From 2cd6f282e4af791f62b26b5321c8054157abea2f Mon Sep 17 00:00:00 2001 From: Pekka Ristola Date: Mon, 8 Apr 2024 20:42:52 +0300 Subject: [PATCH] r-*: use metadata checks for several packages --- BioArchLinux/r-adehabitatma/PKGBUILD | 23 ++++++++++---------- BioArchLinux/r-adehabitatma/lilac.py | 11 +++++----- BioArchLinux/r-adehabitatma/lilac.yaml | 7 +++--- BioArchLinux/r-affyio/PKGBUILD | 23 ++++++++++---------- BioArchLinux/r-affyio/lilac.py | 11 +++++----- BioArchLinux/r-affyio/lilac.yaml | 12 +++++++--- BioArchLinux/r-akima/PKGBUILD | 29 ++++++++++++------------- BioArchLinux/r-akima/lilac.py | 14 +++++++----- BioArchLinux/r-akima/lilac.yaml | 7 +++--- BioArchLinux/r-attempt/PKGBUILD | 24 ++++++++++---------- BioArchLinux/r-attempt/lilac.py | 11 +++++----- BioArchLinux/r-attempt/lilac.yaml | 7 +++--- BioArchLinux/r-coro/PKGBUILD | 22 ++++++++++--------- BioArchLinux/r-coro/lilac.py | 15 ++++++++----- BioArchLinux/r-coro/lilac.yaml | 17 +++++++-------- BioArchLinux/r-diffobj/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-diffobj/lilac.py | 11 +++++----- BioArchLinux/r-diffobj/lilac.yaml | 7 +++--- BioArchLinux/r-genarise/PKGBUILD | 26 ++++++++++++---------- BioArchLinux/r-genarise/lilac.py | 14 +++++++----- BioArchLinux/r-genarise/lilac.yaml | 7 +++--- BioArchLinux/r-grimport/PKGBUILD | 28 ++++++++++-------------- BioArchLinux/r-grimport/lilac.py | 14 +++++++----- BioArchLinux/r-grimport/lilac.yaml | 7 +++--- BioArchLinux/r-htmlutils/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-htmlutils/lilac.py | 11 +++++----- BioArchLinux/r-htmlutils/lilac.yaml | 7 +++--- BioArchLinux/r-irr/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-irr/lilac.py | 11 +++++----- BioArchLinux/r-irr/lilac.yaml | 7 +++--- BioArchLinux/r-pepxmltab/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-pepxmltab/lilac.py | 11 +++++----- BioArchLinux/r-pepxmltab/lilac.yaml | 7 +++--- BioArchLinux/r-polycor/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-polycor/lilac.py | 15 ++++++++----- BioArchLinux/r-polycor/lilac.yaml | 20 ++++++++--------- BioArchLinux/r-prabclus/PKGBUILD | 23 ++++++++++---------- BioArchLinux/r-prabclus/lilac.py | 11 +++++----- BioArchLinux/r-prabclus/lilac.yaml | 7 +++--- BioArchLinux/r-rbiopaxparser/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-rbiopaxparser/lilac.py | 11 +++++----- BioArchLinux/r-rbiopaxparser/lilac.yaml | 7 +++--- BioArchLinux/r-rhtslib/PKGBUILD | 29 ++++++++++++------------- BioArchLinux/r-rhtslib/lilac.py | 14 +++++++----- BioArchLinux/r-rhtslib/lilac.yaml | 27 ++++++++++++++++++++--- BioArchLinux/r-sampling/PKGBUILD | 21 +++++++++--------- BioArchLinux/r-sampling/lilac.py | 11 +++++----- BioArchLinux/r-sampling/lilac.yaml | 11 +++++----- BioArchLinux/r-semisup/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-semisup/lilac.py | 11 +++++----- BioArchLinux/r-semisup/lilac.yaml | 7 +++--- BioArchLinux/r-seqtools/PKGBUILD | 23 ++++++++++---------- BioArchLinux/r-seqtools/lilac.py | 11 +++++----- BioArchLinux/r-seqtools/lilac.yaml | 12 +++++++--- BioArchLinux/r-snowfall/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-snowfall/lilac.py | 11 +++++----- BioArchLinux/r-snowfall/lilac.yaml | 7 +++--- BioArchLinux/r-snpstats/PKGBUILD | 23 ++++++++++---------- BioArchLinux/r-snpstats/lilac.py | 11 +++++----- BioArchLinux/r-snpstats/lilac.yaml | 12 +++++++--- BioArchLinux/r-sparsepca/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-sparsepca/lilac.py | 11 +++++----- BioArchLinux/r-sparsepca/lilac.yaml | 7 +++--- BioArchLinux/r-splancs/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-splancs/lilac.py | 11 +++++----- BioArchLinux/r-splancs/lilac.yaml | 7 +++--- BioArchLinux/r-venn/PKGBUILD | 22 +++++++++---------- BioArchLinux/r-venn/lilac.py | 11 +++++----- BioArchLinux/r-venn/lilac.yaml | 7 +++--- 69 files changed, 564 insertions(+), 468 deletions(-) diff --git a/BioArchLinux/r-adehabitatma/PKGBUILD b/BioArchLinux/r-adehabitatma/PKGBUILD index a2025c765e..0ae96cd4af 100644 --- a/BioArchLinux/r-adehabitatma/PKGBUILD +++ b/BioArchLinux/r-adehabitatma/PKGBUILD @@ -3,29 +3,28 @@ _pkgname=adehabitatMA _pkgver=0.3.16 pkgname=r-${_pkgname,,} -pkgver=0.3.16 +pkgver=${_pkgver//-/.} pkgrel=4 -pkgdesc='Tools to Deal with Raster Maps' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Tools to Deal with Raster Maps" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-sp ) optdepends=( - r-mass r-tkrplot ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('089e415a26b6c45023d04ef64c9cf6d336a233f0b0078fc72adbe601b389b5ca') +md5sums=('8c4f737241fa734be5603a940ae86270') +b2sums=('4bd7a3583331aed034ebab62c2e39ae73cdc5e44e135001f47b23fc50908ce6c4cc5191fd9aa006b4bfa61f65a3f8663c175399b94fe9907af40317eb2594d54') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-adehabitatma/lilac.py b/BioArchLinux/r-adehabitatma/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-adehabitatma/lilac.py +++ b/BioArchLinux/r-adehabitatma/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-adehabitatma/lilac.yaml b/BioArchLinux/r-adehabitatma/lilac.yaml index 07a3077aed..9e60dcf0a0 100644 --- a/BioArchLinux/r-adehabitatma/lilac.yaml +++ b/BioArchLinux/r-adehabitatma/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-sp update_on: -- regex: adehabitatMA_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=adehabitatMA +- source: rpkgs + pkgname: adehabitatMA + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-affyio/PKGBUILD b/BioArchLinux/r-affyio/PKGBUILD index 1f7db51322..5d0f05362d 100644 --- a/BioArchLinux/r-affyio/PKGBUILD +++ b/BioArchLinux/r-affyio/PKGBUILD @@ -3,25 +3,26 @@ _pkgname=affyio _pkgver=1.72.0 pkgname=r-${_pkgname,,} -pkgver=1.72.