R: updates for packages (I)

R/R-DPQmpfr/Portfile

@@ -3,18 +3,19 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran r-project DPQmpfr 0.3-2
-revision            1
+R.setup             cran r-project DPQmpfr 0.3-3
+revision            0
 categories-append   math
+platforms           {darwin any}
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-2+
-description         DPQ (density, probability, quantile) distribution computations using MPFR
+description         DPQ (density, probability, quantile) distribution \
+                    computations using MPFR
 long_description    {*}${description}
-checksums           rmd160  d80101da8292c575db4c9bd66f3f391612f6e921 \
-                    sha256  774f7ec5a953e38963f2c42b3b5526cc2ad10306f4abb56f6aa22f73504cd246 \
-                    size    48065
+checksums           rmd160  9609162f85ac41dd2681e99f8e4dde15037d2d1f \
+                    sha256  c6b70784537974de356277319fa6d0fd6d68e99913a449537939c80a7cf40d54 \
+                    size    63041
 supported_archs     noarch
-platforms           {darwin any}
 
 depends_lib-append  port:R-DPQ \
                     port:R-gmp \

R/R-GpGp/Portfile

@@ -14,6 +14,11 @@ checksums           rmd160  059411e80df66d7a292e668d936db43e66e84e58 \
                     sha256  a3c0bf3df5fb7d766906e7f29c09aa50f77a75e5ffe9abf0e44287909816a267 \
                     size    1378259
 
+# Remove this with the next update. It is a one-time fix.
+if {${os.platform} eq "darwin" && ${configure.cxx_stdlib} eq "libc++"} {
+    incr revision
+}
+
 depends_lib-append  port:R-BH \
                     port:R-FNN \
                     port:R-Rcpp \

R/R-LBI/Portfile

@@ -3,17 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran r-project LBI 0.1.2
+R.setup             cran r-project LBI 0.1.3
 revision            0
 categories-append   math
+platforms           {darwin any}
 maintainers         nomaintainer
 license             GPL-3
 description         Likelihood-Based Inference
 long_description    {*}${description}
-checksums           rmd160  aceb96f459cd16e3f8ede379ed92511b48795a8f \
-                    sha256  0c4cc9e9adc8b96eeb2bab236831227e56860f7721c7ce952c5152411fdc16a2 \
-                    size    105566
+checksums           rmd160  b1a6fb4f7e3950f58de9e1e7cd0b19db44508693 \
+                    sha256  504f8054422796f9d8eb040979de479116fd0f0278c547d7317134425b1001ba \
+                    size    107248
 supported_archs     noarch
-platforms           {darwin any}
 
 test.run            yes

R/R-MBA/Portfile

@@ -3,16 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran cran MBA 0.1-0
-revision            1
+R.setup             cran finleya MBA 0.1-1
+revision            0
 categories-append   math
 maintainers         nomaintainer
 license             GPL-2+
 description         Multilevel b-spline approximation
 long_description    {*}${description}
-checksums           rmd160  213bc8d7e6fc8275a3587ef903e10d5b722470d8 \
-                    sha256  78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af \
-                    size    140852
+checksums           rmd160  651f0e265ea0ed1a2da263e6ba18959028a52362 \
+                    sha256  a22fec16f47f096ddaab2e3a50e1a7378c06f04db26b2c915546a2432d97de9b \
+                    size    140553
 
 depends_lib-append  port:R-BH
 

R/R-NNS/Portfile

@@ -3,22 +3,21 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran OVVO-Financial NNS 10.8.2
-revision            1
+R.setup             cran OVVO-Financial NNS 10.9
+revision            0
 categories-append   math finance
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Non-linear Non-parametric Statistics
 long_description    {*}${description} using partial moments.
-checksums           rmd160  e09a1cceed308172c11c7a022a946471c5824ae8 \
-                    sha256  4de675bb4923a9bbef74453a1a94d587bc0f2b8bd5309e959a871d87ad624a86 \
-                    size    1462012
+checksums           rmd160  ddadc298d3ad068c45f23c9e95fd7e6362f09246 \
+                    sha256  e9356ae7c07d22bf82aebdacb7731bf558868ab411bd26a198af20ed38995598 \
+                    size    1460213
 
 # TODO: https://github.com/OVVO-Financial/NNS/issues/12
 depends_lib-append  port:R-data.table \
                     port:R-doParallel \
                     port:R-foreach \
-                    port:R-plyr \
                     port:R-quantmod \
                     port:R-Rcpp \
                     port:R-RcppParallel \

R/R-OBsMD/Portfile

@@ -3,16 +3,16 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran marta.nairuscone OBsMD 11.1
-revision            1
+R.setup             cran marta.nairuscone OBsMD 12.0
+revision            0
 categories-append   math
 maintainers         nomaintainer
 license             GPL-2+
 description         Objective Bayesian model discrimination in follow-up designs
 long_description    {*}${description}
-checksums           rmd160  139023a956fcca319fc0476674f0686dfef2204a \
-                    sha256  de8456eb18efe0086acb1543c6470ae37dbeb21ce20da275a0b8c448941cbd3f \
-                    size    55690
+checksums           rmd160  8233a95a3e74c55f30e73aa9ad60fe53f3dcec2a \
+                    sha256  781c728bccf3dc5a9347fefb9ace4ab79aa4cd5c675cea01e3b121793709330a \
+                    size    55625
 
 compilers.setup     require_fortran
 

R/R-RcppSimdJson/Portfile

@@ -15,6 +15,11 @@ checksums           rmd160  a48d613836e592fbb082f5529e6bc10312a01b37 \
                     sha256  ffb9cc8fdc869a4d2a2d1fb90bf0ecd57d7134a287a7ae86e3e0a2668a65753b \
                     size    2066347
 
+# Remove this with the next update. It is a one-time fix.
+if {${os.platform} eq "darwin" && ${configure.cxx_stdlib} eq "libc++"} {
+    incr revision
+}
+
 depends_lib-append  port:R-Rcpp
 
 compiler.cxx_standard 2017

R/R-anomaly/Portfile

@@ -3,15 +3,15 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran dan.grose anomaly 4.3.2
-revision            1
+R.setup             cran dan.grose anomaly 4.3.3
+revision            0
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Detect anomalies in data
 long_description    {*}${description}
-checksums           rmd160  2510f28a4645436d40e87ec9054af317f337a4e2 \
-                    sha256  63a75080aa2750b4fb146ab7106d59221ed1583f43b3f1e3541ae74342610bf0 \
-                    size    1044060
+checksums           rmd160  4a9c1a67428ab94c4c67aa2cd5ab1e5c6e658f67 \
+                    sha256  44ec39c7c9320f82020d8090c5d62301582f1d566adb9d788986bd653101b58b \
+                    size    1049371
 
 depends_lib-append  port:R-BH \
                     port:R-cowplot \

R/R-apsimx/Portfile

@@ -3,18 +3,18 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran femiguez apsimx 2.7.7
+R.setup             cran femiguez apsimx 2.8.0
 revision            0
+platforms           {darwin any}
 maintainers         nomaintainer
 license             GPL-3
 description         R package for APSIM-X
 long_description    {*}${description}
 homepage            https://femiguez.github.io/apsimx-docs
-checksums           rmd160  0db9d210db6fdb3f53e0e53f97c8097b0f8ac241 \
-                    sha256  7af53c7ef2fc7c03255618c3548500ad47d6cbb994d12fee52c703efaca709a3 \
-                    size    1216301
+checksums           rmd160  23b6de6cfff37a018e49a61b9f5d9b73b3a219cf \
+                    sha256  016216ce8dd5ad4e92290a7e7d35eb01caf034478147667e69bc4d8179c5244c \
+                    size    1234164
 supported_archs     noarch
-platforms           {darwin any}
 
 depends_lib-append  port:R-DBI \
                     port:R-jsonlite \

R/R-arima2/Portfile

@@ -4,16 +4,17 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # GitHub version is archaic.
-R.setup             cran jeswheel arima2 3.1.0
-revision            1
+R.setup             cran jeswheel arima2 3.3.0
+revision            0
 categories-append   math
 maintainers         nomaintainer
 license             GPL-3+
 description         Likelihood-based inference for ARIMA modelling
 long_description    {*}${description}
-checksums           rmd160  087dde55776160481a946dc1a756df63e4243037 \
-                    sha256  e3a39e959d84e73bdf67a3c0e194add188cc12a9fbc62a97503aef9d0f3ccf69 \
-                    size    210494
+homepage            https://github.com/jeswheel/arima2
+checksums           rmd160  fcf1985beb34a6ba244adf0cc012727ad71a92ee \
+                    sha256  9a53c4f669f49398d3db312f459094d64353328ffa445d3463a041f4467db184 \
+                    size    122018
 
 depends_lib-append  port:R-ggplot2
 

R/R-bayesnec/Portfile

@@ -4,19 +4,19 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # GitHub version is old.
-R.setup             cran open-aims bayesnec 2.1.2.0
-revision            1
+R.setup             cran open-aims bayesnec 2.1.3.0
+revision            0
 categories-append   math
+platforms           {darwin any}
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-2
 description         Bayesian No-Effect-Concentration (NEC) algorithm
 long_description    {*}${description}
 homepage            https://open-aims.github.io/bayesnec
-checksums           rmd160  9dcfdc5273ec8204f28c6c52ffdbac4dda9b2ad5 \
-                    sha256  7528c25bd6ff243aac67c7d70535e3b337a8853af9d887ec78ac68ec06f544c9 \
-                    size    4467652
+checksums           rmd160  8b3529d95afb2ccbb35384b55d46c6fedaafdf5c \
+                    sha256  8158a94d4ffaf92b6e256b88a35461b71a95f79c4212274717df3cfc87464c5d \
+                    size    4452005
 supported_archs     noarch
-platforms           {darwin any}
 
 depends_lib-append  port:R-brms \
                     port:R-chk \

R/R-bnlearn/Portfile

@@ -3,7 +3,7 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran scutari bnlearn 5.0
+R.setup             cran scutari bnlearn 5.0.1
 revision            0
 categories-append   math
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
@@ -12,9 +12,9 @@ description         Bayesian network structure learning, parameter learning \
                     and inference
 long_description    {*}${description}
 homepage            https://www.bnlearn.com
-checksums           rmd160  653925c70d75c5ec90b6544855aeb913ef99e417 \
-                    sha256  e786203121980972c33e1e63736cbc218f9aea8f9b37853a6cd3af762c0279a1 \
-                    size    1325740
+checksums           rmd160  4a270f826b1f34884fa5c29c66625efe0751d32a \
+                    sha256  2452bd9523dbb4d6a44553cd67096523ba4d18800deef7b376e694d7c60af99e \
+                    size    1325437
 
 compilers.setup     require_fortran
 

R/R-clustermq/Portfile

@@ -3,20 +3,22 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             github mschubert clustermq 0.9.4 v
-revision            1
+R.setup             github mschubert clustermq 0.9.5 v
+revision            0
 categories-append   devel
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             Apache-2
 description         Evaluate function calls on HPC schedulers
 long_description    {*}${description}
 homepage            https://mschubert.github.io/clustermq
-checksums           rmd160  4cbb850bbcffbf708e906178912c22eba4d77c27 \
-                    sha256  cf4b5076c7fe9e279312018bfd05ecf4a3ff1be62e137a37ed93f1cb0501b129 \
-                    size    62294
+checksums           rmd160  c9e26c4f6bc6c4ed8d7f57c893f3bf8968a6e1c2 \
+                    sha256  47dc9dbe9fcb98fc889ac4a5dc8e47ef8fb918eca393fa81eadc949bbfae3897 \
+                    size    62952
+github.tarball_from archive
 
 depends_build-append \
-                    port:pkgconfig
+                    path:bin/pkg-config:pkgconfig
+
 # Both zmq variants are needed, one for libzmq, another for zmq.hpp.
 depends_lib-append  port:cppzmq \
                     path:lib/libzmq.dylib:zmq \

R/R-ctsem/Portfile

@@ -4,17 +4,17 @@ PortSystem          1.0
 PortGroup           R 1.0
 
 # GitHub version is old.
-R.setup             cran cdriveraus ctsem 3.10.0
-revision            1
+R.setup             cran cdriveraus ctsem 3.10.1
+revision            0
 categories-append   math
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-3
 description         Continuous Time Structural Equation Modelling
 long_description    {*}${description}
 homepage            https://github.com/cdriveraus/ctsem
-checksums           rmd160  089b4ecde56f35ac5f1928cf21af0416d8c829e6 \
-                    sha256  59fa5316b5b4850c3949a6cf3ba8380938c0355970535c196f31ca013c193782 \
-                    size    1759080
+checksums           rmd160  600eebcb48605f90d6a59fdb1a2d6106268151dd \
+                    sha256  8b373920c18a6e93a78083a4417ca6e8e1a5a8d9eed9989a5d1f2d8c9d8e1910 \
+                    size    1746848
 
 depends_lib-append  port:R-BH \
                     port:R-cOde \

R/R-cv/Portfile

@@ -3,19 +3,19 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran gmonette cv 2.0.0
+R.setup             cran gmonette cv 2.0.2
 revision            0
 categories-append   math
+platforms           {darwin any}
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-2+
 description         Cross-Validation of regression models
 long_description    {*}${description}
 homepage            https://gmonette.github.io/cv
-checksums           rmd160  e642d30c1b55386a2a207112af78a6874ef109e6 \
-                    sha256  686f9e86953b7e06a712a8ee187057faf66f9b038f7a89a7c0c664e416881bca \
-                    size    4172803
+checksums           rmd160  8c7b431294569dd46834c20e6dbf6c0468ef91a6 \
+                    sha256  518926ffd15f72158eea9a6f5b52b71d389f859cd326eb805df5c72ed876e959 \
+                    size    2136477
 supported_archs     noarch
-platforms           {darwin any}
 
 depends_lib-append  port:R-car \
                     port:R-doParallel \

R/R-deepgp/Portfile

@@ -3,16 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran annie_booth deepgp 1.1.2
+R.setup             cran annie_booth deepgp 1.1.3
 revision            0
 categories-append   math
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             LGPL
 description         Bayesian Deep Gaussian Processes using MCMC
-long_description    Performs Bayesian posterior inference for deep Gaussian processes.
-checksums           rmd160  5e51705b96e2f17ce9b0866ef41128ea094a3f90 \
-                    sha256  8b445a0985fd21ae0040801f61ae7bd94cb13c2cba1e077c3020ee958060d92a \
-                    size    676496
+long_description    Performs Bayesian posterior inference \
+                    for deep Gaussian processes.
+checksums           rmd160  62e67e48f42a9dc3abcf3a8c70b93a3e708d86fc \
+                    sha256  d9b7bbf3d587c22cec2938f238734a87ac5598397255a75b09b214fb80d3b8ed \
+                    size    908202
 
 depends_lib-append  port:R-doParallel \
                     port:R-FNN \

R/R-digest/Portfile

@@ -3,17 +3,17 @@
 PortSystem          1.0
 PortGroup           R 1.0
 
-R.setup             cran eddelbuettel digest 0.6.36
+R.setup             cran eddelbuettel digest 0.6.37
 revision            0
 categories-append   devel
 maintainers         {@barracuda156 gmail.com:vital.had} openmaintainer
 license             GPL-2+
 description         Create compact hash digests of R objects
 long_description    {*}${description}
 homepage            http://dirk.eddelbuettel.com/code/digest.html
-checksums           rmd160  dbdca36b4fc996087a0880596f6f6803d465619b \
-                    sha256  d1777364b2358b3ff9d79428fa7c1b280042f88896302765b0d0e2d4dc7ae637 \
-                    size    231298
+checksums           rmd160  7b1dbd207f0651f7de115b4dbd70d5443d34e76d \
+                    sha256  82c4d149994b8a4a9af930f5a8e47420829935abed41f3f9030e94b6a48f0321 \
+                    size    232306
 
 depends_test-append port:R-simplermarkdown \
                     port:R-tinytest