add r-gpart

3 files changed, 105 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..115de887ea95
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,29 @@
+pkgbase = r-gpart
+	pkgdesc = Human genome partitioning of dense sequencing data by identifying haplotype blocks
+	pkgver = 1.13.0
+	pkgrel = 1
+	url = https://bioconductor.org/packages/gpart
+	arch = x86_64
+	license = MIT
+	makedepends = patch
+	depends = r
+	depends = r-annotationdbi
+	depends = r-biomart
+	depends = r-data.table
+	depends = r-genomicranges
+	depends = r-homo.sapiens
+	depends = r-igraph
+	depends = r-iranges
+	depends = r-organismdbi
+	depends = r-rcpp
+	depends = r-txdb.hsapiens.ucsc.hg38.knowngene
+	optdepends = r-biocstyle
+	optdepends = r-knitr
+	optdepends = r-rmarkdown
+	optdepends = r-testthat
+	source = https://bioconductor.org/packages/release/bioc/src/contrib/gpart_1.13.0.tar.gz
+	source = fix_pi.patch
+	sha256sums = 4d8b149f072e10ad1ad149bf09325871cb08d740511bcaef9b4c08aea6e42894
+	sha256sums = 033774f380e8c8edbe056b8dd2b076bcd408895a4ecaa75eb6da5e1c99caae70
+
+pkgname = r-gpart
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..e5c01bbea1bb
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,59 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+
+_pkgname=gpart
+_pkgver=1.13.0
+pkgname=r-${_pkgname,,}
+pkgver=1.13.0
+pkgrel=1
+pkgdesc='Human genome partitioning of dense sequencing data by identifying haplotype blocks'
+arch=('x86_64')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('MIT')
+depends=(
+  r
+  r-annotationdbi
+  r-biomart
+  r-data.table
+  r-genomicranges
+  r-homo.sapiens
+  r-igraph
+  r-iranges
+  r-organismdbi
+  r-rcpp
+  r-txdb.hsapiens.ucsc.hg38.knowngene
+)
+makedepends=(
+  patch
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix_pi.patch")
+sha256sums=('4d8b149f072e10ad1ad149bf09325871cb08d740511bcaef9b4c08aea6e42894'
+            '033774f380e8c8edbe056b8dd2b076bcd408895a4ecaa75eb6da5e1c99caae70')
+
+prepare() {
+  cd "${srcdir}/${_pkgname}"
+
+  # fix misspelled PI macro/variable
+  patch -Np0 -i "${srcdir}/fix_pi.patch"
+}
+
+build() {
+  # create staging directory for installation
+  mkdir -p "${srcdir}/staged"
+
+  R CMD INSTALL "${_pkgname}" -l "${srcdir}/staged"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${srcdir}/staged/${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
+}
+# vim:set ts=2 sw=2 et:
diff --git a/fix_pi.patch b/fix_pi.patch
new file mode 100644
index 000000000000..d6b55dd61a6d
--- /dev/null
+++ b/fix_pi.patch
@@ -0,0 +1,17 @@
+--- src/gpart_cpp.cpp	2021-10-26 22:24:23.000000000 +0300
++++ src/gpart_cpp.cpp	2022-01-24 15:11:39.775657833 +0300
+@@ -617,12 +617,12 @@
+     // three real roots
+     sq = sqrt(qq);
+     dxx = acos(rr / (qq * sq)) * (1.0 / 3.0);
+     sq *= -2;
+     solutions[0] = sq * cos(dxx) - adiv3;
+-    solutions[1] = sq * cos(dxx + (2.0 * PI / 3.0)) - adiv3;
+-    solutions[2] = sq * cos(dxx - (2.0 * PI / 3.0)) - adiv3;
++    solutions[1] = sq * cos(dxx + (2.0 * M_PI / 3.0)) - adiv3;
++    solutions[2] = sq * cos(dxx - (2.0 * M_PI / 3.0)) - adiv3;
+     // now sort and check for within-epsilon equality
+     if (solutions[0] > solutions[1]) {
+       dxx = solutions[0];
+       solutions[0] = solutions[1];
+       if (dxx > solutions[2]) {