<pre style='margin:0'>
Ryan Carsten Schmidt (ryandesign) pushed a commit to branch master
in repository macports-ports.

</pre>
<p><a href="https://github.com/macports/macports-ports/commit/459fffe4a3c71d3475292b97432efc245550695e">https://github.com/macports/macports-ports/commit/459fffe4a3c71d3475292b97432efc245550695e</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 459fffe4a3c71d3475292b97432efc245550695e
</span>Author: barracuda156 <vital.had@gmail.com>
AuthorDate: Sat May 4 19:43:31 2024 +0800

<span style='display:block; white-space:pre;color:#404040;'>    R: update bioconductor stuff to 3.19 release
</span><span style='display:block; white-space:pre;color:#404040;'>    
</span><span style='display:block; white-space:pre;color:#404040;'>    Closes: https://trac.macports.org/ticket/69858
</span>---
 R/{R-yeastNagalakshmi => R-ALL}/Portfile           | 15 +++++---
 R/R-AnnotationDbi/Portfile                         | 13 +++----
 R/R-AnnotationForge/Portfile                       | 13 +++----
 R/R-AnnotationHub/Portfile                         | 12 +++---
 R/R-BSgenome/Portfile                              | 14 ++++---
 R/R-BayesKnockdown/Portfile                        | 11 +++---
 R/R-BioNet/Portfile                                | 11 +++---
 R/R-Biobase/Portfile                               | 25 +++++++++---
 R/R-BiocBaseUtils/Portfile                         | 13 +++----
 R/R-BiocCheck/Portfile                             | 26 +++++++------
 R/R-BiocFileCache/Portfile                         | 13 +++----
 R/R-BiocGenerics/Portfile                          | 17 ++++----
 R/R-BiocIO/Portfile                                | 13 +++----
 R/R-BiocNeighbors/Portfile                         | 20 ++++++----
 R/R-BiocParallel/Portfile                          | 34 ++++++++--------
 .../files/patch-remove-unavailable-suggests.diff   | 19 ++++-----
 R/R-BiocPkgTools/Portfile                          | 11 +++---
 R/R-BiocSingular/Portfile                          | 12 +++---
 R/R-BiocStyle/Portfile                             | 16 ++++----
 R/R-BiocVersion/Portfile                           | 12 +++---
 R/R-Biostrings/Portfile                            | 12 +++---
 R/R-ChemmineDrugs/Portfile                         |  1 +
 R/R-ChemmineOB/Portfile                            | 23 ++++++++---
 R/R-ChemmineOB/files/patch-fix-flags.diff          |  8 ++--
 R/R-ChemmineR/Portfile                             | 22 ++++++-----
 R/R-ComplexHeatmap/Portfile                        | 11 +++---
 R/R-DECIPHER/Portfile                              | 17 ++++----
 R/R-DESeq2/Portfile                                | 14 ++++---
 R/R-DNAcopy/Portfile                               | 11 +++---
 R/R-DelayedArray/Portfile                          | 14 +++----
 R/R-DelayedMatrixStats/Portfile                    | 23 ++++++-----
 R/R-DelayedRandomArray/Portfile                    | 11 +++---
 R/R-DirichletMultinomial/Portfile                  | 11 +++---
 R/R-DynDoc/Portfile                                | 14 ++++---
 R/R-EBImage/Portfile                               | 12 +++---
 R/R-EnrichedHeatmap/Portfile                       | 12 +++---
 R/R-ExperimentHub/Portfile                         | 12 +++---
 R/R-GenomeInfoDb/Portfile                          | 17 ++++----
 R/R-GenomeInfoDbData/Portfile                      | 11 +++---
 R/R-GenomicAlignments/Portfile                     | 11 +++---
 R/R-GenomicFeatures/Portfile                       | 13 +++----
 R/R-GenomicRanges/Portfile                         | 13 +++----
 R/R-HDF5Array/Portfile                             | 13 +++----
 R/R-HilbertCurve/Portfile                          | 12 +++---
 R/R-HilbertVis/Portfile                            | 12 +++---
 R/R-IRanges/Portfile                               | 24 ++++++------
 .../files/patch-remove-unavailable-suggests.diff   | 19 ++++-----
 R/R-Icens/Portfile                                 | 13 +++----
 R/R-InteractionSet/Portfile                        | 11 +++---
 R/R-KEGGREST/Portfile                              | 16 ++++----
 R/R-KEGGgraph/Portfile                             | 22 ++++++-----
 R/R-MassSpecWavelet/Portfile                       | 14 ++++---
 R/R-MatrixGenerics/Portfile                        | 13 +++----
 R/R-MeSHDbi/Portfile                               | 11 +++---
 R/R-MsCoreUtils/Portfile                           | 11 +++---
 R/R-MultiAssayExperiment/Portfile                  | 16 ++++----
 .../files/patch-no-maftools.diff                   | 23 ++++++-----
 R/R-RBGL/Portfile                                  | 21 +++++-----
 R/R-RaggedExperiment/Portfile                      | 13 +++----
 R/R-ResidualMatrix/Portfile                        | 11 +++---
 R/R-Rgraphviz/Portfile                             | 13 ++++---
 R/R-Rhdf5lib/Portfile                              | 11 +++---
 R/R-Rhtslib/Portfile                               | 13 +++----
 R/R-Rsamtools/Portfile                             | 16 ++++----
 R/R-S4Arrays/Portfile                              | 13 +++----
 R/R-S4Vectors/Portfile                             | 20 +++++-----
 R/R-SPIA/Portfile                                  | 17 ++++----
 R/R-SQLDataFrame/Portfile                          | 39 ++++++++-----------
 R/R-ScaledMatrix/Portfile                          | 11 +++---
 R/R-SeqArray/Portfile                              | 11 +++---
 R/R-ShortRead/Portfile                             | 22 ++++++-----
 R/R-SingleCellExperiment/Portfile                  | 12 +++---
 R/R-SparseArray/Portfile                           | 28 +++++++++-----
 R/R-SparseArray/files/patch-disable-openmp.diff    | 45 ++++++++++++++++++++++
 R/R-Structstrings/Portfile                         | 40 +++++++++++++++++++
 .../files/patch-no-tRNAscanImport.diff             | 11 ++++++
 R/R-SummarizedExperiment/Portfile                  | 13 +++----
 R/R-TileDBArray/Portfile                           | 24 +++++++-----
 R/R-UCSC.utils/Portfile                            | 34 ++++++++++++++++
 R/R-VariantAnnotation/Portfile                     | 11 +++---
 R/R-XVector/Portfile                               | 17 ++++----
 R/R-XVector/files/patch-no-drosophila2probe.diff   | 16 ++++----
 R/R-annotate/Portfile                              | 11 +++---
 R/R-apeglm/Portfile                                | 11 +++---
 R/R-aroma.light/Portfile                           | 12 +++---
 R/R-beachmat/Portfile                              | 11 +++---
 R/R-bioDist/Portfile                               | 12 +++---
 R/R-biobroom/Portfile                              | 11 +++---
 R/R-biocViews/Portfile                             | 13 +++----
 R/R-biocthis/Portfile                              | 17 ++++----
 R/R-biomaRt/Portfile                               | 18 +++++----
 R/R-biomaRt/files/patch-no-httptest2.diff          | 11 ++++++
 R/R-bluster/Portfile                               | 11 +++---
 R/R-clustComp/Portfile                             | 11 +++---
 R/R-csaw/Portfile                                  | 11 +++---
 R/R-dcanr/Portfile                                 | 12 +++---
 R/R-dir.expiry/Portfile                            | 11 +++---
 R/R-edgeR/Portfile                                 | 11 +++---
 R/R-fmcsR/Portfile                                 | 11 +++---
 R/R-gdsfmt/Portfile                                | 11 +++---
 R/R-genefilter/Portfile                            | 25 +++++++++---
 R/R-ggtree/Portfile                                | 13 ++++---
 R/R-ggtreeExtra/Portfile                           | 12 +++---
 R/R-golubEsets/Portfile                            | 21 ++++++++++
 R/R-graph/Portfile                                 | 20 +++++-----
 R/R-graphite/Portfile                              | 11 +++---
 R/R-groHMM/Portfile                                | 11 +++---
 R/R-impute/Portfile                                | 11 +++---
 R/R-interactiveDisplayBase/Portfile                | 14 ++++---
 R/R-kebabs/Portfile                                | 11 +++---
 R/R-limma/Portfile                                 | 11 +++---
 R/R-marray/Portfile                                | 11 +++---
 R/R-metapod/Portfile                               | 22 ++++++-----
 R/R-mixOmics/Portfile                              | 11 +++---
 R/R-multtest/Portfile                              | 11 +++---
 R/R-pcaMethods/Portfile                            | 11 +++---
 R/R-preprocessCore/Portfile                        | 11 +++---
 R/R-pwalign/Portfile                               | 28 ++++++++++++++
 R/R-qvalue/Portfile                                | 11 +++---
 R/R-rhdf5/Portfile                                 | 19 +++++----
 R/R-rhdf5filters/Portfile                          | 20 ++++++----
 R/R-rsbml/Portfile                                 | 21 +++++++---
 R/R-rtracklayer/Portfile                           | 16 +++++---
 R/R-sparseMatrixStats/Portfile                     | 13 +++----
 R/R-ssize/Portfile                                 | 11 +++---
 R/R-survcomp/Portfile                              | 11 +++---
 R/R-systemPipeR/Portfile                           | 21 ++++++----
 R/R-systemPipeRdata/Portfile                       | 18 +++++----
 R/R-tkWidgets/Portfile                             | 12 +++---
 R/R-treeio/Portfile                                | 11 +++---
 R/R-vsclust/Portfile                               | 11 +++---
 R/R-widgetTools/Portfile                           | 14 ++++---
 R/R-yeastNagalakshmi/Portfile                      | 11 +++---
 R/R-zlibbioc/Portfile                              | 14 +++----
 134 files changed, 1194 insertions(+), 846 deletions(-)

