From 383b6cc72792b7148c270742fc8cc63ce9187422 Mon Sep 17 00:00:00 2001
From: Juliette Engelaere-Lefebvre
<juliette.engelaere@developpement-durable.gouv.fr>
Date: Fri, 4 Apr 2025 19:24:57 +0200
Subject: [PATCH 1/2] =?UTF-8?q?Modifications=20op=C3=A9r=C3=A9es=20dans=20?=
=?UTF-8?q?l'espoir=20de=20relancer=20le=20d=C3=A9ploiement=20:?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
- déplacement des csv de inst vers data-raw : l'app a priori n'en a pas besoin, c'était peut être à l'origine des problemes de langue (locale) générant le message avec read.table (c'est une fonction qu'il y a derriere read.csv)
- supression de renv/, le déploiement se fait en répliquant les packages du PC de déploiement avec packrat, a priori pas besoin de renv
- ajout de la dépendance au package markdown qui est mal gérée par la fonction includeMarkdown() (c'est une dépendance optionnelle des packages qui la proposent, le problème a été identifié après un premier déploiement infructueux grâce à l'exploration des log de l'app avec `rsconnect::showLogs(appName = "nitrates", account = "ssm-ecologie"))`
- supression de la dépendance de l'app au package nitrates.pdl dans le fichier app.R, shinyApps.io cherche à la réinstaller, mais ne sait pas à partir de où alors que tout est dans le dossier de l'app
---
DESCRIPTION | 1 +
app.R | 3 ++-
.../extdata/Departement_2023.csv | 0
.../extdata/Departement_2024.csv | 0
{inst => data-raw}/extdata/ME_2023.csv | 0
{inst => data-raw}/extdata/ME_2024.csv | 0
...nees_datavisualisation_pression_azotee.ods | Bin
.../extdata/NSA_973_20241205_SANDRE.csv | 0
{inst => data-raw}/extdata/SAGE_2023.csv | 0
{inst => data-raw}/extdata/SAGE_2024.csv | 0
renv/settings.json | 21 ------------------
11 files changed, 3 insertions(+), 22 deletions(-)
rename {inst => data-raw}/extdata/Departement_2023.csv (100%)
rename {inst => data-raw}/extdata/Departement_2024.csv (100%)
rename {inst => data-raw}/extdata/ME_2023.csv (100%)
rename {inst => data-raw}/extdata/ME_2024.csv (100%)
rename {inst => data-raw}/extdata/Metadonnees_datavisualisation_pression_azotee.ods (100%)
rename {inst => data-raw}/extdata/NSA_973_20241205_SANDRE.csv (100%)
rename {inst => data-raw}/extdata/SAGE_2023.csv (100%)
rename {inst => data-raw}/extdata/SAGE_2024.csv (100%)
delete mode 100644 renv/settings.json
diff --git a/DESCRIPTION b/DESCRIPTION
index 4e01ae6..1239d0c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -22,6 +22,7 @@ Imports:
leaflet,
leaflet.extras,
magrittr,
+ markdown,
pkgload,
purrr,
sf,
diff --git a/app.R b/app.R
index 2a37cb8..3bc04f1 100644
--- a/app.R
+++ b/app.R
@@ -3,6 +3,7 @@
# Or use the blue button on top of this file
pkgload::load_all(export_all = FALSE,helpers = FALSE,attach_testthat = FALSE)
+library(markdown)
options( "golem.app.prod" = TRUE)
-nitrates.pdl::run_app() # add parameters here (if any)
+run_app() # add parameters here (if any)
#
diff --git a/inst/extdata/Departement_2023.csv b/data-raw/extdata/Departement_2023.csv
similarity index 100%
rename from inst/extdata/Departement_2023.csv
rename to data-raw/extdata/Departement_2023.csv
diff --git a/inst/extdata/Departement_2024.csv b/data-raw/extdata/Departement_2024.csv
similarity index 100%
rename from inst/extdata/Departement_2024.csv
rename to data-raw/extdata/Departement_2024.csv
diff --git a/inst/extdata/ME_2023.csv b/data-raw/extdata/ME_2023.csv
similarity index 100%
rename from inst/extdata/ME_2023.csv
rename to data-raw/extdata/ME_2023.csv
diff --git a/inst/extdata/ME_2024.csv b/data-raw/extdata/ME_2024.csv
similarity index 100%
rename from inst/extdata/ME_2024.csv
rename to data-raw/extdata/ME_2024.csv
diff --git a/inst/extdata/Metadonnees_datavisualisation_pression_azotee.ods b/data-raw/extdata/Metadonnees_datavisualisation_pression_azotee.ods
similarity index 100%
rename from inst/extdata/Metadonnees_datavisualisation_pression_azotee.ods
rename to data-raw/extdata/Metadonnees_datavisualisation_pression_azotee.ods
diff --git a/inst/extdata/NSA_973_20241205_SANDRE.csv b/data-raw/extdata/NSA_973_20241205_SANDRE.csv
similarity index 100%
rename from inst/extdata/NSA_973_20241205_SANDRE.csv
rename to data-raw/extdata/NSA_973_20241205_SANDRE.csv
diff --git a/inst/extdata/SAGE_2023.csv b/data-raw/extdata/SAGE_2023.csv
