r-performance: fix optdepends

BioArchLinux/r-dharma/PKGBUILD

@@ -0,0 +1,53 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=DHARMa
+_pkgver=0.4.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-or-later')
+depends=(
+  r-ape
+  r-gap
+  r-lme4
+  r-lmtest
+  r-qgam
+)
+checkdepends=(
+  r-glmmadaptive
+  r-glmmtmb
+  r-mgcviz
+  r-spamm
+  r-testthat
+)
+optdepends=(
+  r-glmmadaptive
+  r-glmmtmb
+  r-knitr
+  r-mgcviz
+  r-rmarkdown
+  r-sfsmisc
+  r-spamm
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('1bc0e3ce3b7761689efc8ad828b55e5d')
+b2sums=('c344045c2adeedad2f17f318ddbbe9f8d6214368a50c97d0874f292197941f0c329ba68a18d099a7ec8160ffb294fccb7783762906692203b073bb9e76e0dbca')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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"
+}

BioArchLinux/r-dharma/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-dharma/lilac.yaml

@@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-ape
+- r-gap
+- r-lme4
+- r-lmtest
+- r-qgam
+repo_makedepends:
+- r-glmmadaptive
+- r-glmmtmb
+- r-mgcviz
+- r-spamm
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: DHARMa
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-gamm4/PKGBUILD

@@ -0,0 +1,27 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=gamm4
+_pkgver=0.2-6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Generalized Additive Mixed Models using 'mgcv' and 'lme4'"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
+depends=(
+  r-lme4
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('dff478c7c80f51c0356df39347fdf9f5')
+b2sums=('1d6ea478da815f23c9c986c8d4c3acf9c5b57eaa923e627a3bf8d1b8c07920f48fffd98aaeff5ef8b8afafa5176337f2fb42002633eb0e04b8c6eecec0dce02d')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-gamm4/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-gamm4/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-lme4
+update_on:
+- source: rpkgs
+  pkgname: gamm4
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-genepop/lilac.py

@@ -7,10 +7,7 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
 from lilac_r_utils import r_pre_build
 
 def pre_build():
-    r_pre_build(
+    r_pre_build(_G)
-        _G,
-        expect_license = "CeCILL-2",
-    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-glmmadaptive/PKGBUILD

@@ -0,0 +1,38 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=GLMMadaptive
+_pkgver=0.9-1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Generalized Linear Mixed Models using Adaptive Gaussian Quadrature"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-or-later')
+depends=(
+  r-matrixstats
+)
+optdepends=(
+  r-dharma
+  r-effects
+  r-emmeans
+  r-estimability
+  r-knitr
+  r-multcomp
+  r-optimparallel
+  r-pkgdown
+  r-rmarkdown
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5425f98c02d9ed56c6190b5c2b11dc8e')
+b2sums=('d2e8007729a569ebeb2b7d498bf4ed38076526c3a6610537ef79f28ecb32c757d31b2350b99c17bdea39a3e70276f6fa563001909464c6baa9d47fefe727d75a')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-glmmadaptive/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-glmmadaptive/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-matrixstats
+update_on:
+- source: rpkgs
+  pkgname: GLMMadaptive
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-mgcviz/PKGBUILD

@@ -0,0 +1,52 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=mgcViz
+_pkgver=0.1.11
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Visualisations for Generalized Additive Models"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-gamm4
+  r-ggally
+  r-ggplot2
+  r-gridextra
+  r-matrixstats
+  r-miniui
+  r-plyr
+  r-qgam
+  r-shiny
+  r-viridis
+)
+checkdepends=(
+  r-hexbin
+  r-testthat
+)
+optdepends=(
+  r-knitr
+  r-rgl
+  r-rmarkdown
+  r-testthat
+  r-webshot2
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8b1f6454bc0d2d2a91f638ed6a25cfa6')
+b2sums=('02c27902655eadd9be2b2b7a11b767cbf7d02baf784e4fb03d4428ee52743dd999643a1c70d491eb23dc6617a0133638244b833c3eb893aff29fd61d0e9561e1')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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"
+}

BioArchLinux/r-mgcviz/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-mgcviz/lilac.yaml

@@ -0,0 +1,24 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-gamm4
+- r-ggally
+- r-ggplot2
+- r-gridextra
+- r-matrixstats
+- r-miniui
+- r-plyr
+- r-qgam
+- r-shiny
+- r-viridis
+repo_makedepends:
+- r-hexbin
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: mgcViz
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-performance/PKGBUILD

@@ -2,10 +2,10 @@
 # Contributor: Hu Butui <hot123tea123@gmail.com>
 
 _pkgname=performance
-_pkgver=0.10.9
+_pkgver=0.11.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=0
 pkgdesc="Assessment of Regression Models Performance"
 arch=(any)
 url="https://cran.r-project.org/package=$_pkgname"
@@ -23,6 +23,7 @@ checkdepends=(
   r-bigutilsr
   r-curl
   r-dbscan
+  r-dharma
   r-estimatr
   r-fixest
   r-glmmtmb
@@ -59,6 +60,7 @@ optdepends=(
   r-correlation
   r-cplm
   r-dbscan
+  r-dharma
   r-estimatr
   r-fixest
   r-flextable
@@ -106,8 +108,8 @@ optdepends=(
   r-withr
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-md5sums=('07a07184ab81c70c92646ab990e0fd5f')
+md5sums=('003d46ccb28030be151595396c4315fd')
-b2sums=('029a8b72203e719ac7520d903f3eb510de573fd16a3efc2249a16b22dd11223f25a5e0680a4a114cd87fff4dd0e08504a4f7449e031cea683873059ac7823933')
+b2sums=('1e442ea24bcba7dd8a0a8504adc76a8686aa07e3bb25a73f161d4c2aa92aa2d965c69bde462fe2b7fb0c1ed55e5b10c10f7654dc396de75e277bbfedfe590231')
 
 prepare() {
   # skip failing tests

BioArchLinux/r-performance/lilac.yaml

@@ -14,6 +14,7 @@ repo_makedepends:
 - r-bigutilsr
 - r-curl
 - r-dbscan
+- r-dharma
 - r-estimatr
 - r-fixest
 - r-glmmtmb

BioArchLinux/r-spamm/PKGBUILD

@@ -0,0 +1,71 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=spaMM
+_pkgver=4.4.16
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Mixed-Effect Models, with or without Spatial Random Effects"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('CECILL-2.0')
+depends=(
+  gsl
+  r-backports
+  r-crayon
+  r-geometry
+  r-gmp
+  r-minqa
+  r-nloptr
+  r-numderiv
+  r-pbapply
+  r-proxy
+  r-rcpp
+  r-roi
+)
+makedepends=(
+  r-rcppeigen
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-agridat
+  r-blackbox
+  r-foreach
+  r-future
+  r-future.apply
+  r-infusion
+  r-isorix
+  r-lme4
+  r-maps
+  r-multilevel
+  r-rcdd
+  r-roi.plugin.glpk
+  r-rsae
+  r-rspectra
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "$_pkgname-LICENSE::http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt")
+md5sums=('0e525101ec9034092e125b132e38ee5c'
+         '599cf91b33571e942d3ba5f9623b8011')
+b2sums=('b0a969682e9f004e2a879a4156fe8eede308f5e16c2a7a05fd0e9cd8b46469791df8f094125fe457c75264c6a4d2f50554bddf85c5c1d4679fc7135758cb4d64'
+        'ff97dacc39b8597e670dbaf5bc0f0e4db73eada273708433fc227fa72c054a30a67dbc7b2416089d68f09ab65da721e5b30711022c41047d9cf706731d568038')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test-all.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -Dm644 "$_pkgname-LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}

BioArchLinux/r-spamm/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 = "GNU Scientific Library (GSL)",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-spamm/lilac.yaml

@@ -0,0 +1,29 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-backports
+- r-crayon
+- r-geometry
+- r-gmp
+- r-minqa
+- r-nloptr
+- r-numderiv
+- r-pbapply
+- r-proxy
+- r-rcpp
+- r-roi
+repo_makedepends:
+- r-rcppeigen
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: spaMM
+  repo: cran
+  md5: true
+- alias: r
+- source: alpmfiles
+  pkgname: gsl
+  filename: usr/lib/libgsl\.so\.([^.]+)
+  repo: extra

lilac-extensions/lilac_r_utils.py

@@ -200,6 +200,7 @@ license_map = {
     "CC BY-NC-SA 4.0": "CC-BY-NC-SA-4.0",
     "CC0": "CC0-1.0",
     "CeCILL": "CECILL-2.0",
+    "CeCILL-2": "CECILL-2.0",
     "EPL": "EPL",
     "GNU General Public License version 2": "GPL-2.0-only",
     "GPL": "GPL-2.0-or-later",