diff options
| -rw-r--r-- | doc/guix.texi | 20 | ||||
| -rw-r--r-- | gnu/machine.scm | 12 | ||||
| -rw-r--r-- | gnu/machine/ssh.scm | 148 | ||||
| -rw-r--r-- | gnu/packages/admin.scm | 2 | ||||
| -rw-r--r-- | gnu/packages/audio.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/bioconductor.scm | 20 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 32 | ||||
| -rw-r--r-- | gnu/packages/cran.scm | 319 | ||||
| -rw-r--r-- | gnu/packages/emulators.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/geo.scm | 9 | ||||
| -rw-r--r-- | gnu/packages/image.scm | 9 | ||||
| -rw-r--r-- | gnu/packages/linux.scm | 20 | ||||
| -rw-r--r-- | gnu/packages/machine-learning.scm | 7 | ||||
| -rw-r--r-- | gnu/packages/mail.scm | 16 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/perl.scm | 2 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 139 | ||||
| -rw-r--r-- | gnu/packages/terminals.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/video.scm | 32 | ||||
| -rw-r--r-- | gnu/packages/vpn.scm | 12 | ||||
| -rw-r--r-- | gnu/packages/wm.scm | 2 | ||||
| -rw-r--r-- | gnu/tests/reconfigure.scm | 32 | ||||
| -rw-r--r-- | guix/scripts/deploy.scm | 6 | ||||
| -rw-r--r-- | guix/scripts/system/reconfigure.scm | 20 |
24 files changed, 551 insertions, 334 deletions
diff --git a/doc/guix.texi b/doc/guix.texi index cb60d5c7b7..734206a4b2 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -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} diff --git a/gnu/machine.scm b/gnu/machine.scm index 0b79402b0a..30ae97f6ec 100644 --- a/gnu/machine.scm +++ b/gnu/machine.scm @@ -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 diff --git a/gnu/machine/ssh.scm b/gnu/machine/ssh.scm index 552eafa9de..274d56db26 100644 --- a/gnu/machine/ssh.scm +++ b/gnu/machine/ssh.scm @@ -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) @@ -100,6 +104,145 @@ an environment type of 'managed-host." ;;; +;;; 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)) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index c3b1e04901..393dcb21eb 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -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") diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index c6c42f66c6..fc0d6f80db 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -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"))) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74af02a47d..74620a2cbe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -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))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcec9cd279..956257d7bb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3bd0d664da..4b998eb1fb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -78,14 +78,14 @@ (define-public r-clipr (package (name "r-clipr") - (version "0.6.0") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "clipr" version)) (sha256 (base32 - "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m")))) + "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903")))) (build-system r-build-system) (home-page "https://github.com/mdlincoln/clipr") (synopsis "Read and write from the system clipboard") @@ -97,14 +97,14 @@ the system clipboards.") (define-public r-ellipsis (package (name "r-ellipsis") - (version "0.2.0") + (version "0.2.0.1") (source (origin (method url-fetch) (uri (cran-uri "ellipsis" version)) (sha256 (base32 - "0hdk79q4wn5nq52p8qd65kqz81l0b8gfzsbzyvmfais0p24qclib")))) + "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f")))) (build-system r-build-system) (propagated-inputs `(("r-rlang" ,r-rlang))) @@ -370,14 +370,14 @@ such as copy/paste from an R session.") (define-public r-callr (package (name "r-callr") - (version "3.2.0") + (version "3.3.1") (source (origin (method url-fetch) (uri (cran-uri "callr" version)) (sha256 (base32 - "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b")))) + "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z")))) (build-system r-build-system) (propagated-inputs `(("r-r6" ,r-r6) @@ -500,13 +500,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk")))) + "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) @@ -614,13 +614,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "3.3") + (version "4.0") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c")))) + "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89")))) (build-system r-build-system) (arguments `(#:phases @@ -1205,14 +1205,14 @@ including functions for geolocation and routing.") (define-public r-haven (package (name "r-haven") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (cran-uri "haven" version)) (sha256 (base32 - "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0")))) + "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -1441,14 +1441,14 @@ processes. Most of its code is based on the @code{psutil} Python package.") (define-public