From 743061eabcaa552a3694313ec0c5012c6af99b76 Mon Sep 17 00:00:00 2001 From: BiocondaBot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 15 Nov 2024 00:11:31 +0000 Subject: [PATCH 01/14] Update r-archr to 1.0.3 --- recipes/r-archr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index f5472501bbc18..e44b895a27032 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 '' %} @@ -8,7 +8,7 @@ package: source: url: {{ github }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352 + sha256: 9c07c785a095062a998ed94c65df17a58f273d0d64062c14210f0a2c491304cf patches: - patches/0001-cap-threads.patch From c6d6f773ed3aedd262710b104a3b876a2daf6212 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 09:40:44 +0100 Subject: [PATCH 02/14] update deps; update license; drop patch --- recipes/r-archr/meta.yaml | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index e44b895a27032..7d693d1533e6c 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -9,8 +9,6 @@ package: source: url: {{ github }}/archive/refs/tags/v{{ version }}.tar.gz sha256: 9c07c785a095062a998ed94c65df17a58f273d0d64062c14210f0a2c491304cf - patches: - - patches/0001-cap-threads.patch 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 @@ -37,7 +35,9 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 - bioconductor-summarizedexperiment + - r-chromvarmotifs - r-data.table + - r-devtools - r-ggplot2 - r-ggrepel - r-gridextra @@ -48,11 +48,15 @@ requirements: - 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 @@ -63,7 +67,9 @@ requirements: - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 - bioconductor-summarizedexperiment + - r-chromvarmotifs - r-data.table + - r-devtools - r-ggplot2 - r-ggrepel - r-gridextra @@ -74,7 +80,11 @@ requirements: - r-matrixstats - r-nabor - r-plyr + - r-presto - r-rcpp >=0.12.16 + - r-rcpparmadillo + - r-seurat + - r-seuratobject - r-stringr - r-uwot @@ -86,12 +96,11 @@ 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: From 3aff1ca36b49d2c91399b8985b4b3c4d21a55d47 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 09:41:05 +0100 Subject: [PATCH 03/14] drop patch --- .../r-archr/patches/0001-cap-threads.patch | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 recipes/r-archr/patches/0001-cap-threads.patch 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 From 3fd317732e249cb5108dbbbe1901ecc06f121b9e Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 10:21:24 +0100 Subject: [PATCH 04/14] Update deps --- recipes/r-archr/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 7d693d1533e6c..ffca6fbb5d942 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -34,6 +34,7 @@ requirements: - bioconductor-rhdf5 - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 + - bioconductor-sparsematrixstats - bioconductor-summarizedexperiment - r-chromvarmotifs - r-data.table @@ -43,6 +44,7 @@ requirements: - r-gridextra - r-gtable - r-gtools + - r-harmony - r-magrittr - r-matrix - r-matrixstats @@ -66,6 +68,7 @@ requirements: - bioconductor-rhdf5 - bioconductor-rsamtools - bioconductor-s4vectors >=0.9.25 + - bioconductor-sparsematrixstats - bioconductor-summarizedexperiment - r-chromvarmotifs - r-data.table @@ -75,6 +78,7 @@ requirements: - r-gridextra - r-gtable - r-gtools + - r-harmony - r-magrittr - r-matrix - r-matrixstats From 6414ce49de738e05244904cc5b6b450545da6da9 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 14:53:58 +0100 Subject: [PATCH 05/14] run testthat tests --- recipes/r-archr/meta.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index ffca6fbb5d942..b7e001ef6f90d 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -93,8 +93,13 @@ requirements: - r-uwot test: + requires: + - r-testthat + source_files: + - tests/ commands: - $R -e "library('ArchR')" + - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" about: home: https://www.archrproject.com From 2a10a1c7b7cecfc55c4aa76808e95fdd2cee0002 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 17:08:31 +0100 Subject: [PATCH 06/14] add test dep --- recipes/r-archr/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index b7e001ef6f90d..32a230b17a240 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -95,6 +95,7 @@ requirements: test: requires: - r-testthat + - bioconductor-bsgenome.hsapiens.ucsc.hg19 source_files: - tests/ commands: From c1b05d79cc9f8395e0285f592cc7e5a8b726278d Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 21:03:01 +0100 Subject: [PATCH 07/14] debug --- recipes/r-archr/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 32a230b17a240..218c3401d4b06 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -100,7 +100,7 @@ test: - tests/ commands: - $R -e "library('ArchR')" - - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" + - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=FALSE)" about: home: https://www.archrproject.com From 