From d3e04aa1f7e0a5eda20559b0ba6ecea50da37e83 Mon Sep 17 00:00:00 2001 From: Karl Broman Date: Mon, 15 Jul 2024 09:24:20 -0500 Subject: [PATCH 1/4] Fixed link in genoprob_to_alleleprob_fst Rd file - Problem that showed up on CRAN --- DESCRIPTION | 6 +++--- NEWS.md | 7 +++++++ R/genoprob_to_alleleprob_fst.R | 4 ++-- man/genoprob_to_alleleprob_fst.Rd | 4 ++-- 4 files changed, 14 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5f678fb..6f2d2a4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: qtl2fst -Version: 0.26 -Date: 2021-10-07 +Version: 0.27-1 +Date: 2024-07-15 Title: Database Storage of Genotype Probabilities for QTL Mapping Description: Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time. Author: Karl W Broman [aut, cre] (), @@ -26,5 +26,5 @@ License: GPL-3 URL: https://github.com/rqtl/qtl2fst ByteCompile: true Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.3.2 Roxygen: list(markdown=TRUE) diff --git a/NEWS.md b/NEWS.md index 12fd9b4..a0157e9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +## qtl2fst 0.27-1 (2024-07-15) + +### Minor changes + +- Fixed link in documention. + + ## qtl2fst 0.26 (2021-10-07) ### Minor changes diff --git a/R/genoprob_to_alleleprob_fst.R b/R/genoprob_to_alleleprob_fst.R index 6382efe..36428bf 100644 --- a/R/genoprob_to_alleleprob_fst.R +++ b/R/genoprob_to_alleleprob_fst.R @@ -2,10 +2,10 @@ #' Convert genotype probabilities to allele probabilities and write to fst database #' #' Reduce genotype probabilities (as calculated by -#' [calc_genoprob()]) to allele probabilities, writing them to an fst database. +#' [qtl2::calc_genoprob()]) to allele probabilities, writing them to an fst database. #' #' @param probs Genotype probabilities, as calculated from -#' [calc_genoprob()]. +#' [qtl2::calc_genoprob()]. #' @param fbase Base of filename for fst database. #' @param fdir Directory for fst database. #' @param quiet IF `FALSE`, print progress messages. diff --git a/man/genoprob_to_alleleprob_fst.Rd b/man/genoprob_to_alleleprob_fst.Rd index 44a6117..df35775 100644 --- a/man/genoprob_to_alleleprob_fst.Rd +++ b/man/genoprob_to_alleleprob_fst.Rd @@ -16,7 +16,7 @@ genoprob_to_alleleprob_fst( } \arguments{ \item{probs}{Genotype probabilities, as calculated from -\code{\link[=calc_genoprob]{calc_genoprob()}}.} +\code{\link[qtl2:calc_genoprob]{qtl2::calc_genoprob()}}.} \item{fbase}{Base of filename for fst database.} @@ -39,7 +39,7 @@ collapsed to alleles rather than genotypes. } \description{ Reduce genotype probabilities (as calculated by -\code{\link[=calc_genoprob]{calc_genoprob()}}) to allele probabilities, writing them to an fst database. +\code{\link[qtl2:calc_genoprob]{qtl2::calc_genoprob()}}) to allele probabilities, writing them to an fst database. } \details{ This is like calling \code{qtl2::genoprob_to_alleleprob()} and then From fc7dcd371a7ac1128d4a05ed5b618120e6d0a47e Mon Sep 17 00:00:00 2001 From: Karl Broman Date: Mon, 15 Jul 2024 14:38:09 -0500 Subject: [PATCH 2/4] Add cran branch to github workflows --- .github/workflows/R-CMD-check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..447b6fb 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master] + branches: [main, master, cran] pull_request: - branches: [main, master] + branches: [main, master, cran] name: R-CMD-check From 1a0c9d0c5f331b8205a1dfa97a428b83517e4dcc Mon Sep 17 00:00:00 2001 From: Karl Broman Date: Mon, 15 Jul 2024 14:46:40 -0500 Subject: [PATCH 3/4] Fix typos in NEWS.md --- NEWS.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/NEWS.md b/NEWS.md index a0157e9..e8417ea 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ### Minor changes -- Fixed link in documention. +- Fixed link in documentation. ## qtl2fst 0.26 (2021-10-07) @@ -47,11 +47,11 @@ - Added `calc_genoprob_fst()` which combines `calc_genoprob()` and `fst_genoprob()` to save use of RAM when calculating genotype - probabilties. + probabilities. - Added `genoprob_to_alleleprob_fst()` which combines `genoprob_to_alleleprob()` and `fst_genoprob()` to save use of RAM - when converting genotype probabilties to allele dosages. + when converting genotype probabilities to allele dosages. - Added `summary()` and `print()` functions for `"fst_genoprob"` objects. From 486b87d74594b5891c270906a6620d2b93ce4266 Mon Sep 17 00:00:00 2001 From: Karl Broman Date: Tue, 16 Jul 2024 10:20:29 -0500 Subject: [PATCH 4/4] Bump version for CRAN --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6f2d2a4..11406b2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: qtl2fst -Version: 0.27-1 -Date: 2024-07-15 +Version: 0.28 +Date: 2024-07-16 Title: Database Storage of Genotype Probabilities for QTL Mapping Description: Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time. Author: Karl W Broman [aut, cre] (), diff --git a/NEWS.md b/NEWS.md index e8417ea..5de70bf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -## qtl2fst 0.27-1 (2024-07-15) +## qtl2fst 0.28 (2024-07-16) ### Minor changes