r-pkgbuild (package (name "r-pkgbuild") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (cran-uri "pkgbuild" version)) (sha256 (base32 - "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9")))) + "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19")))) (build-system r-build-system) (propagated-inputs `(("r-callr" ,r-callr) @@ -1497,13 +1497,13 @@ you to rapidly iterate while developing a package.") (define-public r-rcpp (package (name "r-rcpp") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7")))) + (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes @@ -2230,14 +2230,14 @@ topics for ecologists (ISBN 978-0-691-12522-0).") (define-public r-lpsolve (package (name "r-lpsolve") - (version "5.6.13.1") + (version "5.6.13.2") (source (origin (method url-fetch) (uri (cran-uri "lpSolve" version)) (sha256 (base32 - "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a")))) + "0fc5m259ayc880f5hvnq59ih6nb2rlp394n756n1khmxbjpw1w3m")))) (properties `((upstream-name . "lpSolve"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/lpSolve") @@ -2315,14 +2315,14 @@ data). Weighted versions of MLE, MME and QME are available.") (define-public r-energy (package (name "r-energy") - (version "1.7-5") + (version "1.7-6") (source (origin (method url-fetch) (uri (cran-uri "energy" version)) (sha256 (base32 - "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4")))) + "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh")))) (build-system r-build-system) (propagated-inputs `(("r-boot" ,r-boot) @@ -2450,14 +2450,14 @@ available in a vignette.") (define-public r-lava (package (name "r-lava") - (version "1.6.5") + (version "1.6.6") (source (origin (method url-fetch) (uri (cran-uri "lava" version)) (sha256 (base32 - "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f")))) + "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s")))) (build-system r-build-system) (propagated-inputs `(("r-numderiv" ,r-numderiv) @@ -2640,20 +2640,41 @@ to access PostgreSQL database systems.") ;; under the PostgreSQL license. (license license:gpl2))) +(define-public r-linprog + (package + (name "r-linprog") + (version "0.9-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "linprog" version)) + (sha256 + (base32 + "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9")))) + (build-system r-build-system) + (propagated-inputs `(("r-lpsolve" ,r-lpsolve))) + (home-page "http://linprog.r-forge.r-project.org/") + (synopsis "Linear programming and optimization") + (description + "This package can be used to solve Linear Programming / Linear +Optimization problems by using the simplex algorithm.") + (license license:gpl2+))) + (define-public r-geometry (package (name "r-geometry") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (cran-uri "geometry" version)) (sha256 (base32 - "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm")))) + "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz")))) (build-system r-build-system) (propagated-inputs `(("r-magic" ,r-magic) + ("r-linprog" ,r-linprog) ("r-lpsolve" ,r-lpsolve) ("r-rcpp" ,r-rcpp) ("r-rcppprogress" ,r-rcppprogress))) @@ -2871,14 +2892,14 @@ provides a one-row summary of model-level statistics.") (define-public r-recipes (package (name "r-recipes") - (version "0.1.5") + (version "0.1.6") (source (origin (method url-fetch) (uri (cran-uri "recipes" version)) (sha256 (base32 - "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg")))) + "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -2890,7 +2911,6 @@ provides a one-row summary of model-level statistics.") ("r-magrittr" ,r-magrittr) ("r-matrix" ,r-matrix) ("r-purrr" ,r-purrr) - ("r-rcpproll" ,r-rcpproll) ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) @@ -3056,14 +3076,14 @@ Laplace approximation and adaptive Gauss-Hermite quadrature.") (define-public r-jomo (package (name "r-jomo") - (version "2.6-8") + (version "2.6-9") (source (origin (method url-fetch) (uri (cran-uri "jomo" version)) (sha256 (base32 - "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb")))) + "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr")))) (build-system r-build-system) (propagated-inputs `(("r-lme4" ,r-lme4) @@ -3129,14 +3149,14 @@ analysis of multiply imputed data sets.") (define-public r-mice (package (name "r-mice") - (version "3.5.