mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
Merge branch 'master' into core-updates
This commit is contained in:
Mark H Weaver
commit
f67337e23e
80 changed files with 2826 additions and 962 deletions
|
|
@ -31,6 +31,7 @@
|
|||
#:use-module (guix build-system gnu)
|
||||
#:use-module (guix build-system r)
|
||||
#:use-module (guix build-system python)
|
||||
#:use-module (guix build-system trivial)
|
||||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages curl)
|
||||
|
|
@ -99,9 +100,12 @@ can be imported from spreadsheets, text files and database sources and it can
|
|||
be output in text, PostScript, PDF or HTML.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public r
|
||||
;; Update this package together with the set of recommended packages: r-boot,
|
||||
;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice,
|
||||
;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival.
|
||||
(define-public r-minimal
|
||||
(package
|
||||
(name "r")
|
||||
(name "r-minimal")
|
||||
(version "3.3.3")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
|
|
@ -129,17 +133,46 @@ be output in text, PostScript, PDF or HTML.")
|
|||
(substitute* "src/scripts/R.sh.in"
|
||||
(("uname") uname-bin)))
|
||||
#t))
|
||||
(add-after 'unpack 'build-recommended-packages-reproducibly
|
||||
(add-after 'unpack 'build-reproducibly
|
||||
(lambda _
|
||||
(substitute* "src/library/Recommended/Makefile.in"
|
||||
(("INSTALL_OPTS =(.*)" line rest )
|
||||
(string-append "INSTALL_OPTS = --built-timestamp=1970-01-01"
|
||||
rest)))
|
||||
;; Ensure that gzipped files are reproducible
|
||||
;; The documentation contains time stamps to demonstrate
|
||||
;; documentation generation in different phases.
|
||||
(substitute* "src/library/tools/man/Rd2HTML.Rd"
|
||||
(("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S")
|
||||
"(removed for reproducibility)"))
|
||||
|
||||
;; Remove timestamp from tracing environment. This fixes
|
||||
;; reproducibility of "methods.rd{b,x}".
|
||||
(substitute* "src/library/methods/R/trace.R"
|
||||
(("dateCreated = Sys.time\\(\\)")
|
||||
"dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")"))
|
||||
|
||||
;; Ensure that gzipped files are reproducible.
|
||||
(substitute* '("src/library/grDevices/Makefile.in"
|
||||
"doc/manual/Makefile.in")
|
||||
(("R_GZIPCMD\\)" line)
|
||||
(string-append line " -n")))
|
||||
|
||||
;; The "srcfile" procedure in "src/library/base/R/srcfile.R"
|
||||
;; queries the mtime of a given file and records it in an object.
|
||||
;; This is acceptable at runtime to detect stale source files,
|
||||
;; but it destroys reproducibility at build time.
|
||||
;;
|
||||
;; Instead of disabling this feature, which may have unexpected
|
||||
;; consequences, we reset the mtime of generated files before
|
||||
;; passing them to the "srcfile" procedure.
|
||||
(substitute* "src/library/Makefile.in"
|
||||
(("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line)
|
||||
(string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n"))
|
||||
(("@\\$\\(MAKE\\) Rdobjects" line)
|
||||
(string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n "
|
||||
line)))
|
||||
(substitute* "src/library/tools/Makefile.in"
|
||||
(("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line)
|
||||
(string-append
|
||||
line
|
||||
"\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n")))
|
||||
|
||||
;; This library is installed using "install_package_description",
|
||||
;; so we need to pass the "builtStamp" argument.
|
||||
(substitute* "src/library/tools/Makefile.in"
|
||||
|
|
@ -163,7 +196,12 @@ be output in text, PostScript, PDF or HTML.")
|
|||
(add-after 'build 'install-info
|
||||
(lambda _ (zero? (system* "make" "install-info")))))
|
||||
#:configure-flags
|
||||
'("--with-cairo"
|
||||
'(;; Do not build the recommended packages. The build system creates
|
||||
;; random temporary directories and embeds their names in some
|
||||
;; package files. We build these packages with the r-build-system
|
||||
;; instead.
