<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/ac6ff1ecae6b7b68e2259f6ba3606fbe0b986e13">https://github.com/macports/macports-ports/commit/ac6ff1ecae6b7b68e2259f6ba3606fbe0b986e13</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit ac6ff1ecae6b7b68e2259f6ba3606fbe0b986e13
</span>Author: barracuda156 <vital.had@gmail.com>
AuthorDate: Sun Oct 29 04:41:00 2023 +0800
<span style='display:block; white-space:pre;color:#404040;'> R-systemPipeR: update to 2.8.0, support testing
</span>---
R/R-systemPipeR/Portfile | 35 ++++++++++++++++++++++++++----
R/R-systemPipeR/files/patch-no-GO.db.diff | 11 ++++++++++
R/R-systemPipeRdata/Portfile | 36 +++++++++++++++++++++++++++++++
3 files changed, 78 insertions(+), 4 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-systemPipeR/Portfile b/R/R-systemPipeR/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 43931dfe77c..78d55499d45 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-systemPipeR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-systemPipeR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,16 @@
</span> PortSystem 1.0
PortGroup R 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup bioconductor tgirke systemPipeR 2.6.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup bioconductor tgirke systemPipeR 2.8.0
</span> revision 0
maintainers nomaintainer
license Artistic-2
description NGS workflow and report generation environment
long_description {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 0b0df1eca0c2ddc0f4a967ccb5b200da9ac6e337 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 d38f4108a795d607a3759d2359c563be8779c81b66c738237be656383b28e6f9 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 7394851
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://systempipe.org
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 c3ff8d80ab2b12ed586149da7ca4fe66dc6344f6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 ead9681978cbfd512ecffc2d77f8b8fe0ba4b5a63b127f7b0a2e439556c45505 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 7417929
</span> supported_archs noarch
depends_lib-append port:R-BiocGenerics \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -27,3 +28,29 @@ depends_lib-append port:R-BiocGenerics \
</span> port:R-stringr \
port:R-SummarizedExperiment \
port:R-yaml
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-no-GO.db.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-annotate \
</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-batchtools \
</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-DESeq2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-dplyr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DT \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-edgeR \
</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-GenomicAlignments \
</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-IRanges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-kableExtra \
</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-limma \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rjson \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rmarkdown \
</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-testthat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-systemPipeRdata \
</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;'>+test.run yes
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-systemPipeR/files/patch-no-GO.db.diff b/R/R-systemPipeR/files/patch-no-GO.db.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..610a9fdc957
</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-systemPipeR/files/patch-no-GO.db.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,11 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- DESCRIPTION 2023-10-25 07:19:19.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ DESCRIPTION 2023-10-29 03:53:08.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -17,7 +17,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+- AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ AnnotationDbi, kableExtra, GenomeInfoDb, DT,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VignetteBuilder: knitr
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-systemPipeRdata/Portfile b/R/R-systemPipeRdata/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..b3761b9917d
</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-systemPipeRdata/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,36 @@
</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 tgirke systemPipeRdata 2.6.0
</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 Workflow templates and sample data
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://github.com/tgirke/systemPipeRdata
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites https://bioconductor.org/packages/release/data/experiment/src/contrib/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 76e810ec8ade0f4e0e0bc0fd46a0dfd5bcc0c459 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 0ea66cc404368e3456118d2ed696c8bc8a3a679ecaf14a1c0918260bf7939a00 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 283914326
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+supported_archs noarch
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append 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-jsonlite \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-remotes
</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-BiocStyle \
</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-knitr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rmarkdown \
</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-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-systemPipeR
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+test.run yes
</span></pre><pre style='margin:0'>
</pre>