Prepare for CRAN release

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+    paths:
+      - 'R-package/**'
+      - '.github/workflows/R-CMD-check.yaml'
+  pull_request:
+    branches: [main, master]
+    paths:
+      - 'R-package/**'
+      - '.github/workflows/R-CMD-check.yaml'
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+          working-directory: R-package
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          args: 'c("--as-cran", "--no-manual")'
+          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
+          working-directory: R-package

.gitignore

@@ -26,13 +26,6 @@ venv/
 *.asv
 octave-workspace
 
-# Generated R package extdata copied from canonical tests/fixtures sources
-/R-package/inst/extdata/*.bim
-/R-package/inst/extdata/*.bed
-/R-package/inst/extdata/*.fam
-/R-package/inst/extdata/*.ploidy
-/R-package/inst/extdata/*.tsv.gz
-
 # Claude Code
 .claude/
 

R-package/.Rbuildignore

@@ -0,0 +1,3 @@
+^cran-comments\.md$
+^revdep$
+^LICENSE\.md$

R-package/DESCRIPTION

@@ -2,12 +2,11 @@ Package: statgen
 Type: Package
 Title: Statistical Genetics Data Objects and Loaders
 Version: 0.3.0
-Authors@R: person("Oleksandr", "Frei", role = c("aut", "cre"),
+Authors@R: person("Oleksandr", "Frei", role = c("aut", "cre", "cph"),
     email = "oleksandr.frei@gmail.com")
-Author: Oleksandr Frei [aut, cre]
-Maintainer: Oleksandr Frei <oleksandr.frei@gmail.com>
-Description: CRAN-compatible R runtime for statgen statistical genetics
-    reference, genotype, LD, annotation, and summary-statistic objects.
+Description: Loads and manages statistical genetics data objects including reference
+    panels, genotypes, LD matrices, annotations, and summary statistics. Implements the
+    language-agnostic statgen specifications for coordinated multi-runtime analysis.
 License: MIT + file LICENSE
 URL: https://github.com/precimed/statgen
 BugReports: https://github.com/precimed/statgen/issues

R-package/LICENSE.md

@@ -0,0 +1,9 @@
+# MIT License
+
+Copyright (c) 2026 Oleksandr Frei and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

R-package/NEWS.md

@@ -0,0 +1,3 @@
+# statgen 0.3.0
+
+* Initial CRAN submission.

R-package/R/annotations.R

@@ -334,39 +334,48 @@ print.AnnotationPanel <- function(x, ...) {
 }
 
 .parse_bed <- function(path) {
+  # First pass: scan line-by-line to validate structure and count header lines to
+  # skip. Avoids seek(), which R documents as unreliable on Windows text connections.
   con <- file(path, open = "rt")
   on.exit(close(con), add = TRUE)
+
+  skip_count <- 0L
   first_data <- NULL
-  first_pos <- 0
+  found_data <- FALSE
+
   repeat {
-    pos <- seek(con, where = NA)
     line <- readLines(con, n = 1L, warn = FALSE)
     if (!length(line)) {
-      stop(sprintf("%s: BED file is empty", path), call. = FALSE)
-    }
-    if (!identical(line, "") && !startsWith(line, "#")) {
-      first_data <- line
-      first_pos <- pos
+      if (!found_data) {
+        stop(sprintf("%s: BED file is empty", path), call. = FALSE)
+      }
       break
     }
+    if (!found_data) {
+      if (identical(line, "") || startsWith(line, "#")) {
+        skip_count <- skip_count + 1L
+      } else {
+        first_data <- line
+        found_data <- TRUE
+      }
+    } else {
+      if (identical(line, "") || startsWith(line, "#")) {
+        stop(sprintf("%s: blank or comment line after BED data row", path), call. = FALSE)
+      }
+    }
   }
+  close(con)
+  on.exit(NULL)
+
   if (length(strsplit(first_data, "\t", fixed = TRUE)[[1L]]) < 3L) {
     stop(sprintf("%s: BED must have at least 3 tab-separated columns", path), call. = FALSE)
   }
-  seek(con, where = first_pos)
-  repeat {
-    line <- readLines(con, n = 1L, warn = FALSE)
-    if (!length(line)) {
-      break
-    }
-    if (identical(line, "") || startsWith(line, "#")) {
-      stop(sprintf("%s: blank or comment line after BED data row", path), call. = FALSE)
-    }
-  }
-  seek(con, where = first_pos)
+
+  # Second pass: read.table opens the file fresh, no seek() needed.
   df <- tryCatch(
     utils::read.table(
-      file = con,
+      file = path,
+      skip = skip_count,
       header = FALSE,
       sep = "\t",
       quote = "",