|
||||
"--without-recommended-packages"
|
||||
"--with-cairo"
|
||||
"--with-blas=-lopenblas"
|
||||
"--with-libpng"
|
||||
"--with-jpeglib"
|
||||
|
|
@ -221,6 +259,343 @@ publication-quality data plots. A large amount of 3rd-party packages are
|
|||
available, greatly increasing its breadth and scope.")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public r-boot
|
||||
(package
|
||||
(name "r-boot")
|
||||
(version "1.3-18")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "boot" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/boot")
|
||||
(synopsis "Bootstrap functions for R")
|
||||
(description
|
||||
"This package provides functions and datasets for bootstrapping from the
|
||||
book \"Bootstrap Methods and Their Application\" by A.C. Davison and
|
||||
D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
|
||||
;; Unlimited distribution
|
||||
(license (license:non-copyleft "file://R/bootfuns.q"))))
|
||||
|
||||
(define-public r-mass
|
||||
(package
|
||||
(name "r-mass")
|
||||
(version "7.3-45")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "MASS" version))
|
||||
(sha256
|
||||
(base32
|
||||
"13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx"))))
|
||||
(properties `((upstream-name . "MASS")))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
||||
(synopsis "Support functions and datasets for Venables and Ripley's MASS")
|
||||
(description
|
||||
"This package provides functions and datasets for the book \"Modern
|
||||
Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.")
|
||||
;; Either version may be picked.
|
||||
(license (list license:gpl2 license:gpl3))))
|
||||
|
||||
(define-public r-class
|
||||
(package
|
||||
(name "r-class")
|
||||
(version "7.3-14")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "class" version))
|
||||
(sha256
|
||||
(base32
|
||||
"173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-mass" ,r-mass)))
|
||||
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
||||
(synopsis "R functions for classification")
|
||||
(description
|
||||
"This package provides various functions for classification, including
|
||||
k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.")
|
||||
;; Either of the two versions can be picked.
|
||||
(license (list license:gpl2 license:gpl3))))
|
||||
|
||||
(define-public r-cluster
|
||||
(package
|
||||
(name "r-cluster")
|
||||
(version "2.0.5")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "cluster" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/cluster")
|
||||
(synopsis "Methods for cluster analysis")
|
||||
(description
|
||||
"This package provides methods for cluster analysis. It is a much
|
||||
extended version of the original from Peter Rousseeuw, Anja Struyf and Mia
|
||||
Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-codetools
|
||||
(package
|
||||
(name "r-codetools")
|
||||
(version "0.2-15")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "codetools" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/codetools")
|
||||
(synopsis "Code analysis tools for R")
|
||||
(description "This package provides code analysis tools for R.")
|
||||
;; Any version of the GPL.
|
||||
(license (list license:gpl2+ license:gpl3+))))
|
||||
|
||||
(define-public r-foreign
|
||||
(package
|
||||
(name "r-foreign")
|
||||
(version "0.8-67")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "foreign" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/foreign")
|
||||
(synopsis "Read data stored by other statistics software")
|
||||
(description
|
||||
"This package provides functions for reading and writing data stored by
|
||||
some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and
|
||||
for reading and writing some dBase files.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-kernsmooth
|
||||
(package
|
||||
(name "r-kernsmooth")
|
||||
(version "2.23-15")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "KernSmooth" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb"))))
|
||||
(properties `((upstream-name . "KernSmooth")))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/KernSmooth")
|
||||
(synopsis "Functions for kernel smoothing")
|
||||
(description
|
||||
"This package provides functions for kernel smoothing (and density
|
||||
estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
|
||||
\"Kernel Smoothing\".")
