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Merge remote-tracking branch 'origin/master' into wip-texlive

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Ricardo Wurmus 2019-08-07 22:26:55 +02:00
parent 378d94e51b 55e238f2ab
commit 9bd1333e58
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24 changed files with 551 additions and 334 deletions
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20
doc/guix.texi
View File

@ -25510,7 +25510,7 @@ evaluates to. As an example, @var{file} might contain a definition like this:
%base-services))))
(list (machine
(system %system)
(operating-system %system)
(environment managed-host-environment-type)
(configuration (machine-ssh-configuration
(host-name "localhost")
@ -25530,12 +25530,28 @@ complex deployment may involve, for example, starting virtual machines through
a Virtual Private Server (VPS) provider. In such a case, a different
@var{environment} type would be used.
Do note that you first need to generate a key pair on the coordinator machine
to allow the daemon to export signed archives of files from the store
(@pxref{Invoking guix archive}).
@example
# guix archive --generate-key
@end example
@noindent
Each target machine must authorize the key of the master machine so that it
accepts store items it receives from the coordinator:
@example
# guix archive --authorize < coordinator-public-key.txt
@end example
@deftp {Data Type} machine
This is the data type representing a single machine in a heterogeneous Guix
deployment.
@table @asis
@item @code{system}
@item @code{operating-system}
The object of the operating system configuration to deploy.
@item @code{environment}

12
gnu/machine.scm
View File

@ -34,7 +34,7 @@
machine?
this-machine
machine-system
machine-operating-system
machine-environment
machine-configuration
machine-display-name
@ -85,14 +85,14 @@
make-machine
machine?
this-machine
(system machine-system) ; <operating-system>
(environment machine-environment) ; symbol
(configuration machine-configuration ; configuration object
(default #f))) ; specific to environment
(operating-system machine-operating-system) ; <operating-system>
(environment machine-environment) ; symbol
(configuration machine-configuration ; configuration object
(default #f))) ; specific to environment
(define (machine-display-name machine)
"Return the host-name identifying MACHINE."
(operating-system-host-name (machine-system machine)))
(operating-system-host-name (machine-operating-system machine)))
(define (machine-remote-eval machine exp)
"Evaluate EXP, a gexp, on MACHINE. Ensure that all the elements EXP refers to

148
gnu/machine/ssh.scm
View File

@ -20,6 +20,9 @@
#:use-module (gnu machine)
#:autoload (gnu packages gnupg) (guile-gcrypt)
#:use-module (gnu system)
#:use-module (gnu system file-systems)
#:use-module (gnu system uuid)
#:use-module (guix diagnostics)
#:use-module (guix gexp)
#:use-module (guix i18n)
#:use-module (guix modules)
@ -29,6 +32,7 @@
#:use-module (guix scripts system reconfigure)
#:use-module (guix ssh)
#:use-module (guix store)
#:use-module (guix utils)
#:use-module (ice-9 match)
#:use-module (srfi srfi-19)
#:use-module (srfi srfi-26)
@ -98,6 +102,145 @@ an environment type of 'managed-host."
(maybe-raise-unsupported-configuration-error machine)
(remote-eval exp (machine-ssh-session machine)))
;;;
;;; Safety checks.
;;;
(define (machine-check-file-system-availability machine)
"Raise a '&message' error condition if any of the file-systems specified in
MACHINE's 'system' declaration do not exist on the machine."
(define file-systems
(filter (lambda (fs)
(and (file-system-mount? fs)
(not (member (file-system-type fs)
%pseudo-file-system-types))
(not (memq 'bind-mount (file-system-flags fs)))))
(operating-system-file-systems (machine-operating-system machine))))
(define (check-literal-file-system fs)
(define remote-exp
#~(catch 'system-error
(lambda ()
(stat #$(file-system-device fs))
#t)
(lambda args
(system-error-errno args))))
(mlet %store-monad ((errno (machine-remote-eval machine remote-exp)))
(when (number? errno)
(raise (condition
(&message
(message (format #f (G_ "device '~a' not found: ~a")
(file-system-device fs)
(strerror errno)))))))
(return #t)))
(define (check-labeled-file-system fs)
(define remote-exp
(with-imported-modules '((gnu build file-systems))
#~(begin
(use-modules (gnu build file-systems))
(find-partition-by-label #$(file-system-label->string
(file-system-device fs))))))
(mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
(unless result
(raise (condition
(&message
(message (format #f (G_ "no file system with label '~a'")
(file-system-label->string
(file-system-device fs))))))))
(return #t)))
(define (check-uuid-file-system fs)
(define remote-exp
(with-imported-modules (source-module-closure
'((gnu build file-systems)
(gnu system uuid)))
#~(begin
(use-modules (gnu build file-systems)
(gnu system uuid))
(define uuid
(string->uuid #$(uuid->string (file-system-device fs))))
(find-partition-by-uuid uuid))))
(mlet %store-monad ((result (machine-remote-eval machine remote-exp)))
(unless result
(raise (condition
(&message
(message (format #f (G_ "no file system with UUID '~a'")
(uuid->string (file-system-device fs))))))))
(return #t)))
(mbegin %store-monad
(mapm %store-monad check-literal-file-system
(filter (lambda (fs)
(string? (file-system-device fs)))
file-systems))
(mapm %store-monad check-labeled-file-system
(filter (lambda (fs)
(file-system-label? (file-system-device fs)))
file-systems))
(mapm %store-monad check-uuid-file-system
(filter (lambda (fs)
(uuid? (file-system-device fs)))
file-systems))))
(define (machine-check-initrd-modules machine)
"Raise a '&message' error condition if any of the modules needed by
'needed-for-boot' file systems in MACHINE are not available in the initrd."
(define file-systems
(filter file-system-needed-for-boot?
(operating-system-file-systems (machine-operating-system machine))))
(define (missing-modules fs)
(define remote-exp
(let ((device (file-system-device fs)))
(with-imported-modules (source-module-closure
'((gnu build file-systems)
(gnu build linux-modules)
(gnu system uuid)))
#~(begin
(use-modules (gnu build file-systems)
(gnu build linux-modules)
(gnu system uuid))
(define dev
#$(cond ((string? device) device)
((uuid? device) #~(find-partition-by-uuid
(string->uuid
#$(uuid->string device))))
((file-system-label? device)
#~(find-partition-by-label
(file-system-label->string #$device)))))
(missing-modules dev '#$(operating-system-initrd-modules
(machine-operating-system machine)))))))
(mlet %store-monad ((missing (machine-remote-eval machine remote-exp)))
(return (list fs missing))))
(mlet %store-monad ((device (mapm %store-monad missing-modules file-systems)))
(for-each (match-lambda
((fs missing)
(unless (null? missing)
(raise (condition
(&message
(message (format #f (G_ "~a missing modules ~{ ~a~}~%")
(file-system-device fs)
missing))))))))
device)
(return #t)))
(define (check-deployment-sanity machine)
"Raise a '&message' error condition if it is clear that deploying MACHINE's
'system' declaration would fail."
(mbegin %store-monad
(machine-check-file-system-availability machine)
(machine-check-initrd-modules machine)))
;;;
;;; System deployment.
@ -165,8 +308,9 @@ of MACHINE's system profile, ordered from most recent to oldest."
"Internal implementation of 'deploy-machine' for MACHINE instances with an
environment type of 'managed-host."
(maybe-raise-unsupported-configuration-error machine)
(mlet %store-monad ((boot-parameters (machine-boot-parameters machine)))
(let* ((os (machine-system machine))
(mlet %store-monad ((_ (check-deployment-sanity machine))
(boot-parameters (machine-boot-parameters machine)))
(let* ((os (machine-operating-system machine))
(eval (cut machine-remote-eval machine <>))
(menu-entries (map boot-parameters->menu-entry boot-parameters))
(bootloader-configuration (operating-system-bootloader os))

