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authorMarius Bakke <mbakke@fastmail.com>2019-06-11 10:27:09 +0200
committerMarius Bakke <mbakke@fastmail.com>2019-06-11 10:27:09 +0200
commit58bf51b4c0771fb6cfcf22be84d734096e7b11e0 (patch)
tree69c22625468b10e43fd37e7c5ddc420a1de6ab55 /gnu/packages
parent69ecd666d73ebc5ee7a0be54f4e24f000d1d7e31 (diff)
parentbf3005346e6538aba6d077c887f688779b94b274 (diff)
downloadpatches-58bf51b4c0771fb6cfcf22be84d734096e7b11e0.tar
patches-58bf51b4c0771fb6cfcf22be84d734096e7b11e0.tar.gz
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/astronomy.scm8
-rw-r--r--gnu/packages/audio.scm4
-rw-r--r--gnu/packages/bioconductor.scm79
-rw-r--r--gnu/packages/bioinformatics.scm8
-rw-r--r--gnu/packages/cran.scm51
-rw-r--r--gnu/packages/databases.scm25
-rw-r--r--gnu/packages/emacs-xyz.scm45
-rw-r--r--gnu/packages/gl.scm4
-rw-r--r--gnu/packages/gnome.scm10
-rw-r--r--gnu/packages/image.scm8
-rw-r--r--gnu/packages/linux.scm46
-rw-r--r--gnu/packages/mail.scm4
-rw-r--r--gnu/packages/patches/allegro-mesa-18.2.5-and-later.patch41
-rw-r--r--gnu/packages/statistics.scm36
-rw-r--r--gnu/packages/tbb.scm4
-rw-r--r--gnu/packages/terminals.scm4
-rw-r--r--gnu/packages/wine.scm6
17 files changed, 254 insertions, 129 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ab5dcd92a7..9ddb9e1d52 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 John Darrington <jmd@gnu.org>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
@@ -37,15 +37,15 @@
(define-public cfitsio
(package
(name "cfitsio")
- (version "3.450")
+ (version "3.47")
(source
(origin
(method url-fetch)
(uri (string-append
"http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/"
- name (string-replace-substring version "." "") ".tar.gz"))
+ name "-" version ".tar.gz"))
(sha256
- (base32 "0bmrkw6w65zb0k3mszaaqy1f4zjm2hl7njww74nb5v38wvdi4q5z"))))
+ (base32 "1vzlxnrjckz78p2wf148v2z3krkwnykfqvlj42sz3q711vqid1a1"))))
(build-system gnu-build-system)
;; XXX Building with curl currently breaks wcslib. It doesn't use
;; pkg-config and hence won't link with -lcurl.
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index f3f592c58a..9defc59b93 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3701,7 +3701,7 @@ library.")
(define-public faudio
(package
(name "faudio")
- (version "19.06")
+ (version "19.06.07")
(source
(origin
(method git-fetch)
@@ -3710,7 +3710,7 @@ library.")
(commit version)))
(file-name (string-append name "-" version "-checkout"))
(sha256
- (base32 "1azjf972hik1cizsblbvfp38xz7dx368pbpw3pd6z1xk9mnrhi6s"))))
+ (base32 "1w37qp279lgpyvslwz3wlb4fp0i68ncd411rqdlk5s71b1zz466n"))))
(arguments
'(#:tests? #f ; No tests.
#:configure-flags '("-DFFMPEG=ON")))
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ffb7c4e3c..ff159638b3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3621,14 +3621,14 @@ investigation using RNA-seq data.")
(define-public r-aucell
(package
(name "r-aucell")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AUCell" version))
(sha256
(base32
- "025q1as9pifbxa7hidlz634q6d7l73zx8mqy4rjbfrk7d5615xvm"))))
+ "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
@@ -4438,14 +4438,14 @@ interpretation.")
(define-public r-rhisat2
(package
(name "r-rhisat2")
- (version "1.0.1")
+ (version "1.0.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhisat2" version))
(sha256
(base32
- "01jhj5vvfl4n2d0nl3nd1iw9nii85mgw2adnrmxb8wwlxgy240vr"))))
+ "1y3zqvk1vbcb10r1myh6f5yzjvf7bhwhpiq78bs1k6spli4bzj0q"))))
(properties `((upstream-name . "Rhisat2")))
(build-system r-build-system)
(native-inputs
@@ -4606,3 +4606,74 @@ expression data to predict switches in regulatory activity between two
conditions. A Bayesian network is used to model the regulatory structure and
Markov-Chain-Monte-Carlo is applied to sample the activity states.")
