<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/ecdeff505a15314c53b49c4e42518f046f8b2ea8">https://github.com/macports/macports-ports/commit/ecdeff505a15314c53b49c4e42518f046f8b2ea8</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit ecdeff505a15314c53b49c4e42518f046f8b2ea8
</span>Author: barracuda156 <vital.had@gmail.com>
AuthorDate: Mon May 6 10:57:22 2024 +0800
<span style='display:block; white-space:pre;color:#404040;'> R-Seurat and friends, needed for R-nebula update
</span>---
R/R-Seurat/Portfile | 96 ++++++++++++++++++++++++++++++++++++++++++++++++
R/R-glmGamPoi/Portfile | 57 ++++++++++++++++++++++++++++
R/R-harmony/Portfile | 45 +++++++++++++++++++++++
R/R-ica/Portfile | 18 +++++++++
R/R-scattermore/Portfile | 25 +++++++++++++
R/R-sctransform/Portfile | 39 ++++++++++++++++++++
6 files changed, 280 insertions(+)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/R/R-Seurat/Portfile b/R/R-Seurat/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..9d734800753
</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-Seurat/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,96 @@
</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 github satijalab Seurat 5.0.3 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license MIT
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Tools for Single Cell Genomics
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://satijalab.org/seurat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 14bf3e6d49a62dc2f8f614f2893cdfc989dfcc05 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 783f6fdaaf1a1e08717b00368967290fb854f34e4d6805112335f9a971e1cd3a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 3654211
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.tarball_from archive
</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-cowplot \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-fastDummies \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-fitdistrplus \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-future \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-future.apply \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-generics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggplot2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggrepel \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggridges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-httr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ica \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-igraph \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-irlba \
</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-leiden \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-lifecycle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-lmtest \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-matrixStats \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-miniUI \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-patchwork \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-pbapply \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-plotly \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-png \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-progressr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-purrr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RANN \
</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-Rcpp \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppAnnoy \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppEigen \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppHNSW \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppProgress \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-reticulate \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rlang \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ROCR \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RSpectra \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rtsne \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-scales \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-scattermore \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-sctransform \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SeuratObject \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-shiny \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-spatstat.explore \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-spatstat.geom \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-tibble \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-uwot
</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;'>+ # 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-ape \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Biobase \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-data.table \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DelayedArray \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DESeq2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-enrichR \
</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-GenomicRanges \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggrastr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-harmony \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-hdf5r \
</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-limma \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-mixtools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-R.utils \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rfast2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rsvd \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rtracklayer \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-S4Vectors \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SingleCellExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SummarizedExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-testthat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-VGAM
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # On PowerPC 4 tests fail [ FAIL 4 | WARN 0 | SKIP 29 | PASS 532 ]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # https://github.com/satijalab/seurat/issues/8862
</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-glmGamPoi/Portfile b/R/R-glmGamPoi/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..54e055d73af
</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-glmGamPoi/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,57 @@
</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 const-ae glmGamPoi 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><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license GPL-2+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Fit a Gamma-Poisson Generalized Linear Model
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://github.com/const-ae/glmGamPoi
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 9239c7ccd43ff4b927932a8138510d0a47d7bb67 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 723660674f5cfcc758a1798b053b2ce2dc8f9648dc0bd990935df7d23fd8c8d7 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 2109372
</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-beachmat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DelayedArray \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DelayedMatrixStats \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-HDF5Array \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-MatrixGenerics \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-matrixStats \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rcpp \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppArmadillo \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rlang \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SingleCellExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SummarizedExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-vctrs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+compilers.setup require_fortran
</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;'>+ # 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-bench \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocParallel \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-BiocStyle \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-DESeq2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-dplyr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-edgeR \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggplot2 \
</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-rmarkdown \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-statmod \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-testthat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-zoo
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # Two tests fails due to missing test deps.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # [ FAIL 2 | WARN 11 | SKIP 4 | PASS 433 ]
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # For the same reason we disable vignettes here.
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ test.run yes
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ test.args-append \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ --ignore-vignettes
</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-harmony/Portfile b/R/R-harmony/Portfile
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 00000000000..aad746b5453
</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-harmony/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,45 @@
</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 cran broadinstitute harmony 1.2.0 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers nomaintainer
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license GPL-3
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description Fast, sensitive and accurate integration \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ of single cell data
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description {*}${description}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage https://software.broadinstitute.org/harmony
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 4058e9d5336b855ad980ce7ff67d3a217d9bd0d6 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 a63c7d7cbbc5d183e8f919552e9d73044e0a89660856e80861a00eb5d25ac7b5 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 5179505
</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-cowplot \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-dplyr \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggplot2 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-Rcpp \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppArmadillo \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RcppProgress \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-RhpcBLASctl \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-rlang \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-tibble
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+compilers.setup require_fortran
</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-data.table \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggrepel \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-ggthemes \
</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-patchwork \
</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-Seurat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-SingleCellExperiment \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-testthat \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-tidyverse \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ port:R-tidyr
</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-ica/Portfile b/R/R-ica/Portfile
</span>new file mode 100644
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