chore: remove dependency for gencode file from tests

mskilab-org · Jun 14, 2023 · c81dd8f · c81dd8f
1 parent 5e4d4fe
commit c81dd8f
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Showing 5 changed files with 2 additions and 14 deletions.
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -45,12 +45,6 @@ jobs:
         run: |
           Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')"
           Rscript -e "remotes::install_github('mskilab/gGnome', upgrade = 'never')"
-          Rscript -e "remotes::install_github('mskilab/skidb', upgrade = 'never')"
-
-      - name: Setup data for tests
-        run: |
-          mkdir -p ~/DB/GENCODE
-          cp inst/extdata/test_data/gencode.v19.annotation.gtf.gr.rds ~/DB/GENCODE/gencode.v19.annotation.gtf.gr.rds
 
       - name: Test coverage
         run: covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))

diff --git a/.github/workflows/test-only.yaml b/.github/workflows/test-only.yaml
@@ -40,12 +40,6 @@ jobs:
         run: |
           Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')"
           Rscript -e "remotes::install_github('mskilab/gGnome', upgrade = 'never')"
-          Rscript -e "remotes::install_github('mskilab/skidb', upgrade = 'never')"
-
-      - name: Setup data for tests
-        run: |
-          mkdir -p ~/DB/GENCODE
-          cp inst/extdata/test_data/gencode.v19.annotation.gtf.gr.rds ~/DB/GENCODE/gencode.v19.annotation.gtf.gr.rds
 
       - name: Run tests
         run: |

diff --git a/R/gTrack.R b/R/gTrack.R
@@ -2116,7 +2116,7 @@ track.gencode = function(gencode = NULL,
     }
 
     if (is.null(gencode))
-      gencode = skidb::read_gencode()
+      gencode = readRDS(gzcon(url('http://mskilab.com/gTrack/hg19/gencode.v19.annotation.gtf.gr.rds')))
 
     if (is.character(gencode))
     {

diff --git a/inst/extdata/test_data/gencode.v19.annotation.gtf.gr.rds b/inst/extdata/test_data/gencode.v19.annotation.gtf.gr.rds
diff --git a/tests/testthat/test_gTrack.R b/tests/testthat/test_gTrack.R
@@ -69,7 +69,7 @@ create_test_data <- function() {
   )
 }
 
-options(timeout = 60)
+options(timeout = 120)
 test_data <- create_test_data()
 
 test_that("GRanges and gTrack constructors work as expected", {