R: updates to packages

R/R-BiocManager/Portfile

@@ -3,7 +3,7 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran Bioconductor BiocManager 1.30.24
+R.setup             cran Bioconductor BiocManager 1.30.25
 revision            0
 categories-append   bioconductor
 platforms           {darwin any}
@@ -12,9 +12,9 @@ license             Artistic-2
 description         Access the Bioconductor project package repository
 long_description    {*}${description}
 homepage            https://bioconductor.github.io/BiocManager
-checksums           rmd160  811959ffe888e129e26cc6d369c8107836feee27 \
-                    sha256  645c423bb144dbd476cb308678bd36e06c1a3494115f157166dd3f59955ec7d1 \
-                    size    593392
+checksums           rmd160  56554b385cbdb3d13a6f4cbcad1cbcfd17d32b3b \
+                    sha256  83ef8b57dcc7350fe1e8c62590a60d3ad3e1f9c8660930c946b20340a4a81e15 \
+                    size    593414
 supported_archs     noarch
 
 depends_test-append port:R-BiocVersion \

R/R-RSQLite/Portfile

@@ -3,17 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github r-dbi RSQLite 2.3.7.9008 v
+R.setup             github r-dbi RSQLite 2.3.7.9012 v
 revision            0
 categories-append   databases
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             LGPL-2.1+
 description         SQLite interface for R
 long_description    {*}${description}
 homepage            https://rsqlite.r-dbi.org
-checksums           rmd160  3ff3a386df28979177e978d4a1d97232d44a0b82 \
-                    sha256  f69dddc1d9fd8447f38af1003260f766e7c35c0597559d5fd77c2f7870dc9c68 \
-                    size    4232294
+checksums           rmd160  f04c59fe1fbd6b58e5d689037c551633c130fb70 \
+                    sha256  a7a8bf84c212ea195e8e779ee4477ce6830ecd61e944a504b5e22fc870985952 \
+                    size    4237396
 github.tarball_from archive
 
 depends_lib-append  port:R-bit64 \

R/R-RcppBessel/Portfile

@@ -0,0 +1,31 @@
+# -*- 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             cran alexiosg RcppBessel 1.0.0
+revision            0
+categories-append   math
+maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
+license             GPL-2+
+description         Bessel Functions Rcpp Interface
+long_description    ${name} exports an Rcpp interface for the Bessel \
+                    functions in the Bessel package.
+homepage            https://github.com/alexiosg/RcppBessel
+checksums           rmd160  620623e105272b231b1dd369359964ba0e079cd0 \
+                    sha256  a987531b86c18f46f37cd3ecf33a02261b85110a8af7b60045d73a6503d0d4a5 \
+                    size    90820
+
+depends_lib-append  port:R-Rcpp \
+                    port:R-Rdpack
+
+compilers.setup     require_fortran
+
+depends_test-append port:R-Bessel \
+                    port:R-knitr \
+                    port:R-microbenchmark \
+                    port:R-rmarkdown \
+                    port:R-roxygen2 \
+                    port:R-testthat
+
+test.run            yes

R/R-SSN2/Portfile

@@ -3,24 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github USEPA SSN2 0.2.0 v
+# Just use CRAN tarball here.
+R.setup             cran USEPA SSN2 0.2.1
 revision            0
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Spatial modelling on stream networks
 long_description    {*}${description}
 homepage            https://usepa.github.io/SSN2
-checksums           rmd160  bf46772a6eb703278b9759c71c0c8f2b658a5e56 \
-                    sha256  900ef27f5378d7f2647315ad5c47e758fb2293518e5ade0b310256c1a45bfa70 \
-                    size    4074965
-github.tarball_from archive
-
-post-extract {
-    # Trash pre-built Intel binaries, which break powerpc and aarch64 builds:
-    foreach obj [glob ${worksrcpath}/src/*.o] {
-        delete ${obj}
-    }
-}
+checksums           rmd160  84e3c0ac928058e8dbd6fda80ea9f91a9423b230 \
+                    sha256  71d4d379009b6997ee41bff2ae22157a64b26321c363c1d0beebd4ba6f79f07b \
+                    size    1273664
 