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Tools for parsing Affymetrix data files' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') +pkgdesc="Tools for parsing Affymetrix data files" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('LGPL-2.0-or-later') depends=( - r r-zlibbioc + zlib ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('e98fc0f5acba44885b9b7962d2b3d85e8972e8675ab7d9adf7653133d2d95007') +md5sums=('9bd1e4acedbf756386f96d4c1ebb21f3') +b2sums=('f6f89fc05c0da4f2f45fde959387fd133030d179f316adb6d6d8a1cb1483f6e34d111e2015098906a49a40f7efd7bbaf5aa461e8547d96a4fb6eaf96c3a53169') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-affyio/lilac.py b/BioArchLinux/r-affyio/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-affyio/lilac.py +++ b/BioArchLinux/r-affyio/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-affyio/lilac.yaml b/BioArchLinux/r-affyio/lilac.yaml index f8e76f0681..3440729c27 100644 --- a/BioArchLinux/r-affyio/lilac.yaml +++ b/BioArchLinux/r-affyio/lilac.yaml @@ -5,7 +5,13 @@ maintainers: repo_depends: - r-zlibbioc update_on: -- regex: affyio_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/affyio +- source: rpkgs + pkgname: affyio + repo: bioc + md5: true - alias: r +- source: alpm + alpm: zlib + repo: core + provided: libz.so + strip_release: true diff --git a/BioArchLinux/r-akima/PKGBUILD b/BioArchLinux/r-akima/PKGBUILD index a6ecb0eb2d..5be475e138 100644 --- a/BioArchLinux/r-akima/PKGBUILD +++ b/BioArchLinux/r-akima/PKGBUILD @@ -3,32 +3,31 @@ _pkgname=akima _pkgver=0.6-3.4 pkgname=r-${_pkgname,,} -pkgver=0.6.3.4 +pkgver=${_pkgver//-/.} pkgrel=5 -pkgdesc='Interpolation of Irregularly and Regularly Spaced Data' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('ACM') +pkgdesc="Interpolation of Irregularly and Regularly Spaced Data" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('LicenseRef-scancode-acm-sla') depends=( - r r-sp ) -optdepends=( - r-tripack -) makedepends=( gcc-fortran ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('95657592a81d2e3628cb054b60127827ae64e65c58b77d059aa510bc6781ad3e') +md5sums=('55d36a85ecb1c2f82d22bdcec6f9ee3e') +b2sums=('688c8d0319290f16379c526fae9a2b7ee7cd69704dae0a4b8f1387f14d92780f2d3c657d0d1fac3fc3239ae58ba183b1a8a5d522c23c85c88c15452acb9af8c0') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + 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" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-akima/lilac.py b/BioArchLinux/r-akima/lilac.py index bd219c037c..606b2a786a 100644 --- a/BioArchLinux/r-akima/lilac.py +++ b/BioArchLinux/r-akima/lilac.py @@ -1,12 +1,16 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build( + _G, + expect_license = "ACM | file LICENSE", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-akima/lilac.yaml b/BioArchLinux/r-akima/lilac.yaml index 18e0da9c7b..c7a7689ad7 100644 --- a/BioArchLinux/r-akima/lilac.yaml +++ b/BioArchLinux/r-akima/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-sp update_on: -- regex: akima_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=akima +- source: rpkgs + pkgname: akima + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-attempt/PKGBUILD b/BioArchLinux/r-attempt/PKGBUILD index 83fa5af2af..eb8cadcc6a 100644 --- a/BioArchLinux/r-attempt/PKGBUILD +++ b/BioArchLinux/r-attempt/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=attempt _pkgver=0.3.1 pkgname=r-${_pkgname,,} -pkgver=0.3.1 +pkgver=${_pkgver//-/.} pkgrel=6 -pkgdesc='Tools for Defensive Programming' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" +pkgdesc="Tools for Defensive Programming" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" license=('MIT') depends=( - r r-rlang ) optdepends=( @@ -20,15 +19,18 @@ optdepends=( r-testthat ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('15159d3d20198c6300874451e925ca154c23e0b6cdd7e05eaf98a3cbe4798ffa') +md5sums=('b4cbba3e4a87008b3aa8c60251576ccc') +b2sums=('ce366713bd58732895e5fa820221587ab88ab815658a8803516a5f836a7698b7fa3c67ee1ebff3b3876684debadff4033def7b9373c312849968c7a19f60a7c9') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + 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" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-attempt/lilac.py b/BioArchLinux/r-attempt/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-attempt/lilac.py +++ b/BioArchLinux/r-attempt/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-attempt/lilac.yaml b/BioArchLinux/r-attempt/lilac.yaml index 0ddae83941..d6836a3aa2 100644 --- a/BioArchLinux/r-attempt/lilac.yaml +++ b/BioArchLinux/r-attempt/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-rlang update_on: -- regex: attempt_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=attempt +- source: rpkgs + pkgname: attempt + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-coro/PKGBUILD b/BioArchLinux/r-coro/PKGBUILD index 8470895a51..1dcc4d07ae 100644 --- a/BioArchLinux/r-coro/PKGBUILD +++ b/BioArchLinux/r-coro/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=coro _pkgver=1.0.4 pkgname=r-${_pkgname,,} -pkgver=1.0.4 +pkgver=${_pkgver//-/.