diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml index 34577a5b0704b..812be3af50872 100644 --- a/recipes/r-basejump/meta.yaml +++ b/recipes/r-basejump/meta.yaml @@ -1,12 +1,13 @@ -{% set version = "0.9.11" %} +{% set version = "0.10.9" %} +{% set github = "https://github.com/acidgenomics/basejump" %} package: name: r-basejump - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/basejump/archive/v{{ version }}.tar.gz - sha256: c68790afe6c655ec448b39a3afad07f6a13470a295ed9e06c27f30d2dadbfebe + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 2f3735c44df99296c584a1dc4583041a9e5b24b3f8c3146cea1b8c497c05c296 build: number: 0 @@ -18,105 +19,81 @@ build: requirements: host: - r-base - - bioconductor-annotationhub + - r-bioverbs >=0.1.19 + - r-brio >=0.2.1 + - r-freerange >=0.1.6 + - r-goalie >=0.2.16 + - r-syntactic >=0.1.9 + - r-transformer >=0.1.11 - bioconductor-biobase - bioconductor-biocgenerics - - bioconductor-ensembldb - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges - bioconductor-s4vectors - - r-assertive - - r-cowplot >=0.9 - - r-dendsort - - r-matrix.utils >=0.9 - - r-dplyr >=0.7 - - r-pbapply - - r-devtools - - r-ggplot2 >=3.0 - - r-knitr >=1.2.1 + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-dplyr >=0.8 + - r-knitr >=1.22 - r-magrittr >=1.5 - r-matrix >=1.2 - - r-rio - - r-sessioninfo >=1.1 - - r-pheatmap >=1.0 - - r-rcolorbrewer - - r-rcurl >=1.95 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-purrr >=0.2 - r-readr >=1.3 - - r-readxl >=1.0 + - r-reshape2 >=1.4 - r-rlang >=0.3 - - r-r.utils - - r-scales + - r-sessioninfo >=1.1 - r-stringr >=1.3 - r-tibble >=2.0 - r-tidyr >=0.8 - - r-viridis - - r-yaml - - r-bioverbs >=0.1.8 - - r-brio >=0.1.8 - - r-goalie >=0.2.9 - - r-syntactic >=0.1.5 - - r-transformer >=0.1.6 - r-tidyselect >=0.2 - - r-ggrepel >=0.8 - - r-matrixstats >=0.54 - - r-purrr >=0.2 - - r-reshape2 >=1.4 run: - r-base - - bioconductor-annotationhub + - r-bioverbs >=0.1.19 + - r-brio >=0.2.1 + - r-freerange >=0.1.6 + - r-goalie >=0.2.16 + - r-syntactic >=0.1.9 + - r-transformer >=0.1.11 - bioconductor-biobase - bioconductor-biocgenerics - - bioconductor-ensembldb - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges - bioconductor-s4vectors - - r-assertive - - r-cowplot >=0.9 - - r-dendsort - - r-matrix.utils >=0.9 - - r-dplyr >=0.7 - - r-pbapply - - r-devtools - - r-ggplot2 >=3.0 - - r-knitr >=1.2.1 + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-dplyr >=0.8 + - r-knitr >=1.22 - r-magrittr >=1.5 - r-matrix >=1.2 - - r-rio - - r-sessioninfo >=1.1 - - r-pheatmap >=1.0 - - r-rcolorbrewer - - r-rcurl >=1.95 + - r-matrix.utils >=0.9 + - r-matrixstats >=0.54 + - r-purrr >=0.2 - r-readr >=1.3 - - r-readxl >=1.0 + - r-reshape2 >=1.4 - r-rlang >=0.3 - - r-r.utils - - r-scales + - r-sessioninfo >=1.1 - r-stringr >=1.3 - r-tibble >=2.0 - r-tidyr >=0.8 - - r-viridis - - r-yaml - - r-bioverbs >=0.1.8 - - r-brio >=0.1.8 - - r-goalie >=0.2.9 - - r-syntactic >=0.1.5 - - r-transformer >=0.1.6 - r-tidyselect >=0.2 - - r-ggrepel >=0.8 - - r-matrixstats >=0.54 - - r-purrr >=0.2 - - r-reshape2 >=1.4 test: commands: - $R -e "library('basejump')" about: - home: https://github.com/steinbaugh/basejump + home: https://basejump.