(license license:gpl2+)))
+
+(define-public r-ropls
+ (package
+ (name "r-ropls")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ropls" version))
+ (sha256
+ (base32
+ "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
+ (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
+ (synopsis "Multivariate analysis and feature selection of omics data")
+ (description
+ "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
+and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
+regression, classification, and feature selection of omics data where the
+number of variables exceeds the number of samples and with multicollinearity
+among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
+separately model the variation correlated (predictive) to the factor of
+interest and the uncorrelated (orthogonal) variation. While performing
+similarly to PLS, OPLS facilitates interpretation.
+
+This package provides imlementations of PCA, PLS, and OPLS for multivariate
+analysis and feature selection of omics data. In addition to scores, loadings
+and weights plots, the package provides metrics and graphics to determine the
+optimal number of components (e.g. with the R2 and Q2 coefficients), check the
+validity of the model by permutation testing, detect outliers, and perform
+feature selection (e.g. with Variable Importance in Projection or regression
+coefficients).")
+ (license license:cecill)))
+
+(define-public r-biosigner
+ (package
+ (name "r-biosigner")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "biosigner" version))
+ (sha256
+ (base32
+ "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-e1071" ,r-e1071)
+ ("r-randomforest" ,r-randomforest)
+ ("r-ropls" ,r-ropls)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("pandoc" ,ghc-pandoc)
+ ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+ (home-page "https://bioconductor.org/packages/biosigner/")
+ (synopsis "Signature discovery from omics data")
+ (description
+ "Feature selection is critical in omics data analysis to extract
+restricted and meaningful molecular signatures from complex and high-dimension
+data, and to build robust classifiers. This package implements a method to
+assess the relevance of the variables for the prediction performances of the
+classifier. The approach can be run in parallel with the PLS-DA, Random
+Forest, and SVM binary classifiers. The signatures and the corresponding
+'restricted' models are returned, enabling future predictions on new
+datasets.")
+ (license license:cecill)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4b8e662a3a..bb15672d51 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7373,13 +7373,13 @@ S4Vectors package itself.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.18.0")
+ (version "2.18.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0g06y6xlm2q7p7g7phfc8qj14pqpgbb0mkyjzkfgsrwjmzvpwy6m"))))
+ "1d64sh43pfc9vj2l7y7x6sb44l67wlnn3dzygp7ws0smn06mardq"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -9370,14 +9370,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.10.0")
+ (version "2.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "1lqdlyvs2c9g55zf8gnw142ps4jid644fhfvclnax7sjjwrqdjzv"))))
+ "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 005016b984..356595ff33 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -2819,14 +2819,14 @@ color labels, layout, etc.")
(define-public r-stringdist
(package
(name "r-stringdist")
- (version "0.9.5.1")
+ (version "0.9.5.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "stringdist" version))
(sha256
(base32
- "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa"))))
+ "0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l"))))
(build-system r-build-system)
(home-page "https://github.com/markvanderloo/stringdist")
(synopsis "Approximate string matching and string distance functions")
@@ -3583,14 +3583,14 @@ Markdown documents.")
(define-public r-seriation
(package
(name "r-seriation")
- (version "1.2-5")
+ (version "1.2-7")
(source
(origin
(method url-fetch)
(uri (cran-uri "seriation" version))
(sha256
(base32
- "0sk4wfwxxhz3nwbcsfshb93gra4c9p5pvpsz00d7f9nkkmhs97ws"))))
+ "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cluster" ,r-cluster)
@@ -3833,14 +3833,14 @@ supports arbitrary vertex/edge/graph attributes.")
(define-public r-statnet-common
(package
(name "r-statnet-common")
- (version "4.2.0")
+ (version "4.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "statnet.common" version))
(sha256
(base32
- "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi"))))
+ "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
(properties
`((upstream-name . "statnet.common")))
(build-system r-build-system)
@@ -4033,14 +4033,14 @@ financial trading strategies.")