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "mice" version)) (sha256 (base32 - "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g")))) + "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) @@ -3212,14 +3232,14 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9")))) + "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs @@ -3289,14 +3309,14 @@ structure.") (define-public r-vioplot (package (name "r-vioplot") - (version "0.3.0") + (version "0.3.2") (source (origin (method url-fetch) (uri (cran-uri "vioplot" version)) (sha256 (base32 - "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn")))) + "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv")))) (build-system r-build-system) (propagated-inputs `(("r-sm" ,r-sm) @@ -3631,14 +3651,14 @@ constants, and control debugging of packages via environment variables.") (define-public r-processx (package (name "r-processx") - (version "3.3.1") + (version "3.4.1") (source (origin (method url-fetch) (uri (cran-uri "processx" version)) (sha256 (base32 - "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1")))) + "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi")))) (build-system r-build-system) (propagated-inputs `(("r-ps" ,r-ps) @@ -3839,18 +3859,19 @@ to variables on the left-hand side of the assignment.") (define-public r-vctrs (package (name "r-vctrs") - (version "0.1.0") + (version "0.2.0") (source (origin (method url-fetch) (uri (cran-uri "vctrs" version)) (sha256 (base32 - "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c")))) + "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports) ("r-digest" ,r-digest) + ("r-ellipsis" ,r-ellipsis) ("r-glue" ,r-glue) ("r-rlang" ,r-rlang) ("r-zeallot" ,r-zeallot))) @@ -3877,14 +3898,14 @@ to variables on the left-hand side of the assignment.") (define-public r-pillar (package (name "r-pillar") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm")))) + "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) @@ -3923,14 +3944,14 @@ terminals.") (define-public r-tinytex (package (name "r-tinytex") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) (uri (cran-uri "tinytex" version)) (sha256 (base32 - "0aab7ybc6kkxxk3lzdmbla8zcpp6nmlahchc33miv28cmnqw363w")))) + "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax")))) (build-system r-build-system) (propagated-inputs `(("r-xfun" ,r-xfun))) @@ -4628,14 +4649,14 @@ files.") (define-public r-shinyace (package (name "r-shinyace") - (version "0.3.3") + (version "0.4.0") (source (origin (method url-fetch) (uri (cran-uri "shinyAce" version)) (sha256 (base32 - "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j")))) + "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1")))) (properties `((upstream-name . "shinyAce"))) (build-system r-build-system) (propagated-inputs @@ -4678,14 +4699,14 @@ systems.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "0.9.9") + (version "1.0.0") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn")) + "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw")) (modules '((guix build utils))) (snippet '(begin @@ -5140,14 +5161,14 @@ misclassification probabilities of different models.") (define-public r-zip (package (name "r-zip") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "zip" version)) (sha256 (base32 - "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix")))) + "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a")))) (build-system r-build-system) (home-page "https://github.com/gaborcsardi/zip") (synopsis "Cross-platform Zip compression") @@ -5298,14 +5319,14 @@ promises, but with a syntax that is idiomatic R.") (define-public r-dosnow (package (name "r-dosnow") - (version "1.0.16") + (version "1.0.18") (source (origin (method url-fetch) (uri (cran-uri "doSNOW" version)) (sha256 (base32 - "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n")))) + "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh")))) (properties `((upstream-name . "doSNOW"))) (build-system r-build-system) (propagated-inputs @@ -5431,14 +5452,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.12") + (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb")))) + "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs @@ -5548,14 +5569,14 @@ and adds the annotation to the plot.") (define-public r-ggpubr (package (name "r-ggpubr") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "ggpubr" version)) (sha256 (base32 - "0a4dv6a752hwvc7l31xs7bgqhfzfdy94xp6wgwaxf5dxm46na7k1")))) + "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -5569,6 +5590,7 @@ and adds the annotation to the plot.") ("r-magrittr" ,r-magrittr) ("r-polynom" ,r-polynom) ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales) ("r-tidyr" ,r-tidyr))) (home-page "http://www.sthda.com/english/rpkgs/ggpubr") @@ -5628,14 +5650,14 @@ clustering.") (define-public r-factominer (package (name "r-factominer") - (version "1.41") + (version "1.42") (source (origin (method url-fetch) (uri (cran-uri "FactoMineR" version)) (sha256 (base32 - "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259")))) + "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac")))) (properties `((upstream-name . "FactoMineR"))) (build-system r-build-system) (propagated-inputs @@ -5918,20 +5940,19 @@ to help insert or delete content at a specific location in the document.") (define-public r-abn (package (name "r-abn") - (version "1.3") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm")))) + "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-lme4" ,r-lme4) + `(("r-lme4" ,r-lme4) ("r-mass" ,r-mass) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) @@ -6070,14 +6091,14 @@ other add-on packages.") (define-public r-insight (package (name "r-insight") - (version "0.3.