": {
+ "Package": "pool",
+ "Version": "1.0.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DBI",
+ "R",
+ "R6",
+ "later",
+ "methods",
+ "rlang"
+ ],
+ "Hash": "b336b9f1b3cc72033258c70dc17edbf1"
+ },
+ "rappdirs": {
+ "Package": "rappdirs",
+ "Version": "0.3.3",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
+ },
+ "renv": {
+ "Package": "renv",
+ "Version": "1.0.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "utils"
+ ],
+ "Hash": "397b7b2a265bc5a7a06852524dabae20"
+ },
+ "reshape2": {
+ "Package": "reshape2",
+ "Version": "1.4.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "plyr",
+ "stringr"
+ ],
+ "Hash": "bb5996d0bd962d214a11140d77589917"
+ },
+ "rlang": {
+ "Package": "rlang",
+ "Version": "1.1.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "utils"
+ ],
+ "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+ },
+ "rmarkdown": {
+ "Package": "rmarkdown",
+ "Version": "2.28",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "bslib",
+ "evaluate",
+ "fontawesome",
+ "htmltools",
+ "jquerylib",
+ "jsonlite",
+ "knitr",
+ "methods",
+ "tinytex",
+ "tools",
+ "utils",
+ "xfun",
+ "yaml"
+ ],
+ "Hash": "062470668513dcda416927085ee9bdc7"
+ },
+ "rpart": {
+ "Package": "rpart",
+ "Version": "4.1.23",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "b3d390424f41d04174cccf84d49676c2"
+ },
+ "rstudioapi": {
+ "Package": "rstudioapi",
+ "Version": "0.16.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "96710351d642b70e8f02ddeb237c46a7"
+ },
+ "sass": {
+ "Package": "sass",
+ "Version": "0.4.9",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R6",
+ "fs",
+ "htmltools",
+ "rappdirs",
+ "rlang"
+ ],
+ "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
+ },
+ "scales": {
+ "Package": "scales",
+ "Version": "1.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "RColorBrewer",
+ "cli",
+ "farver",
+ "glue",
+ "labeling",
+ "lifecycle",
+ "munsell",
+ "rlang",
+ "viridisLite"
+ ],
+ "Hash": "c19df082ba346b0ffa6f833e92de34d1"
+ },
+ "stacomirtools": {
+ "Package": "stacomirtools",
+ "Version": "0.6.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DBI",
+ "RODBC",
+ "RPostgres",
+ "methods",
+ "pool",
+ "utils",
+ "xtable"
+ ],
+ "Hash": "2b32e7d7b518bc46946e3b020e682d7d"
+ },
+ "stringi": {
+ "Package": "stringi",
+ "Version": "1.8.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "tools",
+ "utils"
+ ],
+ "Hash": "39e1144fd75428983dc3f63aa53dfa91"
+ },
+ "stringr": {
+ "Package": "stringr",
+ "Version": "1.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "magrittr",
+ "rlang",
+ "stringi",
+ "vctrs"
+ ],
+ "Hash": "960e2ae9e09656611e0b8214ad543207"
+ },
+ "tibble": {
+ "Package": "tibble",
+ "Version": "3.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "fansi",
+ "lifecycle",
+ "magrittr",
+ "methods",
+ "pillar",
+ "pkgconfig",
+ "rlang",
+ "utils",
+ "vctrs"
+ ],
+ "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+ },
+ "tidyselect": {
+ "Package": "tidyselect",
+ "Version": "1.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang",
+ "vctrs",
+ "withr"
+ ],
+ "Hash": "829f27b9c4919c16b593794a6344d6c0"
+ },
+ "timechange": {
+ "Package": "timechange",
+ "Version": "0.3.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cpp11"
+ ],
+ "Hash": "c5f3c201b931cd6474d17d8700ccb1c8"
+ },
+ "tinytex": {
+ "Package": "tinytex",
+ "Version": "0.51",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "xfun"
+ ],
+ "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
+ },
+ "utf8": {
+ "Package": "utf8",
+ "Version": "1.2.4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "62b65c52671e6665f803ff02954446e9"
+ },
+ "vctrs": {
+ "Package": "vctrs",
+ "Version": "0.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "cli",
+ "glue",
+ "lifecycle",
+ "rlang"
+ ],
+ "Hash": "c03fa420630029418f7e6da3667aac4a"
+ },
+ "viridis": {
+ "Package": "viridis",
+ "Version": "0.6.5",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "ggplot2",
+ "gridExtra",
+ "viridisLite"
+ ],
+ "Hash": "acd96d9fa70adeea4a5a1150609b9745"
+ },
+ "viridisLite": {
+ "Package": "viridisLite",
+ "Version": "0.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
+ },
+ "withr": {
+ "Package": "withr",
+ "Version": "3.0.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics"
+ ],
+ "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
+ },
+ "xfun": {
+ "Package": "xfun",
+ "Version": "0.44",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "grDevices",
+ "stats",
+ "tools"
+ ],
+ "Hash": "317a0538d32f4a009658bcedb7923f4b"
+ },
+ "xtable": {
+ "Package": "xtable",
+ "Version": "1.8-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "utils"
+ ],
+ "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+ },
+ "yaml": {
+ "Package": "yaml",
+ "Version": "2.3.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "29240487a071f535f5e5d5a323b7afbd"
+ }
+ }
+}
diff --git a/renv/.gitignore b/renv/.gitignore
new file mode 100644
index 0000000..0ec0cbb
--- /dev/null
+++ b/renv/.gitignore
@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
diff --git a/renv/activate.R b/renv/activate.R
new file mode 100644
index 0000000..d13f993
--- /dev/null
+++ b/renv/activate.R
@@ -0,0 +1,1220 @@
+
+local({
+
+ # the requested version of renv
+ version <- "1.0.7"
+ attr(version, "sha") <- NULL
+
+ # the project directory
+ project <- Sys.getenv("RENV_PROJECT")
+ if (!nzchar(project))
+ project <- getwd()
+
+ # use start-up diagnostics if enabled
+ diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
+ if (diagnostics) {
+ start <- Sys.time()
+ profile <- tempfile("renv-startup-", fileext = ".Rprof")
+ utils::Rprof(profile)
+ on.exit({
+ utils::Rprof(NULL)
+ elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L)
+ writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed)))
+ writeLines(sprintf("- Profile: %s", profile))
+ print(utils::summaryRprof(profile))
+ }, add = TRUE)
+ }
+
+ # figure out whether the autoloader is enabled
+ enabled <- local({
+
+ # first, check config option
+ override <- getOption("renv.config.autoloader.enabled")
+ if (!is.null(override))
+ return(override)
+
+ # if we're being run in a context where R_LIBS is already set,
+ # don't load -- presumably we're being run as a sub-process and
+ # the parent process has already set up library paths for us
+ rcmd <- Sys.getenv("R_CMD", unset = NA)
+ rlibs <- Sys.getenv("R_LIBS", unset = NA)
+ if (!is.na(rlibs) && !is.na(rcmd))
+ return(FALSE)
+
+ # next, check environment variables
+ # TODO: prefer using the configuration one in the future
+ envvars <- c(
+ "RENV_CONFIG_AUTOLOADER_ENABLED",
+ "RENV_AUTOLOADER_ENABLED",
+ "RENV_ACTIVATE_PROJECT"
+ )
+
+ for (envvar in envvars) {
+ envval <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(envval))
+ return(tolower(envval) %in% c("true", "t", "1"))
+ }
+
+ # enable by default
+ TRUE
+
+ })
+
+ # bail if we're not enabled
+ if (!enabled) {
+
+ # if we're not enabled, we might still need to manually load
+ # the user profile here
+ profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
+ if (file.exists(profile)) {
+ cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
+ if (tolower(cfg) %in% c("true", "t", "1"))
+ sys.source(profile, envir = globalenv())
+ }
+
+ return(FALSE)
+
+ }
+
+ # avoid recursion
+ if (identical(getOption("renv.autoloader.running"), TRUE)) {
+ warning("ignoring recursive attempt to run renv autoloader")
+ return(invisible(TRUE))
+ }
+
+ # signal that we're loading renv during R startup
+ options(renv.autoloader.running = TRUE)
+ on.exit(options(renv.autoloader.running = NULL), add = TRUE)
+
+ # signal that we've consented to use renv
+ options(renv.consent = TRUE)
+
+ # load the 'utils' package eagerly -- this ensures that renv shims, which
+ # mask 'utils' packages, will come first on the search path
+ library(utils, lib.loc = .Library)
+
+ # unload renv if it's already been loaded
+ if ("renv" %in% loadedNamespaces())
+ unloadNamespace("renv")
+
+ # load bootstrap tools
+ `%||%` <- function(x, y) {
+ if (is.null(x)) y else x
+ }
+
+ catf <- function(fmt, ..., appendLF = TRUE) {
+
+ quiet <- getOption("renv.bootstrap.quiet", default = FALSE)
+ if (quiet)
+ return(invisible())
+
+ msg <- sprintf(fmt, ...)
+ cat(msg, file = stdout(), sep = if (appendLF) "\n" else "")
+
+ invisible(msg)
+
+ }
+
+ header <- function(label,
+ ...,
+ prefix = "#",
+ suffix = "-",
+ n = min(getOption("width"), 78))
+ {
+ label <- sprintf(label, ...)
