Merge branch 'master' into core-updates

Makefile.am

@@ -406,6 +406,7 @@ SH_TESTS =					\
   tests/guix-gc.sh				\
   tests/guix-hash.sh				\
   tests/guix-pack.sh				\
+  tests/guix-pack-relocatable.sh		\
   tests/guix-package.sh				\
   tests/guix-package-net.sh			\
   tests/guix-system.sh				\
@@ -462,8 +463,8 @@ check-system: $(GOBJECTS)
 
 # Public key used to sign substitutes from hydra.gnu.org & co.
 dist_pkgdata_DATA =				\
-  hydra.gnu.org.pub				\
+  etc/substitutes/hydra.gnu.org.pub		\
-  berlin.guixsd.org.pub
+  etc/substitutes/berlin.guixsd.org.pub
 
 # Bash completion file.
 dist_bashcompletion_DATA = etc/completion/bash/guix	\

doc/guix.texi

@@ -31,7 +31,7 @@ Copyright @copyright{} 2016, 2017, 2018 Jan Nieuwenhuizen@*
 Copyright @copyright{} 2016 Julien Lepiller@*
 Copyright @copyright{} 2016 Alex ter Weele@*
 Copyright @copyright{} 2017, 2018 Clément Lassieur@*
-Copyright @copyright{} 2017 Mathieu Othacehe@*
+Copyright @copyright{} 2017, 2018 Mathieu Othacehe@*
 Copyright @copyright{} 2017 Federico Beffa@*
 Copyright @copyright{} 2017, 2018 Carlo Zancanaro@*
 Copyright @copyright{} 2017 Thomas Danckaert@*
@@ -2844,9 +2844,6 @@ The @command{guix pull} command is usually invoked with no arguments,
 but it supports the following options:
 
 @table @code
-@item --verbose
-Produce verbose output, writing build logs to the standard error output.
-
 @item --url=@var{url}
 @itemx --commit=@var{commit}
 @itemx --branch=@var{branch}
@@ -2880,6 +2877,14 @@ current generation only.
 @itemx -p @var{profile}
 Use @var{profile} instead of @file{~/.config/guix/current}.
 
+@item --dry-run
+@itemx -n
+Show which channel commit(s) would be used and what would be built or
+substituted but do not actually do it.
+
+@item --verbose
+Produce verbose output, writing build logs to the standard error output.
+
 @item --bootstrap
 Use the bootstrap Guile to build the latest Guix.  This option is only
 useful to Guix developers.
@@ -10934,6 +10939,10 @@ A gexp denoting the name of the log-in program. The default log-in program is
 @item @code{login-arguments} (default: @code{'("-p")})
 A list of arguments to pass to @command{login}.
 
+@item @code{auto-login} (default: @code{#f})
+When passed a login name, as a string, the specified user will be logged
+in automatically without prompting for their login name or password.
+
 @item @code{hardware-acceleration?} (default: #f)
 Whether to use hardware acceleration.
 
@@ -18663,6 +18672,11 @@ Cuirass jobs.
 Location of sqlite database which contains the build results and previously
 added specifications.
 
+@item @code{ttl} (default: @code{(* 30 24 3600)})
+Specifies the time-to-live (TTL) in seconds of garbage collector roots that
+are registered for build results.  This means that build results are protected
+from garbage collection for at least @var{ttl} seconds.
+
 @item @code{port} (default: @code{8081})
 Port number used by the HTTP server.
 

etc/completion/bash/guix

@@ -1,5 +1,5 @@
 # GNU Guix --- Functional package management for GNU
-# Copyright © 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+# Copyright © 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 #
 # This file is part of GNU Guix.
 #
@@ -172,6 +172,8 @@ _guix_complete ()
                 if _guix_is_dash_L
                 then
                     _guix_complete_file
+		else
+		    _guix_complete_available_package "$word_at_point"
                 fi
 	    elif _guix_is_command "download"
 	    then

gnu/build/install.scm

@@ -18,7 +18,6 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu build install)
-  #:use-module (guix store database)
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (srfi srfi-26)
@@ -27,6 +26,7 @@
             evaluate-populate-directive
             populate-root-file-system
             register-closure
+            install-database-and-gc-roots
             populate-single-profile-directory))
 
 ;;; Commentary:
@@ -141,34 +141,45 @@ includes /etc, /var, /run, /bin/sh, etc., and all the symlinks to SYSTEM."
                 (try))
               (apply throw args)))))))
 
-(define* (register-closure prefix closure
+(define %root-profile
-                           #:key
+  "/var/guix/profiles/per-user/root")
-                           (deduplicate? #t) (reset-timestamps? #t)
+
-                           (schema (sql-schema)))
+(define* (install-database-and-gc-roots root database profile
-  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
+                                        #:key (profile-name "guix-profile"))
-target store and CLOSURE is the name of a file containing a reference graph as
+  "Install DATABASE, the store database, under directory ROOT.  Create
-produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
+PROFILE-NAME and have it link to PROFILE, a store item."
-true, reset timestamps on store files and, if DEDUPLICATE? is true,
+  (define (scope file)
-deduplicates files common to CLOSURE and the rest of PREFIX."
+    (string-append root "/" file))
-  (let ((items (call-with-input-file closure read-reference-graph)))
+
-    (register-items items
+  (define (mkdir-p* dir)
-                    #:prefix prefix
+    (mkdir-p (scope dir)))
-                    #:deduplicate? deduplicate?
+
-                    #:reset-timestamps? reset-timestamps?
+  (define (symlink* old new)
-                    #:registration-time %epoch
+    (symlink old (scope new)))
-                    #:schema schema)))
+
+  (install-file database (scope "/var/guix/db/"))
+  (chmod (scope "/var/guix/db/db.sqlite") #o644)
+  (mkdir-p* "/var/guix/profiles")
+  (mkdir-p* "/var/guix/gcroots")
+  (symlink* "/var/guix/profiles" "/var/guix/gcroots/profiles")
+
+  ;; Make root's profile, which makes it a GC root.
+  (mkdir-p* %root-profile)
+  (symlink* profile
+            (string-append %root-profile "/" profile-name "-1-link"))
+  (symlink* (string-append profile-name "-1-link")
+            (string-append %root-profile "/" profile-name)))
 
 (define* (populate-single-profile-directory directory
                                             #:key profile closure
                                             (profile-name "guix-profile")
-                                            deduplicate?
+                                            database)
-                                            register? schema)
   "Populate DIRECTORY with a store containing PROFILE, whose closure is given
 in the file called CLOSURE (as generated by #:references-graphs.)  DIRECTORY
 is initialized to contain a single profile under /root pointing to PROFILE.
-When REGISTER? is true, initialize DIRECTORY/var/guix/db to reflect the
+
-contents of the store; DEDUPLICATE? determines whether to deduplicate files in
+When DATABASE is true, copy it to DIRECTORY/var/guix/db and create
-the store.
+DIRECTORY/var/guix/gcroots and friends.
 
 PROFILE-NAME is the name of the profile being created under
 /var/guix/profiles, typically either \"guix-profile\" or \"current-guix\".
@@ -177,9 +188,6 @@ This is used to create the self-contained tarballs with 'guix pack'."
   (define (scope file)
     (string-append directory "/" file))
 
-  (define %root-profile
-    "/var/guix/profiles/per-user/root")
-
   (define (mkdir-p* dir)
     (mkdir-p (scope dir)))
 
@@ -189,22 +197,9 @@ This is used to create the self-contained tarballs with 'guix pack'."
   ;; Populate the store.
   (populate-store (list closure) directory)
 
-  (when register?
+  (when database
-    (register-closure (canonicalize-path directory) closure
+    (install-database-and-gc-roots directory database profile
-                      #:deduplicate? deduplicate?
+                                   #:profile-name profile-name))
-                      #:schema schema)
-
-    (mkdir-p* "/var/guix/profiles")
-    (mkdir-p* "/var/guix/gcroots")
-    (symlink* "/var/guix/profiles"
-              "/var/guix/gcroots/profiles"))
-
-  ;; Make root's profile, which makes it a GC root.
-  (mkdir-p* %root-profile)
-  (symlink* profile
-            (string-append %root-profile "/" profile-name "-1-link"))
-  (symlink* (string-append profile-name "-1-link")
-            (string-append %root-profile "/" profile-name))
 
   (match profile-name
     ("guix-profile"

gnu/build/linux-initrd.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -139,6 +139,12 @@ REFERENCES-GRAPHS."
 
     (write-cpio-archive output "." #:gzip gzip))
 
+  ;; Make sure directories are writable so we can delete files.
+  (for-each make-file-writable
+            (find-files "contents"
+                        (lambda (file stat)
+                          (eq? 'directory (stat:type stat)))
+                        #:directories? #t))
   (delete-file-recursively "contents"))
 
 ;;; linux-initrd.scm ends here

gnu/build/vm.scm

@@ -25,7 +25,7 @@
   #:use-module (guix build utils)
   #:use-module (guix build store-copy)
   #:use-module (guix build syscalls)
-  #:use-module ((guix store database) #:select (reset-timestamps))
+  #:use-module (guix store database)
   #:use-module (gnu build linux-boot)
   #:use-module (gnu build install)
   #:use-module (gnu system uuid)
@@ -191,6 +191,23 @@ the #:references-graphs parameter of 'derivation'."
           (mkdir output)
           (copy-recursively "xchg" output)))))
 
+(define* (register-closure prefix closure
+                           #:key
+                           (deduplicate? #t) (reset-timestamps? #t)
+                           (schema (sql-schema)))
+  "Register CLOSURE in PREFIX, where PREFIX is the directory name of the
+target store and CLOSURE is the name of a file containing a reference graph as
+produced by #:references-graphs..  As a side effect, if RESET-TIMESTAMPS? is
+true, reset timestamps on store files and, if DEDUPLICATE? is true,
+deduplicates files common to CLOSURE and the rest of PREFIX."
+  (let ((items (call-with-input-file closure read-reference-graph)))
+    (register-items items
+                    #:prefix prefix
+                    #:deduplicate? deduplicate?
+                    #:reset-timestamps? reset-timestamps?
+                    #:registration-time %epoch
+                    #:schema schema)))
+
 
 ;;;
 ;;; Partitions.

gnu/local.mk

@@ -726,7 +726,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gd-fix-tests-on-i686.patch		\
   %D%/packages/patches/gd-freetype-test-failure.patch		\
   %D%/packages/patches/gdm-CVE-2018-14424.patch			\
-  %D%/packages/patches/gemma-intel-compat.patch			\
   %D%/packages/patches/geoclue-config.patch			\
   %D%/packages/patches/ghc-8.0-fall-back-to-madv_dontneed.patch \
   %D%/packages/patches/ghc-dont-pass-linker-flags-via-response-files.patch	\
@@ -838,7 +837,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/json-glib-fix-tests-32bit.patch		\
-  %D%/packages/patches/jq-CVE-2015-8863.patch			\
   %D%/packages/patches/kdbusaddons-kinit-file-name.patch	\
   %D%/packages/patches/khmer-use-libraries.patch                \
   %D%/packages/patches/libziparchive-add-includes.patch		\
@@ -882,6 +880,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libexif-CVE-2017-7544.patch		\
   %D%/packages/patches/libgcrypt-make-yat2m-reproducible.patch	\
   %D%/packages/patches/libgit2-mtime-0.patch			\
+  %D%/packages/patches/libgit2-oom-test.patch			\
   %D%/packages/patches/libgdata-fix-tests.patch			\
   %D%/packages/patches/libgdata-glib-duplicate-tests.patch	\
   %D%/packages/patches/libgnome-encoding.patch			\

gnu/packages/benchmark.scm

@@ -35,14 +35,14 @@
 (define-public fio
   (package
     (name "fio")
-    (version "3.7")
+    (version "3.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://brick.kernel.dk/snaps/"
-                                  "fio-" version ".tar.gz"))
+                                  "fio-" version ".tar.bz2"))
               (sha256
                (base32
-                "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7"))))
+                "0s8m0wcz5j6sa1hblj80wk3syy5b4shg7y3gabvm9xa3wj0lzasa"))))
     (build-system gnu-build-system)
     (arguments
      '(#:test-target "test"

