Merge branch 'master' into staging

gnu/artwork.scm

@@ -29,7 +29,7 @@ (define-module (gnu artwork)
 ;;; Code:
 
 (define %artwork-repository
-  (let ((commit "e951905f79dcc92fba9cd05d9190afa3ee2d1d50"))
+  (let ((commit "b975164c19c9c0f5d91e5731ec1683e7510c1326"))
     (origin
       (method git-fetch)
       (uri (git-reference
@@ -39,6 +39,6 @@ (define %artwork-repository
                                 "-checkout"))
       (sha256
        (base32
-        "1d79ackvs3bqk43ff91457qmdb6g4nwfknzs3dyrhni1ynk1i976")))))
+        "1fad7az077q9ds3jhp00jfsr8rfw4ws042wmnai52k7jv4kbxwyf")))))
 
 ;;; artwork.scm ends here

gnu/build/linux-modules.scm

@@ -25,6 +25,7 @@ (define-module (gnu build linux-modules)
   #:use-module (rnrs io ports)
   #:use-module (rnrs bytevectors)
   #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-11)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 vlist)
   #:use-module (ice-9 match)
@@ -105,7 +106,8 @@ (define not-softdep-whitespace
   (char-set-complement (char-set #\space #\tab)))
 
 (define (module-soft-dependencies file)
-  "Return a list of (cons section soft-dependency) of module FILE."
+  "Return the list of modules that can be preloaded, and then the list of
+modules that can be postloaded, of the soft dependencies of module FILE."
   ;; TEXT: "pre: baz blubb foo post: bax bar"
   (define (parse-softdep text)
     (let loop ((value '())
@@ -120,13 +122,24 @@ (define (parse-softdep text)
         value))))
 
   ;; Note: Multiple 'softdep sections are allowed.
-  (let ((info (modinfo-section-contents file)))
-    (concatenate
-     (filter-map (match-lambda
-                  (('softdep . value)
-                   (parse-softdep value))
-                  (_ #f))
-                 (modinfo-section-contents file)))))
+  (let* ((info (modinfo-section-contents file))
+         (entries (concatenate
+                   (filter-map (match-lambda
+                                (('softdep . value)
+                                 (parse-softdep value))
+                                (_ #f))
+                               (modinfo-section-contents file)))))
+    (let-values (((pres posts)
+                  (partition (match-lambda
+                              (("pre" . _) #t)
+                              (("post" . _) #f))
+                             entries)))
+      (values (map (match-lambda
+                    ((_ . value) value))
+                   pres)
+              (map (match-lambda
+                    ((_ . value) value))
+                   posts)))))
 
 (define (module-aliases file)
   "Return the list of aliases of module FILE."

gnu/local.mk

@@ -1227,6 +1227,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \
   %D%/packages/patches/rust-bootstrap-stage0-test.patch		\
   %D%/packages/patches/rust-coresimd-doctest.patch		\
+  %D%/packages/patches/rust-1.30-gdb-llvm.patch			\
   %D%/packages/patches/rust-reproducible-builds.patch		 \
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
   %D%/packages/patches/scalapack-blacs-mpi-deprecations.patch	\

gnu/packages/admin.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
 ;;; Copyright © 2014, 2015, 2016, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
@@ -1143,7 +1143,9 @@ (define (copy-man-page target)
 This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
 
     ;; In practice, this is linked against Readline, which makes it GPLv3+.
-    (license license:bsd-3)))
+    (license license:bsd-3)
+
+    (properties `((cpe-name . "wpa_supplicant")))))
 
 (define-public wpa-supplicant
   (package (inherit wpa-supplicant-minimal)

gnu/packages/bioconductor.scm

@@ -170,6 +170,32 @@ (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
 default."  )
     (license license:artistic2.0)))
 
+(define-public r-org-dr-eg-db
+  (package
+    (name "r-org-dr-eg-db")
+    (version "3.7.0")
+    (source (origin
+              (method url-fetch)
+              ;; We cannot use bioconductor-uri here because this tarball is
+              ;; located under "data/annotation/" instead of "bioc/".
+              (uri (string-append "https://www.bioconductor.org/packages/"
+                                  "release/data/annotation/src/contrib/"
+                                  "org.Dr.eg.db_" version ".tar.gz"))
+              (sha256
+               (base32
+                "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
+    (properties
+     `((upstream-name . "org.Dr.eg.db")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
+    (synopsis "Annotation for Zebrafish")
+    (description
+     "This package provides genome wide annotations for Zebrafish, primarily
+based on mapping using Entrez Gene identifiers.")
+    (license license:artistic2.0)))
+
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")

gnu/packages/bioinformatics.scm

@@ -84,6 +84,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages dlang)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages lisp)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages man)
@@ -1384,6 +1385,46 @@ (define-public bowtie
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public bowtie1
+  (package
+    (name "bowtie1")
+    (version "1.2.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
+                                  version "/bowtie-" version "-src.zip"))
+              (sha256
+               (base32
+                "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(substitute* "Makefile"
+                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                      ; no "check" target
+       #:make-flags
+       (list "all"
+             (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure))))
+    (inputs
+     `(("tbb" ,tbb)
+       ("zlib" ,zlib)))
+    (supported-systems '("x86_64-linux"))
+    (home-page "http://bowtie-bio.sourceforge.net/index.shtml")
+    (synopsis "Fast aligner for short nucleotide sequence reads")
+    (description
+     "Bowtie is a fast, memory-efficient short read aligner.  It aligns short
+DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+reads per hour.  Bowtie indexes the genome with a Burrows-Wheeler index to
+keep its memory footprint small: typically about 2.2 GB for the human
+genome (2.9 GB for paired-end).")
+    (license license:artistic2.0)))
+
 (define-public tophat
   (package
     (name "tophat")
@@ -6240,6 +6281,48 @@ (define-public infernal
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-scde
+  (package
+    (name "r-scde")
+    (version "1.99.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/hms-dbmi/scde.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-mgcv" ,r-mgcv)
+       ("r-rook" ,r-rook)
+       ("r-rjson" ,r-rjson)
+       ("r-cairo" ,r-cairo)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-edger" ,r-edger)
+       ("r-quantreg" ,r-quantreg)
+       ("r-nnet" ,r-nnet)
+       ("r-rmtstat" ,r-rmtstat)
+       ("r-extremes" ,r-extremes)
+       ("r-pcamethods" ,r-pcamethods)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-flexmix" ,r-flexmix)))
+    (home-page "https://hms-dbmi.github.io/scde/")
+    (synopsis "R package for analyzing single-cell RNA-seq data")
+    (description "The SCDE package implements a set of statistical methods for
+analyzing single-cell RNA-seq data.  SCDE fits individual error models for
+single-cell RNA-seq measurements.  These models can then be used for
+assessment of differential expression between groups of cells, as well as
+other types of analysis.  The SCDE package also contains the pagoda framework
+which applies pathway and gene set overdispersion analysis to identify aspects
+of transcriptional heterogeneity among single cells.")
+    ;; See https://github.com/hms-dbmi/scde/issues/38
+    (license license:gpl2)))
+
 (define-public r-centipede
   (package
     (name "r-centipede")
@@ -7127,28 +7210,6 @@ (define-public r-optparse
 that accept short and long options.")
     (license license:gpl2+)))
 
-(define-public r-dnacopy
-  (package
-    (name "r-dnacopy")
-    (version "1.56.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "DNAcopy" version))
-              (sha256
-               (base32
-                "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
-    (properties
-     `((upstream-name . "DNAcopy")))
-    (build-system r-build-system)
-    (inputs
-     `(("gfortran" ,gfortran)))
-    (home-page "https://bioconductor.org/packages/DNAcopy")
-    (synopsis "Implementation of a circular binary segmentation algorithm")
-    (description "This package implements the circular binary segmentation (CBS)
-algorithm to segment DNA copy number data and identify genomic regions with
-abnormal copy number.")
-    (license license:gpl2+)))
-
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
@@ -11613,7 +11674,7 @@ (define-public f-seq
 (define-public bismark
   (package
     (name "bismark")
-    (version "0.19.1")
+    (version "0.20.1")
     (source
      (origin
        (method git-fetch)
@@ -11623,18 +11684,25 @@ (define-public bismark
        (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
-       (snippet
-        '(begin
-           ;; highcharts.js is non-free software.  The code is available under
-           ;; CC-BY-NC or proprietary licenses only.
-           (delete-file "bismark_sitrep/highcharts.js")
-           #t))))
+         "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9"))))
     (build-system perl-build-system)
     (arguments
      `(#:tests? #f                      ; there are no tests
+       #:modules ((guix build utils)
+                  (ice-9 popen)
+                  (srfi srfi-26)
+                  (guix build perl-build-system))
        #:phases
        (modify-phases %standard-phases
+         ;; The bundled plotly.js is minified.
+         (add-after 'unpack 'replace-plotly.js
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((file (assoc-ref inputs "plotly.js"))
+                    (installed "plotly/plotly.js"))
+               (let ((minified (open-pipe* OPEN_READ "uglify-js" file)))
+                 (call-with-output-file installed
+                   (cut dump-port minified <>))))
+             #t))
          (delete 'configure)
          (delete 'build)
          (replace 'install
@@ -11653,10 +11721,11 @@ (define-public bismark
                                "deduplicate_bismark"
                                "filter_non_conversion"
                                "bam2nuc"
-                               "bismark2summary")))
+                               "bismark2summary"
+                               "NOMe_filtering")))
                (substitute* "bismark2report"
-                 (("\\$RealBin/bismark_sitrep")
-                  (string-append share "/bismark_sitrep")))
+                 (("\\$RealBin/plotly")
+                  (string-append share "/plotly")))
                (mkdir-p share)
                (mkdir-p docdir)
                (mkdir-p bin)
@@ -11665,8 +11734,8 @@ (define-public bismark
                (for-each (lambda (file) (install-file file docdir))
                          docs)
                (copy-recursively "Docs/Images" (string-append docdir "/Images"))
-               (copy-recursively "bismark_sitrep"
-                                 (string-append share "/bismark_sitrep"))
+               (copy-recursively "plotly"
+                                 (string-append share "/plotly"))
 
                ;; Fix references to gunzip
                (substitute* (map (lambda (file)
@@ -11677,7 +11746,18 @@ (define-public bismark
                                  "/bin/gunzip -c")))
                #t))))))
     (inputs
-     `(("gzip" ,gzip)))
+     `(("gzip" ,gzip)
+       ("perl-carp" ,perl-carp)
+       ("perl-getopt-long" ,perl-getopt-long)))
+    (native-inputs
+     `(("plotly.js"
+        ,(origin
+           (method url-fetch)
+           (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/"
+                               "v1.39.4/dist/plotly.js"))
+           (sha256
+            (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
+       ("uglify-js" ,uglify-js)))
     (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
     (synopsis "Map bisulfite treated sequence reads and analyze methylation")
     (description "Bismark is a program to map bisulfite treated sequencing
@@ -13135,6 +13215,38 @@ (define-public pigx
 HTML reports with interesting findings about your samples.")
     (license license:gpl3+)))
 
