Merge branch 'master' into core-updates-frozen

 Conflicts:
	gnu/packages/bioinformatics.scm
	gnu/packages/chez.scm
	gnu/packages/docbook.scm
	gnu/packages/ebook.scm
	gnu/packages/gnome.scm
	gnu/packages/linux.scm
	gnu/packages/networking.scm
	gnu/packages/python-web.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tex.scm
	gnu/packages/version-control.scm
	gnu/packages/xml.scm
	guix/build-system/dune.scm
	guix/build-system/go.scm
	guix/build-system/linux-module.scm
	guix/packages.scm

1 files changed, 413 insertions, 0 deletions

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 0750c7d507..f288f76e95 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -9390,6 +9390,144 @@ and make comparisons between different methodologies straightforward.")
 several entropy estimators.")
     (license license:gpl3+)))
 
+(define-public r-nsprcomp
+  (package
+    (name "r-nsprcomp")
+    (version "0.5.1-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nsprcomp" version))
+       (sha256
+        (base32
+         "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
+    (properties `((upstream-name . "nsprcomp")))
+    (build-system r-build-system)
+    (home-page "https://sigg-iten.ch/research/")
+    (synopsis "Non-negative and sparse PCA")
+    (description
+     "This package implements two methods for performing a constrained
+principal component analysis (PCA), where non-negativity and/or sparsity
+constraints are enforced on the principal axes (PAs).  The function
+@code{nsprcomp} computes one principal component (PC) after the other.  Each
+PA is optimized such that the corresponding PC has maximum additional variance
+not explained by the previous components.  In contrast, the function
+@code{nscumcomp} jointly computes all PCs such that the cumulative variance is
+maximal.  Both functions have the same interface as the @code{prcomp} function
+from the @code{stats} package (plus some extra parameters).")
+    (license license:gpl2+)))
+
+(define-public r-cmplot
+  (package
+    (name "r-cmplot")
+    (version "3.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "CMplot" version))
+       (sha256
+        (base32
+         "13y05j5gsdc712fn7yvcz5nx2pbcdvl201hfb6jzpvl86qx2l0j1"))))
+    (properties `((upstream-name . "CMplot")))
+    (build-system r-build-system)
+    (home-page "https://github.com/YinLiLin/CMplot")
+    (synopsis "Circle Manhattan plot")
+    (description
+     "Circle Manhattan Plot is an R package that can lay out genome-wide
+association study P-value results in both traditional rectangular patterns,
+QQ-plot and novel circular ones.  United in only one bull's eye style plot,
+association results from multiple traits can be compared interactively,
+thereby to reveal both similarities and differences between signals.
+Additional functions include: highlight signals, a group of SNPs, chromosome
+visualization and candidate genes around SNPs.")
+    (license license:gpl2+)))
+
+(define-public r-precrec
+  (package
+    (name "r-precrec")
+    (version "0.12.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "precrec" version))
+       (sha256
+        (base32
+         "0vwzaqnh9ymrm52dd79bihwqprnygz0d71ay8fv51hdw0zg6saya"))))
+    (properties `((upstream-name . "precrec")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-assertthat" ,r-assertthat)
+       ("r-data-table" ,r-data-table)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridextra" ,r-gridextra)
+       ("r-rcpp" ,r-rcpp)
+       ("r-withr" ,r-withr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://evalclass.github.io/precrec/")
+    (synopsis "Calculate accurate precision-recall and ROC curves")
+    (description
+     "This package provides tools for accurate calculations and visualization
+of precision-recall and ROC (Receiver Operator Characteristics) curves.")
+    (license license:gpl3)))
+
+(define-public r-netrep
+  (package
+    (name "r-netrep")
+    (version "1.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "NetRep" version))
+       (sha256
+        (base32
+         "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
+    (properties `((upstream-name . "NetRep")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-abind" ,r-abind)
+       ("r-bh" ,r-bh)
+       ("r-foreach" ,r-foreach)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rhpcblasctl" ,r-rhpcblasctl)
+       ("r-statmod" ,r-statmod)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://cran.r-project.org/package=NetRep")
+    (synopsis "Permutation testing network module preservation across datasets")
+    (description
+     "This package provides functions for assessing the
+replication/preservation of a network module's topology across datasets
+through permutation testing.")
+    (license license:gpl2)))
+
+(define-public r-intergraph
+  (package
+    (name "r-intergraph")
+    (version "2.0-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "intergraph" version))
+       (sha256
+        (base32
+         "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
+    (properties `((upstream-name . "intergraph")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-igraph" ,r-igraph)
+       ("r-network" ,r-network)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "http://mbojan.github.io/intergraph")
+    (synopsis "Coercion routines for network data objects")
+    (description
+     "Functions implemented in this package allow to coerce (i.e. convert)
+network data between classes provided by other R packages.  Currently
+supported classes are those defined in packages @code{network} and
+@code{igraph}.")
+    (license license:gpl3)))
+
 (define-public r-abcoptim
   (package
     (name "r-abcoptim")
@@ -9517,6 +9655,233 @@ and coverage methods to tune the choice of threshold.")
 @end enumerate")
     (license license:gpl3)))
 