2
gnu/packages/admin.scm
View File

@ -2606,7 +2606,7 @@ buffers.")
`(#:tests? #f ; many of the tests try to load kernel modules
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(replace 'bootstrap
(lambda _
;; Don't run configure in this phase.
(setenv "NOCONFIGURE" "1")

4
gnu/packages/audio.scm
View File

@ -3700,7 +3700,7 @@ library.")
(define-public faudio
(package
(name "faudio")
(version "19.07")
(version "19.08")
(source
(origin
(method git-fetch)
@ -3709,7 +3709,7 @@ library.")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32 "1wf6skc5agaikc9qgwk8bx56sad31fafs53lqqn4jmx8i76pl0lw"))))
(base32 "1v13kfhyr46241vb6a4dcb4gw5f149525sprwa9cj4rv6wlcqgm5"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DFFMPEG=ON")))

20
gnu/packages/bioconductor.scm
View File

@ -1212,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.")
(define-public r-chippeakanno
(package
(name "r-chippeakanno")
(version "3.18.1")
(version "3.18.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ChIPpeakAnno" version))
(sha256
(base32
"1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
"0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
@ -1521,14 +1521,14 @@ experiments.")
(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
"0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
"0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
@ -3529,14 +3529,14 @@ position-specific scores within R and Bioconductor.")
(define-public r-atacseqqc
(package
(name "r-atacseqqc")
(version "1.8.1")
(version "1.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ATACseqQC" version))
(sha256
(base32
"0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
"1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
@ -3621,14 +3621,14 @@ annotations and ontologies.")
(define-public r-abaenrichment
(package
(name "r-abaenrichment")
(version "1.14.0")
(version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ABAEnrichment" version))
(sha256
(base32
"0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
"1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
@ -4841,14 +4841,14 @@ annotations.")
(define-public r-rsubread
(package
(name "r-rsubread")
(version "1.34.4")
(version "1.34.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
"1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
"0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs `(("zlib" ,zlib)))

32
gnu/packages/bioinformatics.scm
View File

@ -7458,13 +7458,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
(version "3.26.5")
(version "3.26.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
"0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m"))))
"17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@ -7525,13 +7525,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
(version "3.40.2")
(version "3.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
"1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7"))))
"166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@ -7658,13 +7658,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
(version "2.40.1")
(version "2.40.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
"1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx"))))
"022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@ -7819,13 +7819,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
(version "1.14.0")
(version "1.14.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
"1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
"0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@ -7883,13 +7883,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
(version "1.44.0")
(version "1.44.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
"161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd"))))
"03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s"))))
(build-system r-build-system)
(arguments
`(#:phases
@ -7930,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
(version "1.36.3")
(version "1.36.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
"0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3"))))
"0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@ -8354,13 +8354,13 @@ paired-end data.")
(define-public r-rcas
(package
(name "r-rcas")
(version "1.10.0")
(version "1.10.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "RCAS" version))
(sha256
(base32
"1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl"))))
"06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz"))))
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
@ -9418,14 +9418,14 @@ of mass spectrometry based proteomics data.")
(define-public r-msnid
(package
(name "r-msnid")
(version "1.18.0")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnID" version))
(sha256
(base32
"18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3"))))
"1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb"))))
(properties `((upstream-name . "MSnID")))
(build-system r-build-system)
(propagated-inputs

319
gnu/packages/cran.scm
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12
gnu/packages/emulators.scm
View File