gnu/packages/bioconductor.scm

@@ -201,14 +201,14 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
 (define-public r-hpar
   (package
     (name "r-hpar")
-    (version "1.22.2")
+    (version "1.24.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "hpar" version))
        (sha256
         (base32
-         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
+         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
     (build-system r-build-system)
     (home-page "https://bioconductor.org/packages/hpar/")
     (synopsis "Human Protein Atlas in R")
@@ -219,23 +219,24 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
-    (version "1.12.0")
+    (version "1.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
-         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
+         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
-     `(("r-memoise" ,r-memoise)
+     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
        ("r-bsgenome" ,r-bsgenome)
-       ("r-rtracklayer" ,r-rtracklayer)
        ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
        ("r-iranges" ,r-iranges)
+       ("r-memoise" ,r-memoise)
+       ("r-rtracklayer" ,r-rtracklayer)
        ("r-s4vectors" ,r-s4vectors)))
     (home-page "https://bioconductor.org/packages/regioneR/")
     (synopsis "Association analysis of genomic regions")
@@ -247,14 +248,14 @@ region sets and other genomic features.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "2.8.0")
+    (version "2.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
+         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (inputs
@@ -292,14 +293,14 @@ occupancy (overlap) analysis and plotting functions.")
 (define-public r-ripseeker
   (package
     (name "r-ripseeker")
-    (version "1.20.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RIPSeeker" version))
        (sha256
         (base32
-         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
+         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
     (properties `((upstream-name . "RIPSeeker")))
     (build-system r-build-system)
     (propagated-inputs
@@ -325,14 +326,14 @@ processing to visualization and annotation.")
 (define-public r-multtest
   (package
     (name "r-multtest")
-    (version "2.36.0")
+    (version "2.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "multtest" version))
        (sha256
         (base32
-         "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
+         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-survival" ,r-survival)
@@ -363,13 +364,13 @@ expressed genes in DNA microarray experiments.")
 (define-public r-graph
   (package
     (name "r-graph")
-    (version "1.58.2")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "graph" version))
               (sha256
                (base32
-                "07smbb3c30pr5r425g181xsg0rs5jx6x2q6xpwb5dqgicxrz30ga"))))
+                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)))
@@ -410,18 +411,19 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.14.2")
+    (version "3.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "13rksc65lxxzyw11galh6xzvgzp5ii0gwiwpvrm395v2r17rhwsc"))))
+         "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
        ("r-biostrings" ,r-biostrings)
        ("r-delayedarray" ,r-delayedarray)
        ("r-go-db" ,r-go-db)
@@ -437,7 +439,6 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-multtest" ,r-multtest)
        ("r-rbgl" ,r-rbgl)
        ("r-graph" ,r-graph)
-       ("r-biocinstaller" ,r-biocinstaller)
        ("r-regioner" ,r-regioner)
        ("r-dbi" ,r-dbi)
        ("r-ensembldb" ,r-ensembldb)
@@ -465,12 +466,12 @@ enrichedGO (addGeneIDs).")
 (define-public r-marray
   (package
     (name "r-marray")
-    (version "1.58.0")
+    (version "1.60.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "marray" version))
               (sha256
-               (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
+               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
@@ -484,12 +485,12 @@ normalization and quality checking.")
 (define-public r-cghbase
   (package
    (name "r-cghbase")
-   (version "1.40.0")
+   (version "1.42.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHbase" version))
             (sha256
-             (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
+             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
    (properties `((upstream-name . "CGHbase")))
    (build-system r-build-system)
    (propagated-inputs
@@ -504,12 +505,12 @@ the @code{arrayCGH} packages.")
 (define-public r-cghcall
   (package
    (name "r-cghcall")
-   (version "2.42.0")
+   (version "2.44.0")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "CGHcall" version))
             (sha256
-             (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
+             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
    (properties `((upstream-name . "CGHcall")))
    (build-system r-build-system)
    (propagated-inputs
@@ -527,12 +528,12 @@ the @code{arrayCGH} packages.")
 (define-public r-qdnaseq
   (package
     (name "r-qdnaseq")
-    (version "1.16.0")
+    (version "1.18.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "QDNAseq" version))
               (sha256
-               (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
+               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
     (properties `((upstream-name . "QDNAseq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -559,14 +560,14 @@ respectively.")
 (define-public r-bayseq
   (package
     (name "r-bayseq")
-    (version "2.14.0")
+    (version "2.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "baySeq" version))
        (sha256
         (base32
-         "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
+         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
     (properties `((upstream-name . "baySeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -585,14 +586,14 @@ more complex hypotheses) via empirical Bayesian methods.")
 (define-public r-chipcomp
   (package
     (name "r-chipcomp")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPComp" version))
        (sha256
         (base32
-         "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
+         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
     (properties `((upstream-name . "ChIPComp")))
     (build-system r-build-system)
     (propagated-inputs
@@ -619,14 +620,14 @@ datasets.")
 (define-public r-riboprofiling
   (package
     (name "r-riboprofiling")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RiboProfiling" version))
        (sha256
         (base32
-         "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
+         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
     (properties `((upstream-name . "RiboProfiling")))
     (build-system r-build-system)
     (propagated-inputs
@@ -658,14 +659,14 @@ assessment, principal component analysis on codon coverage.")
 (define-public r-riboseqr
   (package
     (name "r-riboseqr")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "riboSeqR" version))
        (sha256
         (base32
-         "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
+         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
     (properties `((upstream-name . "riboSeqR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -686,14 +687,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
+         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
@@ -718,14 +719,14 @@ experiments.")
 (define-public r-genomicinteractions
   (package
     (name "r-genomicinteractions")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GenomicInteractions" version))
        (sha256
         (base32
-         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
     (properties
      `((upstream-name . "GenomicInteractions")))
     (build-system r-build-system)
@@ -757,14 +758,14 @@ information and producing various plots and statistics.")
 (define-public r-ctc
   (package
     (name "r-ctc")
-    (version "1.54.0")
+    (version "1.56.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ctc" version))
        (sha256
         (base32
-         "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
+         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-amap" ,r-amap)))
     (home-page "https://bioconductor.org/packages/ctc/")
@@ -777,14 +778,14 @@ trees and clusters to other programs.")
 (define-public r-goseq
   (package
     (name "r-goseq")
-    (version "1.32.0")
+    (version "1.34.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "goseq" version))
        (sha256
         (base32
-         "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
+         "1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -803,14 +804,14 @@ defined categories which are over/under represented in RNA-seq data.")
 (define-public r-glimma
   (package
     (name "r-glimma")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Glimma" version))
        (sha256
         (base32
-         "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
+         "0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"))))
     (properties `((upstream-name . "Glimma")))
     (build-system r-build-system)
     (propagated-inputs
@@ -830,14 +831,14 @@ information.")
 (define-public r-rots
   (package
     (name "r-rots")
-    (version "1.8.0")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ROTS" version))
        (sha256
         (base32
-         "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
+         "137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"))))
     (properties `((upstream-name . "ROTS")))
     (build-system r-build-system)
     (propagated-inputs
@@ -854,14 +855,14 @@ in omics data.")
 (define-public r-inspect
   (package
     (name "r-inspect")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
-         "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
+         "0b671x5v2wyq5np2flq2m1fnjz32f303yjlw64a1inwc9k2w2pz2"))))
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
@@ -890,14 +891,14 @@ modeling the rates that determines changes in mature mRNA levels.")
 (define-public r-dnabarcodes
   (package
     (name "r-dnabarcodes")
-    (version "1.10.0")
+    (version "1.12.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNABarcodes" version))
        (sha256
         (base32
-         "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
+         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
     (properties `((upstream-name . "DNABarcodes")))
     (build-system r-build-system)
     (propagated-inputs
@@ -917,14 +918,14 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 (define-public r-ruvseq
   (package
     (name "r-ruvseq")
-    (version "1.14.0")
+    (version "1.16.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "RUVSeq" version))
        (sha256
         (base32
-         "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
+         "0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"))))
     (properties `((upstream-name . "RUVSeq")))
     (build-system r-build-system)
     (propagated-inputs
@@ -939,3 +940,32 @@ demultiplexed, i.e. assigned to their original reference barcode.")
 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
 samples.")
     (license license:artistic2.0)))
+
+(define-public r-biocneighbors
+  (package
+    (name "r-biocneighbors")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BiocNeighbors" version))
+       (sha256
+        (base32
+         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+    (properties `((upstream-name . "BiocNeighbors")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppannoy" ,r-rcppannoy)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/BiocNeighbors")
+    (synopsis "Nearest Neighbor Detection for Bioconductor packages")
+    (description
+     "This package implements exact and approximate methods for nearest
+neighbor detection, in a framework that allows them to be easily switched
+within Bioconductor packages or workflows.  The exact algorithm is implemented
+using pre-clustering with the k-means algorithm.  Functions are also provided
+to search for all neighbors within a given distance.  Parallelization is
+achieved for all methods using the BiocParallel framework.")
+    (license license:gpl3)))

gnu/packages/ci.scm

@@ -186,8 +186,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "fe2b73c2353d106431ed0659345391f14ed64600")
+  (let ((commit "0b40dca734468e8b12b3ff58e3e779679f17d38e")
-        (revision "20"))
+        (revision "21"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -199,7 +199,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "00ldbig2p14qpwrl2i2hnhb9idgbbf0kqnlh4n79rmz96blm7463"))))
+                  "1kdxs8dzdyldfs4wsz5hb64hprkbrnq5ljdll631f3bj8pbvvvc1"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)

gnu/packages/cran.scm

@@ -492,13 +492,13 @@ print, summary, plot, update, etc.
 (define-public r-ps
   (package
     (name "r-ps")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ps" version))
        (sha256
-        (base32 "0ai8igdkysmks1ihbp3h3s552da2hskxqwrvp4cx7vwn91x9f3wd"))))
+        (base32 "1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx"))))
     (build-system r-build-system)
     (home-page "http://ps.r-lib.org")
     (synopsis "List, query, and manipulate system processes")
@@ -539,14 +539,14 @@ is configured appropriately so R can use them.")
 (define-public r-pkgload
   (package
     (name "r-pkgload")
-    (version "1.0.1")
+    (version "1.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pkgload" version))
        (sha256
         (base32
-         "0mm0avvan528zbrcrxigl5fkd7za01fb0qhlqrqvm3ar0115cqa8"))))
+         "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-desc" ,r-desc)
@@ -891,14 +891,14 @@ in main memory.")
 (define-public r-ffbase
   (package
     (name "r-ffbase")
-    (version "0.12.5")
+    (version "0.12.7")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ffbase" version))
        (sha256
         (base32
-         "1h5x6rbb1nrpzf4ywkizn8ij0bz3mlz46byh46ylxhicg1ribi24"))))
+         "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-bit" ,r-bit)
@@ -1762,14 +1762,14 @@ provided.")
 (define-public r-ipred
   (package
     (name "r-ipred")
-    (version "0.9-7")
+    (version "0.9-8")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ipred" version))
        (sha256
         (base32
-         "0q53cqs46501wsd4cmfsmr78l8nv1hkbamk9m0ns5qy02df5r254"))))
+         "01xcg3c121ndfpz9dirqxszknh4yb1p222p7f1wbwwhdrg1i27cw"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-class" ,r-class)
@@ -1789,14 +1789,14 @@ problems as well as resampling based estimators of prediction error.")
 (define-public r-psych
   (package
     (name "r-psych")
-    (version "1.8.4")
+    (version "1.8.10")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "psych" version))
        (sha256
         (base32
-         "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
+         "0n3frgzsfmnan6cp3yyq5h6c28v5pd7q5a42pp6byaa7n7d1v478"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-foreign" ,r-foreign)
@@ -2319,14 +2319,14 @@ training models for classification or ranking.")
 (define-public r-xts
   (package
     (name "r-xts")
-    (version "0.11-1")
+    (version "0.11-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xts" version))
        (sha256
         (base32
-         "17d3g14xkxa1a5z5gd3gk1xjqfkjg1ik3i12q0arina8frql3jhd"))))
+         "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
     (build-system r-build-system)
     (propagated-inputs `(("r-zoo" ,r-zoo)))
     (home-page "https://github.com/joshuaulrich/xts")
@@ -4814,14 +4814,14 @@ vice versa), or to deal with multiple declared missing values.")
 (define-public r-sjmisc
   (package
     (name "r-sjmisc")
-    (version "2.7.5")
+    (version "2.7.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sjmisc" version))
        (sha256
         (base32
-         "05fjqfr2rfk11065zqkzb9mbqd6mgdkw9jdhq3by425a7f8m2dcg"))))
+         "1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-broom" ,r-broom)
@@ -4829,15 +4829,12 @@ vice versa), or to deal with multiple declared missing values.")
        ("r-dplyr" ,r-dplyr)
        ("r-haven" ,r-haven)
        ("r-magrittr" ,r-magrittr)
-       ("r-pillar" ,r-pillar)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
        ("r-sjlabelled" ,r-sjlabelled)
        ("r-stringdist" ,r-stringdist)
        ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)))
-       ("r-tidyr" ,r-tidyr)
-       ("r-tidyselect" ,r-tidyselect)))
     (home-page "https://github.com/strengejacke/sjmisc")
     (synopsis "Data and variable transformation functions")
     (description
@@ -4899,14 +4896,14 @@ functions.")
 (define-public r-flextable
   (package
     (name "r-flextable")
-    (version "0.4.5")
+    (version "0.4.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "flextable" version))
        (sha256
         (base32
-         "09j2y0z7rkc0w1cl9pp1cpk6fnzzfr6245mxa3ca42z9k2cy2jfl"))))
+         "0fa42dvf0wyl91w4v0rywm3xgw9n03cfyl28ficrv8iabz4k4382"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-gdtools" ,r-gdtools)
@@ -6823,14 +6820,14 @@ Rcpp, RStudio projects, and more.")
 (define-public r-sessioninfo
   (package
     (name "r-sessioninfo")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "sessioninfo" version))
        (sha256
         (base32
-         "01c0m8yzadpwd825hky6as0f8ka4xyz7zfy0ih2iy7qqw11w6qn5"))))
+         "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cli" ,r-cli)
@@ -6846,14 +6843,14 @@ more information about packages, and where they were installed from.")
 (define-public r-remotes
   (package
     (name "r-remotes")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "remotes" version))
        (sha256
         (base32
-         "1xkzlciv68jyf4j8hads0i47nxbgsy1kv7258c6zzyq66z0amhss"))))
+         "0rsjxmhwpr51ilsdjfqn06mj8yr2d7nckcn3arv1ljn23qfkpcxa"))))
     (build-system r-build-system)
     (home-page "https://github.com/r-lib/remotes#readme")
     (synopsis "R package installation from remote repositories")
@@ -6888,14 +6885,14 @@ directories or URLs with their associated programs.")
 (define-public r-rcmdcheck
   (package
     (name "r-rcmdcheck")
-    (version "1.3.0")
+    (version "1.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rcmdcheck" version))
        (sha256
         (base32
-         "13liz9lmx9xgc0f7pjiz3sp8ygvazx2zslbiwz3p9fimfsx1yfsg"))))
+         "1ga19jqix0zs7xyz2j155zyagwbv22r6dgv55g6wdjigc67qfsix"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-callr" ,r-callr)
@@ -6907,6 +6904,7 @@ directories or URLs with their associated programs.")
        ("r-prettyunits" ,r-prettyunits)
        ("r-r6" ,r-r6)
        ("r-rprojroot" ,r-rprojroot)
+       ("r-sessioninfo" ,r-sessioninfo)
        ("r-withr" ,r-withr)
        ("r-xopen" ,r-xopen)))
     (home-page "https://github.com/r-Lib/rcmdcheck#readme")
@@ -6943,14 +6941,14 @@ quick reporting.")
 (define-public r-pander
   (package
     (name "r-pander")
-    (version "0.6.2")
+    (version "0.6.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "pander" version))
        (sha256
         (base32
-         "0gd7rqkpbraznip8jmri9lqa8ajg1sryyplhd6m633wg91whiipi"))))
+         "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-digest" ,r-digest)
@@ -7225,3 +7223,105 @@ R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
 al. (2016)).")
     (license license:gpl2)))
+
+(define-public r-weights
+  (package
+    (name "r-weights")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "weights" version))
+       (sha256
+        (base32
+         "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gdata" ,r-gdata)
+       ("r-hmisc" ,r-hmisc)
+       ("r-mice" ,r-mice)))
+    (home-page
+     "https://cran.r-project.org/web/packages/weights/")
+    (synopsis "Weighting and weighted statistics")
+    (description "This package Provides a variety of functions for producing
+simple weighted statistics, such as weighted Pearson's correlations, partial
+correlations, Chi-Squared statistics, histograms, and t-tests.  Also now
+includes some software for quickly recoding survey data and plotting point
+estimates from interaction terms in regressions (and multiply imputed
+regressions).  NOTE: Weighted partial correlation calculations pulled to
+address a bug.")
+  (license license:gpl2+)))
+
+(define-public r-rcppannoy
+  (package
+    (name "r-rcppannoy")
+    (version "0.0.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppAnnoy" version))
+       (sha256
+        (base32
+         "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1"))))
+    (properties `((upstream-name . "RcppAnnoy")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
+    (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
+    (description
+     "Annoy is a small C++ library for Approximate Nearest Neighbors written
+for efficient memory usage as well an ability to load from and save to disk.
+This package provides an R interface.")
+    ;; Annoy is released under ASL 2.0, but this wrapper is released under
+    ;; GPLv2+.
+    (license (list license:gpl2+ license:asl2.0))))
+
+(define-public r-ncdf4
+  (package
+    (name "r-ncdf4")
+    (version "1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ncdf4" version))
+       (sha256
+        (base32
+         "0lwjjis0b83c4l3xvqai4ckzrskd6mychck1iwxcxgjvh0d77mgd"))))
+    (build-system r-build-system)
+    (inputs
+     `(("netcdf" ,netcdf)
+       ("zlib" ,zlib)))
+    (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
+    (synopsis "R interface to Unidata netCDF format data files")
+    (description
+     "This package provides a high-level R interface to data files written
+using Unidata's netCDF library (version 4 or earlier), which are binary data
+files that are portable across platforms and include metadata information in
+addition to the data sets.  Using this package, netCDF files can be opened and
+data sets read in easily.  It is also easy to create new netCDF dimensions,
+variables, and files, in either version 3 or 4 format, and manipulate existing
+netCDF files.")
+    (license license:gpl3+)))
+
+(define-public r-biocmanager
+  (package
+    (name "r-biocmanager")
+    (version "1.30.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "BiocManager" version))
+       (sha256
+        (base32
+         "0mfvx1xzsgiag9p42kdyqg8fvajyakrdy3z2smhdlaawzbi0qmax"))))
+    (properties `((upstream-name . "BiocManager")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/BiocManager/")
+    (synopsis "Access the Bioconductor project package repository")
+    (description
+     "This package provides a convenient tool to install and update
+Bioconductor packages.")
+    (license license:artistic2.0)))