+ n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L)
+ if (n <= 0)
+ return(paste(prefix, label))
+
+ tail <- paste(rep.int(suffix, n), collapse = "")
+ paste0(prefix, " ", label, " ", tail)
+
+ }
+
+ heredoc <- function(text, leave = 0) {
+
+ # remove leading, trailing whitespace
+ trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+
+ # split into lines
+ lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+
+ # compute common indent
+ indent <- regexpr("[^[:space:]]", lines)
+ common <- min(setdiff(indent, -1L)) - leave
+ paste(substring(lines, common), collapse = "\n")
+
+ }
+
+ startswith <- function(string, prefix) {
+ substring(string, 1, nchar(prefix)) == prefix
+ }
+
+ bootstrap <- function(version, library) {
+
+ friendly <- renv_bootstrap_version_friendly(version)
+ section <- header(sprintf("Bootstrapping renv %s", friendly))
+ catf(section)
+
+ # attempt to download renv
+ catf("- Downloading renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ tarball <- renv_bootstrap_download(version),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to download:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+ on.exit(unlink(tarball), add = TRUE)
+
+ # now attempt to install
+ catf("- Installing renv ... ", appendLF = FALSE)
+ withCallingHandlers(
+ status <- renv_bootstrap_install(version, tarball, library),
+ error = function(err) {
+ catf("FAILED")
+ stop("failed to install:\n", conditionMessage(err))
+ }
+ )
+ catf("OK")
+
+ # add empty line to break up bootstrapping from normal output
+ catf("")
+
+ return(invisible())
+ }
+
+ renv_bootstrap_tests_running <- function() {
+ getOption("renv.tests.running", default = FALSE)
+ }
+
+ renv_bootstrap_repos <- function() {
+
+ # get CRAN repository
+ cran <- getOption("renv.repos.cran", "https://cloud.r-project.org")
+
+ # check for repos override
+ repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+ if (!is.na(repos)) {
+
+ # check for RSPM; if set, use a fallback repository for renv
+ rspm <- Sys.getenv("RSPM", unset = NA)
+ if (identical(rspm, repos))
+ repos <- c(RSPM = rspm, CRAN = cran)
+
+ return(repos)
+
+ }
+
+ # check for lockfile repositories
+ repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity)
+ if (!inherits(repos, "error") && length(repos))
+ return(repos)
+
+ # retrieve current repos
+ repos <- getOption("repos")
+
+ # ensure @CRAN@ entries are resolved
+ repos[repos == "@CRAN@"] <- cran
+
+ # add in renv.bootstrap.repos if set
+ default <- c(FALLBACK = "https://cloud.r-project.org")
+ extra <- getOption("renv.bootstrap.repos", default = default)
+ repos <- c(repos, extra)
+
+ # remove duplicates that might've snuck in
+ dupes <- duplicated(repos) | duplicated(names(repos))
+ repos[!dupes]
+
+ }
+
+ renv_bootstrap_repos_lockfile <- function() {
+
+ lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock")
+ if (!file.exists(lockpath))
+ return(NULL)
+
+ lockfile <- tryCatch(renv_json_read(lockpath), error = identity)
+ if (inherits(lockfile, "error")) {
+ warning(lockfile)
+ return(NULL)
+ }
+
+ repos <- lockfile$R$Repositories
+ if (length(repos) == 0)
+ return(NULL)
+
+ keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1))
+ vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1))
+ names(vals) <- keys
+
+ return(vals)
+
+ }
+
+ renv_bootstrap_download <- function(version) {
+
+ sha <- attr(version, "sha", exact = TRUE)
+
+ methods <- if (!is.null(sha)) {
+
+ # attempting to bootstrap a development version of renv
+ c(
+ function() renv_bootstrap_download_tarball(sha),
+ function() renv_bootstrap_download_github(sha)
+ )
+
+ } else {
+
+ # attempting to bootstrap a release version of renv
+ c(
+ function() renv_bootstrap_download_tarball(version),
+ function() renv_bootstrap_download_cran_latest(version),
+ function() renv_bootstrap_download_cran_archive(version)
+ )
+
+ }
+
+ for (method in methods) {
+ path <- tryCatch(method(), error = identity)
+ if (is.character(path) && file.exists(path))
+ return(path)
+ }
+
+ stop("All download methods failed")
+
+ }
+
+ renv_bootstrap_download_impl <- function(url, destfile) {
+
+ mode <- "wb"
+
+ # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+ fixup <-
+ Sys.info()[["sysname"]] == "Windows" &&
+ substring(url, 1L, 5L) == "file:"
+
+ if (fixup)
+ mode <- "w+b"
+
+ args <- list(
+ url = url,
+ destfile = destfile,
+ mode = mode,
+ quiet = TRUE
+ )
+
+ if ("headers" %in% names(formals(utils::download.file)))
+ args$headers <- renv_bootstrap_download_custom_headers(url)
+
+ 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$pkgType, "source") &&
+ !identical(getOption("pkgType"), "source") &&
+ Sys.info()[["sysname"]] %in% c("Darwin", "Windows")
+
+ types <- c(if (binary) "binary", "source")
+
+ # iterate over types + repositories
+ for (type in types) {
+ for (repos in renv_bootstrap_repos()) {
+
+ # retrieve package database
+ db <- tryCatch(
+ as.data.frame(
+ utils::available.packages(type = type, repos = repos),
+ stringsAsFactors = FALSE
+ ),
+ error = identity
+ )
+
+ if (inherits(db, "error"))
+ next
+
+ # check for compatible entry
+ entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+ if (nrow(entry) == 0)
+ next
+
+ # found it; return spec to caller
+ spec <- list(entry = entry, type = type, repos = repos)
+ return(spec)
+
+ }
+ }
+
+ # if we got here, we failed to find renv
+ fmt <- "renv %s is not available from your declared package repositories"
+ stop(sprintf(fmt, version))
+
+ }
+
+ renv_bootstrap_download_cran_archive <- function(version) {
+
+ name <- sprintf("renv_%s.tar.gz", version)
+ repos <- renv_bootstrap_repos()
+ urls <- file.path(repos, "src/contrib/Archive/renv", name)
+ destfile <- file.path(tempdir(), name)
+
+ for (url in urls) {
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (identical(status, 0L))
+ return(destfile)
+
+ }
+
+ return(FALSE)
+
+ }
+
+ renv_bootstrap_download_tarball <- function(version) {
+
+ # if the user has provided the path to a tarball via
+ # an environment variable, then use it
+ tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA)
+ if (is.na(tarball))
+ return()
+
+ # allow directories
+ if (dir.exists(tarball)) {
+ name <- sprintf("renv_%s.tar.gz", version)
+ tarball <- file.path(tarball, name)
+ }
+
+ # bail if it doesn't exist
+ if (!file.exists(tarball)) {
+
+ # let the user know we weren't able to honour their request
+ fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist."
+ msg <- sprintf(fmt, tarball)
+ warning(msg)
+
+ # bail
+ return()
+
+ }
+
+ catf("- Using local tarball '%s'.", tarball)
+ tarball
+
+ }
+
+ renv_bootstrap_download_github <- function(version) {
+
+ enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+ if (!identical(enabled, "TRUE"))
+ return(FALSE)
+
+ # prepare download options
+ pat <- Sys.getenv("GITHUB_PAT")
+ if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+ fmt <- "--location --fail --header \"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "curl", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+ fmt <- "--header=\"Authorization: token %s\""
+ extra <- sprintf(fmt, pat)
+ saved <- options("download.file.method", "download.file.extra")
+ options(download.file.method = "wget", download.file.extra = extra)
+ on.exit(do.call(base::options, saved), add = TRUE)
+ }
+
+ url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+ name <- sprintf("renv_%s.tar.gz", version)
+ destfile <- file.path(tempdir(), name)
+
+ status <- tryCatch(
+ renv_bootstrap_download_impl(url, destfile),
+ condition = identity
+ )
+
+ if (!identical(status, 0L))
+ return(FALSE)
+
+ renv_bootstrap_download_augment(destfile)
+
+ return(destfile)
+
+ }
+
+ # Add Sha to DESCRIPTION. This is stop gap until #890, after which we
+ # can use renv::install() to fully capture metadata.
+ renv_bootstrap_download_augment <- function(destfile) {
+ sha <- renv_bootstrap_git_extract_sha1_tar(destfile)
+ if (is.null(sha)) {
+ return()
+ }
+
+ # Untar
+ tempdir <- tempfile("renv-github-")
+ on.exit(unlink(tempdir, recursive = TRUE), add = TRUE)
+ untar(destfile, exdir = tempdir)
+ pkgdir <- dir(tempdir, full.names = TRUE)[[1]]
+
+ # Modify description
+ desc_path <- file.path(pkgdir, "DESCRIPTION")
+ desc_lines <- readLines(desc_path)
+ remotes_fields <- c(
+ "RemoteType: github",
+ "RemoteHost: api.github.com",
+ "RemoteRepo: renv",
+ "RemoteUsername: rstudio",
+ "RemotePkgRef: rstudio/renv",
+ paste("RemoteRef: ", sha),
+ paste("RemoteSha: ", sha)
+ )
+ writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path)
+
+ # Re-tar
+ local({
+ old <- setwd(tempdir)
+ on.exit(setwd(old), add = TRUE)
+
+ tar(destfile, compression = "gzip")
+ })
+ invisible()
+ }
+
+ # Extract the commit hash from a git archive. Git archives include the SHA1
+ # hash as the comment field of the tarball pax extended header
+ # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html)
+ # For GitHub archives this should be the first header after the default one
+ # (512 byte) header.
+ renv_bootstrap_git_extract_sha1_tar <- function(bundle) {
+
+ # open the bundle for reading
+ # We use gzcon for everything because (from ?gzcon)
+ # > Reading from a connection which does not supply a 'gzip' magic
+ # > header is equivalent to reading from the original connection
+ conn <- gzcon(file(bundle, open = "rb", raw = TRUE))
+ on.exit(close(conn))
+
+ # The default pax header is 512 bytes long and the first pax extended header
+ # with the comment should be 51 bytes long
+ # `52 comment=` (11 chars) + 40 byte SHA1 hash
+ len <- 0x200 + 0x33
+ res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len])
+
+ if (grepl("^52 comment=", res)) {
+ sub("52 comment=", "", res)
+ } else {
+ NULL
+ }
+ }
+
+ renv_bootstrap_install <- function(version, tarball, library) {
+
+ # attempt to install it into project library
+ dir.create(library, showWarnings = FALSE, recursive = TRUE)
+ output <- renv_bootstrap_install_impl(library, tarball)
+
+ # check for successful install
+ status <- attr(output, "status")
+ if (is.null(status) || identical(status, 0L))
+ return(status)
+
+ # an error occurred; report it
+ header <- "installation of renv failed"
+ lines <- paste(rep.int("=", nchar(header)), collapse = "")
+ text <- paste(c(header, lines, output), collapse = "\n")
+ stop(text)
+
+ }
+
+ renv_bootstrap_install_impl <- function(library, tarball) {
+
+ # invoke using system2 so we can capture and report output
+ bin <- R.home("bin")
+ exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+ R <- file.path(bin, exe)
+
+ args <- c(
+ "--vanilla", "CMD", "INSTALL", "--no-multiarch",
+ "-l", shQuote(path.expand(library)),
+ shQuote(path.expand(tarball))
+ )
+
+ system2(R, args, stdout = TRUE, stderr = TRUE)
+
+ }
+
+ renv_bootstrap_platform_prefix <- function() {
+
+ # construct version prefix
+ version <- paste(R.version$major, R.version$minor, sep = ".")
+ prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+
+ # include SVN revision for development versions of R
+ # (to avoid sharing platform-specific artefacts with released versions of R)
+ devel <-
+ identical(R.version[["status"]], "Under development (unstable)") ||
+ identical(R.version[["nickname"]], "Unsuffered Consequences")
+
+ if (devel)
+ prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+
+ # build list of path components
+ components <- c(prefix, R.version$platform)
+
+ # include prefix if provided by user
+ prefix <- renv_bootstrap_platform_prefix_impl()
+ if (!is.na(prefix) && nzchar(prefix))
+ components <- c(prefix, components)
+
+ # build prefix
+ paste(components, collapse = "/")
+
+ }
+
+ renv_bootstrap_platform_prefix_impl <- function() {
+
+ # if an explicit prefix has been supplied, use it
+ prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA)
+ if (!is.na(prefix))
+ return(prefix)
+
+ # if the user has requested an automatic prefix, generate it
+ auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+ if (is.na(auto) && getRversion() >= "4.4.0")
+ auto <- "TRUE"
+
+ if (auto %in% c("TRUE", "True", "true", "1"))
+ return(renv_bootstrap_platform_prefix_auto())
+
+ # empty string on failure
+ ""
+
+ }
+
+ renv_bootstrap_platform_prefix_auto <- function() {
+
+ prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity)
+ if (inherits(prefix, "error") || prefix %in% "unknown") {
+
+ msg <- paste(
+ "failed to infer current operating system",
+ "please file a bug report at https://github.com/rstudio/renv/issues",
+ sep = "; "
+ )
+
+ warning(msg)
+
+ }
+
+ prefix
+
+ }
+
+ renv_bootstrap_platform_os <- function() {
+
+ sysinfo <- Sys.info()
+ sysname <- sysinfo[["sysname"]]
+
+ # handle Windows + macOS up front
+ if (sysname == "Windows")
+ return("windows")
+ else if (sysname == "Darwin")
+ return("macos")
+
+ # check for os-release files
+ for (file in c("/etc/os-release", "/usr/lib/os-release"))
+ if (file.exists(file))
+ return(renv_bootstrap_platform_os_via_os_release(file, sysinfo))
+
+ # check for redhat-release files
+ if (file.exists("/etc/redhat-release"))
+ return(renv_bootstrap_platform_os_via_redhat_release())
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) {
+
+ # read /etc/os-release
+ release <- utils::read.table(
+ file = file,
+ sep = "=",
+ quote = c("\"", "'"),
+ col.names = c("Key", "Value"),
+ comment.char = "#",
+ stringsAsFactors = FALSE
+ )
+
+ vars <- as.list(release$Value)
+ names(vars) <- release$Key
+
+ # get os name
+ os <- tolower(sysinfo[["sysname"]])
+
+ # read id
+ id <- "unknown"
+ for (field in c("ID", "ID_LIKE")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ id <- vars[[field]]
+ break
+ }
+ }
+
+ # read version
+ version <- "unknown"
+ for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) {
+ if (field %in% names(vars) && nzchar(vars[[field]])) {
+ version <- vars[[field]]
+ break
+ }
+ }
+
+ # join together
+ paste(c(os, id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_platform_os_via_redhat_release <- function() {
+
+ # read /etc/redhat-release
+ contents <- readLines("/etc/redhat-release", warn = FALSE)
+
+ # infer id
+ id <- if (grepl("centos", contents, ignore.case = TRUE))
+ "centos"
+ else if (grepl("redhat", contents, ignore.case = TRUE))
+ "redhat"
+ else
+ "unknown"
+
+ # try to find a version component (very hacky)
+ version <- "unknown"
+
+ parts <- strsplit(contents, "[[:space:]]")[[1L]]
+ for (part in parts) {
+
+ nv <- tryCatch(numeric_version(part), error = identity)
+ if (inherits(nv, "error"))
+ next
+
+ version <- nv[1, 1]
+ break
+
+ }
+
+ paste(c("linux", id, version), collapse = "-")
+
+ }
+
+ renv_bootstrap_library_root_name <- function(project) {
+
+ # use project name as-is if requested
+ asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
+ if (asis)
+ return(basename(project))
+
+ # otherwise, disambiguate based on project's path
+ id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+ paste(basename(project), id, sep = "-")
+
+ }
+
+ renv_bootstrap_library_root <- function(project) {
+
+ prefix <- renv_bootstrap_profile_prefix()
+
+ path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+ if (!is.na(path))
+ return(paste(c(path, prefix), collapse = "/"))
+
+ path <- renv_bootstrap_library_root_impl(project)
+ if (!is.null(path)) {
+ name <- renv_bootstrap_library_root_name(project)
+ return(paste(c(path, prefix, name), collapse = "/"))
+ }
+
+ renv_bootstrap_paths_renv("library", project = project)
+
+ }
+
+ renv_bootstrap_library_root_impl <- function(project) {
+
+ root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+ if (!is.na(root))
+ return(root)
+
+ type <- renv_bootstrap_project_type(project)
+ if (identical(type, "package")) {
+ userdir <- renv_bootstrap_user_dir()
+ return(file.path(userdir, "library"))
+ }
+
+ }
+
+ renv_bootstrap_validate_version <- function(version, description = NULL) {
+
+ # resolve description file
+ #
+ # avoid passing lib.loc to `packageDescription()` below, since R will
+ # use the loaded version of the package by default anyhow. note that
+ # this function should only be called after 'renv' is loaded
+ # https://github.com/rstudio/renv/issues/1625
+ description <- description %||% packageDescription("renv")
+
+ # check whether requested version 'version' matches loaded version of renv
+ sha <- attr(version, "sha", exact = TRUE)
+ valid <- if (!is.null(sha))
+ renv_bootstrap_validate_version_dev(sha, description)
+ else
+ renv_bootstrap_validate_version_release(version, description)
+
+ if (valid)
+ return(TRUE)
+
+ # the loaded version of renv doesn't match the requested version;
+ # give the user instructions on how to proceed
+ dev <- identical(description[["RemoteType"]], "github")
+ remote <- if (dev)
+ paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
+ else
+ paste("renv", description[["Version"]], sep = "@")
+
+ # display both loaded version + sha if available
+ friendly <- renv_bootstrap_version_friendly(
+ version = description[["Version"]],
+ sha = if (dev) description[["RemoteSha"]]
+ )
+
+ fmt <- heredoc("
+ renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+ - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+ - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+ ")
+ catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
+
+ FALSE
+
+ }
+
+ renv_bootstrap_validate_version_dev <- function(version, description) {
+ expected <- description[["RemoteSha"]]
+ is.character(expected) && startswith(expected, version)
+ }
+
+ renv_bootstrap_validate_version_release <- function(version, description) {
+ expected <- description[["Version"]]
+ is.character(expected) && identical(expected, version)
+ }
+
+ renv_bootstrap_hash_text <- function(text) {
+
+ hashfile <- tempfile("renv-hash-")
+ on.exit(unlink(hashfile), add = TRUE)
+
+ writeLines(text, con = hashfile)
+ tools::md5sum(hashfile)
+
+ }
+
+ renv_bootstrap_load <- function(project, libpath, version) {
+
+ # try to load renv from the project library
+ if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+ return(FALSE)
+
+ # warn if the version of renv loaded does not match
+ renv_bootstrap_validate_version(version)
+
+ # execute renv load hooks, if any
+ hooks <- getHook("renv::autoload")
+ for (hook in hooks)
+ if (is.function(hook))
+ tryCatch(hook(), error = warnify)
+
+ # load the project
+ renv::load(project)
+
+ TRUE
+
+ }
+
+ renv_bootstrap_profile_load <- function(project) {
+
+ # if RENV_PROFILE is already set, just use that
+ profile <- Sys.getenv("RENV_PROFILE", unset = NA)
+ if (!is.na(profile) && nzchar(profile))
+ return(profile)
+
+ # check for a profile file (nothing to do if it doesn't exist)
+ path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project)
+ if (!file.exists(path))
+ return(NULL)
+
+ # read the profile, and set it if it exists
+ contents <- readLines(path, warn = FALSE)
+ if (length(contents) == 0L)
+ return(NULL)
+
+ # set RENV_PROFILE
+ profile <- contents[[1L]]
+ if (!profile %in% c("", "default"))
+ Sys.setenv(RENV_PROFILE = profile)
+
+ profile
+
+ }
+
+ renv_bootstrap_profile_prefix <- function() {
+ profile <- renv_bootstrap_profile_get()
+ if (!is.null(profile))
+ return(file.path("profiles", profile, "renv"))
+ }
+
+ renv_bootstrap_profile_get <- function() {
+ profile <- Sys.getenv("RENV_PROFILE", unset = "")
+ renv_bootstrap_profile_normalize(profile)
+ }
+
+ renv_bootstrap_profile_set <- function(profile) {
+ profile <- renv_bootstrap_profile_normalize(profile)
+ if (is.null(profile))
+ Sys.unsetenv("RENV_PROFILE")
+ else
+ Sys.setenv(RENV_PROFILE = profile)
+ }
+
+ renv_bootstrap_profile_normalize <- function(profile) {
+
+ if (is.null(profile) || profile %in% c("", "default"))
+ return(NULL)
+
+ profile
+
+ }
+
+ renv_bootstrap_path_absolute <- function(path) {
+
+ substr(path, 1L, 1L) %in% c("~", "/", "\\") || (
+ substr(path, 1L, 1L) %in% c(letters, LETTERS) &&
+ substr(path, 2L, 3L) %in% c(":/", ":\\")
+ )
+
+ }
+
+ renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) {
+ renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv")
+ root <- if (renv_bootstrap_path_absolute(renv)) NULL else project
+ prefix <- if (profile) renv_bootstrap_profile_prefix()
+ components <- c(root, renv, prefix, ...)
+ paste(components, collapse = "/")
+ }
+
+ renv_bootstrap_project_type <- function(path) {
+
+ descpath <- file.path(path, "DESCRIPTION")
+ if (!file.exists(descpath))
+ return("unknown")
+
+ desc <- tryCatch(
+ read.dcf(descpath, all = TRUE),
+ error = identity
+ )
+
+ if (inherits(desc, "error"))
+ return("unknown")
+
+ type <- desc$Type
+ if (!is.null(type))
+ return(tolower(type))
+
+ package <- desc$Package
+ if (!is.null(package))
+ return("package")
+
+ "unknown"
+
+ }
+
+ renv_bootstrap_user_dir <- function() {
+ dir <- renv_bootstrap_user_dir_impl()
+ path.expand(chartr("\\", "/", dir))
+ }
+
+ renv_bootstrap_user_dir_impl <- function() {
+
+ # use local override if set
+ override <- getOption("renv.userdir.override")
+ if (!is.null(override))
+ return(override)
+
+ # use R_user_dir if available
+ tools <- asNamespace("tools")
+ if (is.function(tools$R_user_dir))
+ return(tools$R_user_dir("renv", "cache"))
+
+ # try using our own backfill for older versions of R
+ envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME")
+ for (envvar in envvars) {
+ root <- Sys.getenv(envvar, unset = NA)
+ if (!is.na(root))
+ return(file.path(root, "R/renv"))
+ }
+
+ # use platform-specific default fallbacks
+ if (Sys.info()[["sysname"]] == "Windows")
+ file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv")
+ else if (Sys.info()[["sysname"]] == "Darwin")
+ "~/Library/Caches/org.R-project.R/R/renv"
+ else
+ "~/.cache/R/renv"
+
+ }
+
+ renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) {
+ sha <- sha %||% attr(version, "sha", exact = TRUE)
+ parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L)))
+ paste(parts, collapse = "")
+ }
+
+ renv_bootstrap_exec <- function(project, libpath, version) {
+ if (!renv_bootstrap_load(project, libpath, version))
+ renv_bootstrap_run(version, libpath)
+ }
+
+ renv_bootstrap_run <- function(version, libpath) {
+
+ # perform bootstrap
+ bootstrap(version, libpath)
+
+ # exit early if we're just testing bootstrap
+ if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+ return(TRUE)
+
+ # try again to load
+ if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+ return(renv::load(project = getwd()))
+ }
+
+ # failed to download or load renv; warn the user
+ msg <- c(
+ "Failed to find an renv installation: the project will not be loaded.",
+ "Use `renv::activate()` to re-initialize the project."