@ -119,8 +119,8 @@
;; Building from recent Git because the official 5.0 release no longer builds.
(define-public dolphin-emu
(let ((commit "2c57e709d0f9e4010a4415de4192de887e37f187")
(revision "5"))
(let ((commit "24718c1a389e4f51db974575cd15c372485b92e2")
(revision "6"))
(package
(name "dolphin-emu")
(version (git-version "5.0" revision commit))
@ -146,7 +146,7 @@
#t))
(sha256
(base32
"0aszfdfvs7yg4bmrd3qxwsiz7hx3mrj29f4aw86bz7h9j7hkh57f"))))
"1d92rhnw307j3m6swk6bycb8fyc7vw2hfgakd5hpsc4qw65vxfq8"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f
@ -250,12 +250,6 @@ turbo speed, networked multiplayer, and graphical enhancements.")
(base32
"02i648i50dwicv1vaql15rccv4g8h5blf5g6inv67lrfxpbkvlf0"))))
(build-system gnu-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
(add-after
'unpack 'autogen.sh
(lambda _
(invoke "sh" "autogen.sh"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))

9
gnu/packages/geo.scm
View File

@ -131,7 +131,12 @@ topology functions.")
(gi-typelib-path (getenv "GI_TYPELIB_PATH"))
(goa-path (string-append
(assoc-ref inputs "gnome-online-accounts")
"/lib:"
(assoc-ref inputs "gnome-online-accounts:lib")
"/lib"))
(geocode-glib-path (string-append
(assoc-ref inputs "geocode-glib")
"/lib"))
(webkitgtk-path (string-append
(assoc-ref inputs "webkitgtk")
"/lib")))
@ -141,7 +146,8 @@ topology functions.")
;; There seems to be no way to embed the path of
;; libgoa-1.0.so.0, libwebkit2gtk-4.0.so.37 and
;; libjavascriptcoregtk-4.0.so.18.
`("LD_LIBRARY_PATH" ":" prefix (,goa-path ,webkitgtk-path)))
`("LD_LIBRARY_PATH" ":" prefix
(,goa-path ,webkitgtk-path ,geocode-glib-path)))
#t))))))
(native-inputs
`(("gobject-introspection" ,gobject-introspection)
@ -163,6 +169,7 @@ topology functions.")
("gjs" ,gjs)
("glib" ,glib)
("gnome-online-accounts" ,gnome-online-accounts)
("gnome-online-accounts:lib" ,gnome-online-accounts "lib")
("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
("rest" ,rest)
("webkitgtk" ,webkitgtk)))

9
gnu/packages/image.scm
View File

@ -595,9 +595,6 @@ collection of tools for doing simple manipulations of TIFF images.")
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autobuild")))
(add-after 'unpack 'patch-reg-wrapper
(lambda _
(substitute* "prog/reg_wrapper.sh"
@ -1240,12 +1237,6 @@ ISO/IEC 15444-1).")
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autogen.sh"))))))
(synopsis "Scaling, colorspace conversion, and dithering library")
(description "Zimg implements the commonly required image processing basics
of scaling, colorspace conversion, and depth conversion. A simple API enables

20
gnu/packages/linux.scm
View File

@ -350,42 +350,42 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
"linux-" version ".tar.xz"))
(sha256 hash)))
(define-public linux-libre-5.2-version "5.2.6")
(define-public linux-libre-5.2-version "5.2.7")
(define-public linux-libre-5.2-pristine-source
(let ((version linux-libre-5.2-version)
(hash (base32 "1whzgdz1wnjzkb78yqz4xs3mad02rv17ksmwaf4ykp4lfgxml45y")))
(hash (base32 "1aazhf0v8bv4py0wnqkdmiy80fchnix431l0hda2fkwsdf9njgnv")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.2)))
(define-public linux-libre-4.19-version "4.19.64")
(define-public linux-libre-4.19-version "4.19.65")
(define-public linux-libre-4.19-pristine-source
(let ((version linux-libre-4.19-version)
(hash (base32 "1gasmcdsrsk81dscslmrsxqsvkfp5xxdx3ay95izggpk7piqnvvs")))
(hash (base32 "1pyyhr2airxzk4c6n7140yl723dc7yw7igy5i5i2ih0nd4c3k6g5")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.19)))
(define-public linux-libre-4.14-version "4.14.136")
(define-public linux-libre-4.14-version "4.14.137")
(define-public linux-libre-4.14-pristine-source
(let ((version linux-libre-4.14-version)
(hash (base32 "0w6z5fhwqgpqnz2js8vj9j5dl6isx8n7rnzrm0vr9r8njaazz396")))
(hash (base32 "0a72pab0zxy28i02glnzj6avzcf0a4gxxnadbdd343rh549yky4k")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.14)))
(define-public linux-libre-4.9-version "4.9.187")
(define-public linux-libre-4.9-version "4.9.188")
(define-public linux-libre-4.9-pristine-source
(let ((version linux-libre-4.9-version)
(hash (base32 "1iyimwl4ysnk6m66m73sg0cnp4vac56d6yy174shfpnj5h2csjq1")))
(hash (base32 "08p2cfc9982b804vmkapfasgipf6969g625ih7z3062xn99rhlr7")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.9)))
(define-public linux-libre-4.4-version "4.4.187")
(define-public linux-libre-4.4-version "4.4.188")
(define-public linux-libre-4.4-pristine-source
(let ((version linux-libre-4.4-version)
(hash (base32 "1dlzb5yzcsicd41myj3q4dq2ql8xcc49brs5f7xjmc5ynvvjjgnc")))
(hash (base32 "1llxamm62kgqd7dig98n8m16qas8dd8rrkmwpfcdgyf8rag216ff")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-4.4)))

7
gnu/packages/machine-learning.scm
View File

@ -193,7 +193,7 @@ classification.")
(uri (svn-reference
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
(revision svn-revision)))
(file-name (string-append name "-" version))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
@ -251,10 +251,7 @@ classification.")
(string-append indent
"@unittest.skip(\"Disabled by Guix\")\n"
line)))
#t))
(add-after 'disable-broken-tests 'autogen
(lambda _
(invoke "bash" "autogen.sh"))))))
#t)))))
(inputs
`(("python" ,python-2) ; only Python 2 is supported
("libxml2" ,libxml2)))

