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-rw-r--r--gnu/packages/cran.scm624
1 files changed, 458 insertions, 166 deletions
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1db2e1c27a..1fe90619cd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -68,6 +68,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages fontutils)
+ #:use-module (gnu packages fribidi)
#:use-module (gnu packages gcc)
#:use-module (gnu packages geo)
#:use-module (gnu packages ghostscript)
@@ -107,14 +108,14 @@
(define-public r-brio
(package
(name "r-brio")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "brio" version))
(sha256
(base32
- "0f7amcd2cjm09aiq39209cz680l5d2gqpp6wwfhz24zagfsa7cvb"))))
+ "0ai2pqw5zk11r0rl2xshsq095ix1sdp2vjlixz2qxvy27x145ykh"))))
(properties `((upstream-name . "brio")))
(build-system r-build-system)
(home-page "https://github.com/r-lib/brio")
@@ -125,6 +126,30 @@ functions always read and write UTF-8 (8-bit Unicode Transformation Format)
files and provide more explicit control over line endings.")
(license license:expat)))
+(define-public r-cachem
+ (package
+ (name "r-cachem")
+ (version "1.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "cachem" version))
+ (sha256
+ (base32
+ "0y3jb96lyn3vc3nq8gs9x669w3xp69vdg5xc69qy0l356r39gp3r"))))
+ (properties `((upstream-name . "cachem")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-fastmap" ,r-fastmap)
+ ("r-rlang" ,r-rlang)))
+ (home-page "https://cachem.r-lib.org/")
+ (synopsis "Cache R objects with automatic pruning")
+ (description
+ "This package provides key-value stores with automatic pruning. Caches
+can limit either their total size or the age of the oldest object (or both),
+automatically pruning objects to maintain the constraints.")
+ (license license:expat)))
+
(define-public r-diffobj
(package
(name "r-diffobj")
@@ -365,17 +390,17 @@ variables.")
(define-public r-ggpmisc
(package
(name "r-ggpmisc")
- (version "0.3.7")
+ (version "0.3.8-1")
(source (origin
(method url-fetch)
(uri (cran-uri "ggpmisc" version))
(sha256
(base32
- "121s6c9k4fn3rcz2myc1kxczllq2826c8zllaii58q8lica7dsyn"))))
+ "0kcrh73nwha52vl6z35wafmqs5lsdh2p4nqvi2ir70cv1k5y46zf"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-broom" ,r-broom)
- ("r-dplyr" ,r-dplyr)
+ `(("r-dplyr" ,r-dplyr)
+ ("r-generics" ,r-generics)
("r-glue" ,r-glue)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
@@ -896,23 +921,27 @@ package is a port of the Python package @code{cssselect}.")
(define-public r-reprex
(package
(name "r-reprex")
- (version "0.3.0")
+ (version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "reprex" version))
(sha256
(base32
- "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
+ "07nzx0fdl48jw95ipx17ql0l13q60yl3rjrkj1m375wrc7h1v5nx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
+ ("r-cli" ,r-cli)
("r-clipr" ,r-clipr)
("r-fs" ,r-fs)
+ ("r-glue" ,r-glue)
+ ("r-knitr" ,r-knitr)
("r-rlang" ,r-rlang)
("r-rmarkdown" ,r-rmarkdown)
- ("r-whisker" ,r-whisker)
("r-withr" ,r-withr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/tidyverse/reprex")
(synopsis "Prepare reproducible R code examples for sharing")
(description
@@ -1130,13 +1159,13 @@ directory.")
(define-public r-htmltools
(package
(name "r-htmltools")
- (version "0.5.1")
+ (version "0.5.1.1")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
- "01v33zcs9rv16r6v8ckqh92k5axj6skmk9hyakmqqmgra522xj3a"))))
+ "1fm4cymz4hz6lds80m9j5q00xy5flkrmfn5dkrn3s3rkzqpyggzh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -1294,14 +1323,14 @@ and vice-versa.")
(define-public r-fastmap
(package
(name "r-fastmap")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastmap" version))
(sha256
(base32
- "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
+ "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
(properties `((upstream-name . "fastmap")))
(build-system r-build-system)
(home-page "https://r-lib.github.io/fastmap/")
@@ -1581,14 +1610,14 @@ well as file saving is available.")
(define-public r-shinythemes
(package
(name "r-shinythemes")
- (version "1.1.2")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "shinythemes" version))
(sha256
(base32
- "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
+ "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
(properties `((upstream-name . "shinythemes")))
(build-system r-build-system)
(propagated-inputs `(("r-shiny" ,r-shiny)))
@@ -2268,13 +2297,13 @@ initiative to bring PASSTEC 2000 functionalities to R.")
(define-public r-partykit
(package
(name "r-partykit")
- (version "1.2-11")
+ (version "1.2-12")
(source (origin
(method url-fetch)
(uri (cran-uri "partykit" version))
(sha256
(base32
- "00n6a74x257m2jk7jadjfxaclihxqpqwh356bgxmq8rag0nk70rs"))))
+ "15d5g89winndv8cy8jjjxy87fliafp5zyb8b58czrijwcmagg50l"))))
(build-system r-build-system)
(propagated-inputs
`(("r-formula" ,r-formula)
@@ -3203,13 +3232,13 @@ and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
(define-public r-inum
(package
(name "r-inum")
- (version "1.0-1")
+ (version "1.0-3")
(source (origin
(method url-fetch)
(uri (cran-uri "inum" version))
(sha256
(base32
- "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
+ "1sz11b4vlpskhmq9vvc1jix63a5g7lij6368w8qbnkjmjd97k7i4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)))
@@ -3946,14 +3975,14 @@ by base R methods related to model fitting.")
(define-public r-broom
(package
(name "r-broom")
- (version "0.7.3")
+ (version "0.7.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "broom" version))
(sha256
(base32
- "0bxwmqj37m06ci378xqlf7kar7pg5g903i1vnrv4i256dkj50mny"))))
+ "1zwdgv59a5c4mdcfn3anvsf83ymi11ij6k9nssw3aqzirp6fwg3w"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@@ -4251,19 +4280,21 @@ clustered data.")
