diff --git a/.Rbuildignore b/.Rbuildignore
index 74e08d25f95aeff6cb535677b434a1b7947c1825..525826344e56d6b28ad4457aab7de0e14293be32 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 cd1bf1b6ea961cd9b5827d1b03bbe25ecbf957f5..ba5263ddfa6a460ebcd55dd85a932633803a12ff 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 53554c036ee8a2cc5fce8e772bb80431d9264797..b518bbca9b5fa3d4cdfdde71604fe0170cb679ac 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 d13f9932a16a92986a514d8cb439662d85db3add..c360bf2962d9071ffee0bcb70101316cef71074b 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)