+ )
+
+ warning(paste(msg, collapse = "\n"), call. = FALSE)
+
+ }
+
+ renv_json_read <- function(file = NULL, text = NULL) {
+
+ jlerr <- NULL
+
+ # if jsonlite is loaded, use that instead
+ if ("jsonlite" %in% loadedNamespaces()) {
+
+ json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ jlerr <- json
+
+ }
+
+ # otherwise, fall back to the default JSON reader
+ json <- tryCatch(renv_json_read_default(file, text), error = identity)
+ if (!inherits(json, "error"))
+ return(json)
+
+ # report an error
+ if (!is.null(jlerr))
+ stop(jlerr)
+ else
+ stop(json)
+
+ }
+
+ renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
+ }
+
+ renv_json_read_default <- function(file = NULL, text = NULL) {
+
+ # find strings in the JSON
+ text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
+ pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
+ locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
+
+ # if any are found, replace them with placeholders
+ replaced <- text
+ strings <- character()
+ replacements <- character()
+
+ if (!identical(c(locs), -1L)) {
+
+ # get the string values
+ starts <- locs
+ ends <- locs + attr(locs, "match.length") - 1L
+ strings <- substring(text, starts, ends)
+
+ # only keep those requiring escaping
+ strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE)
+
+ # compute replacements
+ replacements <- sprintf('"\032%i\032"', seq_along(strings))
+
+ # replace the strings
+ mapply(function(string, replacement) {
+ replaced <<- sub(string, replacement, replaced, fixed = TRUE)
+ }, strings, replacements)
+
+ }
+
+ # transform the JSON into something the R parser understands
+ transformed <- replaced
+ transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE)
+ transformed <- gsub("[[{]", "list(", transformed, perl = TRUE)
+ transformed <- gsub("[]}]", ")", transformed, perl = TRUE)
+ transformed <- gsub(":", "=", transformed, fixed = TRUE)
+ text <- paste(transformed, collapse = "\n")
+
+ # parse it
+ json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]]
+
+ # construct map between source strings, replaced strings
+ map <- as.character(parse(text = strings))
+ names(map) <- as.character(parse(text = replacements))
+
+ # convert to list
+ map <- as.list(map)
+
+ # remap strings in object
+ remapped <- renv_json_read_remap(json, map)
+
+ # evaluate
+ eval(remapped, envir = baseenv())
+
+ }
+
+ renv_json_read_remap <- function(json, map) {
+
+ # fix names
+ if (!is.null(names(json))) {
+ lhs <- match(names(json), names(map), nomatch = 0L)
+ rhs <- match(names(map), names(json), nomatch = 0L)
+ names(json)[rhs] <- map[lhs]
+ }
+
+ # fix values
+ if (is.character(json))
+ return(map[[json]] %||% json)
+
+ # handle true, false, null
+ if (is.name(json)) {
+ text <- as.character(json)
+ if (text == "true")
+ return(TRUE)
+ else if (text == "false")
+ return(FALSE)
+ else if (text == "null")
+ return(NULL)
+ }
+
+ # recurse
+ if (is.recursive(json)) {
+ for (i in seq_along(json)) {
+ json[i] <- list(renv_json_read_remap(json[[i]], map))
+ }
+ }
+
+ json
+
+ }
+
+ # load the renv profile, if any
+ renv_bootstrap_profile_load(project)
+
+ # construct path to library root
+ root <- renv_bootstrap_library_root(project)
+
+ # construct library prefix for platform
+ prefix <- renv_bootstrap_platform_prefix()
+
+ # construct full libpath
+ libpath <- file.path(root, prefix)
+
+ # run bootstrap code
+ renv_bootstrap_exec(project, libpath, version)
+
+ invisible()
+
+})
diff --git a/renv/settings.json b/renv/settings.json
new file mode 100644
index 0000000..74c1d4b
--- /dev/null
+++ b/renv/settings.json
@@ -0,0 +1,19 @@
+{
+ "bioconductor.version": null,
+ "external.libraries": [],
+ "ignored.packages": [],
+ "package.dependency.fields": [
+ "Imports",
+ "Depends",
+ "LinkingTo"
+ ],
+ "ppm.enabled": null,
+ "ppm.ignored.urls": [],
+ "r.version": null,
+ "snapshot.type": "explicit",
+ "use.cache": true,
+ "vcs.ignore.cellar": true,
+ "vcs.ignore.library": true,
+ "vcs.ignore.local": true,
+ "vcs.manage.ignores": true
+}
--
GitLab
From ce82c68c0e59b6b8344c8ba0f87258e8596dda04 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 3 Oct 2024 14:46:55 +0200
Subject: [PATCH 04/11] Renv
---
.Rbuildignore | 1 +
.gitlab-ci.yml | 70 ++++++++++++++++----------------
renv.lock | 80 ++++++++++++++++++------------------
renv/activate.R | 105 +++++++++++++++++++++++++++++++++++++++++++-----
4 files changed, 171 insertions(+), 85 deletions(-)
diff --git a/.Rbuildignore b/.Rbuildignore
index 74e08d2..5258263 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -29,3 +29,4 @@ tests/testhat/\~import_coe20092015\.csv
^public
^ci
^Scripts
+^cache
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cd1bf1b..ba5263d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -35,12 +35,16 @@ variables:
REPO_NAME: "{repo_name}"
R_LIBS: "ci/lib"
R_LIBS_USER: "ci/lib"
+ RENV_PATHS_CACHE: "cache"
+ RENV_PATHS_LIBRARY: "renv/library"
#key for caching per branch
cache:
key: $CI_COMMIT_REF_SLUG
paths:
+ - ${RENV_PATHS_CACHE}
+ - ${RENV_PATHS_LIBRARY}
- ${R_LIBS_USER}
@@ -63,31 +67,16 @@ buildpackage:
only:
- main
- master
- - 0.6.0.7
+ - 0.6.0.7
needs: []
script:
- mkdir -p $R_LIBS_USER
+ - mkdir -p $RENV_PATHS_CACHE
- mkdir -p public
- # from https://www.algorist.co.uk/post/building-a-ci-pipeline-for-r-packages-in-gitlab/
- - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
- - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron
- #- echo 'PGPASSWORD=$POSTGRES_PASSWORD' >> .Renviron # I need to pass the variable to use later in test
- # d --deps dependencies, r
- - apt-get update -y
- - apt-get install -y libpq-dev
- - apt-get install -y r-cran-rodbc
- #- install2.r --deps TRUE --libloc "ci/lib" --repos "https://pbil.univ-lyon1.fr/CRAN/" --error --skipinstalled RODBC
+ - Rscript -e 'source("renv/activate.R")'
- Rscript -e 'if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak")}'
- - Rscript -e 'pak::pkg_install(pkg = c("stacomirtools", "RPostgres", "xtable", "magrittr", "intervals", "RColorBrewer"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
- # these are for code coverage
- - Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
- - Rscript -e 'pak::pkg_install(pkg = c("reshape2", "graphics", "utils", "stats", "lattice", "grDevices", "Hmisc", "lubridate", "mgcv", "withr", "XML"), lib = "'$R_LIBS_USER'", upgrade = TRUE)'
- - rm -rf /tmp/downloaded_packages
- #- r -e 'install.packages(c("stacomirtools","RPostgres","xtable","magrittr","intervals","RColorBrewer"), lib= "ci/lib", dependencies = TRUE, repos =)'> public/logr
- #- r -e 'install.packages(c(), lib= "ci/lib", repos= "https://pbil.univ-lyon1.fr/CRAN/", dependencies = TRUE)'>> public/logr
- #- r -e 'install.packages(c("xml2"), repos= "https://pbil.univ-lyon1.fr/CRAN/", lib= "ci/lib", dependencies = TRUE)'>> public/logr # this one is for test with JUNIT reporter
- #- if [[ $CI_DEFAULT_BRANCH == "master" || $CI_DEFAULT_BRANCH = "main" || $CI_DEFAULT_BRANCH = "0.6.0.7"]]; then echo "OK - default branch is master or main or 0.6.0.7"; else echo "default branch is not master or main or 0.6.0.7, please add yours ($CI_0.6.0.7_BRANCH) where needed, as well as in the present line of code" ; exit 1; fi
+ - Rscript -e 'pak::pkg_install(pkg = c("rcmdcheck", "renv"), upgrade = FALSE)'
+ - Rscript -e 'renv::restore()'
- r -e 'devtools::build(binary = TRUE, path="public", vignettes=TRUE, manual=TRUE)'
- r -e 'devtools::build(binary = FALSE, path="public", vignettes=TRUE)'
artifacts:
@@ -95,8 +84,6 @@ buildpackage:
paths:
- public
- ${R_LIBS_USER}
- - "$(ls -rt *.zip |tail -1)"
- - "$(ls -rt *.tar.gz |tail -1)"
@@ -146,11 +133,27 @@ checkerrors:
- 0.6.0.7
script:
- mkdir -p public/check
- - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
- - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron
- - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
- #- check.r --repo "https://pbil.univ-lyon1.fr/CRAN/" --install-deps --library "ci/lib"
+ - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
+ artifacts:
+ when: always
+ paths:
+ - public/check
+ expire_in: 30 days
+
+checkerrors_update:
+ before_script:
+ - apt-get update
+ - apt-get install -y qpdf
+ stage: check
+ needs: ["buildpackage"]
+ only:
+ - main
+ - master
+ - 0.6.0.7
+ script:
+ - mkdir -p public/check
+ - Rscript -e 'renv::update()'
+ - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
artifacts:
when: always
paths:
@@ -164,13 +167,10 @@ unittests:
only:
- main
- master
- - 0.6.0.7
+ - 0.6.0.7
script:
- export PGPASSWORD=$POSTGRES_PASSWORD
- - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
- - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron
- echo 'PGPASSWORD=$POSTGRES_PASSWORD' >> .Renviron
- r -e 'devtools::load_all();options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password = "postgres"); test <- capture.output(devtools::test(reporter="junit")) ; XML::saveXML(XML::xmlParse(test[grep("?xml version",test):length(test)]), file="public/test.xml")'
- r -e 'a<-1'
@@ -197,13 +197,11 @@ codecov:
- master
- 0.6.0.7
script:
- - echo 'R_LIBS=$R_LIBS_USER' > .Renviron
- - echo 'R_LIBS_USER=$R_LIBS_USER' >> .Renviron
- - echo 'R_LIBS_SITE=$R_LIBS_USER' >> .Renviron
- #- echo 'PGPASSWORD=$POSTGRES_PASSWORD' >> .Renviron
+ # these are for code coverage
+ - Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- r -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password = "postgres");co <- covr::package_coverage(type="all", quiet=FALSE, clean=FALSE);print(co);covr:::print.coverage(co);covr::report(co, file.path("dev/codecoverage_report", paste0("stacomiR-report.html")))'
# the following should be used when pages is set
- #- r -e 'covr::gitlab(file = "public/coverage.html", type = c("all"), quiet = FALSE)'
+ - r -e 'covr::gitlab(file = "public/coverage.html", type = c("all"), quiet = FALSE)'
#A line like Code coverage: 67.89% of lines covered would match.