+(define-public genrich
+  (package
+    (name "genrich")
+    (version "0.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jsh58/Genrich.git")
+                    (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/jsh58/Genrich")
+    (synopsis "Detecting sites of genomic enrichment")
+    (description "Genrich is a peak-caller for genomic enrichment
+assays (e.g. ChIP-seq, ATAC-seq).  It analyzes alignment files generated
+following the assay and produces a file detailing peaks of significant
+enrichment.")
+    (license license:expat)))
+
 (define-public mantis
   (let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84")
         (revision "1"))

gnu/packages/emacs-xyz.scm

@@ -13166,7 +13166,7 @@ (define-public emacs-redshank
 (define-public emacs-disk-usage
   (package
     (name "emacs-disk-usage")
-    (version "1.2.0")
+    (version "1.3.0")
     (home-page "https://gitlab.com/Ambrevar/emacs-disk-usage")
     (source
      (origin
@@ -13177,7 +13177,7 @@ (define-public emacs-disk-usage
              ".el"))
        (sha256
         (base32
-         "13n6bsrz8q07fl6sd7wi5zvf01m5xw11hmrpdz7wcn49v6vs3whl"))))
+         "0ky6c34z7c6hd4yvcrcsidkfk2kvffkg63v02vch2i6hg1n6n028"))))
     (build-system emacs-build-system)
     (synopsis "Sort and browse disk usage listings with Emacs")
     (description "Disk Usage is a file system analyzer: it offers a tabulated

gnu/packages/emacs.scm

@@ -251,8 +251,10 @@ (define-public emacs-no-x-toolkit
     (build-system gnu-build-system)
     (inputs (append `(("inotify-tools" ,inotify-tools))
                     (alist-delete "gtk+" (package-inputs emacs))))
-    (arguments (append '(#:configure-flags '("--with-x-toolkit=no"))
-                       (package-arguments emacs)))))
+    (arguments
+     `(,@(substitute-keyword-arguments (package-arguments emacs)
+           ((#:configure-flags cf)
+            `(cons "--with-x-toolkit=no" ,cf)))))))
 
 (define-public guile-emacs
   (let ((commit "41120e0f595b16387eebfbf731fff70481de1b4b")

gnu/packages/fonts.scm

@@ -344,33 +344,23 @@ (define-public font-linuxlibertine
 (define-public font-terminus
   (package
     (name "font-terminus")
-    (version "4.40")
+    (version "4.47")
     (source
-      (origin
-        (method url-fetch)
-        (uri (string-append
-               "mirror://sourceforge/terminus-font/terminus-font-"
-               version
-               "/terminus-font-"
-               version
-               ".tar.gz"))
-        (sha256
-         (base32
-          "0487cyx5h1f0crbny5sg73a22gmym5vk1i7646gy7hgiscj2rxb4"))))
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/terminus-font/terminus-font-"
+                           version "/terminus-font-" version ".tar.gz"))
+       (sha256
+        (base32 "15qjcpalcxjiwsjgjg5k88vkwp56cs2nnx4ghya6mqp4i1c206qg"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("perl" ,perl)
-       ("bdftopcf" ,bdftopcf)
+     `(("bdftopcf" ,bdftopcf)
        ("font-util" ,font-util)
-       ("mkfontdir" ,mkfontdir)))
+       ("mkfontdir" ,mkfontdir)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)))
     (arguments
-     `(#:configure-flags (list
-                          ;; install fonts into subdirectory of package output
-                          ;; instead of font-util-?.?.?/share/fonts/X11
-                          (string-append "--with-fontrootdir="
-                                         %output "/share/fonts/X11"))
-       #:tests? #f)) ;; No test target in tarball
+     `(#:tests? #f))                    ; no test target in tarball
     (home-page "http://terminus-font.sourceforge.net/")
     (synopsis "Simple bitmap programming font")
     (description "Terminus Font is a clean, fixed-width bitmap font, designed
@@ -505,12 +495,11 @@ (define-public font-wqy-zenhei
                     "mirror://sourceforge/wqy/wqy-zenhei/" version
                     "%20%28Fighting-state%20RC1%29/wqy-zenhei-"
                     version ".tar.gz"))
-              (file-name (string-append "wqy-zenhei-" version ".tar.gz"))
               (sha256
                (base32
                 "1mkmxq8g2hjcglb3zajfqj20r4r88l78ymsp2xyl5yav8w3f7dz4"))))
     (build-system font-build-system)
-    (home-page "http://wenq.org/wqy2/")
+    (home-page "https://wenq.org/wqy2/")
     (synopsis "CJK font")
     (description
      "WenQuanYi Zen Hei is a Hei-Ti style (sans-serif type) Chinese outline
@@ -522,7 +511,7 @@ (define-public font-wqy-zenhei
 full coverage of the GBK (CP936) charset, CJK Unified Ideographs, as well as
 the code-points needed for zh_cn, zh_sg, zh_tw, zh_hk, zh_mo, ja (Japanese) and
 ko (Korean) locales for @code{fontconfig}.")
-    ;; GPLv2 with font embedding exception
+    ;; GPLv2 with font embedding exception.
     (license license:gpl2)))
 
 (define-public font-wqy-microhei
@@ -607,13 +596,13 @@ (define-public font-anonymous-pro
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://www.marksimonson.com/assets/content/fonts/"
+                    "https://www.marksimonson.com/assets/content/fonts/"
                     "AnonymousPro-" version ".zip"))
               (sha256
                (base32
                 "1asj6lykvxh46czbal7ymy2k861zlcdqpz8x3s5bbpqwlm3mhrl6"))))
     (build-system font-build-system)
-    (home-page "http://www.marksimonson.com/fonts/view/anonymous-pro")
+    (home-page "https://www.marksimonson.com/fonts/view/anonymous-pro")
     (synopsis "Fixed-width fonts designed with coding in mind")
     (description "Anonymous Pro is a family of four fixed-width fonts designed
 with coding in mind.  Anonymous Pro features an international, Unicode-based
@@ -948,7 +937,7 @@ (define-public font-fira-sans
 (define-public font-fira-code
   (package
     (name "font-fira-code")
-    (version "1.205")
+    (version "1.206")
     (source (origin
               (method url-fetch/zipbomb)
               (uri (string-append "https://github.com/tonsky/FiraCode/releases/"
@@ -956,7 +945,7 @@ (define-public font-fira-code
                                   "/FiraCode_" version ".zip"))
               (sha256
                (base32
-                "13bxgf59g6fw5191xclcjzn22hj8jk9k5jjwf7vz07mpjbgadcl5"))))
+                "02r1lcp0c9135ps71v66wdvbsrcxwirrp0blqsa1xbjkkq2rwgj3"))))
     (build-system font-build-system)
     (home-page "https://mozilla.github.io/Fira/")
     (synopsis "Monospaced font with programming ligatures")

gnu/packages/games.scm

@@ -4411,7 +4411,7 @@ (define-public fillets-ng
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.22.1")
+    (version "0.23.1")
     (source
      (origin
        (method url-fetch)
@@ -4425,7 +4425,7 @@ (define-public crawl
                             version "-nodeps.tar.xz")))
        (sha256
         (base32
-         "1qc90wwbxvjzqq66n8kfr0a2ny7sfvv2n84si67jiv2887d0ws6k"))
+         "0c3mx49kpz6i2xvv2dwsaj9s7mm4mif1h2qdkfyi80lv2j1ay51h"))
        (patches (search-patches "crawl-upgrade-saves.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -4437,6 +4437,8 @@ (define-public crawl
      `(("bison" ,bison)
        ("flex" ,flex)
        ("perl" ,perl)
+       ("python" ,python)
+       ("python-pyyaml" ,python-pyyaml)
        ("pkg-config" ,pkg-config)))
     (arguments
      '(#:make-flags
@@ -4452,16 +4454,19 @@ (define-public crawl
                "-Csource"))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'patch-python
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "source/util/species-gen.py"
+               (("python") "python3"))
+             #t))
          (delete 'configure)
-         (delete 'check)
-         ;; Test cases require the source to be rebuild with the -DDEBUG define.
-         ;; Do 'check before 'build to avoid a 3rd build on make install.
-         (add-before 'build 'check
+         (replace 'check
            (lambda* (#:key inputs outputs make-flags #:allow-other-keys)
              (setenv "HOME" (getcwd))
              ;; Fake a terminal for the test cases.
              (setenv "TERM" "xterm-256color")
-             (apply invoke "make" "debug" "test"
+             ;; Run the tests that don't require a debug build.
+             (apply invoke "make" "nondebugtest"
                     (format #f "-j~d" (parallel-job-count))
                     ;; Force command line build for test cases.
                     (append make-flags '("GAME=crawl" "TILES="))))))))

gnu/packages/gimp.scm

@@ -80,7 +80,7 @@ (define-public babl
 (define-public gegl
   (package
     (name "gegl")
-    (version "0.4.12")
+    (version "0.4.14")
     (source (origin
               (method url-fetch)
               (uri (list (string-append "https://download.gimp.org/pub/gegl/"
@@ -88,7 +88,7 @@ (define-public gegl
                                         "/gegl-" version ".tar.bz2")))
               (sha256
                (base32
-                "0ljqxc4iyy2hrj31pxcy1xp4xm5zbx1nigqisphmg4p8mcz2jrz9"))))
+                "00crhngwi07f5b9x77kx5p7p4cl6l5g6glpz9rqv7pfqk62xa0ac"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("LDFLAGS=-lm")))

gnu/packages/gl.scm

@@ -9,7 +9,7 @@
 ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -718,7 +718,7 @@ (define-public gl2ps
 (define-public virtualgl
   (package
     (name "virtualgl")
-    (version "2.6")
+    (version "2.6.1")
     (source
      (origin
        (method git-fetch)
@@ -727,8 +727,7 @@ (define-public virtualgl
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0di2igj2bhwb153fndgxks7y57pyhp0gj31n47j93gb7lxc9qcck"))))
+        (base32 "04fdwm6mz76lw4iwd5m7yxjfhpa0rpxd357bv5smk5lclnlbz1bv"))))
     (arguments
      `(#:tests? #f                      ; no tests are available
        #:configure-flags (list

gnu/packages/gnome.scm

@@ -6708,16 +6708,16 @@ (define-public arc-icon-theme
 (define-public folks
   (package
     (name "folks")
-    (version "0.11.2")
+    (version "0.11.4")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "mirror://gnome/sources/" name "/"
+                    "mirror://gnome/sources/folks/"
                     (version-major+minor version) "/"
-                    name "-" version ".tar.xz"))
+                    "folks-" version ".tar.xz"))
               (sha256
                (base32
-                "1f51albxgfqxbax57i3pcgv2fx7i419xaapzdvldas6gw100ma1m"))))
+                "16hqh2gxlbx0b0hgq216hndr1m72vj54jvryzii9zqkk0g9kxc57"))))
     (build-system glib-or-gtk-build-system)
     (inputs
      `(("bdb" ,bdb)

gnu/packages/golang.scm

@@ -668,7 +668,7 @@ (define-public go-gopkg.in-tomb.v2
 (define-public go-github.com-jtolds-gls
   (package
     (name "go-github.com-jtolds-gls")
-    (version "4.2.1")
+    (version "4.20")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -677,7 +677,7 @@ (define-public go-github.com-jtolds-gls
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1vm37pvn0k4r6d3m620swwgama63laz8hhj3pyisdhxwam4m2g1h"))))
+                "1k7xd2q2ysv2xsh373qs801v6f359240kx0vrl0ydh7731lngvk6"))))
     (build-system go-build-system)
     (arguments
      '(#:import-path "github.com/jtolds/gls"))

