R: update bioconductor stuff to 3.19 release

Closes: https://trac.macports.org/ticket/69858
barracuda156 · May 5, 2024 · 05b0e8d · 05b0e8d
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diff --git a/R/R-ALL/Portfile b/R/R-ALL/Portfile
@@ -0,0 +1,21 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+
+PortSystem          1.0
+PortGroup           R 1.0
+
+R.setup             bioconductor Bioconductor ALL 1.46.0
+revision            0
+categories-append   bioconductor
+maintainers         nomaintainer
+license             Artistic-2
+description         A data package
+long_description    {*}${description}
+master_sites        https://bioconductor.org/packages/release/data/experiment/src/contrib/
+checksums           rmd160  4bc9e3055403e27028aca18a7c23eedade95d3df \
+                    sha256  0a660bf324dadfe32e3b75cbe76857a425db13f6d0461e37e9338588305a88fa \
+                    size    11382429
+supported_archs     noarch
+
+depends_lib-append  port:R-Biobase
+
+test.run            yes
diff --git a/R/R-AnnotationDbi/Portfile b/R/R-AnnotationDbi/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor AnnotationDbi 7daf9f47046e11f412e04195a7743a3840541b79
-version             1.65.2
-revision            1
+R.setup             bioconductor Bioconductor AnnotationDbi 1.66.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Manipulation of SQLite-based annotations in Bioconductor
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  14e6cd65be419054465ca9b889ed1d8e78cc6a68 \
-                    sha256  9950ea4c323f4746cb677eb81ef2f718d8b27c9eca03bf6fcdc81ebdf5cdd4ad \
-                    size    3932444
+checksums           rmd160  081469e0c6d4d202377e279fa0a6f30508d8d4c9 \
+                    sha256  3aa793c6888ad50a63d88e2a2df59655c6384ada9db2c5d84473ca76fafa5ebc \
+                    size    4359386
 supported_archs     noarch
 platforms           {darwin any}
 

diff --git a/R/R-AnnotationForge/Portfile b/R/R-AnnotationForge/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor AnnotationForge 2bba05a2305c3c803b8d9747a5c44c0d22fe2631
-version             1.45.0
-revision            1
+R.setup             bioconductor Bioconductor AnnotationForge 1.46.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Tools for building SQLite-based annotation data packages
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  4eb9edad24f2fe2ad6d283a916cfed9f23b472a8 \
-                    sha256  ba6f56a58d2ce9f791bdf89b60f92ab92d6a6bc128b3f0cb1297e3253c0653c0 \
-                    size    3366069
+checksums           rmd160  c647fd409394fc43cd34ee47d273624f049a85d7 \
+                    sha256  c1b234391b582f5d10b87a80a3bbe00d3d2800d5fc3acf03ff12e8b0608a79c6 \
+                    size    3989356
 supported_archs     noarch
 platforms           {darwin any}
 

diff --git a/R/R-AnnotationHub/Portfile b/R/R-AnnotationHub/Portfile
@@ -3,16 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             bioconductor Bioconductor AnnotationHub 3.10.1
-revision            1
-categories-append   www
+R.setup             bioconductor Bioconductor AnnotationHub 3.12.0
+revision            0
+categories-append   bioconductor www
 maintainers         nomaintainer
 license             Artistic-2
 description         Client to access AnnotationHub resources
 long_description    {*}${description}
-checksums           rmd160  522499d73cb02a2303588cb78a383d9738d5ba91 \
-                    sha256  dd974316cea658f5ad099d92fe2cdcb19e77edc11e19a11ce30bbdfac6296c8b \
-                    size    994797
+checksums           rmd160  1571886c70a3738d15fe1fafc7f48e8a724e9094 \
+                    sha256  a138dc289305b598fa7c7ea732c1b5947a54bfd127fe7242b3da772147b042b5 \
+                    size    992371
 supported_archs     noarch
 platforms           {darwin any}
 

