r-mariner: init

BioArchLinux/r-mariner/PKGBUILD

@@ -0,0 +1,77 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=mariner
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Mariner: Explore the Hi-Cs"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-abind
+  r-assertthat
+  r-biocgenerics
+  r-biocmanager
+  r-biocparallel
+  r-colourvalues
+  r-data.table
+  r-dbscan
+  r-delayedarray
+  r-genomeinfodb
+  r-genomicranges
+  r-glue
+  r-hdf5array
+  r-interactionset
+  r-iranges
+  r-magrittr
+  r-plotgardener
+  r-plyranges
+  r-progress
+  r-purrr
+  r-rcolorbrewer
+  r-rhdf5
+  r-rlang
+  r-s4vectors
+  r-strawr
+  r-summarizedexperiment
+)
+checkdepends=(
+  r-marinerdata
+  r-testthat
+)
+optdepends=(
+  r-dplyr
+  r-experimenthub
+  r-knitr
+  r-marinerdata
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-test-snapshot.patch")
+md5sums=('8e7440b7a29afb6f325512a65653b3b9'
+         'd0928c3ea11234e2200f31c9b4ff4ade')
+sha256sums=('90b4563ca30ca8658bf75321ec5940caae3612fbbfe135c4ea82cf6670bb048b'
+            'd4828f9f6fd94b8f60d8a2dd6d093fd5aa1120ccf81426cf0189ccc384d6b00c')
+
+prepare() {
+  # fix snapshot test
+  patch -Np1 -i fix-test-snapshot.patch
+}
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+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"
+}

BioArchLinux/r-mariner/fix-test-snapshot.patch

@@ -0,0 +1,67 @@
+diff --git a/mariner/tests/testthat/_snaps/InteractionArray.md b/mariner/tests/testthat/_snaps/InteractionArray.md
+index 492df25..e6645e7 100644
+--- a/mariner/tests/testthat/_snaps/InteractionArray.md
++++ b/mariner/tests/testthat/_snaps/InteractionArray.md
+@@ -3,7 +3,7 @@
+     Code
+       counts(iarr, TRUE)
+     Output
+-      <11 x 11 x 10 x 2> array of class DelayedArray and type "double":
++      <11 x 11 x 10 x 2> DelayedArray object of type "double":
+       ,,1,FS
+                14740000 14745000 14750000 ... 14785000 14790000
+       14435000        0        0        0   .        0        0
+@@ -39,7 +39,7 @@
+     Code
+       counts(iarr[1:3, 1:2])
+     Output
+-      <11 x 11 x 3 x 2> array of class DelayedArray and type "double":
++      <11 x 11 x 3 x 2> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0
+@@ -64,7 +64,7 @@
+     Code
+       counts(iarr[3:4, 1])
+     Output
+-      <11 x 11 x 2 x 1> array of class DelayedArray and type "double":
++      <11 x 11 x 2 x 1> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0
+@@ -87,7 +87,7 @@
+     Code
+       counts(iarr[1:7, 1:2])
+     Output
+-      <11 x 11 x 7 x 2> array of class DelayedArray and type "double":
++      <11 x 11 x 7 x 2> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0
+@@ -112,7 +112,7 @@
+     Code
+       counts(iarr[1:7, 1])
+     Output
+-      <11 x 11 x 7 x 1> array of class DelayedArray and type "double":
++      <11 x 11 x 7 x 1> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0
+@@ -137,7 +137,7 @@
+     Code
+       counts(iarr[1, 1:2])
+     Output
+-      <11 x 11 x 1 x 2> array of class DelayedArray and type "double":
++      <11 x 11 x 1 x 2> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0
+@@ -160,7 +160,7 @@
+     Code
+       counts(iarr[1, 1])
+     Output
+-      <11 x 11 x 1 x 1> array of class DelayedArray and type "double":
++      <11 x 11 x 1 x 1> DelayedArray object of type "double":
+       ,,1,FS
+              [,1]  [,2]  [,3] ... [,10] [,11]
+        [1,]     0     0     0   .     0     0

BioArchLinux/r-mariner/lilac.py

@@ -0,0 +1,14 @@
+#!/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)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-mariner/lilac.yaml

@@ -0,0 +1,40 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-abind
+- r-assertthat
+- r-biocgenerics
+- r-biocmanager
+- r-biocparallel
+- r-colourvalues
+- r-data.table
+- r-dbscan
+- r-delayedarray
+- r-genomeinfodb
+- r-genomicranges
+- r-glue
+- r-hdf5array
+- r-interactionset
+- r-iranges
+- r-magrittr
+- r-plotgardener
+- r-plyranges
+- r-progress
+- r-purrr
+- r-rcolorbrewer
+- r-rhdf5
+- r-rlang
+- r-s4vectors
+- r-strawr
+- r-summarizedexperiment
+repo_makedepends:
+- r-marinerdata
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: mariner
+  repo: bioc
+  md5: true
+- alias: r