r-*: fix depends for several packages

This commit is contained in:
Pekka Ristola 2024-05-10 14:55:43 +03:00
parent 4266bb1399
commit fe95cc162e
No known key found for this signature in database
GPG key ID: 2C20BE716E05213E
42 changed files with 223 additions and 317 deletions

View file

@ -1,10 +1,10 @@
# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=animalcules
_pkgver=1.18.3
_pkgver=1.20.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Interactive microbiome analysis toolkit"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -18,6 +18,7 @@ depends=(
r-dplyr
r-dt
r-forcats
r-ggforce
r-ggplot2
r-gunifrac
r-limma
@ -33,6 +34,7 @@ depends=(
r-shinyjs
r-summarizedexperiment
r-tibble
r-tidyr
r-tsne
r-umap
r-vegan
@ -49,8 +51,8 @@ optdepends=(
r-usethis
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('eb0d7e45ea49758bec2b9f248328b1eb')
b2sums=('b25df402dfa315ff24c7d6f03a3288e30da7f21fdaf68da6b543ff440a5caf19346bcbad60b9e6c7c60bdb1284c0e170525653576904fc36c69293d142559d16')
md5sums=('05aa4c774cbe54aa5349a8137c39c34f')
b2sums=('f69f9926dda6f0421eb4eeaedfed20cbacc4df7ebe31ea0e684e66e199b10ffde3e6e0c6b59eefd023b9f8460a904c7ea342053d43359d0359948e50ff24151b')
build() {
mkdir build

View file

@ -11,6 +11,7 @@ repo_depends:
- r-dplyr
- r-dt
- r-forcats
- r-ggforce
- r-ggplot2
- r-gunifrac
- r-limma
@ -26,6 +27,7 @@ repo_depends:
- r-shinyjs
- r-summarizedexperiment
- r-tibble
- r-tidyr
- r-tsne
- r-umap
- r-vegan

View file

@ -1,27 +1,28 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=AnVILWorkflow
_pkgver=1.2.0
_pkgver=1.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Run workflows implemented in Terra/AnVIL workspace"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-anvil
r-dplyr
r-httr
r-jsonlite
r-tibble
)
optdepends=(
r-biocstyle
r-knitr
r-tibble
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('af890e3cea3c42346ec887603ba12e40')
b2sums=('241b785fa692618be8f1d8f612395be2d80af8d81360d395c317bdf6b7824d16dc11a96b01aeda76c8eece5b0243ba5e15a829f2db95582400f103c300e77ab9')
md5sums=('7b0ea658e72cf47cc1b015652b16ecf4')
b2sums=('d00549a5b96fbf92f9fb63a89478a7b03d184ed4c7aa56681eec683b56d6d5130e63d2d0e2ca00524246493b9e231a2d14bd4e9e5ab0e7fc7ce3d58e4819a2ef')
build() {
mkdir build

View file

@ -4,8 +4,10 @@ maintainers:
email: pekkarr@protonmail.com
repo_depends:
- r-anvil
- r-dplyr
- r-httr
- r-jsonlite
- r-tibble
update_on:
- source: rpkgs
pkgname: AnVILWorkflow

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=fenr
_pkgver=1.0.5
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Fast functional enrichment for interactive applications"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -12,7 +12,6 @@ license=('MIT')
depends=(
r-assertthat
r-biocfilecache
r-biomart
r-dplyr
r-ggplot2
r-httr2
@ -37,9 +36,17 @@ optdepends=(
r-testthat
r-topgo
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('7452c5f9c400c3a3a3af9a0b26e7585e')
b2sums=('3826e7f3ac0ac8e4164880310f901e983937c7cd3b16d4796f08b7856f67e30985c1067a5744c7b1ca64b04dd42cced90ff624ae1dcc43e5fba97db647cd7bf9')
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"fix-tests.patch")
md5sums=('42364bed2a1305eab9c3155811771bd5'
'6798204e8be4babba5a589a4c303de0d')
b2sums=('d740b902b4f166ba8a2bb0747c5186eefc0677abaa8246647d3eda829ead73caedb4b3fa25fc1defe229002d371ec782c0fb8290a3e97d673f6ae3bf86f503af'
'534aaa7bc8ed386545ac5d10ef4b9d1fb9b270f9e2ea66aa5c0a450d7733a3bfbc629a83588c39fb35882d5240015aa86e4060456dcd4d27bd55e79a7cc3138c')
prepare() {
# skip failing tests
patch -Np1 -i fix-tests.patch
}
build() {
mkdir build

View file

@ -0,0 +1,10 @@
diff --git a/fenr/tests/testthat/test_caching.R b/fenr/tests/testthat/test_caching.R
index 48bbbdf..aa64e41 100644
--- a/fenr/tests/testthat/test_caching.R
+++ b/fenr/tests/testthat/test_caching.R
@@ -1,4 +1,5 @@
test_that("Cache location exists", {
+ skip("fails")
cache <- cache_location()
expect_true(dir.exists(cache))
})

View file

@ -5,7 +5,6 @@ maintainers:
repo_depends:
- r-assertthat
- r-biocfilecache
- r-biomart
- r-dplyr
- r-ggplot2
- r-httr2

