fix

taxonomicallyinformedannotation · Aug 7, 2024 · 291f0a3 · 291f0a3
1 parent eb7e525
commit 291f0a3
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Showing 7 changed files with 34 additions and 10 deletions.
diff --git a/.github/workflows/deploy-app.yaml b/.github/workflows/deploy-app.yaml
@@ -41,7 +41,7 @@ jobs:
  
  - name: Install package
  run: |
- install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
+ install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://bioc.r-universe.dev", "https://cloud.r-project.org"))
  tima::install()
  shell: Rscript {0}
 

diff --git a/.github/workflows/external-use.yaml b/.github/workflows/external-use.yaml
@@ -37,7 +37,7 @@ jobs:
  Ncpus: 2
  - name: Install
  run: |
- install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
+ install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://bioc.r-universe.dev", "https://cloud.r-project.org"))
  tima::install()
  shell: Rscript {0}
  - name: Get example files

diff --git a/R/install.R b/R/install.R
@@ -70,9 +70,10 @@ install <- function(test = FALSE) {
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
+ "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  ),
- INSTALL_opts = "--no-lock"
+ INSTALL_opts = c("--no-test-load")
  )
  TRUE
  },
@@ -81,18 +82,20 @@ install <- function(test = FALSE) {
  }
  )
 
- # If URL installation fails, try installing from source
+ # If installation fails, try installing from source
  if (!success || isTRUE(test)) {
  success <- tryCatch(
  {
- message("Retrying install")
+ message("Retrying install from source")
  install.packages(
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
+ "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  ),
- INSTALL_opts = "--no-lock"
+ type = "source",
+ INSTALL_opts = c("--no-test-load")
  )
  TRUE
  },

diff --git a/README.Rmd b/README.Rmd
@@ -50,7 +50,14 @@ Optionally, you may want to add:
 As the package is not (yet) available on CRAN, you will need to install with:
 
 ``` r
-install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
+install.packages(
+ "tima",
+ repos = c(
+ "https://taxonomicallyinformedannotation.r-universe.dev",
+ "https://bioc.r-universe.dev",
+ "https://cloud.r-project.org"
+ )
+)
 ```
 
 Then, you should be able to install the rest with:

diff --git a/README.md b/README.md
@@ -58,7 +58,14 @@ As the package is not (yet) available on CRAN, you will need to install
 with:
 
 ``` r
-install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
+install.packages(
+ "tima",
+ repos = c(
+ "https://taxonomicallyinformedannotation.r-universe.dev",
+ "https://bioc.r-universe.dev",
+ "https://cloud.r-project.org"
+ )
+)
 ```
 
 Then, you should be able to install the rest with:

diff --git a/codemeta.json b/codemeta.json
@@ -618,7 +618,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3162.851KB",
+ "fileSize": "3163.193KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",

diff --git a/vignettes/tima.Rmd b/vignettes/tima.Rmd
@@ -85,7 +85,14 @@ Each step is detailed in the related [vignettes](https://taxonomicallyinformedan
 All coming steps admit you already installed `tima`:
 
 ```{r eval=FALSE, include=TRUE}
-install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
+install.packages(
+ "tima",
+ repos = c(
+ "https://taxonomicallyinformedannotation.r-universe.dev",
+ "https://bioc.r-universe.dev",
+ "https://cloud.r-project.org"
+ )
+)
 tima::install()
 tima::get_example_files()
 ```