diff --git a/.github/workflows/check-bioc.yaml b/.github/workflows/check-bioc.yaml index 4ae3a6cd..334eb502 100644 --- a/.github/workflows/check-bioc.yaml +++ b/.github/workflows/check-bioc.yaml @@ -52,11 +52,12 @@ jobs: matrix: config: ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - - { os: ubuntu-latest, r: '4.4.1', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } - ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} - - { os: macOS-latest, r: '4.4.1', bioc: '3.20'} + - { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + - { os: ubuntu-devel, r: '4.6.0', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" } + ## - { os: macOS-latest, r: '4.4', bioc: '3.19'} + - { os: macOS-latest, r: '4.5.0', bioc: '3.21'} ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'} - - { os: windows-latest, r: '4.4.1', bioc: '3.20'} + - { os: windows-latest, r: '4.5.0', bioc: '3.21'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true diff --git a/R/gdsWrapper_internal.R b/R/gdsWrapper_internal.R index 0762720c..57672c9c 100644 --- a/R/gdsWrapper_internal.R +++ b/R/gdsWrapper_internal.R @@ -1095,7 +1095,7 @@ runIBDKING <- function(gds, profileID=NULL, snpID=NULL, maf=0.05, verbose) { ## Calculate IBD coefficients by KING method of moment ibd.robust <- snpgdsIBDKING(gdsobj=gds, sample.id=profileID, - snp.id=snpID, maf=maf, + snp.id=snpID, maf=maf, missing.rate=0.01, type="KING-robust", verbose=verbose) diff --git a/tests/testthat/test-gdsWrapper_internal.R b/tests/testthat/test-gdsWrapper_internal.R index 4f4ccb69..1450c352 100644 --- a/tests/testthat/test-gdsWrapper_internal.R +++ b/tests/testthat/test-gdsWrapper_internal.R @@ -132,13 +132,13 @@ test_that("runIBDKING() must return expected results", { maf=0.05, verbose=FALSE) sampleIDs <- c("NA07034", "NA07055", "NA12814") - ibs0 <- matrix(c(0.000000000000000, 0.079705823891870, 0.088194306191519, - 0.079705823891870, 0.000000000000000, 0.094035785288270, - 0.088194306191519, 0.094035785288270, 0.000000000000000), nrow=3, + ibs0 <- matrix(c(0.000000000000000, 0.079928243970500, 0.088100458441300, + 0.079928243970500, 0.000000000000000, 0.093880805262109, + 0.088100458441300, 0.093880805262109, 0.000000000000000), nrow=3, byrow=TRUE) - kinship <- matrix(c(0.500000000000000, 0.017237640936687, 0.001294777729823, - 0.017237640936687, 0.500000000000000, -0.014341590612777, - 0.001294777729823, -0.014341590612777, 0.500000000000000), nrow=3, + kinship <- matrix(c(0.500000000000000, 0.015481901439163, 0.001080847384349, + 0.015481901439163, 0.500000000000000, -0.014173571740078, + 0.001080847384349, -0.014173571740078, 0.500000000000000), nrow=3, byrow=TRUE) expect_equal(result$sample.id, sampleIDs)