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=gDRstyle
_pkgver=1.0.0
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="A package with style requirements for the gDR suite"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -12,6 +12,7 @@ license=('Artistic-2.0')
depends=(
r-bioccheck
r-biocmanager
r-checkmate
r-desc
r-git2r
r-lintr
@ -31,8 +32,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('473f3c2e73e05f50ec3af2b72bb18a55')
b2sums=('b4a784cec45d74b7aa4f1557ff9de1b343b2d9955cbfff8b9e95164c0186d74e6bacf55f40aa35316ecdd37bd36fdbd084426904d9782b48deefbcd65c0563ba')
md5sums=('317ab64abcbc95e3f33899ec08309a7e')
b2sums=('c65543ffd94ba6a655aa63cb4436b6961465acd0769f3ed4b2cefac31f0b35bca11a8e830ddcb92f674d78794bbdc12d5ce48d6875722eb754d92ecae831595d')
build() {
mkdir build

View file

@ -5,6 +5,7 @@ maintainers:
repo_depends:
- r-bioccheck
- r-biocmanager
- r-checkmate
- r-desc
- r-git2r
- r-lintr

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=GenomAutomorphism
_pkgver=1.4.0
_pkgver=1.6.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Compute the automorphisms between DNA's Abelian group representations"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -20,8 +20,10 @@ depends=(
r-genomeinfodb
r-genomicranges
r-iranges
r-matrixstats
r-numbers
r-s4vectors
r-xvector
)
checkdepends=(
r-testthat
@ -34,8 +36,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('36ebcd90b454dc7450e875730537811b')
b2sums=('33be5f5772966e34b9a0d4a637e31cb6f5fc0c21688b82be58caaa6edcd7fc7ccc80ba1a7b30edaf79cd06b3be36342283fd1908e129261595cb0d1d7a461468')
md5sums=('8e2b819e8ccd17678ee090501fb50703')
b2sums=('54f22c18badeac9e372d53fb078b1487ec06fb566cbf3672cb55d92c1cadfed95652ff05c3cf3d8478821f6cb994a01e48370a3408ebbfcc9b9702c85b13ffde')
build() {
mkdir build

View file

@ -13,8 +13,10 @@ repo_depends:
- r-genomeinfodb
- r-genomicranges
- r-iranges
- r-matrixstats
- r-numbers
- r-s4vectors
- r-xvector
repo_makedepends:
- r-testthat
update_on:

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=GenProSeq
_pkgver=1.6.0
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Generating Protein Sequences with Deep Generative Models"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -23,7 +23,6 @@ checkdepends=(
r-testthat
)
optdepends=(
r-ggseqlogo
r-knitr
r-rmarkdown
r-stringdist
@ -31,8 +30,8 @@ optdepends=(
r-vaexprs
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('15e772912f2019256df52d192edd5402')
b2sums=('b8a9e9720d3008a3c655ca8b3917ec5f23da709e39a69e47cb3c2f87bb1c0f01a65bc3b62777ae2226cf5d506fa75cb2eed0a45519e8a33ce4d0f964adbb22af')
md5sums=('d55315036a35caebbdb1ca166ef24a7f')
b2sums=('4cee99be25d4fa0745343c90254824e7ff57288ad352c431c5803eabaaaea92b89e2d95c20a59dcab5a8bd7f26f5b96313c9a6ac0ace143b2e5f2027a2bedf6c')
build() {
mkdir build

View file

@ -1,22 +1,26 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=ggsc
_pkgver=1.0.2
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="Visualizing Single Cell Data"
pkgrel=0
pkgdesc="Visualizing Single Cell and Spatial Transcriptomics"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
blas
onetbb
r-cli
r-dplyr
r-ggfun
r-ggplot2
r-rcolorbrewer
r-rcpp
r-rcppparallel
r-rlang
r-scales
r-scattermore
r-seurat
r-singlecellexperiment
@ -45,6 +49,7 @@ optdepends=(
r-prettydoc
r-rmarkdown
r-scater
r-scatterpie
r-scran
r-scuttle
r-seuratobject
@ -55,8 +60,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('4c0a1656e9943cadf436244c65b18242')
b2sums=('d8d67ddaf34fbdb71347226f6e916c22fd1338716a2b308e15b6d799e133dd9b9b7fba108b7e5792aed38c65efb4469cf9241cb2f3f50b3c2301c79cf169c228')
md5sums=('9b2e1ac75f9a734608bdd581df506a74')
b2sums=('774daf3d454078ef8c355f7817c546e7b84d9006f8ecf994e984ce7e20b1e7943cec296cb7fab90a0c50a55d0fe88f44ed245e252fbf08f0103f878420c99eba')
build() {
mkdir build

View file

@ -5,10 +5,13 @@ maintainers:
repo_depends:
- r-cli
- r-dplyr
- r-ggfun
- r-ggplot2
- r-rcolorbrewer
- r-rcpp
- r-rcppparallel
- r-rlang
- r-scales
- r-scattermore
- r-seurat
- r-singlecellexperiment
@ -31,3 +34,7 @@ update_on:
pkgname: blas
filename: usr/lib/libblas\.so\.([^.]+)
repo: extra
- source: alpmfiles
pkgname: onetbb
filename: usr/lib/libtbb\.so\.([^.]+)
repo: extra