 depends_lib-append  port:R-generics \
                     port:R-RSQLite \

R/R-bigergm/Portfile

@@ -0,0 +1,47 @@
+# -*- 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             cran corneliusfritz2010 bigergm 1.2.1
+revision            0
+categories-append   math
+maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
+license             GPL-3
+description         Hierarchical exponential-family models for big networks
+long_description    A toolbox for analyzing and simulating large networks based \
+                    on hierarchical exponential-family random graph models (HERGMs).
+checksums           rmd160  d0ca43c2937fd081af48661f34c88ab31b57e92a \
+                    sha256  688250b7a20a8ec12bf01fc3ce636368772ab70788c97f4250f3b628a33a1e75 \
+                    size    1754339
+
+depends_lib-append  port:R-cachem \
+                    port:R-dplyr \
+                    port:R-ergm \
+                    port:R-ergm.multi \
+                    port:R-foreach \
+                    port:R-glue \
+                    port:R-igraph \
+                    port:R-intergraph \
+                    port:R-magrittr \
+                    port:R-memoise \
+                    port:R-network \
+                    port:R-purrr \
+                    port:R-Rcpp \
+                    port:R-RcppArmadillo \
+                    port:R-readr \
+                    port:R-reticulate \
+                    port:R-rlang \
+                    port:R-statnet.common \
+                    port:R-stringr \
+                    port:R-tidyr
+
+compilers.setup     require_fortran
+
+depends_test-append port:R-knitr \
+                    port:R-rmarkdown \
+                    port:R-sna \
+                    port:R-testthat \
+                    port:R-tibble
+
+test.run            yes

R/R-boot/Portfile

@@ -6,17 +6,17 @@ PortGroup           R 1.0
 R.recommended       yes
 
 # This is a recommended package. Keep it CRAN-sourced.
-R.setup             cran brazzale boot 1.3-30
-revision            1
+R.setup             cran brazzale boot 1.3-31
+revision            0
+platforms           {darwin any}
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Permissive
 description         Functions and datasets for bootstrapping
 long_description    {*}${description}. Recommended package.
-checksums           rmd160  6381ef1f6477b3b430e97cf1be1c012b8bcd2ce2 \
-                    sha256  5509d62bd6e6c21b6ef352ab7846d89027bddbfb727fd0cf55da59558bd3fe97 \
-                    size    237087
+checksums           rmd160  e4eb916ae1fdbfaae6104d735ff66d5eed508e67 \
+                    sha256  d8542e8cd1b503ca412e774908f386c0522a991296d57560ebded0f3d201c8d2 \
+                    size    238458
 supported_archs     noarch
-platforms           {darwin any}
 
 depends_test-append port:R-MASS \
                     port:R-survival

R/R-broom.helpers/Portfile

@@ -3,20 +3,21 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran larmarange broom.helpers 1.16.0
+R.setup             cran larmarange broom.helpers 1.17.0
 revision            0
 platforms           {darwin any}
 maintainers         nomaintainer
-license             GPL-3
+license             GPL-3+
 description         Helpers for model coefficients tibbles
 long_description    {*}${description}
 homepage            https://larmarange.github.io/broom.helpers
-checksums           rmd160  6c3cc10e866c3da39d0c45a444ef187c656b3a79 \
-                    sha256  9a7bac8678cdcc9a7e0f3b6d287d375fd5f1e880c916ac4d661f02c2c84e2715 \
-                    size    197766
+checksums           rmd160  9f40cacd779ae1ff40645230eeef7c15aecf756c \
+                    sha256  d1e3de2893ccd49408579388604048b808c1f1dbdb0bedde9aedbdfe70d5274d \
+                    size    199679
 supported_archs     noarch
 
 depends_lib-append  port:R-broom \
+                    port:R-cards \
                     port:R-cli \
                     port:R-dplyr \
                     port:R-labelled \