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT summary: Base functions for bioinformatics and R package development. extra: recipe-maintainers: + - mjsteinbaugh - MathiasHaudgaard - FrodePedersen - ArneKr diff --git a/recipes/r-bioverbs/meta.yaml b/recipes/r-bioverbs/meta.yaml index c75ead7a41000..6137018490968 100644 --- a/recipes/r-bioverbs/meta.yaml +++ b/recipes/r-bioverbs/meta.yaml @@ -1,29 +1,36 @@ -{% set version = "0.1.8" %} +{% set version = "0.1.19" %} +{% set github = "https://github.com/acidgenomics/bioverbs" %} package: name: r-bioverbs - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/bioverbs/archive/v{{ version }}.tar.gz - sha256: f5059996e43ca77e690ee6d2e47f8fd04afac7c201733f94bd0175f2f446a348 + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 80dd75330faf4ae2053d23645bc8fddeef14f63051a54657b907c3236373db11 build: number: 0 requirements: - host: - - r-base - run: - - r-base + host: + - r-base + run: + - r-base test: - commands: - - $R -e "library('bioverbs')" + commands: + - $R -e "library('bioverbs')" about: - home: https://github.com/steinbaugh/bioverbs - dev_url: https://github.com/steinbaugh/bioverbs + home: https://bioverbs.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT - summary: S4 generic functions for bioinformatics, part of the basejump toolkit. - license_family: MIT + summary: S4 generic functions for bioinformatics. + +extra: + recipe-maintainers: + - mjsteinbaugh + - pinin4fjords + - chapmanb + diff --git a/recipes/r-brio/meta.yaml b/recipes/r-brio/meta.yaml index e2575ec99c979..6e3dcc7c8d84d 100644 --- a/recipes/r-brio/meta.yaml +++ b/recipes/r-brio/meta.yaml @@ -1,67 +1,66 @@ -{% set version = "0.1.8" %} +{% set version = "0.2.1" %} +{% set github = "https://github.com/acidgenomics/brio" %} package: name: r-brio - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/brio/archive/v{{ version }}.tar.gz - sha256: 7b1ef773fa9255de969abf320401edf87744cdcbecb8a7b87f48ea8ab597d774 + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 2c7c3666f9458f069b10e727a6fc6cc9b538cee87edb3355772c489e08328054 build: number: 0 requirements: - host: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - r-transformer >=0.1.6 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-rtracklayer - - r-matrix >=1.2 - - r-r.utils >=2.7 - - r-curl >=1.95 - - r-data.table >=1.11 - - r-jsonlite >=1.6 - - r-readr >=1.3 - - r-rio >=0.5 - - r-stringr >=1.3 - - r-tibble >=2.0 - - r-yaml >=2.2 + host: + - r-base + - r-bioverbs >=0.1.18 + - r-goalie >=0.2.16 + - r-transformer >=0.1.11 + - bioconductor-genomicranges + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-curl >=1.95 + - r-data.table >=1.12 + - r-jsonlite >=1.6 + - r-matrix >=1.2 + - r-r.utils >=2.8 + - r-readr >=1.3 + - r-rio >=0.5 + - r-stringr >=1.4 + - r-tibble >=2.1 + - r-yaml >=2.2 - run: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - r-transformer >=0.1.6 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-rtracklayer - - r-matrix >=1.2 - - r-r.utils >=2.7 - - r-curl >=1.95 - - r-data.table >=1.11 - - r-jsonlite >=1.6 - - r-readr >=1.3 - - r-rio >=0.5 - - r-stringr >=1.3 - - r-tibble >=2.0 - - r-yaml >=2.2 + run: + - r-base + - r-bioverbs >=0.1.18 + - r-goalie >=0.2.16 + - r-transformer >=0.1.11 + - bioconductor-genomicranges + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-curl >=1.95 + - r-data.table >=1.12 + - r-jsonlite >=1.6 + - r-matrix >=1.2 + - r-r.utils >=2.8 + - r-readr >=1.3 + - r-rio >=0.5 + - r-stringr >=1.4 + - r-tibble >=2.1 + - r-yaml >=2.2 test: - commands: - - $R -e "library('brio')" + commands: + - $R -e "library('brio')" about: - home: https://github.com/steinbaugh/brio - dev_url: https://github.com/steinbaugh/brio + home: https://brio.