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=hermes
_pkgver=1.6.1
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Preprocessing, analyzing, and reporting of RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -54,18 +54,17 @@ optdepends=(
r-statmod
r-testthat
r-vdiffr
r-withr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
"skip-tests.patch")
md5sums=('9e758f81455d5fc7a8b57c3a65b4de5b'
'e228515b639417bea13853cfc94b866a')
b2sums=('224fd9ad63e1bdf566a41e58f90c2cd120008add812f0ff4e777d72d9c3896c7d7ed06b5759b5c5330b2126dfc0cb6097584c7650c8a1f12fd2c1dcdf34ed99c'
'b781820238d74265dce64de9804bd568587c61c0460e15b32eabf27e0f827d673e52e852274e2613a2cf55bd54e218ad21493d78fc16f8fe954a98d3b9970bb7')
"fix-tests.patch")
md5sums=('e2a043604334a9302285e5864ecd72ab'
'029546b1d58fdda69b7ffa514d60f183')
b2sums=('a6264580c5c9d0591e4f5e3c0e9017e3f2666282d627beac7699d83572529646e053e5632de9ef76e615eab2226f5f0a568d22957d4bbe04d659a5f895491af3'
'cc64529e5965906de4292e712770f226e991a549d4bf6fe9b18db1b60fcdd0a4033a9aeb9ff7c59ccf1b2fe94dc69e9e492641a9df5b8579742abf726a36083b')
prepare() {
# skip failing tests
patch -Np1 -i skip-tests.patch
# fix snapshot tests
patch -Np1 -i fix-tests.patch
}
build() {

View file

@ -0,0 +1,52 @@
diff --git a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
index b739901..c6f4aa1 100644
--- a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
+++ b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-custom-options.svg
@@ -18,7 +18,7 @@
</clipPath>
</defs>
<g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
-<rect x='-0.000000000000064' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
+<rect x='0.00' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
</g>
<defs>
<clipPath id='cpMzcuNjl8NjI1Ljg5fDIyLjc4fDU0NS4xMQ=='>
diff --git a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
index 66b9399..8ff2300 100644
--- a/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
+++ b/hermes/tests/testthat/_snaps/graphs/draw-genes-barplot-with-default-options.svg
@@ -18,7 +18,7 @@
</clipPath>
</defs>
<g clip-path='url(#cpMC4wMHw3MjAuMDB8MC4wMHw1NzYuMDA=)'>
-<rect x='-0.000000000000064' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
+<rect x='0.00' y='0.00' width='720.00' height='576.00' style='stroke-width: 1.07; stroke: #FFFFFF; fill: #FFFFFF;' />
</g>
<defs>
<clipPath id='cpMzcuNjl8NjI1Ljg5fDIyLjc4fDU0NS4xMQ=='>
diff --git a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
index 5fb1e94..d8fc8b1 100644
--- a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
+++ b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-custom-options.svg
@@ -54,7 +54,7 @@
<circle cx='378.55' cy='307.48' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
<circle cx='378.55' cy='214.65' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
<circle cx='378.55' cy='104.30' r='1.95' style='stroke-width: 0.71; fill: #000000;' />
-<polygon points='364.29,528.89 392.81,528.89 392.73,528.88 393.07,528.87 393.41,528.80 393.74,528.68 394.04,528.50 394.31,528.28 394.54,528.02 394.73,527.73 394.86,527.41 394.94,527.07 394.97,526.73 394.97,526.73 394.97,516.01 394.97,516.01 394.94,515.67 394.86,515.33 394.73,515.01 394.54,514.72 394.31,514.46 394.04,514.24 393.74,514.06 393.41,513.94 393.07,513.87 392.81,513.85 364.29,513.85 364.55,513.87 364.20,513.86 363.86,513.90 363.52,513.99 363.21,514.14 362.92,514.34 362.67,514.58 362.47,514.86 362.30,515.17 362.19,515.50 362.14,515.84 362.13,516.01 362.13,526.73 362.14,526.55 362.14,526.90 362.19,527.24 362.30,527.57 362.47,527.88 362.67,528.16 362.92,528.40 363.21,528.60 363.52,528.75 363.86,528.84 364.20,528.88 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