gnu/packages/gnupg.scm

@@ -221,14 +221,14 @@ compatible to GNU Pth.")
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.2.10")
+    (version "2.2.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "05f9804g72pffdxgvxjmjzkfcpjg1x221g9rwcr8fi51hrxd77br"))))
+                "1ncwqjhcxh46fgkp84g2lhf91amcha7abk6wdm1kagzm7q93wv29"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

gnu/packages/graph.scm

@@ -156,14 +156,14 @@ model.")
 (define-public r-rgraphviz
   (package
     (name "r-rgraphviz")
-    (version "2.24.0")
+    (version "2.26.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rgraphviz" version))
        (sha256
         (base32
-         "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby"))))
+         "0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"))))
     (properties `((upstream-name . "Rgraphviz")))
     (build-system r-build-system)
     ;; FIXME: Rgraphviz bundles the sources of an older variant of

gnu/packages/guile.scm

@@ -12,7 +12,7 @@
 ;;; Copyright © 2016 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2017 David Thompson <davet@gnu.org>
-;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -68,6 +68,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages image)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages slang)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages networking)
@@ -1112,7 +1113,7 @@ Guile's foreign function interface.")
   (package
     (name "guile-sqlite3")
     (version "0.1.0")
-    (home-page "https://notabug.org/civodul/guile-sqlite3.git")
+    (home-page "https://notabug.org/guile-sqlite3/guile-sqlite3.git")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2243,4 +2244,39 @@ using S-expressions.")
 tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
     (license license:gpl3+)))
 
+;; There has not been any release yet.
+(define-public guile-newt
+  (let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
+        (revision "0"))
+    (package
+      (name "guile-newt")
+      (version (string-append "0-" revision "." (string-take commit 9)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://gitlab.com/mothacehe/guile-newt")
+                      (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
+                (sha256
+                 (base32
+                  "18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
+      (build-system gnu-build-system)
+      (arguments
+       '(#:make-flags
+         '("GUILE_AUTO_COMPILE=0"))) ;to prevent guild warnings
+      (inputs
+       `(("guile" ,guile-2.2)
+         ("newt" ,newt)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (synopsis "Guile bindings to Newt")
+      (description
+       "This package provides bindings for Newt, a programming library for
+color text mode, widget based user interfaces.  The bindings are written in pure
+Scheme by using Guile’s foreign function interface.")
+      (home-page "https://gitlab.com/mothacehe/guile-newt")
+      (license license:gpl3+))))
+
 ;;; guile.scm ends here

gnu/packages/kodi.scm

@@ -317,8 +317,8 @@ generator library for C++.")
                 (string-append (assoc-ref inputs "tzdata")
                                "/share/zoneinfo")))
 
-             ;; Don't phone home to check for updates.¬
+             ;; Don't phone home to check for updates.
-             (substitute* "system/addon-manifest.xml"¬
+             (substitute* "system/addon-manifest.xml"
                (("<addon optional=\\\"true\\\">service.xbmc.versioncheck</addon>")
                 ""))
 

gnu/packages/libreoffice.scm

@@ -939,7 +939,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "6.1.2.1")
+    (version "6.1.3.2")
     (source
      (origin
        (method url-fetch)
@@ -949,7 +949,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
          (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
        (sha256
         (base32
-         "149ziasibplihfxlzafzcm4737ns30hg9175967b43c81yv5f335"))
+         "0i4gf3qi16fg7dxq2l4vhkwh4f5lx7xd1ilpzcw26vccqkv3hvyl"))
        (patches (search-patches "libreoffice-icu.patch"
                                 "libreoffice-glm.patch"))))
     (build-system glib-or-gtk-build-system)

gnu/packages/maths.scm

@@ -884,6 +884,25 @@ extremely large and complex data collections.")
     (license (license:x11-style
               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 
+(define-public hdf5-1.10
+  (package (inherit hdf5)
+    (version "1.10.4")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
+                                "hdf5-" (version-major+minor version)
+                                "/hdf5-" version "/src/hdf5-"
+                                version ".tar.bz2")
+                 (string-append "https://support.hdfgroup.org/ftp/HDF5/"
+                                "current"
+                                (apply string-append
+                                       (take (string-split version #\.) 2))
+                                "/src/hdf5-" version ".tar.bz2")))
+      (sha256
+       (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
+      (patches (list (search-patch "hdf5-config-date.patch")))))))
+
 (define-public hdf-java
   (package
    (name "hdf-java")

gnu/packages/music.scm

@@ -284,7 +284,7 @@ score, keyboard, guitar, drum and controller views.")
          ("pulseaudio" ,pulseaudio)
          ("qtbase" ,qtbase)
          ("qtx11extras" ,qtx11extras)
-         ("sqlite" ,sqlite)
+         ("sqlite" ,sqlite-with-column-metadata)
          ("sparsehash" ,sparsehash)
          ("taglib" ,taglib)))
       (home-page "http://clementine-player.org")

gnu/packages/patches/gemma-intel-compat.patch

@@ -1,44 +0,0 @@
-From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001
-From: Efraim Flashner <efraim@flashner.co.il>
-Date: Tue, 4 Jul 2017 12:44:53 +0300
-Subject: [PATCH] Add NO_INTEL_COMPAT flag to Makefile.
-
-see also: https://github.com/xiangzhou/GEMMA/pull/47
-
----
- Makefile | 12 ++++++++----
- 1 file changed, 8 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5bb8748..712b1ad 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,6 +11,7 @@
- SYS = LNX
- # Leave blank after "=" to disable; put "= 1" to enable
- WITH_LAPACK = 1
-+NO_INTEL_COMPAT = 
- FORCE_32BIT = 
- FORCE_DYNAMIC = 
- DIST_NAME = gemma-0.96
-@@ -64,10 +65,13 @@ endif
-   HDR += $(SRC_DIR)/lapack.h
- endif
- 
--ifdef FORCE_32BIT
--  CPPFLAGS += -m32
--else
--  CPPFLAGS += -m64
-+ifdef NO_INTEL_COMPAT
-+  else
-+  ifdef FORCE_32BIT
-+    CPPFLAGS += -m32
-+  else
-+    CPPFLAGS += -m64
-+  endif
- endif
- 
- ifdef FORCE_DYNAMIC
--- 
-2.13.2
-

gnu/packages/patches/jq-CVE-2015-8863.patch

@@ -1,45 +0,0 @@
-Fix CVE-2015-8863 (Off-by-one error in the tokenadd function in
-jv_parse.c in jq allows remote attackers to cause a denial of service
-(crash) via a long JSON-encoded number, which triggers a heap-based
-buffer overflow):
-
-<https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2015-8863>
-
-Copied from upstream code repository:
-
-<https://github.com/stedolan/jq/commit/8eb1367ca44e772963e704a700ef72ae2e12babd>
-
-From 8eb1367ca44e772963e704a700ef72ae2e12babd Mon Sep 17 00:00:00 2001
-From: Nicolas Williams <nico@cryptonector.com>
-Date: Sat, 24 Oct 2015 17:24:57 -0500
-Subject: [PATCH] Heap buffer overflow in tokenadd() (fix #105)
-
-This was an off-by one: the NUL terminator byte was not allocated on
-resize.  This was triggered by JSON-encoded numbers longer than 256
-bytes.
----
- jv_parse.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/jv_parse.c b/jv_parse.c
-index 3102ed4..84245b8 100644
---- a/jv_parse.c
-+++ b/jv_parse.c
-@@ -383,7 +383,7 @@ static pfunc stream_token(struct jv_parser* p, char ch) {
- 
- static void tokenadd(struct jv_parser* p, char c) {
-   assert(p->tokenpos <= p->tokenlen);
--  if (p->tokenpos == p->tokenlen) {
-+  if (p->tokenpos >= (p->tokenlen - 1)) {
-     p->tokenlen = p->tokenlen*2 + 256;
-     p->tokenbuf = jv_mem_realloc(p->tokenbuf, p->tokenlen);
-   }
-@@ -485,7 +485,7 @@ static pfunc check_literal(struct jv_parser* p) {
-     TRY(value(p, v));
-   } else {
-     // FIXME: better parser
--    p->tokenbuf[p->tokenpos] = 0; // FIXME: invalid
-+    p->tokenbuf[p->tokenpos] = 0;
-     char* end = 0;
-     double d = jvp_strtod(&p->dtoa, p->tokenbuf, &end);
-     if (end == 0 || *end != 0)

gnu/packages/patches/libgit2-oom-test.patch

@@ -0,0 +1,62 @@
+Fix a test failure on 32-bit platforms as reported
+at <https://github.com/libgit2/libgit2/issues/4868>.
+
+From 415a8ae9c9b6ac18f0524b6af8e58408b426457d Mon Sep 17 00:00:00 2001
+From: Edward Thomson <ethomson@edwardthomson.com>
+Date: Thu, 13 Sep 2018 13:27:07 +0100
+Subject: [PATCH] tests: don't run buf::oom on 32-bit systems
+
+On a 32-bit Linux systems, the value large enough to make malloc
+guarantee a failure is also large enough that valgrind considers it
+"fishy".  Skip this test on those systems entirely.
+---
+ tests/buf/oom.c | 14 +++++++++-----
+ 1 file changed, 9 insertions(+), 5 deletions(-)
+
+diff --git a/tests/buf/oom.c b/tests/buf/oom.c
+index 2741a8ddf2..ec3bad9979 100644
+--- a/tests/buf/oom.c
++++ b/tests/buf/oom.c
+@@ -11,12 +11,8 @@
+  */
+ #if defined(GIT_ARCH_64) && defined(__linux__)
+ # define TOOBIG 0x0fffffffffffffff
+-#elif defined(__linux__)
+-# define TOOBIG 0x0fffffff
+ #elif defined(GIT_ARCH_64)
+ # define TOOBIG 0xffffffffffffff00
+-#else
+-# define TOOBIG 0xffffff00
+ #endif
+ 
+ /**
+@@ -25,13 +21,18 @@
+  * will fail.  And because the git_buf_grow() wrapper always
+  * sets mark_oom, the code in git_buf_try_grow() will free
+  * the internal buffer and set it to git_buf__oom.
+- * 
++ *
+  * We initialized the internal buffer to (the static variable)
+  * git_buf__initbuf.  The purpose of this test is to make sure
+  * that we don't try to free the static buffer.
++ *
++ * Skip this test entirely on 32-bit platforms; a buffer large enough
++ * to guarantee malloc failures is so large that valgrind considers
++ * it likely to be an error.
+  */
+ void test_buf_oom__grow(void)
+ {
++#ifdef GIT_ARCH_64
+ 	git_buf buf = GIT_BUF_INIT;
+ 
+ 	git_buf_clear(&buf);
+@@ -40,6 +41,9 @@ void test_buf_oom__grow(void)
+ 	cl_assert(git_buf_oom(&buf));
+ 
+ 	git_buf_free(&buf);
++#else
++    cl_skip();
++#endif
+ }
+ 
+ void test_buf_oom__grow_by(void)