gnu/packages/guile-xyz.scm

@@ -49,9 +49,11 @@ (define-module (gnu packages guile-xyz)
   #:use-module (gnu packages disk)
   #:use-module (gnu packages ed)
   #:use-module (gnu packages emacs)
+  #:use-module (gnu packages emacs-xyz)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
+  #:use-module (gnu packages gnome)
   #:use-module (gnu packages gperf)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages hurd)
@@ -2000,3 +2002,58 @@ (define-public guile-picture-language
        "This package provides a simple SVG-based picture language for Guile.
 The picture values can directly be displayed in Geiser.")
       (license license:lgpl3+))))
+
+(define-public guile-studio
+  (let ((commit "e2da64f014942a73996286c4abe3c3b1f8bd220c")
+        (revision "1"))
+    (package
+      (name "guile-studio")
+      (version (git-version "0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.elephly.net/software/guile-studio.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "10v3kw41bzd8c2a6vxgrwbvl216d0k8f5s9h6pm8hahpd03jl7lm"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                      ; there are none
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (replace 'build
+             (lambda* (#:key source inputs outputs #:allow-other-keys)
+               (let* ((out   (assoc-ref outputs "out"))
+                      (bin   (string-append out "/bin/"))
+                      (share (string-append out "/share/")))
+                 (mkdir-p share)
+                 (mkdir-p bin)
+                 (apply invoke "guile" "-s" "guile-studio-configure.scm"
+                        out
+                        (assoc-ref inputs "emacs")
+                        (assoc-ref inputs "guile-picture-language")
+                        (string-append (assoc-ref inputs "adwaita-icon-theme")
+                                       "/share/icons/Adwaita/")
+                        (map cdr inputs))
+                 #t)))
+           (delete 'install))))
+      (inputs
+       `(("guile" ,guile-2.2)
+         ("guile-picture-language" ,guile-picture-language)
+         ("emacs" ,emacs)
+         ("emacs-geiser" ,emacs-geiser)
+         ("emacs-company" ,emacs-company)
+         ("emacs-flycheck" ,emacs-flycheck)
+         ("emacs-smart-mode-line" ,emacs-smart-mode-line)
+         ("emacs-paren-face" ,emacs-paren-face)
+         ("adwaita-icon-theme" ,adwaita-icon-theme)))
+      (home-page "https://gnu.org/software/guile")
+      (synopsis "IDE for Guile")
+      (description
+       "This is Emacs with a few settings that make working with Guile easier
+for people new to Emacs.  Features include: CUA mode, Geiser, tool bar icons
+to evaluate Guile buffers, support for Guile's very own picture language, code
+completion, a simple mode line, etc.")
+      (license license:gpl3+))))

gnu/packages/java.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
@@ -5452,7 +5452,7 @@ (define-public java-eclipse-osgi
 (define-public java-eclipse-equinox-common
   (package
     (name "java-eclipse-equinox-common")
-    (version "3.8.0")
+    (version "3.10.200")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://repo1.maven.org/maven2/"
@@ -5461,7 +5461,7 @@ (define-public java-eclipse-equinox-common
                                   version "-sources.jar"))
               (sha256
                (base32
-                "12aazpkgw46r1qj0pr421jzwhbmsizd97r37krd7njnbrdgfzksc"))))
+                "1yn8ij6xsljlf35sr2l7wvyvc0ss4n1rv0ry5zkgb49dj4hyrqrj"))))
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f ; no tests included
@@ -5611,7 +5611,7 @@ (define-public java-eclipse-core-contenttype
 (define-public java-eclipse-core-runtime
   (package
     (name "java-eclipse-core-runtime")
-    (version "3.12.0")
+    (version "3.15.100")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://repo1.maven.org/maven2/"
@@ -5620,7 +5620,7 @@ (define-public java-eclipse-core-runtime
                                   version "-sources.jar"))
               (sha256
                (base32
-                "16mkf8jgj35pgzms7w1gyfq0gfm4ixw6c5xbbxzdj1la56c758ya"))))
+                "0l8xayacsbjvz5hypx2fv47vpw2n4dspamcfb3hx30x9hj8vmg7r"))))
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f ; no tests included
@@ -5759,7 +5759,7 @@ (define-public java-eclipse-ant-core
 (define-public java-eclipse-core-resources
   (package
     (name "java-eclipse-core-resources")
-    (version "3.11.1")
+    (version "3.13.200")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://repo1.maven.org/maven2/"
@@ -5768,7 +5768,7 @@ (define-public java-eclipse-core-resources
                                   version "-sources.jar"))
               (sha256
                (base32
-                "1hrfxrll6cpcagfksk2na1ypvkcnsp0fk6n3vcsrn97qayf9mx9l"))))
+                "1sn3b6ky72hkvxcgf9b2jkpbdh3y8lbhi9xxwv1dsiddpkkq91hs"))))
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f ; no tests included
@@ -5935,7 +5935,7 @@ (define-public java-eclipse-text
 (define-public java-eclipse-jdt-core
   (package
     (name "java-eclipse-jdt-core")
-    (version "3.12.3")
+    (version "3.16.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://repo1.maven.org/maven2/"
@@ -5944,11 +5944,28 @@ (define-public java-eclipse-jdt-core
                                   version "-sources.jar"))
               (sha256
                (base32
-                "191xw4lc7mjjkprh4ji5vnpjvr5r4zvbpwkriy4bvsjqrz35vh1j"))))
+                "1g560yr9v2kzv34gc2m3ifpgnj7krcdd6h4gd4z83pwqacwkfz0k"))))
     (build-system ant-build-system)
     (arguments
      `(#:tests? #f ; no tests included
-       #:jar-name "eclipse-jdt-core.jar"))
+       #:jar-name "eclipse-jdt-core.jar"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'move-sources
+           (lambda _
+             (with-directory-excursion "src/jdtCompilerAdaptersrc/"
+               (for-each (lambda (file)
+                           (install-file file (string-append "../" (dirname file))))
+                         (find-files "." ".*")))
+             (delete-file-recursively "src/jdtCompilerAdaptersrc/")
+             #t))
+         (add-before 'build 'copy-resources
+           (lambda _
+             (with-directory-excursion "src"
+               (for-each (lambda (file)
+                           (install-file file (string-append "../build/classes/" (dirname file))))
+                         (find-files "." ".*.(props|properties|rsc)")))
+             #t)))))
     (inputs
      `(("java-eclipse-core-contenttype" ,java-eclipse-core-contenttype)
        ("java-eclipse-core-filesystem" ,java-eclipse-core-filesystem)

gnu/packages/linux.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Mark H Weaver <mhw@netris.org>
@@ -98,6 +98,7 @@ (define-module (gnu packages linux)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages rrdtool)
   #:use-module (gnu packages samba)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages slang)
   #:use-module (gnu packages storage)
   #:use-module (gnu packages texinfo)
@@ -2486,14 +2487,14 @@ (define-public lm-sensors
 (define-public iucode-tool
   (package
     (name "iucode-tool")
-    (version "2.2")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.com/iucode-tool/releases"
                                   "/raw/latest/iucode-tool_" version ".tar.xz"))
               (sha256
                (base32
-                "0w99k1aq1xw148ffk1xykqf60rdbphb1jknw98jcmadq4pwxl44q"))))
+                "159gvf6ljgg3g4vlhyy6pyr0wz11rcyhp985vc4az58d9px8xf0j"))))
     (build-system gnu-build-system)
     (home-page "https://gitlab.com/iucode-tool/iucode-tool/wikis/home")
     (synopsis "Manipulate Intel microcode bundles")
@@ -2662,7 +2663,22 @@ (define-public singularity
                                   "/singularity-" version ".tar.gz"))
               (sha256
                (base32
-                "1whx0hqqi1326scgdxxxa1d94vn95mnq0drid6s8wdp84ni4d3gk"))))
+                "1whx0hqqi1326scgdxxxa1d94vn95mnq0drid6s8wdp84ni4d3gk"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Do not create directories in /var.
+                  (substitute* "Makefile.in"
+                    (("\\$\\(MAKE\\) .*install-data-hook") ""))
+
+                  ;; The original source overrides PATH so that it points to
+                  ;; /bin, /usr/local/bin, etc., which obviously doesn't work
+                  ;; on Guix System.  Leave PATH unchanged so we refer to the
+                  ;; installed Coreutils, grep, etc.
+                  (substitute* "bin/singularity.in"
+                    (("^PATH=.*" all)
+                     (string-append "#" all "\n")))
+                  #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -2670,12 +2686,6 @@ (define-public singularity
              "--localstatedir=/var")
        #:phases
        (modify-phases %standard-phases
-         ;; Do not create directories in /var.
-         (add-after 'unpack 'disable-install-hook
-           (lambda _
-             (substitute* "Makefile.in"
-               (("\\$\\(MAKE\\) .*install-data-hook") ""))
-             #t))
          (add-after 'unpack 'patch-reference-to-squashfs-tools
            (lambda _
              (substitute* "libexec/cli/build.exec"
@@ -3251,6 +3261,32 @@ (define-public fuse-exfat
 write access to exFAT devices.")
     (license license:gpl2+)))
 
+(define-public fuseiso
+  (package
+    (name "fuseiso")
+    (version "20070708")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/fuseiso/fuseiso/"
+                                  version "/fuseiso-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "127xql52dcdhmh7s5m9xc6q39jdlj3zhbjar1j821kb6gl3jw94b"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("fuse" ,fuse)
+       ("glib" ,glib)
+       ("zlib" ,zlib)))
+    (home-page "https://sourceforge.net/projects/fuseiso/")
+    (synopsis "Mount ISO file system images")
+    (description
+     "FuseISO is a FUSE module to mount ISO filesystem images (.iso, .nrg,
+.bin, .mdf and .img files).  It currently support plain ISO9660 Level 1 and 2,
+Rock Ridge, Joliet, and zisofs.")
+    (license license:gpl2)))
+
 (define-public gpm
   (package
     (name "gpm")
@@ -3299,7 +3335,7 @@ (define-public gpm
 (define-public btrfs-progs
   (package
     (name "btrfs-progs")
-    (version "4.17.1")
+    (version "4.20.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -3307,7 +3343,7 @@ (define-public btrfs-progs
                                   "btrfs-progs-v" version ".tar.xz"))
               (sha256
                (base32
-                "0x6d53fbrcmzvhv461575fzsv3373427p4srz646w2wcagqk82xz"))))
+                "0z0fm3j4ajzsf445381ra8r3zzciyyvfh8vvbjmbyarg2rz8n3w9"))))
     (build-system gnu-build-system)
     (outputs '("out"
                "static"))      ; static versions of the binaries in "out"
@@ -3402,7 +3438,7 @@ (define-public f2fs-tools-1.7
               (method url-fetch)
               (uri (string-append
                     "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk"
-                    "/f2fs-tools.git/snapshot/" name "-" version ".tar.gz"))
+                    "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz"))
               (sha256
                (base32
                 "1m6bn1ibq0p53m0n97il91xqgjgn2pzlz74lb5bfzassx7159m1k"))))
@@ -3440,15 +3476,15 @@ (define-public f2fs-tools
   (package
     (inherit f2fs-tools-1.7)
     (name "f2fs-tools")
-    (version "1.11.0")
+    (version "1.12.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "https://git.kernel.org/cgit/linux/kernel/git/jaegeuk"
-                    "/f2fs-tools.git/snapshot/" name "-" version ".tar.gz"))
+                    "/f2fs-tools.git/snapshot/f2fs-tools-" version ".tar.gz"))
               (sha256
                (base32
-                "1qvr3hcic1vzfmyl7c0gnjxfsw8zjaadm66y337h49chv9yaq5mr"))))
+                "15pn2fm9knn7p1vzfzy6msnrdl14p6y1gn4m2ka6ba5bzx6lw4p2"))))
     (inputs
      `(("libuuid" ,util-linux)))))
 