+<polygon points='364.37,528.70 392.74,528.70 392.66,528.70 392.99,528.69 393.31,528.62 393.62,528.50 393.90,528.34 394.16,528.13 394.38,527.88 394.55,527.60 394.68,527.30 394.76,526.98 394.79,526.65 394.79,526.65 394.79,516.09 394.79,516.09 394.76,515.76 394.68,515.44 394.55,515.14 394.38,514.86 394.16,514.61 393.90,514.40 393.62,514.24 393.31,514.12 392.99,514.05 392.74,514.04 364.37,514.04 364.61,514.05 364.28,514.04 363.96,514.08 363.64,514.17 363.34,514.31 363.07,514.50 362.83,514.73 362.63,514.99 362.48,515.29 362.38,515.60 362.32,515.92 362.32,516.09 362.32,526.65 362.32,526.49 362.32,526.82 362.38,527.14 362.48,527.46 362.63,527.75 362.83,528.01 363.07,528.24 363.34,528.43 363.64,528.57 363.96,528.66 364.28,528.70 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
<text x='378.55' y='525.29' text-anchor='middle' style='font-size: 11.38px; font-family: sans;' textLength='25.64px' lengthAdjust='spacingAndGlyphs'>n=20</text>
<rect x='42.58' y='22.78' width='671.94' height='522.33' style='stroke-width: 1.07; stroke: #333333;' />
</g>
diff --git a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
index da75621..821a8d2 100644
--- a/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
+++ b/hermes/tests/testthat/_snaps/graphs/draw-nonzero-boxplot-with-default-options.svg
@@ -54,7 +54,7 @@
<circle cx='380.02' cy='307.69' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
<circle cx='361.44' cy='214.69' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
<circle cx='431.92' cy='104.34' r='1.95' style='stroke-width: 0.71; stroke: #000000; stroke-opacity: 0.25; fill: #000000; fill-opacity: 0.25;' />
-<polygon points='364.29,528.89 392.81,528.89 392.73,528.88 393.07,528.87 393.41,528.80 393.74,528.68 394.04,528.50 394.31,528.28 394.54,528.02 394.73,527.73 394.86,527.41 394.94,527.07 394.97,526.73 394.97,526.73 394.97,516.01 394.97,516.01 394.94,515.67 394.86,515.33 394.73,515.01 394.54,514.72 394.31,514.46 394.04,514.24 393.74,514.06 393.41,513.94 393.07,513.87 392.81,513.85 364.29,513.85 364.55,513.87 364.20,513.86 363.86,513.90 363.52,513.99 363.21,514.14 362.92,514.34 362.67,514.58 362.47,514.86 362.30,515.17 362.19,515.50 362.14,515.84 362.13,516.01 362.13,526.73 362.14,526.55 362.14,526.90 362.19,527.24 362.30,527.57 362.47,527.88 362.67,528.16 362.92,528.40 363.21,528.60 363.52,528.75 363.86,528.84 364.20,528.88 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
+<polygon points='364.37,528.70 392.74,528.70 392.66,528.70 392.99,528.69 393.31,528.62 393.62,528.50 393.90,528.34 394.16,528.13 394.38,527.88 394.55,527.60 394.68,527.30 394.76,526.98 394.79,526.65 394.79,526.65 394.79,516.09 394.79,516.09 394.76,515.76 394.68,515.44 394.55,515.14 394.38,514.86 394.16,514.61 393.90,514.40 393.62,514.24 393.31,514.12 392.99,514.05 392.74,514.04 364.37,514.04 364.61,514.05 364.28,514.04 363.96,514.08 363.64,514.17 363.34,514.31 363.07,514.50 362.83,514.73 362.63,514.99 362.48,515.29 362.38,515.60 362.32,515.92 362.32,516.09 362.32,526.65 362.32,526.49 362.32,526.82 362.38,527.14 362.48,527.46 362.63,527.75 362.83,528.01 363.07,528.24 363.34,528.43 363.64,528.57 363.96,528.66 364.28,528.70 ' style='stroke-width: 0.53; fill: #FFFFFF;' />
<text x='378.55' y='525.29' text-anchor='middle' style='font-size: 11.38px; font-family: sans;' textLength='25.64px' lengthAdjust='spacingAndGlyphs'>n=20</text>
<rect x='42.58' y='22.78' width='671.94' height='522.33' style='stroke-width: 1.07; stroke: #333333;' />
</g>