gnu/packages/slang.scm

@@ -50,13 +50,21 @@
                '(begin
                   (substitute* "src/Makefile.in"
                     (("/bin/ln") "ln"))
-                  (substitute* "configure"
-                    (("-ltermcap") ""))
                   #t))))
     (build-system gnu-build-system)
     (arguments
      '(#:parallel-tests? #f
-       #:parallel-build? #f)) ; there's at least one race
+       #:parallel-build? #f  ; there's at least one race
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'substitute-before-config
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((ncurses (assoc-ref inputs "ncurses")))
+               (substitute* "configure"
+                 (("MISC_TERMINFO_DIRS=\"\"")
+                  (string-append "MISC_TERMINFO_DIRS="
+                                 "\"" ncurses "/share/terminfo" "\"")))
+               #t))))))
     (inputs
      `(("readline" ,readline)
        ("zlib" ,zlib)

gnu/packages/statistics.scm

@@ -339,14 +339,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.")
 (define-public r-mass
   (package
     (name "r-mass")
-    (version "7.3-51")
+    (version "7.3-51.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "MASS" version))
        (sha256
         (base32
-         "0yp5ssfm9mahrp30y1hkqgjg70mzs6w065ba8h7j5ky1z6msdsdy"))))
+         "14907ia8418mp3p1rs1i2f1x5b6kk5z998dk353a29j3xqf3ybyq"))))
     (properties `((upstream-name . "MASS")))
     (build-system r-build-system)
     (home-page "http://www.stats.ox.ac.uk/pub/MASS4/")
@@ -467,13 +467,13 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995)
 (define-public r-lattice
   (package
     (name "r-lattice")
-    (version "0.20-35")
+    (version "0.20-38")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "lattice" version))
               (sha256
                (base32
-                "0pcnmaz3lr62ly0dcy5hnnqxshc4yqd43hrvlz3almgc9l7sna88"))))
+                "0b8abkz7syscq883mrgv63pkwaqkcpwfx8rgbqy9vgfva0z5xszx"))))
     (build-system r-build-system)
     (home-page "http://lattice.r-forge.r-project.org/")
     (synopsis "High-level data visualization system")
@@ -487,14 +487,14 @@ also flexible enough to handle most nonstandard requirements.")
 (define-public r-matrix
   (package
     (name "r-matrix")
-    (version "1.2-14")
+    (version "1.2-15")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Matrix" version))
        (sha256
         (base32
-         "15hknim84nj3f54vkchca5ac0c3ip15v1by18k5parmn8wsl19j9"))))
+         "1mshhyia6imh939p8labxi0wv21lal7csmccxi42klpgdh1j89kv"))))
     (properties `((upstream-name . "Matrix")))
     (build-system r-build-system)
     (propagated-inputs
@@ -614,14 +614,14 @@ analysis.")
 (define-public r-survival
   (package
     (name "r-survival")
-    (version "2.42-6")
+    (version "2.43-1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "survival" version))
        (sha256
         (base32
-         "1bsxc2fir9pbvdzy9n474fkl7har606h9zhspp0z67wnjpp48g73"))))
+         "0220fjsq4ycx1n5zc5h39wdbj5j6xr8rzqbcixx2p25akzdn7kqk"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-matrix" ,r-matrix)))
@@ -2233,13 +2233,13 @@ tables, autolinks and strikethrough text.")
 (define-public r-roxygen2
   (package
     (name "r-roxygen2")
-    (version "6.1.0")
+    (version "6.1.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "roxygen2" version))
               (sha256
                (base32
-                "0ji9k4s1bvfbl8wimfqj1lqr33h1claaz30vb5pgksxyg77j5xaa"))))
+                "0wq29ilqas8yn2z8v49fk0hbgchg29nmyyhwczgdipz0cbhbfipd"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-brew" ,r-brew)
@@ -3085,13 +3085,13 @@ using the multicore functionality of the parallel package.")
 (define-public r-dt
   (package
     (name "r-dt")
-    (version "0.4")
+    (version "0.5")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "DT" version))
               (sha256
                (base32
-                "06gsqz7p2fv6hc3fm3759gaa50krcfrqrmy7qbxyam6a36w9daix"))))
+                "1s5d3sld4l8zygpkvprvlbqa0pm2cv1bm7h7p999wxlap28vnnqf"))))
     (properties
      `((upstream-name . "DT")))
     (build-system r-build-system)
@@ -3099,7 +3099,8 @@ using the multicore functionality of the parallel package.")
      `(("r-crosstalk" ,r-crosstalk)
        ("r-htmltools" ,r-htmltools)
        ("r-htmlwidgets" ,r-htmlwidgets)
-       ("r-magrittr" ,r-magrittr)))
+       ("r-magrittr" ,r-magrittr)
+       ("r-promises" ,r-promises)))
     (home-page "http://rstudio.github.io/DT")
     (synopsis "R wrapper of the DataTables JavaScript library")
     (description
@@ -3665,14 +3666,14 @@ selection.")
 (define-public r-tidyr
   (package
     (name "r-tidyr")
-    (version "0.8.1")
+    (version "0.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "tidyr" version))
        (sha256
         (base32
-         "0485f19mkkglc4bv57y6bm6l9rfgd878hsz2xdg1nwgbqchjhgix"))))
+         "03s9dv6c2dj65a769h8fgy9878y46rdq7x65i53kd44kag80i9cr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-dplyr" ,r-dplyr)
@@ -4031,14 +4032,14 @@ hierarchical clustering dendrograms.")
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.42.0")
+    (version "1.44.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1afar1z7959v7mbzsqa77vqfh0yc7y3nv5ayx71485a8scwsfwbk"))))
+         "0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
@@ -5016,14 +5017,14 @@ decompositions of such matrices, and solutions of linear systems.")
 (define-public r-modelmetrics
   (package
     (name "r-modelmetrics")
-    (version "1.2.0")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
         (uri (cran-uri "ModelMetrics" version))
         (sha256
          (base32
-          "1sgdyrf6fbsn18gk8slir4a1yhv133kfhyg2crfs759nff4aw89h"))))
+          "158ddbw2snlyzd2q6mdaif5i67kq4qfvadylwjxgv1w2cmszrmk6"))))
     (properties `((upstream-name . "ModelMetrics")))
     (build-system r-build-system)
     (propagated-inputs

gnu/packages/syncthing.scm

@@ -30,7 +30,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "0.14.51")
+    (version "0.14.52")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "17phn8l2afhgzh0q9ambi28awj2m905sr1bicq2wc7ghypk5vgqh"))
+                "1hhn72l74vb9l32i1a54ry2l85ji78cq6isd20lxxdk0bjqc4m29"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet '(begin

gnu/packages/terminals.scm

@@ -187,96 +187,112 @@ text-based approach to terminal recording.")
     (license license:gpl3)))
 
 (define-public libtsm
-  (package
+  (let ((commit "f70e37982f382b03c6939dac3d5f814450bda253")
-    (name "libtsm")
+        (revision "1"))
-    (version "3")
+    (package
-    (source (origin
+      (name "libtsm")
-              (method url-fetch)
+      (version (git-version "0.0.0" revision commit))
-              (uri (string-append
+      (source (origin
-                    "https://freedesktop.org/software/kmscon/releases/"
+                (method git-fetch)
-                    "libtsm-" version ".tar.xz"))
+                ;; The freedesktop repository is no longer maintained.
-              (sha256
+                (uri (git-reference
-               (base32
+                      (url (string-append "https://github.com/Aetf/" name))
-                "01ygwrsxfii0pngfikgqsb4fxp8n1bbs47l7hck81h9b9bc1ah8i"))))
+                      (commit commit)))
-    (build-system gnu-build-system)
+                (sha256
-    (native-inputs
+                 (base32
-     `(("pkg-config" ,pkg-config)))
+                  "0mwn91i5h5d518i1s05y7hzv6bc13vzcvxszpfh77473iwg4wprx"))))
-    (inputs
+      (build-system cmake-build-system)
-     `(("libxkbcommon" ,libxkbcommon)))
+      (arguments
-    (synopsis "Xterm state machine library")
+       `(#:configure-flags '("-DBUILD_TESTING=ON")))
-    (description "TSM is a state machine for DEC VT100-VT520 compatible
+      (native-inputs
+       `(("pkg-config" ,pkg-config)))
+      (inputs
+       `(("libxkbcommon" ,libxkbcommon)
+         ("check" ,check)))
+      (synopsis "Xterm state machine library")
+      (description "TSM is a state machine for DEC VT100-VT520 compatible
 terminal emulators.  It tries to support all common standards while keeping
 compatibility to existing emulators like xterm, gnome-terminal, konsole, etc.")
-    (home-page "https://www.freedesktop.org/wiki/Software/libtsm")
+      (home-page "https://www.freedesktop.org/wiki/Software/libtsm")
-    ;; Hash table implementation is lgpl2.1+ licensed.
+      ;; Hash table implementation is lgpl2.1+ licensed.
-    ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
+      ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
-    ;; derived from ISC.
+      ;; derived from ISC.
-    ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
+      ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
-    ;; under the bsd 2 license.
+      ;; under the bsd 2 license.
-    (license (list license:expat license:lgpl2.1+ license:isc license:bsd-2))))
+      (license (list license:expat license:lgpl2.1+ license:isc license:bsd-2)))))
 
 (define-public kmscon
-  (package
+  (let ((commit "01dd0a231e2125a40ceba5f59fd945ff29bf2cdc")
-    (name "kmscon")
+        (revision "1"))
-    (version "8")
+    (package
-    (source (origin
+      (name "kmscon")
-              (method url-fetch)
+      (version (git-version "0.0.0" revision commit))
-              (uri (string-append
+      (source (origin
-                    "https://freedesktop.org/software/kmscon/releases/"
+                (method git-fetch)
-                    "kmscon-" version ".tar.xz"))
+                ;; The freedesktop repository is no longer maintained.
-              (sha256
+                (uri (git-reference
-               (base32
+                      (url (string-append "https://github.com/Aetf/" name))
-                "0axfwrp3c8f4gb67ap2sqnkn75idpiw09s35wwn6kgagvhf1rc0a"))
+                      (commit commit)))
-              (modules '((guix build utils)))
+                (sha256
-              (snippet
+                 (base32
-               ;; Use elogind instead of systemd.
+                  "0q62kjsvy2iwy8adfiygx2bfwlh83rphgxbis95ycspqidg9py87"))
-               '(begin
+                (modules '((guix build utils)))))
-                  (substitute* "configure"
+      (build-system gnu-build-system)
-                    (("libsystemd-daemon libsystemd-login")
+      (arguments
-                     "libelogind"))
+       `(#:phases (modify-phases %standard-phases
-                  (substitute* "src/uterm_systemd.c"
+                    (add-after 'unpack 'autogen.sh
-                    (("#include <systemd/sd-login.h>")
+                      (lambda _
-                     "#include <elogind/sd-login.h>")
+                        (zero? (system* "sh" "autogen.sh"))))
-                    ;; We don't have this header.
+                    ;; Use elogind instead of systemd.
-                    (("#include <systemd/sd-daemon\\.h>")
+                    (add-before 'configure 'remove-systemd
-                     "")
+                      (lambda _
-                    ;; Replace the call to 'sd_booted' by the truth value.
+                        (substitute* "configure"
-                    (("sd_booted\\(\\)")
+                          (("libsystemd-daemon libsystemd-login")
-                     "1"))
+                           "libelogind"))
-                  #t))))
+                        (substitute* "src/uterm_systemd.c"
-    (build-system gnu-build-system)
+                          (("#include <systemd/sd-login.h>")
-    (native-inputs
+                           "#include <elogind/sd-login.h>")
-     `(("pkg-config" ,pkg-config)
+                          ;; We don't have this header.
-       ("libxslt" ,libxslt)                       ;to build the man page
+                          (("#include <systemd/sd-daemon\\.h>")
-       ("libxml2" ,libxml2)                       ;for XML_CATALOG_FILES
+                           "")
-       ("docbook-xsl" ,docbook-xsl)))
+                          ;; Replace the call to 'sd_booted' by the truth value.
-    (inputs
+                          (("sd_booted\\(\\)")
-     `(("libdrm" ,libdrm)
+                           "1")))))))
-       ("libtsm" ,libtsm)
+      (native-inputs
-       ("libxkbcommon" ,libxkbcommon)
+       `(("pkg-config" ,pkg-config)
-       ("logind" ,elogind)
+         ("autoconf" ,autoconf)
-       ("mesa" ,mesa)
+         ("automake" ,automake)
-       ("pango" ,pango)
+         ("libtool" ,libtool)
-       ("udev" ,eudev)))
+         ("libxslt" ,libxslt)                       ;to build the man page
-    (synopsis "Linux KMS-based terminal emulator")
+         ("libxml2" ,libxml2)                       ;for XML_CATALOG_FILES
-    (description "Kmscon is a terminal emulator based on Linux's @dfn{kernel
+         ("docbook-xsl" ,docbook-xsl)))
+      (inputs
+       `(("libdrm" ,libdrm)
+         ("libtsm" ,libtsm)
+         ("libxkbcommon" ,libxkbcommon)
+         ("logind" ,elogind)
+         ("mesa" ,mesa)
+         ("pango" ,pango)
+         ("udev" ,eudev)))
+      (synopsis "Linux KMS-based terminal emulator")
+      (description "Kmscon is a terminal emulator based on Linux's @dfn{kernel
 mode setting} (KMS).  It can replace the in-kernel virtual terminal (VT)
 implementation with a user-space console.  Compared to the Linux console,
 kmscon provides enhanced features including XKB-compatible internationalized
 keyboard support, UTF-8 input/font support, hardware-accelerated rendering,
 multi-seat support, a replacement for @command{mingetty}, and more.")
-    (home-page "https://www.freedesktop.org/wiki/Software/kmscon")
+      (home-page "https://www.freedesktop.org/wiki/Software/kmscon")
-    ;; Hash table implementation is lgpl2.1+ licensed.
+      ;; Hash table implementation is lgpl2.1+ licensed.
-    ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
+      ;; The wcwidth implementation in external/wcwidth.{h,c} uses a license
-    ;; derived from ISC.
+      ;; derived from ISC.
-    ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
+      ;; UCS-4 to UTF-8 encoding is copied from "terminology" which is released
-    ;; under the bsd 2 license.
+      ;; under the bsd 2 license.
-    ;; Unifont-Font is from http://unifoundry.com/unifont.html and licensed
+      ;; Unifont-Font is from http://unifoundry.com/unifont.html and licensed
-    ;; under the terms of the GNU GPL.
+      ;; under the terms of the GNU GPL.
-    (license (list license:expat license:lgpl2.1+ license:bsd-2
+      (license (list license:expat license:lgpl2.1+ license:bsd-2
-                   license:gpl2+))
+                     license:gpl2+))
-    (supported-systems (filter (cut string-suffix? "-linux" <>)
+      (supported-systems (filter (cut string-suffix? "-linux" <>)
-                               %supported-systems))))
+                                 %supported-systems)))))
 