<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-yeastNagalakshmi/Portfile b/R/R-ALL/Portfile
</span>similarity index 52%
copy from R/R-yeastNagalakshmi/Portfile
copy to R/R-ALL/Portfile
<span style='display:block; white-space:pre;color:#808080;'>index 94c97c4f607..95bc6125958 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-yeastNagalakshmi/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ALL/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,19 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor yeastNagalakshmi 1.38.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor ALL 1.46.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Yeast genome RNA sequencing data based on Nagalakshmi et al.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         A data package
</span> long_description    {*}${description}
 master_sites        https://bioconductor.org/packages/release/data/experiment/src/contrib/
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</span> supported_archs     noarch
 
<span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append  port:R-Biobase
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span> test.run            yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-AnnotationDbi/Portfile b/R/R-AnnotationDbi/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 8c009c25bf1..73a2376cf79 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-AnnotationDbi/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-AnnotationDbi/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor AnnotationDbi 7daf9f47046e11f412e04195a7743a3840541b79
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.65.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor AnnotationDbi 1.66.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Manipulation of SQLite-based annotations in Bioconductor
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  3aa793c6888ad50a63d88e2a2df59655c6384ada9db2c5d84473ca76fafa5ebc \
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</span> supported_archs     noarch
 platforms           {darwin any}
 
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-AnnotationForge/Portfile b/R/R-AnnotationForge/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ddafe3b3669..25e07799080 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-AnnotationForge/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-AnnotationForge/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor AnnotationForge 2bba05a2305c3c803b8d9747a5c44c0d22fe2631
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.45.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor AnnotationForge 1.46.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Tools for building SQLite-based annotation data packages
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    3989356
</span> supported_archs     noarch
 platforms           {darwin any}
 
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-AnnotationHub/Portfile b/R/R-AnnotationHub/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 05105d1a275..20650334fe1 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-AnnotationHub/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-AnnotationHub/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor AnnotationHub 3.10.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   www
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor AnnotationHub 3.12.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor www
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Client to access AnnotationHub resources
 long_description    {*}${description}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    992371
</span> supported_archs     noarch
 platforms           {darwin any}
 
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BSgenome/Portfile b/R/R-BSgenome/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 64b45900557..76cb32e4a08 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BSgenome/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BSgenome/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor BSgenome 1.70.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BayesKnockdown/Portfile b/R/R-BayesKnockdown/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 5e57fa9ce9a..c5a63e8336e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BayesKnockdown/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BayesKnockdown/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 Bioconductor BayesKnockdown 1.28.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
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</span> maintainers         nomaintainer
 license             GPL-3
 description         Posterior probabilities for edges from knockdown data
 long_description    {*}${description}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biobase
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BioNet/Portfile b/R/R-BioNet/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 9f3d8c45471..e38c3f3d483 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BioNet/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BioNet/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 Bioconductor BioNet 1.62.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
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</span> maintainers         nomaintainer
 license             GPL-2+
 description         Routines for the functional analysis of biological networks
 long_description    {*}${description}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1680069
</span> supported_archs     noarch
 
 depends_lib-append  port:R-AnnotationDbi \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Biobase/Portfile b/R/R-Biobase/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 8fdb89bc756..9d559d43f33 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Biobase/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Biobase/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,28 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor Biobase 4cf5590294d698b89f77ba639853ebd57a704d53
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Base functions for Bioconductor
 long_description    {*}${description}
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</span> 
 depends_lib-append  port:R-BiocGenerics
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-ALL \
</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-golubEsets \
</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-RUnit \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-tkWidgets
</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;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocBaseUtils/Portfile b/R/R-BiocBaseUtils/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 5e026d156d9..9edea0a220e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocBaseUtils/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocBaseUtils/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocBaseUtils 5bfff695290ae6db7ccbc5ceafdbbc9e5ddb32a7
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.5.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocBaseUtils 1.6.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         nomaintainer
 license             Artistic-2
 description         General utility functions for developing Bioconductor packages
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  19b1135bcdad562ae3539f83fd6df7783cf7ea72 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    228328
</span> supported_archs     noarch
 
 depends_test-append port:R-BiocStyle \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocCheck/Portfile b/R/R-BiocCheck/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index c2c7c1372a9..b748d9b957d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocCheck/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocCheck/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocCheck 7e7e07e1dfd8ddae8bf14d35e9df0add09aad61a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.39.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocCheck 1.40.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Bioconductor-specific package checks
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  6ebe2e08e7a3005db3dba016da76f1fe7a453522 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    4378887
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocBaseUtils \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -22,11 +21,14 @@ depends_lib-append  port:R-BiocBaseUtils \
</span>                     port:R-biocViews \
                     port:R-callr \
                     port:R-graph \
<span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:R-httr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-httr2 \
</span>                     port:R-knitr \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-rvest \
</span>                     port:R-stringdist
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-Biobase \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-Biobase \
</span>                     port:R-BiocGenerics \
                     port:R-BiocStyle \
                     port:R-callr \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -37,5 +39,7 @@ depends_test-append port:R-Biobase \
</span>                     port:R-RUnit \
                     port:R-usethis
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# One test fails on ppc: https://github.com/Bioconductor/BiocCheck/issues/188
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # One test fails, at least on ppc:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # https://github.com/Bioconductor/BiocCheck/issues/188
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocFileCache/Portfile b/R/R-BiocFileCache/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 099a5f71f9c..4087887b83b 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocFileCache/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocFileCache/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocFileCache 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             2.11.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocFileCache 2.12.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Manage files across sessions
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    297080
</span> supported_archs     noarch
 