View file

@ -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(
_G,
expect_license = "Apache License 2.0 | file LICENSE",
)
r_pre_build(_G)
def post_build():
git_pkgbuild_commit()

View file

@ -1,196 +0,0 @@
diff --git a/hermes/tests/testthat/test-calc_cor.R b/hermes/tests/testthat/test-calc_cor.R
index f7c5f29..0010620 100644
--- a/hermes/tests/testthat/test-calc_cor.R
+++ b/hermes/tests/testthat/test-calc_cor.R
@@ -36,6 +36,7 @@ test_that("autoplot method does not give warnings on HermesDataCor objects", {
})
test_that("autoplot for HermesDataCor works as expected with default options", {
+ skip("fails")
object <- correlate(hermes_data)
result <- autoplot(object)
@@ -43,6 +44,7 @@ test_that("autoplot for HermesDataCor works as expected with default options", {
})
test_that("autoplot for HermesDataCor works as expected with custom options", {
+ skip("fails")
object <- correlate(hermes_data)
result <- autoplot(
object,
diff --git a/hermes/tests/testthat/test-connections.R b/hermes/tests/testthat/test-connections.R
index 7a471fa..088f659 100644
--- a/hermes/tests/testthat/test-connections.R
+++ b/hermes/tests/testthat/test-connections.R
@@ -2,7 +2,7 @@
# create object `.mart` with constant Ensembl version.
on_ci <- isTRUE(as.logical(Sys.getenv("CI")))
on_bioc <- !(identical(Sys.getenv("BBS_HOME"), ""))
-.mart <- if (on_ci || on_bioc) {
+.mart <- if (TRUE) {
NULL
} else {
as(
@@ -17,6 +17,7 @@ httr::set_config(httr::config(ssl_verifypeer = FALSE))
# connect_biomart ----
test_that("connect_biomart works as expected", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
@@ -30,6 +31,7 @@ test_that("connect_biomart works as expected", {
})
test_that("connect_biomart can specify older version of Ensembl", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
@@ -45,6 +47,7 @@ test_that("connect_biomart can specify older version of Ensembl", {
# h_get_annotation_biomart ----
test_that("h_get_annotation_biomart works as expected", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
@@ -86,6 +89,7 @@ test_that("h_strip_prefix works as expected", {
# h_get_size_biomart ----
test_that("h_get_size_biomart works as expected", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
@@ -126,6 +130,7 @@ test_that("h_get_size_biomart works as expected", {
# h_ensembl_to_entrez_ids ----
test_that("h_ensembl_to_entrez_ids works as expected", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
@@ -163,6 +168,7 @@ test_that("h_get_granges_by_id works as expected", {
# query-ConnectionBiomart ----
test_that("query to Biomart works as expected", {
+ skip("fails")
skip_on_ci()
skip_on_bioc()
diff --git a/hermes/tests/testthat/test-differential.R b/hermes/tests/testthat/test-differential.R
index 36750a7..31198c1 100644
--- a/hermes/tests/testthat/test-differential.R
+++ b/hermes/tests/testthat/test-differential.R
@@ -123,6 +123,7 @@ test_that("autoplot for HermesDataDiffExpr works as expected with default option
})
test_that("autoplot for HermesDataDiffExpr works as expected with custom options", {
+ skip("fails")
colData(hermes_data) <- df_cols_to_factor(colData(hermes_data))
object <- diff_expression(hermes_data, "SEX", "voom")
result <- autoplot(object, adj_p_val_thresh = 0.92, log2_fc_thresh = 3)
diff --git a/hermes/tests/testthat/test-draw_barplot.R b/hermes/tests/testthat/test-draw_barplot.R
index 4c1787e..980d335 100644
--- a/hermes/tests/testthat/test-draw_barplot.R
+++ b/hermes/tests/testthat/test-draw_barplot.R
@@ -1,4 +1,5 @@
test_that("draw_barplot works when there are duplicate labels in gene spec", {
+ skip("fails")
genes <- gene_spec(c(A = "GeneID:11185", A = "GeneID:10677"), fun = colMeans)
result <- draw_barplot(
hermes_data,
diff --git a/hermes/tests/testthat/test-draw_boxplot.R b/hermes/tests/testthat/test-draw_boxplot.R
index 7e3dcf0..1da1c46 100644
--- a/hermes/tests/testthat/test-draw_boxplot.R
+++ b/hermes/tests/testthat/test-draw_boxplot.R
@@ -1,6 +1,7 @@
# draw_boxplot ----
test_that("draw_boxplot works when there are duplicate labels in gene spec", {
+ skip("fails")
genes <- gene_spec(c(A = "GeneID:11185", A = "GeneID:10677"))
result <- draw_boxplot(
hermes_data,
diff --git a/hermes/tests/testthat/test-draw_scatterplot.R b/hermes/tests/testthat/test-draw_scatterplot.R
index 8c8bf7a..c60e625 100644
--- a/hermes/tests/testthat/test-draw_scatterplot.R
+++ b/hermes/tests/testthat/test-draw_scatterplot.R
@@ -1,4 +1,5 @@
test_that("draw_scatterplot works when there are duplicate labels in gene specs", {
+ skip("fails")
genes_x <- gene_spec(c(A = "GeneID:11185"))
genes_y <- gene_spec(c(A = "GeneID:10677"))
result <- draw_scatterplot(
diff --git a/hermes/tests/testthat/test-graphs.R b/hermes/tests/testthat/test-graphs.R
index 83bd111..ef1b378 100644
--- a/hermes/tests/testthat/test-graphs.R
+++ b/hermes/tests/testthat/test-graphs.R
@@ -1,6 +1,7 @@
# draw_libsize_hist ----
test_that("draw_libsize_hist works as expected", {
+ skip("fails")
result <- draw_libsize_hist(hermes_data, bins = 10L, fill = "blue")
vdiffr::expect_doppelganger("draw_libsize_hist with 10 blue bins", result)
@@ -17,6 +18,7 @@ test_that("draw_libsize_qq works as expected", {
# draw_libsize_densities ----
test_that("draw_libsize_densities works as expected", {
+ skip("fails")
result <- draw_libsize_densities(hermes_data)
vdiffr::expect_doppelganger("draw_libsize_densities with default log", result)
@@ -25,6 +27,7 @@ test_that("draw_libsize_densities works as expected", {
# draw_nonzero_boxplot ----
test_that("draw_nonzero_boxplot works as expected with default options", {
+ skip("fails")
set.seed(123)
result <- draw_nonzero_boxplot(hermes_data)
@@ -32,6 +35,7 @@ test_that("draw_nonzero_boxplot works as expected with default options", {
})
test_that("draw_nonzero_boxplot works as expected with custom options", {
+ skip("fails")
result <- draw_nonzero_boxplot(hermes_data, position = position_identity(), alpha = 1)
vdiffr::expect_doppelganger("draw_nonzero_boxplot with custom options", result)
@@ -40,12 +44,14 @@ test_that("draw_nonzero_boxplot works as expected with custom options", {
# draw_genes_barplot ----
test_that("draw_genes_barplot works as expected with default options", {
+ skip("fails")
result <- draw_genes_barplot(hermes_data)
vdiffr::expect_doppelganger("draw_genes_barplot with default options", result)
})
test_that("draw_genes_barplot works as expected with custom options", {
+ skip("fails")
result <- draw_genes_barplot(hermes_data, chromosomes = c("3", "11"), include_others = FALSE)
vdiffr::expect_doppelganger("draw_genes_barplot with custom options", result)
diff --git a/hermes/tests/testthat/test-top_genes.R b/hermes/tests/testthat/test-top_genes.R
index 9e32b23..2c1712f 100644
--- a/hermes/tests/testthat/test-top_genes.R
+++ b/hermes/tests/testthat/test-top_genes.R
@@ -74,6 +74,7 @@ test_that("top genes gives the names of the genes in the correct order", {
# autoplot-HermesDataTopGenes ----
test_that("autoplot for HermesDataTopGenes works as expected with default options", {
+ skip("fails")
object <- top_genes(hermes_data)
result <- autoplot(object)
@@ -81,6 +82,7 @@ test_that("autoplot for HermesDataTopGenes works as expected with default option
})
test_that("autoplot for HermesDataTopGenes works as expected with custom options", {
+ skip("fails")
object <- top_genes(hermes_data)
result <- autoplot(object, x_lab = "genes", y_lab = "mean count", title = "bla")