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (cran-uri "insight" version)) (sha256 (base32 - "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb")))) + "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82")))) (build-system r-build-system) (home-page "https://easystats.github.io/insight/") (synopsis "Easy access to model information for various model objects") @@ -6527,14 +6548,14 @@ containing one or more SNPs that evolved under directional selection.") (define-public r-proc (package (name "r-proc") - (version "1.15.0") + (version "1.15.3") (source (origin (method url-fetch) (uri (cran-uri "pROC" version)) (sha256 (base32 - "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24")))) + "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h")))) (properties `((upstream-name . "pROC"))) (build-system r-build-system) (propagated-inputs @@ -6900,14 +6921,14 @@ used to teach mathematics, statistics, computation and modeling.") (define-public r-raster (package (name "r-raster") - (version "2.9-5") + (version "2.9-23") (source (origin (method url-fetch) (uri (cran-uri "raster" version)) (sha256 (base32 - "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk")))) + "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -7468,14 +7489,14 @@ multiple-imputation datasets.") (define-public r-magick (package (name "r-magick") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (cran-uri "magick" version)) (sha256 (base32 - "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m")))) + "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg")))) (build-system r-build-system) (inputs `(("imagemagick" ,imagemagick) @@ -7857,14 +7878,14 @@ Hothorn, Westfall, 2010, CRC Press).") (define-public r-emmeans (package (name "r-emmeans") - (version "1.3.5.1") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "emmeans" version)) (sha256 (base32 - "0rgzjvmp3yqhwgfg96v17wi8gbafzbrmz134shj2jsf5bsmw6vbj")))) + "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh")))) (build-system r-build-system) (propagated-inputs `(("r-estimability" ,r-estimability) @@ -8089,14 +8110,14 @@ differentiation.") (define-public r-bayestestr (package (name "r-bayestestr") - (version "0.2.2") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "bayestestR" version)) (sha256 (base32 - "09r654lrhwwnshn5h2s2fbx3c8wigv3j4sva5hmfnkwjg8cclhd9")))) + "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82")))) (properties `((upstream-name . "bayestestR"))) (build-system r-build-system) (propagated-inputs @@ -8114,14 +8135,14 @@ ROPE percentage and pd).") (define-public r-performance (package (name "r-performance") - (version "0.2.0") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "performance" version)) (sha256 (base32 - "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z")))) + "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w")))) (build-system r-build-system) (propagated-inputs `(("r-bayestestr" ,r-bayestestr) @@ -8141,14 +8162,14 @@ effects models and Bayesian models.") (define-public r-ggeffects (package (name "r-ggeffects") - (version "0.10.0") + (version "0.11.0") (source (origin (method url-fetch) (uri (cran-uri "ggeffects" version)) (sha256 (base32 - "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k")))) + "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) @@ -8175,14 +8196,14 @@ results using @code{ggplot2}.") (define-public r-sjplot (package (name "r-sjplot") - (version "2.6.3") + (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "sjPlot" version)) (sha256 (base32 - "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy")))) + "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk")))) (properties `((upstream-name . "sjPlot"))) (build-system r-build-system) (propagated-inputs @@ -8192,6 +8213,7 @@ results using @code{ggplot2}.") ("r-forcats" ,r-forcats) ("r-ggeffects" ,r-ggeffects) ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) ("r-glmmtmb" ,r-glmmtmb) ("r-insight" ,r-insight) ("r-knitr" ,r-knitr) @@ -8311,14 +8333,14 @@ terminals that do not support Unicode.") (define-public r-usethis (package (name "r-usethis") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "usethis" version)) (sha256 (base32 - "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag")))) + "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy")))) (build-system r-build-system) (propagated-inputs `(("r-clipr" ,r-clipr) @@ -8674,14 +8696,14 @@ analysing multivariate abundance data in community ecology.") (define-public r-afex (package (name "r-afex") - (version "0.23-0") + (version "0.24-1") (source (origin (method url-fetch) (uri (cran-uri "afex" version)) (sha256 (base32 - "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7")))) + "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455")))) (build-system r-build-system) (propagated-inputs `(("r-car" ,r-car) @@ -8908,14 +8930,14 @@ Bioconductor packages.") (define-public r-rgl (package (name "r-rgl") - (version "0.100.24") + (version "0.100.26") (source (origin (method url-fetch) (uri (cran-uri "rgl" version)) (sha256 (base32 - "0nm3iyvhhmh0zlywkfmrq3vyh8z1l296xxfmcky0ifd2qnysfcqj")))) + "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271")))) (build-system r-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -9374,14 +9396,14 @@ maps.") (define-public r-tidytree (package (name "r-tidytree") - (version "0.2.4") + (version "0.2.5") (source (origin (method url-fetch) (uri (cran-uri "tidytree" version)) (sha256 (base32 - "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w")))) + "0vfjv33352dmk9cr2qn0knzg761068rdk6jg32csd9vpmcma8awp")))) (build-system r-build-system) (propagated-inputs `(("r-ape" ,r-ape) @@ -9442,14 +9464,14 @@ giving it a description in the specific format.") (define-public r-sparsesvd (package (name "r-sparsesvd") - (version "0.1-4") + (version "0.2") (source (origin (method url-fetch) (uri (cran-uri "sparsesvd" version)) (sha256 (base32 - "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam")))) + "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/") @@ -9664,14 +9686,14 @@ diagnostics for controlling type-1 errors are also provided.") (define-public r-flare (package (name "r-flare") - (version "1.6.0") + (version "1.6.0.2") (source (origin (method url-fetch) (uri (cran-uri "flare" version)) (sha256 (base32 - "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1")))) + "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) @@ -9764,14 +9786,14 @@ Touzet and Varre (2007).") (define-public r-rnifti (package (name "r-rnifti") - (version "0.11.0") + (version "0.11.1") (source (origin (method url-fetch) (uri (cran-uri "RNifti" version)) (sha256 (base32 - "0zs8ffa6gpi9cygxk7xjin6k3vpvfgb540a506zlk50bf6kc5nlf")))) + "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg")))) (properties `((upstream-name . "RNifti"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) @@ -9787,14 +9809,14 @@ used by other packages.") (define-public r-shades (package (name "r-shades") - (version "1.3.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (cran-uri "shades" version)) (sha256 (base32 - "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv")))) + "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj")))) (build-system r-build-system) (home-page "https://github.com/jonclayden/shades") (synopsis "Simple color manipulation") @@ -10143,23 +10165,51 @@ library.") and manipulating sets of ontological terms.") (license license:gpl2+))) +(define-public r-gargle + (package + (name "r-gargle") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "gargle" version)) + (sha256 + (base32 + "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fs" ,r-fs) + ("r-glue" ,r-glue) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-rlang" ,r-rlang) + ("r-withr" ,r-withr))) + (home-page "https://gargle.r-lib.org") + (synopsis "Utilities for working with Google APIs") + (description + "This package provides utilities for working with Google APIs. This +includes functions and classes for handling common credential types and for +preparing, executing, and processing HTTP requests.") + (license license:expat))) + (define-public r-bigrquery (package (name "r-bigrquery") - (version "1.1.1") + (version "1.2.0") (source (origin (method url-fetch) (uri (cran-uri "bigrquery" version)) (sha256 (base32 - "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is")))) + "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-bit64" ,r-bit64) ("r-curl" ,r-curl) ("r-dbi" ,r-dbi) + ("r-gargle" ,r-gargle) ("r-glue" ,r-glue) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) @@ -10167,6 +10217,7 @@ and manipulating sets of ontological terms.") ("r-progress" ,r-progress) ("r-rapidjsonr" ,r-rapidjsonr) ("r-rcpp" ,r-rcpp) + ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble))) (home-page "https://github.com/rstats-db/bigrquery") (synopsis "R interface to Google's BigQuery API") @@ -10724,14 +10775,14 @@ covariance functions for large data sets.") (define-public r-spatialextremes (package (name "r-spatialextremes") - (version "2.0-7") + (version "2.0-7.2") (source (origin (method url-fetch) (uri (cran-uri "SpatialExtremes" version)) (sha256 (base32 - "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050")))) + "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8")))) (properties `((upstream-name . "SpatialExtremes"))) (build-system r-build-system) @@ -10994,14 +11045,14 @@ model with finite state space using the Aalen-Johansen estimator.") (define-public r-epi (package (name "r-epi") - (version "2.37") + (version "2.38") (source (origin (method url-fetch) (uri (cran-uri "Epi" version)) (sha256 (base32 - "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk")))) + "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd")))) (properties `((upstream-name . "Epi"))) (build-system r-build-system) (propagated-inputs @@ -11177,14 +11228,14 @@ them in distributed compute environments.") (define-public r-future (package (name "r-future") - (version "1.13.