From e72077c5356e2db21002b351a7a79901232a2d3b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sat, 17 Mar 2018 04:02:25 -0400 Subject: [PATCH 001/110] download: Remove TU Wien mirror. * guix/download.scm (%mirrors): Remove gd.tuwien.ac.at, which no longer seems to exist. --- guix/download.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/guix/download.scm b/guix/download.scm index 55da2c1d37..5044534bf5 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -66,7 +66,6 @@ "ftp://gcc.gnu.org/pub/gcc/" ,@(map (cut string-append <> "/gcc") gnu-mirrors)) (gnupg - "http://gd.tuwien.ac.at/privacy/gnupg/" "http://artfiles.org/gnupg.org" "http://www.crysys.hu/" "https://gnupg.org/ftp/gcrypt/" @@ -143,7 +142,6 @@ "http://apache.belnet.be/" "http://mirrors.ircam.fr/pub/apache/" "http://apache-mirror.rbc.ru/pub/apache/" - "ftp://gd.tuwien.ac.at/pub/infosys/servers/http/apache/dist/" ;; As a last resort, try the archive. "http://archive.apache.org/dist/") @@ -163,7 +161,6 @@ "ftp://ftp.piotrkosoft.net/pub/mirrors/ftp.x.org/" "ftp://ftp.portal-to-web.de/pub/mirrors/x.org/" "ftp://ftp.solnet.ch/mirror/x.org/" - "ftp://gd.tuwien.ac.at/X11/" "ftp://mi.mirror.garr.it/mirrors/x.org/" "ftp://mirror.cict.fr/x.org/" "ftp://mirror.switch.ch/mirror/X11/" From 4fd09720eed9e0ed314e9a251592d1e3ba2bfd95 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Sat, 17 Mar 2018 13:34:38 +0100 Subject: [PATCH 002/110] gnu: wine-staging-patchset-data: Update to 3.4. * gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.4. --- gnu/packages/wine.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 0327deaf24..07a1244f2e 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -221,7 +221,7 @@ integrate Windows applications into your desktop.") (define-public wine-staging-patchset-data (package (name "wine-staging-patchset-data") - (version "3.3") + (version "3.4") (source (origin (method url-fetch) @@ -230,7 +230,7 @@ integrate Windows applications into your desktop.") (file-name (string-append name "-" version ".zip")) (sha256 (base32 - "16l28vrhqn27kipqwms622jz1prfky8qkjb8pj747k3qjnm2k1g9")))) + "00yzh9bqs2rjgvk78xv3gfkbv4f2bkch9vb1ii4xh883f7wvkz93")))) (build-system trivial-build-system) (native-inputs `(("bash" ,bash) From 732a148995ada989a3e96b460e2a159acf43b373 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Sat, 17 Mar 2018 15:01:35 +0100 Subject: [PATCH 003/110] gnu: wine-staging: Update to 3.4. * gnu/packages/wine.scm (wine-staging): Update to 3.4. --- gnu/packages/wine.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 07a1244f2e..37d36cf922 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -270,12 +270,13 @@ integrate Windows applications into your desktop.") (source (origin (method url-fetch) (uri (string-append - "https://dl.winehq.org/wine/source/3.x/wine-" version - ".tar.xz")) + "https://dl.winehq.org/wine/source/" + (version-major version) ".x" + "/wine-" version ".tar.xz")) (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0cx31jsll7mxd9r7v0vpahajqwb6da6cpwybv06l5ydkgfrbv505")))) + "14wf7536rkmhav9ibbvhqqkfqmbk1dckhd2679i5scizr5x290x4")))) (inputs `(("autoconf" ,autoconf) ; for autoreconf ("gtk+", gtk+) ("libva", libva) From 3bd840e406733694dd240496e1132b8676346d4f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 04:43:08 +0100 Subject: [PATCH 004/110] =?UTF-8?q?gnu:=20Fix=20more=20=E2=80=98filesystem?= =?UTF-8?q?=E2=80=99=20spellings.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python.scm (python-pyinotify)[description]: Spell ‘file system’ as ‘file system’. * gnu/packages/syncthing.scm (go-github-com-zillode-notify)[synopsis]: Likewise. (go-github-com-prometheus-procfs)[description]: Likewise. Minorly tweak grammar. --- gnu/packages/python.scm | 2 +- gnu/packages/syncthing.scm | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 135ea29706..8107c0acfa 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12988,7 +12988,7 @@ interpreter. bpython's main features are (synopsis "Python library for monitoring inotify events") (description "@code{pyinotify} provides a Python interface for monitoring -filesystem events on Linux.") +file system events on Linux.") (license license:expat))) (define-public python2-pyinotify diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 6c3792b92f..04f258481e 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1692,7 +1692,7 @@ using sh's word-splitting rules.") '(#:import-path "github.com/zillode/notify")) (propagated-inputs `(("go-golang-org-x-sys-unix" ,go-golang-org-x-sys-unix))) - (synopsis "Filesystem event notification library") + (synopsis "File system event notification library") (description "This package provides @code{notify}, a file system event notification library in Go.") (home-page "https://github.com/zillode/notify") @@ -1871,8 +1871,8 @@ Prometheus metrics.") (arguments '(#:import-path "github.com/prometheus/procfs")) (synopsis "Go library for reading @file{/proc}") - (description "This Go package @code{procfs} provides functions to retrieve -system, kernel and process metrics from the pseudo-filesystem @file{/proc}.") + (description "The @code{procfs} Go package provides functions to retrieve +system, kernel, and process metrics from the @file{/proc} pseudo file system.") (home-page "https://github.com/prometheus/procfs") (license asl2.0)))) From 111c25fd13e02eed7dd038834730862b7dbfc8a0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 04:45:55 +0100 Subject: [PATCH 005/110] gnu: perl-date-manip: Update to 6.70. * gnu/packages/perl.scm (perl-date-manip): Update to 6.70. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index cf9f21dbc9..e6a656c7b9 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -2043,7 +2043,7 @@ Date::Calc.") (define-public perl-date-manip (package (name "perl-date-manip") - (version "6.50") + (version "6.70") (source (origin (method url-fetch) @@ -2051,7 +2051,7 @@ Date::Calc.") "Date-Manip-" version ".tar.gz")) (sha256 (base32 - "0zd0wbf91i49753rnf7m1lw197hdl5r97mxy0n43zdmcmhvkb3qq")))) + "0r4k4ypb09xwhvq6das0vpx2c0xbhhhx83knq6jfpf8m55h8qi9r")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (arguments From 93e8731dcb60538183ecc6780ce68165deadfb8d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 20:12:54 +0100 Subject: [PATCH 006/110] gnu: perl-sql-abstract: Update to 1.85. * gnu/packages/databases.scm (perl-sql-abstract): Update to 1.85. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index ab8729bde0..58da1f7a90 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1359,7 +1359,7 @@ module, and nothing else.") (define-public perl-sql-abstract (package (name "perl-sql-abstract") - (version "1.84") + (version "1.85") (source (origin (method url-fetch) @@ -1367,7 +1367,7 @@ module, and nothing else.") "SQL-Abstract-" version ".tar.gz")) (sha256 (base32 - "0xayvgv6nic61jm3nhg41rzwgm8h83wfyazvpaks0z7asjillpv5")))) + "1aycggrvppy2zgkwwn85jkdz93n5gsx4dambrjk67k5067hayi4z")))) (build-system perl-build-system) (native-inputs `(("perl-module-install" ,perl-module-install) From d062957a8797d1bd6cc44bdc94259051f42afaab Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 20:29:14 +0100 Subject: [PATCH 007/110] gnu: Use HTTPS for r-project.org home pages. * gnu/packages/cran.scm (r-performanceanalytics, r-qap, r-gclus, r-leaps) (r-splus2r, r-ifultools, r-sapa, r-quantmod, r-tseries, r-wmtsa, r-fractal) (r-urca, r-trend, r-expm, r-complexplus, r-powerplus, r-signal, r-abind) (r-prroc)[home-page]: Use HTTPS. * gnu/packages/emacs.scm (emacs-ess)[home-page]: Likewise. * gnu/packages/graph.scm (r-diffusionmap)[home-page]: Likewise. * gnu/packages/statistics.scm (r-minimal, r-quantreg)[home-page]: Likewise. --- gnu/packages/cran.scm | 38 ++++++++++++++++++------------------- gnu/packages/emacs.scm | 2 +- gnu/packages/graph.scm | 2 +- gnu/packages/statistics.scm | 4 ++-- 4 files changed, 23 insertions(+), 23 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9b045c122f..717fa7fdfa 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1679,7 +1679,7 @@ simplifying cross-class interoperability.") `(("r-quadprog" ,r-quadprog) ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) - (home-page "http://r-forge.r-project.org/projects/returnanalytics/") + (home-page "https://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and @@ -1996,7 +1996,7 @@ traveling salesman problem).") "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/qap/") + (home-page "https://cran.r-project.org/web/packages/qap/") (synopsis "Heuristics for the quadratic assignment problem (QAP)") (description "This package implements heuristics for the @dfn{quadratic assignment problem} (QAP). Currently only a simulated annealing heuristic is @@ -2016,7 +2016,7 @@ available.") "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster))) - (home-page "http://cran.r-project.org/web/packages/gclus/") + (home-page "https://cran.r-project.org/web/packages/gclus/") (synopsis "Clustering graphics") (description "This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices @@ -2355,7 +2355,7 @@ rules with R.") "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/leaps/") + (home-page "https://cran.r-project.org/web/packages/leaps/") (synopsis "Regression subset selection") (description "This package provides tools for regression subset selection, including @@ -2376,7 +2376,7 @@ exhaustive search.") (properties `((upstream-name . "splus2R"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/splus2R/") + (home-page "https://cran.r-project.org/web/packages/splus2R/") (synopsis "Supplemental S-PLUS functionality in R") (description "Currently there are many functions in S-PLUS that are missing in R. To @@ -2399,7 +2399,7 @@ provides some missing S-PLUS functionality in R.") (propagated-inputs `(("r-mass" ,r-mass) ("r-splus2r" ,r-splus2r))) - (home-page "http://cran.r-project.org/web/packages/ifultools/") + (home-page "https://cran.r-project.org/web/packages/ifultools/") (synopsis "Insightful research tools") (description "This package provides C code used by the wmtsa, fractal, and sapa R packages.") @@ -2420,7 +2420,7 @@ sapa R packages.") (propagated-inputs `(("r-ifultools" ,r-ifultools) ("r-splus2r" ,r-splus2r))) - (home-page "http://cran.r-project.org/web/packages/sapa/") + (home-page "https://cran.r-project.org/web/packages/sapa/") (synopsis "Spectral analysis for physical applications") (description "This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, @@ -2444,7 +2444,7 @@ Cambridge University Press, 1993.") ("r-ttr" ,r-ttr) ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) - (home-page "http://cran.r-project.org/web/packages/quantmod/") + (home-page "https://cran.r-project.org/web/packages/quantmod/") (synopsis "Quantitative financial modelling framework") (description "This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative @@ -2469,7 +2469,7 @@ financial trading strategies.") ("r-zoo" ,r-zoo))) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/tseries/") + (home-page "https://cran.r-project.org/web/packages/tseries/") (synopsis "Time series analysis and computational finance") (description "This package provides functions relating to time series analysis and @@ -2492,7 +2492,7 @@ computational finance.") `(("r-ifultools" ,r-ifultools) ("r-mass" ,r-mass) ("r-splus2r" ,r-splus2r))) - (home-page "http://cran.r-project.org/web/packages/wmtsa/") + (home-page "https://cran.r-project.org/web/packages/wmtsa/") (synopsis "Wavelet methods for time series analysis") (description "This package provides software to accompany the book \"Wavelet Methods @@ -2568,7 +2568,7 @@ multivariate distributions.") ("r-scatterplot3d" ,r-scatterplot3d) ("r-splus2r" ,r-splus2r) ("r-wmtsa" ,r-wmtsa))) - (home-page "http://cran.r-project.org/web/packages/fractal/") + (home-page "https://cran.r-project.org/web/packages/fractal/") (synopsis "Fractal time series modeling and analysis") (description "This package provides tools for stochastic fractal and deterministic @@ -2589,7 +2589,7 @@ chaotic time series analysis.") (build-system r-build-system) (propagated-inputs `(("r-nlme" ,r-nlme))) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/urca/") + (home-page "https://cran.r-project.org/web/packages/urca/") (synopsis "Unit root and cointegration tests for time series data") (description "This package provides unit root and cointegration tests encountered in @@ -2637,7 +2637,7 @@ interface.") `(("r-extradistr" ,r-extradistr))) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/trend/") + (home-page "https://cran.r-project.org/web/packages/trend/") (synopsis "Non-parametric trend tests and change-point detection") (description "The analysis of environmental data often requires the detection of @@ -2666,7 +2666,7 @@ sample Robust Rank-Order Distributional Test.") (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://r-forge.r-project.org/projects/expm/") + (home-page "https://r-forge.r-project.org/projects/expm/") (synopsis "Tools for matrix exponentials and related quantities") (description "This package provides tools for the computation of the matrix @@ -2688,7 +2688,7 @@ exponential, logarithm, square root, and related quantities.") (propagated-inputs `(("r-expm" ,r-expm) ("r-matrix" ,r-matrix))) - (home-page "http://cran.r-project.org/web/packages/complexplus/") + (home-page "https://cran.r-project.org/web/packages/complexplus/") (synopsis "Functions of complex or real variables") (description "This package extends several functions to the complex domain, including @@ -2759,7 +2759,7 @@ ordered factor data types.") ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-phontools" ,r-phontools))) - (home-page "http://cran.r-project.org/web/packages/powerplus/") + (home-page "https://cran.r-project.org/web/packages/powerplus/") (synopsis "Exponentiation operations") (description "This package provides tools for the computation of matrix and scalar @@ -2966,7 +2966,7 @@ and within plot factors interact.") (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass))) (native-inputs `(("gfortran" ,gfortran))) - (home-page "http://cran.r-project.org/web/packages/signal/") + (home-page "https://cran.r-project.org/web/packages/signal/") (synopsis "Signal processing") (description "This package provides a set of signal processing functions originally @@ -3075,7 +3075,7 @@ R itself can handle.") (base32 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis")))) (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/abind/") + (home-page "https://cran.r-project.org/web/packages/abind/") (synopsis "Combine multidimensional arrays") (description "This package provides tools to combine multidimensional arrays into a @@ -3098,7 +3098,7 @@ extracting and replacing data in arrays.") "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc")))) (properties `((upstream-name . "PRROC"))) (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/PRROC/") + (home-page "https://cran.r-project.org/web/packages/PRROC/") (synopsis "Precision-Recall and ROC curves for weighted and unweighted data") (description "This package computes the areas under the @dfn{precision-recall} (PR) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index a6c674dfb2..da366441bd 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -3773,7 +3773,7 @@ programming language.") texlive-latex-seminar texlive-latex-hyperref texlive-tex-texinfo))))) - (home-page "http://ess.r-project.org/") + (home-page "https://ess.r-project.org/") (synopsis "Emacs mode for statistical analysis programs") (description "Emacs Speaks Statistics (ESS) is an add-on package for GNU Emacs. It is designed to support editing of scripts and interaction with diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 6a5e0e753f..38924e42b2 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -142,7 +142,7 @@ more.") `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-scatterplot3d" ,r-scatterplot3d))) - (home-page "http://www.r-project.org") + (home-page "https://www.r-project.org") (synopsis "Diffusion map") (description "This package implements the diffusion map method of data parametrization, including creation and visualization of diffusion maps, diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 78afb77a8b..8afccb0737 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -271,7 +271,7 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\ (list (search-path-specification (variable "R_LIBS_SITE") (files (list "site-library/"))))) - (home-page "http://www.r-project.org/") + (home-page "https://www.r-project.org/") (synopsis "Environment for statistical computing and graphics") (description "R is a language and environment for statistical computing and graphics. @@ -5018,7 +5018,7 @@ using modular prediction and response module classes.") `(("r-matrix" ,r-matrix) ("r-matrixmodels" ,r-matrixmodels) ("r-sparsem" ,r-sparsem))) - (home-page "http://www.r-project.org") + (home-page "https://www.r-project.org") (synopsis "Quantile regression") (description "This package provides an estimation and inference methods for models From 132a7e68e4623f0a9d3bde4c40de8ffae5f02f16 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 00:41:00 +0100 Subject: [PATCH 008/110] gnu: python-entrypoints: Update to 0.2.3. * gnu/packages/python.scm (python-entrypoints): Update to 0.2.3. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8107c0acfa..fd4bcd57b6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6485,7 +6485,7 @@ Jupyter Notebook format and Python APIs for working with notebooks.") (define-public python-entrypoints (package (name "python-entrypoints") - (version "0.2.2") + (version "0.2.3") (source (origin (method url-fetch) @@ -6494,7 +6494,7 @@ Jupyter Notebook format and Python APIs for working with notebooks.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0azqlkh3j0za080lsf5crnhaxx3c93k9dpv5ihkhf5cppgw5sjz5")))) + "1pdvgfr5bxyvnfvxbsd3zi0dh3il71pc4k6rinx6zpps91b84a56")))) (build-system python-build-system) ;; The package does not come with a setup.py file, so we have to generate ;; one ourselves. From e4da20ecd82dba88287a60147987e19529f6567b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 01:02:01 +0100 Subject: [PATCH 009/110] gnu: python-bcrypt: Update to 3.1.4. * gnu/packages/password-utils.scm (python-bcrypt): Update to 3.1.4. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 46b6e795ab..8810392530 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -458,14 +458,14 @@ winner of the 2015 Password Hashing Competition.") (define-public python-bcrypt (package (name "python-bcrypt") - (version "3.1.0") + (version "3.1.4") (source (origin (method url-fetch) (uri (pypi-uri "bcrypt" version)) (sha256 (base32 - "1giy0dvd8gvq6flxh44np1v2nqwsji5qsnrz038mgwzgp7c20j75")))) + "13cyrnqwkhc70rs6dg65z4yrrr3dc42fhk11804fqmci9hvimvb7")))) (build-system python-build-system) (native-inputs `(("python-pycparser" ,python-pycparser) From 9b62a6c5eb5409cd7f3c19fad10468e631353836 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 01:10:11 +0100 Subject: [PATCH 010/110] gnu: python-oslotest: Update to 3.3.0. * gnu/packages/openstack.scm (python-oslotest): Update to 3.3.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index f0147bab59..c1380a1af5 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -646,14 +646,14 @@ from the OpenStack project.") (define-public python-oslotest (package (name "python-oslotest") - (version "3.2.0") + (version "3.3.0") (source (origin (method url-fetch) (uri (pypi-uri "oslotest" version)) (sha256 (base32 - "1xay6wjxzqm4bg87fahqas84dhvhgf1gghzldkcczsfx897mqdkh")))) + "006i73w8kbc9s0av2v5mbni6mnkb91c2nq17wa0lz7bwk5zss992")))) (build-system python-build-system) (propagated-inputs `(("python-fixtures" ,python-fixtures) From c9ec726cd8061c8c64d7ea0fcec5bc1f4911cbf1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 01:19:42 +0100 Subject: [PATCH 011/110] gnu: python-protobuf: Update to 3.5.2. * gnu/packages/protobuf.scm (python-protobuf): Update to 3.5.2. --- gnu/packages/protobuf.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index 17d3bacf02..877c9c9c84 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016 Daniel Pimentel ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2017 Ricardo Wurmus -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -149,14 +149,14 @@ code.") (define-public python-protobuf (package (name "python-protobuf") - (version "3.4.0") + (version "3.5.2") (source (origin (method url-fetch) (uri (pypi-uri "protobuf" version)) (sha256 (base32 - "0x33xz85cy5ilg1n2rn92l4qwlcw25vzysx2ldv7k625yjg600pg")))) + "1q4b1m55w4gvcbzklbk8iylaii98n4in41k27d94w8ypbwlrm1q9")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) From f212a85e41a62f01f737c71f96cedcaa789206bd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 02:40:05 +0100 Subject: [PATCH 012/110] gnu: python-jsonschema: Update to 2.6.0. * gnu/packages/python.scm (python-jsonschema): Update to 2.6.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fd4bcd57b6..673d5d3d74 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1857,7 +1857,7 @@ version numbers.") (define-public python-jsonschema (package (name "python-jsonschema") - (version "2.5.1") + (version "2.6.0") (source (origin (method url-fetch) (uri @@ -1866,7 +1866,7 @@ version numbers.") version ".tar.gz")) (sha256 (base32 - "0hddbqjm4jq63y8jf44nswina1crjs16l9snb6m3vvgyg31klrrn")))) + "00kf3zmpp9ya4sydffpifn0j0mzm342a2vzh82p6r0vh10cg7xbg")))) (build-system python-build-system) (arguments '(#:phases From e5fa7df9639205b4fffaec8ebb63ec9773465cd0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 04:39:52 +0100 Subject: [PATCH 013/110] gnu: python-decorator: Update to 4.2.1. * gnu/packages/python.scm (python-decorator): Update to 4.2.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 673d5d3d74..4eb9c9af3e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4056,13 +4056,13 @@ PNG, PostScript, PDF, and SVG file output.") (define-public python-decorator (package (name "python-decorator") - (version "4.1.2") + (version "4.2.1") (source (origin (method url-fetch) (uri (pypi-uri "decorator" version)) (sha256 - (base32 "1d8npb11kxyi36mrvjdpcjij76l5zfyrz2f820brf0l0rcw4vdkw")))) + (base32 "03iaf116rm3w8b4agb8hzf6z9331mrvi4khfxq35zkx17sgxsikx")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; no test target (home-page "https://pypi.python.org/pypi/decorator/") From 34f53e4fbf87d19630dca38216ce3b2e6f5fb5e2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 04:42:42 +0100 Subject: [PATCH 014/110] gnu: python-phonenumbers: Update to 8.9.1. * gnu/packages/python.scm (python-phonenumbers): Update to 8.9.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4eb9c9af3e..fbea6b9fe0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12633,14 +12633,14 @@ and works only with Python 2 and NumPy < 1.9.") (define-public python-phonenumbers (package (name "python-phonenumbers") - (version "8.8.9") + (version "8.9.1") (source (origin (method url-fetch) (uri (pypi-uri "phonenumbers" version)) (sha256 (base32 - "1lhhxmx3hk0b5891nc0p82dl5bq2w9cqbawmh8j5zy587af2j6fq")))) + "03fmrgb4r8x3ykmddjs9i3zhs703in8smikj3a6447blqpimwyh1")))) (build-system python-build-system) (home-page "https://github.com/daviddrysdale/python-phonenumbers") From 96de54114c4486b6a7348335741df281253e60db Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 07:50:09 +0100 Subject: [PATCH 015/110] gnu: python-jupyter-core: Update to 4.4.0. * gnu/packages/python.scm (python-jupyter-core): Update to 4.4.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fbea6b9fe0..28f1c64989 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4428,14 +4428,14 @@ without using the configuration machinery.") (define-public python-jupyter-core (package (name "python-jupyter-core") - (version "4.2.1") + (version "4.4.0") (source (origin (method url-fetch) (uri (string-append (pypi-uri "jupyter_core" version))) (sha256 (base32 - "1cy7inv218dgh4m1fbzbsiqpz733ylgjrj62jxqpfzs3r2cm7ic9")))) + "1dy083rarba8prn9f9srxq3c7n7vyql02ycrqq306c40lr57aw5s")))) (build-system python-build-system) ;; FIXME: not sure how to run the tests (arguments `(#:tests? #f)) From c7bb731af8e052dd35b98d7adcbd5363d366a498 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 07:50:57 +0100 Subject: [PATCH 016/110] gnu: python-kazoo: Update to 2.4.0. * gnu/packages/python.scm (python-kazoo): Update to 2.4.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 28f1c64989..4e2f4b7b54 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8885,14 +8885,14 @@ data in Python.") (define-public python-kazoo (package (name "python-kazoo") - (version "2.2.1") + (version "2.4.0") (source (origin (method url-fetch) (uri (pypi-uri "kazoo" version)) (sha256 (base32 - "10pb864if9qi2pq9lfb9m8f7z7ss6rml80gf1d9h64lap5crjnjj")))) + "16y213k7r8shyn2zw1k6lkzjgcrvm441pqv8scvcjixhvpbx3hm7")))) (build-system python-build-system) (arguments '(#:tests? #f)) ; XXX: needs zookeeper (propagated-inputs From c300630d556a0241ad09949f03ea8e9bcb119f74 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 07:55:00 +0100 Subject: [PATCH 017/110] gnu: python-jupyter-console: Update to 5.2.0. * gnu/packages/python.scm (python-jupyter-console): Update to 5.2.