(define-public r-tseries
(package
(name "r-tseries")
- (version "0.10-46")
+ (version "0.10-47")
(source
(origin
(method url-fetch)
(uri (cran-uri "tseries" version))
(sha256
(base32
- "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j"))))
+ "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-quadprog" ,r-quadprog)
@@ -5933,22 +5933,22 @@ information are missing.")
(define-public r-sjlabelled
(package
(name "r-sjlabelled")
- (version "1.0.17")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjlabelled" version))
(sha256
(base32
- "00c0c22ynpihgf2bvmcfnkvqwqvxax2zzb7wldsmg2f7z5a32aa6"))))
+ "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-dplyr" ,r-dplyr)
- ("r-haven" ,r-haven)
+ `(("r-haven" ,r-haven)
("r-insight" ,r-insight)
("r-magrittr" ,r-magrittr)
("r-purrr" ,r-purrr)
- ("r-rlang" ,r-rlang)))
+ ("r-rlang" ,r-rlang)
+ ("r-tidyselect" ,r-tidyselect)))
(home-page "https://github.com/strengejacke/sjlabelled")
(synopsis "Labelled data utility functions")
(description
@@ -6364,14 +6364,14 @@ containing one or more SNPs that evolved under directional selection.")
(define-public r-proc
(package
(name "r-proc")
- (version "1.14.0")
+ (version "1.15.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "pROC" version))
(sha256
(base32
- "0ki1pvj5iaki81crapvwqllg5avn5qlvv62axnsdkdcmv9xc3wg0"))))
+ "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
(properties `((upstream-name . "pROC")))
(build-system r-build-system)
(propagated-inputs
@@ -7850,25 +7850,26 @@ detection, parallelism through BLAS and parallel user templates.")
(define-public r-sjstats
(package
(name "r-sjstats")
- (version "0.17.4")
+ (version "0.17.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "sjstats" version))
(sha256
(base32
- "012hp9m17xzjnsfvjjz2wdfgxm3irsrfx0zmahfnfmgdrwxd5vk5"))))
+ "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-broom" ,r-broom)
+ `(("r-bayestestr" ,r-bayestestr)
+ ("r-broom" ,r-broom)
("r-dplyr" ,r-dplyr)
("r-emmeans" ,r-emmeans)
("r-insight" ,r-insight)
("r-lme4" ,r-lme4)
("r-magrittr" ,r-magrittr)
("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
("r-modelr" ,r-modelr)
+ ("r-performance" ,r-performance)
("r-purrr" ,r-purrr)
("r-rlang" ,r-rlang)
("r-sjlabelled" ,r-sjlabelled)
@@ -7948,14 +7949,14 @@ ROPE percentage and pd).")
(define-public r-performance
(package
(name "r-performance")
- (version "0.1.0")
+ (version "0.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "performance" version))
(sha256
(base32
- "19lfx25hkavzbycrh6hq4v24a0dz4s60ryq6jyihjlxgrb9g7cnw"))))
+ "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bayestestr" ,r-bayestestr)
@@ -9766,14 +9767,14 @@ the combination of non-negative and non-positive constraints.")
(define-public r-iso
(package
(name "r-iso")
- (version "0.0-17")
+ (version "0.0-18")
(source
(origin
(method url-fetch)
(uri (cran-uri "Iso" version))
(sha256
(base32
- "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0"))))
+ "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
(properties `((upstream-name . "Iso")))
(build-system r-build-system)
(native-inputs `(("gfortran" ,gfortran)))
@@ -11025,14 +11026,14 @@ machine or distributed on a compute cluster.")
(define-public r-rsvd
(package
(name "r-rsvd")
- (version "1.0.0")
+ (version "1.0.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "rsvd" version))
(sha256
(base32
- "0vjhrvnkl9rmvl8sv2kac5sd10z3fgxymb676ynxzc2pmhydy3an"))))
+ "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
(build-system r-build-system)
(propagated-inputs
`(("r-matrix" ,r-matrix)))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 47eaac8e69..55f7a46dc5 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -33,6 +33,7 @@
;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Jack Hill <jackhill@jackhill.us>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -108,6 +109,7 @@
#:use-module (guix download)
#:use-module (guix bzr-download)
#:use-module (guix git-download)
+ #:use-module (guix build-system emacs)
#:use-module (guix build-system gnu)
#:use-module (guix build-system go)
#:use-module (guix build-system perl)
@@ -928,8 +930,7 @@ organized in a hash table or B+ tree.")