 depends_lib-append  port:R-curl \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocGenerics/Portfile b/R/R-BiocGenerics/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 6cf9eed0229..9919629d46e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocGenerics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocGenerics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,14 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocGenerics 2e1a2a6152989cb21ff44eb98906edd486d0eb23
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             0.49.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocGenerics 0.50.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         The package defines many S4 generic functions used in Bioconductor
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description    {*}${description}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  32218f0af24f2562f9e266b410cdff84fac9e2ce \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  8ca9335a97878a84942da0749f505d32d6ed83c9ddb1aabff3312c8363dca08e \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    50319
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         The package defines many S4 generic functions
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description    {*}${description} used in Bioconductor.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  03d7d483fdf4d8d4502b150ddbc185cafdffe374 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  11d72e20c087911a58d08db7898d47424930e00265d6e65ae87d14d786f20014 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    49747
</span> supported_archs     noarch
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocIO/Portfile b/R/R-BiocIO/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index b7e0bd5c05d..dd88d3a8140 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocIO/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocIO/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocIO 96ba3c5d94859e51f551e7278c7b5f7f5fae2421
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.13.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocIO 1.14.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Standard Input and Output for Bioconductor packages
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  aec6fd40c8045983b9100c0e31e9b401ac92ee7a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  6f0806895f5ff31b815ac4e081f9340374edc8290178292918d1abe1b45cd999 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    10336
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  80bef328f46c70e544afb3e2ffc12619dc05f406 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  9010bd8bdf810f571825bc055464219365168c6daadb2d6b8c74ed616fa3fa5e \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    230564
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocNeighbors/Portfile b/R/R-BiocNeighbors/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index bb844e41c03..309d6ee0795 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocNeighbors/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocNeighbors/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,27 +3,31 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor BiocNeighbors 1.20.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocNeighbors 1.22.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-3
 description         Nearest neighbor detection for Bioconductor packages
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  29602eaac6b0dc04eda53a9057e91769ffb67982 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  04123fe8ceb2cc9a17af7d187460e601dcce389adb1fcc6f89ad9c0844e27a53 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    1039738
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  16c2700bbd282314974b3c4003268f68dfc5c9d3 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  2d727fa9e983afd7ff268eef5f6692846e44b50c7248868f98d51b4034232fcf \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1042130
</span> 
 depends_lib-append  port:R-BiocParallel \
                     port:R-Rcpp \
                     port:R-RcppHNSW \
                     port:R-S4Vectors
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-FNN \
                     port:R-knitr \
                     port:R-RcppAnnoy \
                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Tests freeze due to: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Tests freeze due to: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><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 ec348240b8b..8d34f55b888 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;'>@@ -3,27 +3,28 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocParallel 47856deee43f03646f070b2c079a6f1271a0d0e8
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.37.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   parallel
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor BiocParallel 1.38.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor parallel
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             {GPL-2 GPL-3}
 description         Bioconductor facilities for parallel evaluation
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  5ec70fde922c340ba46593093d124015ac837f44 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  245623b3837b86a75a465166f93bdd4ac662cc67ca3fbf4c7af9d2afe2a5135e \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    147091
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  2e14674a9189d3db1f723ddf88a4f8510e3e61cb \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  7e96e07beb4e59ab08d8064aaf6b4e414c9ccd7657e9949d7d9b2325b2113cd6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    995485
</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:#ffe0e0;'>-patchfiles          patch-remove-unavailable-suggests.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    patch-remove-unavailable-suggests.diff
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-batchtools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-batchtools \
</span>                     port:R-BBmisc \
                     port:R-BiocGenerics \
                     port:R-BiocStyle \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -39,9 +40,10 @@ depends_test-append port:R-batchtools \
</span>                     port:R-ShortRead \
                     port:R-VariantAnnotation
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# FIXME: there are MPI-related failures in tests, at least on PowerPC:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# Error in DEACTIVATED("MPI tests not run") : MPI tests not run
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# *** caught segfault ***
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# address 0x11e81414, cause 'memory not mapped'
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# Code from vignettes runs fine, however.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</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;background:#e0ffe0;'>+}
</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><span style='display:block; white-space:pre;color:#808080;'>index 3d3de3496b0..bfc7966476c 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocParallel/files/patch-remove-unavailable-suggests.diff
</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;'>@@ -1,15 +1,12 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- DESCRIPTION    2023-10-24 21:51:58.000000000 +0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ DESCRIPTION    2023-10-26 19:42:16.000000000 +0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -37,10 +37,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- DESCRIPTION    2024-05-01 10:47:25.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ DESCRIPTION    2024-05-04 14:20:45.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -37,8 +37,7 @@
</span>  Depends: methods, R (>= 3.5.0)
  Imports: stats, utils, futile.logger, parallel, snow, codetools
  Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel,
<span style='display:block; white-space:pre;background:#ffe0e0;'>--    GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--    TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--    GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--    data.table
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+    GenomicRanges, VariantAnnotation, Rsamtools, data.table,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+    GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools
</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,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++        GenomicRanges, VariantAnnotation,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         knitr, batchtools, data.table
</span>  Enhances: Rmpi
<span style='display:block; white-space:pre;background:#ffe0e0;'>- Collate: AllGenerics.R DeveloperInterface.R prototype.R
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     bploop.R ErrorHandling.R log.R
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocPkgTools/Portfile b/R/R-BiocPkgTools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 7bb75d2a502..71e1b8aca5f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocPkgTools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocPkgTools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor seandavi BiocPkgTools 1.20.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor seandavi BiocPkgTools 1.22.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             MIT
 description         Collection of simple tools for learning about Bioconductor packages
 long_description    {*}${description}
 homepage            https://github.com/seandavi/BiocPkgTools
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  e063a61fc5c8c05ddac3e835de8324d4e0082396 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  24acf9eacba1c0fec20d7a208d10e380b61d01fc8e09d62ceb61e8a66237916b \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    1478773
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  28f1aeaeb7754c2e4ef6156158a230b431014831 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  dd782d47fa834ebaefeada6ca2da6b3730fbd4b65084c19007b9982f7dc87fd9 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1508067
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocFileCache \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocSingular/Portfile b/R/R-BiocSingular/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 703d1733486..5d996f4a530 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocSingular/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocSingular/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor LTLA BiocSingular 1.18.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
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</span> 
 depends_lib-append  port:R-beachmat \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocStyle/Portfile b/R/R-BiocStyle/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index f3a8f389a28..58f0b41a911 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocStyle/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocStyle/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocStyle 18ce82ef90b5ab7cbdfa45dc0ab16dac0997111e
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Provides standard formatting styles for Bioconductor \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    PDF and HTML documents
</span> long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    787833
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocManager \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-BiocVersion/Portfile b/R/R-BiocVersion/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 1a181b67aa6..90cca85008f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-BiocVersion/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-BiocVersion/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor BiocVersion 1b820443eeff6d0796f2e04ebaba215aa95918f1
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Set the appropriate version of Bioconductor packages
 long_description    {*}${description}
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</span> supported_archs     noarch
 
 test.run            yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Biostrings/Portfile b/R/R-Biostrings/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 4e4f2f3db73..58d49dde350 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Biostrings/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Biostrings/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor Biostrings 8324ca476b7d28e98b03e73c5fe3bba62727b44c
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Efficient manipulation of biological strings
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  3f78f6a9f3a968d805b10cf2d188ae86acba8287 \
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</span> 
 depends_lib-append  port:R-BiocGenerics \
                     port:R-crayon \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ChemmineDrugs/Portfile b/R/R-ChemmineDrugs/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 17d5c5cfec9..f09ca11adaf 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ChemmineDrugs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ChemmineDrugs/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -5,6 +5,7 @@ PortGroup           R 1.0
</span> 
 R.setup             bioconductor Bioconductor ChemmineDrugs 1.0.2
 revision            1
<span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         DrugBank data set
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ChemmineOB/Portfile b/R/R-ChemmineOB/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 4162bd78dc6..f4d08182d54 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ChemmineOB/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ChemmineOB/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor girke-lab ChemmineOB 1.40.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor girke-lab ChemmineOB 1.42.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         R interface to a subset of OpenBabel functionalities
 long_description    {*}${description}
 homepage            https://github.com/girke-lab/ChemmineOB
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  30ebf8641edc7eb8e1e81c03c38a4f8375a24bb5 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1367470
</span> 
 depends_build-append \
                     port:pkgconfig
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -26,7 +27,16 @@ depends_lib-append  path:share/pkgconfig/eigen3.pc:eigen3 \
</span> patchfiles          patch-fix-flags.diff
 
 post-patch {
<span style='display:block; white-space:pre;background:#ffe0e0;'>-    reinplace "s,@PREFIX@,${prefix},g" ${worksrcpath}/src/Makevars.in
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # https://github.com/girke-lab/ChemmineOB/issues/35
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # https://github.com/girke-lab/ChemmineOB/issues/40
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    if {${configure.cxx_stdlib} ne "libc++"} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+        reinplace "s|@PKG_CPPFLAGS@|-D_GLIBCXX_USE_CXX11_ABI=0 -DUSE_BOOST -DHAVE_EIGEN -I${prefix}/include/openbabel3 -I${prefix}/include/eigen3|" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    ${worksrcpath}/src/Makevars.in
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    } else {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+        reinplace "s|@PKG_CPPFLAGS@|-D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION -DUSE_BOOST -DHAVE_EIGEN -I${prefix}/include/openbabel3 -I${prefix}/include/eigen3|" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    ${worksrcpath}/src/Makevars.in
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    reinplace "s|@PKG_LIBS@|-L${prefix}/lib -lopenbabel|" ${worksrcpath}/src/Makevars.in
</span> }
 
 depends_test-append port:R-BiocManager \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -34,6 +44,7 @@ depends_test-append port:R-BiocManager \
</span>                     port:R-ChemmineR \
                     port:R-knitr \
                     port:R-knitrBootstrap \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-rmarkdown \
</span>                     port:R-RUnit
 
 test.run            yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ChemmineOB/files/patch-fix-flags.diff b/R/R-ChemmineOB/files/patch-fix-flags.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index f4420616643..0e1d1664528 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ChemmineOB/files/patch-fix-flags.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ChemmineOB/files/patch-fix-flags.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,12 +1,10 @@
</span> --- src/Makevars.in       2023-10-25 02:13:48.000000000 +0800
 +++ src/Makevars.in    2023-10-27 04:21:49.000000000 +0800
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -6,5 +6,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -6,5 +6,5 @@
</span>  #      endif
  #endif 
  
 -PKG_CPPFLAGS = -I/usr/include/openbabel3  -I/usr/include/eigen3  -DUSE_BOOST -DHAVE_EIGEN  -I/usr/local/include/eigen3 -I/usr/local/include/openbabel3  @OPENBABEL_CFLAGS@ 
 -PKG_LIBS =  -L/usr/local/lib/openbabel3  @OPENBABEL_LIBS@
<span style='display:block; white-space:pre;background:#ffe0e0;'>-+PKG_CPPFLAGS = -DUSE_BOOST -DHAVE_EIGEN -I@PREFIX@/include/openbabel3 -I@PREFIX@/include/eigen3
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+PKG_LIBS = -L@PREFIX@/lib -lopenbabel
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+PKG_CXXFLAGS = -D_GLIBCXX_USE_CXX11_ABI=0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++PKG_CPPFLAGS = @PKG_CPPFLAGS@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++PKG_LIBS = @PKG_LIBS@
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ChemmineR/Portfile b/R/R-ChemmineR/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 9e89baae34c..5e8cb1cfc54 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ChemmineR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ChemmineR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,20 +3,21 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor girke-lab ChemmineR 3.54.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor girke-lab ChemmineR 3.56.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Cheminformatics toolkit for R
 long_description    {*}${description}
 homepage            https://github.com/girke-lab/ChemmineR
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  c9ea71d72f93cc4bca758fbdf55d764cc39550f5 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  01297549b77098b794d22158253a30989b8111a6998d1872dc993af82aaf488c \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  49c555dd3bd671d8bb085b8adcfe9058891f8e79 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  ac6550157293f9a2b2ec7feb631c153ef747e77f196a021f6959be3586efa288 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    2062989
</span> 
 depends_lib-append  port:R-base64enc \
<span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:R-BiocGenerics \
</span>                     port:R-BH \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocGenerics \
</span>                     port:R-DBI \
                     port:R-digest \
                     port:R-DT \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -30,7 +31,9 @@ depends_lib-append  port:R-base64enc \
</span>                     port:R-rsvg \
                     port:R-stringi
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-bibtex \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
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                     port:R-BiocStyle \
                     port:R-ChemmineDrugs \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -46,5 +49,6 @@ depends_test-append port:R-bibtex \
</span>                     port:R-scatterplot3d \
                     port:R-snow
 