@@ -3490,49 +3526,51 @@ (define-public freefall
 (define-public thinkfan
   (package
     (name "thinkfan")
-    (version "0.9.3")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://sourceforge/thinkfan/"
-                                  "/thinkfan-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0nz4c48f0i0dljpk5y33c188dnnwg8gz82s4grfl8l64jr4n675n"))
-              (modules '((guix build utils)))
-              ;; Fix erroneous man page location in Makefile leading to
-              ;; a compilation failure.
-              (snippet '(begin
-                          (substitute* "CMakeLists.txt"
-                            (("thinkfan\\.1") "src/thinkfan.1"))
-                          #t))))
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/vmatare/thinkfan.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "107vw0962hrwva3wra9n3hxlbfzg82ldc10qssv3dspja88g8psr"))))
     (build-system cmake-build-system)
     (arguments
      `(#:modules ((guix build cmake-build-system)
                   (guix build utils)
                   (srfi srfi-26))
-       #:tests? #f                      ;no test target
+       #:tests? #f                      ; no test target
        #:configure-flags
        ;; Enable reading temperatures from hard disks via S.M.A.R.T.
+       ;; Upstream ‘defaults to OFF because libatasmart seems to be horribly
+       ;; inefficient’.
        `("-DUSE_ATASMART:BOOL=ON")
        #:phases
        (modify-phases %standard-phases
-         ;; Install scripts for various foreign init systems. Also fix
-         ;; hard-coded path for daemon.
-         (add-after 'install 'install-rc-scripts
+         (add-after 'unpack 'create-init-scripts
+           ;; CMakeLists.txt relies on build-time symptoms of OpenRC and
+           ;; systemd to patch and install their service files.  Fake their
+           ;; presence rather than duplicating the build system below.  Leave
+           ;; things like ‘/bin/kill’ because they're not worth a dependency.
+           ;; The sysvinit needs manual patching, but since upstream doesn't
+           ;; even provide the option to install it: don't.
            (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (files (find-files
-                           (string-append "../thinkfan-" ,version "/rcscripts")
-                           ".*")))
-               (substitute* files
-                 (("/usr/sbin/(\\$NAME|thinkfan)" _ name)
-                  (string-append out "/sbin/" name)))
-               (for-each (cute install-file <>
-                               (string-append out "/share/thinkfan"))
-                         files))
-             #t)))))
+             (let* ((out   (assoc-ref outputs "out"))
+                    (share (string-append out "/share/" ,name)))
+               (substitute* "CMakeLists.txt"
+                 (("pkg_check_modules\\((OPENRC|SYSTEMD) .*" _ package)
+                  (format "option(~a_FOUND \"Faked\" ON)\n" package))
+                 ;; That was easy!  Now we just need to fix the destinations.
+                 (("/etc" directory)
+                  (string-append out directory)))
+               #t))))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (inputs
-     `(("libatasmart" ,libatasmart)))
+     `(("libatasmart" ,libatasmart)
+       ("yaml-cpp" ,yaml-cpp)))
     (home-page "http://thinkfan.sourceforge.net/")
     (synopsis "Simple fan control program")
     (description
@@ -4387,15 +4425,14 @@ (define-public libmnl
 (define-public libnftnl
   (package
     (name "libnftnl")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
-      (origin
-        (method url-fetch)
-        (uri (string-append "mirror://netfilter.org/libnftnl/"
-                            "libnftnl-" version ".tar.bz2"))
-        (sha256
-         (base32
-          "1wmgjfcb35mscb2srzia5931srygywrs1aznxmg67v177x0nasjx"))))
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://netfilter.org/libnftnl/"
+                           "libnftnl-" version ".tar.bz2"))
+       (sha256
+        (base32 "0pffmsv41alsn5ac7mwnb9fh3qpwzqk13jrzn6c5i71wq6kbgix5"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -5023,7 +5060,7 @@ (define-public libnfnetlink
 (define-public xfsprogs
   (package
     (name "xfsprogs")
-    (version "4.19.0")
+    (version "4.20.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -5031,10 +5068,10 @@ (define-public xfsprogs
                     "xfsprogs-" version ".tar.gz"))
               (sha256
                (base32
-                "0gs39yiyamjw516jbak3nj4dy4h2a2g48c1mmv4wbppsccvwmwh5"))))
+                "0ss0r6jlxxinf9fhpc0fgf7b89n9mzirpa85xxjmi1ix9l6cls6x"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f)) ; Kernel/user integration tests are in package "xfstests"
+     `(#:tests? #f)) ; kernel/user integration tests are in package "xfstests"
     (native-inputs
      `(("gettext" ,gettext-minimal)
        ("util-linux" ,util-linux)))
@@ -5049,17 +5086,34 @@ (define-public xfsprogs
 (define-public genext2fs
   (package
     (name "genext2fs")
-    (version "1.4.1")
+    (version "1.4.1-4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/jeremie-koenig/genext2fs.git")
-                    (commit (string-append "genext2fs-" version))))
+                    ;; 1.4.1-3 had a VCS tag but 1.4.1-4 doesn't.
+                    (commit "9ee43894634998b0b2b309d636f25c64314c9421")))
               (file-name (git-file-name name version))
               (sha256
-               (base32
-                "1r0n74pyypv63qfqqpvx75dwijcsvcrvqrlv8sldbhv0nwr1gk53"))))
+               (base32 "0ib5icn78ciz00zhc1bgdlrwaxvsdz7wnplwblng0jirwi9ml7sq"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'apply-debian-patches
+           ;; Debian changes (the revision after ‘-’ in VERSION) are
+           ;; maintained as separate patches.  Apply those relevant to us.
+           (lambda _
+             (for-each
+              (lambda (file-name)
+                (invoke "patch" "-p1" "-i"
+                        (string-append "debian/patches/" file-name)))
+              (list "blocksize+creator.diff" ; add -B/-o options
+                    "byteswap_fix.diff"))
+             #t)))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
     (home-page "https://github.com/jeremie-koenig/genext2fs")
     (synopsis "Generate ext2 filesystem as a normal user")
     (description "This package provides a program to general an ext2

gnu/packages/man.scm

@@ -241,7 +241,7 @@ (define-public help2man/latest
 (define-public scdoc
   (package
    (name "scdoc")
-   (version "1.8.1")
+   (version "1.9.4")
    (source
     (origin
      (method url-fetch)
@@ -250,7 +250,7 @@ (define-public scdoc
      (file-name (string-append name "-" version ".tar.gz"))
      (sha256
       (base32
-       "1f3qrnbjr9ikbdvpsyx726nyiz4f7ka38rimy9fvbl7kmi62w1v7"))))
+       "00zc3rzj97gscby31djlqyczvqpyhrl66i44czwzmmn7rc5j03m1"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags '("CC=gcc")

gnu/packages/maths.scm

@@ -1397,7 +1397,7 @@ (define-public ceres
 (define-public octave-cli
   (package
     (name "octave-cli")
-    (version "4.4.1")
+    (version "5.1.0")
     (source
      (origin
       (method url-fetch)
@@ -1405,7 +1405,7 @@ (define-public octave-cli
                           version ".tar.lz"))
       (sha256
        (base32
-        "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
+        "11wwxpy2q1bhxs2v41bqn05i2sb0905cj1xil6mg8l4k2kka4cq6"))))
     (build-system gnu-build-system)
     (inputs
      `(("lapack" ,lapack)

gnu/packages/mpd.scm

@@ -91,7 +91,7 @@ (define-public libmpdclient
 (define-public mpd
   (package
     (name "mpd")
-    (version "0.21.4")
+    (version "0.21.5")
     (source (origin
               (method url-fetch)
               (uri
@@ -100,7 +100,7 @@ (define-public mpd
                               "/mpd-" version ".tar.xz"))
               (sha256
                (base32
-                "1ix52vfa8k8my4xyr8b0phg8605b2xchyzyva908m08vpzm14w94"))))
+                "1y8fbch4xp96i4mz6czivnwvaf7g8pnfix5d0pbybnkv7bmz1a9f"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=true") ; The default is 'false'...