 (define-public libtermkey
   (package

gnu/packages/terraform.scm

@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,13 +22,12 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix build-system go)
+  #:use-module (guix build-system go))
-  #:use-module (gnu packages golang))
 
 (define-public terraform-docs
   (package
     (name "terraform-docs")
-    (version "0.3.0")
+    (version "0.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -36,11 +36,8 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xchpik32ab8m89s6jv671vswg8xhprfvh6s5md0zd36482d2nmm"))))
+                "12w2yr669hk5kxdb9rrzsn8hwvx8rzrc1rmn8hs9l8z1bkfhr4gg"))))
     (build-system go-build-system)
-    (native-inputs
-     `(("go-github-com-hashicorp-hcl" ,go-github-com-hashicorp-hcl)
-       ("go-github-com-tj-docopt" ,go-github-com-tj-docopt)))
     (arguments
      '(#:import-path "github.com/segmentio/terraform-docs"))
     (synopsis "Generate documentation from Terraform modules")

gnu/packages/version-control.scm

@@ -469,7 +469,8 @@ everything from small to very large projects with speed and efficiency.")
               (sha256
                (base32
                 "15kp4sq72kh762bm7dgspyrk0a6siarvll3k7nrhs0xy77idf80g"))
-              (patches (search-patches "libgit2-mtime-0.patch"))
+              (patches (search-patches "libgit2-mtime-0.patch"
+                                       "libgit2-oom-test.patch"))
 
               ;; Remove bundled software.
               (snippet '(begin

gnu/packages/video.scm

@@ -614,14 +614,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
 (define-public ffmpeg
   (package
     (name "ffmpeg")
-    (version "4.0.3")
+    (version "4.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1vg229mxcrm415cq6q1nfm891hm4x56mb5p4cqjnlqnky7ikfg15"))))
+               "150rrm549fy1x71c9whmyi5knyd9sliwvmcsm438bdgg4v8c93m3"))))
     (build-system gnu-build-system)
     (inputs
      `(("fontconfig" ,fontconfig)
@@ -1269,7 +1269,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.10.05")
+    (version "2018.11.03")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1277,7 +1277,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1iq02kwxdgh07bf0w0fvbsjbdshs4kja35gy8m70ji9cj10l1mbw"))))
+                "11phhwhr1g050h4625d5jsgcsjnnv7jc6xcrbn7zdzd32f6gy2lj"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion

gnu/packages/web.scm

@@ -195,14 +195,14 @@ Interface} specification.")
     (name "nginx")
     ;; Consider updating the nginx-documentation package if the nginx package is
     ;; updated.
-    (version "1.14.0")
+    (version "1.14.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nginx.org/download/nginx-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1d9c0avfpbwvzyg53b59ks8shpnrxnbnshcd7ziizflsyv5vw5ax"))))
+                "19542jxcjf4dvrqvgb5vr36mhbzcjrxc3v0xh451rm60610rf2dz"))))
     (build-system gnu-build-system)
     (inputs `(("openssl" ,openssl)
               ("pcre" ,pcre)
@@ -4166,19 +4166,15 @@ It uses the uwsgi protocol for all the networking/interprocess communications.")
 (define-public jq
   (package
     (name "jq")
-    (version "1.5")
+    (version "1.6")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/stedolan/" name
+              (uri (string-append "https://github.com/stedolan/jq"
-                                  "/releases/download/" name "-" version
+                                  "/releases/download/jq-" version
-                                  "/" name "-" version ".tar.gz"))
+                                  "/jq-" version ".tar.gz"))
               (sha256
                (base32
-                "0g29kyz4ykasdcrb0zmbrp2jqs9kv1wz9swx849i2d1ncknbzln4"))
+                "1a76f46a652i2g333kfvrl6mp2w7whf6h1yly519izg4y967h9cn"))))
-              ;; This patch has been pushed and the vulnerability will be
-              ;; fixed in the next release after 1.5.
-              ;; https://github.com/stedolan/jq/issues/995
-              (patches (search-patches "jq-CVE-2015-8863.patch"))))
     (inputs
      `(("oniguruma" ,oniguruma)))
     (native-inputs

gnu/packages/xorg.scm

@@ -5453,6 +5453,58 @@ The XCB util module provides the following libraries:
       "file://COPYING"
       "See COPYING in the distribution."))))
 
+(define-public xcb-util-errors
+  (let ((commit "5d660ebe872cadcdc85de9d6f9afe05de629c030")
+        (revision "1"))
+    (package
+      (name "xcb-util-errors")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://anongit.freedesktop.org/git/xcb/util-errors.git")
+                      (commit commit)
+                      (recursive? #t)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "12bah0iz5k6b9hwlc5zffyfg2gnrajll3gn5s8zmazgynvw72ahg"))))
+     (build-system gnu-build-system)
+     (outputs '("out"))
+     (inputs
+      `(("util-macros" ,util-macros)
+        ("xcb-proto" ,xcb-proto)))
+     (propagated-inputs
+      `(("libxcb" ,libxcb)))
+     (native-inputs
+      `(("autoconf" ,autoconf)
+        ("automake" ,automake)
+        ("libtool" ,libtool)
+        ("python-2" ,python-2)
+        ("pkg-config" ,pkg-config)))
+     (arguments
+      `(#:phases
+        (modify-phases %standard-phases
+          (replace 'bootstrap
+            (lambda _
+              ;; The default 'bootstrap' phase would run 'autogen.sh', which
+              ;; would try to run ./configure and fail due to unpatched
+              ;; shebangs.
+              (invoke "autoreconf" "-v" "--install"))))))
+     (home-page "https://cgit.freedesktop.org/xcb/util-errors/")
+     (synopsis "XCB helper library for printing information about X11 errors")
+     (description
+      "The XCB util module provides a number of libraries which sit on
+top of libxcb, the core X protocol library, and some of the extension
+libraries.  These experimental libraries provide convenience functions
+and interfaces which make the raw X protocol more usable.  Some of the
+libraries also provide client-side code which is not strictly part of
+the X protocol but which has traditionally been provided by Xlib.
+
+The XCB util-errors module provides a utility library that gives human
+readable names to error codes, event codes, and also to major and minor
+numbers.")
+     (license license:x11))))
 
 (define-public xcb-util-image
   (package

gnu/services/base.scm

@@ -6,6 +6,7 @@
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2040,6 +2041,8 @@ This service is not part of @var{%base-services}."
                            (default (file-append shadow "/bin/login")))
   (login-arguments         kmscon-configuration-login-arguments
                            (default '("-p")))
+  (auto-login              kmscon-configuration-auto-login
+                           (default #f))
   (hardware-acceleration?  kmscon-configuration-hardware-acceleration?
                            (default #f))) ; #t causes failure
 
@@ -2051,14 +2054,20 @@ This service is not part of @var{%base-services}."
            (virtual-terminal (kmscon-configuration-virtual-terminal config))
            (login-program (kmscon-configuration-login-program config))
            (login-arguments (kmscon-configuration-login-arguments config))
+           (auto-login (kmscon-configuration-auto-login config))
            (hardware-acceleration? (kmscon-configuration-hardware-acceleration? config)))
 
        (define kmscon-command
          #~(list
             #$(file-append kmscon "/bin/kmscon") "--login"
             "--vt" #$virtual-terminal
+            "--no-switchvt" ;Prevent a switch to the virtual terminal.
             #$@(if hardware-acceleration? '("--hwaccel") '())
-            "--" #$login-program #$@login-arguments))
+            "--login" "--"
+            #$login-program #$@login-arguments
+            #$@(if auto-login
+                   #~(#$auto-login)
+                   #~())))
 
        (shepherd-service
         (documentation "kmscon virtual terminal")

gnu/services/cuirass.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
@@ -54,6 +54,8 @@
                     (default "/var/log/cuirass.log"))
   (cache-directory  cuirass-configuration-cache-directory ;string (dir-name)
                     (default "/var/cache/cuirass"))
+  (ttl              cuirass-configuration-ttl     ;integer
+                    (default (* 30 24 3600)))
   (user             cuirass-configuration-user ;string
                     (default "cuirass"))
   (group            cuirass-configuration-group ;string
@@ -86,6 +88,7 @@
          (group            (cuirass-configuration-group config))
          (interval         (cuirass-configuration-interval config))
          (database         (cuirass-configuration-database config))
+         (ttl              (cuirass-configuration-ttl config))
          (port             (cuirass-configuration-port config))
          (host             (cuirass-configuration-host config))
          (specs            (cuirass-configuration-specifications config))
@@ -102,6 +105,7 @@
                             "--specifications"
                             #$(scheme-file "cuirass-specs.scm" specs)
                             "--database" #$database
+                            "--ttl" #$(string-append (number->string ttl) "s")
                             "--port" #$(number->string port)
                             "--listen" #$host
                             "--interval" #$(number->string interval)

gnu/services/dns.scm

@@ -763,9 +763,9 @@ manually.")
         (use-modules (guix build utils)
                      (ice-9 rdelim))
         (let ((ddclient-user
-               #$(passwd:uid (getpw (ddclient-configuration-user config))))
+               (passwd:uid (getpw #$(ddclient-configuration-user config))))
               (ddclient-group
-               #$(passwd:gid (getpw (ddclient-configuration-group config))))
+               (passwd:gid (getpw #$(ddclient-configuration-group config))))
               (ddclient-secret-file
                #$(ddclient-configuration-secret-file config)))
           ;; 'ddclient' complains about ddclient.conf file permissions, which

guix/build-system/r.scm

@@ -53,7 +53,7 @@ release corresponding to NAME and VERSION."
   (list (string-append "https://bioconductor.org/packages/release/bioc/src/contrib/"
                        name "_" version ".tar.gz")
         ;; TODO: use %bioconductor-version from (guix import cran)
-        (string-append "https://bioconductor.org/packages/3.7/bioc/src/contrib/Archive/"
+        (string-append "https://bioconductor.org/packages/3.8/bioc/src/contrib/Archive/"
                        name "_" version ".tar.gz")))
 
 (define %r-build-system-modules

guix/build/store-copy.scm

@@ -168,6 +168,28 @@ REFERENCE-GRAPHS, a list of reference-graph files."
 
   (reduce + 0 (map file-size items)))
 
+(define (reset-permissions file)
+  "Reset the permissions on FILE and its sub-directories so that they are all
+read-only."
+  ;; XXX: This procedure exists just to work around the inability of
+  ;; 'copy-recursively' to preserve permissions.
+  (file-system-fold (const #t)                    ;enter?
+                    (lambda (file stat _)         ;leaf
+                      (unless (eq? 'symlink (stat:type stat))
+                        (chmod file
+                               (if (zero? (logand (stat:mode stat)
+                                                  #o100))
+                                   #o444
+                                   #o555))))
+                    (const #t)                    ;down
+                    (lambda (directory stat _)    ;up
+                      (chmod directory #o555))
+                    (const #f)                    ;skip
+                    (const #f)                    ;error
+                    #t
+                    file
+                    lstat))
+
 (define* (populate-store reference-graphs target
                          #:key (log-port (current-error-port)))
   "Populate the store under directory TARGET with the items specified in
@@ -197,7 +219,13 @@ REFERENCE-GRAPHS, a list of reference-graph files."
         (for-each (lambda (thing)
                     (copy-recursively thing
                                       (string-append target thing)
+                                      #:keep-mtime? #t
                                       #:log (%make-void-port "w"))
+
+                    ;; XXX: Since 'copy-recursively' doesn't allow us to
+                    ;; preserve permissions, we have to traverse TARGET to
+                    ;; make sure everything is read-only.
+                    (reset-permissions (string-append target thing))
                     (report))
                   things)))))
 

guix/docker.scm

@@ -26,6 +26,7 @@
                           delete-file-recursively
                           with-directory-excursion
                           invoke))
+  #:use-module (gnu build install)
   #:use-module (json)                             ;guile-json
   #:use-module (srfi srfi-19)
   #:use-module (srfi srfi-26)
@@ -108,11 +109,15 @@ return \"a\"."
                              (symlinks '())
                              (transformations '())
                              (system (utsname:machine (uname)))
+                             database
                              compressor
                              (creation-time (current-time time-utc)))
   "Write to IMAGE a Docker image archive containing the given PATHS.  PREFIX
 must be a store path that is a prefix of any store paths in PATHS.
 