similarity index 100%
rename from inst/extdata/SAGE_2023.csv
rename to data-raw/extdata/SAGE_2023.csv
diff --git a/inst/extdata/SAGE_2024.csv b/data-raw/extdata/SAGE_2024.csv
similarity index 100%
rename from inst/extdata/SAGE_2024.csv
rename to data-raw/extdata/SAGE_2024.csv
diff --git a/renv/settings.json b/renv/settings.json
deleted file mode 100644
index 0ecea91..0000000
--- a/renv/settings.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
- "bioconductor.version": null,
- "external.libraries": [],
- "ignored.packages": [
- "nitrates.pdl"
- ],
- "package.dependency.fields": [
- "Imports",
- "Depends",
- "LinkingTo"
- ],
- "ppm.enabled": null,
- "ppm.ignored.urls": [],
- "r.version": null,
- "snapshot.type": "implicit",
- "use.cache": true,
- "vcs.ignore.cellar": true,
- "vcs.ignore.library": true,
- "vcs.ignore.local": true,
- "vcs.manage.ignores": true
-}
--
GitLab
From 0e4af56a3c15ce9f30f18d8d8645a050b285b9de Mon Sep 17 00:00:00 2001
From: Franck Gaspard <franck.gaspard@developpement-durable.gouv.fr>
Date: Mon, 14 Apr 2025 16:27:26 +0200
Subject: [PATCH 2/2] =?UTF-8?q?modification=20de=20prepa=5Fpression=5Fazot?=
=?UTF-8?q?ee.R=20pour=20prendre=20en=20compte=20le=20fait=20que=20les=20.?=
=?UTF-8?q?csv=20ont=20=C3=A9t=C3=A9=20d=C3=A9plac=C3=A9=20de=20inst/extda?=
=?UTF-8?q?ta=20=C3=A0=20data-raw/exdatdata?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
ajout des package markdown et pkgload dans DESCRIPTION du fait de leur nécessité pour le déploiement de l'application
0 errors ✔ | 0 warnings ✔ | 3 notes ✖
── R CMD check results ─────────────────────── nitrates.pdl 0.0.0.9000 ────
Duration: 3m 8.9s
⯠checking installed package size ... NOTE
installed size is 14.6Mb
sub-directories of 1Mb or more:
app 3.4Mb
data 10.8Mb
⯠checking for future file timestamps ... NOTE
unable to verify current time
⯠checking dependencies in R code ... NOTE
Espaces de noms dans le champ Imports non importés depuis :
'markdown' 'pkgload'
All declared Imports should be used.
R CMD check succeeded
---
data-raw/prepa_pression_azotee.R | 6 +++---
data/departement_pa_telecharger.rda | Bin 940 -> 942 bytes
dev/02_dev.R | 2 ++
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/data-raw/prepa_pression_azotee.R b/data-raw/prepa_pression_azotee.R
index 0044db7..5e4201f 100644
--- a/data-raw/prepa_pression_azotee.R
+++ b/data-raw/prepa_pression_azotee.R
@@ -26,21 +26,21 @@ rm(list=ls())
# importation des données de la DRAAF 2024 --------
-Departement_2024 <- utils::read.csv2("inst/extdata/Departement_2024.csv")
+Departement_2024 <- utils::read.csv2("data-raw/extdata/Departement_2024.csv")
# names(Departement_2024)
# [1] "ANNEE_DECLARATION" "DEPARTEMENT" "Code" "SAU_recensee"
# [5] "QTE_ORG_MIN" "QTE_N_MIN_EPAN" "ORG_EPAN_THEORIQ" "QTE_N_ORG_NON_MAITRI"
# [9] "nb_occurences" "pression_azote_globale" "pression_azote_mineral" "pression_azote_orga"
# [13] "pression_azote_orga_non_maitri"
-ME_2024 <- utils::read.csv2("inst/extdata/ME_2024.csv")
+ME_2024 <- utils::read.csv2("data-raw/extdata/ME_2024.csv")
# names(ME_2024)
# [1] "ANNEE_DECLARATION" "CODE_ME" "Nom" "SAU_recensee"
# [5] "QTE_ORG_MIN" "QTE_N_MIN_EPAN" "ORG_EPAN_THEORIQ" "QTE_N_ORG_NON_MAITRI"
# [9] "Comptage" "pression_azote_globale" "pression_azote_mineral" "pression_azote_orga"
# [13] "pression_azote_orga_non_maitri"
-SAGE_2024 <- utils::read.csv2("inst/extdata/SAGE_2024.csv") %>%
+SAGE_2024 <- utils::read.csv2("data-raw/extdata/SAGE_2024.csv") %>%
dplyr::mutate(Code = as.character(Code))
# names(SAGE_2024)
# [1] "ANNEE_DECLARATION" "nom" "Code" "SAU_recensee"
diff --git a/data/departement_pa_telecharger.rda b/data/departement_pa_telecharger.rda
index 2e2b74365d7017994e21c08c5231ae909a0e12e3..c1a0f910bc9382ebb1b515d834beb9d11b4a2e56 100644
GIT binary patch
delta 919
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diff --git a/dev/02_dev.R b/dev/02_dev.R
index 0cf6fa0..758d091 100644
--- a/dev/02_dev.R
+++ b/dev/02_dev.R
@@ -17,6 +17,8 @@
## Amend DESCRIPTION with dependencies read from package code parsing
## install.packages('attachment') # if needed.
attachment::att_amend_desc()
+usethis::use_package("markdown")
+usethis::use_package("pkgload")
## Add modules ----
## Create a module infrastructure in R/
--
GitLab