From c1313913952383777d663213c10eea10fca7f26f Mon Sep 17 00:00:00 2001
From: Arya Massarat <23412689+aryarm@users.noreply.github.com>
Date: Fri, 8 Nov 2024 16:14:58 -0800
Subject: [PATCH] add r-pgenlibr recipe

---
 recipes/r-pgenlibr/bld.bat   |  2 +
 recipes/r-pgenlibr/build.sh  |  3 ++
 recipes/r-pgenlibr/meta.yaml | 90 ++++++++++++++++++++++++++++++++++++
 3 files changed, 95 insertions(+)
 create mode 100644 recipes/r-pgenlibr/bld.bat
 create mode 100644 recipes/r-pgenlibr/build.sh
 create mode 100644 recipes/r-pgenlibr/meta.yaml

diff --git a/recipes/r-pgenlibr/bld.bat b/recipes/r-pgenlibr/bld.bat
new file mode 100644
index 0000000000000..9d97015ce956c
--- /dev/null
+++ b/recipes/r-pgenlibr/bld.bat
@@ -0,0 +1,2 @@
+"%R%" CMD INSTALL --build . %R_ARGS%
+IF %ERRORLEVEL% NEQ 0 exit /B 1
diff --git a/recipes/r-pgenlibr/build.sh b/recipes/r-pgenlibr/build.sh
new file mode 100644
index 0000000000000..b8d2635525637
--- /dev/null
+++ b/recipes/r-pgenlibr/build.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-pgenlibr/meta.yaml b/recipes/r-pgenlibr/meta.yaml
new file mode 100644
index 0000000000000..9e4fe4006f498
--- /dev/null
+++ b/recipes/r-pgenlibr/meta.yaml
@@ -0,0 +1,90 @@
+{% set version = '0.3.7' %}
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-pgenlibr
+  version: {{ version|replace("-", "_") }}
+
+source:
+  url:
+    - {{ cran_mirror }}/src/contrib/pgenlibr_{{ version }}.tar.gz
+    - {{ cran_mirror }}/src/contrib/Archive/pgenlibr/pgenlibr_{{ version }}.tar.gz
+  sha256: 03928d827ef296b49819892db75eb621c009a40de88ff5ea519cd3982ca96bf1
+
+build:
+  merge_build_host: True  # [win]
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  missing_dso_whitelist:
+    - '*/R.dll'        # [win]
+    - '*/Rblas.dll'    # [win]
+    - '*/Rlapack.dll'  # [win]
+
+requirements:
+  run_exports:
+    - {{ pin_subpackage('r-pgenlibr', max_pin="x.x") }}
+  build:
+    - {{ compiler('c') }}              # [not win]
+    - {{ compiler('m2w64_c') }}        # [win]
+    - {{ compiler('cxx') }}            # [not win]
+    - {{ compiler('m2w64_cxx') }}      # [win]
+    - {{ posix }}filesystem        # [win]
+    - {{ posix }}sed               # [win]
+    - {{ posix }}grep              # [win]
+    - {{ posix }}autoconf
+    - {{ posix }}automake          # [not win]
+    - {{ posix }}automake-wrapper  # [win]
+    - {{ posix }}pkg-config
+    - {{ posix }}make
+    - {{ posix }}coreutils         # [win]
+    - {{ posix }}zip               # [win]
+    - cross-r-base {{ r_base }}    # [build_platform != target_platform]
+  host:
+    - r-base
+    - r-rcpp >=1.0.1
+  run:
+    - r-base
+    - {{ native }}gcc-libs         # [win]
+    - r-rcpp >=1.0.1
+
+test:
+  commands:
+    - $R -e "library('pgenlibr')"           # [not win]
+    - "\"%R%\" -e \"library('pgenlibr')\""  # [win]
+
+about:
+  home: https://CRAN.R-project.org/package=pgenlibr
+  license: LGPL-3
+  summary: A thin wrapper over PLINK 2's core libraries which provides an R interface for reading
+    .pgen files.  A minimal .pvar loader is also included.  Chang et al. (2015) \doi{10.1186/s13742-015-0047-8}.
+  license_family: LGPL
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3'
+
+extra:
+  recipe-maintainers:
+    - aryarm
+
+# Package: pgenlibr
+# Type: Package
+# Title: PLINK 2 Binary (.pgen) Reader
+# Version: 0.3.7
+# Date: 2024-06-03
+# Authors@R: c(person(given = "Christopher", family = "Chang", role = c("aut", "cre"), email = "chrchang@alumni.caltech.edu"), person(given = "Eric", family = "Biggers", role = c("ctb", "cph"), comment = "Author of included libdeflate library"), person(given = "Yann", family = "Collet", role = c("ctb"), comment = "Author of included Zstd library"), person(given = "Meta Platforms, Inc.", role = c("cph"), comment = "Zstd library"), person(given = "Evan", family = "Nemerson", role = c("ctb", "cph"), comment = "Author of included SIMDe library"), person(given = "Przemyslaw", family = "Skibinski", role = c("ctb"), comment = "Author of included Zstd library"), person(given = "Nick", family = "Terrell", role = c("ctb"), comment = "Author of included Zstd library"))
+# Description: A thin wrapper over PLINK 2's core libraries which provides an R interface for reading .pgen files.  A minimal .pvar loader is also included.  Chang et al. (2015) \doi{10.1186/s13742-015-0047-8}.
+# Encoding: UTF-8
+# License: LGPL (>= 3)
+# Copyright: This package includes sources of the libdeflate library owned by Eric Biggers, sources of the SIMDe library owned by Evan Nemerson, sources of the Zstd library owned by Meta Platforms, Inc., and sources of the pgenlib library owned by Christopher Chang.
+# BugReports: https://github.com/chrchang/plink-ng/issues
+# Imports: Rcpp (>= 1.0.1)
+# LinkingTo: Rcpp
+# RoxygenNote: 7.3.1
+# NeedsCompilation: yes
+# Packaged: 2024-06-03 23:04:04 UTC; chrchang
+# Author: Christopher Chang [aut, cre], Eric Biggers [ctb, cph] (Author of included libdeflate library), Yann Collet [ctb] (Author of included Zstd library), Meta Platforms, Inc. [cph] (Zstd library), Evan Nemerson [ctb, cph] (Author of included SIMDe library), Przemyslaw Skibinski [ctb] (Author of included Zstd library), Nick Terrell [ctb] (Author of included Zstd library)
+# Maintainer: Christopher Chang <chrchang@alumni.caltech.edu>
+# Repository: CRAN
+# Date/Publication: 2024-06-04 14:10:02 UTC