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT - summary: Biological R input/output. This package is part of the basejump - toolkit. - license_family: MIT + summary: Biological R input/output. diff --git a/recipes/r-freerange/build.sh b/recipes/r-freerange/build.sh new file mode 100644 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-freerange/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build . diff --git a/recipes/r-freerange/meta.yaml b/recipes/r-freerange/meta.yaml new file mode 100644 index 0000000000000..ae4e9cb81391f --- /dev/null +++ b/recipes/r-freerange/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "0.1.6" %} +{% set github = "https://github.com/acidgenomics/freerange" %} + +package: + name: r-freerange + version: "{{ version }}" + +source: + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: a9161118bc9b82ccc5e3d7556b44d7e654506c3eec20a67a3139c1e5a95b6c62 + +build: + number: 0 + +requirements: + host: + - r-base + - r-brio >=0.2.0 + - r-goalie >=0.2.16 + - r-syntactic >=0.1.9 + - r-transformer >=0.1.11 + - bioconductor-annotationhub + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-dplyr >=0.8 + - r-magrittr >=1.5 + - r-rlang >=0.3 + - r-tibble >=2.1 + + run: + - r-base + - r-brio >=0.2.0 + - r-goalie >=0.2.16 + - r-syntactic >=0.1.9 + - r-transformer >=0.1.11 + - bioconductor-annotationhub + - bioconductor-biocgenerics + - bioconductor-ensembldb + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-dplyr >=0.8 + - r-magrittr >=1.5 + - r-rlang >=0.3 + - r-tibble >=2.1 + +test: + commands: + - $R -e "library('freerange')" + +about: + home: https://freerange.acidgenomics.com/ + dev_url: "{{ github }}" + license: MIT + summary: Generate and manipulate genomic ranges. diff --git a/recipes/r-goalie/meta.yaml b/recipes/r-goalie/meta.yaml index 33325908420fc..6eb13343ec52a 100644 --- a/recipes/r-goalie/meta.yaml +++ b/recipes/r-goalie/meta.yaml @@ -1,39 +1,40 @@ -{% set version = "0.2.9" %} +{% set version = "0.2.16" %} +{% set github = "https://github.com/acidgenomics/goalie" %} package: name: r-goalie - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/goalie/archive/v{{ version }}.tar.gz - sha256: 69b76b66415ab9fd8fca78549c936f8561dff4298f555fdebd8f01697103ac45 + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 0fbe297255077f0d43d5f38f6a5d58d607ec43e040c10849f966d16cbd5b69a3 build: number: 0 requirements: - host: - - r-base - - r-backports - - r-curl >=3.2.* - - run: - - r-curl >=3.2.* - - r-base + host: + - r-base + - r-backports + - r-curl >=3.2 + + run: + - r-base + - r-backports + - r-curl >=3.2 test: - commands: - - $R -e "library('goalie')" + commands: + - $R -e "library('goalie')" about: - home: https://github.com/steinbaugh/goalie - dev_url: https://github.com/steinbaugh/goalie + home: https://goalie.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT - summary: Assertive check functions for defensive R programming. - goalie is an attempt to incorporate elements of multiple assertive check - packages into a single package with as few dependencies as possible. All - assertive checks are written in the most basic R code possible, without - reliance on compilation (e.g. C++/Rcpp). It is still a work in progress, - and feature requests are welcome. + summary: Assertive check functions for defensive R programming. - license_family: MIT +extra: + recipe-maintainers: + - mjsteinbaugh + - pinin4fjords + - chapmanb diff --git a/recipes/r-syntactic/meta.yaml b/recipes/r-syntactic/meta.yaml index 5909163e07c82..77c191ac5fd37 100644 --- a/recipes/r-syntactic/meta.yaml +++ b/recipes/r-syntactic/meta.yaml @@ -1,47 +1,42 @@ -{% set version = "0.1.5" %} +{% set version = "0.1.9" %} +{% set github = "https://github.com/acidgenomics/syntactic" %} package: name: r-syntactic - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/syntactic/archive/v{{ version }}.tar.gz - sha256: 0df38399bbaa8c55a679eeae83720276a859e0764411928495add703001e0a7f + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 023ae015d91d7ec6bd33de5ec8e627b7138547abe339872da953cdc1fff9725c build: number: 0 requirements: - host: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - r-matrix - - r-r.utils - - r-magrittr + host: + - r-base + - r-bioverbs >=0.1.10 + - r-goalie >=0.2.12 + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-matrix - run: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - r-matrix - - r-r.utils - - r-magrittr + run: + - r-base + - r-bioverbs >=0.1.10 + - r-goalie >=0.2.12 + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-matrix test: - commands: - - $R -e "library('syntactic')" + commands: + - $R -e "library('syntactic')" about: - home: https://github.com/steinbaugh/syntactic - dev_url: https://github.com/steinbaugh/syntactic + home: https://syntactic.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT - summary: Make syntactically valid names out of character vectors. This - package is part of the basejump toolkit. - license_family: MIT + summary: Make syntactically valid names out of character vectors. diff --git a/recipes/r-transformer/meta.yaml b/recipes/r-transformer/meta.yaml index aa6802bac9eb5..65bdaabe1e08a 100644 --- a/recipes/r-transformer/meta.yaml +++ b/recipes/r-transformer/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "0.1.6" %} +{% set version = "0.1.11" %} +{% set github = "https://github.com/acidgenomics/transformer" %} package: name: r-transformer - version: {{ version }} + version: "{{ version }}" source: - url: https://github.com/steinbaugh/transformer/archive/v{{ version }}.tar.gz - sha256: 05edb2c71a15b74b87f56efb7ff6e9bd1bc7ce659eef52e442ed44d19ae45f7f + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 2a84e481dc9363097b69e447f6e48ba09e35aff39b85d40bb56a7c5e5430858a build: number: 0 requirements: - host: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - r-data.table >=1.12 - - r-matrix >=1.2 - - r-tibble >=2.0.1 - - run: - - r-base - - r-bioverbs >=0.1.8 - - r-goalie >=0.2.9 - - bioconductor-genomicranges - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - r-data.table >=1.12 - - r-matrix >=1.2 - - r-tibble >=2.0.1 + host: + - r-base + - r-bioverbs >=0.1.9 + - r-goalie >=0.2.12 + - bioconductor-biocgenerics + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-data.table >=1.12 + - r-matrix >=1.2 + - r-tibble >=2.1 + + run: + - r-base + - r-bioverbs >=0.1.9 + - r-goalie >=0.2.12 + - bioconductor-biocgenerics + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-data.table >=1.12 + - r-matrix >=1.2 + - r-tibble >=2.1 test: - commands: - - $R -e "library('transformer')" + commands: + - $R -e "library('transformer')" about: - home: https://github.com/steinbaugh/transformer - dev_url: https://github.com/steinbaugh/transformer + home: https://transformer.acidgenomics.com/ + dev_url: "{{ github }}" license: MIT summary: Additional S3 and S4 coercion methods for easy interconversion - between Bioconductor and tidyverse data classes. This package is part of - the basejump toolkit. - license_family: MIT + between Bioconductor and tidyverse data classes. + +extra: + recipe-maintainers: + - mjsteinbaugh + - pinin4fjords + - chapmanb