gnu/packages/patches/rust-1.30-gdb-llvm.patch

@@ -0,0 +1,89 @@
+Tweak some gdb tests which were broken during LLVM upgrades.
+This has been subsequently fixed upstream in later rustc versions,
+but still needed to bootstrap some earlier versions of the compiler.
+
+diff -r -u rustc-1.30.1-src-orig/src/test/debuginfo/borrowed-c-style-enum.rs rustc-1.30.1-src/src/test/debuginfo/borrowed-c-style-enum.rs
+--- rustc-1.30.1-src-orig/src/test/debuginfo/borrowed-c-style-enum.rs	2019-02-04 12:49:34.055483896 -0800
++++ rustc-1.30.1-src/src/test/debuginfo/borrowed-c-style-enum.rs	2019-02-04 13:01:10.915950356 -0800
+@@ -18,15 +18,15 @@
+ 
+ // gdb-command:print *the_a_ref
+ // gdbg-check:$1 = TheA
+-// gdbr-check:$1 = borrowed_c_style_enum::ABC::TheA
++// gdbr-check:$1 = borrowed_c_style_enum::TheA
+ 
+ // gdb-command:print *the_b_ref
+ // gdbg-check:$2 = TheB
+-// gdbr-check:$2 = borrowed_c_style_enum::ABC::TheB
++// gdbr-check:$2 = borrowed_c_style_enum::TheB
+ 
+ // gdb-command:print *the_c_ref
+ // gdbg-check:$3 = TheC
+-// gdbr-check:$3 = borrowed_c_style_enum::ABC::TheC
++// gdbr-check:$3 = borrowed_c_style_enum::TheC
+ 
+ 
+ // === LLDB TESTS ==================================================================================
+diff -r -u rustc-1.30.1-src-orig/src/test/debuginfo/c-style-enum-in-composite.rs rustc-1.30.1-src/src/test/debuginfo/c-style-enum-in-composite.rs
+--- rustc-1.30.1-src-orig/src/test/debuginfo/c-style-enum-in-composite.rs	2019-02-04 12:49:34.051483727 -0800
++++ rustc-1.30.1-src/src/test/debuginfo/c-style-enum-in-composite.rs	2019-02-04 13:02:00.981997525 -0800
+@@ -19,31 +19,31 @@
+ 
+ // gdb-command:print tuple_interior_padding
+ // gdbg-check:$1 = {__0 = 0, __1 = OneHundred}
+-// gdbr-check:$1 = (0, c_style_enum_in_composite::AnEnum::OneHundred)
++// gdbr-check:$1 = (0, c_style_enum_in_composite::OneHundred)
+ 
+ // gdb-command:print tuple_padding_at_end
+ // gdbg-check:$2 = {__0 = {__0 = 1, __1 = OneThousand}, __1 = 2}
+-// gdbr-check:$2 = ((1, c_style_enum_in_composite::AnEnum::OneThousand), 2)
++// gdbr-check:$2 = ((1, c_style_enum_in_composite::OneThousand), 2)
+ 
+ // gdb-command:print tuple_different_enums
+ // gdbg-check:$3 = {__0 = OneThousand, __1 = MountainView, __2 = OneMillion, __3 = Vienna}
+-// gdbr-check:$3 = (c_style_enum_in_composite::AnEnum::OneThousand, c_style_enum_in_composite::AnotherEnum::MountainView, c_style_enum_in_composite::AnEnum::OneMillion, c_style_enum_in_composite::AnotherEnum::Vienna)
++// gdbr-check:$3 = (c_style_enum_in_composite::OneThousand, c_style_enum_in_composite::MountainView, c_style_enum_in_composite::OneMillion, c_style_enum_in_composite::Vienna)
+ 
+ // gdb-command:print padded_struct
+ // gdbg-check:$4 = {a = 3, b = OneMillion, c = 4, d = Toronto, e = 5}
+-// gdbr-check:$4 = c_style_enum_in_composite::PaddedStruct {a: 3, b: c_style_enum_in_composite::AnEnum::OneMillion, c: 4, d: c_style_enum_in_composite::AnotherEnum::Toronto, e: 5}
++// gdbr-check:$4 = c_style_enum_in_composite::PaddedStruct {a: 3, b: c_style_enum_in_composite::OneMillion, c: 4, d: c_style_enum_in_composite::Toronto, e: 5}
+ 
+ // gdb-command:print packed_struct
+ // gdbg-check:$5 = {a = 6, b = OneHundred, c = 7, d = Vienna, e = 8}
+-// gdbr-check:$5 = c_style_enum_in_composite::PackedStruct {a: 6, b: c_style_enum_in_composite::AnEnum::OneHundred, c: 7, d: c_style_enum_in_composite::AnotherEnum::Vienna, e: 8}
++// gdbr-check:$5 = c_style_enum_in_composite::PackedStruct {a: 6, b: c_style_enum_in_composite::OneHundred, c: 7, d: c_style_enum_in_composite::Vienna, e: 8}
+ 
+ // gdb-command:print non_padded_struct
+ // gdbg-check:$6 = {a = OneMillion, b = MountainView, c = OneThousand, d = Toronto}
+-// gdbr-check:$6 = c_style_enum_in_composite::NonPaddedStruct {a: c_style_enum_in_composite::AnEnum::OneMillion, b: c_style_enum_in_composite::AnotherEnum::MountainView, c: c_style_enum_in_composite::AnEnum::OneThousand, d: c_style_enum_in_composite::AnotherEnum::Toronto}
++// gdbr-check:$6 = c_style_enum_in_composite::NonPaddedStruct {a: c_style_enum_in_composite::OneMillion, b: c_style_enum_in_composite::MountainView, c: c_style_enum_in_composite::OneThousand, d: c_style_enum_in_composite::Toronto}
+ 
+ // gdb-command:print struct_with_drop
+ // gdbg-check:$7 = {__0 = {a = OneHundred, b = Vienna}, __1 = 9}
+-// gdbr-check:$7 = (c_style_enum_in_composite::StructWithDrop {a: c_style_enum_in_composite::AnEnum::OneHundred, b: c_style_enum_in_composite::AnotherEnum::Vienna}, 9)
++// gdbr-check:$7 = (c_style_enum_in_composite::StructWithDrop {a: c_style_enum_in_composite::OneHundred, b: c_style_enum_in_composite::Vienna}, 9)
+ 
+ // === LLDB TESTS ==================================================================================
+ 
+diff -r -u rustc-1.30.1-src-orig/src/test/debuginfo/gdb-pretty-struct-and-enums-pre-gdb-7-7.rs rustc-1.30.1-src/src/test/debuginfo/gdb-pretty-struct-and-enums-pre-gdb-7-7.rs
+--- rustc-1.30.1-src-orig/src/test/debuginfo/gdb-pretty-struct-and-enums-pre-gdb-7-7.rs	2019-02-04 12:49:34.043483393 -0800
++++ rustc-1.30.1-src/src/test/debuginfo/gdb-pretty-struct-and-enums-pre-gdb-7-7.rs	2019-02-04 13:02:17.954691634 -0800
+@@ -27,15 +27,15 @@
+ 
+ // gdb-command: print c_style_enum1
+ // gdbg-check:$3 = CStyleEnumVar1
+-// gdbr-check:$3 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnum::CStyleEnumVar1
++// gdbr-check:$3 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnumVar1
+ 
+ // gdb-command: print c_style_enum2
+ // gdbg-check:$4 = CStyleEnumVar2
+-// gdbr-check:$4 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnum::CStyleEnumVar2
++// gdbr-check:$4 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnumVar2
+ 
+ // gdb-command: print c_style_enum3
+ // gdbg-check:$5 = CStyleEnumVar3
+-// gdbr-check:$5 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnum::CStyleEnumVar3
++// gdbr-check:$5 = gdb_pretty_struct_and_enums_pre_gdb_7_7::CStyleEnumVar3
+ 
+ #![allow(dead_code, unused_variables)]

gnu/packages/perl.scm

@@ -1647,9 +1647,8 @@ (define-public perl-czplib
           (lambda* (#:key outputs #:allow-other-keys)
             (copy-recursively "."
                               (string-append (assoc-ref outputs "out")
-                                             "/plib/perl5/site_perl/"
-                                             ,(package-version perl)
-                                             "/czplib/"))
+                                             "/lib/perl5/site_perl/"
+                                             ,(package-version perl)))
             #t)))))
     (home-page "https://sourceforge.net/projects/czplib/")
     (synopsis "Library for genomic analysis")
@@ -1751,6 +1750,27 @@ (define-public perl-data-dump
 code that, when \"eval\"ed, produces a deep copy of the original arguments.")
     (license (package-license perl))))
 
+(define-public perl-data-dumper
+  (package
+    (name "perl-data-dumper")
+    (version "2.173")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/X/XS/XSAWYERX/"
+                           "Data-Dumper-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1yknbp86md6mjlhbs1lzz6mals3iyizndgiij58qx61hjfrhhxk9"))))
+    (build-system perl-build-system)
+    (home-page "https://metacpan.org/release/Data-Dumper")
+    (synopsis "Convert data structures to strings")
+    (description "Given a list of scalars or reference variables,
+@code{Data::Dumper} writes out their contents in Perl syntax.  The references
+can also be objects.  The content of each variable is output in a single Perl
+statement.  It handles self-referential structures correctly.")
+    (license perl-license)))
+
 (define-public perl-data-dumper-concise
   (package
     (name "perl-data-dumper-concise")

gnu/packages/python-xyz.scm

@@ -2631,14 +2631,14 @@ (define-public python-pydocstyle
 (define-public python-language-server
   (package
     (name "python-language-server")
-    (version "0.23.2")
+    (version "0.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "python-language-server" version))
        (sha256
         (base32
-         "1h83x5widj9p630ha9yv39cpp3djxppll3iww9nc8i3hdmyrbnnh"))))
+         "05zmv6jr7qbgnkz0lqh5pr7kr4lm12i8ljm2k5h5kz3q9m8d4mm0"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-pluggy" ,python-pluggy)
@@ -8032,7 +8032,7 @@ (define-public python-mako
      `(("python-mock" ,python-mock)
        ("python-nose" ,python-nose)
        ("python-pytest" ,python-pytest)))
-    (home-page "http://www.makotemplates.org/")
+    (home-page "https://www.makotemplates.org/")
     (synopsis "Templating language for Python")
     (description "Mako is a templating language for Python that compiles
 templates into Python modules.")

gnu/packages/ruby.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2017, 2018, 2019 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
+;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -4982,14 +4983,14 @@ (define-public ruby-rack-test
 (define-public ruby-rack-protection
   (package
     (name "ruby-rack-protection")
-    (version "2.0.3")
+    (version "2.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (rubygems-uri "rack-protection" version))
        (sha256
         (base32
-         "1z5598qipilmnf45428jnxi63ykrgvnyywa5ckpr52zv2vpd8jdp"))))
+         "15167q25rmxipqwi6hjqj3i1byi9iwl3xq9b7mdar7qiz39pmjsk"))))
     (build-system ruby-build-system)
     (arguments
      '(;; Tests missing from the gem.
@@ -8379,3 +8380,164 @@ (define-public ruby-sprockets
 serves JavaScript, CoffeeScript, CSS, LESS, Sass, and SCSS.")
     (home-page "https://github.com/rails/sprockets")
     (license license:expat)))
+
+(define-public ruby-mustermann
+  (package
+    (name "ruby-mustermann")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "mustermann" version))
+       (sha256
+        (base32
+         "0lycgkmnyy0bf29nnd2zql5a6pcf8sp69g9v4xw0gcfcxgpwp7i1"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; No tests.
+     '(#:tests? #f))
+    (synopsis "Library implementing patterns that behave like regular expressions")
+    (description "Given a string pattern, Mustermann will turn it into an
+object that behaves like a regular expression and has comparable performance
+characteristics.")
+    (home-page "https://github.com/sinatra/mustermann")
+    (license license:expat)))
+
+(define-public ruby-sinatra
+  (package
+    (name "ruby-sinatra")
+    (version "2.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "sinatra" version))
+       (sha256
+        (base32
+         "1gasgn5f15myv08k10i16p326pchxjsy37pgqfw0xm66kcc5d7ry"))))
+    (build-system ruby-build-system)
+    (propagated-inputs
+     `(("ruby-mustermann" ,ruby-mustermann)
+       ("ruby-rack" ,ruby-rack)
+       ("ruby-rack-protection" ,ruby-rack-protection)
+       ("ruby-tilt" ,ruby-tilt)))
+    (synopsis "DSL for quick web applications creation in Ruby")
+    (description
+     "Sinatra is a DSL for quickly creating web applications in Ruby with
+minimal effort.")
+    (home-page "http://sinatrarb.com/")
+    (license license:expat)))
+
+(define-public ruby-thin
+  (package
+    (name "ruby-thin")
+    (version "1.7.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "thin" version))
+       (sha256
+        (base32
+         "0nagbf9pwy1vg09k6j4xqhbjjzrg5dwzvkn4ffvlj76fsn6vv61f"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; No tests.
+     '(#:tests? #f))
+    (propagated-inputs
+     `(("ruby-daemons" ,ruby-daemons)
+       ("ruby-eventmachine" ,ruby-eventmachine)
+       ("ruby-rack" ,ruby-rack)))
+    (synopsis "Thin and fast web server for Ruby")
+    (description "Thin is a Ruby web server that glues together 3 Ruby libraries:
+@itemize
+@item the Mongrel parser,
+@item Event Machine, a network I/O library with high scalability, performance
+and stability,
+@item Rack, a minimal interface between webservers and Ruby frameworks.
+@end itemize\n")
+    (home-page "http://code.macournoyer.com/thin/")
+    (license license:ruby)))
+
+(define-public ruby-skinny
+  (package
+    (name "ruby-skinny")
+    (version "0.2.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "skinny" version))
+       (sha256
+        (base32
+         "1y3yvx88ylgz4d2s1wskjk5rkmrcr15q3ibzp1q88qwzr5y493a9"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f ; No included tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'patch-gemspec
+           (lambda _
+             (substitute* ".gemspec"
+               (("<eventmachine>.freeze, \\[\\\"~> 1.0.0\"")
+                "<eventmachine>, [\">= 1.0.0\"")
+               (("<thin>.freeze, \\[\\\"< 1.7\", ") "<thin>, ["))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-eventmachine" ,ruby-eventmachine)
+       ("ruby-thin" ,ruby-thin)))
+    (synopsis "Simple, upgradable WebSockets for Ruby Thin")
+    (description "Skinny is a simple, upgradable WebSockets for Ruby, using
+the Thin library.")
+    (home-page "https://github.com/sj26/skinny")
+    (license license:expat)))
+
+(define-public mailcatcher
+  (package
+    (name "mailcatcher")
+    (version "0.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "mailcatcher" version))
+       (sha256
+        (base32
+         "02w1ycyfv7x0sh9799lz7xa65p5qvl5z4pa8a7prb68h2zwkfq0n"))))
+    (build-system ruby-build-system)
+    (arguments
+     ;; Tests require web/assets which is not included in the output.  We
+     ;; might be able to fix this by adding the Git repository to the GEM_PATH
+     ;; of the tests.  See ruby-mysql2.
+     '(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'patch-gemspec
+           (lambda _
+             (substitute* ".gemspec"
+               (("<eventmachine>.freeze, \\[\\\"= 1.0.9.1")
+                "<eventmachine>, [\">= 1.0.9.1")
+               (("<rack>.freeze, \\[\\\"~> 1.5") "<rack>, [\">= 1.5")
+               (("<thin>.freeze, \\[\\\"~> 1.5.0") "<thin>, [\">= 1.5.0")
+               (("<sinatra>.freeze, \\[\\\"~> 1.2") "<sinatra>, [\">= 1.2"))
+             #t))
+         (add-before 'build 'loosen-dependency-contraint
+             (lambda _
+               (substitute* "lib/mail_catcher.rb"
+                 (("\"eventmachine\", \"1.0.9.1\"") "\"eventmachine\", \">= 1.0.9.1\"")
+                 (("\"rack\", \"~> 1.5\"") "\"rack\", \">= 1.5\"")
+                 (("\"thin\", \"~> 1.5.0\"") "\"thin\", \">= 1.5.0\"")
+                 (("\"sinatra\", \"~> 1.2\"") "\"sinatra\", \">= 1.2\""))
+               #t)))))
+    (inputs
+     `(("ruby-eventmachine" ,ruby-eventmachine)
+       ("ruby-mail" ,ruby-mail)
+       ("ruby-rack" ,ruby-rack)
+       ("ruby-sinatra" ,ruby-sinatra)
+       ("ruby-skinny" ,ruby-skinny)
+       ("ruby-sqlite3" ,ruby-sqlite3)
+       ("ruby-thin" ,ruby-thin)))
+    (synopsis "SMTP server which catches messages to display them a browser")
+    (description
+     "MailCatcher runs a super simple SMTP server which catches any message
+sent to it to display in a web interface.  Run mailcatcher, set your favourite
+app to deliver to smtp://127.0.0.1:1025 instead of your default SMTP server,
+then check out http://127.0.0.1:1080 to see the mail.")
+    (home-page "https://mailcatcher.me")
+    (license license:expat)))