R-package/README.md

@@ -0,0 +1,30 @@
+# statgen R Package
+
+Statistical genetics data objects and loaders for R. This package is part of the larger `statgen` repository, which also includes Python and MATLAB/Octave implementations.
+
+## Installation
+
+### From GitHub (development)
+
+```r
+# Install devtools if needed
+if (!require("devtools")) install.packages("devtools")
+
+# Install from the R-package directory
+devtools::install()
+
+# Or from the repository root
+devtools::install("R-package")
+```
+
+### From CRAN (release)
+
+```r
+install.packages("statgen")
+```
+
+## Documentation
+
+- [Main statgen repository](https://github.com/precimed/statgen)
+- Package vignette: `vignette("statgen")`
+

R-package/cran-comments.md

@@ -0,0 +1,9 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.
+
+* NOTE: "Possibly misspelled words in DESCRIPTION: LD, statgen"
+  Both are intentional: 'LD' is a standard abbreviation for Linkage Disequilibrium
+  in statistical genetics; 'statgen' is the name of this package and software suite.

R-package/inst/extdata/anno1.bed

@@ -0,0 +1,5 @@
+1	99	150
+1	120	200
+1	299	350
+1	350	400
+1	499	500

R-package/inst/extdata/anno2.bed

@@ -0,0 +1,3 @@
+X	99	100
+X	195	205
+X	198	302

R-package/inst/extdata/genotype_1.bim

@@ -0,0 +1,5 @@
+1	rs1001	0	100	A	G
+1	rs1002	0	200	C	T
+1	rs1003	0	300	A	C
+1	rs1004	0	400	G	A
+1	rs1005	0	500	T	C

R-package/inst/extdata/genotype_1.fam

@@ -0,0 +1,4 @@
+FAM1	IND1	0	0	1	-9
+FAM1	IND2	0	0	2	-9
+FAM2	IND3	0	0	1	-9
+FAM2	IND4	0	0	2	-9

R-package/inst/extdata/genotype_X.bim

@@ -0,0 +1,3 @@
+X	rsX001	0	100	A	G
+X	rsX002	0	200	C	T
+X	rsX003	0	300	A	C

R-package/inst/extdata/genotype_X.fam

@@ -0,0 +1,4 @@
+FAM1	IND1	0	0	1	-9
+FAM1	IND2	0	0	2	-9
+FAM2	IND3	0	0	1	-9
+FAM2	IND4	0	0	2	-9

R-package/inst/extdata/genotype_X.ploidy

@@ -0,0 +1,3 @@
+1	2
+1	2
+1	2

R-package/inst/extdata/reference_chr1.bim

@@ -0,0 +1,5 @@
+1	rs1001	0	100	A	G
+1	rs1002	0	200	C	T
+1	rs1003	0	300	A	C
+1	rs1004	0	400	G	A
+1	rs1005	0	500	T	C

R-package/inst/extdata/reference_chrX.bim

@@ -0,0 +1,3 @@
+X	rsX001	0	100	A	G
+X	rsX002	0	200	C	T
+X	rsX003	0	300	A	C

R-package/man/ld.Rd

@@ -68,4 +68,23 @@ a vector or matrix with the same shape as \code{M}, and \code{fast_prune()}
 returns a numeric vector or one-dimensional matrix with pruned entries set to
 \code{NaN}.
 }
+\examples{
+ld_src <- system.file("extdata", "ld", "python", package = "statgen")
+if (nzchar(ld_src)) {
+  ld_root <- tempfile("ld_npz_")
+  dir.create(ld_root)
+  file.copy(list.files(ld_src, full.names = TRUE), ld_root, recursive = TRUE)
+
+  prepare_ld_npz_for_r(ld_root)
+  ld <- load_ld(ld_root)
+
+  num_snp(ld)
+  head(a1freq(ld))
+
+  scores <- seq_len(num_snp(ld))
+  multiply_r2(ld, scores)
+
+  fast_prune(c(9, 9, 7, 1, 2, 6, 5, 4), ld, r2_threshold = 0.35)
+}
+}
 \keyword{datasets}