coverage: '/Coverage: \d+\.\d+/'
artifacts:
diff --git a/renv.lock b/renv.lock
index 53554c0..b518bbc 100644
--- a/renv.lock
+++ b/renv.lock
@@ -143,24 +143,24 @@
},
"Rcpp": {
"Package": "Rcpp",
- "Version": "1.0.12",
+ "Version": "1.0.13",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"methods",
"utils"
],
- "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+ "Hash": "f27411eb6d9c3dada5edd444b8416675"
},
"backports": {
"Package": "backports",
- "Version": "1.4.1",
+ "Version": "1.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R"
],
- "Hash": "c39fbec8a30d23e721980b8afb31984c"
+ "Hash": "e1e1b9d75c37401117b636b7ae50827a"
},
"base64enc": {
"Package": "base64enc",
@@ -210,7 +210,7 @@
},
"bslib": {
"Package": "bslib",
- "Version": "0.7.0",
+ "Version": "0.8.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -228,7 +228,7 @@
"rlang",
"sass"
],
- "Hash": "8644cc53f43828f19133548195d7e59e"
+ "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
},
"cachem": {
"Package": "cachem",
@@ -243,7 +243,7 @@
},
"checkmate": {
"Package": "checkmate",
- "Version": "2.3.1",
+ "Version": "2.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -251,18 +251,18 @@
"backports",
"utils"
],
- "Hash": "c01cab1cb0f9125211a6fc99d540e315"
+ "Hash": "0e14e01ce07e7c88fd25de6d4260d26b"
},
"cli": {
"Package": "cli",
- "Version": "3.6.2",
+ "Version": "3.6.3",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"utils"
],
- "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
+ "Hash": "b21916dd77a27642b447374a5d30ecf3"
},
"cluster": {
"Package": "cluster",
@@ -280,7 +280,7 @@
},
"colorspace": {
"Package": "colorspace",
- "Version": "2.1-0",
+ "Version": "2.1-1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -290,39 +290,39 @@
"methods",
"stats"
],
- "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
+ "Hash": "d954cb1c57e8d8b756165d7ba18aa55a"
},
"cpp11": {
"Package": "cpp11",
- "Version": "0.4.7",
+ "Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R"
],
- "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
+ "Hash": "91570bba75d0c9d3f1040c835cee8fba"
},
"data.table": {
"Package": "data.table",
- "Version": "1.15.4",
+ "Version": "1.16.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
],
- "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e"
+ "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a"
},
"digest": {
"Package": "digest",
- "Version": "0.6.35",
+ "Version": "0.6.37",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"utils"
],
- "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
+ "Hash": "33698c4b3127fc9f506654607fb73676"
},
"dplyr": {
"Package": "dplyr",
@@ -349,14 +349,13 @@
},
"evaluate": {
"Package": "evaluate",
- "Version": "0.23",
+ "Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
- "R",
- "methods"
+ "R"
],
- "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
+ "Hash": "6b567375113ceb7d9f800de4dd42218e"
},
"fansi": {
"Package": "fansi",
@@ -398,7 +397,7 @@
},
"foreign": {
"Package": "foreign",
- "Version": "0.8-86",
+ "Version": "0.8-87",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -407,7 +406,7 @@
"stats",
"utils"
],
- "Hash": "550170303dbb19d07b2bcc288068e7dc"
+ "Hash": "81fc09bdeab0077a73927ed1243404b6"
},
"fs": {
"Package": "fs",
@@ -458,14 +457,14 @@
},
"glue": {
"Package": "glue",
- "Version": "1.7.0",
+ "Version": "1.8.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"methods"
],
- "Hash": "e0b3a53876554bd45879e596cdb10a52"
+ "Hash": "5899f1eaa825580172bb56c08266f37c"
},
"gridExtra": {
"Package": "gridExtra",
@@ -523,7 +522,7 @@
},
"htmlTable": {
"Package": "htmlTable",
- "Version": "2.4.2",
+ "Version": "2.4.3",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -537,7 +536,7 @@
"rstudioapi",
"stringr"
],
- "Hash": "0164d8cade33fac2190703da7e6e3241"
+ "Hash": "ca027d8771f2c039aed82f00a81e725b"
},
"htmltools": {
"Package": "htmltools",
@@ -606,13 +605,13 @@
},
"jsonlite": {
"Package": "jsonlite",
- "Version": "1.8.8",
+ "Version": "1.8.9",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"methods"
],
- "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+ "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
},
"knitr": {
"Package": "knitr",
@@ -754,7 +753,7 @@
},
"nlme": {
"Package": "nlme",
- "Version": "3.1-165",
+ "Version": "3.1-166",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -764,7 +763,7 @@
"stats",
"utils"
],
- "Hash": "2769a88be217841b1f33ed469675c3cc"
+ "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
},
"nnet": {
"Package": "nnet",
@@ -850,13 +849,13 @@
},
"renv": {
"Package": "renv",
- "Version": "1.0.7",
+ "Version": "1.0.9",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"utils"
],
- "Hash": "397b7b2a265bc5a7a06852524dabae20"
+ "Hash": "ef233f0e9064fc88c898b340c9add5c2"
},
"reshape2": {
"Package": "reshape2",
@@ -1053,13 +1052,13 @@
},
"tinytex": {
"Package": "tinytex",
- "Version": "0.51",
+ "Version": "0.53",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"xfun"
],
- "Hash": "d44e2fcd2e4e076f0aac540208559d1d"
+ "Hash": "9db859e8aabbb474293dde3097839420"
},
"utf8": {
"Package": "utf8",
@@ -1122,15 +1121,16 @@
},
"xfun": {
"Package": "xfun",
- "Version": "0.44",
+ "Version": "0.47",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
+ "R",
"grDevices",
"stats",
"tools"
],
- "Hash": "317a0538d32f4a009658bcedb7923f4b"
+ "Hash": "36ab21660e2d095fef0d83f689e0477c"
},
"xtable": {
"Package": "xtable",
@@ -1146,10 +1146,10 @@
},
"yaml": {
"Package": "yaml",
- "Version": "2.3.8",
+ "Version": "2.3.10",
"Source": "Repository",
"Repository": "CRAN",
- "Hash": "29240487a071f535f5e5d5a323b7afbd"
+ "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
}
}
}
diff --git a/renv/activate.R b/renv/activate.R
index d13f993..c360bf2 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,7 +2,7 @@
local({
# the requested version of renv
- version <- "1.0.7"
+ version <- "1.0.9"
attr(version, "sha") <- NULL
# the project directory
@@ -98,6 +98,66 @@ local({
unloadNamespace("renv")
# load bootstrap tools
+ ansify <- function(text) {
+ if (renv_ansify_enabled())
+ renv_ansify_enhanced(text)
+ else
+ renv_ansify_default(text)
+ }
+
+ renv_ansify_enabled <- function() {
+
+ override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+ if (!is.na(override))
+ return(as.logical(override))
+
+ pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+ if (identical(pane, "build"))
+ return(FALSE)
+
+ testthat <- Sys.getenv("TESTTHAT", unset = "false")
+ if (tolower(testthat) %in% "true")
+ return(FALSE)
+
+ iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+ if (tolower(iderun) %in% "false")
+ return(FALSE)
+
+ TRUE
+
+ }
+
+ renv_ansify_default <- function(text) {
+ text
+ }
+
+ renv_ansify_enhanced <- function(text) {
+
+ # R help links
+ pattern <- "`\\?(renv::(?:[^`])+)`"
+ replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+ text <- gsub(pattern, replacement, text, perl = TRUE)
+
+ # runnable code
+ pattern <- "`(renv::(?:[^`])+)`"
+ replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+ text <- gsub(pattern, replacement, text, perl = TRUE)
+
+ # return ansified text
+ text
+
+ }
+
+ renv_ansify_init <- function() {
+
+ envir <- renv_envir_self()
+ if (renv_ansify_enabled())
+ assign("ansify", renv_ansify_enhanced, envir = envir)
+ else
+ assign("ansify", renv_ansify_default, envir = envir)
+
+ }
+
`%||%` <- function(x, y) {
if (is.null(x)) y else x
}
@@ -142,7 +202,10 @@ local({
# compute common indent
indent <- regexpr("[^[:space:]]", lines)
common <- min(setdiff(indent, -1L)) - leave
- paste(substring(lines, common), collapse = "\n")
+ text <- paste(substring(lines, common), collapse = "\n")
+
+ # substitute in ANSI links for executable renv code
+ ansify(text)
}
@@ -306,7 +369,11 @@ local({
)
if ("headers" %in% names(formals(utils::download.file)))
- args$headers <- renv_bootstrap_download_custom_headers(url)
+ {
+ headers <- renv_bootstrap_download_custom_headers(url)
+ if (length(headers) && is.character(headers))
+ args$headers <- headers
+ }
do.call(utils::download.file, args)
@@ -385,10 +452,22 @@ local({
for (type in types) {
for (repos in renv_bootstrap_repos()) {
+ # build arguments for utils::available.packages() call
+ args <- list(type = type, repos = repos)
+
+ # add custom headers if available -- note that
+ # utils::available.packages() will pass this to download.file()
+ if ("headers" %in% names(formals(utils::download.file)))
+ {
+ headers <- renv_bootstrap_download_custom_headers(url)
+ if (length(headers) && is.character(headers))
+ args$headers <- headers
+ }
+
# retrieve package database
db <- tryCatch(
as.data.frame(
- utils::available.packages(type = type, repos = repos),
+ do.call(utils::available.packages, args),
stringsAsFactors = FALSE
),
error = identity
@@ -470,6 +549,14 @@ local({
}
+ 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")
@@ -477,16 +564,16 @@ local({
return(FALSE)
# prepare download options
- pat <- Sys.getenv("GITHUB_PAT")
- if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+ token <- renv_bootstrap_github_token()
+ if (nzchar(Sys.which("curl")) && nzchar(token)) {
fmt <- "--location --fail --header \"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