gnu/packages/rust.scm

@@ -786,7 +786,7 @@ (define-public rust-1.28
              ;; The thinlto test should pass with llvm 6.
              (delete 'disable-thinlto-test))))))))
 
-(define-public rust
+(define-public rust-1.29
   (let ((base-rust
          (rust-bootstrapped-package rust-1.28 "1.29.2"
                                     "1jb787080z754caa2w3w1amsygs4qlzj9rs1vy64firfmabfg22h"
@@ -795,3 +795,84 @@ (define-public rust
                                       "rust-reproducible-builds.patch"))))
     (package
       (inherit base-rust))))
+
+(define-public rust-1.30
+  (let ((base-rust
+         (rust-bootstrapped-package rust-1.29 "1.30.1"
+                                    "0aavdc1lqv0cjzbqwl5n59yd0bqdlhn0zas61ljf38yrvc18k8rn"
+                                    #:patches
+                                    '("rust-1.25-accept-more-detailed-gdb-lines.patch"
+                                      "rust-1.30-gdb-llvm.patch"
+                                      "rust-reproducible-builds.patch"))))
+    (package
+      (inherit base-rust)
+      (inputs
+       ;; Use LLVM 7.0
+       (alist-replace "llvm" (list llvm)
+                      (package-inputs base-rust)))
+      (arguments
+       (substitute-keyword-arguments (package-arguments base-rust)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'patch-cargo-tests 'patch-cargo-env-shebang
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (let ((coreutils (assoc-ref inputs "coreutils")))
+                   (substitute* "src/tools/cargo/tests/testsuite/fix.rs"
+                     ;; Cargo has a test which explicitly sets a
+                     ;; RUSTC_WRAPPER environment variable which points
+                     ;; to /usr/bin/env. Since it's not a shebang, it
+                     ;; needs to be manually patched
+                     (("\"/usr/bin/env\"")
+                      (string-append "\"" coreutils "/bin/env\"")))
+                   #t)))
+             (add-after 'patch-cargo-env-shebang 'ignore-cargo-package-tests
+               (lambda* _
+                 (substitute* "src/tools/cargo/tests/testsuite/package.rs"
+                   ;; These tests largely check that cargo outputs warning/error
+                   ;; messages as expected. It seems that cargo outputs an
+                   ;; absolute path to something in the store instead of the
+                   ;; expected relative path (e.g. `[..]`) so we'll ignore
+                   ;; these for now
+                   (("fn include") "#[ignore]\nfn include")
+                   (("fn exclude") "#[ignore]\nfn exclude"))
+                   #t))
+             ;; Appears that this test isn't currently running and has been
+             ;; moved elsewhere, so the patch doesn't apply.
+             (delete 'disable-amd64-avx-test))))))))
+
+(define-public rust
+  (let ((base-rust
+         (rust-bootstrapped-package rust-1.30 "1.31.1"
+                                    "0sk84ff0cklybcp0jbbxcw7lk7mrm6kb6km5nzd6m64dy0igrlli"
+                                    #:patches
+                                    '("rust-1.25-accept-more-detailed-gdb-lines.patch"
+                                      "rust-1.30-gdb-llvm.patch"
+                                      "rust-reproducible-builds.patch"))))
+    (package
+      (inherit base-rust)
+      (arguments
+       (substitute-keyword-arguments (package-arguments base-rust)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-after 'patch-tests 'patch-command-exec-tests
+               (lambda* (#:key inputs #:allow-other-keys)
+                 (let ((coreutils (assoc-ref inputs "coreutils")))
+                   (substitute* "src/test/run-pass/command-exec.rs"
+                     ;; This test suite includes some tests that the stdlib's
+                     ;; `Command` execution properly handles situations where
+                     ;; the environment or PATH variable are empty, but this
+                     ;; fails since we don't have `echo` available in the usual
+                     ;; Linux directories.
+                     ;; NB: the leading space is so we don't fail a tidy check
+                     ;; for trailing whitespace, and the newlines are to ensure
+                     ;; we don't exceed the 100 chars tidy check as well
+                     ((" Command::new\\(\"echo\"\\)")
+                      (string-append "\nCommand::new(\"" coreutils "/bin/echo\")\n")))
+                   #t)))
+             (add-after 'patch-tests 'patch-process-docs-rev-cmd
+               (lambda* _
+                 ;; Disable some doc tests which depend on the "rev" command
+                 ;; https://github.com/rust-lang/rust/pull/58746
+                 (substitute* "src/libstd/process.rs"
+                   (("```rust") "```rust,no_run"))
+                 #t)))))))))

gnu/packages/syncthing.scm

@@ -30,7 +30,7 @@ (define-module (gnu packages syncthing)
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "1.0.1")
+    (version "1.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@ (define-public syncthing
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "0gas07lxm5d2c21axgcs90r779rj9sk3jymnnffxz457rvpr2qn3"))
+                "1iks1a3149gj89yqmqa5iry2ik2sj9sjhlhc6nfh7xq4swqgsrb5"))
               ;; Since the update to Go 1.11, Go programs have been keeping
               ;; spurious references to all their dependencies:
               ;; <https://bugs.gnu.org/33620>.

gnu/packages/uml.scm

@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2019 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,17 +30,17 @@ (define-module (gnu packages uml)
 (define-public plantuml
   (package
     (name "plantuml")
-    (version "1.2019.0")
+    (version "1.2019.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/plantuml/"
                                   version "/plantuml-" version ".tar.gz"))
               (sha256
                (base32
-                "0mws7g0w3fn0wxizccg2iqisq9ljkn95i5qf8ma07lbw3nj0h48n"))))
+                "0hqj2crf6yg40naiwlnnym4c6r0wbz5vr8729z0daggnyg8vqniz"))))
     (build-system ant-build-system)
     (arguments
-     `(#:tests? #f ; no tests
+     `(#:tests? #f                      ; no tests
        #:build-target "dist"
        #:phases
        (modify-phases %standard-phases

gnu/packages/valgrind.scm

@@ -35,13 +35,15 @@ (define-public valgrind
     (version "3.13.0")
     (source (origin
               (method url-fetch)
-             (uri (string-append "ftp://sourceware.org/pub/valgrind/valgrind-"
-                                 version ".tar.bz2"))
-             (sha256
-              (base32
-               "0fqc3684grrbxwsic1rc5ryxzxmigzjx9p5vf3lxa37h0gpq0rnp"))
-             (patches (search-patches "valgrind-enable-arm.patch"
-                                      "valgrind-glibc-compat.patch"))))
+              (uri (list (string-append "http://www.valgrind.org/downloads"
+                                        "/valgrind-" version ".tar.bz2")
+                         (string-append "ftp://sourceware.org/pub/valgrind"
+                                        "/valgrind-" version ".tar.bz2")))
+              (sha256
+               (base32
+                "0fqc3684grrbxwsic1rc5ryxzxmigzjx9p5vf3lxa37h0gpq0rnp"))
+              (patches (search-patches "valgrind-enable-arm.patch"
+                                       "valgrind-glibc-compat.patch"))))
     (build-system gnu-build-system)
     (outputs '("doc"                              ;16 MB
                "out"))

gnu/packages/video.scm

@@ -33,6 +33,7 @@
 ;;; Copyright © 2018 Gábor Boskovit <boskovits@gmail.com>
 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Timo Eisenmann <eisenmann@fn.de>
+;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -240,6 +241,43 @@ (define-public liba52
 television and DVD.  It is also known as AC-3.")
     (license license:gpl2+)))
 
+(define-public libaom
+  ;; The 1.0.0-errata1 release installs a broken pkg-config .pc file.  This
+  ;; is fixed in libaom commit 0ddc150, but we use an even later commit.
+  (let ((commit "22b150bf040608028a56d8bf39e72f771383d836")
+        (revision "0"))
+    (package
+      (name "libaom")
+      (version (git-version "1.0.0-errata1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://aomedia.googlesource.com/aom/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1pdd5h3n42607n6qmggz4yv8izhjr2kl6knb3kh7gh4v0vy47h1r"))))
+      (build-system cmake-build-system)
+      (native-inputs
+       `(("perl" ,perl)
+         ("pkg-config" ,pkg-config)
+         ("python" ,python))) ; to detect the version
+      (arguments
+       `(#:tests? #f  ;no check target
+         #:configure-flags
+           ;; build dynamic library
+         (list "-DBUILD_SHARED_LIBS=YES"
+               "-DENABLE_PIC=TRUE"
+               "-DAOM_TARGET_CPU=generic"
+               (string-append "-DCMAKE_INSTALL_PREFIX="
+                                (assoc-ref %outputs "out")))))
+      (home-page "https://aomedia.googlesource.com/aom/")
+      (synopsis "AV1 video codec")
+      (description "Libaom is the reference implementation of AV1.  It includes
+a shared library and encoder and decoder command-line executables.")
+      (license license:bsd-2))))
+
 (define-public libmpeg2
   (package
     (name "libmpeg2")
@@ -707,6 +745,7 @@ (define-public ffmpeg
        ("opus" ,opus)
        ("ladspa" ,ladspa)
        ("lame" ,lame)
+       ("libaom" ,libaom)
        ("libass" ,libass)
        ("libbluray" ,libbluray)
        ("libcaca" ,libcaca)
@@ -793,6 +832,7 @@ (define-public ffmpeg
          "--enable-fontconfig"
          "--enable-gnutls"
          "--enable-ladspa"
+         "--enable-libaom"
          "--enable-libass"
          "--enable-libbluray"
          "--enable-libcaca"
@@ -875,7 +915,13 @@ (define-public ffmpeg-3.4
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0b59qk5wpc5ksiha76jbhb859g5gxa4w0k6afh3kgvgajiivs73l"))))))
+               "0b59qk5wpc5ksiha76jbhb859g5gxa4w0k6afh3kgvgajiivs73l"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments ffmpeg)
+       ((#:configure-flags flags)
+        `(delete "--enable-libaom" ,flags))))
+    (inputs (alist-delete "libaom"
+                          (package-inputs ffmpeg)))))
 
 (define-public ffmpeg-for-stepmania
   (hidden-package
@@ -1366,7 +1412,7 @@ (define-public libvpx-1.7
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2019.02.18")
+    (version "2019.03.01")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/rg3/youtube-dl/releases/"
@@ -1374,7 +1420,7 @@ (define-public youtube-dl
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1sr0f6ixpaqyp3cf29zswx84y3nfabwnk3sljcgvgnmjp73zzfv1"))))
+                "0bxk6adyppdv50jnp5cika8wc6wfgd6d8zbg1njgmcs1pxskllmf"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
@@ -1485,7 +1531,7 @@ (define-public youtube-dl-gui
 (define-public you-get
   (package
     (name "you-get")
-    (version "0.4.1210")
+    (version "0.4.1256")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1494,7 +1540,7 @@ (define-public you-get
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1plw518hzpzzcr38phlnsbpq7aqnps8iwrgr68f6d41rppl1qb25"))))
+                "1hzr7ha1jvbc0v2bwl7s08ymwdmvb0f2jz4xp1fi6agq5y3ca1iv"))))
     (build-system python-build-system)
     (inputs
      `(("ffmpeg" ,ffmpeg)))             ; for multi-part and >=1080p videos
@@ -3319,15 +3365,20 @@ (define-public openshot
 (define-public dav1d
   (package
     (name "dav1d")
-    (version "0.1.0")
+    (version "0.2.0")
     (source
       (origin
         (method url-fetch)
-        (uri (string-append "https://downloads.videolan.org/pub/videolan/"
-                            "dav1d/" version "/dav1d-" version ".tar.xz"))
+        (uri (list ;; The canonical download site
+                   (string-append "https://downloads.videolan.org/pub/videolan/"
+                                  "dav1d/" version "/dav1d-" version ".tar.xz")
+
+                   ;; Auto-generated tarballs from the Git repo?
+                   (string-append "https://code.videolan.org/videolan/dav1d/-/"
+                                  "archive/" version "/dav1d-" version ".tar.bz2")))
         (sha256
          (base32
-          "0dw0liday8cbyrirhm6bgzhxg4cdy66nspfkdlq338gdsfqcvrsc"))))
+          "0q0dbbl91syjnkygz268gh4b7mdcgl6hldj300a4cbqidsadpl5p"))))
     (build-system meson-build-system)
     (native-inputs `(("nasm" ,nasm)))
     (home-page "https://code.videolan.org/videolan/dav1d")

gnu/packages/virtualization.scm

@@ -354,7 +354,7 @@ (define-public libosinfo
 (define-public lxc
   (package
     (name "lxc")
-    (version "3.0.2")
+    (version "3.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -362,7 +362,7 @@ (define-public lxc
                     version ".tar.gz"))
               (sha256
                (base32
-                "0p1gy553cm4mhwxi85fl6qiwz61rjmvysm8c8pd20qh62xxi3dva"))))
+                "1igxqgx8q9cp15mcp1y8j564bl85ijw04jcmgb1s5bmfbg1751sd"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
@@ -372,9 +372,11 @@ (define-public lxc
        ("libseccomp" ,libseccomp)
        ("libselinux" ,libselinux)))
     (arguments
-     '(#:configure-flags
-       '("--sysconfdir=/etc"
-         "--localstatedir=/var")
+     `(#:configure-flags
+       (list (string-append "--docdir=" (assoc-ref %outputs "out")
+                            "/share/doc/" ,name "-" ,version)
+             "--sysconfdir=/etc"
+             "--localstatedir=/var")
        #:phases
        (modify-phases %standard-phases
          (replace 'install

gnu/packages/vulkan.scm

@@ -32,6 +32,7 @@ (define-module (gnu packages vulkan)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages pkg-config)
@@ -42,8 +43,8 @@ (define-module (gnu packages vulkan)
 (define-public spirv-headers
   ;; Keep updated in accordance with
   ;; https://github.com/google/shaderc/blob/known-good/known_good.json
-  (let ((commit "3ce3e49d73b8abbf2ffe33f829f941fb2a40f552")
-        (revision "3"))
+  (let ((commit "8bea0a266ac9b718aa0818d9e3a47c0b77c2cb23")
+        (revision "4"))
     (package
       (name "spirv-headers")
       (version (string-append "0.0-" revision "." (string-take commit 9)))
@@ -55,7 +56,7 @@ (define-public spirv-headers
                (commit commit)))
          (sha256
           (base32
-           "0yk4bzqifdqpmdxkhvrxbdqhf5ngkga0ig1yyz7khr7rklqfz7wp"))
+           "01qyjghjz42hmyw9111zz20a1paf37ps39p4xbj8abjba65d8lqx"))
          (file-name (string-append name "-" version "-checkout"))))
       (build-system cmake-build-system)
       (arguments
@@ -83,82 +84,81 @@ (define-public spirv-headers
                                commit "/LICENSE"))))))
 
 (define-public spirv-tools
-  ;; Keep updated in accordance with
-  ;; https://github.com/google/shaderc/blob/known-good/known_good.json
-  (let ((commit "fe2fbee294a8ad4434f828a8b4d99eafe9aac88c")
-        (revision "2"))
-    (package
-     (name "spirv-tools")
-     (version (string-append "0.0-" revision "." (string-take commit 9)))
-     (source
-      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/KhronosGroup/SPIRV-Tools")
-             (commit commit)))
-       (sha256
-        (base32
-         "03rq4ypwqnz34n8ip85n95a3b9rxb34j26azzm3b3invaqchv19x"))
-       (file-name (string-append name "-" version "-checkout"))))
-     (build-system cmake-build-system)
-     (arguments
-      `(#:tests? #f ; FIXME: Tests fail.
-        #:configure-flags (list (string-append "-DSPIRV-Headers_SOURCE_DIR="
-                                               (assoc-ref %build-inputs
-                                                          "spirv-headers")))))
-     (inputs `(("spirv-headers" ,spirv-headers)))
-     (native-inputs `(("pkg-config" ,pkg-config)
-                      ("python" ,python)))
-     (home-page "https://github.com/KhronosGroup/SPIRV-Tools")
-     (synopsis "API and commands for processing SPIR-V modules")
-     (description
-      "The SPIR-V Tools project provides an API and commands for processing
-SPIR-V modules.  The project includes an assembler, binary module parser,
-disassembler, validator, and optimizer for SPIR-V.")
-     (license license:asl2.0))))
+  (package
+    (name "spirv-tools")
+    (version "2019.1")
+    (source
+     (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/KhronosGroup/SPIRV-Tools")
+            (commit (string-append "v" version))))
+      (sha256
+       (base32
+        "0vddjzhkrhrm3l3i57nxmq2smv3r1s0ka5ff2kziaahr4hqb479r"))
+      (file-name (string-append name "-" version "-checkout"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f ; FIXME: Tests fail.
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'fixgcc7
+           (lambda _
+             (unsetenv "C_INCLUDE_PATH")
+             (unsetenv "CPLUS_INCLUDE_PATH")
+             #t)))
+       #:configure-flags (list (string-append "-DSPIRV-Headers_SOURCE_DIR="
+                               (assoc-ref %build-inputs "spirv-headers")))))
+    (inputs `(("spirv-headers" ,spirv-headers)))
+    (native-inputs `(("gcc" ,gcc-7)
+                     ("pkg-config" ,pkg-config)
+                     ("python" ,python)))
+    (home-page "https://github.com/KhronosGroup/SPIRV-Tools")
+    (synopsis "API and commands for processing SPIR-V modules")
+    (description
+     "The SPIR-V Tools project provides an API and commands for processing
+SPIR-V modules.  The project includes an assembler, binary module
+parser,disassembler, validator, and optimizer for SPIR-V.")
+    (license license:asl2.0)))
 
 (define-public glslang
-  ;; Keep updated in accordance with
-  ;; https://github.com/google/shaderc/blob/known-good/known_good.json
-  (let ((commit "32d3ec319909fcad0b2b308fe1635198773e8316")
-        (revision "3"))
-    (package
-      (name "glslang")
-      (version (string-append "3.0-" revision "." (string-take commit 9)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/KhronosGroup/glslang")
-               (commit commit)))
-         (sha256
-          (base32
-           "1kmgjv5kbrjy6azpgwnjcn3cj8vg5i8hnyk3m969sc0gq2j1rbjj"))
-         (file-name (string-append name "-" version "-checkout"))))
-      (build-system cmake-build-system)
-      (arguments
-       `(#:tests? #f ;; No tests
-         ;; glslang tries to set CMAKE_INSTALL_PREFIX manually. Remove the
-         ;; offending line.
-         #:phases (modify-phases %standard-phases
-                    (add-after 'patch-source-shebangs 'fix-cmakelists
-                      (lambda _
-                        (substitute* "CMakeLists.txt"
-                          (("set.*CMAKE_INSTALL_PREFIX.*") ""))
-                        #t)))))
-      (native-inputs `(("bison" ,bison)
-                       ("pkg-config" ,pkg-config)))
-      (home-page "https://github.com/KhronosGroup/glslang")
-      (synopsis "OpenGL and OpenGL ES shader front end and validator")
-      (description
-       "Glslang is the official reference compiler front end for the
+  (package
+    (name "glslang")
+    (version "7.11.3113")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/KhronosGroup/glslang")
+             (commit version)))
+       (sha256
+        (base32
+         "1kzv2b4q1fddxd7c0hc754nd6rw6y9vijb9fsi13xzzq9dficgb6"))
+       (file-name (string-append name "-" version "-checkout"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f ;; No tests
+       ;; glslang tries to set CMAKE_INSTALL_PREFIX manually. Remove the
+       ;; offending line.
+       #:phases (modify-phases %standard-phases
+                  (add-after 'patch-source-shebangs 'fix-cmakelists
+                    (lambda _
+                      (substitute* "CMakeLists.txt"
+                        (("set.*CMAKE_INSTALL_PREFIX.*") ""))
+                      #t)))))
+    (native-inputs `(("bison" ,bison)
+                     ("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/KhronosGroup/glslang")
+    (synopsis "OpenGL and OpenGL ES shader front end and validator")
+    (description
+     "Glslang is the official reference compiler front end for the
 OpenGL@tie{}ES and OpenGL shading languages.  It implements a strict
 interpretation of the specifications for these languages.")
-      ;; Modified BSD license. See "copyright" section of
-      ;; https://www.khronos.org/opengles/sdk/tools/Reference-Compiler/
-      (license (list license:bsd-3
-                     ;; include/SPIRV/{bitutils,hex_float}.h are Apache 2.0.
-                     license:asl2.0)))))
+    ;; Modified BSD license. See "copyright" section of
+    ;; https://www.khronos.org/opengles/sdk/tools/Reference-Compiler/
+    (license (list license:bsd-3
+                   ;; include/SPIRV/{bitutils,hex_float}.h are Apache 2.0.
+                   license:asl2.0))))
 