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ComplexHeatmap/Portfile b/R/R-ComplexHeatmap/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 8d0d4bcce6c..bcc7a98e817 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ComplexHeatmap/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ComplexHeatmap/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
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 depends_lib-append  port:R-circlize \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DECIPHER/Portfile b/R/R-DECIPHER/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-DECIPHER/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,21 +3,24 @@
</span> PortSystem          1.0
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                     port:R-XVector
 
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DESeq2/Portfile b/R/R-DESeq2/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,17 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor mikelove DESeq2 1.42.1
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</span> maintainers         nomaintainer
 license             LGPL-3+
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 depends_lib-append  port:R-Biobase \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DNAcopy/Portfile b/R/R-DNAcopy/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 04b9032735f..1276c0f267e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-DNAcopy/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,14 +3,15 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor DNAcopy 1.76.0
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</span> maintainers         nomaintainer
 license             GPL-2+
 description         DNA copy number data analysis
 long_description    {*}${description}
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 compilers.setup     require_fortran
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DelayedArray/Portfile b/R/R-DelayedArray/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 0d46789c53e..3981cc54c13 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-DelayedArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-DelayedArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,18 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor DelayedArray 700cfdc38e0f97a67942963c1555d0fd83a7bc41
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         Unified framework for working transparently with on-disk and in-memory array-like datasets
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DelayedMatrixStats/Portfile b/R/R-DelayedMatrixStats/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 850d2ec4473..62330d4fa92 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-DelayedMatrixStats/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-DelayedMatrixStats/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github PeteHaitch DelayedMatrixStats ef5c2cb5517b9705b1a50a241b57cdb822447253
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             MIT
 description         Functions that apply to rows and columns of DelayedMatrix objects
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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 depends_lib-append  port:R-DelayedArray \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -22,7 +22,9 @@ depends_lib-append  port:R-DelayedArray \
</span>                     port:R-S4Vectors \
                     port:R-sparseMatrixStats
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
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</span>                     port:R-HDF5Array \
                     port:R-knitr \
                     port:R-matrixStats \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -31,5 +33,6 @@ depends_test-append port:R-BiocStyle \
</span>                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# One test fails on ppc: https://github.com/PeteHaitch/DelayedMatrixStats/issues/90
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # One test fails on ppc: https://github.com/PeteHaitch/DelayedMatrixStats/issues/90
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-DelayedRandomArray/Portfile b/R/R-DelayedRandomArray/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-DelayedRandomArray/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
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</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Delayed arrays of random values
 long_description    {*}${description}
 homepage            https://github.com/LTLA/DelayedRandomArray
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-GenomicFeatures/Portfile b/R/R-GenomicFeatures/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-GenomicFeatures/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-GenomicFeatures/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor GenomicFeatures 723829e39f9790ad50bc4b5f3081a6d6866449fe
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-GenomicRanges/Portfile b/R/R-GenomicRanges/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-GenomicRanges/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-GenomicRanges/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor GenomicRanges 910b78473ca2d8c961732549565696616774c3fd
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-HDF5Array/Portfile b/R/R-HDF5Array/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor HDF5Array 01340131dd044f92e0597a32b4e066a2454d62de
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</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
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 depends_lib-append  port:R-BiocGenerics \
                     port:R-DelayedArray \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-HilbertCurve/Portfile b/R/R-HilbertCurve/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index e86eba20138..b4bfbc545cb 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-HilbertCurve/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   graphics
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor jokergoo HilbertCurve 1.34.0
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</span> maintainers         nomaintainer
 license             MIT
 description         Make a 2D Hilbert curve
 long_description    {*}${description}
 homepage            http://jokergoo.github.io/HilbertCurve
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-circlize \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-HilbertVis/Portfile b/R/R-HilbertVis/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index edc7c11841c..d08314cc163 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-HilbertVis/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-HilbertVis/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor HilbertVis 1.60.0
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</span> maintainers         nomaintainer
 license             GPL-3+
 description         Hilbert curve visualization
 long_description    {*}${description}
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 depends_test-append port:R-EBImage \
                     port:R-IRanges
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-IRanges/Portfile b/R/R-IRanges/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 627e1b15998..de81eb6551f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-IRanges/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-IRanges/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,25 +3,26 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor IRanges 60cf5502ce421eee47dfc14841cc8ccbc57381df
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</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         Foundation of integer range manipulation
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
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</span>                     port:R-GenomicAlignments \
                     port:R-GenomicFeatures \
                     port:R-GenomicRanges \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -29,4 +30,5 @@ depends_test-append port:R-BiocStyle \
</span>                     port:R-RUnit \
                     port:R-XVector
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,11 +1,12 @@
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++        GenomicFeatures, RUnit, BiocStyle
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         AtomicList-utils.R Ranges-and-RangesList-classes.R
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Icens/Portfile b/R/R-Icens/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 190549c5b43..6bdf304e6de 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Icens/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Icens/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor Icens 233ce54178261214adc78a05e4badcc0896cf778
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.75.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor Icens 1.76.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         NPMLE for censored and truncated data
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  6c4da5a74662302cad53ac1aafc2d35b2f891772 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  d02cff849ae3e42e314ed1fbebba73dba8d6b81b28b697ef6e9e7815c3d03eb8 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    21516
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  5f03fca5787379076c478eda80d99c0463e5b2a4 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  7f8ddee8ca6452401ef0c53184471bc16f241d05e3d6efbac2475e74fba46b99 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    21053
</span> supported_archs     noarch
 
 # https://github.com/Bioconductor/Icens/issues/2
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-InteractionSet/Portfile b/R/R-InteractionSet/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 7d1ae312211..4a4e318d927 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-InteractionSet/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-InteractionSet/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 Bioconductor InteractionSet 1.30.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor InteractionSet 1.32.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-3
 description         Base classes for storing genomic interaction data
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  fea87cd65bff77933912112081e4855cf1b0b16c \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  1a372f3d5e9908caf13ceaf67ca7cc9e80b3ecec23c965acbf649c0539ebef56 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  f229c7ce5f7097678da8d111a4687c67772f801c \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  1a06acb7baab7846de9fa437c0f9634453ba2a86495eefab9eb0e6673eac7346 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    401992
</span> 
 depends_lib-append  port:R-BiocGenerics \
                     port:R-GenomeInfoDb \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-KEGGREST/Portfile b/R/R-KEGGREST/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index d5ee06d0120..0c63810d0ea 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-KEGGREST/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-KEGGREST/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor KEGGREST 192ddeea5f674dd66c18bf56c1cbe1e16dbba549
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.43.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor KEGGREST 1.44.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor www
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Client-side REST access to the Kyoto Encyclopedia \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    of Genes and Genomes (KEGG)
</span> long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  d670cc94279b3f6170b92cade3665947959e7171 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  22c12d375b8204536df1fe86687c35ae90ece6c2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  c079a74d37d4246ef67bcfa1da00d33bc87ac5fb74e1eb5015728fcc7d0871f7 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    23171
</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biostrings \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-KEGGgraph/Portfile b/R/R-KEGGgraph/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index f768e816113..d81da278b2b 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-KEGGgraph/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-KEGGgraph/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,15 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor KEGGgraph 1.62.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor KEGGgraph 1.64.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span> maintainers         nomaintainer
 license             GPL-2+
 description         A graph approach to KEGG pathway in R and Bioconductor
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  5e8717906e65e508de0189f3223082359a019de1 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  7412ccf6f30faf1cd5ef6081c5eef7ce933ed0507c74b9660630e27a50c63145 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  108f5eba850d6b270280bfe7e3419b0438e67c61 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  e71a46e0d81999c3b473fc07fc1c5e7094b5ed4f26e55e7de14bbacaf7c2ce51 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1363503
</span> supported_archs     noarch
 
 depends_lib-append  port:R-graph \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -19,12 +19,16 @@ depends_lib-append  port:R-graph \
</span>                     port:R-Rgraphviz \
                     port:R-XML
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles          patch-missing-test-deps.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    patch-missing-test-deps.diff
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-RBGL \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-RBGL \
</span>                     port:R-RColorBrewer \
                     port:R-SPIA \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# There are no specific tests though.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # There are no specific tests though.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MassSpecWavelet/Portfile b/R/R-MassSpecWavelet/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 627f195b42b..02a6923d97d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MassSpecWavelet/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MassSpecWavelet/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,18 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor zeehio MassSpecWavelet 1.68.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor zeehio MassSpecWavelet 1.70.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL-2+
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Peak detection for mass spectrometry data using wavelet-based algorithms
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Peak detection for mass spectrometry data \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    using wavelet-based algorithms
</span> long_description    {*}${description}
 homepage            https://github.com/zeehio/MassSpecWavelet
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  ef55b2d26d120d35976eb4ed34e8e1d5403138fc \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  0ed56568634fa76e138ef64c5efc210202dc410e \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  426a6dfa39f95fbfca9f04f940ac67b7dbe0c70493e7471533bf4c06a0b27b32 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1962420
</span> 
 depends_test-append port:R-bench \
                     port:R-BiocStyle \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MatrixGenerics/Portfile b/R/R-MatrixGenerics/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 819a59b7954..337a8b89642 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MatrixGenerics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MatrixGenerics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor MatrixGenerics 7287502c7b94f9572c8b1fbd385e0e88a04c1fcb
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.15.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor MatrixGenerics 1.16.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor math
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         S4 generic summary statistic functions that operate on matrix-like objects
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    31669
</span> supported_archs     noarch
 