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (cran-uri "future" version)) (sha256 (base32 - "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz")))) + "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) @@ -11237,14 +11288,14 @@ machine or distributed on a compute cluster.") (define-public r-rsvd (package (name "r-rsvd") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "rsvd" version)) (sha256 (base32 - "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz")))) + "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) @@ -11445,14 +11496,14 @@ identifying outliers.") (define-public r-bayesm (package (name "r-bayesm") - (version "3.1-1") + (version "3.1-3") (source (origin (method url-fetch) (uri (cran-uri "bayesm" version)) (sha256 (base32 - "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28")))) + "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) @@ -11849,14 +11900,14 @@ probabilities from a standard bivariate normal CDF.") (define-public r-lavaan (package (name "r-lavaan") - (version "0.6-3") + (version "0.6-4") (source (origin (method url-fetch) (uri (cran-uri "lavaan" version)) (sha256 (base32 - "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz")))) + "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) @@ -12073,14 +12124,14 @@ running IRkernel session.") (define-public r-irkernel (package (name "r-irkernel") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "IRkernel" version)) (sha256 (base32 - "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s")))) + "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp")))) (properties `((upstream-name . "IRkernel"))) (build-system r-build-system) (arguments @@ -12192,14 +12243,14 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-rematch2 (package (name "r-rematch2") - (version "2.0.1") + (version "2.1.0") (source (origin (method url-fetch) (uri (cran-uri "rematch2" version)) (sha256 (base32 - "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6")))) + "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq")))) (build-system r-build-system) (propagated-inputs `(("r-tibble" ,r-tibble))) @@ -12541,14 +12592,14 @@ classes.") (define-public r-classint (package (name "r-classint") - (version "0.3-3") + (version "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "classInt" version)) (sha256 (base32 - "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9")))) + "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir")))) (properties `((upstream-name . "classInt"))) (build-system r-build-system) (propagated-inputs @@ -12616,14 +12667,14 @@ sampling.") (define-public r-deldir (package (name "r-deldir") - (version "0.1-21") + (version "0.1-23") (source (origin (method url-fetch) (uri (cran-uri "deldir" version)) (sha256 (base32 - "03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr")))) + "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://cran.r-project.org/web/packages/deldir") @@ -12640,14 +12691,14 @@ tessellation.") (define-public r-sf (package (name "r-sf") - (version "0.7-4") + (version "0.7-7") (source (origin (method url-fetch) (uri (cran-uri "sf" version)) (sha256 (base32 - "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1")))) + "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i")))) (build-system r-build-system) (inputs `(("gdal" ,gdal) @@ -13022,18 +13073,19 @@ inbred lines, F2 intercrosses, and association mapping populations.") (define-public r-ldheatmap (package (name "r-ldheatmap") - (version "0.99-5") + (version "0.99-7") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 - "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s")))) + "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs `(("r-genetics" ,r-genetics) + ("r-rcpp" ,r-rcpp) ("r-snpstats" ,r-snpstats))) (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") @@ -13112,13 +13164,13 @@ SELECT or UPDATE queries to an end-point.