+(define-public r-ggnetwork
+  (package
+    (name "r-ggnetwork")
+    (version "0.5.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ggnetwork" version))
+       (sha256
+        (base32
+         "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
+    (properties `((upstream-name . "ggnetwork")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ggplot2" ,r-ggplot2)
+       ("r-ggrepel" ,r-ggrepel)
+       ("r-igraph" ,r-igraph)
+       ("r-network" ,r-network)
+       ("r-sna" ,r-sna)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/briatte/ggnetwork")
+    (synopsis "Geometries to plot networks with ggplot2")
+    (description
+     "This package provides geometries to plot network objects with the
+ggplot2 package.")
+    (license license:gpl3)))
+
+(define-public r-cvauc
+  (package
+    (name "r-cvauc")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "cvAUC" version))
+       (sha256
+        (base32
+         "13bk97l5nn97h85iz93zxazhr63n21nwyrpnl856as9qp59yvn64"))))
+    (properties `((upstream-name . "cvAUC")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-rocr" ,r-rocr)))
+    (home-page "https://github.com/ledell/cvAUC")
+    (synopsis "Cross-validated area under the ROC curve confidence intervals")
+    (description
+     "This package contains various tools for working with and evaluating
+cross-validated area under the ROC curve (AUC) estimators.  The primary
+functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
+report cross-validated AUC and compute confidence intervals for
+cross-validated AUC estimates based on influence curves for i.i.d. and pooled
+repeated measures data, respectively.")
+    (license license:asl2.0)))
+
+(define-public r-gam
+  (package
+    (name "r-gam")
+    (version "1.20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gam" version))
+       (sha256
+        (base32
+         "1zhy2fp7pxac8xp3z3hndhprj4s5gx3305b627vc78bal1ml3swi"))))
+    (properties `((upstream-name . "gam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-foreach" ,r-foreach)))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/package=gam")
+    (synopsis "Generalized additive models")
+    (description
+     "This package provides functions for fitting and working with generalized
+additive models, as described in chapter 7 of \"Statistical Models in
+S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
+Models\" (Hastie and Tibshirani, 1990).")
+    (license license:gpl2)))
+
+(define-public r-superlearner
+  (package
+    (name "r-superlearner")
+    (version "2.0-28")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "SuperLearner" version))
+       (sha256
+        (base32
+         "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
+    (properties `((upstream-name . "SuperLearner")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cvauc" ,r-cvauc)
+       ("r-gam" ,r-gam)
+       ("r-nnls" ,r-nnls)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/ecpolley/SuperLearner")
+    (synopsis "Super learner prediction")
+    (description
+     "This package implements the super learner prediction method and contains
+a library of prediction algorithms to be used in the super learner.")
+    (license license:gpl3)))
+
+(define-public r-drtmle
+  (package
+    (name "r-drtmle")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "drtmle" version))
+       (sha256
+        (base32
+         "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa"))))
+    (properties `((upstream-name . "drtmle")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-future-apply" ,r-future-apply)
+       ("r-np" ,r-np)
+       ("r-superlearner" ,r-superlearner)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/benkeser/drtmle")
+    (synopsis "Doubly-robust nonparametric estimation and inference")
+    (description
+     "This package implements targeted minimum loss-based estimators of
+counterfactual means and causal effects that are doubly-robust with respect
+both to consistency and asymptotic normality.")
+    (license license:expat)))
+
+(define-public r-dofuture
+  (package
+    (name "r-dofuture")
+    (version "0.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "doFuture" version))
+       (sha256
+        (base32
+         "1hqzdlgcrc5l6xjwdylsc9iiysi2wx8k1j1vmw3wryj26057c9y4"))))
+    (properties `((upstream-name . "doFuture")))
+    (build-system r-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     `(("r-foreach" ,r-foreach)
+       ("r-future" ,r-future)
+       ("r-globals" ,r-globals)
+       ("r-iterators" ,r-iterators)))
+    (native-inputs
+     `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
+    (home-page "https://github.com/HenrikBengtsson/doFuture")
+    (synopsis "Foreach parallel adapter using the future API")
+    (description
+     "This package provides a @code{%dopar%} adapter such that any type of
+futures can be used as backends for the @code{foreach} framework.")
+    (license license:lgpl2.1+)))
+
+(define-public r-superheat
+  (package
+    (name "r-superheat")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "superheat" version))
+       (sha256
+        (base32
+         "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
+    (properties `((upstream-name . "superheat")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dplyr" ,r-dplyr)
+       ("r-ggdendro" ,r-ggdendro)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtable" ,r-gtable)
+       ("r-magrittr" ,r-magrittr)
+       ("r-plyr" ,r-plyr)
+       ("r-scales" ,r-scales)))
+    (home-page "https://cran.r-project.org/package=superheat")
+    (synopsis "Graphical tool for exploring complex datasets using heatmaps")
+    (description
+     "This package provides a system for generating extendable and
+customizable heatmaps for exploring complex datasets, including big data and
+data with multiple data types.")
+    (license license:cc0)))
+
+(define-public r-qualv
+  (package
+    (name "r-qualv")
+    (version "0.3-3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "qualV" version))
+       (sha256
+        (base32
+         "1yyqk223ydcc0125gsn33a4mcdp8bd76fpn8kj9bfz9g78b8dqmx"))))
+    (properties `((upstream-name . "qualV")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-kernsmooth" ,r-kernsmooth)))
+    (home-page "http://qualV.R-Forge.R-Project.org/")
+    (synopsis "Qualitative Validation Methods")
+    (description
+     "This package provides qualitative methods for the validation of dynamic
+models.  It contains
+
+@enumerate
+@item an orthogonal set of deviance measures for absolute, relative and
+  ordinal scale and
+@item approaches accounting for time shifts.
+@end enumerate
+
+The first approach transforms time to take time delays and speed differences
+into account.  The second divides the time series into interval units
+according to their main features and finds the @dfn{longest common
+subsequence} (LCS) using a dynamic programming algorithm.")
+    (license license:gpl2+)))
+
 (define-public r-mosaiccore
   (package
     (name "r-mosaiccore")
@@ -11745,6 +12110,54 @@ builders who wish to wrap command line software, and to help analysts stay
 inside R when they might usually leave to execute non-R software.")
     (license license:expat)))
 