} pkgrel=1 pkgdesc="'Coroutines' for R" -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" license=('MIT') depends=( - r r-rlang ) optdepends=( @@ -23,15 +22,18 @@ optdepends=( r-testthat ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('8f21bf44ec46fa1da88e9232db5536f494cbd87aade3ef16957d27919f58cc64') +md5sums=('20d535e6d36920c23c8e74442977806a') +b2sums=('b164beab9bf7818939e835071b0b85a162505bd0eff42f87b751385f99d990ee4907ac6ac8097c75147cec5b12882ab26ab9cac4ccbd46cd7e34119d1a32104a') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + 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" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-coro/lilac.py b/BioArchLinux/r-coro/lilac.py index cc91618b28..b5cdb057c5 100644 --- a/BioArchLinux/r-coro/lilac.py +++ b/BioArchLinux/r-coro/lilac.py @@ -1,9 +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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-coro/lilac.yaml b/BioArchLinux/r-coro/lilac.yaml index a0cda72717..68fcb3a5fe 100644 --- a/BioArchLinux/r-coro/lilac.yaml +++ b/BioArchLinux/r-coro/lilac.yaml @@ -1,13 +1,12 @@ build_prefix: extra-x86_64 maintainers: - - github: sukanka - email: su975853527@gmail.com -post_build_script: | - git_pkgbuild_commit() - update_aur_repo() +- github: sukanka + email: su975853527@gmail.com repo_depends: - - r-rlang +- r-rlang update_on: - - regex: coro_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=coro +- source: rpkgs + pkgname: coro + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-diffobj/PKGBUILD b/BioArchLinux/r-diffobj/PKGBUILD index f1e84e9d2b..2300be6d6f 100644 --- a/BioArchLinux/r-diffobj/PKGBUILD +++ b/BioArchLinux/r-diffobj/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=diffobj _pkgver=0.3.5 pkgname=r-${_pkgname,,} -pkgver=0.3.5 +pkgver=${_pkgver//-/.} pkgrel=6 -pkgdesc='Diffs for R Objects' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Diffs for R Objects" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-only OR GPL-3.0-only') depends=( - r r-crayon ) optdepends=( @@ -18,14 +17,15 @@ optdepends=( r-rmarkdown ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60') +md5sums=('dffa0a111b1f8766d0b64a2cd7138d09') +b2sums=('c593f790c121d53c540fc52fcf25aded44d0f56c696a7c2d222afed4f337c2b61331c5dd6058f0ee48959a1feb5d9cd11f6b81cf296244eb89ce116183b41e10') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-diffobj/lilac.py b/BioArchLinux/r-diffobj/lilac.py index 620556bc87..9244fd6914 100644 --- a/BioArchLinux/r-diffobj/lilac.py +++ b/BioArchLinux/r-diffobj/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-diffobj/lilac.yaml b/BioArchLinux/r-diffobj/lilac.yaml index a8615f88b4..4157e2b551 100644 --- a/BioArchLinux/r-diffobj/lilac.yaml +++ b/BioArchLinux/r-diffobj/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-crayon update_on: -- regex: diffobj_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=diffobj +- source: rpkgs + pkgname: diffobj + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-genarise/PKGBUILD b/BioArchLinux/r-genarise/PKGBUILD index b41134f93c..b8e0bd1c00 100644 --- a/BioArchLinux/r-genarise/PKGBUILD +++ b/BioArchLinux/r-genarise/PKGBUILD @@ -3,28 +3,30 @@ _pkgname=genArise _pkgver=1.78.0 pkgname=r-${_pkgname,,} -pkgver=1.78.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Microarray Analysis tool' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('custom') +pkgdesc="Microarray Analysis tool" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('LicenseRef-genArise') depends=( - r r-locfit r-tkrplot r-xtable ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('e095e1c32a8eac4d36e7a5387e86b03a23d65e24234967e3f72387ec9a7e6199') +md5sums=('d81489147ccfe688c07c228b7fcfcf7d') +b2sums=('95a674942bf301f6b4e8c227ac25d7810eec88e497448aa0b852d3701136b1ac4c05f590b6bb7082fef11186bca9536bcd7665ca826b66c703ba46ce2fd654d4') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + 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" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-genarise/lilac.py b/BioArchLinux/r-genarise/lilac.py index bd219c037c..c808eaf563 100644 --- a/BioArchLinux/r-genarise/lilac.py +++ b/BioArchLinux/r-genarise/lilac.py @@ -1,12 +1,16 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build( + _G, + expect_license = "file LICENSE", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-genarise/lilac.yaml b/BioArchLinux/r-genarise/lilac.yaml index 797aa49e16..bad6ec48e5 100644 --- a/BioArchLinux/r-genarise/lilac.yaml +++ b/BioArchLinux/r-genarise/lilac.yaml @@ -7,7 +7,8 @@ repo_depends: - r-tkrplot - r-xtable update_on: -- regex: genArise_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/genArise +- source: rpkgs + pkgname: genArise + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-grimport/PKGBUILD b/BioArchLinux/r-grimport/PKGBUILD index 11d3c8f249..cbbf7418ba 100644 --- a/BioArchLinux/r-grimport/PKGBUILD +++ b/BioArchLinux/r-grimport/PKGBUILD @@ -1,35 +1,31 @@ -# system requirements: ghostscript # Maintainer: Guoyi Zhang _pkgname=grImport _pkgver=0.9-7 pkgname=r-${_pkgname,,} -pkgver=0.9.7 +pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc='Importing Vector Graphics' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Importing Vector Graphics" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r - r-xml ghostscript + r-xml ) optdepends=( - r-cluster r-colorspace - r-lattice - r-survival ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('05f8b65a55c5fabce2afb74c2b843f5df772d1f931d1ba3ce5f3bfe0493cd0a4') +md5sums=('15b22fb059f5cc409231f1af50b7316d') +b2sums=('e35f32334da85d0bfdce10443aed632637e21c18d96c148d0968711e154c7f5508c9c694f7905e0456a1137c451aaaaa96189cd10784646acc34a93bdcc55359') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-grimport/lilac.py b/BioArchLinux/r-grimport/lilac.py index bd219c037c..a6c8cadf49 100644 --- a/BioArchLinux/r-grimport/lilac.py +++ b/BioArchLinux/r-grimport/lilac.py @@ -1,12 +1,16 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build( + _G, + expect_systemrequirements = "ghostscript", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-grimport/lilac.yaml b/BioArchLinux/r-grimport/lilac.yaml index 63d2ea234f..d72e9ed7a5 100644 --- a/BioArchLinux/r-grimport/lilac.yaml +++ b/BioArchLinux/r-grimport/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-xml update_on: -- regex: grImport_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=grImport +- source: rpkgs + pkgname: grImport + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-htmlutils/PKGBUILD b/BioArchLinux/r-htmlutils/PKGBUILD index 2251d96eec..d7af44edb8 100644 --- a/BioArchLinux/r-htmlutils/PKGBUILD +++ b/BioArchLinux/r-htmlutils/PKGBUILD @@ -3,25 +3,25 @@ _pkgname=HTMLUtils _pkgver=0.1.9 pkgname=r-${_pkgname,,} -pkgver=0.1.9 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Facilitates Automated HTML Report Creation' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Facilitates Automated HTML Report Creation" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-r2html ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('14e92d45743a9adf21aab726be7d1aacdc901eae443da896b149a657183a8ec4') +md5sums=('dfdfd0071ccdaf1d589c20a8513d9752') +b2sums=('5b395b687bd257a77f271b4ae03893f94d26e9f3a8cb3bef0b06772240b736bcd7696b81c4dc96c1c6e1baad89c4af72fccb39e9e4a2355ec1fe3c79955f0849') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-htmlutils/lilac.py b/BioArchLinux/r-htmlutils/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-htmlutils/lilac.py +++ b/BioArchLinux/r-htmlutils/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-htmlutils/lilac.yaml b/BioArchLinux/r-htmlutils/lilac.yaml index 1f684f6243..bcad34e250 100644 --- a/BioArchLinux/r-htmlutils/lilac.yaml +++ b/BioArchLinux/r-htmlutils/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-r2html update_on: -- regex: HTMLUtils_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=HTMLUtils +- source: rpkgs + pkgname: HTMLUtils + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-irr/PKGBUILD b/BioArchLinux/r-irr/PKGBUILD index d8197aef50..1025dcf95d 100644 --- a/BioArchLinux/r-irr/PKGBUILD +++ b/BioArchLinux/r-irr/PKGBUILD @@ -3,25 +3,25 @@ _pkgname=irr _pkgver=0.84.1 pkgname=r-${_pkgname,,} -pkgver=0.84.1 +pkgver=${_pkgver//-/.} pkgrel=6 -pkgdesc='Various Coefficients of Interrater Reliability and Agreement' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Various Coefficients of Interrater Reliability and Agreement" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-lpsolve ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('e7bae8476b723a2246564c013194e8b7fcc9b34affc0ab5fcd55875231f544c3') +md5sums=('802ae19d1fc45cede1afafb5012cfdf0') +b2sums=('41f6e4046a498394cb53a1c4599a7ac6ec66b9301272f7bb523740887bd8c8ed3b23a74c48e5eb177042c36a9f968fb7e47b55426ea1318a71183c01e4c537fa') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-irr/lilac.py b/BioArchLinux/r-irr/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-irr/lilac.py +++ b/BioArchLinux/r-irr/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-irr/lilac.yaml b/BioArchLinux/r-irr/lilac.yaml index d5602b3804..d0a7ba5750 100644 --- a/BioArchLinux/r-irr/lilac.yaml +++ b/BioArchLinux/r-irr/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-lpsolve update_on: -- regex: irr_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=irr +- source: rpkgs + pkgname: irr + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-pepxmltab/PKGBUILD b/BioArchLinux/r-pepxmltab/PKGBUILD index a5222e0c6d..465d4efc72 100644 --- a/BioArchLinux/r-pepxmltab/PKGBUILD +++ b/BioArchLinux/r-pepxmltab/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=pepXMLTab _pkgver=1.36.0 pkgname=r-${_pkgname,,} -pkgver=1.36.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Parsing pepXML files and filter based on peptide FDR.' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="Parsing pepXML files and filter based on peptide FDR" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( - r r-xml ) optdepends=( @@ -18,14 +17,15 @@ optdepends=( r-runit ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('441a1a4c73d083e10cc95f4f80209f02f523af9085079d9857bd61effa1116b4') +md5sums=('71d6bcb41c5a79bc2cfdd375c6468250') +b2sums=('37e0d23e667c4f3720a7bf0305152c7f4540058cdba396edb13e7c1848b26a806bdbd840f6d133c9124ad7202c940e5c7963b8fa004420b6f94592e4404074e8') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-pepxmltab/lilac.py b/BioArchLinux/r-pepxmltab/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-pepxmltab/lilac.py +++ b/BioArchLinux/r-pepxmltab/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-pepxmltab/lilac.yaml b/BioArchLinux/r-pepxmltab/lilac.yaml index 59f3d1dcd5..edb594ce60 100644 --- a/BioArchLinux/r-pepxmltab/lilac.yaml +++ b/BioArchLinux/r-pepxmltab/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-xml update_on: -- regex: pepXMLTab_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/pepXMLTab +- source: rpkgs + pkgname: pepXMLTab + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-polycor/PKGBUILD b/BioArchLinux/r-polycor/PKGBUILD index 287fc3ec75..16165aa751 100644 --- a/BioArchLinux/r-polycor/PKGBUILD +++ b/BioArchLinux/r-polycor/PKGBUILD @@ -3,26 +3,26 @@ _pkgname=polycor _pkgver=0.8-1 pkgname=r-${_pkgname,,} -pkgver=0.8.1 +pkgver=${_pkgver//-/.} pkgrel=5 -pkgdesc='Polychoric and Polyserial Correlations' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Polychoric and Polyserial Correlations" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-admisc r-mvtnorm ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509') +md5sums=('bcf23e352787794c7e36875d6cd8d6f6') +b2sums=('040a667cc6a0dceeac6fe85e011e54605c081259f998deb8aae3be4f6c57820aa34f63f1b27c2e7a40e9099b35c8e57ba6b1d76488e6389a7f8eb0c2f80ed57a') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-polycor/lilac.py b/BioArchLinux/r-polycor/lilac.py index cc91618b28..b5cdb057c5 100644 --- a/BioArchLinux/r-polycor/lilac.py +++ b/BioArchLinux/r-polycor/lilac.py @@ -1,9 +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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-polycor/lilac.yaml b/BioArchLinux/r-polycor/lilac.yaml index b2c69d77a1..7f97273908 100644 --- a/BioArchLinux/r-polycor/lilac.yaml +++ b/BioArchLinux/r-polycor/lilac.yaml @@ -1,15 +1,13 @@ build_prefix: extra-x86_64 maintainers: - - github: sukanka - email: su975853527@gmail.com -post_build_script: | - git_pkgbuild_commit() - update_aur_repo() +- github: sukanka + email: su975853527@gmail.com repo_depends: - - r-admisc - - r-mvtnorm +- r-admisc +- r-mvtnorm update_on: - - regex: polycor_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=polycor - - alias: r +- source: rpkgs + pkgname: polycor + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-prabclus/PKGBUILD b/BioArchLinux/r-prabclus/PKGBUILD index 310a6ebb88..3c46170478 100644 --- a/BioArchLinux/r-prabclus/PKGBUILD +++ b/BioArchLinux/r-prabclus/PKGBUILD @@ -3,32 +3,31 @@ _pkgname=prabclus _pkgver=2.3-3 pkgname=r-${_pkgname,,} -pkgver=2.3.3 +pkgver=${_pkgver//-/.} pkgrel=3 -pkgdesc='Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-mclust ) optdepends=( r-bootstrap - r-foreign r-mvtnorm r-spatialreg r-spdep ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('005d000a9ac357e670de26e5b8fc4ddb1617351275fa43bf6d2e88b8774358c1') +md5sums=('a978397e43f43298a994a0c8fcc450c7') +b2sums=('fe4edb65112dfec49f2ce877931d539a93fe478b106e4c45e429de9e850c9f4e4ef064164905b23999c548be5345944b58e8da7db4780904d245423a2b0d74eb') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-prabclus/lilac.py b/BioArchLinux/r-prabclus/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-prabclus/lilac.py +++ b/BioArchLinux/r-prabclus/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-prabclus/lilac.yaml b/BioArchLinux/r-prabclus/lilac.yaml index 567745daf4..8298d80a64 100644 --- a/BioArchLinux/r-prabclus/lilac.yaml +++ b/BioArchLinux/r-prabclus/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-mclust update_on: -- regex: prabclus_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=prabclus +- source: rpkgs + pkgname: prabclus + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-rbiopaxparser/PKGBUILD b/BioArchLinux/r-rbiopaxparser/PKGBUILD index c60aedb7c8..d59b71bc6e 100644 --- a/BioArchLinux/r-rbiopaxparser/PKGBUILD +++ b/BioArchLinux/r-rbiopaxparser/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=rBiopaxParser _pkgver=2.42.0 pkgname=r-${_pkgname,,} -pkgver=2.42.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Parses BioPax files and represents them in R' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Parses BioPax files and represents them in R" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-data.table r-xml ) @@ -24,14 +23,15 @@ optdepends=( r-runit ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('275cb296a6e9d262a2c853d85c0954fcf72a87197b482adfbb4c8e045346caff') +md5sums=('53e24a8896bf17bd56fe48d62427eb33') +b2sums=('46186aa0fd6c43330d8d928e39f3e4fda57afb0fab3e46f67c160ead21ff5260e35541ef1246f97b88d3df012c0fbafb4fbf13aa13ea8e7c737d2704eb9f359b') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-rbiopaxparser/lilac.py b/BioArchLinux/r-rbiopaxparser/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-rbiopaxparser/lilac.py +++ b/BioArchLinux/r-rbiopaxparser/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-rbiopaxparser/lilac.yaml b/BioArchLinux/r-rbiopaxparser/lilac.yaml index 2c85006caf..c695cfdc27 100644 --- a/BioArchLinux/r-rbiopaxparser/lilac.yaml +++ b/BioArchLinux/r-rbiopaxparser/lilac.yaml @@ -6,7 +6,8 @@ repo_depends: - r-data.table - r-xml update_on: -- regex: rBiopaxParser_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/rBiopaxParser +- source: rpkgs + pkgname: rBiopaxParser + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-rhtslib/PKGBUILD b/BioArchLinux/r-rhtslib/PKGBUILD index 4ea7077d76..603becc784 100644 --- a/BioArchLinux/r-rhtslib/PKGBUILD +++ b/BioArchLinux/r-rhtslib/PKGBUILD @@ -1,22 +1,20 @@ -# system requirements: libbz2 & liblzma & libcurl (with header files), GNUmake # Maintainer: Guoyi Zhang _pkgname=Rhtslib _pkgver=2.4.1 pkgname=r-${_pkgname,,} -pkgver=2.4.1 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='HTSlib high-throughput sequencing library as an R package' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('LGPL') -options=(!lto staticlibs) +pkgdesc="HTSlib high-throughput sequencing library as an R package" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('LGPL-2.0-or-later') depends=( - r - r-zlibbioc bzip2 - xz curl + r-zlibbioc + xz + zlib ) optdepends=( r-biocstyle @@ -24,14 +22,15 @@ optdepends=( r-rmarkdown ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('0c34b951a0f15c26222a3dfd96700a0905c16c4cbe59db36374cf1ceab2a2b21') +md5sums=('b7d295a694e865f4f4060c94c4bca446') +b2sums=('003d61f9455981794724ab4e65eaf7f557d2bd394b58ba4e61eb895fbceb8117cb8a8fc6b99f7be71f2ec1b1641ea71867c6a083deba29991c630716de48e82c') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-rhtslib/lilac.py b/BioArchLinux/r-rhtslib/lilac.py index 620556bc87..e4064d3fda 100644 --- a/BioArchLinux/r-rhtslib/lilac.py +++ b/BioArchLinux/r-rhtslib/lilac.py @@ -1,12 +1,16 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build( + _G, + expect_systemrequirements = "libbz2 & liblzma & libcurl (with header files), GNU make", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-rhtslib/lilac.yaml b/BioArchLinux/r-rhtslib/lilac.yaml index 515eb1b0a9..247031b009 100644 --- a/BioArchLinux/r-rhtslib/lilac.yaml +++ b/BioArchLinux/r-rhtslib/lilac.yaml @@ -5,7 +5,28 @@ maintainers: repo_depends: - r-zlibbioc update_on: -- regex: Rhtslib_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/Rhtslib +- source: rpkgs + pkgname: Rhtslib + repo: bioc + md5: true - alias: r +- source: alpm + alpm: bzip2 + repo: core + provided: libbz2.so + strip_release: true +- source: alpm + alpm: curl + repo: core + provided: libcurl.so + strip_release: true +- source: alpm + alpm: xz + repo: core + provided: liblzma.so + strip_release: true +- source: alpm + alpm: zlib + repo: core + provided: libz.so + strip_release: true diff --git a/BioArchLinux/r-sampling/PKGBUILD b/BioArchLinux/r-sampling/PKGBUILD index d2efd76d1a..7fdbc82407 100644 --- a/BioArchLinux/r-sampling/PKGBUILD +++ b/BioArchLinux/r-sampling/PKGBUILD @@ -3,26 +3,25 @@ _pkgname=sampling _pkgver=2.10 pkgname=r-${_pkgname,,} -pkgver=2.10 +pkgver=${_pkgver//-/.} pkgrel=1 pkgdesc="Survey Sampling" -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-lpsolve ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775') +md5sums=('42f9a999adb8edaa1aa1199d1774b8aa') +b2sums=('022baa77d2b46732f55c5bfc451cc6cf900d8d9c5709dd35ca8f73b62e9ef49337c57d28eba01b73180d7f4bb4f83a6eb85d7a860683d6c20a37cd2b1c168bdb') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" -# install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-sampling/lilac.py b/BioArchLinux/r-sampling/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-sampling/lilac.py +++ b/BioArchLinux/r-sampling/lilac.py @@ -1,12 +1,13 @@ #!/usr/bin/env python3 from lilaclib import * +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + def pre_build(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-sampling/lilac.yaml b/BioArchLinux/r-sampling/lilac.yaml index a8a95290bb..64c590f7fe 100644 --- a/BioArchLinux/r-sampling/lilac.yaml +++ b/BioArchLinux/r-sampling/lilac.yaml @@ -2,10 +2,11 @@ build_prefix: extra-x86_64 maintainers: - github: starsareintherose email: kuoi@bioarchlinux.org -update_on: -- regex: sampling_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=sampling -- alias: r repo_depends: - r-lpsolve +update_on: +- source: rpkgs + pkgname: sampling + repo: cran + md5: true +- alias: r diff --git a/BioArchLinux/r-semisup/PKGBUILD b/BioArchLinux/r-semisup/PKGBUILD index b15e85a18c..e9dab434bd 100644 --- a/BioArchLinux/r-semisup/PKGBUILD +++ b/BioArchLinux/r-semisup/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=semisup _pkgver=1.26.0 pkgname=r-${_pkgname,,} -pkgver=1.26.