(assoc-ref %build-inputs "bash:include")
"/include/bash"))))
- (native-inputs `(("emacs" ,emacs-minimal)
- ("bc" ,bc)
+ (native-inputs `(("bc" ,bc)
("bash:include" ,bash "include")
("check" ,check)
("libuuid" ,util-linux)
@@ -948,6 +949,26 @@ types are supported, as is encryption.")
(license license:gpl3+)
(home-page "https://www.gnu.org/software/recutils/")))
+(define-public emacs-recutils
+ (package
+ (inherit recutils)
+ (name "emacs-recutils")
+ (build-system emacs-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'change-directory
+ (lambda _
+ (chdir "etc")
+ #t)))))
+ (native-inputs '())
+ (inputs '())
+ (synopsis "Emacs mode for working with recutils database files")
+ (description "This package provides an Emacs major mode @code{rec-mode}
+for working with GNU Recutils text-based, human-editable databases. It
+supports editing, navigation, and querying of recutils database files
+including field and record folding.")))
+
(define-public rocksdb
(package
(name "rocksdb")
diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm
index 7db46e81c5..2eb705dedd 100644
--- a/gnu/packages/emacs-xyz.scm
+++ b/gnu/packages/emacs-xyz.scm
@@ -8534,29 +8534,32 @@ key. Optionally, a mouse pop-up can be added by binding
(license license:gpl3+)))
(define-public emacs-idris-mode
- (package
- (name "emacs-idris-mode")
- (version "0.9.19")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "http://stable.melpa.org/packages/idris-mode-"
- version ".tar"))
- (sha256
- (base32
- "16hl2s22l3wc9drnwzw6hn7xrm49ml9lii0s6k218dgahdgsncmf"))))
- (build-system emacs-build-system)
- (propagated-inputs
- `(("emacs-prop-menu" ,emacs-prop-menu)))
- (home-page
- "https://github.com/idris-hackers/idris-mode")
- (synopsis "Major mode for editing Idris code")
- (description
- "This is an Emacs mode for editing Idris code. It requires the latest
+ (let ((commit "acc8835449475d7cd205aba213fdd3d41c38ba40")
+ (revision "0"))
+ (package
+ (name "emacs-idris-mode")
+ (version (git-version "0.9.19" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/idris-hackers/idris-mode.git")
+ (commit commit)))
+ (file-name (git-file-name name commit))
+ (sha256
+ (base32
+ "0n9xbknc68id0mf8hbfmawi8qpvrs47ix807sk9ffv2g3ik32kk6"))))
+ (build-system emacs-build-system)
+ (propagated-inputs
+ `(("emacs-prop-menu" ,emacs-prop-menu)))
+ (home-page
+ "https://github.com/idris-hackers/idris-mode")
+ (synopsis "Major mode for editing Idris code")
+ (description
+ "This is an Emacs mode for editing Idris code. It requires the latest
version of Idris, and some features may rely on the latest Git version of
Idris.")
- (license license:gpl3+)))
+ (license license:gpl3+))))
(define-public emacs-browse-at-remote
(package
diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm
index 3680a8979d..96e7fc7165 100644
--- a/gnu/packages/gl.scm
+++ b/gnu/packages/gl.scm
@@ -733,7 +733,7 @@ mixed vector/bitmap output.")
(define-public virtualgl
(package
(name "virtualgl")
- (version "2.6.1")
+ (version "2.6.2")
(source
(origin
(method git-fetch)
@@ -742,7 +742,7 @@ mixed vector/bitmap output.")
(commit version)))
(file-name (git-file-name name version))
(sha256
- (base32 "04fdwm6mz76lw4iwd5m7yxjfhpa0rpxd357bv5smk5lclnlbz1bv"))))
+ (base32 "0yyc553xsb5n0rx7jp9p4wdbd7md07b3qrkf3ssyjavqqg908qg9"))))
(arguments
`(#:tests? #f ; no tests are available
#:configure-flags (list
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index c77baad1f2..875d28caee 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2115,7 +2115,7 @@ Hints specification (EWMH).")