diff --git a/R/R-BSgenome/Portfile b/R/R-BSgenome/Portfile
@@ -3,15 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             bioconductor Bioconductor BSgenome 1.70.2
-revision            1
+R.setup             bioconductor Bioconductor BSgenome 1.72.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
-description         Software infrastructure for efficient representation of full genomes and their SNPs
+description         Software infrastructure for efficient representation \
+                    of full genomes and their SNPs
 long_description    {*}${description}
-checksums           rmd160  2ca505383589549ece1b22cfaa57ba617ea1e592 \
-                    sha256  2d1879cc4aaab1ebdeeb36228143800dcbdee17cc13aba1f21524747cfc3190b \
-                    size    5909171
+checksums           rmd160  1526c109a69a66c046695640b3e2b51673cce55b \
+                    sha256  98541684ea234a3c102338b4a4d055817d92a088b9e67ea88b6a339fa79a4bde \
+                    size    5718748
 supported_archs     noarch
 
 depends_lib-append  port:R-BiocGenerics \

diff --git a/R/R-BayesKnockdown/Portfile b/R/R-BayesKnockdown/Portfile
@@ -3,15 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             bioconductor Bioconductor BayesKnockdown 1.28.0
-revision            1
+R.setup             bioconductor Bioconductor BayesKnockdown 1.30.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             GPL-3
 description         Posterior probabilities for edges from knockdown data
 long_description    {*}${description}
-checksums           rmd160  a8d33e78796ffaf4214308899281148691c8d731 \
-                    sha256  88869bc99b67d947642bcf38110e2ab13e65ea9965bdbb37585e34ea1e692fab \
-                    size    116534
+checksums           rmd160  4790eac1899f84f11ee90e15be4c3148d6820b29 \
+                    sha256  0aefd1850059bbf595f6bf0ee135ed15a9eb9316713f36198112006d06acf416 \
+                    size    117801
 supported_archs     noarch
 
 depends_lib-append  port:R-Biobase

diff --git a/R/R-BioNet/Portfile b/R/R-BioNet/Portfile
@@ -3,15 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             bioconductor Bioconductor BioNet 1.62.0
-revision            1
+R.setup             bioconductor Bioconductor BioNet 1.64.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             GPL-2+
 description         Routines for the functional analysis of biological networks
 long_description    {*}${description}
-checksums           rmd160  fc20c5cf00d92fba4fc7d0db41d192502592eccd \
-                    sha256  78012ebdb0dc4acfbb179a1030b76a835617129b2bfb0ef34a3849f2b2915988 \
-                    size    1687581
+checksums           rmd160  bd34049a504ac6d8657c82f2bb38a0455283c7e8 \
+                    sha256  06828daef6fdd94068b29dc7e63b015b70107a22ca1e28535af69ece40ddf852 \
+                    size    1680069
 supported_archs     noarch
 
 depends_lib-append  port:R-AnnotationDbi \

diff --git a/R/R-Biobase/Portfile b/R/R-Biobase/Portfile
@@ -3,15 +3,28 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor Biobase 4cf5590294d698b89f77ba639853ebd57a704d53
-version             2.63.0
-revision            1
+R.setup             bioconductor Bioconductor Biobase 2.64.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Base functions for Bioconductor
 long_description    {*}${description}
-checksums           rmd160  7daa612d833d4b86f6bcb8079949b8295c7fac3a \
-                    sha256  96491344516448fde15ccfb9560b370134795c12a79ee385d654b05d68fde5ca \
-                    size    1182396
+checksums           rmd160  821f629260b6c9acc2cdc79941fa65e4ac936f4c \
+                    sha256  a21e35cdf4eeb71fc144712bb619d4ea5124c4013ceb14034a4d638231a0b627 \
+                    size    1792985
 
 depends_lib-append  port:R-BiocGenerics
+
+variant tests description "Enable testing" {
+    depends_test-append \
+                    port:R-ALL \
+                    port:R-BiocStyle \
+                    port:R-golubEsets \
+                    port:R-knitr \
+                    port:R-limma \
+                    port:R-RUnit \
+                    port:R-tkWidgets
+
+    test.run        yes
+}
diff --git a/R/R-BiocBaseUtils/Portfile b/R/R-BiocBaseUtils/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor BiocBaseUtils 5bfff695290ae6db7ccbc5ceafdbbc9e5ddb32a7
-version             1.5.0
-revision            1
+R.setup             bioconductor Bioconductor BiocBaseUtils 1.6.0
+revision            0
+categories-append   bioconductor devel
 maintainers         nomaintainer
 license             Artistic-2
 description         General utility functions for developing Bioconductor packages
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  19b1135bcdad562ae3539f83fd6df7783cf7ea72 \
-                    sha256  aeddaed86f897f20f14d5d4ae1b5e3458775c20952f0894a13e7974ed6c78b92 \
-                    size    8212
+checksums           rmd160  b965c45d366bb2911345adc085ea613aa988c2a3 \
+                    sha256  a4d8aa652a1ab929cd66172b315d2fb79e489f06a2ddbdb4288a76132ffc0b39 \
+                    size    228328
 supported_archs     noarch
 
 depends_test-append port:R-BiocStyle \

diff --git a/R/R-BiocCheck/Portfile b/R/R-BiocCheck/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor BiocCheck 7e7e07e1dfd8ddae8bf14d35e9df0add09aad61a
-version             1.39.0
-revision            1
+R.setup             bioconductor Bioconductor BiocCheck 1.40.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Bioconductor-specific package checks
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  6ebe2e08e7a3005db3dba016da76f1fe7a453522 \
-                    sha256  9284956381683f6fd7db8d3baa9a2e828d3afb69569b76e1dcc54361c1202e76 \
-                    size    4136699
+checksums           rmd160  f193aae4052999471553abd374b583c3e3f12e8a \
+                    sha256  e885ee791975e4b69a94dbb1a6761370c4231de7dd8e90e43a395a551a327967 \
+                    size    4378887
 supported_archs     noarch
 
 depends_lib-append  port:R-BiocBaseUtils \
@@ -22,11 +21,14 @@ depends_lib-append  port:R-BiocBaseUtils \
                     port:R-biocViews \
                     port:R-callr \
                     port:R-graph \
-                    port:R-httr \
+                    port:R-httr2 \
                     port:R-knitr \
+                    port:R-rvest \
                     port:R-stringdist
 
-depends_test-append port:R-Biobase \
+variant tests description "Enable testing" {
+    depends_test-append \
+                    port:R-Biobase \
                     port:R-BiocGenerics \
                     port:R-BiocStyle \
                     port:R-callr \
@@ -37,5 +39,7 @@ depends_test-append port:R-Biobase \
                     port:R-RUnit \
                     port:R-usethis
 
-# One test fails on ppc: https://github.com/Bioconductor/BiocCheck/issues/188
-test.run            yes
+    # One test fails, at least on ppc:
+    # https://github.com/Bioconductor/BiocCheck/issues/188
+    test.run        yes
+}
diff --git a/R/R-BiocFileCache/Portfile b/R/R-BiocFileCache/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor BiocFileCache 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
-version             2.11.2
-revision            1
+R.setup             bioconductor Bioconductor BiocFileCache 2.12.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Manage files across sessions
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  e6cf87e3e167b7ce2f6eb0ce0883a1e062f5b70f \
-                    sha256  e0aa9ef23a9e9c802d075fabbf46336381f74f2cb37156408e3735f025df91d4 \
-                    size    52473
+checksums           rmd160  7537ab402764ab6bb14222a4fb3caec7e6455973 \
+                    sha256  2e716d10a27ecb677095144dd707273c534f8d1f11d248fed63aa45ea285664b \
+                    size    297080
 supported_archs     noarch
 