+(define-public r-rslurm
+  (package
+    (name "r-rslurm")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rslurm" version))
+       (sha256
+        (base32
+         "0fn2na8prsaxa03x5wi3105gpsxc35qvgmik7wy3nylvx4wdfv9g"))))
+    (properties `((upstream-name . "rslurm")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-whisker" ,r-whisker)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "http://cyberhelp.sesync.org/rslurm/")
+    (synopsis "Submit R calculations to a Slurm cluster")
+    (description
+     "This package provides functions that simplify submitting R scripts to a
+Slurm workload manager, in part by automating the division of embarrassingly
+parallel calculations across cluster nodes.")
+    (license license:gpl3)))
+
+(define-public r-chk
+  (package
+    (name "r-chk")
+    (version "0.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "chk" version))
+       (sha256
+        (base32
+         "1fxsxgvd08lkb6amjgs4x48dhqr046mmjngjfgy2ya9cl2shd7ls"))))
+    (properties `((upstream-name . "chk")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-lifecycle" ,r-lifecycle)
+       ("r-rlang" ,r-rlang)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/poissonconsulting/chk")
+    (synopsis "Check user-supplied function arguments")
+    (description
+     "This is a package for developers to check user-supplied function
+arguments.  It is designed to be simple, fast and customizable.  Error
+messages follow the tidyverse style guide.")
+    (license license:expat)))
+
 (define-public r-weights
   (package
     (name "r-weights")