(define-public gnumeric
(package
(name "gnumeric")
- (version "1.12.44")
+ (version "1.12.45")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/gnumeric/"
@@ -2123,7 +2123,7 @@ Hints specification (EWMH).")
"gnumeric-" version ".tar.xz"))
(sha256
(base32
- "0147962c6ybdsj57rz95nla0rls7g545wc2n7pz59zmzyd5pksk0"))))
+ "0c8dl1kvnj3g32qy3s92qpqpqfy0in59cx005gjvvzsflahav61h"))))
(build-system glib-or-gtk-build-system)
(arguments
`(;; The gnumeric developers don't worry much about failing tests.
@@ -5467,7 +5467,7 @@ to virtual private networks (VPNs) via OpenVPN.")
(define-public mobile-broadband-provider-info
(package
(name "mobile-broadband-provider-info")
- (version "20170310")
+ (version "20190116")
(source (origin
(method url-fetch)
(uri (string-append
@@ -5476,10 +5476,10 @@ to virtual private networks (VPNs) via OpenVPN.")
"mobile-broadband-provider-info-" version ".tar.xz"))
(sha256
(base32
- "0fxm11x8k9hxjg8l5inaldfmmjnwkay3ibjv899jra03bv4h6kql"))))
+ "16y5lc7pfdvai9c8xwb825zc3v46039gghbip13fqslf5gw11fic"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f)) ; No tests
+ `(#:tests? #f)) ; no tests
(home-page "https://wiki.gnome.org/Projects/NetworkManager")
(synopsis "Database of broadband connection configuration")
(description "Database of broadband connection configuration.")
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index e3956394cc..f9709e2b19 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -1600,7 +1600,7 @@ identical visual appearance.")
(define-public grim
(package
(name "grim")
- (version "1.1")
+ (version "1.2.0")
(source
(origin
(method git-fetch)
@@ -1609,7 +1609,7 @@ identical visual appearance.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1bcvkggqszcwy6hg8g4mch3yr25ic0baafbd90af5s5mrhrjxxxz"))))
+ (base32 "0brljl4zfbn5mh9hkfrfkvd27c5y9vdkgap9r1hrfy9r1x20sskn"))))
(build-system meson-build-system)
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("cairo" ,cairo)
@@ -1626,7 +1626,7 @@ identical visual appearance.")
(define-public slurp
(package
(name "slurp")
- (version "1.0.1")
+ (version "1.2.0")
(source
(origin
(method git-fetch)
@@ -1635,7 +1635,7 @@ identical visual appearance.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "072lkwhpvr753wfqzmd994bnhbrgfavxcgqcyml7abab28sdhs1y"))))
+ (base32 "0580m6kaiilgsrcj608r837r37sl6a25y7w21p7d6ij20fs3gvg1"))))
(build-system meson-build-system)
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("cairo" ,cairo)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 5401b1ad97..b6887349fa 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -430,8 +430,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration."
It has been modified to remove all non-free binary blobs.")
(license license:gpl2)))
-(define %linux-libre-version "5.1.7")
-(define %linux-libre-hash "0hr4sbapdpgdkb6xg1f7bpc31242yiqdvy5sfpymsrzfslr8vwy1")
+(define %linux-libre-version "5.1.8")
+(define %linux-libre-hash "1vkirlz9vsvym8fdbvj308n3hj8f9j8n9m267x0dhlgbmig570j2")
(define %linux-libre-5.1-patches
(list %boot-logo-patch
@@ -448,8 +448,8 @@ It has been modified to remove all non-free binary blobs.")
(make-linux-libre-headers %linux-libre-version
%linux-libre-hash))
-(define %linux-libre-4.19-version "4.19.48")
-(define %linux-libre-4.19-hash "04jwwzc9wbhx33i4bhm3vbs52vxlb8kjdmfjpfild94xbk8m2wy4")
+(define %linux-libre-4.19-version "4.19.49")
+(define %linux-libre-4.19-hash "0dxmm8190h0g5indj3sqfipkji10y3icr8xnf7bbz7086nkkrcvz")
(define %linux-libre-4.19-patches
(list %boot-logo-patch
@@ -466,22 +466,8 @@ It has been modified to remove all non-free binary blobs.")
