Merge remote-tracking branch 'origin/master' into core-updates

gnu/packages/bioconductor.scm

@@ -2098,6 +2098,96 @@ impute GReX can be trained with a training dataset where the real total
 expression values are known.")
     (license license:gpl3)))
 
+(define-public r-affyilm
+  (package
+    (name "r-affyilm")
+    (version "1.50.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyILM" version))
+       (sha256
+        (base32 "0i2hjaqjz06ym5kbw5da1h3cahc630mjwljsji1l2ks0gjcipll0"))))
+    (properties `((upstream-name . "affyILM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affxparser
+           r-affy
+           r-biobase
+           r-gcrma))
+    (home-page "https://bioconductor.org/packages/affyILM")
+    (synopsis
+     "Linear model of background subtraction and the Langmuir isotherm")
+    (description
+     "The affyILM package is a preprocessing tool which estimates gene
+expression levels for Affymetrix Gene Chips.  Input from physical chemistry is
+employed to first background subtract intensities before calculating
+concentrations on behal of the Langmuir model.")
+    (license license:gpl3)))
+
+(define-public r-affylmgui
+  (package
+    (name "r-affylmgui")
+    (version "1.72.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affylmGUI" version))
+       (sha256
+        (base32 "0jds73pxqf522wcg8qd4b4k1qbhn51av5md1nhgcdnb6is0lzvxi"))))
+    (properties `((upstream-name . "affylmGUI")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-affy
+           r-affyio
+           r-affyplm
+           r-annotationdbi
+           r-biocgenerics
+           r-biocmanager
+           r-gcrma
+           r-limma
+           r-r2html
+           r-tkrplot
+           r-xtable))
+    (home-page "https://bioinf.wehi.edu.au/affylmGUI/")
+    (synopsis "GUI for limma package with Affymetrix microarrays")
+    (description
+     "This package provides a @acronym{GUI, Graphical User Interface} for
+analysis of Affymetrix microarray gene expression data using the affy and
+limma packages.")
+    (license license:gpl2+)))
+
+(define-public r-affyplm
+  (package
+    (name "r-affyplm")
+    (version "1.74.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyPLM" version))
+       (sha256
+        (base32 "0f0faxjzlg0znhjfvf1490yc54npkx659jx76cddm5hk7q0blv3v"))))
+    (properties `((upstream-name . "affyPLM")))
+    (build-system r-build-system)
+    (inputs (list zlib))
+    (propagated-inputs
+     (list r-affy
+           r-biobase
+           r-biocgenerics
+           r-gcrma
+           r-preprocesscore
+           r-zlibbioc))
+    (home-page "https://github.com/bmbolstad/affyPLM")
+    (synopsis "Methods for fitting probe-level models")
+    (description
+     "The affyPLM provides a package that extends and improves the
+functionality of the base affy package.  For speeding up the runs, it includes
+routines that make heavy use of compiled code.  The central focus is on
+implementation of methods for fitting probe-level models and tools using these
+models.  @acronym{PLM, probe-level models} based quality assessment tools are
+also provided.")
+    (license license:gpl2+)))
+
 (define-public r-affyrnadegradation
   (package
     (name "r-affyrnadegradation")
@@ -2617,6 +2707,57 @@ Powerful interactive and dynamic figures generated by animalcules enable users
 to understand their data better and discover new insights.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhubdata
+  (package
+    (name "r-annotationhubdata")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHubData" version))
+       (sha256
+        (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"))))
+    (properties `((upstream-name . "AnnotationHubData")))
+    (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'install 'set-home
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     (list r-annotationdbi
+           r-annotationforge
+           r-annotationhub
+           r-biobase
+           r-bioccheck
+           r-biocgenerics
+           r-biocmanager
+           r-biocviews
+           r-biostrings
+           r-dbi
+           r-futile-logger
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-graph
+           r-iranges
+           r-jsonlite
+           r-organismdbi
+           r-rcurl
+           r-rsamtools
+           r-rsqlite
+           r-rtracklayer
+           r-s4vectors
+           r-xml))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/AnnotationHubData")
+    (synopsis "Transform public data resources into Bioconductor data structures")
+    (description
+     "This package provides tools to acquire, annotate, convert and store data
+for use in Bioconductor’s AnnotationHub.")
+    (license license:artistic2.0)))
+
 (define-public r-anvil
   (package
     (name "r-anvil")

gnu/packages/cran.scm

@@ -2818,6 +2818,27 @@ designed to make it easy to install and load multiple tidyverse packages in a
 single step.")
     (license license:gpl3)))
 
+(define-public r-tkrplot
+  (package
+    (name "r-tkrplot")
+    (version "0.0-27")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "tkrplot" version))
+       (sha256
+        (base32 "19bj4wn1fs4wrx5k4gakhpz4q59fgx0584wyaw7hnh0ljj8i34n9"))))
+    (properties `((upstream-name . "tkrplot")))
+    (build-system r-build-system)
+    (inputs (list libx11))
+    (home-page "https://cran.r-project.org/package=tkrplot")
+    (synopsis "Place R graphics in a Tk widget")
+    (description
+     "The tkrplot package lets you place R graphics in a @dfn{Tk,
+cross-platform graphical user interface toolkit} widget.")
+    ;; Any version of the GPL.
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-rvest
   (package
     (name "r-rvest")

gnu/packages/java.scm

@@ -1054,7 +1054,9 @@ new Date();"))
                                     (find-files "." ".*.(bin|exe|jar)$"))))
               (sha256
                (base32
-                "0i47ar8lxzjrkkiwbzybfxs473390h4jq9ahm3xqdvy5zpchxy3y"))))
+                "0i47ar8lxzjrkkiwbzybfxs473390h4jq9ahm3xqdvy5zpchxy3y"))
+              (patches (search-patches
+                        "openjdk-10-idlj-reproducibility.patch"))))
     (arguments
      (substitute-keyword-arguments (package-arguments openjdk9)
        ((#:phases phases)