|
||||
;; Unlimited distribution
|
||||
(license (license:non-copyleft "file://LICENCE.note"))))
|
||||
|
||||
(define-public r-lattice
|
||||
(package
|
||||
(name "r-lattice")
|
||||
(version "0.20-34")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "lattice" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://lattice.r-forge.r-project.org/")
|
||||
(synopsis "High-level data visualization system")
|
||||
(description
|
||||
"The lattice package provides a powerful and elegant high-level data
|
||||
visualization system inspired by Trellis graphics, with an emphasis on
|
||||
multivariate data. Lattice is sufficient for typical graphics needs, and is
|
||||
also flexible enough to handle most nonstandard requirements.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-matrix
|
||||
(package
|
||||
(name "r-matrix")
|
||||
(version "1.2-7.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Matrix" version))
|
||||
(sha256
|
||||
(base32
|
||||
"09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
|
||||
(properties `((upstream-name . "Matrix")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(home-page "http://Matrix.R-forge.R-project.org/")
|
||||
(synopsis "Sparse and dense matrix classes and methods")
|
||||
(description
|
||||
"This package provides classes and methods for dense and sparse matrices
|
||||
and operations on them using LAPACK and SuiteSparse.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-nlme
|
||||
(package
|
||||
(name "r-nlme")
|
||||
(version "3.1-131")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "nlme" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(native-inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(home-page "http://cran.r-project.org/web/packages/nlme")
|
||||
(synopsis "Linear and nonlinear mixed effects models")
|
||||
(description
|
||||
"This package provides tools to fit and compare Gaussian linear and
|
||||
nonlinear mixed-effects models.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-mgcv
|
||||
(package
|
||||
(name "r-mgcv")
|
||||
(version "1.8-16")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "mgcv" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-matrix" ,r-matrix)
|
||||
("r-nlme" ,r-nlme)))
|
||||
(home-page "http://cran.r-project.org/web/packages/mgcv")
|
||||
(synopsis "Mixed generalised additive model computation")
|
||||
(description
|
||||
"GAMs, GAMMs and other generalized ridge regression with multiple smoothing
|
||||
parameter estimation by GCV, REML or UBRE/AIC. The library includes a
|
||||
@code{gam()} function, a wide variety of smoothers, JAGS support and
|
||||
distributions beyond the exponential family.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-nnet
|
||||
(package
|
||||
(name "r-nnet")
|
||||
(version "7.3-12")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "nnet" version))
|
||||
(sha256
|
||||
(base32
|
||||
"17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
||||
(synopsis "Feed-forward neural networks and multinomial log-linear models")
|
||||
(description
|
||||
"This package provides functions for feed-forward neural networks with a
|
||||
single hidden layer, and for multinomial log-linear models.")
|
||||
(license (list license:gpl2+ license:gpl3+))))
|
||||
|
||||
(define-public r-rpart
|
||||
(package
|
||||
(name "r-rpart")
|
||||
(version "4.1-10")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "rpart" version))
|
||||
(sha256
|
||||
(base32
|
||||
"119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/rpart")
|
||||
(synopsis "Recursive partitioning and regression trees")
|
||||
(description
|
||||
"This package provides recursive partitioning functions for
|
||||
classification, regression and survival trees.")
|
||||
(license (list license:gpl2+ license:gpl3+))))
|
||||
|
||||
(define-public r-spatial
|
||||
(package
|
||||
(name "r-spatial")
|
||||
(version "7.3-11")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "spatial" version))
|
||||
(sha256
|
||||
(base32
|
||||
"04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
|
||||
(synopsis "Functions for kriging and point pattern analysis")
|
||||
(description
|
||||
"This package provides functions for kriging and point pattern
|
||||
analysis.")
|
||||
;; Either version may be picked.
|
||||
(license (list license:gpl2 license:gpl3))))
|
||||
|
||||
(define-public r-survival
|
||||
(package
|
||||
(name "r-survival")
|
||||
(version "2.40-1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "survival" version))
|
||||
(sha256
|
||||
(base32
|
||||
"10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-matrix" ,r-matrix)))
|
||||
(home-page "https://github.com/therneau/survival")
|
||||
(synopsis "Survival analysis")
|
||||
(description
|
||||
"This package contains the core survival analysis routines, including
|
||||
definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
|
||||
curves, Cox models, and parametric accelerated failure time models.")