R/R-cubble/Portfile

@@ -4,17 +4,17 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # GitHub version lags behind.
-R.setup             cran huizezhang-sherry cubble 0.3.2
+R.setup             cran huizezhang-sherry cubble 1.0.0
 revision            0
 categories-append   math
 platforms           {darwin any}
 maintainers         nomaintainer
 license             MIT
 description         Vector spatio-temporal data structure for data analysis
 long_description    {*}${description}
-checksums           rmd160  3fd61ae03529f773a3c18fc28298dc185cfc32af \
-                    sha256  31c147ee195db518362fa983fb00ce51a382c39d847d1d087e4b7dfaffac6ad9 \
-                    size    3517288
+checksums           rmd160  1c0f12b5e0758e6d519976adf702fc026fc49741 \
+                    sha256  e5ed70bd0bd1e1231c9d42669206064b6882027ac553b8a318c357087fac0574 \
+                    size    3519407
 supported_archs     noarch
 
 depends_lib-append  port:R-cli \

R/R-extras/Portfile

@@ -4,7 +4,7 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # GitHub version lags behind.
-R.setup             cran poissonconsulting extras 0.7.2
+R.setup             cran poissonconsulting extras 0.7.3
 revision            0
 categories-append   math
 platforms           {darwin any}
@@ -13,9 +13,9 @@ license             MIT
 description         Helper functions for Bayesian analyses
 long_description    {*}${description}
 homepage            https://poissonconsulting.github.io/extras
-checksums           rmd160  0a4aacb381f35d4a2cc42f6f200a1678a4219109 \
-                    sha256  8436d18e1fc1645a52056c58cc52d0df659ea88a7aed20d1a0796b9d9c96a289 \
-                    size    244259
+checksums           rmd160  016efa554a8f56d7bcd299e389dc996a3cba958b \
+                    sha256  e1f5fd70e5b59c6d80d182d47f6b4f16f7ba361f4132ead78a7bd299084d11e4 \
+                    size    244648
 supported_archs     noarch
 
 depends_lib-append  port:R-chk \

R/R-garchx/Portfile

@@ -0,0 +1,23 @@
+# -*- 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             cran gsucarrat garchx 1.5
+revision            0
+categories-append   finance
+maintainers         nomaintainer
+license             GPL-2+
+description         Flexible and robust GARCH-X modelling
+long_description    {*}${description}
+homepage            https://github.com/gsucarrat/garchx
+checksums           rmd160  71ffa89167558b68a850d0240455774b4252933c \
+                    sha256  ab98f3b0a8ee302dece8d3b23eae99558e39f8c84080eb4d76dbb4a5732bcb7e \
+                    size    20582
+
+depends_lib-append  port:R-zoo
+
+depends_test-append port:R-lgarch \
+                    port:R-tvgarch
+
+test.run            yes

R/R-gdtools/Portfile

@@ -3,29 +3,31 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran davidgohel gdtools 0.3.7
-revision            1
+R.setup             cran davidgohel gdtools 0.4.0
+revision            0
+categories-append   graphics
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Utilities for graphical rendering and fonts management
 long_description    {*}${description}
 homepage            https://davidgohel.github.io/gdtools
-checksums           rmd160  8b674fe83f6ae383d59673fc1a659af468e15f1f \
-                    sha256  d292c3b8574adc38007662085c3d1cf5d17e8019f085295d594380d85cf2b394 \
-                    size    72067
+checksums           rmd160  85c2c0257fb7658ee24674d9b8365f683fa3627d \
+                    sha256  e1136e9a997ba653ae05bc8feaf6a7241b889712c47e69cf31ec1a4506402f6b \
+                    size    74178
 
 depends_build-append \
-                    port:pkgconfig
+                    path:bin/pkg-config:pkgconfig
+
 depends_lib-append  path:lib/pkgconfig/cairo.pc:cairo \
                     port:fontconfig \
                     port:freetype \
-                    port:R-curl \
                     port:R-fontquiver \
-                    port:R-gfonts \
                     port:R-htmltools \
                     port:R-Rcpp \
                     port:R-systemfonts
 
