r-demuxsnp: fix depends

BioArchLinux/r-demuxsnp/PKGBUILD

@@ -1,21 +1,22 @@
 # Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
 
 _pkgname=demuxSNP
-_pkgver=1.0.0
+_pkgver=1.2.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=3
+pkgrel=0
 pkgdesc="scRNAseq demultiplexing using cell hashing and SNPs"
 arch=(any)
 url="https://bioconductor.org/packages/$_pkgname"
 license=('GPL-3.0-only')
 depends=(
   r-biocgenerics
-  r-combinat
   r-demuxmix
+  r-dplyr
   r-ensembldb
   r-genomeinfodb
   r-iranges
+  r-kernelknn
   r-matrixgenerics
   r-singlecellexperiment
   r-summarizedexperiment
@@ -40,8 +41,8 @@ optdepends=(
   r-viridislite
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-md5sums=('66a0ed302acbc18c7a106d99bf645133')
-b2sums=('eb2a41ca87b50cd53d98fa5de81ee0c75d6d356c100d5f49e1108cf6aeea73ec7aaaa090f23b92dbd0494253368e8996236a62ffa38e6612f32e09d9a63a5f21')
+md5sums=('696b03cdca6d6ff4288288ca4e8a636d')
+b2sums=('2a6ae121f0592df9f936bf6bc48a4408f9d6dae89d4448edc0c7abb517e74c9d08ec6b467bfa1288ed2abdc7d07bb12262da9c7e6fea3e27bd2472dcb8cdce84')
 
 build() {
   mkdir build

BioArchLinux/r-demuxsnp/lilac.yaml

@@ -4,11 +4,12 @@ maintainers:
   email: pekkarr@protonmail.com
 repo_depends:
 - r-biocgenerics
-- r-combinat
 - r-demuxmix
+- r-dplyr
 - r-ensembldb
 - r-genomeinfodb
 - r-iranges
+- r-kernelknn
 - r-matrixgenerics
 - r-singlecellexperiment
 - r-summarizedexperiment

BioArchLinux/r-kernelknn/PKGBUILD

@@ -0,0 +1,49 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=KernelKnn
+_pkgver=1.1.5
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Kernel k Nearest Neighbors"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('MIT')
+depends=(
+  blas
+  lapack
+  r-rcpp
+)
+makedepends=(
+  r-rcpparmadillo
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-covr
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('1f67b9a401d36132a78e36f09bbe8be2')
+b2sums=('6d7db2dde893e6c3bacea87b6bb34748b5bd01d62064bc41215186bdc02a3f61646a7cebb0845d3d92a8006b47c55addd2a732507111b7fd3d877731a2323ff4')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-kernelknn/lilac.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(
+        _G,
+        expect_systemrequirements = "libarmadillo: apt-get install -y libarmadillo-dev (deb), libblas: apt-get install -y libblas-dev (deb), liblapack: apt-get install -y liblapack-dev (deb), libarpack++2: apt-get install -y libarpack++2-dev (deb), gfortran: apt-get install -y gfortran (deb)",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-kernelknn/lilac.yaml

@@ -0,0 +1,23 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rcpp
+repo_makedepends:
+- r-rcpparmadillo
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: KernelKnn
+  repo: cran
+  md5: true
+- alias: r
+- source: alpmfiles
+  pkgname: blas
+  filename: usr/lib/libblas\.so\.([^.]+)
+  repo: extra
+- source: alpmfiles
+  pkgname: lapack
+  filename: usr/lib/liblapack\.so\.([^.]+)
+  repo: extra