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4e2f4b7b54..adac8e9f48 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6691,14 +6691,14 @@ in the data.") (define-public python-jupyter-console (package (name "python-jupyter-console") - (version "5.0.0") + (version "5.2.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_console" version)) (sha256 (base32 - "04acmkwsi99rcg3vb54c6n492zv35s92h2ahabc0w6wj976cipvx")))) + "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal")))) (build-system python-build-system) ;; FIXME: it's not clear how to run the tests. (arguments `(#:tests? #f)) From e83539e8cc9fb323f2d0e104e967386f5a6182d0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 07:56:35 +0100 Subject: [PATCH 018/110] gnu: python-chai: Update to 1.1.2. * gnu/packages/python.scm (python-chai): Update to 1.1.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index adac8e9f48..d586eb94ba 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8992,13 +8992,13 @@ etc.") (define-public python-chai (package (name "python-chai") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (pypi-uri "chai" version)) (sha256 (base32 - "016kf3irrclpkpvcm7q0gmkfibq7jgy30a9v73pp42bq9h9a32bl")))) + "1k6n6zbgrrs83crp6mr3yqj9zlv40b8rpisyrliwsq7naml2p3gz")))) (build-system python-build-system) (home-page "https://github.com/agoragames/chai") (synopsis "Mocking framework for Python") From c8674cf5fedbc6d4f69b363e74e7326c477eb7e4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 09:03:00 +0100 Subject: [PATCH 019/110] gnu: python-ptyprocess: Update to 0.5.2. * gnu/packages/python.scm (python-ptyprocess): Update to 0.5.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d586eb94ba..f9818417a6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5614,7 +5614,7 @@ markdown_py is also provided to convert Markdown files to HTML.") (define-public python-ptyprocess (package (name "python-ptyprocess") - (version "0.5.1") + (version "0.5.2") (source (origin (method url-fetch) @@ -5623,7 +5623,7 @@ markdown_py is also provided to convert Markdown files to HTML.") version ".tar.gz")) (sha256 (base32 - "19l1xrjn4l9gjz01s3vg92gn2dd9d8mw1v86ppkzlnr9m5iwwc05")))) + "0ra31k10v3629xq0kdn8lwmfbi97anmk48r03yvh7mks0kq96hg6")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose))) From 40a1020240d21700810f8efe4e505cd72bab0b3f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 09:04:57 +0100 Subject: [PATCH 020/110] gnu: python-simplejson: Update to 3.13.2. * gnu/packages/python.scm (python-simplejson): Update to 3.13.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f9818417a6..d64c7e7e6f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1164,14 +1164,14 @@ after Andy Lester’s Perl module WWW::Mechanize.") (define-public python-simplejson (package (name "python-simplejson") - (version "3.10.0") + (version "3.13.2") (source (origin (method url-fetch) (uri (pypi-uri "simplejson" version)) (sha256 (base32 - "1qhwsykjlb85igb4cfl6v6gkprzbbg8gyqdd7zscc8w3x0ifcfwm")))) + "02jg5nixffqyicfqdl4dil82fh1z9p2as758wp0nqwalw0hcykjc")))) (build-system python-build-system) (home-page "http://simplejson.readthedocs.org/en/latest/") (synopsis From 4bd77a5dd0f55a8e121deb714a3c337786386753 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 09:33:39 +0100 Subject: [PATCH 021/110] gnu: python-nbformat: Update to 4.4.0. * gnu/packages/python.scm (python-nbformat): Update to 4.4.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d64c7e7e6f..6cdf13db11 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6433,14 +6433,14 @@ Debian-related files, such as: (define-public python-nbformat (package (name "python-nbformat") - (version "4.3.0") + (version "4.4.0") (source (origin (method url-fetch) (uri (pypi-uri "nbformat" version)) (sha256 (base32 - "12s7j4qja8b5bs1kyw5dzmrqbjxxj8wk52cyasbiqbv7fblcrssz")))) + "00nlf08h8yc4q73nphfvfhxrcnilaqanb8z0mdy6nxk0vzq4wjgp")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; no test target (propagated-inputs From f17f9984c372ff88ee8e8b6b5601f1be8dd4a2e6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 09:34:45 +0100 Subject: [PATCH 022/110] gnu: python-pkginfo: Update to 1.4.2. * gnu/packages/python.scm (python-pkginfo): Update to 1.4.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6cdf13db11..aef63f334b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12117,14 +12117,14 @@ design and layout.") (define-public python-pkginfo (package (name "python-pkginfo") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (pypi-uri "pkginfo" version)) (sha256 (base32 - "17pqjfpq3c6xzdmk8pski6jcjgjv78q00zjf2bgzb668pzm6l6mv")))) + "0x6lm17p1ks031mj6pajyp4rkq74vpqq8qwjb7ikgwmkli1day2q")))) (build-system python-build-system) (arguments ;; The tests are broken upstream. From 36a17f056c097d548e56558a99f276bca61d9825 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 16:04:49 +0100 Subject: [PATCH 023/110] gnu: texlive-latex-type1cm: Fix description typo. * gnu/packages/tex.scm (texlive-latex-type1cm)[description]: Fix typo. --- gnu/packages/tex.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 30033e1041..1416a00251 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3591,7 +3591,7 @@ this is particularly useful when using scalable versions of the CM fonts (Bakoma, or the versions from BSR/Y&Y, or True Type versions from Kinch, PCTeX, etc.). In fact, since modern distributions will automatically generate any bitmap font you might need, @code{type1cm} has wider application than just -those using scaleable versions of the fonts. Note that the LaTeX distribution +those using scalable versions of the fonts. Note that the LaTeX distribution now contains a package @code{fix-cm},f which performs the task of @code{type1cm}, as well as doing the same job for T1- and TS1-encoded @code{ec} fonts.") From 49c4c4de8575821b0ba08b5c980b996577bcb9ec Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 16:33:16 +0100 Subject: [PATCH 024/110] gnu: shaderc: Fix formatting. * gnu/packages/vulkan.scm (shaderc): Use conventional indentation. [native-inputs]: Move unquotes to their operands. --- gnu/packages/vulkan.scm | 142 ++++++++++++++++++++-------------------- 1 file changed, 72 insertions(+), 70 deletions(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 478de6a444..2daa857394 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -210,74 +210,76 @@ and the ICD.") (let ((commit "773ec22d49f40b7161820f29d953be4a7e40190d") (revision "1")) (package - (name "shaderc") - (version (string-append "0.0-" revision "." (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/google/shaderc") - (commit commit))) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f")))) - (build-system meson-build-system) - (arguments - `(#:tests? #f ;; Tests don't work yet. - #:phases - (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; Remove various lines and touch build-version.inc or - ;; configuring won't work. - (invoke "touch" "glslc/src/build-version.inc") - (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") "")) - (substitute* "CMakeLists.txt" - ((".*update_build_version.py..*") "")) - (substitute* "CMakeLists.txt" - ((".*add_custom_target.build-version.*") "")) - (substitute* "CMakeLists.txt" - ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*") - "")) - (substitute* "CMakeLists.txt" - ((".*Update build-version.inc.*") "")) - (substitute* "CMakeLists.txt" ((".*--check.*") "")) - (substitute* "glslc/src/main.cc" ((".*build-version.inc.*") - "\"1\"")) - (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release" - "-DSHADERC_SKIP_TESTS=ON" - "-DCMAKE_INSTALL_LIBDIR=lib" - (string-append "-DCMAKE_INSTALL_PREFIX=" - out))))) - (add-after 'unpack 'unpack-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((spirv-tools-source (assoc-ref %build-inputs - "spirv-tools-source")) - (spirv-headers-source (assoc-ref %build-inputs - "spirv-headers-source")) - (glslang-source (assoc-ref %build-inputs - "glslang-source"))) - (mkdir-p "third-party/spirv-tools") - (copy-recursively spirv-tools-source - "third_party/spirv-tools") - (mkdir-p "third-party/spirv-tools/external/spirv-headers") - (copy-recursively spirv-headers-source - (string-append "third_party/spirv-tools" - "/external/spirv-headers")) - (mkdir-p "third-party/glslang") - (copy-recursively glslang-source - "third_party/glslang") - #t)))))) - (inputs `(("python" ,python))) - (native-inputs `(("cmake" ,cmake) - ("glslang-source", (package-source glslang)) - ("pkg-config", pkg-config) - ("spirv-headers-source", (package-source spirv-headers)) - ("spirv-tools-source", (package-source spirv-tools)))) - (home-page "https://github.com/google/shaderc") - (synopsis "Tools for shader compilation") - (description "Shaderc is a collection of tools, libraries and tests for + (name "shaderc") + (version (string-append "0.0-" revision "." (string-take commit 9))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/google/shaderc") + (commit commit))) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f")))) + (build-system meson-build-system) + (arguments + `(#:tests? #f ; tests don't work yet. + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Remove various lines and touch build-version.inc or + ;; configuring won't work. + (invoke "touch" "glslc/src/build-version.inc") + (substitute* "CMakeLists.txt" (("..PYTHON_EXE..