-depends_test-append port:R-testthat
+depends_test-append port:R-curl \
+                    port:R-gfonts \
+                    port:R-testthat
 
 test.run            yes

R/R-glmmTMB/Portfile

@@ -5,12 +5,13 @@ PortGroup           R 1.0
 
 # GitHub version is old.
 R.setup             cran glmmTMB glmmTMB 1.1.9
-revision            1
+revision            2
 categories-append   math
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             AGPL-3
 description         Generalized Linear Mixed Models using Template Model Builder
 long_description    {*}${description}
+homepage            https://github.com/glmmTMB/glmmTMB
 checksums           rmd160  4d1da5480eefbb01b0b137f48bd87eb6871160be \
                     sha256  93d5a6b907b0f71f97c13134e0c450c951b3636365a369f48edb804207e78963 \
                     size    4362034

R/R-golem/Portfile

@@ -4,7 +4,7 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # Revert to GitHub once updated there.
-R.setup             cran ThinkR-open golem 0.5.0 v
+R.setup             cran ThinkR-open golem 0.5.1 v
 revision            0
 categories-append   devel
 platforms           {darwin any}
@@ -13,9 +13,9 @@ license             MIT
 description         Framework for robust Shiny applications
 long_description    {*}${description}
 homepage            https://thinkr-open.github.io/golem
-checksums           rmd160  ee4f416628be0f8de8a7c815741b6f9b0fa66ac1 \
-                    sha256  fd47eb3b2029135bf942c09e9ea6000b9efa402e3603b135fe1c4cdc71bfc10a \
-                    size    1675193
+checksums           rmd160  30edca1c27267ecc15bc6c844ae245ce3bdf79dd \
+                    sha256  86d66415cb117c7a0ad186f174c1d3482565266cbc8b226f9a6853bdf1973f1d \
+                    size    1675221
 # github.tarball_from archive
 supported_archs     noarch
 

R/R-greybox/Portfile

@@ -3,16 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran config-i1 greybox 2.0.1
+R.setup             cran config-i1 greybox 2.0.2
 revision            0
 categories-append   math
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             LGPL-2.1
 description         Toolbox for model building and forecasting
 long_description    {*}${description}
-checksums           rmd160  b58647a011922846e9ff30934c2b347453de48ac \
-                    sha256  13aad1a480df6ccf6ddd303fc9c065b145717c1ad19b97696f9ee0d3a6687114 \
-                    size    2258596
+homepage            https://github.com/config-i1/greybox
+checksums           rmd160  b27e69920d60acb3ea64c9d9995fd7e1b2343c72 \
+                    sha256  5fa926854dd23b04b2dda97b28d81f00cf3b0c80af55754bb855f24b976a7e62 \
+                    size    2336126
 
 depends_lib-append  port:R-generics \
                     port:R-nloptr \

R/R-harmony/Portfile

@@ -3,17 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran broadinstitute harmony 1.2.0 v
+R.setup             cran broadinstitute harmony 1.2.1 v
 revision            0
 maintainers         nomaintainer
 license             GPL-3
 description         Fast, sensitive and accurate integration \
                     of single cell data
 long_description    {*}${description}
 homepage            https://software.broadinstitute.org/harmony
-checksums           rmd160  4058e9d5336b855ad980ce7ff67d3a217d9bd0d6 \
-                    sha256  a63c7d7cbbc5d183e8f919552e9d73044e0a89660856e80861a00eb5d25ac7b5 \
-                    size    5179505
+checksums           rmd160  5dae1f8bd60870549a65332225b92c1f26d4e978 \
+                    sha256  240ae45bf97311371aa132db1ff6725dd287ee2b98620c0f23d88ab00b633bdd \
+                    size    5004595
 
 depends_lib-append  port:R-cowplot \
                     port:R-dplyr \