16
gnu/packages/mail.scm
View File

@ -1051,7 +1051,7 @@ useful features.")
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(replace 'bootstrap
(lambda _
(setenv "NOCONFIGURE" "true")
(invoke "sh" "autogen.sh"))))
@ -1365,12 +1365,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.")
`(#:tests? #f ;No tests exist.
#:configure-flags (list (string-append "--with-dovecot="
(assoc-ref %build-inputs "dovecot")
"/lib/dovecot"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autogen.sh"))))))
"/lib/dovecot"))))
(home-page "https://0xacab.org/riseuplabs/trees")
(synopsis "NaCL-based Dovecot email storage encryption plugin")
(description
@ -1421,12 +1416,7 @@ using libsodium sealed boxes.
`(#:tests? #f ;No tests exist.
#:configure-flags (list (string-append "--with-dovecot="
(assoc-ref %build-inputs "dovecot")
"/lib/dovecot"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autogen.sh"))))))
"/lib/dovecot"))))
(home-page "https://github.com/LuckyFellow/dovecot-libsodium-plugin")
(synopsis "Libsodium password hashing schemes plugin for Dovecot")
(description

4
gnu/packages/maths.scm
View File

@ -4333,14 +4333,14 @@ are noisy or are discontinuous at the solution.")
(define-public r-desolve
(package
(name "r-desolve")
(version "1.21")
(version "1.24")
(source
(origin
(method url-fetch)
(uri (cran-uri "deSolve" version))
(sha256
(base32
"0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"))))
"0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
(properties `((upstream-name . "deSolve")))
(build-system r-build-system)
(native-inputs

2
gnu/packages/perl.scm
View File

@ -4082,7 +4082,7 @@ relic support.")
(base32
"0h3wfnpv5d4d3f9xzmwkchay6251nhzngdv3f6xia56mj4hxabs0"))))
(build-system perl-build-system)
(inputs
(propagated-inputs
`(("perl-clone-choose" ,perl-clone-choose)))
(home-page "https://metacpan.org/release/Hash-Merge")
(synopsis "Merge arbitrarily deep hashes into a single hash")