+When DATABASE is true, copy it to /var/guix/db in the image and create
+/var/guix/gcroots and friends.
+
 SYMLINKS must be a list of (SOURCE -> TARGET) tuples describing symlinks to be
 created in the image, where each TARGET is relative to PREFIX.
 TRANSFORMATIONS must be a list of (OLD -> NEW) tuples describing how to
@@ -188,10 +193,15 @@ SRFI-19 time-utc object, as the creation time in metadata."
                                 source))))
                   symlinks)
 
+        (when database
+          ;; Initialize /var/guix, assuming PREFIX points to a profile.
+          (install-database-and-gc-roots "." database prefix))
+
         (apply invoke "tar" "-cf" "layer.tar"
                `(,@transformation-options
                  ,@%tar-determinism-options
                  ,@paths
+                 ,@(if database '("var") '())
                  ,@(map symlink-source symlinks)))
         ;; It is possible for "/" to show up in the archive, especially when
         ;; applying transformations.  For example, the transformation
@@ -203,7 +213,11 @@ SRFI-19 time-utc object, as the creation time in metadata."
         (system* "tar" "--delete" "/" "-f" "layer.tar")
         (for-each delete-file-recursively
                   (map (compose topmost-component symlink-source)
-                       symlinks)))
+                       symlinks))
+
+        ;; Delete /var/guix.
+        (when database
+          (delete-file-recursively "var")))
 
       (with-output-to-file "config.json"
         (lambda ()

guix/import/cran.scm

@@ -127,9 +127,9 @@ package definition."
 (define %cran-url "http://cran.r-project.org/web/packages/")
 (define %bioconductor-url "https://bioconductor.org/packages/")
 
-;; The latest Bioconductor release is 3.7.  Bioconductor packages should be
+;; The latest Bioconductor release is 3.8.  Bioconductor packages should be
 ;; updated together.
-(define %bioconductor-version "3.7")
+(define %bioconductor-version "3.8")
 
 (define %bioconductor-packages-list-url
   (string-append "https://bioconductor.org/packages/"

guix/scripts/pack.scm

@@ -52,6 +52,9 @@
   #:export (compressor?
             lookup-compressor
             self-contained-tarball
+            docker-image
+            squashfs-image
+
             guix-pack))
 
 ;; Type of a compression tool.
@@ -103,6 +106,47 @@ found."
                       (package-transitive-propagated-inputs package)))
               (list guile-gcrypt guile-sqlite3)))
 
+(define (store-database items)
+  "Return a directory containing a store database where all of ITEMS and their
+dependencies are registered."
+  (define schema
+    (local-file (search-path %load-path
+                             "guix/store/schema.sql")))
+
+
+  (define labels
+    (map (lambda (n)
+           (string-append "closure" (number->string n)))
+         (iota (length items))))
+
+  (define build
+    (with-extensions gcrypt-sqlite3&co
+      ;; XXX: Adding (gnu build install) just to work around
+      ;; <https://bugs.gnu.org/15602>: that way, (guix build store-copy) is
+      ;; copied last and the 'store-info-XXX' macros are correctly expanded.
+      (with-imported-modules (source-module-closure
+                              '((guix build store-copy)
+                                (guix store database)
+                                (gnu build install)))
+        #~(begin
+            (use-modules (guix store database)
+                         (guix build store-copy)
+                         (srfi srfi-1))
+
+            (define (read-closure closure)
+              (call-with-input-file closure read-reference-graph))
+
+            (let ((items (append-map read-closure '#$labels)))
+              (register-items items
+                              #:state-directory #$output
+                              #:deduplicate? #f
+                              #:reset-timestamps? #f
+                              #:registration-time %epoch
+                              #:schema #$schema))))))
+
+  (computed-file "store-database" build
+                 #:options `(#:references-graphs ,(zip labels items))))
+
 (define* (self-contained-tarball name profile
                                  #:key target
                                  deduplicate?
@@ -117,121 +161,116 @@ with a properly initialized store database.
 
 SYMLINKS must be a list of (SOURCE -> TARGET) tuples denoting symlinks to be
 added to the pack."
-  (define schema
+  (define database
     (and localstatedir?
-         (local-file (search-path %load-path
+         (file-append (store-database (list profile))
-                                  "guix/store/schema.sql"))))
+                      "/db/db.sqlite")))
 
   (define build
-    (with-imported-modules `(((guix config) => ,(make-config.scm))
+    (with-imported-modules (source-module-closure
-                             ,@(source-module-closure
+                            `((guix build utils)
-                                `((guix build utils)
+                              (guix build union)
-                                  (guix build union)
+                              (gnu build install))
-                                  (guix build store-copy)
+                            #:select? not-config?)
-                                  (gnu build install))
+      #~(begin
-                                #:select? not-config?))
+          (use-modules (guix build utils)
-      (with-extensions gcrypt-sqlite3&co
+                       ((guix build union) #:select (relative-file-name))
-        #~(begin
+                       (gnu build install)
-            (use-modules (guix build utils)
+                       (srfi srfi-1)
-                         ((guix build union) #:select (relative-file-name))
+                       (srfi srfi-26)
-                         (gnu build install)
+                       (ice-9 match))
-                         (srfi srfi-1)
-                         (srfi srfi-26)
-                         (ice-9 match))
 
-            (define %root "root")
+          (define %root "root")
 
-            (define symlink->directives
+          (define symlink->directives
-              ;; Return "populate directives" to make the given symlink and its
+            ;; Return "populate directives" to make the given symlink and its
-              ;; parent directories.
+            ;; parent directories.
-              (match-lambda
+            (match-lambda
-                ((source '-> target)
+              ((source '-> target)
-                 (let ((target (string-append #$profile "/" target))
+               (let ((target (string-append #$profile "/" target))
-                       (parent (dirname source)))
+                     (parent (dirname source)))
-                   ;; Never add a 'directory' directive for "/" so as to
+                 ;; Never add a 'directory' directive for "/" so as to
-                   ;; preserve its ownnership when extracting the archive (see
+                 ;; preserve its ownnership when extracting the archive (see
-                   ;; below), and also because this would lead to adding the
+                 ;; below), and also because this would lead to adding the
-                   ;; same entries twice in the tarball.
+                 ;; same entries twice in the tarball.
-                   `(,@(if (string=? parent "/")
+                 `(,@(if (string=? parent "/")
-                           '()
+                         '()
-                           `((directory ,parent)))
+                         `((directory ,parent)))
-                     (,source
+                   (,source
-                      -> ,(relative-file-name parent target)))))))
+                    -> ,(relative-file-name parent target)))))))
 
-            (define directives
+          (define directives
-              ;; Fully-qualified symlinks.
+            ;; Fully-qualified symlinks.
-              (append-map symlink->directives '#$symlinks))
+            (append-map symlink->directives '#$symlinks))
 
-            ;; The --sort option was added to GNU tar in version 1.28, released
+          ;; The --sort option was added to GNU tar in version 1.28, released
-            ;; 2014-07-28.  For testing, we use the bootstrap tar, which is
+          ;; 2014-07-28.  For testing, we use the bootstrap tar, which is
-            ;; older and doesn't support it.
+          ;; older and doesn't support it.
-            (define tar-supports-sort?
+          (define tar-supports-sort?
-              (zero? (system* (string-append #+archiver "/bin/tar")
+            (zero? (system* (string-append #+archiver "/bin/tar")
-                              "cf" "/dev/null" "--files-from=/dev/null"
+                            "cf" "/dev/null" "--files-from=/dev/null"
-                              "--sort=name")))
+                            "--sort=name")))
 
-            ;; Add 'tar' to the search path.
+          ;; Add 'tar' to the search path.
-            (setenv "PATH" #+(file-append archiver "/bin"))
+          (setenv "PATH" #+(file-append archiver "/bin"))
 
-            ;; Note: there is not much to gain here with deduplication and there
+          ;; Note: there is not much to gain here with deduplication and there
-            ;; is the overhead of the '.links' directory, so turn it off.
+          ;; is the overhead of the '.links' directory, so turn it off.
-            ;; Furthermore GNU tar < 1.30 sometimes fails to extract tarballs
+          ;; Furthermore GNU tar < 1.30 sometimes fails to extract tarballs
-            ;; with hard links:
+          ;; with hard links:
-            ;; <http://lists.gnu.org/archive/html/bug-tar/2017-11/msg00009.html>.
+          ;; <http://lists.gnu.org/archive/html/bug-tar/2017-11/msg00009.html>.
-            (populate-single-profile-directory %root
+          (populate-single-profile-directory %root
-                                               #:profile #$profile
+                                             #:profile #$profile
-                                               #:closure "profile"
+                                             #:closure "profile"
-                                               #:deduplicate? #f
+                                             #:database #+database)
-                                               #:register? #$localstatedir?
-                                               #:schema #$schema)
 
-            ;; Create SYMLINKS.
+          ;; Create SYMLINKS.
-            (for-each (cut evaluate-populate-directive <> %root)
+          (for-each (cut evaluate-populate-directive <> %root)
-                      directives)
+                    directives)
 
-            ;; Create the tarball.  Use GNU format so there's no file name
+          ;; Create the tarball.  Use GNU format so there's no file name
-            ;; length limitation.
+          ;; length limitation.
-            (with-directory-excursion %root
+          (with-directory-excursion %root
-              (exit
+            (exit
-               (zero? (apply system* "tar"
+             (zero? (apply system* "tar"
-                             #+@(if (compressor-command compressor)
+                           #+@(if (compressor-command compressor)
-                                    #~("-I"
+                                  #~("-I"
-                                       (string-join
+                                     (string-join
-                                        '#+(compressor-command compressor)))
+                                      '#+(compressor-command compressor)))
-                                    #~())
+                                  #~())
-                             "--format=gnu"
+                           "--format=gnu"
 
-                             ;; Avoid non-determinism in the archive.  Use
+                           ;; Avoid non-determinism in the archive.  Use
-                             ;; mtime = 1, not zero, because that is what the
+                           ;; mtime = 1, not zero, because that is what the
-                             ;; daemon does for files in the store (see the
+                           ;; daemon does for files in the store (see the
-                             ;; 'mtimeStore' constant in local-store.cc.)
+                           ;; 'mtimeStore' constant in local-store.cc.)
-                             (if tar-supports-sort? "--sort=name" "--mtime=@1")
+                           (if tar-supports-sort? "--sort=name" "--mtime=@1")
-                             "--mtime=@1"         ;for files in /var/guix
+                           "--mtime=@1"           ;for files in /var/guix
-                             "--owner=root:0"
+                           "--owner=root:0"
-                             "--group=root:0"
+                           "--group=root:0"
 
-                             "--check-links"
+                           "--check-links"
-                             "-cvf" #$output
+                           "-cvf" #$output
-                             ;; Avoid adding / and /var to the tarball, so
+                           ;; Avoid adding / and /var to the tarball, so
-                             ;; that the ownership and permissions of those
+                           ;; that the ownership and permissions of those
-                             ;; directories will not be overwritten when
+                           ;; directories will not be overwritten when
-                             ;; extracting the archive.  Do not include /root
+                           ;; extracting the archive.  Do not include /root
-                             ;; because the root account might have a
+                           ;; because the root account might have a
-                             ;; different home directory.
+                           ;; different home directory.
-                             #$@(if localstatedir?
+                           #$@(if localstatedir?
-                                    '("./var/guix")
+                                  '("./var/guix")
-                                    '())
+                                  '())
 
-                             (string-append "." (%store-directory))
+                           (string-append "." (%store-directory))
 
-                             (delete-duplicates
+                           (delete-duplicates
-                              (filter-map (match-lambda
+                            (filter-map (match-lambda
-                                            (('directory directory)
+                                          (('directory directory)
-                                             (string-append "." directory))
+                                           (string-append "." directory))
-                                            ((source '-> _)
+                                          ((source '-> _)
-                                             (string-append "." source))
+                                           (string-append "." source))
-                                            (_ #f))
+                                          (_ #f))
-                                          directives))))))))))
+                                        directives)))))))))
 
   (gexp->derivation (string-append name ".tar"
                                    (compressor-extension compressor))
@@ -240,7 +279,6 @@ added to the pack."
 
 (define* (squashfs-image name profile
                          #:key target
-                         deduplicate?
                          (compressor (first %compressors))
                          localstatedir?
                          (symlinks '())
@@ -251,75 +289,85 @@ points for virtual file systems (like procfs), and optional symlinks.
 
 SYMLINKS must be a list of (SOURCE -> TARGET) tuples denoting symlinks to be
 added to the pack."
+  (define database
+    (and localstatedir?
+         (file-append (store-database (list profile))
+                      "/db/db.sqlite")))
+
   (define build
-    (with-imported-modules `(((guix config) => ,(make-config.scm))
+    (with-imported-modules (source-module-closure
-                             ,@(source-module-closure
+                            '((guix build utils)
-                                '((guix build utils)
+                              (guix build store-copy)
-                                  (guix build store-copy)
+                              (gnu build install))
-                                  (gnu build install))
+                            #:select? not-config?)
-                                #:select? not-config?))
+      #~(begin
-      (with-extensions gcrypt-sqlite3&co
+          (use-modules (guix build utils)
-        #~(begin
+                       (guix build store-copy)
-            (use-modules (guix build utils)
+                       (gnu build install)
-                         (gnu build install)
+                       (srfi srfi-1)
-                         (guix build store-copy)
+                       (srfi srfi-26)
-                         (srfi srfi-1)
+                       (ice-9 match))
-                         (srfi srfi-26)
-                         (ice-9 match))
 
-            (setenv "PATH" (string-append #$archiver "/bin"))
+          (define database #+database)
 
-            ;; We need an empty file in order to have a valid file argument when
+          (setenv "PATH" (string-append #$archiver "/bin"))
-            ;; we reparent the root file system.  Read on for why that's
-            ;; necessary.
-            (with-output-to-file ".empty" (lambda () (display "")))
 
-            ;; Create the squashfs image in several steps.
+          ;; We need an empty file in order to have a valid file argument when
-            ;; Add all store items.  Unfortunately mksquashfs throws away all
+          ;; we reparent the root file system.  Read on for why that's
-            ;; ancestor directories and only keeps the basename.  We fix this
+          ;; necessary.
-            ;; in the following invocations of mksquashfs.
+          (with-output-to-file ".empty" (lambda () (display "")))
-            (apply invoke "mksquashfs"
-                   `(,@(map store-info-item
-                            (call-with-input-file "profile"
-                              read-reference-graph))
-                     ,#$output
 
