diff --git a/recipes/r-archr/build.sh b/recipes/r-archr/build.sh index b8d2635525637..612617da660c2 100644 --- a/recipes/r-archr/build.sh +++ b/recipes/r-archr/build.sh @@ -1,3 +1,3 @@ #!/bin/bash export DISABLE_AUTOBREW=1 -${R} CMD INSTALL --build . ${R_ARGS} +${R} CMD INSTALL --build --install-tests . ${R_ARGS} diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index f5472501bbc18..4051558d4a6df 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.0.2' %} +{% set version = '1.0.3' %} {% set github = 'https://github.com/GreenleafLab/ArchR' %} {% set posix = 'm2-' if win else '' %} @@ -8,9 +8,7 @@ package: source: url: {{ github }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352 - patches: - - patches/0001-cap-threads.patch + sha256: 9c07c785a095062a998ed94c65df17a58f273d0d64062c14210f0a2c491304cf build: number: 0 @@ -26,7 +24,7 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} host: - - r-base =4.1 + - r-base - bioconductor-biocgenerics - bioconductor-biostrings - bioconductor-chromvar @@ -36,23 +34,31 @@ requirements: - bioconductor-rhdf5 - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 + - bioconductor-sparsematrixstats - bioconductor-summarizedexperiment + - r-chromvarmotifs - r-data.table - - r-ggplot2 + - r-devtools + - r-ggplot2 <3.5 - r-ggrepel - r-gridextra - r-gtable - r-gtools + - r-harmony - r-magrittr - r-matrix - r-matrixstats - r-nabor - r-plyr + - r-presto - r-rcpp >=0.12.16 + - r-rcpparmadillo + - r-seurat + - r-seuratobject - r-stringr - r-uwot run: - - r-base =4.1 + - r-base - bioconductor-biocgenerics - bioconductor-biostrings - bioconductor-chromvar @@ -62,36 +68,51 @@ requirements: - bioconductor-rhdf5 - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 + - bioconductor-sparsematrixstats - bioconductor-summarizedexperiment + - r-chromvarmotifs - r-data.table - - r-ggplot2 + - r-devtools + - r-ggplot2 <3.5 + ## ggrastr is optional lib, but plotting defaults assume it + - r-ggrastr - r-ggrepel - r-gridextra - r-gtable - r-gtools + - r-harmony - r-magrittr - r-matrix - r-matrixstats - r-nabor - r-plyr + - r-presto - r-rcpp >=0.12.16 + - r-rcpparmadillo + - r-seurat + - r-seuratobject - r-stringr - r-uwot test: + requires: + - r-testthat + - macs2 + - bioconductor-bsgenome.hsapiens.ucsc.hg19 commands: - $R -e "library('ArchR')" + ## NB: this tightly-couples to `macs2` coming from `test.requires` and avoids running against the container + - if command -v macs2; then $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)"; fi about: home: https://www.archrproject.com dev_url: {{ github }} doc_url: https://www.archrproject.com/bookdown/index.html - license: GPL-2.0-or-later + license: MIT summary: This package is designed to streamline scATAC analyses in R. - license_family: GPL2 + license_family: MIT license_file: - - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-2 - - {{ environ['PREFIX'] }}/lib/R/share/licenses/GPL-3 + - {{ environ['PREFIX'] }}/lib/R/share/licenses/MIT extra: recipe-maintainers: diff --git a/recipes/r-archr/patches/0001-cap-threads.patch b/recipes/r-archr/patches/0001-cap-threads.patch deleted file mode 100644 index b1384bd55b381..0000000000000 --- a/recipes/r-archr/patches/0001-cap-threads.patch +++ /dev/null @@ -1,36 +0,0 @@ -From f512a5eaab8b12ef4c78414ffdf813c7ebc872c5 Mon Sep 17 00:00:00 2001 -From: Mervin Fansler -Date: Fri, 11 Oct 2024 12:50:25 +0200 -Subject: [PATCH] bugfix threads not capped to threads input - ---- - R/CreateArrow.R | 2 +- - R/MatrixGeneScores.R | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/R/CreateArrow.R b/R/CreateArrow.R -index ac0be626..08243139 100644 ---- a/R/CreateArrow.R -+++ b/R/CreateArrow.R -@@ -205,7 +205,7 @@ createArrowFiles <- function( - if(subThreading){ - h5disableFileLocking() - }else{ -- args$threads <- length(inputFiles) -+ args$threads <- min(length(inputFiles), threads) - } - - args$minTSS <- NULL -diff --git a/R/MatrixGeneScores.R b/R/MatrixGeneScores.R -index 1d1d10b3..fd342a1a 100644 ---- a/R/MatrixGeneScores.R -+++ b/R/MatrixGeneScores.R -@@ -125,7 +125,7 @@ addGeneScoreMatrix <- function( - if(subThreading){ - h5disableFileLocking() - }else{ -- args$threads <- length(ArrowFiles) -+ args$threads <- min(length(ArrowFiles), threads) - } - - #Remove Input from args