139
gnu/packages/statistics.scm
View File

@ -75,6 +75,7 @@
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages base)
#:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@ -396,14 +397,14 @@ available, greatly increasing its breadth and scope.")
(define-public r-boot
(package
(name "r-boot")
(version "1.3-22")
(version "1.3-23")
(source
(origin
(method url-fetch)
(uri (cran-uri "boot" version))
(sha256
(base32
"1z2dig1mi76b3b9ck6qlkh07l3hs478gaf70db5nv8x7w2qhq7yg"))))
"0bx07zbb5nfz2xfgnzbspg7r5vxz4bjdz1ry4d1vk434vlcrxj1h"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/boot")
(synopsis "Bootstrap functions for R")
@ -501,14 +502,14 @@ code for possible problems.")
(define-public r-foreign
(package
(name "r-foreign")
(version "0.8-71")
(version "0.8-72")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreign" version))
(sha256
(base32
"1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"))))
"124c9229is44p2rv7xyh2q86nsfi7vzyyh5n3c5ihziqrp4ig723"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/foreign")
(synopsis "Read data stored by other statistics software")
@ -587,14 +588,14 @@ and operations on them using LAPACK and SuiteSparse.")
(define-public r-nlme
(package
(name "r-nlme")
(version "3.1-140")
(version "3.1-141")
(source
(origin
(method url-fetch)
(uri (cran-uri "nlme" version))
(sha256
(base32
"0k9x5j34fx093a023da9ny3b3101lbwpmfm27mkvfj950l22z88x"))))
"0ml00g79bimjcl0sgn6h55l5b4gfmnsnc1vvmivggn0318k4c04i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@ -803,13 +804,13 @@ effects of different types of color-blindness.")
(define-public r-digest
(package
(name "r-digest")
(version "0.6.19")
(version "0.6.20")
(source
(origin
(method url-fetch)
(uri (cran-uri "digest" version))
(sha256
(base32 "1x6cbj9qvkk7pxv9xdqibazw3x8psjp6x0m0ildx1jwyb2ymkl98"))))
(base32 "1irhk2jaj9cg57cxprgyn1if06x121xwcxh1fzzn3148bl5lnrq5"))))
(build-system r-build-system)
;; Vignettes require r-knitr, which requires r-digest, so we have to
;; disable them and the tests.
@ -1602,18 +1603,19 @@ R packages that praise their users.")
(define-public r-testthat
(package
(name "r-testthat")
(version "2.1.1")
(version "2.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "testthat" version))
(sha256
(base32
"03jgr0hlr77yp0aib4v30yjyjrjsa8dczr02yk21m93vl25vqvkp"))))
"0y0bvggm4pzkzp6xn7b8cf3ybqp9ijxkhhyp3z49a9iipc90bvk7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
("r-crayon" ,r-crayon)
("r-digest" ,r-digest)
("r-evaluate" ,r-evaluate)
("r-magrittr" ,r-magrittr)
("r-praise" ,r-praise)
("r-r6" ,r-r6)
@ -1695,13 +1697,13 @@ and printing capabilities than traditional data frames.")
(define-public r-dplyr
(package
(name "r-dplyr")
(version "0.8.1")
(version "0.8.3")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
"1nw12hzk1jcac5879nfmf1yp98jpb3i59qkb8sfpk2cd6zqgfgjz"))))
"032c89wa04g9rih9shyvwl3il0bsrv3xk489x6867sk9bb3amd38"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@ -1978,13 +1980,13 @@ inference for statistical models.")
(define-public r-coda
(package
(name "r-coda")
(version "0.19-2")
(version "0.19-3")
(source (origin
(method url-fetch)
(uri (cran-uri "coda" version))
(sha256
(base32
"03fs3sdrrym3is92dgpa6ydk3m63gaihwy7bva4k0wm2hxm7x2k7"))))
"1mn50bshky968gn4nf6vnkaa768fnvm1xmhkms7szwdw9341zpyk"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@ -2020,14 +2022,14 @@ and environmental data in the framework of Euclidean exploratory methods.")
(define-public r-xml2
(package
(name "r-xml2")
(version "1.2.0")
(version "1.2.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "xml2" version))
(sha256
(base32
"154lmksfiwkhnlmryas25mjhfg6k4mmnnk7bbb29mnn5x5pr2yha"))))
"0186d7r36xw1z9f8ajz35a0dz4ch6hmrjl9536yc7vq78v4vn5an"))))
(build-system r-build-system)
(inputs
`(("libxml2" ,libxml2)
@ -2135,14 +2137,14 @@ R version.")
(define-public r-checkmate
(package
(name "r-checkmate")
(version "1.9.3")
(version "1.9.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "checkmate" version))
(sha256
(base32
"15ccwvmw73c2zz1k10k5zdn8px0rrbnvs1b4nzvlb0iwj7cimhp4"))))
"08ddpgs4mv5d5y4j054pm8drmxkn7yvhfpbghwxlizjpnxa5g8ps"))))
(build-system r-build-system)
(propagated-inputs
`(("r-backports" ,r-backports)))
@ -2332,14 +2334,14 @@ collation, and NAMESPACE files.")
(define-public r-openssl
(package
(name "r-openssl")
(version "1.4")
(version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "openssl" version))
(sha256
(base32
"0mh4xwb9wnn5j2n1zzmjldqjqv2nn4wdidiixxciaqrqsi0l9834"))))
"1ihz2qi33lhngl19xdanq0pbmfaacy63794mg8ll7z2lab3yryzp"))))
(build-system r-build-system)
(inputs
`(("libressl" ,libressl)))
@ -2365,13 +2367,13 @@ integers.")
(define-public r-httr
(package
(name "r-httr")
(version "1.4.0")
(version "1.4.1")
(source (origin
(method url-fetch)
(uri (cran-uri "httr" version))
(sha256
(base32
"0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"))))
"0mp1il13q6n49n2hv1p2p8x6avjan6dr5az19ql4hb78pc3pwp37"))))
(build-system r-build-system)
(propagated-inputs
`(("r-curl" ,r-curl)
@ -2391,20 +2393,16 @@ functions make it easy to control additional request components.")
(define-public r-git2r
(package
(name "r-git2r")
(version "0.25.2")
(version "0.26.1")
(source (origin
(method url-fetch)
(uri (cran-uri "git2r" version))
(sha256
(base32
"15kpvz6ry2r8ii5hzinjwkggc5kgmkbcpsdwzahsf8gha52w80p0"))))
"0dbl845sahv2i641ncaf06w06djravwc5wknp9syzx0ad8l0kmhk"))))
(build-system r-build-system)
;; This R package contains modified sources of libgit2. This modified
;; version of libgit2 is built as the package is built. Hence libgit2 is
;; not among the inputs of this package.
(inputs
`(("libssh2" ,libssh2) ; for SSH transport
("openssl" ,openssl)
`(("libgit2" ,libgit2)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -2437,13 +2435,13 @@ informative error messages when it's not available.")
(define-public r-devtools
(package
(name "r-devtools")
(version "2.0.2")
(version "2.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "devtools" version))
(sha256
(base32
"028pppj39ng7q17k27531s8k00lmw982vz5krn74n9b8f2azm8lr"))))
"0393v7nr22gr5g9afgrhq4ab3lwbqy6fd3shnmlhdpqam5357xy1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-callr" ,r-callr)
@ -2456,9 +2454,11 @@ informative error messages when it's not available.")
("r-pkgbuild" ,r-pkgbuild)
("r-pkgload" ,r-pkgload)
("r-rcmdcheck" ,r-rcmdcheck)
("r-roxygen2" ,r-roxygen2)
("r-remotes" ,r-remotes)
("r-rstudioapi" ,r-rstudioapi)
("r-sessioninfo" ,r-sessioninfo)
("r-testthat" ,r-testthat)
("r-usethis" ,r-usethis)
("r-withr" ,r-withr)))
(home-page "https://github.com/hadley/devtools")
@ -2489,18 +2489,19 @@ were originally a part of the r-devtools package.")
(define-public r-hms
(package
(name "r-hms")
(version "0.4.2")
(version "0.5.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hms" version))
(sha256
(base32
"1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"))))
"06snfqdczr0x0nbp7qnvwhlp2pw0wx9c2y3xb4gr1wrvbik74y58"))))
(build-system r-build-system)
(propagated-inputs
`(("r-rlang" ,r-rlang)
("r-pkgconfig" ,r-pkgconfig)))
("r-pkgconfig" ,r-pkgconfig)
("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/rstats-db/hms")
(synopsis "Pretty time of day")
(description
@ -2596,13 +2597,13 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.9.500.2.0")
(version "0.9.600.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"1lyvpb7n54ijlqns29qiixqr39334knf67cnixvlic58945glrhv"))))