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Semi-Supervised Mixture Model' -arch=('any') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="Semi-Supervised Mixture Model" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( - r r-vgam ) optdepends=( @@ -19,14 +18,15 @@ optdepends=( r-testthat ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('a9b0a2eb85fe87ff5f7397d5a966637f07cbbe66b88a1ebb72391cfef8676376') +md5sums=('fb3d32c07acbfadbbee01f9a6c8333fe') +b2sums=('0f2feb4757068304cac0398c4bbf5d79ac07cefa2e191703cedea9e5fc446cababbac8ec9c5ef9f82ab36a9e904a563eb2b1b995f7c7379692b6b0ffcede6c32') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-semisup/lilac.py b/BioArchLinux/r-semisup/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-semisup/lilac.py +++ b/BioArchLinux/r-semisup/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-semisup/lilac.yaml b/BioArchLinux/r-semisup/lilac.yaml index 5baa71c9dc..05c3b1f7f8 100644 --- a/BioArchLinux/r-semisup/lilac.yaml +++ b/BioArchLinux/r-semisup/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-vgam update_on: -- regex: semisup_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/semisup +- source: rpkgs + pkgname: semisup + repo: bioc + md5: true - alias: r diff --git a/BioArchLinux/r-seqtools/PKGBUILD b/BioArchLinux/r-seqtools/PKGBUILD index 98f717887a..2d86772208 100644 --- a/BioArchLinux/r-seqtools/PKGBUILD +++ b/BioArchLinux/r-seqtools/PKGBUILD @@ -3,29 +3,30 @@ _pkgname=seqTools _pkgver=1.36.0 pkgname=r-${_pkgname,,} -pkgver=1.36.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Analysis of nucleotide, sequence and quality content on fastq files' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +pkgdesc="Analysis of nucleotide, sequence and quality content on fastq files" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('Artistic-2.0') depends=( - r r-zlibbioc + zlib ) optdepends=( r-biocgenerics r-runit ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('559031059a9315d8b0912d5334c91cb5176427e09586df400b3eeff58b9a1584') +md5sums=('be9be6eb0ee1ff4ab001720970d68da8') +b2sums=('d813ac5feb6ac445a2462b4ac4aeb2c36837cb7101a210c64922561051b222c2c3126f11c1121f3a36e56a64fe903229a42495a72547ab7376ff1499ba2be96f') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-seqtools/lilac.py b/BioArchLinux/r-seqtools/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-seqtools/lilac.py +++ b/BioArchLinux/r-seqtools/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-seqtools/lilac.yaml b/BioArchLinux/r-seqtools/lilac.yaml index 8462698cbe..5f527c7688 100644 --- a/BioArchLinux/r-seqtools/lilac.yaml +++ b/BioArchLinux/r-seqtools/lilac.yaml @@ -5,7 +5,13 @@ maintainers: repo_depends: - r-zlibbioc update_on: -- regex: seqTools_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/seqTools +- source: rpkgs + pkgname: seqTools + repo: bioc + md5: true - alias: r +- source: alpm + alpm: zlib + repo: core + provided: libz.so + strip_release: true diff --git a/BioArchLinux/r-snowfall/PKGBUILD b/BioArchLinux/r-snowfall/PKGBUILD index 1782421ecd..270670ca3b 100644 --- a/BioArchLinux/r-snowfall/PKGBUILD +++ b/BioArchLinux/r-snowfall/PKGBUILD @@ -3,28 +3,28 @@ _pkgname=snowfall _pkgver=1.84-6.3 pkgname=r-${_pkgname,,} -pkgver=1.84.6.3 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Easier cluster computing (based on snow).' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Easier Cluster Computing (Based on 'snow')" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-snow ) optdepends=( r-rmpi ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('2641932b01041e34b7afb1261f649755b4c8d6560080e0e2ee549ffdf3b8b143') +md5sums=('4ca758a26dd4e862cc9ffd43ae16b2d3') +b2sums=('f641aeef1a201c75424f61db662bf523fc277ac4d4abfb113588f52757c5b93c77af17bf97282dbd85604ff7099e9b62f6f80b7a672064447a9dc5512850e61e') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-snowfall/lilac.py b/BioArchLinux/r-snowfall/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-snowfall/lilac.py +++ b/BioArchLinux/r-snowfall/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-snowfall/lilac.yaml b/BioArchLinux/r-snowfall/lilac.yaml index 0829de9b7d..e1fda6553f 100644 --- a/BioArchLinux/r-snowfall/lilac.yaml +++ b/BioArchLinux/r-snowfall/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-snow update_on: -- regex: snowfall_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=snowfall +- source: rpkgs + pkgname: snowfall + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-snpstats/PKGBUILD b/BioArchLinux/r-snpstats/PKGBUILD index 474ecd1be2..d85c504b1e 100644 --- a/BioArchLinux/r-snpstats/PKGBUILD +++ b/BioArchLinux/r-snpstats/PKGBUILD @@ -3,29 +3,30 @@ _pkgname=snpStats _pkgver=1.52.0 pkgname=r-${_pkgname,,} -pkgver=1.52.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='SnpMatrix and XSnpMatrix classes and methods' -arch=('x86_64') -url="https://bioconductor.org/packages/${_pkgname}" -license=('GPL') +pkgdesc="SnpMatrix and XSnpMatrix classes and methods" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') depends=( - r r-biocgenerics r-zlibbioc + zlib ) optdepends=( r-hexbin ) source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('d9af4679d0dcb74895b62825902925826b8303a2c674f884b1674b3ad2f69328') +md5sums=('0625c920470937a31fd278cf8bd8982a') +b2sums=('2ada9c7f21a9f59558519c9e34328101acd7815e153674a17cb65815471b6ec3570da2daf9f9cf5d4c78fa0c496b350973de312bfdbd223a5180f5ca4e21e2c0') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-snpstats/lilac.py b/BioArchLinux/r-snpstats/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-snpstats/lilac.py +++ b/BioArchLinux/r-snpstats/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-snpstats/lilac.yaml b/BioArchLinux/r-snpstats/lilac.yaml index 8f128c9600..9da8d649f2 100644 --- a/BioArchLinux/r-snpstats/lilac.yaml +++ b/BioArchLinux/r-snpstats/lilac.yaml @@ -6,7 +6,13 @@ repo_depends: - r-biocgenerics - r-zlibbioc update_on: -- regex: snpStats_([\d._-]+).tar.gz - source: regex - url: https://bioconductor.org/packages/snpStats +- source: rpkgs + pkgname: snpStats + repo: bioc + md5: true - alias: r +- source: alpm + alpm: zlib + repo: core + provided: libz.so + strip_release: true diff --git a/BioArchLinux/r-sparsepca/PKGBUILD b/BioArchLinux/r-sparsepca/PKGBUILD index a9daa6797b..c96b7415c9 100644 --- a/BioArchLinux/r-sparsepca/PKGBUILD +++ b/BioArchLinux/r-sparsepca/PKGBUILD @@ -3,25 +3,25 @@ _pkgname=sparsepca _pkgver=0.1.2 pkgname=r-${_pkgname,,} -pkgver=0.1.2 +pkgver=${_pkgver//-/.