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=hicVennDiagram
_pkgver=1.0.2
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Venn Diagram for genomic interaction data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -12,29 +12,31 @@ license=('GPL-3.0-only')
depends=(
r-complexupset
r-eulerr
r-genomeinfodb
r-genomicranges
r-ggplot2
r-htmlwidgets
r-interactionset
r-iranges
r-reshape2
r-rtracklayer
r-s4vectors
r-svglite
)
checkdepends=(
r-genomicranges
r-testthat
)
optdepends=(
r-biocstyle
r-chippeakanno
r-genomicranges
r-knitr
r-rmarkdown
r-testthat
r-txdb.hsapiens.ucsc.hg38.knowngene
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('61651aeae22cb23e4e66b3a7b9d0896f')
b2sums=('f6e5af8063c103b62b53ff38c80ee2b8441ebf4395bf92a0c42a81d868c738c2f5059ce366438cbac9eae4859b53a3abdcf3b5d39be1da103be3d1b3fa6db52d')
md5sums=('313574d5ead069cabeb5aafa7bbae093')
b2sums=('66953fd68d7e4bda96027956cc5e782dad88e34bf1f543a80699c6f1e6970af305050d932c68e73c740a13e49137eb2f5616d0cad9d6088baea2f486a4c2ff02')
build() {
mkdir build

View file

@ -5,15 +5,17 @@ maintainers:
repo_depends:
- r-complexupset
- r-eulerr
- r-genomeinfodb
- r-genomicranges
- r-ggplot2
- r-htmlwidgets
- r-interactionset
- r-iranges
- r-reshape2
- r-rtracklayer
- r-s4vectors
- r-svglite
repo_makedepends:
- r-genomicranges
- r-testthat
update_on:
- source: rpkgs

View file

@ -2,15 +2,16 @@
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=HumanTranscriptomeCompendium
_pkgver=1.17.0
_pkgver=1.20.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Tools to work with a Compendium of 181000 human transcriptome sequencing studies"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-biocmanager
r-s4vectors
r-shiny
r-ssrch
@ -18,7 +19,6 @@ depends=(
)
checkdepends=(
r-biocfilecache
r-biocmanager
r-rhdf5client
r-testthat
)
@ -37,8 +37,8 @@ optdepends=(
r-tximportdata
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('00689fd704a35eea4e0ba38516603b49')
b2sums=('8b74cc6ea362178bd614539615e2fe6e1b5738dc7e22f534136c861a9fe59ef9442c04ccf4f5ae34fcbefb3eda9ff72376117ee710b27f3179d8f00c185f1b4a')
md5sums=('27bbd86aebf51ff0bfbfad400b80d69b')
b2sums=('078fedc4db598d81b05076b4f043e38b34d0e1ab9f6521d0c25f86b19d1dc811b61fd46a641b043ecaf090c609b87ca963a830c01cc51be3995e5a81b0daf44c')
build() {
mkdir build

View file

@ -3,13 +3,13 @@ maintainers:
- github: pekkarr
email: pekkarr@protonmail.com
repo_depends:
- r-biocmanager
- r-s4vectors
- r-shiny
- r-ssrch
- r-summarizedexperiment
repo_makedepends:
- r-biocfilecache
- r-biocmanager
- r-rhdf5client
- r-testthat
update_on:

View file

@ -2,10 +2,10 @@
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=IgGeneUsage
_pkgver=1.16.0
_pkgver=1.18.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=4
pkgrel=0
pkgdesc="Differential gene usage in immune repertoires"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
@ -33,17 +33,19 @@ optdepends=(
r-ggforce
r-ggplot2
r-ggrepel
r-gridextra
r-knitr
r-patchwork
r-rmarkdown
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('231f1af3465f435ca3bb099a93e51e5b')
b2sums=('6b645f318f8017a9ca973f869b5924899aaf39262e46e920d7757c8361d847ac4c623811df25dfbbeb12087fca01875edd6bbc84d2989c0d381f5e3c6bb6ed35')
md5sums=('6b09f356086c2d9d212b6b64973d69a9')
b2sums=('fa24145aaf622951e6439e2ee8859e7ce3cf5f133be0ff1828a46bbede22d787cf6af5b689cc33244d70bdf308d60e9470f1d130879bfa74eeb9d45245d4eaf6')
build() {
mkdir build
# compilation needs a lot of memory
MAKEFLAGS+=" -j1"
R CMD INSTALL -l build "$_pkgname"
}

View file

@ -2,16 +2,17 @@
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=lefser
_pkgver=1.12.1
_pkgver=1.14.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="R implementation of the LEfSE method for microbiome biomarker discovery"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-coin
r-dplyr
r-ggplot2
r-s4vectors
r-summarizedexperiment
@ -28,8 +29,8 @@ optdepends=(
r-withr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('c3b2deaf4b58de1bb930164df11a388f')
b2sums=('2dba16640a6e47d68966e0ad01d6dce44c5f909b0a51262258d271bfeec0b2a303d0702e63847e077a2a1e22efb1520594011260cb182e266150417003aef91a')
md5sums=('f092ce758deedacc39855a98cfc06849')
b2sums=('404f6a5b4eaf7b74020ca95e47d31e6aa2a783aa9d14a1b4ea95e8e41e65174a092febad84fbe79c23a1b4b1e69b53e01625c13d16103f007545d442b31472ec')
build() {
mkdir build

View file

@ -4,6 +4,7 @@ maintainers:
email: pekkarr@protonmail.com
repo_depends:
- r-coin
- r-dplyr
- r-ggplot2
- r-s4vectors
- r-summarizedexperiment

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=LinTInd
_pkgver=1.6.0
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Lineage tracing by indels"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -23,6 +23,7 @@ depends=(
r-networkd3
r-pheatmap
r-purrr
r-pwalign
r-reshape2
r-rlist
r-s4vectors
@ -34,8 +35,8 @@ optdepends=(
r-rmarkdown
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('3dd8f8601ee8df3a0a53a02dc0c4d272')
b2sums=('97f130b23e117677ffda7c12e814f8ff33989f7309d2d67c4f84c2b3e1e690e77550076bbb86035ed338d94671bce72e92f4728c8f45c66f84e6ed57bed1b68e')
md5sums=('bd5c8c848408028ffc8fd1bd5529d586')
b2sums=('ea8db25d21644283bebf9bd52de15deb8bfaca0991abe5548b379730929e10c9b630c9a483acf82b56d0900816a191910a7fede32958dd936bf9e489ff9207d0')
build() {
mkdir build