 depends_lib-append  port:R-curl \

diff --git a/R/R-BiocGenerics/Portfile b/R/R-BiocGenerics/Portfile
@@ -3,15 +3,14 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor BiocGenerics 2e1a2a6152989cb21ff44eb98906edd486d0eb23
-version             0.49.1
-revision            1
+R.setup             bioconductor Bioconductor BiocGenerics 0.50.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
-description         The package defines many S4 generic functions used in Bioconductor
-long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  32218f0af24f2562f9e266b410cdff84fac9e2ce \
-                    sha256  8ca9335a97878a84942da0749f505d32d6ed83c9ddb1aabff3312c8363dca08e \
-                    size    50319
+description         The package defines many S4 generic functions
+long_description    {*}${description} used in Bioconductor.
+checksums           rmd160  03d7d483fdf4d8d4502b150ddbc185cafdffe374 \
+                    sha256  11d72e20c087911a58d08db7898d47424930e00265d6e65ae87d14d786f20014 \
+                    size    49747
 supported_archs     noarch
diff --git a/R/R-BiocIO/Portfile b/R/R-BiocIO/Portfile
@@ -3,17 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github Bioconductor BiocIO 96ba3c5d94859e51f551e7278c7b5f7f5fae2421
-version             1.13.0
-revision            1
+R.setup             bioconductor Bioconductor BiocIO 1.14.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             Artistic-2
 description         Standard Input and Output for Bioconductor packages
 long_description    {*}${description}
-homepage            https://bioconductor.org/packages/${R.package}
-checksums           rmd160  aec6fd40c8045983b9100c0e31e9b401ac92ee7a \
-                    sha256  6f0806895f5ff31b815ac4e081f9340374edc8290178292918d1abe1b45cd999 \
-                    size    10336
+checksums           rmd160  80bef328f46c70e544afb3e2ffc12619dc05f406 \
+                    sha256  9010bd8bdf810f571825bc055464219365168c6daadb2d6b8c74ed616fa3fa5e \
+                    size    230564
 supported_archs     noarch
 
 depends_lib-append  port:R-BiocGenerics \

diff --git a/R/R-BiocNeighbors/Portfile b/R/R-BiocNeighbors/Portfile
@@ -3,27 +3,31 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             bioconductor Bioconductor BiocNeighbors 1.20.2
-revision            1
+R.setup             bioconductor Bioconductor BiocNeighbors 1.22.0
+revision            0
+categories-append   bioconductor
 maintainers         nomaintainer
 license             GPL-3
 description         Nearest neighbor detection for Bioconductor packages
 long_description    {*}${description}
-checksums           rmd160  29602eaac6b0dc04eda53a9057e91769ffb67982 \
-                    sha256  04123fe8ceb2cc9a17af7d187460e601dcce389adb1fcc6f89ad9c0844e27a53 \
-                    size    1039738
+checksums           rmd160  16c2700bbd282314974b3c4003268f68dfc5c9d3 \
+                    sha256  2d727fa9e983afd7ff268eef5f6692846e44b50c7248868f98d51b4034232fcf \
+                    size    1042130
 
 depends_lib-append  port:R-BiocParallel \
                     port:R-Rcpp \
                     port:R-RcppHNSW \
                     port:R-S4Vectors
 
-depends_test-append port:R-BiocStyle \
+variant tests description "Enable testing" {
+    depends_test-append \
+                    port:R-BiocStyle \
                     port:R-FNN \
                     port:R-knitr \
                     port:R-RcppAnnoy \
                     port:R-rmarkdown \
                     port:R-testthat
 
-# Tests freeze due to: https://trac.macports.org/ticket/67059
-test.run            yes
+    # Tests freeze due to: https://trac.macports.org/ticket/67059
+    test.run        yes
+}