} pkgrel=6 -pkgdesc='Sparse Principal Component Analysis (SPCA)' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Sparse Principal Component Analysis (SPCA)" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-or-later') depends=( - r r-rsvd ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('646f2244a57ae8d2e490e0913d4dc9dcf3dafeffb1104d225aaf847b46b56272') +md5sums=('fbbc7e20a66da7f318e3d8f87791a201') +b2sums=('5a484f636279744d341f83c50280821b3fe72daee1de596a22e07f743879674f654e5935bfd29779980f2b9c1ff5251a94c45403f9396b378e1c59db959b3ad8') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-sparsepca/lilac.py b/BioArchLinux/r-sparsepca/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-sparsepca/lilac.py +++ b/BioArchLinux/r-sparsepca/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-sparsepca/lilac.yaml b/BioArchLinux/r-sparsepca/lilac.yaml index 2d3efa3fa0..d90ecef4de 100644 --- a/BioArchLinux/r-sparsepca/lilac.yaml +++ b/BioArchLinux/r-sparsepca/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-rsvd update_on: -- regex: sparsepca_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=sparsepca +- source: rpkgs + pkgname: sparsepca + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-splancs/PKGBUILD b/BioArchLinux/r-splancs/PKGBUILD index 5fbdbd1aaa..1cd1dc47d3 100644 --- a/BioArchLinux/r-splancs/PKGBUILD +++ b/BioArchLinux/r-splancs/PKGBUILD @@ -3,28 +3,28 @@ _pkgname=splancs _pkgver=2.01-44 pkgname=r-${_pkgname,,} -pkgver=2.01.44 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Spatial and Space-Time Point Pattern Analysis' -arch=('x86_64') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Spatial and Space-Time Point Pattern Analysis" +arch=(x86_64) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-2.0-or-later') depends=( - r r-sp ) makedepends=( gcc-fortran ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('08d46df9b56488925cc1b66261cf1134292ce4b5174b45e066eeb1e951dec171') +md5sums=('44e5896425648e699fb0fe15fef191fc') +b2sums=('5a5b355941c1fc3da3ac67b34c0b132aa6b2cb20b21dcc1f01cc3fa9a09146b9bbfea3ed0fb67d89a4828edfc93550ed8377deac6fad535ec61a7414faf6df05') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-splancs/lilac.py b/BioArchLinux/r-splancs/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-splancs/lilac.py +++ b/BioArchLinux/r-splancs/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-splancs/lilac.yaml b/BioArchLinux/r-splancs/lilac.yaml index d2fe4ff2a3..0331c8889f 100644 --- a/BioArchLinux/r-splancs/lilac.yaml +++ b/BioArchLinux/r-splancs/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-sp update_on: -- regex: splancs_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=splancs +- source: rpkgs + pkgname: splancs + repo: cran + md5: true - alias: r diff --git a/BioArchLinux/r-venn/PKGBUILD b/BioArchLinux/r-venn/PKGBUILD index 9f9ba8869f..28c1fa8817 100644 --- a/BioArchLinux/r-venn/PKGBUILD +++ b/BioArchLinux/r-venn/PKGBUILD @@ -3,14 +3,13 @@ _pkgname=venn _pkgver=1.12 pkgname=r-${_pkgname,,} -pkgver=1.12 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Draw Venn Diagrams' -arch=('any') -url="https://cran.r-project.org/package=${_pkgname}" -license=('GPL') +pkgdesc="Draw Venn Diagrams" +arch=(any) +url="https://cran.r-project.org/package=$_pkgname" +license=('GPL-3.0-or-later') depends=( - r r-admisc ) optdepends=( @@ -19,14 +18,15 @@ optdepends=( r-qca ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('ed86b69bd99ceea93352a30699a0baba3fd8cdcde907a9476e92be202ad8721d') +md5sums=('29b0e3dd951c8626b126705d88f8303a') +b2sums=('09b3727890b2b2447a076c94e8449e20e39c4cf2eaaf9c8ff9573dd1ede01ae6ea8f10f3a0342910e717bf49b6079329fcf66184c30ea215198d24c514ec9102') build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir build + R CMD INSTALL -l build "$_pkgname" } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/BioArchLinux/r-venn/lilac.py b/BioArchLinux/r-venn/lilac.py index bd219c037c..b5cdb057c5 100644 --- a/BioArchLinux/r-venn/lilac.py +++ b/BioArchLinux/r-venn/lilac.py @@ -1,12 +1,13 @@ #!/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(): - for line in edit_file('PKGBUILD'): - if line.startswith('_pkgver='): - line = f'_pkgver={_G.newver}' - print(line) - update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.')) + r_pre_build(_G) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-venn/lilac.yaml b/BioArchLinux/r-venn/lilac.yaml index 7c2ca9dbf9..3e0a450e72 100644 --- a/BioArchLinux/r-venn/lilac.yaml +++ b/BioArchLinux/r-venn/lilac.yaml @@ -5,7 +5,8 @@ maintainers: repo_depends: - r-admisc update_on: -- regex: venn_([\d._-]+).tar.gz - source: regex - url: https://cran.r-project.org/package=venn +- source: rpkgs + pkgname: venn + repo: cran + md5: true - alias: r