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R: update bioconductor stuff to 3.19 release

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Closes: https://trac.macports.org/ticket/69858
This commit is contained in:
barracuda156
2024-05-04 19:43:31 +08:00
committed by Ryan Carsten Schmidt
parent f0f2a8059f
commit 459fffe4a3
134 changed files with 1207 additions and 841 deletions
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R/R-ALL/Portfile
+21
View File
@@ -0,0 +1,21 @@
# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor ALL 1.46.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description A data package
long_description {*}${description}
master_sites https://bioconductor.org/packages/release/data/experiment/src/contrib/
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size 11382429
supported_archs noarch
depends_lib-append port:R-Biobase
test.run yes
R/R-AnnotationDbi/Portfile
+6 -7
View File
@@ -3,17 +3,16 @@
PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor AnnotationDbi 7daf9f47046e11f412e04195a7743a3840541b79
version 1.65.2
revision 1
R.setup bioconductor Bioconductor AnnotationDbi 1.66.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Manipulation of SQLite-based annotations in Bioconductor
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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platforms {darwin any}
R/R-AnnotationForge/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor AnnotationForge 2bba05a2305c3c803b8d9747a5c44c0d22fe2631
version 1.45.0
revision 1
R.setup bioconductor Bioconductor AnnotationForge 1.46.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Tools for building SQLite-based annotation data packages
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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R/R-AnnotationHub/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor AnnotationHub 3.10.1
revision 1
categories-append www
R.setup bioconductor Bioconductor AnnotationHub 3.12.0
revision 0
categories-append bioconductor www
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license Artistic-2
description Client to access AnnotationHub resources
long_description {*}${description}
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R/R-BSgenome/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor BSgenome 1.70.2
revision 1
R.setup bioconductor Bioconductor BSgenome 1.72.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Software infrastructure for efficient representation of full genomes and their SNPs
description Software infrastructure for efficient representation \
of full genomes and their SNPs
long_description {*}${description}
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R/R-BayesKnockdown/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor BayesKnockdown 1.28.0
revision 1
R.setup bioconductor Bioconductor BayesKnockdown 1.30.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license GPL-3
description Posterior probabilities for edges from knockdown data
long_description {*}${description}
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R/R-BioNet/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor BioNet 1.62.0
revision 1
R.setup bioconductor Bioconductor BioNet 1.64.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license GPL-2+
description Routines for the functional analysis of biological networks
long_description {*}${description}
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R/R-Biobase/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor Biobase 4cf5590294d698b89f77ba639853ebd57a704d53
version 2.63.0
revision 1
R.setup bioconductor Bioconductor Biobase 2.64.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Base functions for Bioconductor
long_description {*}${description}
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size 1792985
depends_lib-append port:R-BiocGenerics
variant tests description "Enable testing" {
depends_test-append \
port:R-ALL \
port:R-BiocStyle \
port:R-golubEsets \
port:R-knitr \
port:R-limma \
port:R-RUnit \
port:R-tkWidgets
test.run yes
}
R/R-BiocBaseUtils/Portfile
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@@ -3,17 +3,16 @@
PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocBaseUtils 5bfff695290ae6db7ccbc5ceafdbbc9e5ddb32a7
version 1.5.0
revision 1
R.setup bioconductor Bioconductor BiocBaseUtils 1.6.0
revision 0
categories-append bioconductor devel
maintainers nomaintainer
license Artistic-2
description General utility functions for developing Bioconductor packages
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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R/R-BiocCheck/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocCheck 7e7e07e1dfd8ddae8bf14d35e9df0add09aad61a
version 1.39.0
revision 1
R.setup bioconductor Bioconductor BiocCheck 1.40.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Bioconductor-specific package checks
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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depends_lib-append port:R-BiocBaseUtils \
@@ -22,11 +21,14 @@ depends_lib-append port:R-BiocBaseUtils \
port:R-biocViews \
port:R-callr \
port:R-graph \
port:R-httr \
port:R-httr2 \
port:R-knitr \
port:R-rvest \
port:R-stringdist
depends_test-append port:R-Biobase \
variant tests description "Enable testing" {
depends_test-append \
port:R-Biobase \
port:R-BiocGenerics \
port:R-BiocStyle \
port:R-callr \
@@ -37,5 +39,7 @@ depends_test-append port:R-Biobase \
port:R-RUnit \
port:R-usethis
# One test fails on ppc: https://github.com/Bioconductor/BiocCheck/issues/188
test.run yes
# One test fails, at least on ppc:
# https://github.com/Bioconductor/BiocCheck/issues/188
test.run yes
}
R/R-BiocFileCache/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocFileCache 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
version 2.11.2
revision 1
R.setup bioconductor Bioconductor BiocFileCache 2.12.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license Artistic-2
description Manage files across sessions
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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depends_lib-append port:R-curl \
R/R-BiocGenerics/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocGenerics 2e1a2a6152989cb21ff44eb98906edd486d0eb23
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revision 1
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homepage https://bioconductor.org/packages/${R.package}
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long_description {*}${description} used in Bioconductor.
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R/R-BiocIO/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocIO 96ba3c5d94859e51f551e7278c7b5f7f5fae2421
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R.setup bioconductor Bioconductor BiocIO 1.14.0
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maintainers nomaintainer
license Artistic-2
description Standard Input and Output for Bioconductor packages
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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R/R-BiocNeighbors/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup bioconductor Bioconductor BiocNeighbors 1.20.2
revision 1
R.setup bioconductor Bioconductor BiocNeighbors 1.22.0
revision 0
categories-append bioconductor
maintainers nomaintainer
license GPL-3
description Nearest neighbor detection for Bioconductor packages
long_description {*}${description}
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port:R-Rcpp \
port:R-RcppHNSW \
port:R-S4Vectors
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variant tests description "Enable testing" {
depends_test-append \
port:R-BiocStyle \
port:R-FNN \
port:R-knitr \
port:R-RcppAnnoy \
port:R-rmarkdown \
port:R-testthat
# Tests freeze due to: https://trac.macports.org/ticket/67059
test.run yes
# Tests freeze due to: https://trac.macports.org/ticket/67059
test.run yes
}
R/R-BiocParallel/Portfile
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PortSystem 1.0
PortGroup R 1.0
R.setup github Bioconductor BiocParallel 47856deee43f03646f070b2c079a6f1271a0d0e8
version 1.37.1
revision 1
categories-append parallel
R.setup bioconductor Bioconductor BiocParallel 1.38.0
revision 0
categories-append bioconductor parallel
maintainers {@barracuda156 gmail.com:vital.had} openmaintainer
license {GPL-2 GPL-3}
description Bioconductor facilities for parallel evaluation
long_description {*}${description}
homepage https://bioconductor.org/packages/${R.package}
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port:R-cpp11 \
port:R-futile.logger \
port:R-snow
patchfiles patch-remove-unavailable-suggests.diff
variant tests description "Enable testing" {
patchfiles-append \
patch-remove-unavailable-suggests.diff
depends_test-append port:R-batchtools \
depends_test-append \
port:R-batchtools \
port:R-BBmisc \
port:R-BiocGenerics \
port:R-BiocStyle \
@@ -39,9 +40,10 @@ depends_test-append port:R-batchtools \
port:R-ShortRead \
port:R-VariantAnnotation
# FIXME: there are MPI-related failures in tests, at least on PowerPC:
# Error in DEACTIVATED("MPI tests not run") : MPI tests not run
# *** caught segfault ***
# address 0x11e81414, cause 'memory not mapped'
# Code from vignettes runs fine, however.
test.run yes
# FIXME: there are MPI-related failures in tests, at least on PowerPC:
# Error in DEACTIVATED("MPI tests not run") : MPI tests not run
# *** caught segfault ***
# address 0x11e81414, cause 'memory not mapped'
# Code from vignettes runs fine, however.
test.run yes
}
R/R-BiocParallel/files/patch-remove-unavailable-suggests.diff
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--- DESCRIPTION 2023-10-24 21:51:58.000000000 +0800
+++ DESCRIPTION 2023-10-26 19:42:16.000000000 +0800
@@ -37,10 +37,8 @@
--- DESCRIPTION 2024-05-01 10:47:25.000000000 +0800
+++ DESCRIPTION 2024-05-04 14:20:45.000000000 +0800
@@ -37,8 +37,7 @@
Depends: methods, R (>= 3.5.0)
Imports: stats, utils, futile.logger, parallel, snow, codetools
Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel,
- GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
- TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools,
- GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools,
- data.table
+ GenomicRanges, VariantAnnotation, Rsamtools, data.table,
+ GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools
- GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
- TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
+ GenomicRanges, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
Enhances: Rmpi
Collate: AllGenerics.R DeveloperInterface.R prototype.R
bploop.R ErrorHandling.R log.R
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R.setup bioconductor seandavi BiocPkgTools 1.20.0
revision 1
R.setup bioconductor seandavi BiocPkgTools 1.22.0
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license MIT
description Collection of simple tools for learning about Bioconductor packages
long_description {*}${description}
homepage https://github.com/seandavi/BiocPkgTools
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description Set the appropriate version of Bioconductor packages
long_description {*}${description}
checksums rmd160 e08f94b041e92ac49bae1adcf41c449258290964 \
sha256 5d508bbc2f05d870864663f465be5b34684aacb01641e8dc41e887b0f06dc60f \
size 826
checksums rmd160 979b54de95618a6c8337a74da08787ed2dd88884 \
sha256 b096e4e98c2000dcc3aaf2aa0628b1c7ecb2f68f7835071dd34bbf11061215fe \
size 987
supported_archs noarch
test.run yes

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