(define-public r-mitml
(package
(name "r-mitml")
- (version "0.3-7")
+ (version "0.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "mitml" version))
(sha256
(base32
- "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
+ "1bw92fl6xp3yvawh3nbjzs4hp4alpwj6vnv6lsysd74aqndw447c"))))
(build-system r-build-system)
(propagated-inputs
`(("r-haven" ,r-haven)
("r-jomo" ,r-jomo)
("r-pan" ,r-pan)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/mitml/")
(synopsis "Tools for multiple imputation in multilevel modeling")
(description
@@ -4276,14 +4307,14 @@ analysis of multiply imputed data sets.")
(define-public r-mice
(package
(name "r-mice")
- (version "3.12.0")
+ (version "3.13.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "mice" version))
(sha256
(base32
- "0i7i9r0ipn7fypzp5xv1dnr54l30b7kg38mmq1kcvj2z1mjrwpap"))))
+ "11cpyqlilakan2pwjzacb9jjlazazsqdngy237nnrj8j6mky822i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-broom" ,r-broom)
@@ -4717,19 +4748,17 @@ plots in @code{ggplot2}.")
(define-public r-cli
(package
(name "r-cli")
- (version "2.2.0")
+ (version "2.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "cli" version))
(sha256
(base32
- "1f20mk9pb9kqn0ni2z0sqsx8qj1apcbiw08pa4gwry142zv7m9rr"))))
+ "128bx3bds0dnkixc4frbky11rz1ilnvdfzz9mggajj690i11b62q"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
- ("r-crayon" ,r-crayon)
- ("r-fansi" ,r-fansi)
("r-glue" ,r-glue)))
(home-page "https://github.com/r-lib/cli#readme")
(synopsis "Helpers for developing command line interfaces")
@@ -4929,13 +4958,13 @@ iVAT).")
(define-public r-xfun
(package
(name "r-xfun")
- (version "0.20")
+ (version "0.21")
(source
(origin
(method url-fetch)
(uri (cran-uri "xfun" version))
(sha256
- (base32 "043wv9qihs3r29810mf8ajpn2iks1bxq44wbxz8sfpix5b8kjhi8"))))
+ (base32 "18qjs81fn8q2d2drcan8gpgvrbgxgd0b659c92z19kg2h4c1g3k4"))))
(build-system r-build-system)
;; knitr itself depends on xfun
#;
@@ -5079,14 +5108,14 @@ terminals.")
(define-public r-tinytex
(package
(name "r-tinytex")
- (version "0.28")
+ (version "0.29")
(source
(origin
(method url-fetch)
(uri (cran-uri "tinytex" version))
(sha256
(base32
- "11pa1q7gl17ala74lz10qbghk2yqanl9pylwvi9b4kmhx856b83n"))))
+ "0my1412vn5zri01w2myzn268lfwinbhfgdj4bbcib3s48i9djw0n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-xfun" ,r-xfun)))
@@ -5160,27 +5189,29 @@ supports arbitrary vertex/edge/graph attributes.")
(define-public r-stabs
(package
- (name "r-stabs")
- (version "0.6-3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "stabs" version))
- (sha256
+ (name "r-stabs")
+ (version "0.6-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "stabs" version))
+ (sha256
(base32
- "17sa0sjxf6h7gx1ga1pxhv17yrz3qisaivbf5cbc3asvshhswqg9"))))
- (build-system r-build-system)
- (home-page "https://github.com/hofnerb/stabs")
- (synopsis "Stability selection with error control")
- (description
- "This package provides resampling procedures to assess the stability of
+ "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/hofnerb/stabs")
+ (synopsis "Stability selection with error control")
+ (description
+ "This package provides resampling procedures to assess the stability of
selected variables with additional finite sample error control for
high-dimensional variable selection procedures such as Lasso or boosting.
Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
complementary pairs stability selection with improved error bounds
(Shah & Samworth, 2013) are implemented. The package can be combined with
arbitrary user specified variable selection approaches.")
- (license license:gpl2)))
+ (license license:gpl2)))
(define-public r-rle
(package
@@ -5350,17 +5381,16 @@ exhaustive search.")
(define-public r-splus2r
(package
(name "r-splus2r")
- (version "1.2-2")
+ (version "1.3-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "splus2R" version))
(sha256
(base32
- "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
+ "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
(properties `((upstream-name . "splus2R")))
(build-system r-build-system)
- (native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/splus2R/")
(synopsis "Supplemental S-PLUS functionality in R")
(description
@@ -5804,14 +5834,14 @@ functions to enforce symmetric scales or add tags to facetted plots.")
(define-public r-heatmaply
(package
(name "r-heatmaply")
- (version "1.1.1")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "heatmaply" version))
(sha256
(base32
- "02fv66h61y55bn5wrnlvhj7v6xwqs3pddyp3jgk554s1zv4qs2fr"))))
+ "0hspfkninwy62sf8gkdcsvwnvl66bbnjs2dpah9rr95a3rsgdp9d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -6296,15 +6326,19 @@ are included.")
(define-public r-riverplot
(package
(name "r-riverplot")
- (version "0.6")
+ (version "0.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "riverplot" version))
(sha256
(base32
- "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
+ "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
(build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://logfc.wordpress.com")
(synopsis "Sankey or ribbon plots")
(description
@@ -6871,14 +6905,14 @@ the source data frame.")
(define-public r-rappdirs
(package
(name "r-rappdirs")
- (version "0.3.1")
+ (version "0.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "rappdirs" version))
(sha256
(base32
- "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
+ "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/rappdirs/")
(synopsis "Determine where to save data, caches, and logs")
@@ -7966,14 +8000,14 @@ functions.")
(define-public r-flextable
(package
(name "r-flextable")
- (version "0.6.1")
+ (version "0.6.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "flextable" version))
(sha256
(base32
- "06nzyd2a9yaf9hmn740xrgxw0448z5dvlplcj3kizz9sm23aw9li"))))
+ "0as80m19lvajc0vzllq9d9p63zglsm2ph7vdfg3jgk90jp8j76dg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -8098,14 +8132,14 @@ support for default values, positional argument support, etc.")
(define-public r-findpython
(package
(name "r-findpython")
- (version "1.0.5")
+ (version "1.0.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "findpython" version))
(sha256
(base32
- "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
+ "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
(build-system r-build-system)
(home-page "https://github.com/trevorld/findpython")
(synopsis "Functions to find an acceptable Python binary")
@@ -8934,14 +8968,14 @@ genotypes as \"graphical genotypes\".")
(define-public r-furrr
(package
(name "r-furrr")
- (version "0.2.1")
+ (version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "furrr" version))
(sha256
(base32
- "16s6sgfgh1ayzhf3kvpy9vhsd5h6p57waj1xgbksgdmf4j1wkcq7"))))
+ "0kfd4hw1yn2mfxzjgiz4r6yi2vsp1j0wy5hdhzd6wha7vi9h7hg5"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ellipsis" ,r-ellipsis)
@@ -9186,13 +9220,13 @@ singular or ill-conditioned Jacobian.")
(define-public r-physicalactivity
(package
(name "r-physicalactivity")
- (version "0.2-2")
+ (version "0.2-4")
(source
(origin
(method url-fetch)
(uri (cran-uri "PhysicalActivity" version))
(sha256
- (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
+ (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
(properties
`((upstream-name . "PhysicalActivity")))
(build-system r-build-system)
@@ -9741,14 +9775,14 @@ packages maintained by Torsten Hothorn.")
(define-public r-multcomp
(package
(name "r-multcomp")
- (version "1.4-15")
+ (version "1.4-16")
(source
(origin
(method url-fetch)
(uri (cran-uri "multcomp" version))
(sha256
(base32
- "1klvn4a1rlrzwhy1cjrkbbh6jspgzbrdm0jxsb1lmf1yzdz609wr"))))
+ "1s8qmljawalisggniy7va5l5cicsgvs0lp20c33vxlvyiy0dbb1s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
@@ -9769,14 +9803,14 @@ Hothorn, Westfall, 2010, CRC Press).")
(define-public r-emmeans
(package
(name "r-emmeans")
- (version "1.5.3")
+ (version "1.5.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "emmeans" version))
(sha256
(base32
- "11x7bn260v91gb7qri1pq54l339zm4msa5frc8saqb9ykbg4dby5"))))
+ "1rbh3ls23fazrwpsam5llk3kqdzz2zvsms3i4f1cgn34ky3w8361"))))
(build-system r-build-system)
(propagated-inputs
`(("r-estimability" ,r-estimability)
@@ -9820,13 +9854,13 @@ Cohen (1988).")
(define-public r-libcoin
(package
(name "r-libcoin")
- (version "1.0-7")
+ (version "1.0-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "libcoin" version))
(sha256
- (base32 "1vb21pw3vpv2pdnfcddw2bax13v0dg656r28j0p8njcyhwk89xln"))))
+ (base32 "0izgnr4zdrbz3a05b0s28xfly4izp2zslgh282l9ads4skrmj3hl"))))
(build-system r-build-system)
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
(home-page "https://cran.r-project.org/web/packages/libcoin")
@@ -9839,14 +9873,14 @@ and permutation inference in the framework of Strasser and Weber (1999).")
(define-public r-coin
(package
(name "r-coin")
- (version "1.4-0")
+ (version "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "coin" version))
(sha256
(base32
- "1n2ad4m3zw8px6yc0h750k59pci3fqpnr742hhvsqirrwcdzp6zv"))))
+ "15xvhnbyg34aacn6jfz4bsa1f7wq2ci0hslj8mgymql90k50x1qi"))))
(build-system r-build-system)
(propagated-inputs
`(("r-libcoin" ,r-libcoin)
@@ -9902,14 +9936,14 @@ Bayesian modeling.")
(define-public r-tmb
(package
(name "r-tmb")
- (version "1.7.18")
+ (version "1.7.19")
(source
(origin
(method url-fetch)
(uri (cran-uri "TMB" version))
(sha256
(base32
- "0dbps92sni9rnynj31z9zhg6l0vbczxhzlw7gnhpxjlzfnsglp3y"))))
+ "0vnjh8d5gnjswil8ld3gbbspy4m5l2pzar1mpj62qxn2mwx0cc4s"))))
(properties `((upstream-name . "TMB")))
(build-system r-build-system)
(propagated-inputs
@@ -10005,14 +10039,14 @@ differentiation.")
(define-public r-bayestestr
(package
(name "r-bayestestr")
- (version "0.8.0")
+ (version "0.8.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "bayestestR" version))
(sha256
(base32
- "11mxnpqc85y13wf8mnnrh0k8d3jqdsr99hkv4cgvwav38qpvjhhw"))))
+ "06y7vccgln1882yv04may9p6s915py8nnhg82d5ppbpxzcifi7l4"))))
(properties `((upstream-name . "bayestestR")))
(build-system r-build-system)
(propagated-inputs
@@ -10032,14 +10066,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.6.1")
+ (version "0.7.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "0wz2zc98r99pg6r4l09qxxzv1fwxwp1md6wmhay401568kd8h5zn"))))
+ "1z45vy8gg77c2imcspwqf94anzi6c40wwbq0h7hg6zy76jsgvbyj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -10317,14 +10351,14 @@ user credentials.")
(define-public r-gert
(package
(name "r-gert")
- (version "1.0.2")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gert" version))
(sha256
(base32
- "1lq4hgv2727lwcv8vha5af26nslj99rjxjrgflshmmcihawpls1n"))))
+ "09har6mj7qy813s6dxyzfzmjwg60m8c01yx3q6lfsnvwqzxlqxv8"))))
(properties `((upstream-name . "gert")))
(build-system r-build-system)
(inputs
@@ -10335,6 +10369,7 @@ user credentials.")
("r-credentials" ,r-credentials)
("r-openssl" ,r-openssl)
("r-rstudioapi" ,r-rstudioapi)
+ ("r-sys" ,r-sys)
("r-zip" ,r-zip)))
(native-inputs
`(("pkg-config" ,pkg-config)
@@ -10352,14 +10387,14 @@ User credentials are shared with command line git through the
(define-public r-usethis
(package
(name "r-usethis")
- (version "2.0.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "usethis" version))
(sha256
(base32
- "0m4qnnkdiizsdvq33x502zwkn98hw2qcfm45cjj031vaydcjpai2"))))
+ "1j6nzzrm2m6vi1gq0d5kxnnr9d8cy88wpmgigz3inych65x9w9pg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -10645,14 +10680,14 @@ algorithms, clusterings, and individual clusters.")
(define-public r-tweedie
(package
(name "r-tweedie")
- (version "2.3.2")
+ (version "2.3.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "tweedie" version))
(sha256
(base32
- "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
+ "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
(home-page "https://cran.r-project.org/web/packages/tweedie/")
@@ -11036,13 +11071,13 @@ isosurfaces.")
(define-public r-ks
(package
(name "r-ks")
- (version "1.11.7")
+ (version "1.12.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ks" version))
(sha256
- (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
+ (base32 "1sff6rlpq64lqyvwgral9zbcan30wpgmfb26hw9y6wzypd9gxbz6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fnn" ,r-fnn)
@@ -11052,7 +11087,8 @@ isosurfaces.")
("r-mclust" ,r-mclust)
("r-mgcv" ,r-mgcv)
("r-multicool" ,r-multicool)
- ("r-mvtnorm" ,r-mvtnorm)))
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-plot3d" ,r-plot3d)))
(home-page "http://www.mvstat.net/tduong/")
(synopsis "Kernel smoothing")
(description
@@ -11066,17 +11102,18 @@ hypothesis testing.")
(define-public r-feature
(package
(name "r-feature")
- (version "1.2.14")
+ (version "1.2.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "feature" version))
(sha256
(base32
- "1c12rny9nx8dynzxbcf49h76a7wlmsk1m131wh0jiyqx3c3y41y1"))))
+ "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-ks" ,r-ks)))
+ `(("r-ks" ,r-ks)
+ ("r-plot3d" ,r-plot3d)))
(native-inputs
`(("r-knitr" ,r-knitr)))
(home-page "http://www.mvstat.net/tduong/")
@@ -12208,14 +12245,14 @@ Emphasis is always given to methods for visualizing the data.")
(define-public r-pixmap
(package
(name "r-pixmap")
- (version "0.4-11")
+ (version "0.4-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "pixmap" version))
(sha256
(base32
- "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
+ "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pixmap")
(synopsis "Tools for bitmap images")
@@ -12246,16 +12283,18 @@ library.")
(define-public r-ontologyindex
(package
(name "r-ontologyindex")
- (version "2.5")
+ (version "2.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "ontologyIndex" version))
(sha256
(base32
- "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
+ "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
(properties `((upstream-name . "ontologyIndex")))
(build-system r-build-system)
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/ontologyIndex")
(synopsis "Functions for processing ontologies in R")
(description
@@ -12384,14 +12423,14 @@ Precision Floating-Point Reliable} (MPFR) library.")
(define-public r-assertive-base
(package
(name "r-assertive-base")
- (version "0.0-7")
+ (version "0.0-9")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertive.base" version))
(sha256
(base32
- "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
+ "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
(properties
`((upstream-name . "assertive.base")))
(build-system r-build-system)
@@ -13146,14 +13185,14 @@ model with finite state space using the Aalen-Johansen estimator.")
(define-public r-epi
(package
(name "r-epi")
- (version "2.42")
+ (version "2.43")
(source
(origin
(method url-fetch)
(uri (cran-uri "Epi" version))
(sha256
(base32
- "1vsyxlxl6n5y3wr8w7ji17hnhvbr0xsawqbdl1ajcfg5faizm9sl"))))
+ "0wsjvilcivrhy2kh2dcagkzy7bjmfa0sq9xjpv6qb4b0nc0mv089"))))
(properties `((upstream-name . "Epi")))
(build-system r-build-system)
(propagated-inputs
@@ -13166,6 +13205,7 @@ model with finite state space using the Aalen-Johansen estimator.")
("r-mgcv" ,r-mgcv)
("r-numderiv" ,r-numderiv)
("r-plyr" ,r-plyr)
+ ("r-purrr" ,r-purrr)
("r-survival" ,r-survival)
("r-zoo" ,r-zoo)))
(home-page "https://BendixCarstensen.com/Epi/")
@@ -14228,14 +14268,14 @@ graphs.")
(define-public r-pbdzmq
(package
(name "r-pbdzmq")
- (version "0.3-4")
+ (version "0.3-5")
(source
(origin
(method url-fetch)
(uri (cran-uri "pbdZMQ" version))
(sha256
(base32
- "0adiac53yq305ymhrds1gas4jm0rn1ddv7c7df5ky2cfhpb4ny87"))))
+ "1v8iv1pzs4j3ics9k9h4xjkv6z1ma2xbqy003xk2lqax6srqi02d"))))
(properties `((upstream-name . "pbdZMQ")))
(build-system r-build-system)
(inputs
@@ -14256,14 +14296,14 @@ compatible with @code{rzmq} are also provided.")
(define-public r-repr
(package
(name "r-repr")
- (version "1.1.0")
+ (version "1.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "repr" version))
(sha256
(base32
- "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
+ "0qimllv9pn8wsl550bjkp5dkknbmr69j85mrwfbbq75m2ga466sk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-base64enc" ,r-base64enc)
@@ -14280,14 +14320,14 @@ several formats and MIME types.")
(define-public r-irdisplay
(package
(name "r-irdisplay")
- (version "0.7.0")
+ (version "1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "IRdisplay" version))
(sha256
(base32
- "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
+ "15jbjrihm1mk899357h9xb08iq3xyagds1xb40fmdpkfcmcfqrw9"))))
(properties `((upstream-name . "IRdisplay")))
(build-system r-build-system)
(propagated-inputs
@@ -14804,6 +14844,27 @@ is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
classes.")
(license license:gpl2)))
+(define-public r-udunits2
+ (package
+ (name "r-udunits2")
+ (version "0.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "udunits2" version))
+ (sha256
+ (base32
+ "0yav7rm2afcx67xqrknybxgz7x63w78zyxa0xifvc0k2gz0d6mfi"))))
+ (properties `((upstream-name . "udunits2")))
+ (build-system r-build-system)
+ (inputs
+ `(("udunits" ,udunits)))
+ (home-page "https://cran.r-project.org/package=udunits2")
+ (synopsis "Udunits-2 bindings for R")
+ (description
+ "This package provides simple bindings to Unidata's udunits library.")
+ (license license:gpl2)))
+
(define-public r-classint
(package
(name "r-classint")
@@ -15151,13 +15212,13 @@ lspec, polyclass, and polymars.")
(define-public r-rms
(package
(name "r-rms")
- (version "6.1-0")
+ (version "6.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rms" version))
(sha256
- (base32 "0llz519rgnc7v2jqhfrjgixkpkmmi5wi1a52hgz3n28s46ww77mq"))))
+ (base32 "1zgfd60lzbakcv7x0i5k3lkw3s0xx5bzssjgangna5lq2j17cdli"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
@@ -15197,14 +15258,14 @@ generalized linear models, and quantile regression.")
(define-public r-arsenal
(package
(name "r-arsenal")
- (version "3.5.0")
+ (version "3.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "arsenal" version))
(sha256
(base32
- "0avi434wkk3w7axd89a4jwsbb11fi0239mkkla6zasnjwbqgjim0"))))
+ "13ql3rb79a764ppsc1sqi8glzzkw79la0j2ahzbxgz7cz879sazy"))))
(properties `((upstream-name . "arsenal")))
(build-system r-build-system)
(propagated-inputs `(("r-knitr" ,r-knitr)))
@@ -16280,14 +16341,14 @@ using the three.js visualization library.")
(define-public r-mlbench
(package
(name "r-mlbench")
- (version "2.1-1")
+ (version "2.1-3")
(source
(origin
(method url-fetch)
(uri (cran-uri "mlbench" version))
(sha256
(base32
- "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
+ "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/mlbench/")
(synopsis "Machine learning benchmark problems")
@@ -16933,14 +16994,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
(define-public r-ingredients
(package
(name "r-ingredients")
- (version "2.0")
+ (version "2.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ingredients" version))
(sha256
(base32
- "084ywbq0dwnf075bazz40n23wh7r1fwl6zs7xqkcg07kfzqkzb2w"))))
+ "0w46h1f28y5ypqm3ypsvk7yk9v7k8p21f1pzjl3ima8r1ivmhv12"))))
(properties `((upstream-name . "ingredients")))
(build-system r-build-system)
(propagated-inputs
@@ -17067,19 +17128,22 @@ and model output.")
(define-public r-enrichr
(package
(name "r-enrichr")
- (version "2.1")
+ (version "3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "enrichR" version))
(sha256
(base32
- "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
+ "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
(properties `((upstream-name . "enrichR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-httr" ,r-httr)
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-httr" ,r-httr)
("r-rjson" ,r-rjson)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/enrichR/")
(synopsis "R Interface to Enrichr database for analyzing gene sets")
(description
@@ -17427,14 +17491,14 @@ computed using the L1 (Manhattan, taxicab) metric.")
(define-public r-leiden
(package
(name "r-leiden")
- (version "0.3.6")
+ (version "0.3.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "leiden" version))
(sha256
(base32
- "1k1250bjgf2cb1whp2sl1r6b88156qwi2zkamw5iy2q1qhw6w2d7"))))
+ "14iqn5iqcya6bqbjvjivpd7q9gwc323sj29y7ssrbhb3sz9982bp"))))
(properties `((upstream-name . "leiden")))
(build-system r-build-system)
(propagated-inputs
@@ -17632,14 +17696,14 @@ both R code and compiled C/C++/FORTRAN code.")
(define-public r-systemfonts
(package
(name "r-systemfonts")
- (version "0.3.2")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "systemfonts" version))
(sha256
(base32
- "12hdvv66kkd3b4rs82blc3c4ifz2dw1048sqpkbz6vkk1zqpc53x"))))
+ "15x7qx8iigkybgz6b6s66i3mh75vgynzpd50nw05wflfwzcv87a0"))))
(properties `((upstream-name . "systemfonts")))
(build-system r-build-system)
(propagated-inputs
@@ -17753,14 +17817,14 @@ cell RNA-seq experiments.")
(define-public r-assertr
(package
(name "r-assertr")
- (version "2.7")
+ (version "2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertr" version))
(sha256
(base32
- "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
+ "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)
@@ -17809,13 +17873,13 @@ effect size.")
(define-public r-rgdal
(package
(name "r-rgdal")
- (version "1.5-19")
+ (version "1.5-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "rgdal" version))
(sha256
- (base32 "1cii2azm3zv5l6fn33xzwahp8349z3pb2769vpdxkf7734dxggvg"))))
+ (base32 "0vnb7kw762y349pda4aq1hx0smafylmn3635l963qykfji5p99cw"))))
(properties `((upstream-name . "rgdal")))
(build-system r-build-system)
(inputs
@@ -17838,14 +17902,14 @@ PROJ.4 library.")
(define-public r-insol
(package
(name "r-insol")
- (version "1.2.1")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "insol" version))
(sha256
(base32
- "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
+ "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
(properties `((upstream-name . "insol")))
(build-system r-build-system)
(propagated-inputs
@@ -17895,17 +17959,19 @@ signalled with increasing levels of non-invasive verbosity.")
(define-public r-assertable
(package
(name "r-assertable")
- (version "0.2.7")
+ (version "0.2.8")
(source
(origin
(method url-fetch)
(uri (cran-uri "assertable" version))
(sha256
(base32
- "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
+ "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
(build-system r-build-system)
(propagated-inputs
`(("r-data-table" ,r-data-table)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/assertable/")
(synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
(description "This package provides simple, flexible assertions on
@@ -17971,12 +18037,12 @@ to ODEs by numerical differencing.")
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.2.9")
+ (version "2.3.3")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
+ (base32 "0g5r5ir5k43ba0ngnsanp108k479l2dnsjd5w6idk1d34ivqs7yg"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/pracma/")
(synopsis "Practical numerical math functions")
@@ -20309,14 +20375,14 @@ API; see the package vignette for details.")
(define-public r-actuar
(package
(name "r-actuar")
- (version "3.1-0")
+ (version "3.1-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "actuar" version))
(sha256
(base32
- "15a8axb2ym46j8vlm7icwnsc950p8m66hp0armha7drk0725y77k"))))
+ "0sxn1mskh7x164f1vbrqnadgxnq7y2p3a9mlmqc0sp6cqkw9lhp9"))))
(properties `((upstream-name . "actuar")))
(build-system r-build-system)
(propagated-inputs `(("r-expint" ,r-expint)))
@@ -21202,14 +21268,14 @@ both exclusive and shared locking.")
(define-public r-archivist
(package
(name "r-archivist")
- (version "2.3.4")
+ (version "2.3.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "archivist" version))
(sha256
(base32
- "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
+ "0sk16bcafgswrvwh39ysbgm6jvsg20yil4pdsg3wsp81nnsrb43k"))))
(properties `((upstream-name . "archivist")))
(build-system r-build-system)
(propagated-inputs
@@ -21221,6 +21287,8 @@ both exclusive and shared locking.")
("r-magrittr" ,r-magrittr)
("r-rcurl" ,r-rcurl)
("r-rsqlite" ,r-rsqlite)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://pbiecek.github.io/archivist/")
(synopsis "Tools for storing, restoring and searching for R objects")
(description
@@ -21480,20 +21548,18 @@ character codes as well as the UN M.49 area codes.")
(define-public r-stopwords
(package
(name "r-stopwords")
- (version "2.1")
+ (version "2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "stopwords" version))
(sha256
(base32
- "1g2p8gsj7xjck7idcwczgc7fmv72lzwjw00qarrj0cv44kypmiq8"))))
+ "1f862y30c4r0phamlp7shzkpxg0vh3i410xy0336w310hv3wqsxn"))))
(properties `((upstream-name . "stopwords")))
(build-system r-build-system)
(propagated-inputs
- `(("r-desc" ,r-desc)
- ("r-isocodes" ,r-isocodes)
- ("r-usethis" ,r-usethis)))
+ `(("r-isocodes" ,r-isocodes)))
(home-page "https://github.com/quanteda/stopwords")
(synopsis "Multilingual stopword lists")
(description
@@ -21598,17 +21664,17 @@ machine learning, visually representing text and text analyses, and more.")
(define-public r-topicmodels
(package
(name "r-topicmodels")
- (version "0.2-11")
+ (version "0.2-12")
(source
(origin
(method url-fetch)
(uri (cran-uri "topicmodels" version))
(sha256
(base32
- "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
+ "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
(properties `((upstream-name . "topicmodels")))
(build-system r-build-system)
- (native-inputs
+ (inputs
`(("gsl" ,gsl)))
(propagated-inputs
`(("r-modeltools" ,r-modeltools)
@@ -22097,30 +22163,26 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
(define-public r-qgraph
(package
(name "r-qgraph")
- (version "1.6.5")
+ (version "1.6.9")
(source
(origin
(method url-fetch)
(uri (cran-uri "qgraph" version))
(sha256
(base32
- "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
+ "153bqfmsrghkg7598nfr57r3cxv6dn6ir084njl2sqq5np0sj9di"))))
(properties `((upstream-name . "qgraph")))
(build-system r-build-system)
(propagated-inputs
`(("r-abind" ,r-abind)
- ("r-bdgraph" ,r-bdgraph)
("r-colorspace" ,r-colorspace)
("r-corpcor" ,r-corpcor)
- ("r-d3network" ,r-d3network)
("r-dplyr" ,r-dplyr)
("r-fdrtool" ,r-fdrtool)
("r-ggplot2" ,r-ggplot2)
- ("r-ggraph" ,r-ggraph)
("r-glasso" ,r-glasso)
("r-gtools" ,r-gtools)
("r-hmisc" ,r-hmisc)
- ("r-huge" ,r-huge)
("r-igraph" ,r-igraph)
("r-jpeg" ,r-jpeg)
("r-lavaan" ,r-lavaan)
@@ -22130,8 +22192,7 @@ network, tree, dendrogram, and Sankey graphs from R using data frames.")
("r-png" ,r-png)
("r-psych" ,r-psych)
("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-tidygraph" ,r-tidygraph)))
+ ("r-reshape2" ,r-reshape2)))
(home-page "http://sachaepskamp.com/qgraph/")
(synopsis "Weighted network visualization and analysis")
(description
@@ -24274,14 +24335,14 @@ diagonals. This package allows you to compute the tensor product of arrays.")
(define-public r-spatstat-utils
(package
(name "r-spatstat-utils")
- (version "1.20-2")
+ (version "2.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.utils" version))
(sha256
(base32
- "066f35017wpbz9plwc14gji3ddq4a1h2lx4mcgxajrcrk0zl3hk2"))))
+ "1li0vksxpkvgyx3j2wi40kj5687vwakkfdix6icm6g01a0lb2m5d"))))
(properties
`((upstream-name . "spatstat.utils")))
(build-system r-build-system)
@@ -24295,14 +24356,14 @@ which may also be useful for other purposes.")
(define-public r-spatstat-data
(package
(name "r-spatstat-data")
- (version "1.7-0")
+ (version "2.0-0")
(source
(origin
(method url-fetch)
(uri (cran-uri "spatstat.data" version))
(sha256
(base32
- "0by10dx72jjn6rvgrdj4xwh4zg6vxi4cp536aq4b6drb7za95hdv"))))
+ "1z1jb1yzb7qhfg55dhzcrdvn5x8hpg9xif0hpnapddbmhxd1hbb7"))))
(properties `((upstream-name . "spatstat.data")))
(build-system r-build-system)
(propagated-inputs
@@ -24385,14 +24446,14 @@ for linear mixed models (AIREML).")
(define-public r-cpp11
(package
(name "r-cpp11")
- (version "0.2.5")
+ (version "0.2.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "cpp11" version))
(sha256
(base32
- "081f3b98mcxyilqsxbzzdnj2x6v7xycprrw7r5934163q0397vvg"))))
+ "118i8s7978vl9xyhnb47wcbd6rcc6b958mq2w8s3rdsd4pxv62gz"))))
(properties `((upstream-name . "cpp11")))
(build-system r-build-system)
(native-inputs `(("r-knitr" ,r-knitr)))
@@ -25811,16 +25872,45 @@ as allowing spectra with different resolutions.")
data to rasters. It speeds up plotting of data with millions of points.")
(license license:gpl3+)))
+(define-public r-seuratobject
+ (package
+ (name "r-seuratobject")
+ (version "4.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "SeuratObject" version))
+ (sha256
+ (base32
+ "03k27z7g76wy7mfja2cpxq183xk0906k9gxb2j6p1zw341gv4gii"))))
+ (properties `((upstream-name . "SeuratObject")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rlang" ,r-rlang)
+ ("r-sctransform" ,r-sctransform)))
+ (home-page "https://satijalab.org/seurat")
+ (synopsis "Data structures for single cell data")
+ (description
+ "This package defines S4 classes for single-cell genomic data and
+associated information, such as dimensionality reduction embeddings,
+nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
+access methods and R-native hooks to ensure the Seurat object is familiar to
+other R users.")
+ (license license:gpl3)))
+
(define-public r-seurat
(package
(name "r-seurat")
- (version "3.2.3")
+ (version "4.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "11rzc7h2ad8z8k5r1sbz4d7y4rl3080qp2hh7vibwmipbkvlial3"))))
+ "1mp3py00bmzj4541d8ry5sfzkpfzvnl9dpa8n4qhakd13dl30xdn"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@@ -25857,11 +25947,11 @@ data to rasters. It speeds up plotting of data with millions of points.")
("r-reticulate" ,r-reticulate)
("r-rlang" ,r-rlang)
("r-rocr" ,r-rocr)
- ("r-rsvd" ,r-rsvd)
("r-rtsne" ,r-rtsne)
("r-scales" ,r-scales)
("r-scattermore" ,r-scattermore)
("r-sctransform" ,r-sctransform)
+ ("r-seuratobject" ,r-seuratobject)
("r-shiny" ,r-shiny)
("r-spatstat" ,r-spatstat)
("r-tibble" ,r-tibble)
@@ -26208,13 +26298,13 @@ package also supersedes the package @code{BBmisc}.")
(define-public r-paradox
(package
(name "r-paradox")
- (version "0.6.0")
+ (version "0.7.0")
(source (origin
(method url-fetch)
(uri (cran-uri "paradox" version))
(sha256
(base32
- "1zv0q411wcwigkf4yggs3w2gz48lvv3jhnrddrv40qih8b70ywi3"))))
+ "1fz6sdwvvifm4qbmwgm27dil278mswvcfw8bbsvli5v4l1ghw8kj"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)
@@ -26233,13 +26323,13 @@ implemented as @code{R6} classes.")
(define-public r-mlr3
(package
(name "r-mlr3")
- (version "0.9.0")
+ (version "0.10.0")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3" version))
(sha256
(base32
- "0gg7rrzxwrnpg6sgm0aa6bmfwmqv3d3za0ghnqrnibg33p9ynpgb"))))
+ "1arqijbbmhv57mj8kyq30zxykah83ab1d1c7gs0cxs0xhfwln66g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-r6" ,r-r6)
@@ -26293,14 +26383,14 @@ vector machines, and gradient boosting.")
(define-public r-bbotk
(package
(name "r-bbotk")
- (version "0.2.2")
+ (version "0.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "bbotk" version))
(sha256
(base32
- "06iz6gyymcxkbjiw049v1dk3vjfni646z247q08i2s0x59sqfqxv"))))
+ "0kbjbwwq1fdfpl4xzy08hz4qvhjjchvz58icxq0dlbsmdyqwhwv0"))))
(properties `((upstream-name . "bbotk")))
(build-system r-build-system)
(propagated-inputs
@@ -26310,6 +26400,8 @@ vector machines, and gradient boosting.")
("r-mlr3misc" ,r-mlr3misc)
("r-paradox" ,r-paradox)
("r-r6" ,r-r6)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bbotk.mlr-org.com")
(synopsis "Black-Box Optimization Toolkit")
(description "This package provides a common framework for optimization of
@@ -26321,13 +26413,13 @@ annealing.")
(define-public r-mlr3tuning
(package
(name "r-mlr3tuning")
- (version "0.5.0")
+ (version "0.6.0")
(source (origin
(method url-fetch)
(uri (cran-uri "mlr3tuning" version))
(sha256
(base32
- "1pn80qjxzj2pivgs6qgairci6yh1bdnl2zbgl9ykdip2rqzv6r6m"))))
+ "0kxf9wl1jnwyrj2zfmiz12w2594407y44m0xxwp9b2lrwxk31wm7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bbotk" ,r-bbotk)
@@ -26559,3 +26651,203 @@ unit tests of graphics).")
to add graphical unit tests. It provides a Shiny application to manage the
test cases.")