(make-linux-libre-headers %linux-libre-4.19-version
%linux-libre-4.19-hash))
-(define %linux-libre-4.15-version "4.15.18")
-(define %linux-libre-4.15-hash "0f0s4drx888ydlwjcm9qcxqian4850yiv2vamyw9bbjf83frwxyw")
-
-(define-public linux-libre-4.15
- (make-linux-libre %linux-libre-4.15-version
- %linux-libre-4.15-hash
- '("x86_64-linux" "i686-linux" "armhf-linux")
- #:configuration-file kernel-config))
-
-(define-public linux-libre-headers-4.15
- (make-linux-libre-headers %linux-libre-4.15-version
- %linux-libre-4.15-hash))
-
-
-(define %linux-libre-4.14-version "4.14.123")
-(define %linux-libre-4.14-hash "185kf576rwhsaq7jqrnmg8r5fh2nh4k8lifxaxwi3amshnwbj2qg")
+(define %linux-libre-4.14-version "4.14.124")
+(define %linux-libre-4.14-hash "0z9iaz1rcm9472rjvcihmq65ygyks07j6kbiqm989r9rb4dw6ghg")
(define-public linux-libre-4.14
(make-linux-libre %linux-libre-4.14-version
@@ -4405,15 +4391,16 @@ developers.")
(define-public radeontop
(package
(name "radeontop")
- (version "1.1")
- (home-page "https://github.com/clbr/radeontop/")
- (source (origin
- (method url-fetch)
- (uri (string-append home-page "archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "1fv06j5c99imvzkac3j40lgjhr5b2i77fnyffhlvj92bli1fm1c6"))))
+ (version "1.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/clbr/radeontop.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1b1m30r2nfwqkajqw6m01xmfhlq83z1qylyijxg7962mp9x2k0gw"))))
(build-system gnu-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@@ -4437,6 +4424,7 @@ developers.")
("libpciaccess" ,libpciaccess)
("libxcb" ,libxcb)
("ncurses" ,ncurses)))
+ (home-page "https://github.com/clbr/radeontop/")
(synopsis "Usage monitor for AMD Radeon graphics")
(description "RadeonTop monitors resource consumption on supported AMD
Radeon Graphics Processing Units (GPUs), either in real time as bar graphs on
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 35a2c3048d..7f9dc8e13f 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -581,7 +581,7 @@ and corrections. It is based on a Bayesian filter.")
(define-public offlineimap
(package
(name "offlineimap")
- (version "7.2.3")
+ (version "7.2.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -590,7 +590,7 @@ and corrections. It is based on a Bayesian filter.")
(file-name (git-file-name name version))
(sha256
(base32
- "18sdnhjldn8zs03bgqy1qa3ikmlfvyxcvwp3nbnv1a74biccqbpa"))))
+ "0h5q5nk2p2vx86w6rrbs7v70h81dpqqr68x6l3klzl3m0yj9agb1"))))
(build-system python-build-system)
(native-inputs
`(("asciidoc" ,asciidoc)))
diff --git a/gnu/packages/patches/allegro-mesa-18.2.5-and-later.patch b/gnu/packages/patches/allegro-mesa-18.2.5-and-later.patch
new file mode 100644
index 0000000000..fa273a5dfa
--- /dev/null
+++ b/gnu/packages/patches/allegro-mesa-18.2.5-and-later.patch
@@ -0,0 +1,41 @@
+Fixes compilation with Mesa >= 18.2.5.