 depends_lib-append  port:R-matrixStats
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MeSHDbi/Portfile b/R/R-MeSHDbi/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index b6ea1c15f71..87dc2cbbf5d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MeSHDbi/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MeSHDbi/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 Bioconductor MeSHDbi 1.38.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         DBI to construct MeSH-related package from sqlite file
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  05cc5b6bae40982c36119c079c291396c62365e9 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  adaeb97e7a112ad76b0acc9a73ed5c733bc4da57 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  bc4e5d4abea6b8a0bdcb0b28d63ab9e3cfab733495b658c219a250f68689a634 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    50417
</span> supported_archs     noarch
 
 depends_lib-append  port:R-AnnotationDbi \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MsCoreUtils/Portfile b/R/R-MsCoreUtils/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index e3bb881a3ce..08753f5ff94 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MsCoreUtils/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MsCoreUtils/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor RforMassSpectrometry MsCoreUtils 1.14.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor RforMassSpectrometry MsCoreUtils 1.16.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Core utils for mass spectrometry data
 long_description    {*}${description}
 homepage            https://github.com/RforMassSpectrometry/MsCoreUtils
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</span> 
 depends_lib-append  port:R-clue \
                     port:R-Rcpp \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MultiAssayExperiment/Portfile b/R/R-MultiAssayExperiment/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 802aa59848b..70ba0d9ca0d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MultiAssayExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MultiAssayExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github waldronlab MultiAssayExperiment a04fa9191a6939f5a77f1cccc66ae89242a431af
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.29.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor waldronlab MultiAssayExperiment 1.30.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Software for the integration of multi-omics experiments in Bioconductor
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description    {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Software for the integration of multi-omics experiments
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description    {*}${description} in Bioconductor.
</span> homepage            https://waldronlab.io/MultiAssayExperiment
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biobase \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-MultiAssayExperiment/files/patch-no-maftools.diff b/R/R-MultiAssayExperiment/files/patch-no-maftools.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index 72ed421e132..8cbd091ce80 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-MultiAssayExperiment/files/patch-no-maftools.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-MultiAssayExperiment/files/patch-no-maftools.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,10 +1,13 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- DESCRIPTION    2023-10-24 22:49:00.000000000 +0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ DESCRIPTION    2023-10-27 01:32:33.000000000 +0800
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -33,7 +33,6 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     BiocStyle,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     HDF5Array (>= 1.19.17),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     knitr,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--    maftools (>= 2.7.10),
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     rmarkdown,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     R.rsp,
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-     RaggedExperiment,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- DESCRIPTION    2024-05-03 06:49:42.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ DESCRIPTION    2024-05-04 21:03:38.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -26,8 +26,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         GenomicRanges (>= 1.25.93), IRanges, methods, S4Vectors (>=
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         0.23.19), tidyr, utils
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>=
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-        2.7.10), R.rsp, RaggedExperiment, reshape2, rmarkdown,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, R.rsp,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++        RaggedExperiment, reshape2, rmarkdown,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         survival, survminer, testthat, UpSetR
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VignetteBuilder: knitr, R.rsp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ biocViews: Infrastructure, DataRepresentation
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-RBGL/Portfile b/R/R-RBGL/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 6c6ec255429..1c7e1593fec 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-RBGL/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-RBGL/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,27 +3,28 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor RBGL ebeedfab659b89f99ad5fe216f4d28c71299b588
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.79.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   devel
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         Interface to the graph algorithms contained in the Boost library
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span> 
 depends_lib-append  port:R-BH \
                     port:R-graph
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
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</span>                     port:R-BiocStyle \
                     port:R-knitr \
                     port:R-Rgraphviz \
                     port:R-RUnit \
                     port:R-XML
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
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</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-RaggedExperiment/Portfile b/R/R-RaggedExperiment/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 1d836d7b6b1..0d01489873d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-RaggedExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-RaggedExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor RaggedExperiment 1fbbbdc0f3ebc9af41ae5a13045830a08367f001
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.27.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor RaggedExperiment 1.28.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Representation of sparse experiments and assays across samples
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocBaseUtils \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ResidualMatrix/Portfile b/R/R-ResidualMatrix/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 303d0ac918e..1d3e0438684 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ResidualMatrix/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ResidualMatrix/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor LTLA ResidualMatrix 1.12.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Creating a DelayedMatrix of regression residuals
 long_description    {*}${description}
 homepage            https://github.com/LTLA/ResidualMatrix
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-DelayedArray \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Rgraphviz/Portfile b/R/R-Rgraphviz/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 688792d7f2a..45c1abbfbe7 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Rgraphviz/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Rgraphviz/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor kasperdanielhansen Rgraphviz 2.46.0
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   graphics
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor kasperdanielhansen Rgraphviz 2.48.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor graphics
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             EPL
 description         Interfaces R with graphviz library for plotting R graph objects
 long_description    {*}${description}
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 # Not using MacPorts Graphviz due to: https://github.com/kasperdanielhansen/Rgraphviz/issues/19
 depends_lib-append  port:R-graph
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Rhdf5lib/Portfile b/R/R-Rhdf5lib/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index e5720310a5a..a2a5ebc7ce4 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Rhdf5lib/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor grimbough Rhdf5lib 1.24.2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         HDF5 library as an R package
 long_description    {*}${description}
 homepage            https://github.com/grimbough/Rhdf5lib
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 # FIXME: reason is unknown at the moment, but recent versions may fail to build on Rosetta:
 # See: https://github.com/grimbough/Rhdf5lib/issues/53
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Rhtslib/Portfile b/R/R-Rhtslib/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 0ddbbcfd004..f8091d0259f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Rhtslib/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Rhtslib/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor Rhtslib 4e1c963a6ef8f73163ebbd3793fa97b69f22dbb5
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             2.5.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor Rhtslib 3.0.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL
 description         HTSlib high-throughput sequencing library as an R package
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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 depends_lib-append  port:bzip2 \
                     port:curl \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Rsamtools/Portfile b/R/R-Rsamtools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 76c918607d5..4956129ec07 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-Rsamtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-Rsamtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor Rsamtools cb532a85d712c82431ed72e874f97e71e08d588a
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             2.19.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor Rsamtools 2.20.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Binary alignment (BAM), FASTA, variant call (BCF) and tabix file import
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Binary alignment (BAM), FASTA, variant call (BCF) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    and tabix file import
</span> long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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 depends_lib-append  port:curl \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-S4Arrays/Portfile b/R/R-S4Arrays/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 63e068faef3..60aba1a8878 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-S4Arrays/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-S4Arrays/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,18 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor S4Arrays c1f8e6f1f5008a04d336454254302b040229d6db
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.3.7
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   devel
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor S4Arrays 1.4.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         Foundation of array-like containers in Bioconductor
 long_description    {*}${description}
 homepage            https://bioconductor.org/packages/${R.package}
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 depends_lib-append  port:R-abind \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-S4Vectors/Portfile b/R/R-S4Vectors/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 5fb96482352..3472510517e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-S4Vectors/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-S4Vectors/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,21 +3,22 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor S4Vectors c54a595b76e7d2ae52ef4906ef4b1389b47df9e4
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             0.41.6
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor S4Vectors 0.42.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Foundation of vector-like and list-like containers
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage-append     https://bioconductor.org/packages/${R.package}
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 depends_lib-append  port:R-BiocGenerics
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
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</span>                     port:R-data.table \
                     port:R-DelayedArray \
                     port:R-GenomicRanges \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -28,4 +29,5 @@ depends_test-append port:R-BiocStyle \
</span>                     port:R-ShortRead \
                     port:R-SummarizedExperiment
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
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</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SPIA/Portfile b/R/R-SPIA/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 91dc18f1af1..3a8ca943953 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SPIA/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SPIA/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,19 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor SPIA 2.54.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor SPIA 2.56.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Restrictive
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         Signaling Pathway Impact Analysis (SPIA) using combined evidence \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    of pathway over-representation and unusual signaling perturbations
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://bioconductor.org/packages/release/bioc/licenses/SPIA/LICENSE
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Signaling Pathway Impact Analysis (SPIA) \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    using combined evidence of pathway over-representation \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    and unusual signalling perturbations
</span> long_description    {*}${description}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-KEGGgraph
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SQLDataFrame/Portfile b/R/R-SQLDataFrame/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index e3acf2effed..626db395c20 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SQLDataFrame/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SQLDataFrame/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,38 +3,33 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor SQLDataFrame 6eced9bdf3a8ba4fc1fa3aecbf3203a1c4bcbd84
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   databases
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor SQLDataFrame 1.18.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor databases
</span> maintainers         nomaintainer
<span style='display:block; white-space:pre;background:#ffe0e0;'>-license             GPL-3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license             LGPL-3
</span> description         Representation of SQL database in DataFrame metaphor
 long_description    {*}${description}
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 depends_lib-append  port:R-BiocGenerics \
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</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# There are some warnings during checks:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# https://github.com/Bioconductor/SQLDataFrame/issues/7
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-S4Vectors
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-bigrquery \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Some tests fail: https://github.com/Bioconductor/SQLDataFrame/issues/10
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# On PowerPC [ FAIL 11 | WARN 0 | SKIP 0 | PASS 96 ]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-knitr \
                     port:R-rmarkdown \
<span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:R-RMySQL \
</span>                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ScaledMatrix/Portfile b/R/R-ScaledMatrix/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 60525b1a874..9ba93050052 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ScaledMatrix/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ScaledMatrix/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor LTLA ScaledMatrix 1.10.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor LTLA ScaledMatrix 1.12.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Creating a DelayedMatrix of scaled and centered values
 long_description    {*}${description}
 homepage            https://github.com/LTLA/ScaledMatrix
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  37ccfcec8d7cd0b93a2461248fd69d121e6cd192 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  8a40a14537c47caaf9aa1dc4b7b8c2354fca77ba895e548821b132a481622faa \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    313034
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  4029c4afd6af6fa9b11483b39ccb5653c8ca60fa \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  f15ea729ef6162a68c437d887d40981aa7f0d613ac777a727e3e0c7d6db9da30 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    311705
</span> supported_archs     noarch
 
