<pre style='margin:0'>
Herby Gillot (herbygillot) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/b66b2c707cc364b2b163c532d6f2479503efe9eb">https://github.com/macports/macports-ports/commit/b66b2c707cc364b2b163c532d6f2479503efe9eb</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit b66b2c707cc364b2b163c532d6f2479503efe9eb
</span>Author: barracuda156 <vital.had@gmail.com>
AuthorDate: Thu Oct 26 20:06:58 2023 +0800
<span style='display:block; white-space:pre;color:#404040;'> R-BiocParallel: update to 1.37.0, add support for testing
</span>---
R/R-BiocParallel/Portfile | 37 ++++++++++++++++++----
.../files/patch-remove-unavailable-suggests.diff | 15 +++++++++
R/R-VariantAnnotation/Portfile | 34 ++++++++++++++++++++
3 files changed, 80 insertions(+), 6 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocParallel/Portfile b/R/R-BiocParallel/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 7c830c87867..7767227e3a6 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocParallel/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocParallel/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,20 +3,45 @@
</span> PortSystem 1.0
PortGroup R 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup github Bioconductor BiocParallel e80f4e7a76f46c6a11e0be681a80a5aeab55f05e
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version 1.35.4
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup github Bioconductor BiocParallel 79a1b2de06ce6f95e6b716d041b5636e26608195
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version 1.37.0
</span> revision 0
categories-append parallel
maintainers {@barracuda156 gmail.com:vital.had} openmaintainer
license {GPL-2 GPL-3}
description Bioconductor facilities for parallel evaluation
long_description {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage https://bioconductor.org/packages/release/bioc/html/BiocParallel.html
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 ed68340d1c7325fbe3975a2a66df24d26618c5ff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 b3cb5ff6fdda466eb715b274021a768f051c56ac672dcd52c66793126929e45a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 147087
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 ea9816ec940161d70d574a5e1faafd3cbfd7c260 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 e508a8da15bb2a5339619af31e6b7340ead400d6d1e6369e1d83fbe42bc44e42 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 147084
</span>
depends_lib-append port:R-BH \
port:R-cpp11 \
port:R-futile.logger \
port:R-snow
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-remove-unavailable-suggests.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_test-append port:R-batchtools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BBmisc \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-data.table \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-doParallel \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-foreach \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-GenomicAlignments \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-GenomicRanges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-knitr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rmpi \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rsamtools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RUnit \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ShortRead \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-VariantAnnotation
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# FIXME: there are MPI-related failures in tests, at least on PowerPC:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Error in DEACTIVATED("MPI tests not run") : MPI tests not run
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# *** caught segfault ***
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# address 0x11e81414, cause 'memory not mapped'
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Code from vignettes runs fine, however.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+test.run yes
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocParallel/files/patch-remove-unavailable-suggests.diff b/R/R-BiocParallel/files/patch-remove-unavailable-suggests.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..3d3de3496b0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocParallel/files/patch-remove-unavailable-suggests.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,15 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- DESCRIPTION 2023-10-24 21:51:58.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ DESCRIPTION 2023-10-26 19:42:16.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -37,10 +37,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Depends: methods, R (>= 3.5.0)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Imports: stats, utils, futile.logger, parallel, snow, codetools
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- data.table
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ GenomicRanges, VariantAnnotation, Rsamtools, data.table,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Enhances: Rmpi
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Collate: AllGenerics.R DeveloperInterface.R prototype.R
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ bploop.R ErrorHandling.R log.R
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-VariantAnnotation/Portfile b/R/R-VariantAnnotation/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..02fc1f4be5d
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-VariantAnnotation/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,34 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# -*- 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
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup R 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup bioconductor Bioconductor VariantAnnotation 1.48.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license Artistic-2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Annotation of genetic variants
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 3599ddd8c9639c08be59d3862589b82eb136d797 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 1795cc947cdbee1ec6afc9f3e6e80c6efc5d11dea3e6bafbfbb2d0926bf42ce4 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 1886463
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:curl \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-AnnotationDbi \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Biobase \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Biostrings \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BSgenome \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DBI \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-GenomeInfoDb \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-GenomicFeatures \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-GenomicRanges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-IRanges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-MatrixGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rhtslib \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rsamtools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rtracklayer \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-S4Vectors \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SummarizedExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-XVector \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-zlibbioc
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