+
+Taken from upstream:
+
+https://github.com/liballeg/allegro5/commit/a40d30e21802ecf5c9382cf34af9b01bd3781e47
+
+diff --git a/include/allegro5/allegro_opengl.h b/include/allegro5/allegro_opengl.h
+index 0f86a6768..652dd024e 100644
+--- a/include/allegro5/allegro_opengl.h
++++ b/include/allegro5/allegro_opengl.h
+@@ -103,10 +103,14 @@
+
+ /* HACK: Prevent both Mesa and SGI's broken headers from screwing us */
+ #define __glext_h_
++#define __gl_glext_h_
+ #define __glxext_h_
++#define __glx_glxext_h_
+ #include <GL/gl.h>
+ #undef __glext_h_
++#undef __gl_glext_h_
+ #undef __glxext_h_
++#undef __glx_glxext_h_
+
+ #endif /* ALLEGRO_MACOSX */
+
+diff --git a/include/allegro5/opengl/GLext/glx_ext_defs.h b/include/allegro5/opengl/GLext/glx_ext_defs.h
+index 49c502091..fba8aea5d 100644
+--- a/include/allegro5/opengl/GLext/glx_ext_defs.h
++++ b/include/allegro5/opengl/GLext/glx_ext_defs.h
+@@ -1,7 +1,9 @@
+ /* HACK: Prevent both Mesa and SGI's broken headers from screwing us */
+ #define __glxext_h_
++#define __glx_glxext_h_
+ #include <GL/glx.h>
+ #undef __glxext_h_
++#undef __glx_glxext_h_
+
+ #ifndef GLX_VERSION_1_3
+ #define _ALLEGRO_GLX_VERSION_1_3
+--
+2.20.0
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index e845fc0bb0..156a329627 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1404,13 +1404,13 @@ data derived from /etc/mime.types in UNIX-type systems.")
(define-public r-markdown
(package
(name "r-markdown")
- (version "0.9")
+ (version "1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "markdown" version))
(sha256
(base32
- "08xzs4bcf12jxp0276m6xqvq8kcgg5qp6fxrvsz6r9x73jjccs1h"))))
+ "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p"))))
(build-system r-build-system)
;; Skip check phase because the tests require the r-knitr package to be
;; installed. This prevents installation failures. Knitr normally
@@ -1670,14 +1670,14 @@ like tidy evaluation.")
(define-public r-tibble
(package
(name "r-tibble")
- (version "2.1.2")
+ (version "2.1.3")
(source
(origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
(base32
- "1sb5j6k8hp7yf7grjjhn45hhc163fcndiw9zw976zc74f1856kpj"))))
+ "06jfayiip8j8ibdhw3fvxn4n8aqbqhwanrszpzlsf92xdfgfm34s"))))
(build-system r-build-system)
(propagated-inputs
`(("r-cli" ,r-cli)
@@ -1731,14 +1731,14 @@ database.")
(define-public r-dbplyr
(package
(name "r-dbplyr")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "dbplyr" version))
(sha256
(base32
- "0f4gfkzl07gfwihyc747kdnzxahaw2g28wli4jmikrvczldvjqjx"))))
+ "15fs66qq2p20gi3y2jlcsw27ach8rwkkkgr1mz2qbiyddbsjks6g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@@ -2882,13 +2882,13 @@ ldap, and also supports cookies, redirects, authentication, etc.")
(define-public r-xml
(package
(name "r-xml")
- (version "3.98-1.19")
+ (version "3.98-1.20")
(source (origin
(method url-fetch)
(uri (cran-uri "XML" version))
(sha256
(base32
- "1axyfa56q45x7z4zd56aasdn9hz9niv2vv5qm1zp9i94vyic9cc1"))))
+ "0n28m8iz1wfgixr7fjswl238c5w9kggsrw0c8hdzp859dqvqdbs6"))))
(properties
`((upstream-name . "XML")))
(build-system r-build-system)
@@ -3365,14 +3365,14 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.")
(define-public r-e1071
(package
(name "r-e1071")
- (version "1.7-1")
+ (version "1.7-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "e1071" version))
(sha256
(base32
- "1zlxz3da216q6v6r4ff60il121xwz7g7m639vzdwglhw3jjh8psw"))))
+ "0lipj692rjjw8rrhqh2k9i5dh8y2sjrw9q53rwm32irhx2f2j73j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)))
@@ -4772,14 +4772,14 @@ and resampling-based inference.")
(define-public r-prabclus
(package
(name "r-prabclus")
- (version "2.2-7.1")
+ (version "2.3-1")
(source
(origin
(method url-fetch)
(uri (cran-uri "prabclus" version))
(sha256
(base32
- "0x998nidd7abq5nqynyr8q79z056qbli23mvad6f09fjn2xz6nrc"))))
+ "1h5k13w8mmmdy74l145zh64f339wy78z1nlg8xr3zg23gmv98cpg"))))
(build-system r-build-system)
(propagated-inputs
`(("r-mass" ,r-mass)
@@ -4968,14 +4968,14 @@ of the points.")