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r")))) + "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -13585,14 +13637,14 @@ package.") (define-public r-ggplotify (package (name "r-ggplotify") - (version "0.0.3") + (version "0.0.4") (source (origin (method url-fetch) (uri (cran-uri "ggplotify" version)) (sha256 (base32 - "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby")))) + "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -14562,14 +14614,14 @@ engine (Salmon et al., 2011) as provided by the package @code{sitmo}.") (define-public r-dalex (package (name "r-dalex") - (version "0.4") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "DALEX" version)) (sha256 (base32 - "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a")))) + "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r")))) (properties `((upstream-name . "DALEX"))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) @@ -14588,14 +14640,14 @@ and model output.") (define-public r-enrichr (package (name "r-enrichr") - (version "1.0") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "enrichR" version)) (sha256 (base32 - "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn")))) + "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz")))) (properties `((upstream-name . "enrichR"))) (build-system r-build-system) (propagated-inputs @@ -14698,18 +14750,17 @@ into R and converted to @code{BibEntry} objects.") (define-public r-citr (package (name "r-citr") - (version "0.3.0") + (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "citr" version)) (sha256 (base32 - "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g")))) + "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) - ("r-bibtex" ,r-bibtex) ("r-curl" ,r-curl) ("r-httr" ,r-httr) ("r-miniui" ,r-miniui) @@ -14729,14 +14780,14 @@ the current document.") (define-public r-xgboost (package (name "r-xgboost") - (version "0.82.1") + (version "0.90.0.2") (source (origin (method url-fetch) (uri (cran-uri "xgboost" version)) (sha256 (base32 - "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq")))) + "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194")))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 8d0162a2d1..257591c8d3 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -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))) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 8005c46129..edb3b49841 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -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))) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index d4273c6fa1..6928246509 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -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 diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9f20d2bace..a5b9f6bfed 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -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))) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index dd5ee1e9ee..e48c91a2cf 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -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))) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 40fe7d9450..b81b15d80c 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -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 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b204b314c6..e3c7d9ce91 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -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 diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 2a40b2c736..5628a4b93f 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -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") diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6ed1e40108..f27f2229f7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -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))) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index df8d1e4b79..9077d295db 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -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) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 04715a5ce1..eda5b8fc39 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -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 diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index c7046b7f50..d1a7248536 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -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))) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index c56cf406ee..160c267882 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -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")) diff --git a/gnu/tests/reconfigure.scm b/gnu/tests/reconfigure.scm index 3a2f0a2e53..fb11e6164e 100644 --- a/gnu/tests/reconfigure.scm +++ b/gnu/tests/reconfigure.scm @@ -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))))) diff --git a/guix/scripts/deploy.scm b/guix/scripts/deploy.scm index 52bba3f3bf..ebc99e52cc 100644 --- a/guix/scripts/deploy.scm +++ b/guix/scripts/deploy.scm @@ -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) diff --git a/guix/scripts/system/reconfigure.scm b/guix/scripts/system/reconfigure.scm index dee0c24bd2..579b7fffbe 100644 --- a/guix/scripts/system/reconfigure.scm +++ b/guix/scripts/system/reconfigure.scm @@ -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 |