+ 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(pat)) {
+ } else if (nzchar(Sys.which("wget")) && nzchar(token)) {
fmt <- "--header=\"Authorization: token %s\""
- extra <- sprintf(fmt, pat)
+ 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)
--
GitLab
From b7c6faf9a0fdbf8d9bd22033a7a092cb5048f74d Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Thu, 3 Oct 2024 22:43:51 +0200
Subject: [PATCH 05/11] Draft: Resolve "Bugs in test on gitlab"
---
.Rbuildignore | 5 +-
.gitignore | 2 +
.gitlab-ci.yml | 201 +++----------------
_pkgdown.yml | 4 +
gitlab-ci/buildpackage.gitlab-ci.yml | 35 ++++
gitlab-ci/check.gitlab-ci.yml | 32 +++
gitlab-ci/codecov.gitlab-ci.yml | 32 +++
gitlab-ci/image.gitlab-ci.yml | 11 +
gitlab-ci/integration.gitlab-ci.yml | 31 +++
gitlab-ci/pkgdown.gitlab-ci.yml | 32 +++
gitlab-ci/rules.gitlab-ci.yml | 19 ++
gitlab-ci/service.gitlab-ci.yml | 10 +
gitlab-ci/testdb.gitlab-ci.yml | 25 +++
gitlab-ci/unittests.gitlab-ci.yml | 37 ++++
gitlab-ci/update_check.gitlab-ci.yml | 33 +++
pkgdown/favicon/apple-touch-icon-120x120.png | Bin 0 -> 6541 bytes
pkgdown/favicon/apple-touch-icon-152x152.png | Bin 0 -> 8870 bytes
pkgdown/favicon/apple-touch-icon-180x180.png | Bin 0 -> 11015 bytes
pkgdown/favicon/apple-touch-icon-60x60.png | Bin 0 -> 2478 bytes
pkgdown/favicon/apple-touch-icon-76x76.png | Bin 0 -> 3423 bytes
pkgdown/favicon/apple-touch-icon.png | Bin 0 -> 11015 bytes
pkgdown/favicon/favicon-16x16.png | Bin 0 -> 877 bytes
pkgdown/favicon/favicon-32x32.png | Bin 0 -> 1754 bytes
pkgdown/favicon/favicon.ico | Bin 0 -> 15086 bytes
24 files changed, 331 insertions(+), 178 deletions(-)
create mode 100644 _pkgdown.yml
create mode 100644 gitlab-ci/buildpackage.gitlab-ci.yml
create mode 100644 gitlab-ci/check.gitlab-ci.yml
create mode 100644 gitlab-ci/codecov.gitlab-ci.yml
create mode 100644 gitlab-ci/image.gitlab-ci.yml
create mode 100644 gitlab-ci/integration.gitlab-ci.yml
create mode 100644 gitlab-ci/pkgdown.gitlab-ci.yml
create mode 100644 gitlab-ci/rules.gitlab-ci.yml
create mode 100644 gitlab-ci/service.gitlab-ci.yml
create mode 100644 gitlab-ci/testdb.gitlab-ci.yml
create mode 100644 gitlab-ci/unittests.gitlab-ci.yml
create mode 100644 gitlab-ci/update_check.gitlab-ci.yml
create mode 100644 pkgdown/favicon/apple-touch-icon-120x120.png
create mode 100644 pkgdown/favicon/apple-touch-icon-152x152.png
create mode 100644 pkgdown/favicon/apple-touch-icon-180x180.png
create mode 100644 pkgdown/favicon/apple-touch-icon-60x60.png
create mode 100644 pkgdown/favicon/apple-touch-icon-76x76.png
create mode 100644 pkgdown/favicon/apple-touch-icon.png
create mode 100644 pkgdown/favicon/favicon-16x16.png
create mode 100644 pkgdown/favicon/favicon-32x32.png
create mode 100644 pkgdown/favicon/favicon.ico
diff --git a/.Rbuildignore b/.Rbuildignore
index 5258263..fb2cf7d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -29,4 +29,7 @@ tests/testhat/\~import_coe20092015\.csv
^public
^ci
^Scripts
-^cache
\ No newline at end of file
+^cache
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
diff --git a/.gitignore b/.gitignore
index 39bebef..479a553 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ stacomir.Rproj
/doc/
/Meta/
/~import_coe20092015.csv
+.dbeaver/project-settings.json
+docs
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ba5263d..0b405e5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,87 +7,53 @@
# public
# For more information, see: https://docs.gitlab.com/ee/ci/yaml/index.html#stages
-image: rocker/tidyverse
-
-services:
- - name: registry.forgemia.inra.fr/stacomi/stacomi_db/$imagedb_name:$db_version-pg$postgres_version-ps$postgis_version
- alias: host_db
-
stages: # List of stages for jobs, and their order of execution
- testdb
- build
- #- document
+ - document
- check
- test
- codecoverage
- deploy
variables:
- tag_dev: "dev"
- imagedb_name: "stacomi_db"
+ POSTGRES_PASSWORD: "postgres"
+ POSTGRES_HOSTNAME: "host_db"
+ stacomi_db_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
+ db_image_name: "stacomi_db"
db_version: "0.6.1"
postgres_version: "14"
postgis_version: "3.2"
- _R_CHECK_CRAN_INCOMING_: "false"
- _R_CHECK_FORCE_SUGGESTS_: "true"
- CODECOV_TOKEN: "CODECOV_TOKEN_STRING"
- POSTGRES_PASSWORD: postgres
- REPO_NAME: "{repo_name}"
- R_LIBS: "ci/lib"
+ db_image_tagdev: "$db_version-pg$postgres_version-ps$postgis_version"
R_LIBS_USER: "ci/lib"
RENV_PATHS_CACHE: "cache"
RENV_PATHS_LIBRARY: "renv/library"
-
+ R_LIBS: "ci/lib"
+ CHECK_DIR: "$CI_PROJECT_DIR/ci/logs"
+ BUILD_DIR: "$CI_PROJECT_DIR/ci/build"
+ BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs/$CI_PROJECT_NAME.Rcheck"
-#key for caching per branch
+#key for caching per branch
cache:
key: $CI_COMMIT_REF_SLUG
paths:
- ${RENV_PATHS_CACHE}
- ${RENV_PATHS_LIBRARY}
- ${R_LIBS_USER}
-
-
-
-test_db:
- before_script:
- - sleep 120 # waiting postgresql
- - psql --version
- - export PGPASSWORD=$POSTGRES_PASSWORD
- image: postgres:${postgres_version}
- stage: testdb
- script:
- - psql -U postgres -h host_db -c "SELECT * FROM pg_catalog.pg_tables WHERE schemaname != 'pg_catalog' AND schemaname != 'information_schema';"
- - psql -U postgres -h host_db -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat
- - export PGPASSWORD=test && psql -U test -h host_db -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat # test avec l'utilisateur iav pour vérfier les droits
-
-
-buildpackage:
- stage: build
- only:
- - main
- - master
- - 0.6.0.7
- needs: []
- script:
- - mkdir -p $R_LIBS_USER
- - mkdir -p $RENV_PATHS_CACHE
- - mkdir -p public
- - Rscript -e 'source("renv/activate.R")'
- - Rscript -e 'if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak")}'
- - Rscript -e 'pak::pkg_install(pkg = c("rcmdcheck", "renv"), upgrade = FALSE)'
- - Rscript -e 'renv::restore()'
- - r -e 'devtools::build(binary = TRUE, path="public", vignettes=TRUE, manual=TRUE)'
- - r -e 'devtools::build(binary = FALSE, path="public", vignettes=TRUE)'
- artifacts:
- when: always
- paths:
- - public
- - ${R_LIBS_USER}
+include:
+ - local: '/gitlab-ci/rules.gitlab-ci.yml'
+ - local: '/gitlab-ci/image.gitlab-ci.yml'
+ - local: '/gitlab-ci/service.gitlab-ci.yml'
+ - local: '/gitlab-ci/testdb.gitlab-ci.yml'
+ - local: '/gitlab-ci/buildpackage.gitlab-ci.yml'
+ - local: '/gitlab-ci/check.gitlab-ci.yml'
+ - local: '/gitlab-ci/update_check.gitlab-ci.yml'
+ - local: '/gitlab-ci/unittests.gitlab-ci.yml'
+ - local: '/gitlab-ci/codecov.gitlab-ci.yml'
+ - local: '/gitlab-ci/integration.gitlab-ci.yml'
+ - local: '/gitlab-ci/pkgdown.gitlab-ci.yml'
-
-
# pour lancer celui là il faudrait avoir un accès à un runner.... pour l'instant j'ai pas....
#https://guillaumebriday.fr/installer-et-utiliser-les-gitlab-runners
#https://forgemia.inra.fr/gaev/usecases/macosr
@@ -120,121 +86,6 @@ buildpackage:
# - r -e 'devtools::load_all()'
# - r -e 'devtools::document()'
-# https://cran.r-project.org/web/packages/littler/vignettes/littler-examples.html
-checkerrors:
- before_script:
- - apt-get update
- - apt-get install -y qpdf
- stage: check
- needs: ["buildpackage"]
- only:
- - main
- - master
- - 0.6.0.7
- script:
- - mkdir -p public/check
- - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
- artifacts:
- when: always
- paths:
- - public/check
- expire_in: 30 days
-
-checkerrors_update:
- before_script:
- - apt-get update
- - apt-get install -y qpdf
- stage: check
- needs: ["buildpackage"]
- only:
- - main
- - master
- - 0.6.0.7
- script:
- - mkdir -p public/check
- - Rscript -e 'renv::update()'
- - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
- artifacts:
- when: always
- paths:
- - public/check
- expire_in: 30 days
-
-# https://docs.gitlab.com/ee/ci/testing/unit_test_reports.html
-unittests:
- stage: test
- needs: ["buildpackage"]
- only:
- - main
- - master
- - 0.6.0.7
- script:
-
- - export PGPASSWORD=$POSTGRES_PASSWORD
- - echo 'PGPASSWORD=$POSTGRES_PASSWORD' >> .Renviron
- - r -e 'devtools::load_all();options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password = "postgres"); test <- capture.output(devtools::test(reporter="junit")) ; XML::saveXML(XML::xmlParse(test[grep("?xml version",test):length(test)]), file="public/test.xml")'
- - r -e 'a<-1'
- - r -e 'print(a)'
- - r -e 'devtools::test'
- artifacts:
- when: always
- # You should set the job that uploads the screenshot to
- #artifacts:when: always so that it still uploads a screenshot
- #when a test fails.
- paths:
- - public/test.xml
- reports:
- junit: public/test.xml
- expire_in: 30 days
-
-# here covr:codecov publishes the report on codecov, this function writes
-# the coverage.html in public
-codecov:
- stage: codecoverage
- needs: ["buildpackage"]
- only:
- - main
- - master
- - 0.6.0.7
- script:
- # these are for code coverage
- - Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- - r -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password = "postgres");co <- covr::package_coverage(type="all", quiet=FALSE, clean=FALSE);print(co);covr:::print.coverage(co);covr::report(co, file.path("dev/codecoverage_report", paste0("stacomiR-report.html")))'
- # the following should be used when pages is set
- - r -e 'covr::gitlab(file = "public/coverage.html", type = c("all"), quiet = FALSE)'
- #A line like Code coverage: 67.89% of lines covered would match.