(define-public r-fpc
(package
(name "r-fpc")
- (version "2.2-1")
+ (version "2.2-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "fpc" version))
(sha256
(base32
- "183awn9fbigsy3rwmg5l39zpfg2zpbb94hkx7k99v2dir8dpdy85"))))
+ "1lzqxi2jzc753j4356b949isx2nccd32mw2ch665q78nxccp145n"))))
(build-system r-build-system)
(propagated-inputs
`(("r-class" ,r-class)
@@ -5139,14 +5139,14 @@ using modular prediction and response module classes.")
(define-public r-quantreg
(package
(name "r-quantreg")
- (version "5.38")
+ (version "5.40")
(source
(origin
(method url-fetch)
(uri (cran-uri "quantreg" version))
(sha256
(base32
- "1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"))))
+ "1srni6lkgvy44ljxndz2j9ca702z2wy81f6z6mbbi6h06ni11qw6"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
@@ -5377,14 +5377,14 @@ are computed via non-Monte Carlo methods.")
(define-public r-numderiv
(package
(name "r-numderiv")
- (version "2016.8-1")
+ (version "2016.8-1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "numDeriv" version))
(sha256
(base32
- "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
+ "0idk02pqkziik932bd8k72d1q775g1is3m4bc861pcxfz6gx3i6q"))))
(properties `((upstream-name . "numDeriv")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/numDeriv")
diff --git a/gnu/packages/tbb.scm b/gnu/packages/tbb.scm
index b8f324274a..5e427ffe63 100644
--- a/gnu/packages/tbb.scm
+++ b/gnu/packages/tbb.scm
@@ -28,7 +28,7 @@
(define-public tbb
(package
(name "tbb")
- (version "2019_U6")
+ (version "2019_U8")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -37,7 +37,7 @@
(file-name (git-file-name name version))
(sha256
(base32
- "1zbf06l659vq6s5wp3ln96ycwcd42caffan5vilqvqyxqvjljyic"))
+ "0z0kh1a5g28gckcxlv3x7qqskh5fsl8knf2ypbbvk7z9ln9k3wfq"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index 0ef9b0079d..f742e86a6b 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -924,7 +924,7 @@ tmux.")
(define-public kitty
(package
(name "kitty")
- (version "0.14.1")
+ (version "0.14.2")
(home-page "https://sw.kovidgoyal.net/kitty/")
(source
(origin
@@ -935,7 +935,7 @@ tmux.")
(file-name (git-file-name name version))
(sha256
(base32
- "0nm8l8ki0csdapf5mj3vg605ki5hjsx7h7i3m01x1a4vjzjmk8bv"))
+ "15iv3k7iryf10n8n67d37x24pzcarq97a3dr42lbld00k1lx19az"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index eb8ac81930..63916d1cc3 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -310,7 +310,7 @@ integrate Windows applications into your desktop.")
(define-public wine-staging-patchset-data
(package
(name "wine-staging-patchset-data")
- (version "4.9")
+ (version "4.10")
(source
(origin
(method git-fetch)
@@ -320,7 +320,7 @@ integrate Windows applications into your desktop.")
(file-name (git-file-name name version))
(sha256
(base32
- "17v66rsxvm3grglidxxzllw4msfrgwg35hmzanvrf8x8jfzjlvv2"))))
+ "0kl5718c4xk8d1va1jb5jaa2n0vw3l0hi6bpc7siaww1fp64hy98"))))
(build-system trivial-build-system)
(native-inputs
`(("bash" ,bash)
@@ -366,7 +366,7 @@ integrate Windows applications into your desktop.")
(file-name (string-append name "-" version ".tar.xz"))
(sha256
(base32
- "16vrzhhk0x862mfhninx5515s76j2kbjgmz7gzdigjzkzwi8x14i"))))
+ "041d3km85iqbshspy9av1fxjwq18xldrb18j04xl2fmpv1hq3pas"))))
(inputs `(("autoconf" ,autoconf) ; for autoreconf
("faudio" ,faudio)
("ffmpeg" ,ffmpeg)