View file

@ -16,6 +16,7 @@ repo_depends:
- r-networkd3
- r-pheatmap
- r-purrr
- r-pwalign
- r-reshape2
- r-rlist
- r-s4vectors

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=Macarron
_pkgver=1.6.0
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -15,11 +15,11 @@ depends=(
r-delayedarray
r-dynamictreecut
r-ff
r-httr
r-logging
r-maaslin2
r-plyr
r-psych
r-rcurl
r-rjsonio
r-summarizedexperiment
r-wgcna
@ -37,8 +37,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('525669e56fccd2be5524315ee6a0eafb')
b2sums=('9e5ae37af40ba687647a95c75b60c86cd3586de67ca7aa0ec3bb103faa59e13f7a29b1c216d9adfdd43c2a85b841cb9f2d2b9f16011a8be8efed2876a4e4c7a3')
md5sums=('f0ab96828900fe45d5eb914afa5baf89')
b2sums=('50a17512558616fdda67f672898a0d11cd2bf6ebcb8c57f41b77d22628abcefc5fc1b8752d4c1b8d37bcf9aaa785dbdc0e0e60a733b6260570a4d0ce494bef5d')
build() {
mkdir build

View file

@ -8,11 +8,11 @@ repo_depends:
- r-delayedarray
- r-dynamictreecut
- r-ff
- r-httr
- r-logging
- r-maaslin2
- r-plyr
- r-psych
- r-rcurl
- r-rjsonio
- r-summarizedexperiment
- r-wgcna

View file

@ -2,10 +2,10 @@
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=methylscaper
_pkgver=1.10.0
_pkgver=1.12.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=2
pkgrel=0
pkgdesc="Visualization of Methylation Data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -14,6 +14,7 @@ depends=(
r-biocparallel
r-biostrings
r-data.table
r-pwalign
r-rfast
r-seqinr
r-seriation
@ -30,8 +31,8 @@ optdepends=(
r-rmarkdown
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('0fae72e2aac98ec4a55d8aa4343039ba')
b2sums=('a0e2d398a8a537dd26314c6c60cbfe5cc6211c22223a866f3bbb56304793547f1211c7f77487ef478e0df69ddeb60cafbf747ed150d8798dc1aea2ea3c284f68')
md5sums=('da76dd45cdba774ec799f415e5a95743')
b2sums=('afc889892c8050ab087f2a360290fdf478f2a9b03bd53870b15e8a419dbc42a37ab60bd733b6a43479d5d2e5411453f237b9c559667150171bdb7577eba1b83b')
build() {
mkdir build

View file

@ -6,6 +6,7 @@ repo_depends:
- r-biocparallel
- r-biostrings
- r-data.table
- r-pwalign
- r-rfast
- r-seqinr
- r-seriation

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=MsBackendMsp
_pkgver=1.6.0
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Mass Spectrometry Data Backend for NIST msp Files"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -13,6 +13,7 @@ depends=(
r-biocparallel
r-iranges
r-mscoreutils
r-protgenerics
r-s4vectors
r-spectra
)
@ -27,8 +28,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('805d831547106b2f232bb9eda75172bc')
b2sums=('2164f6a771b0d4fa1d33e8d2c6d6043a20fed24bc35feaeb8445287084bc488fb6f184039c4d878a998ebdeca09ae78ceec43042e81479442a990b73918255f3')
md5sums=('0c1449c171d9dbb52f4a1f3815716b86')
b2sums=('0c395932dfbccac200fbb1a2e54bac293de9513a052e19b4bb11a5bc0d770030f0146c1787729b76517a991274ecab4c9236b36a8be1cda73a878fbf85b60230')
build() {
mkdir build

View file

@ -6,6 +6,7 @@ repo_depends:
- r-biocparallel
- r-iranges
- r-mscoreutils
- r-protgenerics
- r-s4vectors
- r-spectra
repo_makedepends:

View file

@ -1,11 +1,11 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=MultiRNAflow
_pkgver=1.0.0
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgdesc="An R package for analysing RNA-seq raw counts with several biological conditions and different time points"
pkgrel=0
pkgdesc="An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
@ -17,18 +17,14 @@ depends=(
r-factominer
r-ggalluvial
r-ggplot2
r-ggplotify
r-ggrepel
r-ggsci
r-gprofiler2
r-mfuzz
r-plot3d
r-plot3drgl
r-plyr
r-rcolorbrewer
r-reshape2
r-rlang
r-s4vectors
r-scales
r-summarizedexperiment
r-upsetr
)
@ -44,8 +40,8 @@ optdepends=(
r-testthat
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('cefc109896f4cb34b4ee6a09ae966f42')
b2sums=('f177caeb4ada5c30e51d852e816b2bfaad64149e2b6cba1a287f0b799a000998684bb54f6bb77cb49050a507a5cee5c5b9456ae3084362519ff8e67045321e41')
md5sums=('223e9edd588edeb351f343daffb27bd3')
b2sums=('c582f6e4081d04c5c7558def452d5f7b6c274382f52131316cd2ecc73e692ecbf9983b12c8ed29c9b9f49c24a910130c3d62bb43d54518bf0cb344e4c79fdcca')
build() {
mkdir build