*") "")) + (substitute* "CMakeLists.txt" + ((".*update_build_version.py..*") "")) + (substitute* "CMakeLists.txt" + ((".*add_custom_target.build-version.*") "")) + (substitute* "CMakeLists.txt" + ((".*spirv-tools_SOURCE_DIR.*glslang_SOURCE_DIR.*") + "")) + (substitute* "CMakeLists.txt" + ((".*Update build-version.inc.*") "")) + (substitute* "CMakeLists.txt" ((".*--check.*") "")) + (substitute* "glslc/src/main.cc" ((".*build-version.inc.*") + "\"1\"")) + (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release" + "-DSHADERC_SKIP_TESTS=ON" + "-DCMAKE_INSTALL_LIBDIR=lib" + (string-append "-DCMAKE_INSTALL_PREFIX=" + out))))) + (add-after 'unpack 'unpack-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((spirv-tools-source (assoc-ref %build-inputs + "spirv-tools-source")) + (spirv-headers-source (assoc-ref %build-inputs + "spirv-headers-source")) + (glslang-source (assoc-ref %build-inputs + "glslang-source"))) + (mkdir-p "third-party/spirv-tools") + (copy-recursively spirv-tools-source + "third_party/spirv-tools") + (mkdir-p "third-party/spirv-tools/external/spirv-headers") + (copy-recursively spirv-headers-source + (string-append "third_party/spirv-tools" + "/external/spirv-headers")) + (mkdir-p "third-party/glslang") + (copy-recursively glslang-source + "third_party/glslang") + #t)))))) + (inputs + `(("python" ,python))) + (native-inputs + `(("cmake" ,cmake) + ("glslang-source" ,(package-source glslang)) + ("pkg-config" ,pkg-config) + ("spirv-headers-source" ,(package-source spirv-headers)) + ("spirv-tools-source" ,(package-source spirv-tools)))) + (home-page "https://github.com/google/shaderc") + (synopsis "Tools for shader compilation") + (description "Shaderc is a collection of tools, libraries, and tests for shader compilation.") - (license license:asl2.0)))) + (license license:asl2.0)))) From 8696fbbad1904e6c5edb59f334f9d9ab7ddeeba7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 16:36:10 +0100 Subject: [PATCH 025/110] gnu: shaderc: Use standard versioning scheme. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/vulkan.scm (shaderc)[version]: Use GIT-VERSION with a ‘0.0.0’ prefix. --- gnu/packages/vulkan.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 2daa857394..6ba9b94a3d 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Rutger Helling +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -211,7 +212,7 @@ and the ICD.") (revision "1")) (package (name "shaderc") - (version (string-append "0.0-" revision "." (string-take commit 9))) + (version (git-version "0.0.0-" revision commit)) (source (origin (method git-fetch) From 9bc0591bc11190ac49c8ea3cf44c4903c924f6c7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 16:44:36 +0100 Subject: [PATCH 026/110] gnu: shaderc: Use more standard keys. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/vulkan.scm (shaderc)[arguments]: Move cmake options from the raw INVOKE call to #:build-type and #:configure-flags. Adjust the ‘configure’ phase accordingly. --- gnu/packages/vulkan.scm | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 6ba9b94a3d..dc73ce3cad 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -225,11 +225,18 @@ and the ICD.") "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f")))) (build-system meson-build-system) (arguments - `(#:tests? #f ; tests don't work yet. + `(#:build-type "Release" + #:configure-flags + (list "-GNinja" + "-DSHADERC_SKIP_TESTS=ON" + "-DCMAKE_INSTALL_LIBDIR=lib" + (string-append "-DCMAKE_INSTALL_PREFIX=" + (assoc-ref %outputs "out"))) + #:tests? #f ; tests don't work yet. #:phases (modify-phases %standard-phases (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key build-type configure-flags #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) ;; Remove various lines and touch build-version.inc or ;; configuring won't work. @@ -247,11 +254,8 @@ and the ICD.") (substitute* "CMakeLists.txt" ((".*--check.*") "")) (substitute* "glslc/src/main.cc" ((".*build-version.inc.*") "\"1\"")) - (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release" - "-DSHADERC_SKIP_TESTS=ON" - "-DCMAKE_INSTALL_LIBDIR=lib" - (string-append "-DCMAKE_INSTALL_PREFIX=" - out))))) + (invoke "cmake" (cons build-type configure-flags)) + #t))) (add-after 'unpack 'unpack-sources (lambda* (#:key inputs #:allow-other-keys) (let ((spirv-tools-source (assoc-ref %build-inputs From c695fb769c94623371c5997da1dc454b0a4f58a8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 16 Mar 2018 16:50:14 +0100 Subject: [PATCH 027/110] gnu: Fix common unquote typos. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit It's easy to mistype ‘("foo" foo)’ as ‘("foo", foo)’ (which also works). Fix such typos for the proper edification of our young. * gnu/packages/android.scm: Move unquotes to their operands. * gnu/packages/bootloaders.scm: Likewise. * gnu/packages/build-tools.scm: Likewise. * gnu/packages/chemistry.scm: Likewise. * gnu/packages/compression.scm: Likewise. * gnu/packages/connman.scm: Likewise. * gnu/packages/django.scm: Likewise. * gnu/packages/emulators.scm: Likewise. * gnu/packages/engineering.scm: Likewise. * gnu/packages/file-systems.scm: Likewise. * gnu/packages/freedesktop.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gimp.scm: Likewise. * gnu/packages/gl.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/graphics.scm: Likewise. * gnu/packages/haskell.scm: Likewise. * gnu/packages/irc.scm: Likewise. * gnu/packages/julia.scm: Likewise. * gnu/packages/kde-frameworks.scm: Likewise. * gnu/packages/linux.scm: Likewise. * gnu/packages/lua.scm: Likewise. * gnu/packages/mail.scm: Likewise. * gnu/packages/make-bootstrap.scm: Likewise. * gnu/packages/messaging.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/networking.scm: Likewise. * gnu/packages/ocaml.scm: Likewise. * gnu/packages/perl.scm: Likewise. * gnu/packages/python.scm: Likewise. * gnu/packages/python-web.scm: Likewise. * gnu/packages/qt.scm: Likewise. * gnu/packages/ratpoison.scm: Likewise. * gnu/packages/sdl.scm: Likewise. * gnu/packages/sml.scm: Likewise. * gnu/packages/terminals.scm: Likewise. * gnu/packages/text-editors.scm: Likewise. * gnu/packages/video.scm: Likewise. * gnu/packages/virtualization.scm: Likewise. * gnu/packages/vulkan.scm: Likewise. * gnu/packages/wget.scm: Likewise. * gnu/packages/wine.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/xdisorg.scm: Likewise. * gnu/packages/xml.scm: Likewise. * gnu/packages/xorg.scm: Likewise. --- gnu/packages/android.scm | 2 +- gnu/packages/bootloaders.scm | 2 +- gnu/packages/build-tools.scm | 2 +- gnu/packages/chemistry.scm | 4 ++-- gnu/packages/compression.scm | 2 +- gnu/packages/connman.scm | 4 ++-- gnu/packages/django.scm | 4 ++-- gnu/packages/emulators.scm | 2 +- gnu/packages/engineering.scm | 2 +- gnu/packages/file-systems.scm | 2 +- gnu/packages/flashing-tools.scm | 2 +- gnu/packages/freedesktop.scm | 2 +- gnu/packages/games.scm | 26 ++++++++++++------------ gnu/packages/gimp.scm | 12 +++++------ gnu/packages/gl.scm | 2 +- gnu/packages/gnome.scm | 2 +- gnu/packages/graphics.scm | 14 ++++++------- gnu/packages/haskell.scm | 8 ++++---- gnu/packages/irc.scm | 2 +- gnu/packages/kde-frameworks.scm | 36 ++++++++++++++++----------------- gnu/packages/linux.scm | 24 +++++++++++----------- gnu/packages/lua.scm | 10 ++++----- gnu/packages/mail.scm | 2 +- gnu/packages/make-bootstrap.scm | 2 +- gnu/packages/messaging.scm | 12 +++++------ gnu/packages/music.scm | 6 +++--- gnu/packages/networking.scm | 20 +++++++++--------- gnu/packages/ocaml.scm | 6 +++--- gnu/packages/perl.scm | 2 +- gnu/packages/python-web.scm | 2 +- gnu/packages/python.scm | 8 ++++---- gnu/packages/qt.scm | 2 +- gnu/packages/ratpoison.scm | 2 +- gnu/packages/sdl.scm | 6 +++--- gnu/packages/sml.scm | 2 +- gnu/packages/terminals.scm | 16 +++++++-------- gnu/packages/text-editors.scm | 8 ++++---- gnu/packages/video.scm | 4 ++-- gnu/packages/virtualization.scm | 2 +- gnu/packages/vulkan.scm | 4 ++-- gnu/packages/web.scm | 8 ++++---- gnu/packages/wget.scm | 28 ++++++++++++------------- gnu/packages/wine.scm | 4 ++-- gnu/packages/wm.scm | 2 +- gnu/packages/xdisorg.scm | 6 +++--- gnu/packages/xml.scm | 4 ++-- gnu/packages/xorg.scm | 2 +- 47 files changed, 163 insertions(+), 163 deletions(-) diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm index 6baefbca96..637cda0205 100644 --- a/gnu/packages/android.scm +++ b/gnu/packages/android.scm @@ -457,7 +457,7 @@ def _FindRepo(): ;; TODO: Add git-remote-persistent-https once it is available in guix `(("git" ,git) ("gnupg" ,gnupg) - ("ssh", openssh))) + ("ssh" ,openssh))) (native-inputs `(("nose" ,python2-nose))) (home-page "https://code.google.com/p/git-repo/") diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 9ea8748a5b..582c71cc4a 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -181,7 +181,7 @@ menu to select one of the installed operating systems.") (synopsis "GRand Unified Boot loader (UEFI version)") (inputs `(("efibootmgr" ,efibootmgr) - ("mtools", mtools) + ("mtools" ,mtools) ,@(package-inputs grub))) (arguments `(;; TODO: Tests need a UEFI firmware for qemu. There is one at diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 2abb44fdb8..73eacf7df2 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -81,7 +81,7 @@ makes a few sacrifices to acquire fast full and incremental build times.") (base32 "06r8limj38mv884s5riiz6lpzw37cvhbf9jd0smzcbi7fwmv3yah")))) (build-system python-build-system) - (inputs `(("ninja", ninja))) + (inputs `(("ninja" ,ninja))) (propagated-inputs `(("python" ,python))) (home-page "https://mesonbuild.com/") (synopsis "Build system designed to be fast and user-friendly") diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index ed883072b4..f1359b2cf6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -73,8 +73,8 @@ only with Python 2 and NumPy < 1.9.") (build-system python-build-system) (inputs `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib)) - ("python-scientific", python2-scientific) - ("netcdf", netcdf) + ("python-scientific" ,python2-scientific) + ("netcdf" ,netcdf) ("gv" ,gv))) (propagated-inputs `(("python-mmtk" ,python2-mmtk))) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 05442024f6..f92239d505 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1657,7 +1657,7 @@ speed.") (source (package-source zstd)) (build-system gnu-build-system) (native-inputs - `(("googletest", googletest))) + `(("googletest" ,googletest))) (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/connman.scm b/gnu/packages/connman.scm index 25756019fd..7e87cd8968 100644 --- a/gnu/packages/connman.scm +++ b/gnu/packages/connman.scm @@ -70,7 +70,7 @@ (string-append "--with-dbusdatadir=" (assoc-ref %outputs "out") "/share")))) (native-inputs - `(("pkg-config", pkg-config) + `(("pkg-config" ,pkg-config) ("python" ,python-2))) (inputs `(("dbus" ,dbus) @@ -84,7 +84,7 @@ ;; TODO: add neard, ofono ("openconnect" ,openconnect) ("openvpn" ,openvpn) - ("ppp", ppp) + ("ppp" ,ppp) ("vpnc" ,vpnc) ("wpa-supplicant" ,wpa-supplicant))) (home-page "https://01.org/connman") diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index a901af6f14..4501b5c745 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -75,7 +75,7 @@ (zero? (system* "python" "tests/runtests.py"))))))) ;; TODO: Install extras/django_bash_completion. (native-inputs - `(("tzdata", tzdata-for-tests) + `(("tzdata" ,tzdata-for-tests) ;; bcrypt and argon2-cffi are extra requirements not yet in guix ;;("python-argon2-cffi" ,python-argon2-cffi) ; >= 16.1.0 ;;("python-bcrypt" ,python-bcrypt) ; not py-bcrypt! @@ -199,7 +199,7 @@ useful tools for testing Django applications and projects.") (native-inputs `(("python-django" ,python-django) ("python-djangorestframework" ,python-djangorestframework) - ("python-django-crispy-forms", python-django-crispy-forms) + ("python-django-crispy-forms" ,python-django-crispy-forms) ("python-mock" ,python-mock))) (home-page "https://django-filter.readthedocs.io/en/latest/") (synopsis "Reusable Django application to filter querysets dynamically") diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index 142603b082..9d8e7fa1ae 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1095,7 +1095,7 @@ emulation community. It provides highly accurate emulation.") ("sdl" ,sdl2) ("udev" ,eudev) ("vulkan-icd-loader" ,vulkan-icd-loader) - ("wayland", wayland) + ("wayland" ,wayland) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 449584f57e..076d4b6094 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -862,7 +862,7 @@ the 'showing the effect of'-style of operation.") (inputs `(("boost" ,boost))) (native-inputs - `(("python-2", python-2) + `(("python-2" ,python-2) ("python2-cheetah" ,python2-cheetah))) (home-page "http://libvolk.org/") (synopsis "Vector-Optimized Library of Kernels") diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 0e65213c72..6522662c4e 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -236,7 +236,7 @@ All of this is accomplished without a centralized metadata server.") (inputs `(("curl" ,curl) ("glib" ,glib) - ("fuse", fuse))) + ("fuse" ,fuse))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://curlftpfs.sourceforge.net/") diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index 192f84c36c..51b259a5cf 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -104,7 +104,7 @@ programmer devices.") "1g4032c81wkk37wvbg1dxcqq6mnd76y9x7f2crmzqi6z4q9jcxmj")))) (build-system gnu-build-system) (inputs - `(("libusb",libusb-0.1))) ; doesn't work with libusb-compat + `(("libusb" ,libusb-0.1))) ; doesn't work with libusb-compat (arguments '(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 366fcecea2..f673c4bf34 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -357,7 +357,7 @@ of a the system to know what users are logged in, and where.") ("glib:bin" ,glib "bin"))) (inputs `(("glib" ,glib) - ("bash-completion", bash-completion) + ("bash-completion" ,bash-completion) ("polkit" ,polkit))) (propagated-inputs `(("sqlite" ,sqlite))) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index a33da03ad5..a03e58b0ad 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -234,7 +234,7 @@ settings to tweak as well.") ("libvorbis" ,libvorbis) ("ncurses" ,ncurses) ("sdl2" ,sdl2) - ("sdl2-image", sdl2-image) + ("sdl2-image" ,sdl2-image) ("sdl2-ttf" ,sdl2-ttf) ("sdl2-mixer" ,sdl2-mixer))) (home-page "http://en.cataclysmdda.com/") @@ -2230,19 +2230,19 @@ Transport Tycoon Deluxe.") (substitute* "cmake_install.cmake" (("EXPECTED_HASH SHA1=b587d83de508d0b104d14c599b76f8565900fce0") ""))))))) - (inputs `(("curl", curl) - ("fontconfig", fontconfig) - ("freetype", freetype) - ("jansson", jansson) - ("libpng", libpng) - ("libzip", libzip) - ("mesa", mesa) - ("openssl", openssl) - ("sdl2", sdl2) - ("speexdsp", speexdsp) - ("zlib", zlib))) + (inputs `(("curl" ,curl) + ("fontconfig" ,fontconfig) + ("freetype" ,freetype) + ("jansson" ,jansson) + ("libpng" ,libpng) + ("libzip" ,libzip) + ("mesa" ,mesa) + ("openssl" ,openssl) + ("sdl2" ,sdl2) + ("speexdsp" ,speexdsp) + ("zlib" ,zlib))) (native-inputs - `(("pkg-config", pkg-config))) + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/OpenRCT2/OpenRCT2") (synopsis "Free software re-implementation of RollerCoaster Tycoon 2") (description "OpenRCT2 is a free software re-implementation of diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index c98f686d41..2483885c95 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -175,12 +175,12 @@ buffers.") ("libjpeg" ,libjpeg-8) ("atk" ,atk) ("gtk+" ,gtk+-2) - ("exif" ,libexif) ;optional, EXIF + XMP support - ("lcms" ,lcms) ;optional, color management - ("librsvg" ,librsvg) ;optional, SVG support - ("poppler", poppler) ; optional, PDF support - ("python" ,python-2) ;optional, Python support - ("python2-pygtk" ,python2-pygtk) ;optional, Python support + ("exif" ,libexif) ; optional, EXIF + XMP support + ("lcms" ,lcms) ; optional, color management + ("librsvg" ,librsvg) ; optional, SVG support + ("poppler" ,poppler) ; optional, PDF support + ("python" ,python-2) ; optional, Python support + ("python2-pygtk" ,python2-pygtk) ; optional, Python support ("gegl" ,gegl))) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm index 0e416a9efd..f46c4b4d4b 100644 --- a/gnu/packages/gl.scm +++ b/gnu/packages/gl.scm @@ -756,7 +756,7 @@ mixed vector/bitmap output.") ("libjpeg-turbo" ,libjpeg-turbo) ("mesa" ,mesa) ("openssl" ,openssl))) - (native-inputs `(("pkg-config", pkg-config))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://www.virtualgl.org") (synopsis "Redirects 3D commands from an OpenGL application onto a 3D graphics card") diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 56ee1aa885..8ce36430ee 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -273,7 +273,7 @@ features to enable users to create their discs easily and quickly.") ("gettext" ,gettext-minimal) ("itstool" ,itstool) ("intltool" ,intltool) - ("cmake", cmake))) + ("cmake" ,cmake))) (home-page "https://launchpad.net/deja-dup") (synopsis "Simple backup tool, for regular encrypted backups") (description diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 8504b2f11e..8ea9c74cec 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -435,13 +435,13 @@ visual effects work for film.") (native-inputs `(("unzip" ,unzip))) (inputs - `(("giflib", giflib) - ("jasper", jasper) - ("librsvg", librsvg) - ("pth", pth) - ("qtbase", qtbase) - ("ffmpeg", ffmpeg) - ("mesa", mesa))) + `(("giflib" ,giflib) + ("jasper" ,jasper) + ("librsvg" ,librsvg) + ("pth" ,pth) + ("qtbase" ,qtbase) + ("ffmpeg" ,ffmpeg) + ("mesa" ,mesa))) (synopsis "High performance real-time graphics toolkit") (description "The OpenSceneGraph is a high performance 3D graphics toolkit diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index c5408f8627..9c59f56139 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -7881,7 +7881,7 @@ files in Haskell.") (inputs `(("ghc-mtl" ,ghc-mtl) ("ghc-network" ,ghc-network) - ("ghc-directory", ghc-directory) + ("ghc-directory" ,ghc-directory) ("ghc-old-locale" ,ghc-old-locale))) (native-inputs `(("ghc-hunit" ,ghc-hunit))) @@ -8458,7 +8458,7 @@ that are much lighter weight than IO-threads.") (native-inputs `(("ghc-hunit" ,ghc-hunit) ("ghc-quickcheck" ,ghc-quickcheck) - ("ghc-ieee754", ghc-ieee754) + ("ghc-ieee754" ,ghc-ieee754) ("ghc-test-framework" ,ghc-test-framework) ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2))) @@ -8582,7 +8582,7 @@ statically known size.") (build-system haskell-build-system) (inputs `(("ghc-tuple-th" ,ghc-tuple-th) ("ghc-contravariant" ,ghc-contravariant) - ("ghc-base-prelude",ghc-base-prelude))) + ("ghc-base-prelude" ,ghc-base-prelude))) (home-page "https://github.com/nikita-volkov/contravariant-extras") (synopsis "Extras for the @code{ghc-contravariant} Haskell package") (description "This Haskell package provides extras for the @@ -8897,7 +8897,7 @@ and are often as efficient as hand-written folds.") ("ghc-vector-algorithms" ,ghc-vector-algorithms) ("ghc-split" ,ghc-split))) (native-inputs `(("ghc-hspec" ,ghc-hspec) - ("ghc-hunit",ghc-hunit) + ("ghc-hunit" ,ghc-hunit) ("ghc-quickcheck" ,ghc-quickcheck) ("ghc-semigroups" ,ghc-semigroups) ("ghc-foldl" ,ghc-foldl))) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index e59b34417b..bad27dacb6 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -100,7 +100,7 @@ ("qttools" ,qttools))) (inputs `(("qca" ,qca) - ("qtbase", qtbase) + ("qtbase" ,qtbase) ("qtscript" ,qtscript) ("snorenotify" ,snorenotify) ("zlib" ,zlib))) diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm index 246860e3f3..b763a03476 100644 --- a/gnu/packages/kde-frameworks.scm +++ b/gnu/packages/kde-frameworks.scm @@ -157,7 +157,7 @@ common build settings used in software produced by the KDE community.") ;; TODO: Add building the super experimental QML support `(("extra-cmake-modules" ,extra-cmake-modules) ("pkg-config" ,pkg-config) - ("qttools", qttools))) + ("qttools" ,qttools))) (inputs `(("qtbase" ,qtbase))) (arguments @@ -1186,7 +1186,7 @@ lower level classes for interaction with the X Windowing System.") ("pkg-config" ,pkg-config))) (propagated-inputs ;; Headers contain #include - `(("modem-manager", modem-manager))) + `(("modem-manager" ,modem-manager))) (inputs `(("qtbase" ,qtbase))) (arguments @@ -1284,7 +1284,7 @@ which are used in DBus communication.") (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules))) (inputs - `(("libdmtx", libdmtx) + `(("libdmtx" ,libdmtx) ("qrencode" ,qrencode) ("qtbase" ,qtbase))) ;; TODO: rethink: nix propagates this (home-page "https://api.kde.org/frameworks/prison/html/index.html") @@ -2209,7 +2209,7 @@ their settings.") ("kwidgetsaddons" ,kwidgetsaddons) ("kwindowsystem" ,kwindowsystem) ("kxmlgui" ,kxmlgui) - ("libepoxy", libepoxy) + ("libepoxy" ,libepoxy) ("qtbase" ,qtbase) ("qtdeclarative" ,qtdeclarative) ("solid" ,solid))) @@ -3003,7 +3003,7 @@ types or handled by application specific code.") ("libgit2" ,libgit2) ("perl" ,perl) ("qtbase" ,qtbase) - ("qtdeclarative", qtdeclarative) + ("qtdeclarative" ,qtdeclarative) ("qtscript" ,qtscript) ("qtxmlpatterns" ,qtxmlpatterns) ("solid" ,solid) @@ -3071,7 +3071,7 @@ library.") ("kwidgetsaddons" ,kwidgetsaddons) ("kwindowsystem" ,kwindowsystem) ("qtbase" ,qtbase) - ("qtspeech", qtspeech))) + ("qtspeech" ,qtspeech))) (arguments `(#:phases (modify-phases %standard-phases @@ -3150,7 +3150,7 @@ the passwords on KDE work spaces.") `(("extra-cmake-modules" ,extra-cmake-modules))) (inputs `(("attica" ,attica) - ("kauth", kauth) + ("kauth" ,kauth) ("kcodecs" ,kcodecs) ("kcoreaddons" ,kcoreaddons) ("kglobalaccel" ,kglobalaccel) @@ -3395,7 +3395,7 @@ workspace.") `(("dbus" ,dbus) ("docbook-xml" ,docbook-xml-4.4) ; optional ("extra-cmake-modules" ,extra-cmake-modules) - ("perl", perl) + ("perl" ,perl) ("perl-uri" ,perl-uri) ("pkg-config" ,pkg-config) ("shared-mime-info" ,shared-mime-info) @@ -3421,7 +3421,7 @@ workspace.") ("knotifications" ,knotifications) ("kparts" ,kparts) ("ktextwidgets" ,ktextwidgets) - ("kunitconversion", kunitconversion) + ("kunitconversion" ,kunitconversion) ("kwindowsystem" ,kwindowsystem) ("qtbase" ,qtbase))) (inputs @@ -3434,9 +3434,9 @@ workspace.") ("kservice" ,kservice) ("kwidgetsaddons" ,kwidgetsaddons) ("kxmlgui" ,kxmlgui) - ("libsm", libsm) - ("networkmanager-qt", networkmanager-qt) - ("openssl", openssl) + ("libsm" ,libsm) + ("networkmanager-qt" ,networkmanager-qt) + ("openssl" ,openssl) ("qtsvg" ,qtsvg) ("qttools" ,qttools) ("qtx11extras" ,qtx11extras))) @@ -3507,7 +3507,7 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") (build-system cmake-build-system) (native-inputs `(("extra-cmake-modules" ,extra-cmake-modules) - ("perl", perl))) + ("perl" ,perl))) (inputs `(("giflib" ,giflib) ("gperf" ,gperf) @@ -3521,14 +3521,14 @@ http://community.kde.org/Frameworks/Porting_Notes should help with this.") ("knotifications" ,knotifications) ("kparts" ,kparts) ("ktextwidgets" ,ktextwidgets) - ("kwallet", kwallet) + ("kwallet" ,kwallet) ("kwidgetsaddons" ,kwidgetsaddons) ("kwindowsystem" ,kwindowsystem) ("kxmlgui" ,kxmlgui) - ("libjpeg", libjpeg) - ("libpng", libpng) - ("openssl", openssl) - ("phonon", phonon) + ("libjpeg" ,libjpeg) + ("libpng" ,libpng) + ("openssl" ,openssl) + ("phonon" ,phonon) ("qtbase" ,qtbase) ("qtx11extras" ,qtx11extras) ("sonnet" ,sonnet))) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index df6d7468ac..a268c4db0d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1778,9 +1778,9 @@ file system is as easy as logging into the server with an SSH client.") (base32 "0v4si1ri6lhnq9q87gkx7fsh6lv6xz4bynknwndqncpvfp5cy1jg")))) (build-system gnu-build-system) - (inputs `(("fuse", fuse) - ("libarchive", libarchive))) - (native-inputs `(("pkg-config", pkg-config))) + (inputs `(("fuse" ,fuse) + ("libarchive" ,libarchive))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://www.cybernoia.de/software/archivemount") (synopsis "Tool for mounting archive files with FUSE") (description "archivemount is a FUSE-based file system for Unix variants, @@ -2034,7 +2034,7 @@ from the module-init-tools project.") ("docbook-xml" ,docbook-xml-4.2) ("docbook-xsl" ,docbook-xsl) ("libxml2" ,libxml2) ;for $XML_CATALOG_FILES - ("xsltproc", libxslt))) + ("xsltproc" ,libxslt))) (inputs ;; When linked against libblkid, eudev can populate /dev/disk/by-label ;; and similar; it also installs the '60-persistent-storage.rules' file, @@ -3707,7 +3707,7 @@ are