|
||||
(license license:lgpl2.0+)))
|
||||
|
||||
(define-public r
|
||||
(package (inherit r-minimal)
|
||||
(name "r")
|
||||
(source #f)
|
||||
(build-system trivial-build-system)
|
||||
(arguments '(#:builder (mkdir %output)))
|
||||
(propagated-inputs
|
||||
`(("r-minimal" ,r-minimal)
|
||||
("r-boot" ,r-boot)
|
||||
("r-class" ,r-class)
|
||||
("r-cluster" ,r-cluster)
|
||||
("r-codetools" ,r-codetools)
|
||||
("r-foreign" ,r-foreign)
|
||||
("r-kernsmooth" ,r-kernsmooth)
|
||||
("r-lattice" ,r-lattice)
|
||||
("r-mass" ,r-mass)
|
||||
("r-matrix" ,r-matrix)
|
||||
("r-mgcv" ,r-mgcv)
|
||||
("r-nlme" ,r-nlme)
|
||||
("r-nnet" ,r-nnet)
|
||||
("r-rpart" ,r-rpart)
|
||||
("r-spatial" ,r-spatial)
|
||||
("r-survival" ,r-survival)))))
|
||||
|
||||
(define-public r-bit
|
||||
(package
|
||||
(name "r-bit")
|
||||
|
|
@ -460,49 +835,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
|
|||
'citation(\"Rcpp\")' for details on these last two.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-matrix
|
||||
(package
|
||||
(name "r-matrix")
|
||||
(version "1.2-7.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "Matrix" version))
|
||||
(sha256
|
||||
(base32
|
||||
"09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa"))))
|
||||
(properties `((upstream-name . "Matrix")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(home-page "http://Matrix.R-forge.R-project.org/")
|
||||
(synopsis "Sparse and dense matrix classes and methods")
|
||||
(description
|
||||
"This package provides classes and methods for dense and sparse matrices
|
||||
and operations on them using LAPACK and SuiteSparse.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-mgcv
|
||||
(package
|
||||
(name "r-mgcv")
|
||||
(version "1.8-16")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "mgcv" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/mgcv")
|
||||
(synopsis "Mixed generalised additive model computation")
|
||||
(description
|
||||
"GAMs, GAMMs and other generalized ridge regression with multiple smoothing
|
||||
parameter estimation by GCV, REML or UBRE/AIC. The library includes a
|
||||
@code{gam()} function, a wide variety of smoothers, JAGS support and
|
||||
distributions beyond the exponential family.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-permute
|
||||
(package
|
||||
(name "r-permute")
|
||||
|
|
@ -722,6 +1054,7 @@ legends.")
|
|||
("r-gtable" ,r-gtable)
|
||||
("r-plyr" ,r-plyr)
|
||||
("r-lazyeval" ,r-lazyeval)
|
||||
("r-mass" ,r-mass)
|
||||
("r-tibble" ,r-tibble)
|
||||
("r-reshape2" ,r-reshape2)
|
||||
("r-scales" ,r-scales)
|
||||
|
|
@ -1342,6 +1675,8 @@ side.")
|
|||
(base32
|
||||
"0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(home-page "http://cran.r-project.org/web/packages/locfit")
|
||||
(synopsis "Local regression, likelihood and density estimation")
|
||||
(description
|
||||
|
|
@ -1519,6 +1854,8 @@ inference for statistical models.")
|
|||
(base32
|
||||
"14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(home-page "http://cran.r-project.org/web/packages/coda")
|
||||
(synopsis "This is a package for Output Analysis and Diagnostics for MCMC")
|
||||
(description "This package provides functions for summarizing and plotting
|
||||
|
|
@ -2028,26 +2365,6 @@ scaling functions for R.")
|
|||
"This package provides an integration of base and grid graphics for R.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-lattice
|
||||
(package
|
||||
(name "r-lattice")
|
||||
(version "0.20-34")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "lattice" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://lattice.r-forge.r-project.org/")
|
||||
(synopsis "High-level data visualization system")
|
||||
(description
|
||||
"The lattice package provides a powerful and elegant high-level data
|
||||
visualization system inspired by Trellis graphics, with an emphasis on
|
||||
multivariate data. Lattice is sufficient for typical graphics needs, and is
|
||||
also flexible enough to handle most nonstandard requirements.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-latticeextra
|
||||
(package
|
||||
(name "r-latticeextra")
|
||||
|
|
@ -2687,6 +3004,8 @@ flexible than the orphaned \"base64\" package.")
|
|||
(base32
|
||||
"1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-matrix" ,r-matrix)))
|
||||
(home-page "http://cran.r-project.org/web/packages/irlba")
|
||||
(synopsis "Methods for eigendecomposition of large matrices")
|
||||
(description
|
||||
|
|
@ -2707,10 +3026,11 @@ analysis of large sparse or dense matrices.")
|
|||
(base32
|
||||
"1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c"))))
|
||||
(build-system r-build-system)
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(inputs
|
||||
`(("gfortran" ,gfortran)))
|
||||
(propagated-inputs
|
||||
`(("r-foreach" ,r-foreach)))
|
||||
`(("r-foreach" ,r-foreach)
|
||||
("r-matrix" ,r-matrix)))
|
||||
(home-page "http://www.jstatsoft.org/v33/i01")
|
||||
(synopsis "Lasso and elastic-net regularized generalized linear models")
|
||||
(description
|
||||
|
|
@ -2828,6 +3148,8 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
|
|||
(base32
|
||||
"1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-class" ,r-class)))
|
||||
(home-page "http://cran.r-project.org/web/packages/e1071")
|
||||
(synopsis "Miscellaneous functions for probability theory")
|
||||
(description
|
||||
|
|
@ -3439,6 +3761,9 @@ from within R.")