View file

@ -10,18 +10,14 @@ repo_depends:
- r-factominer
- r-ggalluvial
- r-ggplot2
- r-ggplotify
- r-ggrepel
- r-ggsci
- r-gprofiler2
- r-mfuzz
- r-plot3d
- r-plot3drgl
- r-plyr
- r-rcolorbrewer
- r-reshape2
- r-rlang
- r-s4vectors
- r-scales
- r-summarizedexperiment
- r-upsetr
repo_makedepends:

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=nipalsMCIA
_pkgver=1.0.0
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Multiple Co-Inertia Analysis via the NIPALS Method"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -25,6 +25,7 @@ checkdepends=(
r-testthat
)
optdepends=(
r-biocfilecache
r-biocstyle
r-circlize
r-ggpubr
@ -39,8 +40,8 @@ optdepends=(
r-tidyverse
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('0558d05ea61523c6fcaed9d8ed9b0ded')
b2sums=('1b4f12364525b2732899e332a90c97b3ba68320a996442e94cf67c983c97e5ad98c2ce65f6e85b2bcc5410118a1f279514199dfd35b4432651094f5beafe8e91')
md5sums=('4092618c668e796e5fbaa4f6fe34bc2f')
b2sums=('331f310aa90a60f66efaf44d30118d37c038330e3c8bc23cabffeccb8768924f985bfd89ab0ff0aa6fb921c53136df7e9e8792d33b8a31bd6e40a51b5d6c6dcb')
build() {
mkdir build

View file

@ -1,10 +1,10 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=omicsViewer
_pkgver=1.6.0
_pkgver=1.8.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
@ -13,6 +13,7 @@ depends=(
r-beeswarm
r-biobase
r-curl
r-drc
r-dt
r-fastmatch
r-fgsea
@ -48,8 +49,8 @@ optdepends=(
r-unittest
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('7d650ff242a133610199a574a29abfde')
b2sums=('f97ece507080b043c87e59f55c3a84bfb391264a62ed1b1e67169794774e3e521c7ff904584199eae21b83c96f25a22335eb1625d6c284acf34a00dc7b2ab1e1')
md5sums=('99de2e1df69e1e064471746fd94fb31f')
b2sums=('cf4c1ae23e1dd6f1d44a7dcb0cce741dece1c1a8eb9e965464851f7b60b3fc8863b1fbdeb2626848bb78dc874d3de2f0afc199208f0bec35acc94ae1543fe990')
build() {
mkdir build

View file

@ -6,6 +6,7 @@ repo_depends:
- r-beeswarm
- r-biobase
- r-curl
- r-drc
- r-dt
- r-fastmatch
- r-fgsea

View file

@ -1,16 +1,17 @@
# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=RNAseqCovarImpute
_pkgver=1.0.2
_pkgver=1.2.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=3
pkgrel=0
pkgdesc="Impute Covariate Data in RNA Sequencing Studies"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('GPL-3.0-only')
depends=(
r-biobase
r-biocgenerics
r-biocparallel
r-dplyr
r-edger
@ -26,14 +27,15 @@ checkdepends=(
optdepends=(
r-biocstyle
r-knitr
r-pcatools
r-rmarkdown
r-stringr
r-testthat
r-tidyr
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('17d14273ae359562d3f0cbf1c45b10a7')
b2sums=('48f75a62b283ba85cc581266360abebb252ac32a9e3e8193ed11b5c68deb9df4d2ffd41903cbfa41855ab99a77a2a61b1837aa21cec74ed940fd298d5b915367')
md5sums=('0ec9872567c7b1063c7d9fb1f20a3517')
b2sums=('c2a263fd3922a217da2be63f8d43b4cea88792014abcaa97a2f89279898e09581fe706e10375315e847a557c2a1f3b21b896025db04a49b41e135a19e01fc962')
build() {
mkdir build

View file

@ -4,6 +4,7 @@ maintainers:
email: pekkarr@protonmail.com
repo_depends:
- r-biobase
- r-biocgenerics
- r-biocparallel
- r-dplyr
- r-edger

View file

@ -2,10 +2,10 @@
# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
_pkgname=SAIGEgds
_pkgver=2.2.1
_pkgver=2.4.0
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=4
pkgrel=0
pkgdesc="Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association Studies"
arch=(x86_64)
url="https://bioconductor.org/packages/$_pkgname"
@ -14,17 +14,18 @@ depends=(
blas
lapack
onetbb
r-compquadform
r-gdsfmt
r-rcpp
r-rcppparallel
r-seqarray
r-survey
)
makedepends=(
r-rcpparmadillo
)
optdepends=(
r-biocgenerics
r-compquadform
r-crayon
r-ggmanh
r-knitr
@ -32,11 +33,10 @@ optdepends=(
r-rmarkdown
r-runit
r-snprelate
r-survey
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('1187edceb086e860386386db76896e83')
b2sums=('4088bd9e28b66232c74cc1e12291eb5799a231adfb00d7c200f161a20998552df3fb7097c3f16b88ce99cb9816f9cddfd0225af0c08171881a635e1d2037cc26')
md5sums=('874595e6351ae7cceea8a4f4d92cd6db')
b2sums=('d9301bcf684f4806895315ca3dcfe8f97d94c7756be80a55cb6fd35f8254915a107338dc341810f52a0141f16aefc7c6eea99fee2a871a9d5537c0e4e6a5243a')
build() {
mkdir build

View file

@ -3,10 +3,12 @@ maintainers:
- github: pekkarr
email: pekkarr@protonmail.com
repo_depends:
- r-compquadform
- r-gdsfmt
- r-rcpp
- r-rcppparallel
- r-seqarray
- r-survey
repo_makedepends:
- r-rcpparmadillo
update_on: