mirror of
https://codeberg.org/guix/guix.git
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Merge branch 'master' into core-updates-frozen
Conflicts: gnu/packages/bioinformatics.scm gnu/packages/cmake.scm gnu/packages/curl.scm gnu/packages/emacs-xyz.scm gnu/packages/gpodder.scm gnu/packages/music.scm gnu/packages/patches/glibc-bootstrap-system.patch gnu/packages/python-xyz.scm gnu/packages/shells.scm gnu/packages/statistics.scm
This commit is contained in:
Marius Bakke
commit
b029be2ee0
100 changed files with 5664 additions and 43929 deletions
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@ -214,11 +214,14 @@ This package also provides @command{xls2csv} to export Excel files to CSV.")
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(substitute* "src/library/base/makebasedb.R"
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(("compress = TRUE") "compress = FALSE"))
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#t))
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(add-before 'configure 'patch-uname
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(add-before 'configure 'patch-coreutils-paths
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((uname-bin (search-input-file inputs "/bin/uname")))
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(let ((uname-bin (search-input-file inputs "/bin/uname"))
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(rm-bin (search-input-file inputs "/bin/rm")))
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(substitute* "src/scripts/R.sh.in"
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(("uname") uname-bin)))
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(("uname") uname-bin))
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(substitute* "src/unix/sys-std.c"
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(("rm -Rf ") (string-append rm-bin " -Rf "))))
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#t))
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(add-after 'unpack 'build-reproducibly
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(lambda _
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@ -1041,14 +1044,14 @@ solution for sending email, including attachments, from within R.")
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(define-public r-stringi
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(package
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(name "r-stringi")
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(version "1.6.2")
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(version "1.7.3")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "stringi" version))
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(sha256
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(base32
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"1bidc1xzsv5nz2glf6z4sjxqlbs6zq595wwdmiq66sc2p7cis59s"))))
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"0mhz7dkjdm8ap2zav1pmivhr8s0l6p2f6piij2hy08nwszqk51nr"))))
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(build-system r-build-system)
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(inputs `(("icu4c" ,icu4c)))
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(native-inputs `(("pkg-config" ,pkg-config)))
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@ -1513,19 +1516,19 @@ the execution time of R expressions.")
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(define-public r-pryr
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(package
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(name "r-pryr")
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(version "0.1.4")
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(version "0.1.5")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "pryr" version))
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(sha256
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(base32
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"06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"))))
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"02vp1y7zhv22id43j5c0gdcgn9171dyypqp8rqrlc3w5a7n565kv"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-stringr" ,r-stringr)
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("r-codetools" ,r-codetools)))
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(native-inputs
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`(("r-rcpp" ,r-rcpp)))
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`(("r-codetools" ,r-codetools)
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("r-lobstr" ,r-lobstr)
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("r-rcpp" ,r-rcpp)
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("r-stringr" ,r-stringr)))
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(home-page "https://github.com/hadley/pryr")
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(synopsis "Tools for computing on the R language")
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(description
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@ -1677,14 +1680,14 @@ like tidy evaluation.")
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(define-public r-tibble
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(package
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(name "r-tibble")
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(version "3.1.2")
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(version "3.1.3")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "tibble" version))
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(sha256
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(base32
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"1vmwz1a756lar0jsigx6dhmj9mwk5mhywhq0prifwih3abhvszmn"))))
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"1gpy90hg0bd4an0wqj0xx16a6x37fhc94z1v63y46dpiz231xfks"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-ellipsis" ,r-ellipsis)
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@ -2552,13 +2555,13 @@ time-of-day values, based on the @code{difftime} class.")
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(define-public r-readr
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(package
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(name "r-readr")
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(version "1.4.0")
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(version "2.0.0")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "readr" version))
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(sha256
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(base32
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"1fa67h4l9d30ig460xizgzl115i9pm3bk9dvsbrw6awbmf51ic82"))))
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"1738nccg0msrhmzsasp19i0dpqi3m1nqbbg3nf1iiyp0mqc1dl8r"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-cli" ,r-cli)
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@ -2570,7 +2573,8 @@ time-of-day values, based on the @code{difftime} class.")
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("r-tibble" ,r-tibble)
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("r-r6" ,r-r6)
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("r-rlang" ,r-rlang)
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("r-bh" ,r-bh)))
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("r-tzdb" ,r-tzdb)
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("r-vroom" ,r-vroom)))
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(native-inputs
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`(("r-knitr" ,r-knitr)))
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(home-page "https://github.com/hadley/readr")
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@ -2644,13 +2648,13 @@ well as additional utilities such as panel and axis annotation functions.")
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(define-public r-rcpparmadillo
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(package
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(name "r-rcpparmadillo")
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(version "0.10.5.0.0")
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(version "0.10.6.0.0")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "RcppArmadillo" version))
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(sha256
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(base32
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"059qi872f9h40ns65166qsq1i1jq1mvizm29a0xmqlyn7a5y9ca3"))))
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"1bcx8fk5l5mmwb6cw36ndvld9v3amkz6vyc19059dw0xp7mxx04v"))))
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(properties `((upstream-name . "RcppArmadillo")))
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(build-system r-build-system)
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(propagated-inputs
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@ -2829,13 +2833,13 @@ that package, other packages are unaffected.")