|
|||
(("if isnan\\(lambda\\) \\{")
|
||||
"if (isnan(lambda)) {"))
|
||||
#t)))))
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)
|
||||
("r-matrix" ,r-matrix)))
|
||||
(home-page "http://spams-devel.gforge.inria.fr")
|
||||
(synopsis "Toolbox for solving sparse estimation problems")
|
||||
(description "SPAMS (SPArse Modeling Software) is an optimization toolbox
|
||||
|
|
@ -3456,45 +3781,6 @@ following problems:
|
|||
@end enumerate\n")
|
||||
(license license:gpl3+)))
|
||||
|
||||
(define-public r-rpart
|
||||
(package
|
||||
(name "r-rpart")
|
||||
(version "4.1-10")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "rpart" version))
|
||||
(sha256
|
||||
(base32
|
||||
"119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "http://cran.r-project.org/web/packages/rpart")
|
||||
(synopsis "Recursive partitioning and regression trees")
|
||||
(description
|
||||
"This package provides recursive partitioning functions for
|
||||
classification, regression and survival trees.")
|
||||
(license (list license:gpl2+ license:gpl3+))))
|
||||
|
||||
(define-public r-survival
|
||||
(package
|
||||
(name "r-survival")
|
||||
(version "2.40-1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (cran-uri "survival" version))
|
||||
(sha256
|
||||
(base32
|
||||
"10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
|
||||
(build-system r-build-system)
|
||||
(home-page "https://github.com/therneau/survival")
|
||||
(synopsis "Survival analysis")
|
||||
(description
|
||||
"This package contains the core survival analysis routines, including
|
||||
definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
|
||||
curves, Cox models, and parametric accelerated failure time models.")
|
||||
(license license:lgpl2.0+)))
|
||||
|
||||
(define-public r-base64
|
||||
(package
|
||||
(name "r-base64")
|
||||
|
|
@ -3536,17 +3822,20 @@ package instead.")
|
|||
`(("r-acepack" ,r-acepack)
|
||||
("r-base64" ,r-base64)
|
||||
("r-base64enc" ,r-base64enc)
|
||||
("r-cluster" ,r-cluster)
|
||||
("r-data-table" ,r-data-table)
|
||||
("r-foreign" ,r-foreign)
|
||||
("r-formula" ,r-formula)
|
||||
("r-ggplot2" ,r-ggplot2)
|
||||
("r-gridextra" ,r-gridextra)
|
||||
("r-gtable" ,r-gtable)
|
||||
;; Hmisc needs survival >= 2.40.1, so it cannot use the survival
|
||||
;; package that comes with R 3.3.2.
|
||||
("r-survival" ,r-survival)
|
||||
("r-lattice" ,r-lattice)
|
||||
("r-latticeextra" ,r-latticeextra)
|
||||
("r-htmltable" ,r-htmltable)
|
||||
("r-htmltools" ,r-htmltools)
|
||||
("r-nnet" ,r-nnet)
|
||||
("r-rpart" ,r-rpart)
|
||||
("r-survival" ,r-survival)
|
||||
("r-viridis" ,r-viridis)))
|
||||
(home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
|
||||
(synopsis "Miscellaneous data analysis and graphics functions")
|
||||
|
|
@ -3831,6 +4120,8 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
|
|||
(base32
|
||||
"167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lattice" ,r-lattice)))
|
||||
(home-page "http://zoo.R-Forge.R-project.org/")
|
||||
(synopsis "S3 infrastructure for regular and irregular time series")
|
||||
(description "This package contains an S3 class with methods for totally
|
||||
|
|
@ -4097,7 +4388,9 @@ letters, as is often required for scientific publications.")
|
|||
"133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-segmented" ,r-segmented)))
|
||||
`(("r-boot" ,r-boot)
|
||||
("r-mass" ,r-mass)
|
||||
("r-segmented" ,r-segmented)))
|
||||
(home-page "http://cran.r-project.org/web/packages/mixtools")
|
||||
(synopsis "Tools for analyzing finite mixture models")
|
||||
(description
|
||||
|
|
@ -4227,7 +4520,9 @@ to change in the future.")