-                     ;; Do not perform duplicate checking because we
+          ;; Create the squashfs image in several steps.
-                     ;; don't have any dupes.
+          ;; Add all store items.  Unfortunately mksquashfs throws away all
-                     "-no-duplicates"
+          ;; ancestor directories and only keeps the basename.  We fix this
-                     "-comp"
+          ;; in the following invocations of mksquashfs.
-                     ,#+(compressor-name compressor)))
+          (apply invoke "mksquashfs"
+                 `(,@(map store-info-item
+                          (call-with-input-file "profile"
+                            read-reference-graph))
+                   ,#$output
 
-            ;; Here we reparent the store items.  For each sub-directory of
+                   ;; Do not perform duplicate checking because we
-            ;; the store prefix we need one invocation of "mksquashfs".
+                   ;; don't have any dupes.
-            (for-each (lambda (dir)
+                   "-no-duplicates"
-                        (apply invoke "mksquashfs"
+                   "-comp"
-                               `(".empty"
+                   ,#+(compressor-name compressor)))
-                                 ,#$output
-                                 "-root-becomes" ,dir)))
-                      (reverse (string-tokenize (%store-directory)
-                                                (char-set-complement (char-set #\/)))))
 
-            ;; Add symlinks and mount points.
+          ;; Here we reparent the store items.  For each sub-directory of
-            (apply invoke "mksquashfs"
+          ;; the store prefix we need one invocation of "mksquashfs".
-                   `(".empty"
+          (for-each (lambda (dir)
-                     ,#$output
+                      (apply invoke "mksquashfs"
-                     ;; Create SYMLINKS via pseudo file definitions.
+                             `(".empty"
-                     ,@(append-map
+                               ,#$output
-                        (match-lambda
+                               "-root-becomes" ,dir)))
-                          ((source '-> target)
+                    (reverse (string-tokenize (%store-directory)
-                           (list "-p"
+                                              (char-set-complement (char-set #\/)))))
-                                 (string-join
-                                  ;; name s mode uid gid symlink
-                                  (list source
-                                        "s" "777" "0" "0"
-                                        (string-append #$profile "/" target))))))
-                        '#$symlinks)
 
-                     ;; Create empty mount points.
+          ;; Add symlinks and mount points.
-                     "-p" "/proc d 555 0 0"
+          (apply invoke "mksquashfs"
-                     "-p" "/sys d 555 0 0"
+                 `(".empty"
-                     "-p" "/dev d 555 0 0"))))))
+                   ,#$output
+                   ;; Create SYMLINKS via pseudo file definitions.
+                   ,@(append-map
+                      (match-lambda
+                        ((source '-> target)
+                         (list "-p"
+                               (string-join
+                                ;; name s mode uid gid symlink
+                                (list source
+                                      "s" "777" "0" "0"
+                                      (string-append #$profile "/" target))))))
+                      '#$symlinks)
+
+                   ;; Create empty mount points.
+                   "-p" "/proc d 555 0 0"
+                   "-p" "/sys d 555 0 0"
+                   "-p" "/dev d 555 0 0"))
+
+          (when database
+            ;; Initialize /var/guix.
+            (install-database-and-gc-roots "var-etc" database #$profile)
+            (invoke "mksquashfs" "var-etc" #$output)))))
 
   (gexp->derivation (string-append name
                                    (compressor-extension compressor)
@@ -329,7 +377,6 @@ added to the pack."
 
 (define* (docker-image name profile
                        #:key target
-                       deduplicate?
                        (compressor (first %compressors))
                        localstatedir?
                        (symlinks '())
@@ -339,6 +386,11 @@ image is a tarball conforming to the Docker Image Specification, compressed
 with COMPRESSOR.  It can be passed to 'docker load'.  If TARGET is true, it
 must a be a GNU triplet and it is used to derive the architecture metadata in
 the image."
+  (define database
+    (and localstatedir?
+         (file-append (store-database (list profile))
+                      "/db/db.sqlite")))
+
   (define defmod 'define-module)                  ;trick Geiser
 
   (define build
@@ -357,6 +409,7 @@ the image."
                                      (call-with-input-file "profile"
                                        read-reference-graph))
                                 #$profile
+                                #:database #+database
                                 #:system (or #$target (utsname:machine (uname)))
                                 #:symlinks '#$symlinks
                                 #:compressor '#$(compressor-command compressor)

guix/scripts/pull.scm

@@ -86,6 +86,8 @@ Download and deploy the latest version of Guix.\n"))
                          list generations matching PATTERN"))
   (display (G_ "
   -p, --profile=PROFILE  use PROFILE instead of ~/.config/guix/current"))
+  (display (G_ "
+  -n, --dry-run          show what would be pulled and built"))
   (display (G_ "
       --bootstrap        use the bootstrap Guile to build the new Guix"))
   (newline)
@@ -164,15 +166,18 @@ Download and deploy the latest version of Guix.\n"))
     (_ #t)))
 
 (define* (build-and-install instances profile
-                            #:key verbose?)
+                            #:key verbose? dry-run?)
-  "Build the tool from SOURCE, and install it in PROFILE."
+  "Build the tool from SOURCE, and install it in PROFILE.  When DRY-RUN? is
+true, display what would be built without actually building it."
   (define update-profile
     (store-lift build-and-use-profile))
 
   (mlet %store-monad ((manifest (channel-instances->manifest instances)))
     (mbegin %store-monad
-      (update-profile profile manifest)
+      (update-profile profile manifest
-      (return (display-profile-news profile)))))
+                      #:dry-run? dry-run?)
+      (munless dry-run?
+        (display-profile-news profile)))))
 
 (define (honor-lets-encrypt-certificates! store)
   "Tell Guile-Git to use the Let's Encrypt certificates."
@@ -497,8 +502,6 @@ Use '~/.config/guix/channels.scm' instead."))
        (ensure-default-profile)
        (cond ((assoc-ref opts 'query)
               (process-query opts profile))
-             ((assoc-ref opts 'dry-run?)
-              #t)                                 ;XXX: not very useful
              (else
               (with-store store
                 (with-status-report print-build-event
@@ -531,6 +534,8 @@ Use '~/.config/guix/channels.scm' instead."))
                                            (canonical-package guile-2.2)))))
                         (run-with-store store
                           (build-and-install instances profile
+                                             #:dry-run?
+                                             (assoc-ref opts 'dry-run?)
                                              #:verbose?
                                              (assoc-ref opts 'verbose?))))))))))))))
 

guix/self.scm

@@ -206,21 +206,22 @@ list of file-name/file-like objects suitable as inputs to 'imported-files'."
                (local-file file #:recursive? #t)))
        (find-files (string-append directory "/" sub-directory) pred)))
 
-(define* (sub-directory item sub-directory)
+(define* (file-append* item file #:key (recursive? #t))
-  "Return SUB-DIRECTORY within ITEM, which may be a file name or a file-like
+  "Return FILE within ITEM, which may be a file name or a file-like object.
-object."
+When ITEM is a plain file name (a string), simply return a 'local-file'
+record with the new file name."
   (match item
     ((? string?)
      ;; This is the optimal case: we return a new "source".  Thus, a
      ;; derivation that depends on this sub-directory does not depend on ITEM
      ;; itself.
-     (local-file (string-append item "/" sub-directory)
+     (local-file (string-append item "/" file)
-                 #:recursive? #t))
+                 #:recursive? recursive?))
     ;; TODO: Add 'local-file?' case.
     (_
      ;; In this case, anything that refers to the result also depends on ITEM,
      ;; which isn't great.
-     (file-append item "/" sub-directory))))
+     (file-append item "/" file))))
 
 (define* (locale-data source domain
                       #:optional (directory domain))
@@ -238,7 +239,7 @@ DOMAIN, a gettext domain."
                        (ice-9 match) (ice-9 ftw))
 
           (define po-directory
-            #+(sub-directory source (string-append "po/" directory)))
+            #+(file-append* source (string-append "po/" directory)))
 
           (define (compile language)
             (let ((gmo (string-append #$output "/" language "/LC_MESSAGES/"
@@ -273,10 +274,10 @@ DOMAIN, a gettext domain."
                 'graphviz))
 
   (define documentation
-    (sub-directory source "doc"))
+    (file-append* source "doc"))
 
   (define examples
-    (sub-directory source "gnu/system/examples"))
+    (file-append* source "gnu/system/examples"))
 
   (define build
     (with-imported-modules '((guix build utils))
@@ -290,7 +291,7 @@ DOMAIN, a gettext domain."
           ;; doesn't change at each commit?
           (call-with-output-file "version.texi"
             (lambda (port)
-              (let ((version "0.0-git)"))
+              (let ((version "0.0-git"))
                 (format port "
 @set UPDATED 1 January 1970
 @set UPDATED-MONTH January 1970
@@ -404,11 +405,29 @@ load path."
                       (apply guix-main (command-line))))
                 #:guile guile))
 
+(define (miscellaneous-files source)
+  "Return data files taken from SOURCE."
+  (file-mapping "guix-misc"
+                `(("etc/bash_completion.d/guix"
+                   ,(file-append* source "/etc/completion/bash/guix"))
+                  ("etc/bash_completion.d/guix-daemon"
+                   ,(file-append* source "/etc/completion/bash/guix-daemon"))
+                  ("share/zsh/site-functions/_guix"
+                   ,(file-append* source "/etc/completion/zsh/_guix"))
+                  ("share/fish/vendor_completions.d/guix.fish"
+                   ,(file-append* source "/etc/completion/fish/guix.fish"))
+                  ("share/guix/hydra.gnu.org.pub"
+                   ,(file-append* source
+                                  "/etc/substitutes/hydra.gnu.org.pub"))
+                  ("share/guix/berlin.guixsd.org.pub"
+                   ,(file-append* source "/etc/substitutes/berlin.guixsd.org.pub")))))
+
 (define* (whole-package name modules dependencies
                         #:key
                         (guile-version (effective-version))
                         compiled-modules
-                        info daemon guile
+                        info daemon miscellany
+                        guile
                         (command (guix-command modules
                                                #:dependencies dependencies
                                                #:guile guile
@@ -422,6 +441,7 @@ assumed to be part of MODULES."
                  (with-imported-modules '((guix build utils))
                    #~(begin
                        (use-modules (guix build utils))
+
                        (mkdir-p (string-append #$output "/bin"))
                        (symlink #$command
                                 (string-append #$output "/bin/guix"))
@@ -441,6 +461,10 @@ assumed to be part of MODULES."
                                     (string-append #$output
                                                    "/share/info"))))
 
+                       (when #$miscellany
+                         (copy-recursively #$miscellany #$output
+                                           #:log (%make-void-port "w")))
+
                        ;; Object files.
                        (when #$compiled-modules
                          (let ((modules (string-append #$output "/lib/guile/"
@@ -666,6 +690,7 @@ assumed to be part of MODULES."
                                                'guix-daemon)
 
                           #:info (info-manual source)
+                          #:miscellany (miscellaneous-files source)
                           #:guile-version guile-version)))
         ((= 0 pull-version)
          ;; Legacy 'guix pull': return the .scm and .go files as one

guix/ssh.scm

@@ -161,7 +161,7 @@ Throw an error on failure."
                                     "/var/guix/daemon-socket/socket"))
   "Connect to the remote build daemon listening on SOCKET-NAME over SESSION,
 an SSH session.  Return a <nix-server> object."
-  (open-connection #:port (remote-daemon-channel session)))
+  (open-connection #:port (remote-daemon-channel session socket-name)))
 
 
 (define (store-import-channel session)

po/guix/de.po

@@ -9,7 +9,7 @@ msgstr ""
 "Project-Id-Version: guix 0.15.0\n"
 "Report-Msgid-Bugs-To: ludo@gnu.org\n"
 "POT-Creation-Date: 2018-06-22 14:08+0200\n"
-"PO-Revision-Date: 2018-08-24 20:57+0200\n"
+"PO-Revision-Date: 2018-10-27 02:22+0200\n"
 "Last-Translator: Mario Blättermann <mario.blaettermann@gmail.com>\n"
 "Language-Team: German <translation-team-de@lists.sourceforge.net>\n"
 "Language: de\n"
@@ -437,7 +437,7 @@ msgid ""
 "      --no-build-hook    do not attempt to offload builds via the build hook"
 msgstr ""
 "\n"
-"      --no-build-hook    nicht versuchen, Erstellungen über den »build hook«\n"
+"      --no-build-hook    nicht versuchen, Erstellungen über den »Build-Hook«\n"
 "                           auszulagern"
 
 #: guix/scripts/build.scm:362
@@ -497,7 +497,7 @@ msgstr ""
 #: guix/scripts/build.scm:479 guix/scripts/build.scm:486
 #, scheme-format
 msgid "not a number: '~a' option argument: ~a~%"
-msgstr "Keine Zahl: Kommandozeilenargument von »~a«: ~a~%"
+msgstr "Keine Zahl: Befehlszeilenargument von »~a«: ~a~%"
 
 #: guix/scripts/build.scm:505
 msgid ""
@@ -658,7 +658,7 @@ msgid ""
 "invalid argument: '~a' option argument: ~a, ~\n"
 "must be one of 'package', 'all', or 'transitive'~%"
 msgstr ""
-"Ungültiges Argument der Kommandozeilenoption »~a«: ~a, ~\n"
+"Ungültiges Argument der Befehlszeilenoption »~a«: ~a, ~\n"
 "muss entweder »package«, »all« oder »transitive« sein~%"
 
 #: guix/scripts/build.scm:621
@@ -1018,7 +1018,7 @@ msgstr ""
 msgid "upgrade regexp '~a' looks like a command-line option~%"
 msgstr ""
 "--upgrade: Der reguläre Ausdruck »~a«\n"
-"sieht wie eine Kommandozeilenoption aus"
+"sieht wie eine Befehlszeilenoption aus"
 
 #: guix/scripts/package.scm:443
 #, scheme-format
@@ -1183,7 +1183,7 @@ msgstr "Es sind bereits ~h Bytes verfügbar auf ~a, nichts zu tun~%"
 
 #: guix/scripts/gc.scm:205
 msgid "freeing ~h bytes~%"
-msgstr "Gebe ~h Bytes frei~%"
+msgstr "~h Bytes werden freigegeben~%"
 
 #: guix/scripts/gc.scm:217
 #, scheme-format
@@ -1192,7 +1192,7 @@ msgstr "Zusätzliche Argumente: ~{~a ~}~%"
 
 #: guix/scripts/gc.scm:237 guix/scripts/gc.scm:240
 msgid "freed ~h bytes~%"
-msgstr "~h Bytes freigegeben"
+msgstr "~h Bytes wurden freigegeben"
 
 #: guix/scripts/hash.scm:47
 msgid ""
@@ -2885,7 +2885,7 @@ msgid ""
 "  -R, --relocatable      produce relocatable executables"
 msgstr ""
 "\n"
-"  -R, --relocatable      »portable« ausführbare Datei erzeugen"
+"  -R, --relocatable      pfad-agnostische ausführbare Datei erzeugen"
 
 #: guix/scripts/pack.scm:650
 msgid ""
@@ -3331,7 +3331,7 @@ msgstr "Generation ~a des Profils »~a« existiert nicht~%"
 #: guix/ui.scm:628
 #, scheme-format
 msgid "   ... propagated from ~a@~a~%"
-msgstr "   … propagatiert von ~a@~a~%"
+msgstr "   … propagiert von ~a@~a~%"
 
 #: guix/ui.scm:638
 #, scheme-format
@@ -3703,7 +3703,7 @@ msgstr "URLS als die vorgegebene Liste von Substitutsanbietern nutzen"
 
 #: nix/nix-daemon/guix-daemon.cc:117
 msgid "do not use the 'build hook'"
-msgstr "den »build hook« nicht benutzen"
+msgstr "den »Build-Hook« nicht benutzen"
 
 #: nix/nix-daemon/guix-daemon.cc:119
 msgid "cache build failures"

tests/guix-pack-relocatable.sh

@@ -0,0 +1,61 @@
+# GNU Guix --- Functional package management for GNU
+# Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+#
+# This file is part of GNU Guix.
+#
+# GNU Guix is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or (at
+# your option) any later version.
+#
+# GNU Guix is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+#
+# Test the 'guix pack --relocatable' using the external store, if any.
+#
+
+guix pack --version
+
+# 'guix pack --relocatable' requires a C compiler and libc.a, which our
+# bootstrap binaries don't provide.  To make the test relatively inexpensive,
+# run it on the user's global store if possible, on the grounds that binaries
+# may already be there or can be built or downloaded inexpensively.
+
+NIX_STORE_DIR="`guile -c '(use-modules (guix config))(display %storedir)'`"
+localstatedir="`guile -c '(use-modules (guix config))(display %localstatedir)'`"
+GUIX_DAEMON_SOCKET="$localstatedir/guix/daemon-socket/socket"
+export NIX_STORE_DIR GUIX_DAEMON_SOCKET
+
+if ! guile -c '(use-modules (guix)) (exit (false-if-exception (open-connection)))'
+then
+    exit 77
+fi
+
+STORE_PARENT="`dirname $NIX_STORE_DIR`"
+export STORE_PARENT
+if test "$STORE_PARENT" = "/"; then exit 77; fi
+
+# This test requires user namespaces and associated command-line tools.
+if ! unshare -mrf sh -c 'mount -t tmpfs none "$STORE_PARENT"'
+then
+    exit 77
+fi
+
+test_directory="`mktemp -d`"
+export test_directory
+trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT
+
+tarball="`guix pack -R -S /Bin=bin sed`"
+(cd "$test_directory"; tar xvf "$tarball")
+
+# Run that relocatable 'sed' in a user namespace where we "erase" the store by
+# mounting an empty file system on top of it.  That way, we exercise the
+# wrapper code that creates the user namespace and bind-mounts the store.
+unshare -mrf sh -c 'mount -t tmpfs none "$STORE_PARENT"; echo "$STORE_PARENT"/*; "$test_directory/Bin/sed" --version > "$test_directory/output"'
+grep 'GNU sed' "$test_directory/output"

tests/guix-pack.sh

@@ -29,39 +29,27 @@ fi
 
 guix pack --version
 
-# Starting from commit 66e9944e078cbb9e0d618377dd6df6e639640efa, 'guix pack'
+# Use --no-substitutes because we need to verify we can do this ourselves.
-# produces derivations that refer to guile-sqlite3 and libgcrypt.  To make
+GUIX_BUILD_OPTIONS="--no-substitutes"
-# that relatively inexpensive, run the test in the user's global store if
+export GUIX_BUILD_OPTIONS
-# possible, on the grounds that binaries may already be there or can be built
-# or downloaded inexpensively.
-
-NIX_STORE_DIR="`guile -c '(use-modules (guix config))(display %storedir)'`"
-localstatedir="`guile -c '(use-modules (guix config))(display %localstatedir)'`"
-GUIX_DAEMON_SOCKET="$localstatedir/guix/daemon-socket/socket"
-export NIX_STORE_DIR GUIX_DAEMON_SOCKET
-
-if ! guile -c '(use-modules (guix)) (exit (false-if-exception (open-connection)))'
-then
-    exit 77
-fi
 
 # Build a tarball with no compression.
-guix pack --compression=none guile-bootstrap
+guix pack --compression=none --bootstrap guile-bootstrap
 
 # Build a tarball (with compression).  Check that '-e' works as well.
-out1="`guix pack guile-bootstrap`"
+out1="`guix pack --bootstrap guile-bootstrap`"
-out2="`guix pack -e '(@ (gnu packages bootstrap) %bootstrap-guile)'`"
+out2="`guix pack --bootstrap -e '(@ (gnu packages bootstrap) %bootstrap-guile)'`"
 test -n "$out1"
 test "$out1" = "$out2"
 
 # Build a tarball with a symlink.
-the_pack="`guix pack -S /opt/gnu/bin=bin guile-bootstrap`"
+the_pack="`guix pack --bootstrap -S /opt/gnu/bin=bin guile-bootstrap`"
 
 # Try to extract it.  Note: we cannot test whether /opt/gnu/bin/guile itself
 # exists because /opt/gnu/bin may be an absolute symlink to a store item that
 # has been GC'd.
 test_directory="`mktemp -d`"
-trap 'rm -rf "$test_directory"' EXIT
+trap 'chmod -Rf +w "$test_directory"; rm -rf "$test_directory"' EXIT
 cd "$test_directory"
 tar -xf "$the_pack"
 test -L opt/gnu/bin

tests/pack.scm

@@ -22,20 +22,26 @@
   #:use-module (guix store)
   #:use-module (guix derivations)
   #:use-module (guix profiles)
+  #:use-module (guix packages)
   #:use-module (guix monads)
   #:use-module (guix grafts)
   #:use-module (guix tests)
   #:use-module (guix gexp)
   #:use-module (gnu packages bootstrap)
+  #:use-module ((gnu packages compression) #:select (squashfs-tools-next))
   #:use-module (srfi srfi-64))
 
+(define %store
+  (open-connection-for-tests))
+
 ;; Globally disable grafts because they can trigger early builds.
 (%graft? #f)
 
 (define-syntax-rule (test-assertm name store exp)
   (test-assert name
-    (run-with-store store exp
+    (let ((guile (package-derivation store %bootstrap-guile)))
-                    #:guile-for-build (%guile-for-build))))
+      (run-with-store store exp
+                      #:guile-for-build guile))))
 
 (define %gzip-compressor
   ;; Compressor that uses the bootstrap 'gzip'.
@@ -48,6 +54,58 @@
 
 (test-begin "pack")
 
+(unless (network-reachable?) (test-skip 1))
+(test-assertm "self-contained-tarball" %store
+  (mlet* %store-monad
+      ((profile (profile-derivation (packages->manifest
+                                     (list %bootstrap-guile))
+                                    #:hooks '()
+                                    #:locales? #f))
+       (tarball (self-contained-tarball "pack" profile
+                                        #:symlinks '(("/bin/Guile"
+                                                      -> "bin/guile"))
+                                        #:compressor %gzip-compressor
+                                        #:archiver %tar-bootstrap))
+       (check   (gexp->derivation
+                 "check-tarball"
+                 (with-imported-modules '((guix build utils))
+                   #~(begin
+                       (use-modules (guix build utils)
+                                    (srfi srfi-1))
+
+                       (define store
+                         ;; The unpacked store.
+                         (string-append "." (%store-directory) "/"))
+
+                       (define (canonical? file)
+                         ;; Return #t if FILE is read-only and its mtime is 1.
+                         (let ((st (lstat file)))
+                           (or (not (string-prefix? store file))
+                               (eq? 'symlink (stat:type st))
+                               (and (= 1 (stat:mtime st))
+                                    (zero? (logand #o222
+                                                   (stat:mode st)))))))
+
+                       (define bin
+                         (string-append "." #$profile "/bin"))
+
+                       (setenv "PATH"
+                               (string-append #$%tar-bootstrap "/bin"))
+                       (system* "tar" "xvf" #$tarball)
+                       (mkdir #$output)
+                       (exit
+                        (and (file-exists? (string-append bin "/guile"))
+                             (file-exists? store)
+                             (every canonical?
+                                    (find-files "." (const #t)
+                                                #:directories? #t))
+                             (string=? (string-append #$%bootstrap-guile "/bin")
+                                       (readlink bin))
+                             (string=? (string-append ".." #$profile
+                                                      "/bin/guile")
+                                       (readlink "bin/Guile")))))))))
+    (built-derivations (list check))))
+
 ;; The following test needs guile-sqlite3, libgcrypt, etc. as a consequence of
 ;; commit c45477d2a1a651485feede20fe0f3d15aec48b39 and related changes.  Thus,
 ;; run it on the user's store, if it's available, on the grounds that these
@@ -56,17 +114,15 @@
 
 (with-external-store store
   (unless store (test-skip 1))
-  (test-assertm "self-contained-tarball" store
+  (test-assertm "self-contained-tarball + localstatedir" store
     (mlet* %store-monad
-        ((profile (profile-derivation (packages->manifest
+        ((guile   (set-guile-for-build (default-guile)))
+         (profile (profile-derivation (packages->manifest
                                        (list %bootstrap-guile))
                                       #:hooks '()
                                       #:locales? #f))
-         (tarball (self-contained-tarball "pack" profile
+         (tarball (self-contained-tarball "tar-pack" profile
-                                          #:symlinks '(("/bin/Guile"
+                                          #:localstatedir? #t))
-                                                        -> "bin/guile"))
-                                          #:compressor %gzip-compressor
-                                          #:archiver %tar-bootstrap))
          (check   (gexp->derivation
                    "check-tarball"
                    #~(let ((bin (string-append "." #$profile "/bin")))
@@ -75,12 +131,84 @@
                        (system* "tar" "xvf" #$tarball)
                        (mkdir #$output)
                        (exit
-                        (and (file-exists? (string-append bin "/guile"))
+                        (and (file-exists? "var/guix/db/db.sqlite")
                              (string=? (string-append #$%bootstrap-guile "/bin")
-                                       (readlink bin))
+                                       (readlink bin))))))))
-                             (string=? (string-append ".." #$profile
+      (built-derivations (list check))))
-                                                      "/bin/guile")
+
-                                       (readlink "bin/Guile"))))))))
+  (unless store (test-skip 1))
+  (test-assertm "docker-image + localstatedir" store
+    (mlet* %store-monad
+        ((guile   (set-guile-for-build (default-guile)))
+         (profile (profile-derivation (packages->manifest
+                                       (list %bootstrap-guile))
+                                      #:hooks '()
+                                      #:locales? #f))
+         (tarball (docker-image "docker-pack" profile
+                                #:symlinks '(("/bin/Guile" -> "bin/guile"))
+                                #:localstatedir? #t))
+         (check   (gexp->derivation
+                   "check-tarball"
+                   (with-imported-modules '((guix build utils))
+                     #~(begin
+                         (use-modules (guix build utils)
+                                      (ice-9 match))
+
+                         (define bin
+                           (string-append "." #$profile "/bin"))
+
+                         (setenv "PATH" (string-append #$%tar-bootstrap "/bin"))
+                         (mkdir "base")
+                         (with-directory-excursion "base"
+                           (invoke "tar" "xvf" #$tarball))
+
+                         (match (find-files "base" "layer.tar")
+                           ((layer)
+                            (invoke "tar" "xvf" layer)))
+
+                         (when
+                          (and (file-exists? (string-append bin "/guile"))
+                               (file-exists? "var/guix/db/db.sqlite")
+                               (string=? (string-append #$%bootstrap-guile "/bin")
+                                         (pk 'binlink (readlink bin)))
+                               (string=? (string-append #$profile "/bin/guile")
+                                         (pk 'guilelink (readlink "bin/Guile"))))
+                          (mkdir #$output)))))))
+      (built-derivations (list check))))
+
+  (unless store (test-skip 1))
+  (test-assertm "squashfs-image + localstatedir" store
+    (mlet* %store-monad
+        ((guile   (set-guile-for-build (default-guile)))
+         (profile (profile-derivation (packages->manifest
+                                       (list %bootstrap-guile))
+                                      #:hooks '()
+                                      #:locales? #f))
+         (image   (squashfs-image "squashfs-pack" profile
+                                  #:symlinks '(("/bin" -> "bin"))
+                                  #:localstatedir? #t))
+         (check   (gexp->derivation
+                   "check-tarball"
+                   (with-imported-modules '((guix build utils))
+                     #~(begin
+                         (use-modules (guix build utils)
+                                      (ice-9 match))
+
+                         (define bin
+                           (string-append "." #$profile "/bin"))
+
+                         (setenv "PATH"
+                                 (string-append #$squashfs-tools-next "/bin"))
+                         (invoke "unsquashfs" #$image)
+                         (with-directory-excursion "squashfs-root"
+                           (when (and (file-exists? (string-append bin
+                                                                   "/guile"))
+                                      (file-exists? "var/guix/db/db.sqlite")
+                                      (string=? (string-append #$%bootstrap-guile "/bin")
+                                                (pk 'binlink (readlink bin)))
+                                      (string=? (string-append #$profile "/bin")
+                                                (pk 'guilelink (readlink "bin"))))
+                             (mkdir #$output))))))))
       (built-derivations (list check)))))
 
 (test-end)