"07jg2667xyhmp1fbcdi5nnhmkk81da76s9rlswfq4k2sjsmbfmr0"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
;; All needed for vignettes
@ -2694,14 +2695,14 @@ certain criterion, e.g., it contains a certain regular file.")
(define-public r-rmarkdown
(package
(name "r-rmarkdown")
(version "1.13")
(version "1.14")
(source
(origin
(method url-fetch)
(uri (cran-uri "rmarkdown" version))
(sha256
(base32
"1vv3b8nlw8ra19492rjg3na42lwh3xr5a2jy2ia81fvvs846pywn"))))
"0qfw5rkvwqpgix32g6qy9xrr50awmm146aqbm836xravih2b2dpn"))))
(properties `((upstream-name . "rmarkdown")))
(build-system r-build-system)
(propagated-inputs
@ -2787,17 +2788,18 @@ that package, other packages are unaffected.")
(define-public r-blob
(package
(name "r-blob")
(version "1.1.1")
(version "1.2.0")
(source (origin
(method url-fetch)
(uri (cran-uri "blob" version))
(sha256
(base32
"0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"))))
"08z071jzac4gasgfgab0y5g3ilfmlw08ln813wphxg07hsiczw8s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-prettyunits" ,r-prettyunits)
("r-tibble" ,r-tibble)))
("r-rlang" ,r-rlang)
("r-vctrs" ,r-vctrs)))
(home-page "https://github.com/hadley/blob")
(synopsis "Simple S3 Class for representing vectors of binary data")
(description "Raw vectors in R are useful for storing a single binary
@ -2809,13 +2811,13 @@ a column in data frame.")
(define-public r-rsqlite
(package
(name "r-rsqlite")
(version "2.1.1")
(version "2.1.2")
(source (origin
(method url-fetch)
(uri (cran-uri "RSQLite" version))
(sha256
(base32
"1giwk4335sc6yhj3rs8h070g1mwy38kyqyqv6vcfxvskykj7vp6z"))))
"1inrhap5cs0wry2jbw42fx9wwxb3qdzlpy0ba4f6a29bs8jx9nk6"))))
(properties `((upstream-name . "RSQLite")))
(build-system r-build-system)
(propagated-inputs
@ -3068,14 +3070,14 @@ standard R subsetting and Kronecker products.")
(define-public r-iterators
(package
(name "r-iterators")
(version "1.0.10")
(version "1.0.12")
(source
(origin
(method url-fetch)
(uri (cran-uri "iterators" version))
(sha256
(base32
"1s3iykfvccpnzs73z90rx18qvbvgw2dgl4nfcrvm5m1850qb5qd9"))))
"0jwzxaa3jm1xzgfv5pn0xqkk7rhm0xwvgn85w7xaw8xx1vb33gwn"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/iterators")
(synopsis "Iterator construct for R")
@ -3088,14 +3090,14 @@ data.")
(define-public r-foreach
(package
(name "r-foreach")
(version "1.4.4")
(version "1.4.7")
(source
(origin
(method url-fetch)
(uri (cran-uri "foreach" version))
(sha256
(base32
"0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"))))
"0q7iyniw5iri4hl57bhil3r69s5wnaijzn0q0x4h3z42245jqqwm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-codetools" ,r-codetools)
@ -3116,14 +3118,14 @@ parallel.")
(define-public r-doparallel
(package
(name "r-doparallel")
(version "1.0.14")
(version "1.0.15")
(source
(origin
(method url-fetch)
(uri (cran-uri "doParallel" version))
(sha256
(base32
"01qjs4iw9f1kgymcypj0m2s4pvgqhxaycpli0fb8lq3dc0vpzfyb"))))
"0vnqbha3gig3awbfvsfx3ni5jir398md1n7xmsb8jihnjsk7xbbi"))))
(properties `((upstream-name . "doParallel")))
(build-system r-build-system)
(propagated-inputs
@ -3139,14 +3141,14 @@ using the parallel package.")
(define-public r-domc
(package
(name "r-domc")
(version "1.3.5")
(version "1.3.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "doMC" version))
(sha256
(base32
"1vfrykvfvsyq12mypd266867ml1dcwc3rj5k9c3wrn5bddcm88kr"))))
"1cn9gxavhvjswip8pwvkpi7q6wpzdllcsdjabga8akf55nggqxr9"))))
(properties `((upstream-name . "doMC")))
(build-system r-build-system)
(propagated-inputs
@ -3162,13 +3164,13 @@ using the multicore functionality of the parallel package.")
(define-public r-dt
(package
(name "r-dt")
(version "0.7")
(version "0.8")
(source (origin
(method url-fetch)
(uri (cran-uri "DT" version))
(sha256
(base32
"0b6ywgzk9b35y5f69zwfz3vv7qwqqj3xsmy0xymf7nfcvrqg3qqx"))))
"08cfmv3d5awvd9h8648bvidcg2ak5pvl2p6vqwqwy1l82ia506ch"))))
(properties
`((upstream-name . "DT")))
(build-system r-build-system)
@ -3176,6 +3178,7 @@ using the multicore functionality of the parallel package.")
`(("r-crosstalk" ,r-crosstalk)
("r-htmltools" ,r-htmltools)
("r-htmlwidgets" ,r-htmlwidgets)
("r-jsonlite" ,r-jsonlite)
("r-magrittr" ,r-magrittr)
("r-promises" ,r-promises)))
(home-page "http://rstudio.github.io/DT")
@ -3314,14 +3317,14 @@ package registries.")
(define-public r-rngtools
(package
(name "r-rngtools")
(version "1.3.1.1")
(version "1.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "rngtools" version))
(sha256
(base32
"0k1nlcxggflq0043m15dfclnqnzchkpw2ik7jk82h4dqwvysiqcr"))))
"1kivj594bn774lbn29ws2rmzy2km99sza0j3jqvhal6hwmk27a9s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-digest" ,r-digest)
@ -4565,19 +4568,19 @@ Farebrother's algorithm or Liu et al.'s algorithm.")
(define-public r-cowplot
(package
(name "r-cowplot")
(version "0.9.4")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "cowplot" version))
(sha256
(base32
"0yvalwalvyddyqk0q66y8361nxlh2cvp3ssazax9g5q89lghjmzv"))))
"19cqdhgfyr1wj0fz0c5ly8f0aiy9sfgzq6lzb78hkx0hdp2agybh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-ggplot2" ,r-ggplot2)
("r-gtable" ,r-gtable)
("r-plyr" ,r-plyr)
("r-rlang" ,r-rlang)
("r-scales" ,r-scales)))
(home-page "https://github.com/wilkelab/cowplot")
(synopsis "Streamlined plot theme and plot annotations for ggplot2")
@ -4639,14 +4642,14 @@ regression.")
(define-public r-fastica
(package
(name "r-fastica")
(version "1.2-1")
(version "1.2-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "fastICA" version))
(sha256
(base32
"108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg"))))
"1zpijqcipm0aa3rxj0mys06lskqy4dbppjpxr1aby0j16y9ka8ij"))))
(properties `((upstream-name . "fastICA")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/fastICA")
@ -4748,14 +4751,14 @@ models, generalized linear models and model-based clustering.")
(define-public r-mclust
(package
(name "r-mclust")
(version "5.4.4")
(version "5.4.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "mclust" version))
(sha256
(base32
"039ymr57bq5327gypizw0v2qb81j6bkqhjdh8yj23qa5sh51phyc"))))
"0whandnda1fnjn5k3hgxdbp3b0xr7nlzy1j37saqb536h8q9dwkm"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@ -4918,14 +4921,14 @@ generally.")
(define-public r-robust
(package
(name "r-robust")
(version "0.4-18")
(version "0.4-18.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "robust" version))
(sha256
(base32
"1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4"))))
"0xs098pfw5zdcdk3rsxkylfl6d2pyp566s5v92bzhgl7h8c90cfy"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fit-models" ,r-fit-models)
@ -5024,14 +5027,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.")
(define-public r-pbapply
(package
(name "r-pbapply")
(version "1.4-0")
(version "1.4-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "pbapply" version))
(sha256
(base32
"0bn7a9ni36xy5acnrl9ky3gd1k8jr5kxgazzh3pzd1q6bri1nx7k"))))
"1bbws9n90cqnnp5k58hp852jwmm6513jnhn4vzhl9f8x314k6qxk"))))
(build-system r-build-system)
(home-page "https://github.com/psolymos/pbapply")
(synopsis "Adding progress bar to apply functions")
@ -5137,14 +5140,14 @@ using modular prediction and response module classes.")
(define-public r-quantreg
(package
(name "r-quantreg")
(version "5.41")
(version "5.42.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
(base32
"110ax3ngn6i94h7iw7ha67kfsmj94hycp7lk62nmyvkp34vpfykh"))))
"1aycnghci329yqw63kybv7sfjjx5whq3xs7xzic4wsaj7j4b1hjc"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))