 depends_lib-append  port:R-DelayedArray \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SeqArray/Portfile b/R/R-SeqArray/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 51dc6fd3bcb..7bbdd2a85a2 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SeqArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SeqArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor zhengxwen SeqArray 1.42.4
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor zhengxwen SeqArray 1.44.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-3
 description         Data management of large-scale whole-genome sequence variant calls
 long_description    {*}${description}
 homepage            https://github.com/zhengxwen/SeqArray
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  8b8524693e0695593a4dd540e58afaf01ceea809 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  2d55f287546a9cfa5e02923e934a1318bdf22b6d6bac67bcbc65d0202727ef4c \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    3594809
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  9fcaf5f207f8dda2d8745844157548935c95a2b6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  13a1b9b44dd66e6e4141ae089f2c9f762bdbf9090c6ac14186113963fc3108bd \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    3580975
</span> 
 depends_lib-append  port:R-Biostrings \
                     port:R-gdsfmt \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ShortRead/Portfile b/R/R-ShortRead/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 9ef9cc9ac94..aa3313b51d7 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ShortRead/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ShortRead/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor ShortRead 6b48c2b6a26162a3ebd7eb610a88875b1e899d3d
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.61.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor ShortRead 1.62.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         FASTQ input and manipulation
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  e1afa20e00c55d33739bc1a590497fbc87f7995f \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  d13774360749fc42412828943aaecd3374da6dc35a8bc460feee0ecfc1ce0438 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    5009082
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  da8875044bccc06edae361e1845e5c96373aeac4 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  550ead16ef1aa2dca0f221a570ca8216b077d1627701c824cf45773145c7b174 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    5313872
</span> 
 depends_lib-append  port:R-Biobase \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -24,17 +24,21 @@ depends_lib-append  port:R-Biobase \
</span>                     port:R-hwriter \
                     port:R-IRanges \
                     port:R-latticeExtra \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-pwalign \
</span>                     port:R-Rhtslib \
                     port:R-Rsamtools \
                     port:R-S4Vectors \
                     port:R-XVector \
                     port:R-zlibbioc
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-biomaRt \
                     port:R-RUnit \
                     port:R-GenomicFeatures \
                     port:R-yeastNagalakshmi
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# One example fails: https://github.com/Bioconductor/ShortRead/issues/13
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # One example fails: https://github.com/Bioconductor/ShortRead/issues/13
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SingleCellExperiment/Portfile b/R/R-SingleCellExperiment/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 132fbdafc01..b731abe5ced 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SingleCellExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SingleCellExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor SingleCellExperiment 1.24.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor SingleCellExperiment 1.26.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-3
 description         S4 classes for single-cell data
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  c21b6f47471ede03cd2d5ee8065361c4a740df3a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  c4670774e28468028bc62971a78f2576a10fb90c4b832c0a6c34785a4fb28460 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    985002
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  7a39ab4cb45fa4004a11b7450ac465ce5d36ea18 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  76e080bbed5634caf152a02799d722750ede9ecf2b97bd9743bd949732984b27 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    979460
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SparseArray/Portfile b/R/R-SparseArray/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index e94d34b34a7..c030fe368fa 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SparseArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SparseArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,18 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor SparseArray 25665f0500c9b59b8ba7d97a5b136708697a3255
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.3.5
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   devel
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor SparseArray 1.4.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         Efficient in-memory representation of multi-dimensional sparse arrays
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  820c678c2e5f0c595a1d648d098d2ac5d6394af3 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  9778f025dcbca98e3ccccd5c4e195659f1be07fa555b7c927024c991b3a003d7 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    142659
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  6bfa03fb02a070445feaca70edcda09073ef9498 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  0d2cfd75da16c471713b0d9e0c9b83ae21c6467779231ec6ddd1de151668617f \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    374420
</span> 
 depends_lib-append  port:R-BiocGenerics \
                     port:R-IRanges \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -24,10 +22,20 @@ depends_lib-append  port:R-BiocGenerics \
</span>                     port:R-S4Vectors \
                     port:R-XVector
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Temporarily disable OpenMP with Clang due to:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# https://github.com/Bioconductor/SparseArray/issues/9
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+if {[string match *clang* ${configure.compiler}]} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    patch-disable-openmp.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-DelayedArray \
                     port:R-knitr \
                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SparseArray/files/patch-disable-openmp.diff b/R/R-SparseArray/files/patch-disable-openmp.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..fd00832f1a3
</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-SparseArray/files/patch-disable-openmp.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,45 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/Makevars   2024-05-01 08:54:02.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/Makevars   2024-05-05 04:55:32.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1,2 +1,2 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++PKG_CFLAGS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++PKG_LIBS =
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/thread_control.c   2024-05-01 08:54:02.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/thread_control.c   2024-05-05 04:57:12.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -3,14 +3,14 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+  ****************************************************************************/
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include "thread_control.h"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ifdef _OPENMP
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#if defined(_OPENMP) && !defined(__clang__)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <omp.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static int get_num_procs(void)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ifdef _OPENMP
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#if defined(_OPENMP) && !defined(__clang__)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   return omp_get_num_procs();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #else
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   return 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -19,7 +19,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static int get_max_threads(void)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ifdef _OPENMP
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#if defined(_OPENMP) && !defined(__clang__)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   return omp_get_max_threads();
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #else
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   return 0;
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -28,7 +28,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static void set_max_threads(int nthread)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-#ifdef _OPENMP
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#if defined(_OPENMP) && !defined(__clang__)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   omp_set_num_threads(nthread);
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+   return;
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Structstrings/Portfile b/R/R-Structstrings/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..e680e3515e7
</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-Structstrings/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,40 @@
</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 FelixErnst Structstrings 1.20.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</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         Implementation of the dot bracket annotations with Biostrings
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description    ${name} implements the widely used dot bracket annotation \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    for storing base pairing information in structured RNA.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage            https://github.com/FelixErnst/Structstrings
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  4034158efe7a6042dd258d96959a43d2c84d2e37 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  e9efa165ccff880429acba1b2d149ead365fda46ed3b14b2723bb1077b9c49cd \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    375653
</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-crayon \
</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-S4Vectors \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-stringi \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-stringr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-XVector
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    patchfiles-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    patch-no-tRNAscanImport.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</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-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-testthat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Tests pass, one example from vignettes fails.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Structstrings/files/patch-no-tRNAscanImport.diff b/R/R-Structstrings/files/patch-no-tRNAscanImport.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..a9a56f2d488
</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-Structstrings/files/patch-no-tRNAscanImport.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    2024-05-02 07:40:27.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ DESCRIPTION    2024-05-05 05:08:04.000000000 +0800
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -24,7 +24,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ LinkingTo: IRanges, S4Vectors
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon,
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         grDevices
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++Suggests: testthat, knitr, rmarkdown, BiocStyle
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ VignetteBuilder: knitr
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ RoxygenNote: 7.3.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ Collate: 'Structstrings.R' 'AllGenerics.R'
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-SummarizedExperiment/Portfile b/R/R-SummarizedExperiment/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 00522139f8e..3c8a5b96dd2 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-SummarizedExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-SummarizedExperiment/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor SummarizedExperiment 6393bb8e050f3a02d4aaad4b82582353a76b8efb
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.33.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor SummarizedExperiment 1.34.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         SummarizedExperiment container
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  c364962f883df538d6e0bf16e908bdeb797bda56 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  eae7af1c67c5772025e6f3b598ddc9a5c323a06e7b8b0430b2592459c3fc6f74 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    93765
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  a6a120b3351243d5cf7a655f792a8bc640765779 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  e0c2b2c512dcf273b6c74115bac49093932753b69bb0d95ff80fbcb7057e9b09 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    688177
</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biobase \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-TileDBArray/Portfile b/R/R-TileDBArray/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 911933be260..f1e3b54e6de 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-TileDBArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-TileDBArray/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,18 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor LTLA TileDBArray 1.12.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor LTLA TileDBArray 1.14.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> categories-append   databases
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             MIT
 description         Use TileDB as a DelayedArray backend
 long_description    {*}${description}
 homepage            https://github.com/LTLA/TileDBArray
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  994f49297750004ecba3e17a2c6b276f831a877a \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  920703cc68b3dbad43aaac626efb3d8a1e5c7f18fbdf95f9ade80ef878ada1d7 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    size    313671
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  c768ef48ad6e5025856ad5fef33288923b467ec5 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  030096dc995559762968fa785a420fda55b80f0480de3596741694e75c67fcc1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    312953
</span> 
 depends_lib-append  port:R-DelayedArray \
                     port:R-Rcpp \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -22,13 +23,16 @@ depends_lib-append  port:R-DelayedArray \
</span> 
 compiler.cxx_standard 2017
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocParallel \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocParallel \
</span>                     port:R-BiocStyle \
                     port:R-knitr \
                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Status of tests on ppc: [ FAIL 5 | WARN 0 | SKIP 0 | PASS 28 ]
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# Those failing spit out the same message: [TileDB::ArrayDirectory] Error: FilterCreate: Deserialization error; not enough data in buffer for metadata
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# See notes in TileDB and R-tiledb ports; also: https://github.com/TileDB-Inc/TileDB/issues/4096
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Status of tests on ppc: [ FAIL 5 | WARN 0 | SKIP 0 | PASS 28 ]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Those failing spit out the same message: [TileDB::ArrayDirectory] Error: FilterCreate: Deserialization error; not enough data in buffer for metadata
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # See notes in TileDB and R-tiledb ports; also: https://github.com/TileDB-Inc/TileDB/issues/4096
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-UCSC.utils/Portfile b/R/R-UCSC.utils/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..de8a4c2cba3
</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-UCSC.utils/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 UCSC.utils 1.0.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</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         Low-level utilities to retrieve data \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    from the UCSC Genome Browser
</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  d313396ce690328a86d8712b1b8f6d9e041e82ad \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  349de171d96d28875fdbac104e4a10f0d6c891fdec6676d755d1fa6c5a2f2e71 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    236116
</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-httr \
</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-S4Vectors
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</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-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-knitr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-RMariaDB \
</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-testthat
</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;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-VariantAnnotation/Portfile b/R/R-VariantAnnotation/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 7fdc37dfaa7..47c0d7ac7f4 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-VariantAnnotation/Portfile
</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;'>@@ -3,15 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor VariantAnnotation 1.48.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor VariantAnnotation 1.50.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biobase \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-biocViews/Portfile b/R/R-biocViews/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-biocViews/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-biocViews/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor biocViews e4a1a5ac568fb07e03f7b700c2fcda049f367a37
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 description         Categorized views of R package repositories
 long_description    {*}${description}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-Biobase \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-biocthis/Portfile b/R/R-biocthis/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-biocthis/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,18 +3,19 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-biomaRt/Portfile b/R/R-biomaRt/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-biomaRt/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,32 +3,34 @@
</span> PortSystem          1.0
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-AnnotationDbi \
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                     port:R-digest \
<span style='display:block; white-space:pre;background:#ffe0e0;'>-                    port:R-httr \
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</span> depends_test-append port:R-BiocStyle \
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                     port:R-mockery \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-testthat
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 test.run            yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-biomaRt/files/patch-no-httptest2.diff b/R/R-biomaRt/files/patch-no-httptest2.diff
</span>new file mode 100644
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
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 description         Clustering algorithms for Bioconductor
 long_description    {*}${description}
 homepage            https://github.com/LTLA/bluster
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 depends_lib-append  port:R-BiocNeighbors \
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-clustComp/Portfile b/R/R-clustComp/Portfile
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 description         Clustering Comparison
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-csaw/Portfile b/R/R-csaw/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,15 +3,16 @@
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 long_description    {*}${description}
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 depends_lib-append  port:curl \
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-dcanr/Portfile b/R/R-dcanr/Portfile
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</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Differential co-expression/association network analysis
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-circlize \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-dir.expiry/Portfile b/R/R-dir.expiry/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 4bf3f745b69..0a606194659 100644
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-dir.expiry/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 Bioconductor dir.expiry 1.10.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor devel
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 license             GPL-3
 description         Managing expiration for cache directories
 long_description    {*}${description}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-filelock
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-edgeR/Portfile b/R/R-edgeR/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-edgeR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-edgeR/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 Bioconductor edgeR 4.0.16
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            2
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 license             GPL-2+
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 long_description    {*}${description}
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 depends_lib-append  port:R-limma \
                     port:R-locfit \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-fmcsR/Portfile b/R/R-fmcsR/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-fmcsR/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor girke-lab fmcsR 1.44.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Mismatch-tolerant maximum common substructure searching
 long_description    {*}${description}
 homepage            https://github.com/girke-lab/fmcsR
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</span> 
 depends_build-append \
                     port:grep
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-gdsfmt/Portfile b/R/R-gdsfmt/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 98cf20c4de0..db6c0ada286 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-gdsfmt/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-gdsfmt/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor zhengxwen gdsfmt 1.38.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor zhengxwen gdsfmt 1.40.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL-3
 description         R interface to CoreArray Genomic Data Structure (GDS) files
 long_description    {*}${description}
 homepage            https://github.com/zhengxwen/gdsfmt
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</span> 
 # TODO: consider switching to external libs: https://github.com/zhengxwen/gdsfmt/issues/35
 