 (define-public vulkan-headers
   (package
@@ -281,75 +281,73 @@ (define-public vulkan-tools
     (license (list license:asl2.0)))) ;LICENSE.txt
 
 (define-public shaderc
-  (let ((commit "be8e0879750303a1de09385465d6b20ecb8b380d")
-        (revision "2"))
-    (package
-      (name "shaderc")
-      (version (git-version "0.0.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/google/shaderc")
-               (commit commit)))
-         (file-name (string-append name "-" version ".tar.gz"))
-         (sha256
-          (base32
-           "16p25ry2i4zrj00zihfpf210f8xd7g398ffbw25igvi9mbn4nbfd"))))
-      (build-system meson-build-system)
-      (arguments
-       `(#:tests? #f ; FIXME: Tests fail.
-         #:phases
-         (modify-phases %standard-phases
-           (replace 'configure
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((out (assoc-ref outputs "out")))
-                 ;; Remove various lines and touch build-version.inc or
-                 ;; configuring won't work.
-                 (invoke "touch" "glslc/src/build-version.inc")
-                 (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") ""))
-                 (substitute* "CMakeLists.txt"
-                   ((".*update_build_version.py..*") ""))
-                 (substitute* "CMakeLists.txt"
-                   ((".*add_custom_target.build-version.*") ""))
-                 (substitute* "CMakeLists.txt"
-                   ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*")
-                    ""))
-                 (substitute* "CMakeLists.txt"
-                   ((".*Update build-version.inc.*") ""))
-                 (substitute* "CMakeLists.txt" ((".*--check.*") ""))
-                 (substitute* "glslc/src/main.cc" ((".*build-version.inc.*")
-                                                   "\"1\""))
-                 (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release"
-                         "-DSHADERC_SKIP_TESTS=ON"
-                         "-DCMAKE_INSTALL_LIBDIR=lib"
-                         (string-append "-DCMAKE_INSTALL_PREFIX="
-                                        out)))))
-           (add-after 'unpack 'unpack-sources
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((spirv-tools-source (assoc-ref inputs "spirv-tools-source"))
-                     (spirv-headers-source (assoc-ref inputs "spirv-headers-source"))
-                     (glslang-source (assoc-ref inputs "glslang-source")))
-                 (copy-recursively spirv-tools-source "third_party/spirv-tools")
-                 (copy-recursively spirv-headers-source
-                                   (string-append "third_party/spirv-tools"
-                                                  "/external/spirv-headers"))
-                 (copy-recursively glslang-source "third_party/glslang")
-                 #t))))))
-      (inputs
-       `(("googletest" ,googletest)
-         ("python" ,python)))
-      (native-inputs
-       `(("cmake" ,cmake)
-         ("glslang-source" ,(package-source glslang))
-         ("pkg-config" ,pkg-config)
-         ("spirv-headers-source" ,(package-source spirv-headers))
-         ("spirv-tools-source" ,(package-source spirv-tools))))
-      (home-page "https://github.com/google/shaderc")
-      (synopsis "Tools for shader compilation")
-      (description "Shaderc is a collection of tools, libraries, and tests for
+  (package
+    (name "shaderc")
+    (version "2018.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/google/shaderc")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0qigmj0riw43pgjn5f6kpvk72fajssz1lc2aiqib5qvmj9rqq3hl"))))
+    (build-system meson-build-system)
+    (arguments
+     `(#:tests? #f ; FIXME: Tests fail.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               ;; Remove various lines and touch build-version.inc or
+               ;; configuring won't work.
+               (invoke "touch" "glslc/src/build-version.inc")
+               (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") ""))
+               (substitute* "CMakeLists.txt"
+                 ((".*update_build_version.py..*") ""))
+               (substitute* "CMakeLists.txt"
+                 ((".*add_custom_target.build-version.*") ""))
+               (substitute* "CMakeLists.txt"
+                 ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*")
+                  ""))
+               (substitute* "CMakeLists.txt"
+                 ((".*Update build-version.inc.*") ""))
+               (substitute* "CMakeLists.txt" ((".*--check.*") ""))
+               (substitute* "glslc/src/main.cc" ((".*build-version.inc.*")
+                                                 "\"1\""))
+               (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release"
+                       "-DSHADERC_SKIP_TESTS=ON"
+                       "-DCMAKE_INSTALL_LIBDIR=lib"
+                       (string-append "-DCMAKE_INSTALL_PREFIX="
+                                      out)))))
+         (add-after 'unpack 'unpack-sources
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((spirv-tools-source (assoc-ref inputs "spirv-tools-source"))
+                   (spirv-headers-source (assoc-ref inputs "spirv-headers-source"))
+                   (glslang-source (assoc-ref inputs "glslang-source")))
+               (copy-recursively spirv-tools-source "third_party/spirv-tools")
+               (copy-recursively spirv-headers-source
+                                 (string-append "third_party/spirv-tools"
+                                                "/external/spirv-headers"))
+               (copy-recursively glslang-source "third_party/glslang")
+               #t))))))
+    (inputs
+     `(("googletest" ,googletest)
+       ("python" ,python)))
+    (native-inputs
+     `(("cmake" ,cmake)
+       ("glslang-source" ,(package-source glslang))
+       ("pkg-config" ,pkg-config)
+       ("spirv-headers-source" ,(package-source spirv-headers))
+       ("spirv-tools-source" ,(package-source spirv-tools))))
+    (home-page "https://github.com/google/shaderc")
+    (synopsis "Tools for shader compilation")
+    (description "Shaderc is a collection of tools, libraries, and tests for
 shader compilation.")
-      (license license:asl2.0))))
+    (license license:asl2.0)))
 
 (define-public vkd3d
   (let ((commit "ecda316ef54d70bf1b3e860755241bb75873e53f")) ; Release 1.1.

gnu/packages/wget.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2014, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
@@ -111,48 +111,60 @@ (define-public wgetpaste
 (define-public wget2
   (package
    (name "wget2")
-   (version "1.0.0")
+   (version "1.99.1")
    (source
-    (origin
-     (method git-fetch)
-     (uri (git-reference
-           (url "https://gitlab.com/gnuwget/wget2.git")
-           (commit "b45709d3d21714135ce79df6abbdcb704684063d")
-           (recursive? #t))) ;; Needed for 'gnulib' git submodule.
-     (file-name (string-append name "-" version "-checkout"))
-     (sha256
-      (base32
-       "0ww84wwzmpyylkz8rnb6nk6f7x040132z81x52w7rjhk68p9mm24"))))
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://gitlab.com/gnuwget/wget2.git")
+              (commit (string-append name "-" version))
+              (recursive? #t))) ;; Needed for 'gnulib' git submodule.
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "15wxsnjhc6bzk7f60i1djmsarh1w31gwi5h2gh9k19ncwypfj5dm"))))
    (build-system gnu-build-system)
    (arguments
-    `(#:phases (modify-phases %standard-phases
-      (replace 'bootstrap
-        (lambda _
-          ;; Make sure all the files are writable so that ./bootstrap
-          ;; can proceed.
-          (for-each (lambda (file)
-                      (chmod file #o755))
-                      (find-files "."))
-          (substitute* "./gnulib/gnulib-tool.py"
-                       (("/usr/bin/python") (which "python3")))
-          (invoke "sh" "./bootstrap"
-                          "--gnulib-srcdir=gnulib"
-                          "--no-git"))))))
-   (inputs `(("autoconf" ,autoconf)
-             ("automake" ,automake)
-             ("doxygen" ,doxygen)
-             ("flex" ,flex)
-             ("gettext" ,gettext-minimal)
-             ("gnutls" ,gnutls/dane)
-             ("libiconv" ,libiconv)
-             ("libidn2" ,libidn2)
-             ("libmicrohttpd" ,libmicrohttpd)
-             ("libpsl" ,libpsl)
-             ("libtool" ,libtool)
-             ("pcre2" ,pcre2)
-             ("python" ,python)))
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'skip-network-test
+          (lambda _
+            (substitute* "tests/Makefile.am"
+              (("test-auth-digest\\$\\(EXEEXT)") ""))
+            #t))
+        (replace 'bootstrap
+          (lambda _
+            ;; Make sure all the files are writable so that ./bootstrap
+            ;; can proceed.
+            (for-each (lambda (file)
+                        (chmod file #o755))
+                        (find-files "."))
+            (patch-shebang "./gnulib/gnulib-tool.py")
+            ;; Remove unnecessary inputs from bootstrap.conf
+            (substitute* "bootstrap.conf"
+              (("flex.*") "")
+              (("makeinfo.*") "")
+              (("lzip.*") "")
+              (("rsync.*") ""))
+            (invoke "sh" "./bootstrap"
+                    "--gnulib-srcdir=gnulib"
+                    "--no-git"))))))
+   (inputs
+    `(("gnutls" ,gnutls/dane)
+      ("libiconv" ,libiconv)
+      ("libidn2" ,libidn2)
+      ("libmicrohttpd" ,libmicrohttpd)
+      ("libpsl" ,libpsl)
+      ("pcre2" ,pcre2)))
    ;; TODO: Add libbrotlidec, libnghttp2.
-   (native-inputs `(("pkg-config" ,pkg-config)))
+   (native-inputs
+    `(("autoconf" ,autoconf)
+      ("automake" ,automake)
+      ("flex" ,flex)
+      ("gettext" ,gettext-minimal)
+      ("libtool" ,libtool)
+      ("pkg-config" ,pkg-config)
+      ("python" ,python-2)))
    (home-page "https://gitlab.com/gnuwget/wget2")
    (synopsis "Successor of GNU Wget")
    (description "GNU Wget2 is the successor of GNU Wget, a file and recursive

gnu/packages/xorg.scm

@@ -5663,14 +5663,14 @@ (define-public xcb-util-wm
 (define-public xinit
   (package
     (name "xinit")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://xorg/individual/app/xinit-"
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1vw2wlg74ig52naw0cha3pgzcwwk25l834j42cg8m5zmybp3a213"))))
+                "1fdbakx59vyh474skjydj1bbglpby3y03nl7mxn0z9v8gdhqz6yy"))))
     (build-system gnu-build-system)
     (inputs
      `(("xorgproto" ,xorgproto)