- coverage: '/Coverage: \d+\.\d+/'
- artifacts:
- when: always
- paths:
- - dev/codecoverage_report/stacomiR-report.html
- expire_in: 30 days
-
-
-# adapted from
-# https://github.com/statnmap/gitlabr/blob/main/inst/gitlab-ci/check-coverage-pkgdown-renv.yml
-# https://gist.github.com/artemklevtsov/785ed0472c167246e947a75216852e10#file-gitlab-ci-yml-L15
-# ? need to create CI_JOB_TOKEN
-
-integration:
- stage: deploy
- allow_failure: true
- only:
- - main
- - master
- - 0.6.0.7
- script:
- - echo "copy package to public"
- - cp -r "$(ls -rt *_*.zip |tail -1)" public
- - cp -r "$(ls -rt *_*.tar.gz |tail -1)" public
- - mkdir -p public/check
- - cp -r check public/check
- artifacts:
- when: on_success
- paths:
- - public
- expire_in: 30 days
-
# https://about.gitlab.com/blog/2016/11/03/publish-code-coverage-report-with-gitlab-pages/
# A job that is meant to publish your code coverage report with GitLab Pages has to be placed in the separate stage.
# Stages test, build and deploy are specified by 0.6.0.7, but you can change that if needed.
@@ -257,8 +108,4 @@ integration:
# - echo "deployment with cache"
# artifacts:
# paths:
-# - public
-
-
-
-
+# - public
\ No newline at end of file
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..d71acfb
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: ~
+template:
+ bootstrap: 5
+
diff --git a/gitlab-ci/buildpackage.gitlab-ci.yml b/gitlab-ci/buildpackage.gitlab-ci.yml
new file mode 100644
index 0000000..248b5bc
--- /dev/null
+++ b/gitlab-ci/buildpackage.gitlab-ci.yml
@@ -0,0 +1,35 @@
+.buildpackage:
+ stage: build
+ needs: []
+ script:
+ - mkdir -p $R_LIBS_USER
+ - mkdir -p $RENV_PATHS_CACHE
+ - mkdir -p public
+ - Rscript -e 'source("renv/activate.R")'
+ - Rscript -e 'if(!requireNamespace("pak", quietly = TRUE)) {install.packages("pak")}'
+ - Rscript -e 'pak::pkg_install(pkg = c("rcmdcheck", "renv"), upgrade = FALSE)'
+ - Rscript -e 'renv::restore()'
+ - r -e 'devtools::build(binary = TRUE, path="public", vignettes=TRUE, manual=TRUE)'
+ - r -e 'devtools::build(binary = FALSE, path="public", vignettes=TRUE)'
+
+ artifacts:
+ when: always
+ paths:
+ - public
+ - ${R_LIBS_USER}
+
+# en dev
+buildpackage-dev:
+ extends:
+ - .rules_other
+ - .buildpackage
+ - .image-dev
+ - .service-dev
+
+# en prod
+buildpackage-prod:
+ extends:
+ - .rules_main
+ - .buildpackage
+ - .image-prod
+ - .service-prod
\ No newline at end of file
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
new file mode 100644
index 0000000..3714e3e
--- /dev/null
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -0,0 +1,32 @@
+# https://cran.r-project.org/web/packages/littler/vignettes/littler-examples.html
+.checkerrors:
+ before_script:
+ - apt-get update
+ - apt-get install -y qpdf
+ stage: check
+ script:
+ - mkdir -p public/check
+ - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
+ artifacts:
+ when: always
+ paths:
+ - public/check
+ expire_in: 30 days
+
+# en dev
+checkerrors-dev:
+ extends:
+ - .rules_other
+ - .checkerrors
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+checkerrors-prod:
+ extends:
+ - .rules_main
+ - .checkerrors
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
new file mode 100644
index 0000000..ae5def6
--- /dev/null
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -0,0 +1,32 @@
+# here covr:codecov publishes the report on codecov, this function writes
+# the coverage.html in public
+.codecov:
+ stage: codecoverage
+ script:
+ - Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
+ - Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
+ - Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password ="${POSTGRES_PASSWORD}");covr::gitlab(quiet = FALSE)'
+ coverage: '/Coverage: \d+\.\d+/'
+ artifacts:
+ when: always
+ paths:
+ - public
+ expire_in: 30 days
+
+# en dev
+codecov-dev:
+ extends:
+ - .rules_other
+ - .codecov
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+codecov-prod:
+ extends:
+ - .rules_main
+ - .codecov
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
\ No newline at end of file
diff --git a/gitlab-ci/image.gitlab-ci.yml b/gitlab-ci/image.gitlab-ci.yml
new file mode 100644
index 0000000..d483c19
--- /dev/null
+++ b/gitlab-ci/image.gitlab-ci.yml
@@ -0,0 +1,11 @@
+# to use the right docker db image
+
+#######################
+# for any branch, but main
+.image-dev:
+ image: rocker/tidyverse:latest
+
+#######################
+# for main branch only
+.image-prod:
+ image: rocker/tidyverse:latest
\ No newline at end of file
diff --git a/gitlab-ci/integration.gitlab-ci.yml b/gitlab-ci/integration.gitlab-ci.yml
new file mode 100644
index 0000000..fa38992
--- /dev/null
+++ b/gitlab-ci/integration.gitlab-ci.yml
@@ -0,0 +1,31 @@
+.integration:
+ stage: deploy
+ allow_failure: true
+ script:
+ - echo "copy package to public"
+ - cp -r "$(ls -rt *_*.tar.gz |tail -1)" public
+ - mkdir -p public/check
+ - cp -r check public/check
+ artifacts:
+ when: on_success
+ paths:
+ - public
+ expire_in: 30 days
+
+# en dev
+integration-dev:
+ extends:
+ - .rules_other
+ - .integration
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+integration-prod:
+ extends:
+ - .rules_main
+ - .integration
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
\ No newline at end of file
diff --git a/gitlab-ci/pkgdown.gitlab-ci.yml b/gitlab-ci/pkgdown.gitlab-ci.yml
new file mode 100644
index 0000000..eb6133d
--- /dev/null
+++ b/gitlab-ci/pkgdown.gitlab-ci.yml
@@ -0,0 +1,32 @@
+.pkgdown:
+ stage: document
+ allow_failure: true
+ when: on_success
+ script:
+ - mkdir -p public/documentation
+ - Rscript -e 'pak::pkg_install(pkg = c("pkgdown"), upgrade = FALSE)'
+ - Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
+ - Rscript -e 'pkgdown::build_site()'
+ - cp -r docs/* public/documentation
+ artifacts:
+ paths:
+ - public
+ expire_in: 30 days
+
+# en dev
+pkgdown-dev:
+ extends:
+ - .rules_other
+ - .pkgdown
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+pkgdown-prod:
+ extends:
+ - .rules_main
+ - .pkgdown
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
\ No newline at end of file
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
new file mode 100644
index 0000000..fe008cc
--- /dev/null
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -0,0 +1,19 @@
+# generic rules to be used for main branch or others
+
+#######################
+# for any branch, but main
+.rules_other:
+ rules:
+ - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH != "main" && $CI_COMMIT_REF_PROTECTED != "true" # only if there is changes in branch other than main
+
+#######################
+# for main banch only
+.rules_main:
+ rules:
+ - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "main" || $CI_COMMIT_REF_PROTECTED == "true" # only if there is changes in the main branch
+
+#######################
+# for shutting down the job
+.rules_shut_down:
+ rules:
+ - when: never
\ No newline at end of file
diff --git a/gitlab-ci/service.gitlab-ci.yml b/gitlab-ci/service.gitlab-ci.yml
new file mode 100644
index 0000000..9cca718
--- /dev/null
+++ b/gitlab-ci/service.gitlab-ci.yml
@@ -0,0 +1,10 @@
+.service-dev:
+ services:
+ - name: ${stacomi_db_path}/${db_image_name}:${db_image_tagdev}
+ alias: ${POSTGRES_HOSTNAME}
+
+
+.service-prod:
+ services:
+ - name: ${stacomi_db_path}/${db_image_name}:latest
+ alias: ${POSTGRES_HOSTNAME}
diff --git a/gitlab-ci/testdb.gitlab-ci.yml b/gitlab-ci/testdb.gitlab-ci.yml
new file mode 100644
index 0000000..4aa10e4
--- /dev/null
+++ b/gitlab-ci/testdb.gitlab-ci.yml
@@ -0,0 +1,25 @@
+.test_db:
+ stage: testdb
+ image: postgres:${postgres_version}
+ before_script:
+ - sleep 120 # waiting postgresql
+ - psql --version
+ - export PGPASSWORD=$POSTGRES_PASSWORD
+ - psql -U postgres -h ${POSTGRES_HOSTNAME} -c "SELECT * FROM pg_catalog.pg_tables WHERE schemaname != 'pg_catalog' AND schemaname != 'information_schema';"
+ script:
+ - psql -U postgres -h ${POSTGRES_HOSTNAME} -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat
+ - export PGPASSWORD=test && psql -U test -h ${POSTGRES_HOSTNAME} -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat # test avec l'utilisateur
+
+# en dev
+test_db-dev:
+ extends:
+ - .rules_other
+ - .test_db
+ - .service-dev
+
+# en prod
+test_db-prod:
+ extends:
+ - .rules_main
+ - .test_db
+ - .service-prod
\ No newline at end of file
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
new file mode 100644
index 0000000..8a6312a
--- /dev/null
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -0,0 +1,37 @@
+# https://docs.gitlab.com/ee/ci/testing/unit_test_reports.html
+.unittests:
+ stage: test
+ script:
+ - Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
+ - r -e "devtools::load_all();
+ options(stacomiR.dbname = 'bd_contmig_nat', stacomiR.host = '${POSTGRES_HOSTNAME}', stacomiR.port = '5432', stacomiR.user = 'postgres', stacomiR.password = '${POSTGRES_PASSWORD}');
+ test <- capture.output(devtools::test(reporter='junit')) ;
+ XML::saveXML(XML::xmlParse(test[grep('?xml version', test):length(test)]), file = 'public/test.xml')"
+ artifacts:
+ when: always
+ # You should set the job that uploads the screenshot to
+ #artifacts:when: always so that it still uploads a screenshot
+ #when a test fails.