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-genefilter/Portfile b/R/R-genefilter/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 3abeb288afc..82fd076ec44 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-genefilter/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-genefilter/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 Bioconductor genefilter 1.84.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor genefilter 1.86.0
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Methods for filtering genes from high-throughput experiments
 long_description    {*}${description}
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 depends_lib-append  port:R-annotate \
                     port:R-AnnotationDbi \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -19,3 +20,17 @@ depends_lib-append  port:R-annotate \
</span>                     port:R-MatrixGenerics
 
 compilers.setup     require_fortran
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Some optional deps are omitted.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-ALL \
</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-knitr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-RColorBrewer \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-tkWidgets
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Some examples gonna fail since they rely
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # on a missing package.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
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</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ggtree/Portfile b/R/R-ggtree/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 82708158187..af973a7c193 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ggtree/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ggtree/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         R package for visualization of tree and annotation data
 long_description    {*}${description}
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</span> supported_archs     noarch
 
 depends_lib-append  port:R-ape \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ggtreeExtra/Portfile b/R/R-ggtreeExtra/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 22a31e05db3..aaffa98aaac 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ggtreeExtra/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ggtreeExtra/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor YuLab-SMU ggtreeExtra 1.12.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   graphics
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor YuLab-SMU ggtreeExtra 1.14.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor graphics
</span> maintainers         nomaintainer
 license             GPL-3+
 description         Add geometric layers on circular or other layout tree of ggtree
 long_description    {*}${description}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    526655
</span> supported_archs     noarch
 
 depends_lib-append  port:R-cli \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-golubEsets/Portfile b/R/R-golubEsets/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..fc37bbb81a4
</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-golubEsets/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,21 @@
</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
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor marray 1.82.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL
 description         Exploratory analysis for two-color spotted microarray data
 long_description    {*}${description}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    5054750
</span> supported_archs     noarch
 
 depends_lib-append  port:R-limma
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-metapod/Portfile b/R/R-metapod/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 474a8a55cad..c53f78ad572 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-metapod/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-metapod/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,23 +3,27 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor metapod 1.10.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor metapod 1.12.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-3
 description         Meta-analyses on p-values of differential analyses
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  2155316098c3057d60d7402df090001c4832ba16 \
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</span> 
 depends_lib-append  port:R-Rcpp
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-knitr \
                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Tests err out due to a broken R-BATCH.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-# See: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Tests err out due to a broken R-BATCH.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # See: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-mixOmics/Portfile b/R/R-mixOmics/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index c8a7a65ef87..f8c98db7986 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-mixOmics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-mixOmics/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor Bioconductor mixOmics 6.26.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor mixOmics 6.28.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             GPL-2+
 description         Omics Data Integration Project
 long_description    {*}${description}
 homepage            http://www.mixOmics.org
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    18848374
</span> supported_archs     noarch
 
 depends_lib-append  port:R-BiocParallel \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-multtest/Portfile b/R/R-multtest/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 754d21d27c3..7509868f6fe 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-multtest/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-multtest/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 Bioconductor multtest 2.58.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor multtest 2.60.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL
 description         Resampling-based multiple hypothesis testing
 long_description    {*}${description}
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1295259
</span> 
 depends_lib-append  port:R-Biobase \
                     port:R-BiocGenerics
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-pcaMethods/Portfile b/R/R-pcaMethods/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ba05aebae96..db7a4a36c0d 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-pcaMethods/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-pcaMethods/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor hredestig pcaMethods 1.94.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor hredestig pcaMethods 1.96.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3+
 description         Collection of PCA methods
 long_description    {*}${description}
 homepage            https://github.com/hredestig/pcamethods
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  b26b9cdef7f482e4d0d80fb5ef763cf1acfaf2f4 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  54a78e03edb36daade8ca1ac67d353b83e358afe \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  f15662bdd30fa86cde65a7a2bc17cbc271a80cca4953133d2c89867c6b0738c3 \
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</span> 
 depends_lib-append  port:R-Biobase \
                     port:R-BiocGenerics \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-preprocessCore/Portfile b/R/R-preprocessCore/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index d170ddfb369..e674c8d63e7 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-preprocessCore/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-preprocessCore/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor bmbolstad preprocessCore 1.64.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor bmbolstad preprocessCore 1.66.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             LGPL-2+
 description         Collection of pre-processing functions
 long_description    {*}${description}
 homepage            https://github.com/bmbolstad/preprocessCore
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  b4c0c3801e88ac042258cd2ee4b0fc763ba768a3 \
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</span> 
 compilers.setup     require_fortran
 
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-pwalign/Portfile b/R/R-pwalign/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..dad5c59548f
</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-pwalign/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,28 @@
</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 pwalign 1.0.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</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         Perform pairwise sequence alignments
</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  6b17459360d7ec92a1f0fbd45f3040fc20515f62 \
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</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-IRanges \
</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-XVector
</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-RUnit
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# Optional, avoid for now:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+# depends_test-append port:R-Rmpi
</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-qvalue/Portfile b/R/R-qvalue/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 801356c5c50..9f8aaccf79e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-qvalue/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-qvalue/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor StoreyLab qvalue 2.34.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor StoreyLab qvalue 2.36.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL
 description         Q-value estimation for false discovery rate control
 long_description    {*}${description}
 homepage            https://github.com/StoreyLab/qvalue
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  1a09573322afc59dfab507e54a560c075449d8b6 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  15fe5b6ae7b461a5fa7af2aa2cb4f6b5b3fc6873 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  4a3cf7ec1f241779f893e15858c44ea4b74f4a5669c602c26ac8e5a0d7cef3c1 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    2760802
</span> supported_archs     noarch
 
 depends_lib-append  port:R-ggplot2 \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-rhdf5/Portfile b/R/R-rhdf5/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ed0b2d6ac5a..e36f42ca6b5 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-rhdf5/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-rhdf5/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,22 +3,24 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor grimbough rhdf5 2.46.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor grimbough rhdf5 2.48.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         R Interface to HDF5
 long_description    {*}${description}
 homepage            https://github.com/grimbough/rhdf5
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  617ed55b8d9317431badba04292d131e57c672f5 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  b68f4960bf8498e83984467b07ed8fa10b3ef68fb5abbc776d6b7dee9307de79 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  09fee5f05ed08f1f221819809275e205280fef98 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  9683e5b11da8bda62894f1fefd488490592ed6b739ac4954fa03735a3fb7cb20 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1269365
</span> 
 depends_lib-append  port:R-rhdf5filters \
                     port:R-Rhdf5lib \
                     port:R-S4Vectors
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-bench \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append port:R-bench \
</span>                     port:R-BiocParallel \
                     port:R-BiocStyle \
                     port:R-bit64 \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -29,5 +31,6 @@ depends_test-append port:R-bench \
</span>                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Some tests fail on PPC: https://github.com/grimbough/rhdf5/issues/122
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Some tests fail on PPC: https://github.com/grimbough/rhdf5/issues/122
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-rhdf5filters/Portfile b/R/R-rhdf5filters/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 3d175ed68a8..dfa6cbc8f22 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-rhdf5filters/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-rhdf5filters/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,8 +3,9 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor grimbough rhdf5filters 1.14.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor grimbough rhdf5filters 1.16.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             BSD
 description         HDF5 compression filters
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -12,9 +13,9 @@ long_description    Provides a collection of additional compression filters for
</span>                     The package is intended to provide seemless integration with rhdf5, \
                     however the compiled filters can also be used with external applications.
 homepage            https://github.com/grimbough/rhdf5filters
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  92bc6ddd0ad716a43400dca7f00341e23ed343bd \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  ff6c91e582b31dd887194bbd0e349990c60ffb7a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  1df1452264bdb9057c682d6c5d90178046bdd34addd923c100b32c77c9b84e3b \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    1176741
</span> 
 depends_lib-append  port:R-Rhdf5lib
 
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -28,11 +29,14 @@ platform darwin 10 {
</span>     }
 }
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_test-append port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+variant tests description "Enable testing" {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_test-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-BiocStyle \
</span>                     port:R-knitr \
                     port:R-rhdf5 \
                     port:R-rmarkdown \
                     port:R-testthat
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-# Tests may fail to run due to: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # Tests may fail to run due to: https://trac.macports.org/ticket/67059
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-rsbml/Portfile b/R/R-rsbml/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 08344bdcfda..84eb296cb2b 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-rsbml/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-rsbml/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 Bioconductor rsbml 2.60.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor rsbml 2.62.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         R support for SBML, using libsbml
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  8ff3ca4d6c2aea16e5d0724e8c64c81799095931 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  caddc5dd6bc4cf7471ff5160d55fbce694334494 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    565386
</span> 
 depends_build-append \
                     port:pkgconfig
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -19,4 +20,12 @@ depends_lib-append  port:libsbml \
</span>                     port:R-BiocGenerics \
                     port:R-graph
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+platform darwin {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    if {${os.major} > 10 && ${configure.cxx_stdlib} eq "libc++"} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    build.args-append   --configure-vars=' \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                        RSBML_CPPFLAGS="-D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                        '
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    }
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+test.run            no
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-rtracklayer/Portfile b/R/R-rtracklayer/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 1c490d847cc..05932bdc01e 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-rtracklayer/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-rtracklayer/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -4,23 +4,27 @@ PortSystem          1.0
</span> PortGroup           openssl 1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             bioconductor lawremi rtracklayer 1.62.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor lawremi rtracklayer 1.64.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
<span style='display:block; white-space:pre;background:#ffe0e0;'>-description         R interface to genome annotation files and the UCSC genome browser
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         R interface to genome annotation files \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    and the UCSC genome browser
</span> long_description    {*}${description}
 homepage            https://github.com/lawremi/rtracklayer
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  b17725f5955503ba182d83c03f162fc0e8f18d1f \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    3951281
</span> 
 depends_lib-append  port:R-BiocGenerics \
                     port:R-BiocIO \
                     port:R-Biostrings \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-curl \
</span>                     port:R-GenomeInfoDb \
                     port:R-GenomicAlignments \
                     port:R-GenomicRanges \
<span style='display:block; white-space:pre;background:#e0ffe0;'>+                    port:R-httr \
</span>                     port:R-IRanges \
                     port:R-RCurl \
                     port:R-restfulr \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-sparseMatrixStats/Portfile b/R/R-sparseMatrixStats/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index aae0b3ed9b9..ffc7f2d7647 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-sparseMatrixStats/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-sparseMatrixStats/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,17 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github const-ae sparseMatrixStats 511322bbf36176b6150534c742ed3ab0caf08328
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.15.1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor const-ae sparseMatrixStats 1.16.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             MIT
 description         Summary statistics for rows and columns of sparse matrices
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  c9c7bd5e93ade8fc75078545f294fbfcd4e695e6 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  9d0dabb36aac2a09fb5e32757feb5e86d6127de7 \
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</span> 
 depends_lib-append  port:R-MatrixGenerics \
                     port:R-matrixStats \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-ssize/Portfile b/R/R-ssize/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ebb26242ddb..c2b665a581f 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-ssize/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-ssize/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 Bioconductor ssize 1.76.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor ssize 1.78.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             LGPL
 description         Estimate microarray sample size
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  5f901947b9d3f77a5a18698af424acb92cf1093d \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  b326624303774a945e3d884ceb8399b0cda87302 \
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</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    size    373307
</span> supported_archs     noarch
 
 depends_lib-append  port:R-gdata \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-survcomp/Portfile b/R/R-survcomp/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index ccfc0736f57..5c87b3b3779 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-survcomp/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-survcomp/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 Bioconductor survcomp 1.52.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor survcomp 1.54.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   bioconductor
</span> maintainers         nomaintainer
 license             Artistic-2
 description         Performance assessment and comparison for survival analysis
 long_description    {*}${description}
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 depends_lib-append  port:R-bootstrap \
                     port:R-ipred \
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-systemPipeR/Portfile b/R/R-systemPipeR/Portfile
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,17 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -29,9 +30,12 @@ depends_lib-append  port:R-BiocGenerics \
</span>                     port:R-SummarizedExperiment \
                     port:R-yaml
 
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                     port:R-batchtools \
                     port:R-BiocStyle \
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -53,4 +57,5 @@ depends_test-append port:R-annotate \
</span>                     port:R-systemPipeRdata \
                     port:R-VariantAnnotation
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    test.run        yes
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</span> PortSystem          1.0
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 license             Artistic-2
 description         Workflow templates and sample data
 long_description    {*}${description}
 homepage            https://github.com/tgirke/systemPipeRdata
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<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -21,7 +22,9 @@ depends_lib-append  port:R-BiocGenerics \
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                     port:R-remotes
 
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</span>                     port:R-ShortRead \
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<span style='display:block; white-space:pre;background:#ffe0e0;'>-test.run            yes
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</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,16 +3,16 @@
</span> PortSystem          1.0
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<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-treeio/Portfile b/R/R-treeio/Portfile
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</span> supported_archs     noarch
 
 test.run            yes
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-zlibbioc/Portfile b/R/R-zlibbioc/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 545a09f1b34..b5123035695 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/R/R-zlibbioc/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/R/R-zlibbioc/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,18 +3,16 @@
</span> PortSystem          1.0
 PortGroup           R 1.0
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-R.setup             github Bioconductor zlibbioc 77920bcab5ef50132fbcbf9e1e13ddb04692c2db
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version             1.49.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision            1
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append   archivers
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+R.setup             bioconductor Bioconductor zlibbioc 1.50.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision            0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   archivers bioconductor
</span> maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Artistic-2
 description         An R-packaged zlib-1.2.5
 long_description    {*}${description}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage            https://bioconductor.org/packages/${R.package}
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</span> 
 depends_test-append port:R-BiocStyle
 
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