fix

taxonomicallyinformedannotation · Aug 7, 2024 · a391bc8 · a391bc8
1 parent edb2f76
commit a391bc8
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Showing 9 changed files with 8 additions and 13 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://bioc.r-universe.dev", "https://cloud.r-project.org"))
+ install.packages("tima", repos = c("https://taxonomicallyinformedannotation.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://bioc.r-universe.dev", "https://cloud.r-project.org"))
+ install.packages("tima", repos = c("https://taxonomicallyinformedannotation.r-universe.dev", "https://cloud.r-project.org"))
  tima::install()
  shell: Rscript {0}
  - name: Get example files

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ Imports:
  fs (>= 1.6.4),
  glue (>= 1.7.0),
  gt (>= 0.11.0),
- httr2 (>= 1.0.2),
+ httr2 (>= 1.0.1),
  igraph (>= 2.0.3),
  import (>= 1.3.2),
  installr (>= 0.23.4),
@@ -51,7 +51,7 @@ Imports:
  stats,
  stringi (>= 1.8.4),
  targets (>= 1.7.1),
- tidyfst (>= 1.7.9),
+ tidyfst (>= 1.7.8),
  tidytable (>= 0.11.1),
  utils,
  visNetwork (>= 2.1.2),

diff --git a/Dockerfile b/Dockerfile
@@ -24,7 +24,7 @@ COPY --chown=tima-user:tima-user inst ./inst
 COPY --chown=tima-user:tima-user R ./R
 
 # Run R script to install dependencies
-RUN Rscript -e "install.packages('tima', repos = c('https://taxonomicallyinformedannotation.r-universe.dev', 'https://bioc.r-universe.dev', 'https://cloud.r-project.org')); tima::install()"
+RUN Rscript -e "install.packages('tima', repos = c('https://taxonomicallyinformedannotation.r-universe.dev', 'https://cloud.r-project.org')); tima::install()"
 
 # Expose the necessary ports for Shiny
 EXPOSE 3838

diff --git a/R/install.R b/R/install.R
@@ -70,7 +70,6 @@ install <- function(test = FALSE) {
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
- "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  ),
  INSTALL_opts = c("--no-test-load")
@@ -91,7 +90,6 @@ install <- function(test = FALSE) {
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
- "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  ),
  INSTALL_opts = c("--no-test-load"),

diff --git a/README.Rmd b/README.Rmd
@@ -54,7 +54,6 @@ install.packages(
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
- "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  )
 )

diff --git a/README.md b/README.md
@@ -62,7 +62,6 @@ install.packages(
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
- "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  )
 )

diff --git a/codemeta.json b/codemeta.json
@@ -245,7 +245,7 @@
  "@type": "SoftwareApplication",
  "identifier": "httr2",
  "name": "httr2",
- "version": ">= 1.0.2",
+ "version": ">= 1.0.1",
  "provider": {
  "@id": "https://cran.r-project.org",
  "@type": "Organization",
@@ -562,7 +562,7 @@
  "@type": "SoftwareApplication",
  "identifier": "tidyfst",
  "name": "tidyfst",
- "version": ">= 1.7.9",
+ "version": ">= 1.7.8",
  "provider": {
  "@id": "https://cran.r-project.org",
  "@type": "Organization",
@@ -618,7 +618,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "3162.98KB",
+ "fileSize": "3162.793KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",

diff --git a/vignettes/tima.Rmd b/vignettes/tima.Rmd
@@ -89,7 +89,6 @@ install.packages(
  "tima",
  repos = c(
  "https://taxonomicallyinformedannotation.r-universe.dev",
- "https://bioc.r-universe.dev",
  "https://cloud.r-project.org"
  )
 )