31ca6a6706f78b8e926e0671fc25824d34dfb7fd Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Fri, 15 Nov 2024 23:28:43 +0100 Subject: [PATCH 08/14] debug --- recipes/r-archr/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 218c3401d4b06..ea1f0b2a30d5d 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -100,7 +100,7 @@ test: - tests/ commands: - $R -e "library('ArchR')" - - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=FALSE)" + #- $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" about: home: https://www.archrproject.com From 0c2f8231a5c89e62fa8f6a1d1ae737edbb195b8e Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Sat, 16 Nov 2024 11:53:39 +0100 Subject: [PATCH 09/14] reenable tests; add deps --- recipes/r-archr/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index ea1f0b2a30d5d..6be092c061b69 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -74,6 +74,8 @@ requirements: - r-data.table - r-devtools - r-ggplot2 + ## ggrastr is optional lib, but plotting defaults assume it + - r-ggrastr - r-ggrepel - r-gridextra - r-gtable @@ -95,12 +97,13 @@ requirements: test: requires: - r-testthat + - macs2 - bioconductor-bsgenome.hsapiens.ucsc.hg19 source_files: - tests/ commands: - $R -e "library('ArchR')" - #- $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" + - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" about: home: https://www.archrproject.com From d06ad7003f6e5769ccd0d70a8dc1c28b9d53044a Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Tue, 19 Nov 2024 13:20:31 +0100 Subject: [PATCH 10/14] upper bound ggplot2 --- recipes/r-archr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 6be092c061b69..abfcf7c55bd9d 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -39,7 +39,7 @@ requirements: - r-chromvarmotifs - r-data.table - r-devtools - - r-ggplot2 + - r-ggplot2 <3.5 - r-ggrepel - r-gridextra - r-gtable @@ -73,7 +73,7 @@ requirements: - r-chromvarmotifs - r-data.table - r-devtools - - r-ggplot2 + - r-ggplot2 <3.5 ## ggrastr is optional lib, but plotting defaults assume it - r-ggrastr - r-ggrepel From b3738aca8437e7ce07ce7e18474ce01b9b98b49e Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Tue, 19 Nov 2024 14:12:03 +0100 Subject: [PATCH 11/14] install tests --- recipes/r-archr/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-archr/build.sh b/recipes/r-archr/build.sh index b8d2635525637..612617da660c2 100644 --- a/recipes/r-archr/build.sh +++ b/recipes/r-archr/build.sh @@ -1,3 +1,3 @@ #!/bin/bash export DISABLE_AUTOBREW=1 -${R} CMD INSTALL --build . ${R_ARGS} +${R} CMD INSTALL --build --install-tests . ${R_ARGS} From b18f160a069808cd27aae0ecab4b1a8213f8ff58 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Tue, 19 Nov 2024 14:13:41 +0100 Subject: [PATCH 12/14] test installed tests --- recipes/r-archr/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index abfcf7c55bd9d..6d5b35a53ceb4 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -99,11 +99,9 @@ test: - r-testthat - macs2 - bioconductor-bsgenome.hsapiens.ucsc.hg19 - source_files: - - tests/ commands: - $R -e "library('ArchR')" - - $R -e "testthat::test_file('tests/testthat.R', stop_on_failure=TRUE)" + - $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)" about: home: https://www.archrproject.com From e833ba81b35ae3fa9c423cc741af4e940ac7e97b Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Wed, 20 Nov 2024 10:30:56 +0100 Subject: [PATCH 13/14] avoid container unit tests this depends that `test.requires` are not installed for the container and checks lack of macs2 to skip --- recipes/r-archr/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 6d5b35a53ceb4..912dbde12a7ff 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -101,7 +101,8 @@ test: - bioconductor-bsgenome.hsapiens.ucsc.hg19 commands: - $R -e "library('ArchR')" - - $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)" + ## NB: this tightly-couples to `macs2` coming from `test.requires` and avoids running against the container + - command -v macs2 && $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)" about: home: https://www.archrproject.com From c3139b952c51ace815438abc3e530f9b3fed08f3 Mon Sep 17 00:00:00 2001 From: Mervin Fansler Date: Wed, 20 Nov 2024 13:37:31 +0100 Subject: [PATCH 14/14] conditional --- recipes/r-archr/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-archr/meta.yaml b/recipes/r-archr/meta.yaml index 912dbde12a7ff..4051558d4a6df 100644 --- a/recipes/r-archr/meta.yaml +++ b/recipes/r-archr/meta.yaml @@ -102,7 +102,7 @@ test: commands: - $R -e "library('ArchR')" ## NB: this tightly-couples to `macs2` coming from `test.requires` and avoids running against the container - - command -v macs2 && $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)" + - if command -v macs2; then $R -e "testthat::test_package('ArchR', stop_on_failure=TRUE)"; fi about: home: https://www.archrproject.com