(license license:gpl3)))
+
+(define-public r-highlight
+ (package
+ (name "r-highlight")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "highlight" version))
+ (sha256
+ (base32
+ "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
+ (properties `((upstream-name . "highlight")))
+ (build-system r-build-system)
+ (home-page "https://github.com/hadley/highlight")
+ (synopsis "Syntax highlighter for R code")
+ (description
+ "This package provides a syntax highlighter for R code based on the
+results of the R parser. It supports rendering in HTML and LaTeX markup. It
+includes a custom Sweave driver performing syntax highlighting of R code
+chunks.")
+ (license license:gpl3+)))
+
+(define-public r-clustree
+ (package
+ (name "r-clustree")
+ (version "0.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "clustree" version))
+ (sha256
+ (base32
+ "0lxydy2f83qqd5dhlp2l546jax759l43b29j6g82079yzg1szwsz"))))
+ (properties `((upstream-name . "clustree")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-checkmate" ,r-checkmate)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggraph" ,r-ggraph)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-igraph" ,r-igraph)
+ ("r-rlang" ,r-rlang)
+ ("r-tidygraph" ,r-tidygraph)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/lazappi/clustree")
+ (synopsis "Visualize clusterings at different resolutions")
+ (description
+ "Deciding what resolution to use can be a difficult question when
+approaching a clustering analysis. One way to approach this problem is to
+look at how samples move as the number of clusters increases. This package
+allows you to produce clustering trees, a visualization for interrogating
+clusterings as resolution increases.")
+ (license license:gpl3)))
+
+(define-public r-textshaping
+ (package
+ (name "r-textshaping")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "textshaping" version))
+ (sha256
+ (base32
+ "053pbw45by96q62kjfnyc3d0ssar9svssrdqy6a09kdmdh75xdar"))))
+ (properties `((upstream-name . "textshaping")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("fribidi" ,fribidi)
+ ("harfbuzz" ,harfbuzz)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-cpp11" ,r-cpp11)
+ ("r-systemfonts" ,r-systemfonts)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/r-lib/textshaping")
+ (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
+ (description
+ "This package provides access to the text shaping functionality in the
+HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
+is a low-level utility package mainly for graphic devices that expands upon
+the font tool-set provided by the @code{systemfonts} package.")
+ (license license:expat)))
+
+(define-public r-ragg
+ (package
+ (name "r-ragg")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ragg" version))
+ (sha256
+ (base32
+ "0443dhfi7bjfpap041vrnslw3ql3vpsxx18raz2w9nfdb7id8lsc"))))
+ (properties `((upstream-name . "ragg")))
+ (build-system r-build-system)
+ (inputs
+ `(("freetype" ,freetype)
+ ("libjpeg" ,libjpeg-turbo)
+ ("libpng" ,libpng)
+ ("libtiff" ,libtiff)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-systemfonts" ,r-systemfonts)
+ ("r-textshaping" ,r-textshaping)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://ragg.r-lib.org")
+ (synopsis "Graphic devices based on AGG")
+ (description
+ "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
+drawing library. The ragg package provides a set of graphic devices based on
+AGG to use as alternative to the raster devices provided through the
+@code{grDevices} package.")
+ (license license:expat)))
+
+(define-public r-downlit
+ (package
+ (name "r-downlit")
+ (version "0.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "downlit" version))
+ (sha256
+ (base32
+ "0z4fz7c9kyd9v72wl3iqs2wxspi975d6b0rgjr9lvg8a18maa9z6"))))
+ (properties `((upstream-name . "downlit")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-brio" ,r-brio)
+ ("r-digest" ,r-digest)
+ ("r-evaluate" ,r-evaluate)
+ ("r-fansi" ,r-fansi)
+ ("r-rlang" ,r-rlang)
+ ("r-vctrs" ,r-vctrs)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://downlit.r-lib.org/")
+ (synopsis "Syntax highlighting and automatic linking")
+ (description
+ "This package provides syntax highlighting of R code, specifically
+designed for the needs of RMarkdown packages like @code{pkgdown},
+@code{hugodown}, and @code{bookdown}. It includes linking of function calls
+to their documentation on the web, and automatic translation of ANSI escapes
+in output to the equivalent HTML.")
+ (license license:expat)))
+
+(define-public r-pkgdown
+ (package
+ (name "r-pkgdown")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pkgdown" version))
+ (sha256
+ (base32
+ "1k31biyvxkv3xjc1yy3nzb9wfza3vbx97fv17nly5a6vlv7zqbs4"))))
+ (properties `((upstream-name . "pkgdown")))
+ (build-system r-build-system)
+ (inputs `(("pandoc" ,pandoc)))
+ (propagated-inputs
+ `(("r-callr" ,r-callr)
+ ("r-crayon" ,r-crayon)
+ ("r-desc" ,r-desc)
+ ("r-digest" ,r-digest)
+ ("r-downlit" ,r-downlit)
+ ("r-fs" ,r-fs)
+ ("r-httr" ,r-httr)
+ ("r-magrittr" ,r-magrittr)
+ ("r-memoise" ,r-memoise)
+ ("r-openssl" ,r-openssl)
+ ("r-purrr" ,r-purrr)
+ ("r-ragg" ,r-ragg)
+ ("r-rematch2" ,r-rematch2)
+ ("r-rlang" ,r-rlang)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-tibble" ,r-tibble)
+ ("r-whisker" ,r-whisker)
+ ("r-withr" ,r-withr)
+ ("r-xml2" ,r-xml2)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://pkgdown.r-lib.org")
+ (synopsis "Make static HTML documentation for an R package")
+ (description
+ "The goal of this package is to generate an attractive and useful website
+from a source package. @code{pkgdown} converts your documentation, vignettes,
+README file, and more to HTML making it easy to share information about your
+package online.")
+ (license license:expat)))
generated by cgit v1.2.3 (git 2.50.1) at 2025-09-25 20:01:29 +0000