6
gnu/packages/terminals.scm
View File

@ -57,6 +57,7 @@
#:use-module (gnu packages golang)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages libcanberra)
#:use-module (gnu packages libevent)
#:use-module (gnu packages linux)
#:use-module (gnu packages ncurses)
@ -954,7 +955,7 @@ tmux.")
(define-public kitty
(package
(name "kitty")
(version "0.14.2")
(version "0.14.3")
(home-page "https://sw.kovidgoyal.net/kitty/")
(source
(origin
@ -965,7 +966,7 @@ tmux.")
(file-name (git-file-name name version))
(sha256
(base32
"15iv3k7iryf10n8n67d37x24pzcarq97a3dr42lbld00k1lx19az"))
"0wi6b6b1nyp16rcpcghk6by62wy6qsamv1xdymyn0zbqgd8h9n6b"))
(modules '((guix build utils)))
(snippet
'(begin
@ -984,6 +985,7 @@ tmux.")
`(("python" ,python)
("harfbuzz" ,harfbuzz)
("zlib" ,zlib)
("libcanberra" ,libcanberra)
("libpng" ,libpng)
("freetype" ,freetype)
("fontconfig" ,fontconfig)

32
gnu/packages/video.scm
View File

@ -792,17 +792,18 @@ operate properly.")
(define-public ffmpeg
(package
(name "ffmpeg")
(version "4.1.4")
(version "4.2")
(source (origin
(method url-fetch)
(uri (string-append "https://ffmpeg.org/releases/ffmpeg-"
version ".tar.xz"))
(sha256
(base32
"1qd7a10gs12ifcp31gramcgqjl77swskjfp7cijibgyg5yl4kw7i"))))
"1mgcxm7sqkajx35px05szsmn9mawwm03cfpmk3br7bcp3a1i0gq2"))))
(build-system gnu-build-system)
(inputs
`(("fontconfig" ,fontconfig)
`(("dav1d" ,dav1d)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
("frei0r-plugins" ,frei0r-plugins)
("gnutls" ,gnutls)
@ -901,6 +902,7 @@ operate properly.")
"--enable-libbluray"
"--enable-libcaca"
"--enable-libcdio"
"--enable-libdav1d"
"--enable-libfreetype"
"--enable-libmp3lame"
"--enable-libopus"
@ -983,9 +985,10 @@ audio/video codec library.")
(arguments
(substitute-keyword-arguments (package-arguments ffmpeg)
((#:configure-flags flags)
`(delete "--enable-libaom" ,flags))))
(inputs (alist-delete "libaom"
(package-inputs ffmpeg)))))
`(delete "--enable-libdav1d" (delete "--enable-libaom"
,flags)))))
(inputs (alist-delete "dav1d" (alist-delete "libaom"
(package-inputs ffmpeg))))))
(define-public ffmpeg-for-stepmania
(hidden-package
@ -2063,12 +2066,6 @@ capabilities.")
("libass" ,libass)
("tesseract-ocr" ,tesseract-ocr)
("zimg" ,zimg)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(invoke "sh" "autogen.sh"))))))
(home-page "http://www.vapoursynth.com/")
(synopsis "Video processing framework")
(description "VapourSynth is a C++ library and Python module for video
@ -2511,12 +2508,6 @@ Other features include a live preview and live streaming.")
(base32
"18yfkr70lr1x1hc8snn2ldnbzdcc7b64xmkqrfk8w59gpg7sl1xn"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen.sh
(lambda _
(invoke "sh" "autogen.sh"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)))
@ -2896,10 +2887,7 @@ practically any type of media.")
(add-after 'unpack 'change-to-build-dir
(lambda _
(chdir "Project/GNU/Library")
#t))
(add-after 'change-to-build-dir 'autogen
(lambda _
(invoke "sh" "autogen.sh"))))))
#t)))))
(home-page "https://mediaarea.net/en/MediaInfo")
(synopsis "Library for retrieving media metadata")
(description "MediaInfo is a library used for retrieving technical