|
|||
"1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-modeltools" ,r-modeltools)))
|
||||
`(("r-lattice" ,r-lattice)
|
||||
("r-modeltools" ,r-modeltools)
|
||||
("r-nnet" ,r-nnet)))
|
||||
(home-page "http://cran.r-project.org/web/packages/flexmix")
|
||||
(synopsis "Flexible mixture modeling")
|
||||
(description
|
||||
|
|
@ -4274,7 +4569,8 @@ and resampling-based inference.")
|
|||
"0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-mclust" ,r-mclust)))
|
||||
`(("r-mass" ,r-mass)
|
||||
("r-mclust" ,r-mclust)))
|
||||
(home-page "https://cran.r-project.org/web/packages/prabclus")
|
||||
(synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
|
||||
(description
|
||||
|
|
@ -4363,9 +4659,12 @@ of the points.")
|
|||
"15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-diptest" ,r-diptest)
|
||||
`(("r-class" ,r-class)
|
||||
("r-cluster" ,r-cluster)
|
||||
("r-diptest" ,r-diptest)
|
||||
("r-flexmix" ,r-flexmix)
|
||||
("r-kernlab" ,r-kernlab)
|
||||
("r-mass" ,r-mass)
|
||||
("r-mclust" ,r-mclust)
|
||||
("r-mvtnorm" ,r-mvtnorm)
|
||||
("r-prabclus" ,r-prabclus)
|
||||
|
|
@ -4484,7 +4783,8 @@ based on an interface to Fortran implementations by M. J. D. Powell.")
|
|||
(properties `((upstream-name . "RcppEigen")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-rcpp" ,r-rcpp)))
|
||||
`(("r-rcpp" ,r-rcpp)
|
||||
("r-matrix" ,r-matrix)))
|
||||
(home-page "http://eigen.tuxfamily.org")
|
||||
(synopsis "Rcpp integration for the Eigen templated linear algebra library")
|
||||
(description
|
||||
|
|
@ -4529,6 +4829,8 @@ metrics for evaluating models.")
|
|||
"0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
|
||||
(properties `((upstream-name . "MatrixModels")))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-matrix" ,r-matrix)))
|
||||
(home-page "https://cran.r-project.org/web/packages/MatrixModels")
|
||||
(synopsis "Modelling with sparse and dense matrices")
|
||||
(description
|
||||
|
|
@ -4606,7 +4908,9 @@ algorithms.")
|
|||
("r-rcppeigen" ,r-rcppeigen)))
|
||||
(propagated-inputs
|
||||
`(("r-minqa" ,r-minqa)
|
||||
("r-nloptr" ,r-nloptr)))
|
||||
("r-nloptr" ,r-nloptr)
|
||||
("r-mass" ,r-mass)
|
||||
("r-nlme" ,r-nlme)))
|
||||
(home-page "http://cran.r-project.org/web/packages/lme4")
|
||||
(synopsis "Linear mixed-effects models using eigen and S4")
|
||||
(description
|
||||
|
|
@ -4629,7 +4933,9 @@ C++ library for numerical linear algebra and RcppEigen glue.")
|
|||
"00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-lme4" ,r-lme4)))
|
||||
`(("r-lme4" ,r-lme4)
|
||||
("r-mass" ,r-mass)
|
||||
("r-matrix" ,r-matrix)))
|
||||
(home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
|
||||
(synopsis "Methods for linear mixed model comparison")
|
||||
(description
|
||||
|
|
@ -4651,7 +4957,10 @@ bootstrap test for generalized linear mixed models.")
|
|||
"0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-pbkrtest" ,r-pbkrtest)
|
||||
`(("r-mass" ,r-mass)
|
||||
("r-mgcv" ,r-mgcv)
|
||||
("r-nnet" ,r-nnet)
|
||||
("r-pbkrtest" ,r-pbkrtest)
|
||||
("r-quantreg" ,r-quantreg)))
|
||||
(home-page "https://r-forge.r-project.org/projects/car/")
|
||||
(synopsis "Companion to applied regression")
|
||||
|
|
@ -4790,7 +5099,8 @@ multivariate case.")
|
|||
"0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
|
||||
(build-system r-build-system)
|
||||
(propagated-inputs
|
||||
`(("r-mclust" ,r-mclust)
|
||||
`(("r-cluster" ,r-cluster)
|
||||
("r-mclust" ,r-mclust)
|
||||
("r-mvtnorm" ,r-mvtnorm)
|
||||
("r-sn" ,r-sn)))
|
||||
(home-page "http://cran.r-project.org/web/packages/tclust")
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue