diff --git a/DESCRIPTION b/DESCRIPTION index 91ed8e8..9b14196 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: easylift Title: An R package to perform genomic liftover -Version: 0.99.92 +Version: 0.99.93 Date: 2023-09-25 Authors@R: c( diff --git a/README.Rmd b/README.Rmd index 13ec605..3a5764f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -79,7 +79,7 @@ gr |> easylift("hg38") To cite package `easylift` in publications use: Al Nahid A, Love M (2023). _easylift: An R package to perform - genomic liftover_. R package version 0.99.92, + genomic liftover_. R package version 0.99.93, . @@ -90,7 +90,7 @@ A BibTeX entry for LaTeX users is title = {easylift: An R package to perform genomic liftover}, author = {Abdullah Al Nahid and Michael Love}, year = {2023}, - note = {R package version 0.99.92}, + note = {R package version 0.99.93}, url = {https://github.com/nahid18/easylift}, } ``` diff --git a/README.md b/README.md index fe25810..64de725 100644 --- a/README.md +++ b/README.md @@ -77,7 +77,7 @@ gr |> easylift("hg38") To cite package `easylift` in publications use: Al Nahid A, Love M (2023). *easylift: An R package to perform genomic -liftover*. R package version 0.99.92, +liftover*. R package version 0.99.93, . A BibTeX entry for LaTeX users is @@ -86,7 +86,7 @@ A BibTeX entry for LaTeX users is title = {easylift: An R package to perform genomic liftover}, author = {Abdullah Al Nahid and Michael Love}, year = {2023}, - note = {R package version 0.99.92}, + note = {R package version 0.99.93}, url = {https://github.com/nahid18/easylift}, } diff --git a/tests/testthat/test-easylift.R b/tests/testthat/test-easylift.R index ab0b4a6..9d56c48 100644 --- a/tests/testthat/test-easylift.R +++ b/tests/testthat/test-easylift.R @@ -30,11 +30,9 @@ test_that("easylift function tests with valid chain files", { easylift(x = gr2, to = "hg38", chain = chain_path), easylift(x = gr2, to = "hg38", chain = chain_path_gz) ) - expect_error(easylift(gr2, "hg38", BiocFileCache::BiocFileCache())) + expect_no_error(easylift(gr2, "hg38")) expect_no_error(gr2 |> easylift("hg38")) - expect_error(gr2 |> easylift("hg38", BiocFileCache::BiocFileCache())) - expect_no_error(easylift(gr2, "hg38", NULL, BiocFileCache::BiocFileCache())) expect_no_error(gr2 |> easylift("hg38", NULL, NULL)) expect_no_error(gr2 |> easylift("hg38", NULL)) }) @@ -99,6 +97,10 @@ test_that("easylift succeeds with BiocFileCache", { genome(gr) <- "hg19" + expect_error(easylift(gr, "hg38", bfc)) + expect_error(gr |> easylift("hg38", bfc)) + expect_no_error(easylift(gr, "hg38", NULL, bfc)) + # Test success when bfc is provided tryCatch({ result <- easylift(x = gr, to = "hg38", bfc = bfc)