12
gnu/packages/vpn.scm
View File

@ -3,7 +3,7 @@
;;; Copyright © 2013, 2016, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
@ -227,11 +227,6 @@ the entire VPN in a network namespace accessible only through SSH.")
("automake" ,automake)))
(inputs
`(("libevent" ,libevent)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _ (invoke "sh" "autogen.sh"))))))
(home-page "https://github.com/cernekee/ocproxy")
(synopsis "OpenConnect proxy")
(description
@ -252,11 +247,12 @@ the user specifically asks to proxy, so the @dfn{VPN} interface no longer
(sha256 (base32
"1wlypi68kqqg2mdck8wvf6aanhrmf9i7z6lngyxvcrp23jdzz34h"))))
(build-system gnu-build-system)
(inputs
(propagated-inputs
`(("libxml2" ,libxml2)
("gnutls" ,gnutls)
("vpnc-scripts" ,vpnc-scripts)
("zlib" ,zlib)))
(inputs
`(("vpnc-scripts" ,vpnc-scripts)))
(native-inputs
`(("gettext" ,gettext-minimal)
("pkg-config" ,pkg-config)))

2
gnu/packages/wm.scm
View File

@ -290,8 +290,6 @@ Despite the name it should work with any X11 window manager.")
(arguments
`(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
#:phases (modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _ (invoke "sh" "autogen.sh")))
(add-after 'install 'install-doc
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))

32
gnu/tests/reconfigure.scm
View File

@ -19,8 +19,10 @@
(define-module (gnu tests reconfigure)
#:use-module (gnu bootloader)
#:use-module (gnu services shepherd)
#:use-module (gnu system vm)
#:use-module (gnu system)
#:use-module (gnu system accounts)
#:use-module (gnu system shadow)
#:use-module (gnu system vm)
#:use-module (gnu tests)
#:use-module (guix derivations)
#:use-module (guix gexp)
@ -43,7 +45,13 @@
generation of the system profile."
(define os
(marionette-operating-system
(simple-operating-system)
(operating-system
(inherit (simple-operating-system))
(users (cons (user-account
(name "jakob")
(group "users")
(home-directory "/home/jakob"))
%base-user-accounts)))
#:imported-modules '((gnu services herd)
(guix combinators))))
@ -84,7 +92,25 @@ generation of the system profile."
(test-equal "script created new generation"
(length (system-generations marionette))
(1+ (length generations-prior))))
(1+ (length generations-prior)))
(test-assert "script activated the new generation"
(and (eqv? 'symlink
(marionette-eval
'(stat:type (lstat "/run/current-system"))
marionette))
(string= #$os
(marionette-eval
'(readlink "/run/current-system")
marionette))))
(test-assert "script activated user accounts"
(marionette-eval
'(string-contains (call-with-input-file "/etc/passwd"
(lambda (port)
(get-string-all port)))
"jakob")
marionette)))
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0)))))

6
guix/scripts/deploy.scm
View File

@ -19,6 +19,7 @@
(define-module (guix scripts deploy)
#:use-module (gnu machine)
#:use-module (guix discovery)
#:use-module (guix scripts)
#:use-module (guix scripts build)
#:use-module (guix store)
@ -74,7 +75,10 @@ Perform the deployment specified by FILE.\n"))
(define (load-source-file file)
"Load FILE as a user module."
(let ((module (make-user-module '((gnu) (gnu machine) (gnu machine ssh)))))
(let* ((guix-path (dirname (search-path %load-path "guix.scm")))
(environment-modules (scheme-modules* guix-path "gnu/machine"))
(module (make-user-module (append '((gnu) (gnu machine))
environment-modules))))
(load* file module)))
(define (guix-deploy . args)

20
guix/scripts/system/reconfigure.scm
View File

@ -195,21 +195,31 @@ BOOTLOADER-PACKAGE."
(srfi srfi-34)
(srfi srfi-35))
(let* ((gc-root (string-append #$target %gc-roots-directory "/bootcfg"))
(temp-gc-root (string-append gc-root ".new")))
(switch-symlinks temp-gc-root gc-root)
(install-boot-config #$bootcfg #$bootcfg-file #$target)
(new-gc-root (string-append gc-root ".new")))
;; #$bootcfg has dependencies.
;; The bootloader magically loads the configuration from
;; (string-append #$target #$bootcfg-file) (for example
;; "/boot/grub/grub.cfg").
;; If we didn't do something special, the garbage collector
;; would remove the dependencies of #$bootcfg.
;; Register #$bootcfg as a GC root.
;; Preserve the previous activation's garbage collector root
;; until the bootloader installer has run, so that a failure in
;; the bootloader's installer script doesn't leave the user with
;; a broken installation.
(switch-symlinks new-gc-root #$bootcfg)
(install-boot-config #$bootcfg #$bootcfg-file #$target)
(when #$installer
(catch #t
(lambda ()
(#$installer #$bootloader-package #$device #$target))
(lambda args
(delete-file temp-gc-root)
(delete-file new-gc-root)
(apply throw args))))
(rename-file temp-gc-root gc-root)))))))
;; We are sure that the installation of the bootloader
;; succeeded, so we can replace the old GC root by the new
;; GC root now.
(rename-file new-gc-root gc-root)))))))
(define* (install-bootloader eval configuration bootcfg
#:key