+ paths:
+ - public/test.xml
+ reports:
+ junit: public/test.xml
+ expire_in: 30 days
+
+# en dev
+unittests-dev:
+ extends:
+ - .rules_other
+ - .unittests
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+unittests-prod:
+ extends:
+ - .rules_main
+ - .unittests
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
\ No newline at end of file
diff --git a/gitlab-ci/update_check.gitlab-ci.yml b/gitlab-ci/update_check.gitlab-ci.yml
new file mode 100644
index 0000000..2e32a75
--- /dev/null
+++ b/gitlab-ci/update_check.gitlab-ci.yml
@@ -0,0 +1,33 @@
+# https://cran.r-project.org/web/packages/littler/vignettes/littler-examples.html
+.checkerrors_update:
+ before_script:
+ - apt-get update
+ - apt-get install -y qpdf
+ stage: check
+ script:
+ - mkdir -p public/check
+ - Rscript -e 'renv::update()'
+ - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
+ artifacts:
+ when: always
+ paths:
+ - public/check
+ expire_in: 30 days
+
+# en dev
+checkerrors_update-dev:
+ extends:
+ - .rules_other
+ - .checkerrors_update
+ - .image-dev
+ - .service-dev
+ needs: ["buildpackage-dev"]
+
+# en prod
+checkerrors_update-prod:
+ extends:
+ - .rules_main
+ - .checkerrors_update
+ - .image-prod
+ - .service-prod
+ needs: ["buildpackage-prod"]
diff --git a/pkgdown/favicon/apple-touch-icon-120x120.png b/pkgdown/favicon/apple-touch-icon-120x120.png
new file mode 100644
index 0000000000000000000000000000000000000000..92e8e41c614a687a80e66433a24583ad9f37259c
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diff --git a/pkgdown/favicon/favicon.ico b/pkgdown/favicon/favicon.ico
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literal 0
HcmV?d00001
--
GitLab
From 2960a866687b606e3b836c71f604aa7b7ef10b16 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 4 Oct 2024 08:03:58 +0200
Subject: [PATCH 06/11] fix codecov
---
gitlab-ci/codecov.gitlab-ci.yml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index ae5def6..41eaed0 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -5,7 +5,7 @@
script:
- Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- - Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host ="db", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password ="${POSTGRES_PASSWORD}");covr::gitlab(quiet = FALSE)'
+ - Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host = "${POSTGRES_HOSTNAME}", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password ="${POSTGRES_PASSWORD}");covr::gitlab(quiet = FALSE)'
coverage: '/Coverage: \d+\.\d+/'
artifacts:
when: always
--
GitLab
From 5e405ed937f16eca65f3f6d74b7341c9d1d82632 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 4 Oct 2024 09:02:43 +0200
Subject: [PATCH 07/11] fix: helper for gitlab-ci
---
.gitlab-ci.yml | 3 ++-
gitlab-ci/codecov.gitlab-ci.yml | 2 +-
gitlab-ci/testdb.gitlab-ci.yml | 4 ++--
gitlab-ci/unittests.gitlab-ci.yml | 2 +-
tests/testthat/helper.R | 14 +++++++-------
5 files changed, 13 insertions(+), 12 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0b405e5..5bd68db 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,7 +17,8 @@ stages: # List of stages for jobs, and their order of execution
- deploy
variables:
- POSTGRES_PASSWORD: "postgres"
+ POSTGRES_USER: "test"
+ POSTGRES_PASSWORD: "test"
POSTGRES_HOSTNAME: "host_db"
stacomi_db_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
db_image_name: "stacomi_db"
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index 41eaed0..599977e 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -5,7 +5,7 @@
script:
- Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- - Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host = "${POSTGRES_HOSTNAME}", stacomiR.port = "5432", stacomiR.user = "postgres", stacomiR.password ="${POSTGRES_PASSWORD}");covr::gitlab(quiet = FALSE)'
+ - Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all(); options(stacomiR.dbname = "bd_contmig_nat",stacomiR.host = "${POSTGRES_HOSTNAME}", stacomiR.port = "5432", stacomiR.user = "${POSTGRES_USER}", stacomiR.password ="${POSTGRES_PASSWORD}");covr::gitlab(quiet = FALSE)'
coverage: '/Coverage: \d+\.\d+/'
artifacts:
when: always
diff --git a/gitlab-ci/testdb.gitlab-ci.yml b/gitlab-ci/testdb.gitlab-ci.yml
index 4aa10e4..d53a046 100644
--- a/gitlab-ci/testdb.gitlab-ci.yml
+++ b/gitlab-ci/testdb.gitlab-ci.yml
@@ -5,9 +5,9 @@
- sleep 120 # waiting postgresql
- psql --version
- export PGPASSWORD=$POSTGRES_PASSWORD
- - psql -U postgres -h ${POSTGRES_HOSTNAME} -c "SELECT * FROM pg_catalog.pg_tables WHERE schemaname != 'pg_catalog' AND schemaname != 'information_schema';"
+ - psql -U ${POSTGRES_USER} -h ${POSTGRES_HOSTNAME} -c "SELECT * FROM pg_catalog.pg_tables WHERE schemaname != 'pg_catalog' AND schemaname != 'information_schema';"
script:
- - psql -U postgres -h ${POSTGRES_HOSTNAME} -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat
+ - psql -U ${POSTGRES_USER} -h ${POSTGRES_HOSTNAME} -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat
- export PGPASSWORD=test && psql -U test -h ${POSTGRES_HOSTNAME} -c "select * from test.t_dispositifcomptage_dic" bd_contmig_nat # test avec l'utilisateur
# en dev
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index 8a6312a..1170a9a 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -4,7 +4,7 @@
script:
- Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
- r -e "devtools::load_all();
- options(stacomiR.dbname = 'bd_contmig_nat', stacomiR.host = '${POSTGRES_HOSTNAME}', stacomiR.port = '5432', stacomiR.user = 'postgres', stacomiR.password = '${POSTGRES_PASSWORD}');
+ options(stacomiR.dbname = 'bd_contmig_nat', stacomiR.host = '${POSTGRES_HOSTNAME}', stacomiR.port = '5432', stacomiR.user = '${POSTGRES_USER}', stacomiR.password = '${POSTGRES_PASSWORD}');
test <- capture.output(devtools::test(reporter='junit')) ;
XML::saveXML(XML::xmlParse(test[grep('?xml version', test):length(test)]), file = 'public/test.xml')"
artifacts:
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 9ba852e..f857709 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -3,13 +3,13 @@
# this file is called before testhat so funcion will be available in all test
# https://testthat.r-lib.org/articles/test-fixtures.html#withr-defer-
# could have used with_envvar and local_envvar but had to set them each time
-options(
- stacomiR.dbname = "bd_contmig_nat_test",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = "test",
- stacomiR.password = "test"
-)
+# options(
+# stacomiR.dbname = "bd_contmig_nat_test",
+# stacomiR.host ="localhost",
+# stacomiR.port = "5432",
+# stacomiR.user = "test",
+# stacomiR.password = "test"
+# )
password <- getOption("stacomiR.password") #if not set will be ""
dbname <- getOption("stacomiR.dbname") #if not set will be ""
user <- getOption("stacomiR.user")
--
GitLab
From 67feb7e83856b30a3c8eeab0f689601b75deefa3 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 4 Oct 2024 09:53:05 +0200
Subject: [PATCH 08/11] retour au user postgres
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5bd68db..10770d6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,8 +17,8 @@ stages: # List of stages for jobs, and their order of execution
- deploy
variables:
- POSTGRES_USER: "test"
- POSTGRES_PASSWORD: "test"
+ POSTGRES_USER: "postgres"
+ POSTGRES_PASSWORD: "postgres"
POSTGRES_HOSTNAME: "host_db"
stacomi_db_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
db_image_name: "stacomi_db"
--
GitLab
From af06c75973ba40fa1019ebc842925316eddbf1b3 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 4 Oct 2024 10:03:53 +0200
Subject: [PATCH 09/11] =?UTF-8?q?retour=20=C3=A0=20test?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 10770d6..5bd68db 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,8 +17,8 @@ stages: # List of stages for jobs, and their order of execution
- deploy
variables:
- POSTGRES_USER: "postgres"
- POSTGRES_PASSWORD: "postgres"
+ POSTGRES_USER: "test"
+ POSTGRES_PASSWORD: "test"
POSTGRES_HOSTNAME: "host_db"
stacomi_db_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
db_image_name: "stacomi_db"
--
GitLab
From 9dbacb5bf0cd07ad4e1d13ae56b4614be9178079 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 4 Oct 2024 10:05:56 +0200
Subject: [PATCH 10/11] =?UTF-8?q?retour=20=C3=A0=20user=20postgres?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
.gitlab-ci.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5bd68db..10770d6 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,8 +17,8 @@ stages: # List of stages for jobs, and their order of execution
- deploy
variables:
- POSTGRES_USER: "test"
- POSTGRES_PASSWORD: "test"
+ POSTGRES_USER: "postgres"
+ POSTGRES_PASSWORD: "postgres"
POSTGRES_HOSTNAME: "host_db"
stacomi_db_path: "registry.forgemia.inra.fr/stacomi/stacomi_db"
db_image_name: "stacomi_db"
--
GitLab
From 4edf10a9f3569f039ef75eebeb4e3a67a3b8c4fe Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Mon, 7 Oct 2024 11:11:10 +0200
Subject: [PATCH 11/11] Resolve "pkgdown"
---
.gitlab-ci.yml | 1 +
gitlab-ci/pkgdown.gitlab-ci.yml | 2 +-
gitlab-ci/publication.gitlab-ci.yml | 45 +++++++++++++++++++++++++++++
gitlab-ci/rules.gitlab-ci.yml | 4 +--
4 files changed, 49 insertions(+), 3 deletions(-)
create mode 100644 gitlab-ci/publication.gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 10770d6..fddc64a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,6 +54,7 @@ include:
- local: '/gitlab-ci/codecov.gitlab-ci.yml'
- local: '/gitlab-ci/integration.gitlab-ci.yml'
- local: '/gitlab-ci/pkgdown.gitlab-ci.yml'
+ - local: '/gitlab-ci/publication.gitlab-ci.yml'
# pour lancer celui là il faudrait avoir un accès à un runner.... pour l'instant j'ai pas....
#https://guillaumebriday.fr/installer-et-utiliser-les-gitlab-runners
diff --git a/gitlab-ci/pkgdown.gitlab-ci.yml b/gitlab-ci/pkgdown.gitlab-ci.yml
index eb6133d..c9c252d 100644
--- a/gitlab-ci/pkgdown.gitlab-ci.yml
+++ b/gitlab-ci/pkgdown.gitlab-ci.yml
@@ -7,7 +7,7 @@
- Rscript -e 'pak::pkg_install(pkg = c("pkgdown"), upgrade = FALSE)'
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- Rscript -e 'pkgdown::build_site()'
- - cp -r docs/* public/documentation
+ - cp -r docs/* public
artifacts:
paths:
- public
diff --git a/gitlab-ci/publication.gitlab-ci.yml b/gitlab-ci/publication.gitlab-ci.yml
new file mode 100644
index 0000000..14621dc
--- /dev/null
+++ b/gitlab-ci/publication.gitlab-ci.yml
@@ -0,0 +1,45 @@
+.publication:
+ stage: deploy
+ allow_failure: true
+ when: on_success
+ script:
+ - echo "publication"
+ artifacts:
+ paths:
+ - public
+ expire_in: 30 days
+
+# en dev
+publication-dev:
+ extends:
+ - .rules_other
+ - .publication
+ - .image-dev
+ needs: ["pkgdown-dev"]
+ environment:
+ name: $CI_COMMIT_REF_SLUG
+ url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN/-/$CI_PROJECT_NAME/-/jobs/$CI_JOB_ID/artifacts/public/index.html
+ on_stop: stop-pkgdown-dev
+
+stop-pkgdown-dev:
+ stage: deploy
+ extends:
+ - .rules_other
+ script:
+ - echo "Supprime l'environnement de test"
+ environment:
+ name: $CI_COMMIT_REF_SLUG
+ action: stop
+ when: manual
+
+# en prod
+pages:
+ extends:
+ - .rules_main
+ stage: deploy
+ script:
+ - echo "deployment"
+ artifacts:
+ paths:
+ - public
+ needs: ["pkgdown-prod"]
\ No newline at end of file
diff --git a/gitlab-ci/rules.gitlab-ci.yml b/gitlab-ci/rules.gitlab-ci.yml
index fe008cc..1294670 100644
--- a/gitlab-ci/rules.gitlab-ci.yml
+++ b/gitlab-ci/rules.gitlab-ci.yml
@@ -4,13 +4,13 @@
# for any branch, but main
.rules_other:
rules:
- - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH != "main" && $CI_COMMIT_REF_PROTECTED != "true" # only if there is changes in branch other than main
+ - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH && $CI_COMMIT_BRANCH != "main" && $CI_COMMIT_REF_PROTECTED != "true" # only if there is changes in branch other than main
#######################
# for main banch only
.rules_main:
rules:
- - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "main" || $CI_COMMIT_REF_PROTECTED == "true" # only if there is changes in the main branch
+ - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH == "main" || $CI_COMMIT_REF_PROTECTED == "true" # only if there is changes in the main branch
#######################
# for shutting down the job
--
GitLab