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(define-public r-blob
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(package
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(name "r-blob")
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(version "1.2.1")
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(version "1.2.2")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "blob" version))
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(sha256
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(base32
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"1slb5mvxfyi92i8ifx2qa31hp57inilwhq1g9lzvgha6jrxbqm7g"))))
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"1yn7f13icaix0apxp4drnciwdn8bx8xmbd129jd7ck4rcly0axj9"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-rlang" ,r-rlang)
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@ -3410,14 +3414,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
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(define-public r-e1071
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(package
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(name "r-e1071")
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(version "1.7-7")
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(version "1.7-8")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "e1071" version))
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(sha256
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(base32
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"1phqrx787fkiamgx56sjjmzl9nh5wgpffah0mlwd7ijrf446qz3r"))))
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"16lw0pr71h00whndkkv9zh2ixm6vc8bkp8m4i5wwhmihd9abdkdb"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-class" ,r-class)
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@ -3658,13 +3662,13 @@ t-probabilities, quantiles, random deviates and densities.")
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(define-public r-matrixstats
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(package
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(name "r-matrixstats")
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(version "0.59.0")
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(version "0.60.0")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "matrixStats" version))
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(sha256
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(base32
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"178baqrd7rbin3l10zyrkps5sda0q9mdqil9r12b3n99mlk8fhh7"))))
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"08azjib5pwqs683dpgr3p5gid0silddcq6baqmvmazncrw1r7q0f"))))
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(properties `((upstream-name . "matrixStats")))
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(build-system r-build-system)
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(arguments
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@ -5444,14 +5448,14 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
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(define-public r-ranger
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(package
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(name "r-ranger")
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(version "0.12.1")
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(version "0.13.1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "ranger" version))
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(sha256
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(base32
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"1vr5akgh388iivrxi0g4pl2npq9dc4cim3ljk4kjf637q058wc7w"))))
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"02idcc6zbdz4wsi1mcwh7qyhmlbwvnzxwkdvvppxw7n2rh54z4v0"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-rcpp" ,r-rcpp)
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@ -6215,3 +6219,85 @@ various statistical models with linear predictors.")
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factors for simple designs, including contingency tables, one- and two-sample
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designs, one-way designs, general ANOVA designs, and linear regression.")
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(license license:gpl2)))
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(define-public r-norm
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(package
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(name "r-norm")
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(version "1.0-9.5")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "norm" version))
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(sha256
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(base32
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"01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h"))))
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(build-system r-build-system)
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(native-inputs
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`(("gfortran" ,gfortran)))
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(home-page "https://cran.r-project.org/web/packages/norm/")
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(synopsis "Analysis of multivariate normal datasets with missing values")
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(description "Multiple imputation of multivariate continuous data under a
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normal model.")
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;; Custom license, see https://cran.r-project.org/web/packages/norm/LICENSE.
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(license (license:non-copyleft "file://LICENSE"))))
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(define-public r-naniar
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(package
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(name "r-naniar")
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(version "0.6.1")
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(source (origin
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(method url-fetch)
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(uri (cran-uri "naniar" version))
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(sha256
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(base32
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"0l3l2x85v3srilww483kpgp4zlwixyml257b0cqly8kcpwawlinm"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-dplyr" ,r-dplyr)
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("r-norm" ,r-norm)
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("r-forcats" ,r-forcats)
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("r-ggplot2" ,r-ggplot2)
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("r-glue" ,r-glue)
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("r-magrittr" ,r-magrittr)
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("r-purrr" ,r-purrr)
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("r-rlang" ,r-rlang)
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("r-tibble" ,r-tibble)
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("r-tidyr" ,r-tidyr)
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("r-upsetr" ,r-upsetr)
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("r-viridis" ,r-viridis)
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("r-visdat" ,r-visdat)))
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(native-inputs
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`(("r-knitr" ,r-knitr)))
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(home-page "https://github.com/njtierney/naniar")
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(synopsis
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"Data structures, summaries, and visualisations for missing data")
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(description
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"Missing values are ubiquitous in data and need to be explored and
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handled in the initial stages of analysis. The package provides data structures
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and functions that facilitate the plotting of missing values and examination of
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imputations. This allows missing data dependencies to be explored with minimal
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deviation from the common work patterns of @code{ggplot2} and tidy data.")
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(license license:expat)))
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(define-public r-glinternet
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(package
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(name "r-glinternet")
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(version "1.0.11")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "glinternet" version))
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(sha256
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(base32
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"1lqph2hj0h826gcfyk290ahkfalpnrd6jzymm60xi2qxia14lzk5"))))
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(build-system r-build-system)
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(home-page "http://web.stanford.edu/~hastie/Papers/glinternet_jcgs.pdf")
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(synopsis "Learning interactions via hierarchical group-lasso regularization")
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(description "Group-Lasso INTERaction-NET. Fits linear pairwise-interaction
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models that satisfy strong hierarchy: if an interaction coefficient is estimated
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to be nonzero, then its two associated main effects also have nonzero estimated
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coefficients. Accommodates categorical variables (factors) with arbitrary
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numbers of levels, continuous variables, and combinations thereof. Implements
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the machinery described in the paper \"Learning interactions via hierarchical
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group-lasso regularization\" (JCGS 2015, Volume 24, Issue 3).
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Michael Lim & Trevor Hastie (2015)")
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(license license:gpl2)))
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