exceeded.") (inputs `(("acl" ,acl) ("libuuid" ,util-linux) - ("lzo", lzo) + ("lzo" ,lzo) ("zlib" ,zlib))) (build-system gnu-build-system) (arguments @@ -4137,13 +4137,13 @@ used by nftables.") (base32 "1i1gfy8l7qyhc5vlrpp63s0n5kybmc9pi4dywiq8rmkhrrnddsla")))) (build-system gnu-build-system) - (inputs `(("bison", bison) - ("flex", flex) - ("gmp", gmp) - ("libmnl", libmnl) - ("libnftnl", libnftnl) - ("readline", readline))) - (native-inputs `(("pkg-config", pkg-config))) + (inputs `(("bison" ,bison) + ("flex" ,flex) + ("gmp" ,gmp) + ("libmnl" ,libmnl) + ("libnftnl" ,libnftnl) + ("readline" ,readline))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://www.nftables.org") (synopsis "Userspace utility for Linux packet filtering") (description "nftables is the project that aims to replace the existing diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 0d4bf12817..69180abeac 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -354,12 +354,12 @@ secure session between the peers.") (inputs `(("gobject-introspection" ,gobject-introspection) ("glib" ,glib) - ("pango", pango) - ("gtk", gtk+-2) + ("pango" ,pango) + ("gtk" ,gtk+-2) ("lua" ,lua) ("cairo" ,cairo) ("libffi" ,libffi) - ("xorg-server", xorg-server))) + ("xorg-server" ,xorg-server))) (native-inputs `(("pkg-config" ,pkg-config) ("dbus" ,dbus))) ;tests use 'dbus-run-session' @@ -397,7 +397,7 @@ Notable examples are GTK+, GStreamer and Webkit.") (string-append out "/share/lua/" lua-version)) #t)))) #:test-target "test")) - (inputs `(("lua", lua))) + (inputs `(("lua" ,lua))) (synopsis "Pattern-matching library for Lua") (description "LPeg is a pattern-matching library for Lua, based on Parsing Expression @@ -436,7 +436,7 @@ Grammars (PEGs).") #:phases (modify-phases %standard-phases (delete 'configure)))) - (inputs `(("lua", lua))) + (inputs `(("lua" ,lua))) (home-page "https://bitop.luajit.org/index.html") (synopsis "Bitwise operations on numbers for Lua") (description diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 7986671e97..1d52b35929 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1812,7 +1812,7 @@ in Perl.") (patch-shebang "mb2md" (list (string-append perl "/bin"))) (chmod "mb2md" #o555)) #t)))) - (native-inputs `(("gzip", gzip))) + (native-inputs `(("gzip" ,gzip))) (inputs `(("perl" ,perl) ("perl-timedate" ,perl-timedate))) (home-page "http://batleth.sapienti-sat.org/projects/mb2md/") diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm index 779b7ef5aa..99488fb4c4 100644 --- a/gnu/packages/make-bootstrap.scm +++ b/gnu/packages/make-bootstrap.scm @@ -108,7 +108,7 @@ for `sh' in $PATH, and without nscd, and with static NSS modules." ("gcc" ,(package (inherit gcc) (outputs '("out")) ; all in one so libgcc_s is easily found (inputs - `(("libc",(glibc-for-bootstrap)) + `(("libc" ,(glibc-for-bootstrap)) ("libc:static" ,(glibc-for-bootstrap) "static") ,@(package-inputs gcc))))) ,@(fold alist-delete (%final-inputs) '("libc" "gcc"))))) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index ae489e1586..6ce8b258bb 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -144,9 +144,9 @@ keys, no previous conversation is compromised.") #:configure-flags '("-DBUILD_SHARED_LIBS=on" "-DBUILD_TESTING=1"))) (build-system cmake-build-system) (inputs `( ;; Required for tests: - ("check", check) - ("openssl", openssl))) - (native-inputs `(("pkg-config", pkg-config))) + ("check" ,check) + ("openssl" ,openssl))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://github.com/WhisperSystems/libsignal-protocol-c") (synopsis "Implementation of a ratcheting forward secrecy protocol") (description "libsignal-protocol-c is an implementation of a ratcheting @@ -613,8 +613,8 @@ end-to-end encryption support; XML console.") (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))))) (inputs `(("libgee" ,libgee) - ("libsignal-protocol-c", libsignal-protocol-c) - ("libgcrypt", libgcrypt) + ("libsignal-protocol-c" ,libsignal-protocol-c) + ("libgcrypt" ,libgcrypt) ("libsoup" ,libsoup) ("sqlite" ,sqlite) ("gpgme" ,gpgme) @@ -623,7 +623,7 @@ end-to-end encryption support; XML console.") ("gsettings-desktop-schemas" ,gsettings-desktop-schemas))) (native-inputs `(("pkg-config" ,pkg-config) - ("libsignal-protocol-c-source", (package-source libsignal-protocol-c)) + ("libsignal-protocol-c-source" ,(package-source libsignal-protocol-c)) ("glib" ,glib "bin") ("vala" ,vala) ("gettext" ,gettext-minimal))) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 4bd58d9733..c7c4913bf0 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -399,7 +399,7 @@ many input formats and provides a customisable Vi-style user interface.") "Clarinet in Bb.denemo")) #t))))) (native-inputs - `(("glib:bin", glib "bin") ; for gtester + `(("glib:bin" ,glib "bin") ; for gtester ("pkg-config" ,pkg-config))) (inputs `(("alsa-lib" ,alsa-lib) @@ -417,7 +417,7 @@ many input formats and provides a customisable Vi-style user interface.") ("libsndfile" ,libsndfile) ("libtool" ,libtool) ("libxml2" ,libxml2) - ("lilypond", lilypond) + ("lilypond" ,lilypond) ("portaudio" ,portaudio) ("portmidi" ,portmidi) ("rubberband" ,rubberband))) @@ -2518,7 +2518,7 @@ websites such as Libre.fm.") (build-system python-build-system) (propagated-inputs `(("python-requests" ,python-requests) - ("eyed3", eyed3) + ("eyed3" ,eyed3) ("python-beautifulsoup4" ,python-beautifulsoup4) ("youtube-dl" ,youtube-dl))) (arguments diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 395e75afa6..999f0578d7 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1225,11 +1225,11 @@ gone wild and are suddenly taking up your bandwidth.") (assoc-ref %build-inputs "ncurses") "/lib") (string-append "--with-tlslib=GnuTLS")))) (build-system gnu-build-system) - (inputs `(("gnutls", gnutls) - ("libxml2", libxml2) - ("ncurses", ncurses) - ("zlib", zlib))) - (native-inputs `(("pkg-config", pkg-config))) + (inputs `(("gnutls" ,gnutls) + ("libxml2" ,libxml2) + ("ncurses" ,ncurses) + ("zlib" ,zlib))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://github.com/nzbget/nzbget") (synopsis "Usenet binary file downloader") (description @@ -1455,11 +1455,11 @@ does not use SSH and requires a pre-shared symmetric key.") (patches (search-patches "quagga-reproducible-build.patch")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config",pkg-config) - ("perl",perl) - ("dejagnu",dejagnu))) - (inputs `(("readline",readline) - ("c-ares",c-ares))) + (native-inputs `(("pkg-config" ,pkg-config) + ("perl" ,perl) + ("dejagnu" ,dejagnu))) + (inputs `(("readline" ,readline) + ("c-ares" ,c-ares))) (synopsis "Routing Software Suite") (description "Quagga is a routing software suite, providing implementations of OSPFv2, OSPFv3, RIP v1 and v2, RIPng and BGP-4 for Unix platforms. diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 24f402128c..9346012390 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3755,7 +3755,7 @@ sensitive completion, colors, and more.") (delete 'configure)))) (inputs `(("topkg" ,ocaml-topkg) - ("opam", opam))) + ("opam" ,opam))) (synopsis "Various signed and unsigned integer types for OCaml") (description "The ocaml-integers library provides a number of 8-, 16-, 32- and 64-bit signed and unsigned integer types, together with aliases such as @@ -3789,7 +3789,7 @@ long and size_t whose sizes depend on the host platform.") ("integers" ,ocaml-integers) ("lwt" ,ocaml-lwt) ("topkg" ,ocaml-topkg) - ("opam", opam))) + ("opam" ,opam))) (synopsis "Library for binding to C libraries using pure OCaml") (description "Ctypes is a library for binding to C libraries using pure OCaml. The primary aim is to make writing C extensions as straightforward as @@ -3822,7 +3822,7 @@ without writing or generating any C!") (delete 'configure)))) (inputs `(("topkg" ,ocaml-topkg) - ("opam", opam))) + ("opam" ,opam))) (native-inputs `(("astring" ,ocaml-astring))) (synopsis "OCamlbuild plugin for C stubs") diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index e6a656c7b9..0bc4697229 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -5759,7 +5759,7 @@ most specific one) is instantiated.") ("perl-file-configdir" ,perl-file-configdir) ("perl-file-find-rule" ,perl-file-find-rule) ("perl-hash-merge" ,perl-hash-merge) - ("perl-moo", perl-moo) + ("perl-moo" ,perl-moo) ("perl-moox-file-configdir" ,perl-moox-file-configdir) ("perl-namespace-clean" ,perl-namespace-clean))) (home-page "http://search.cpan.org/dist/MooX-ConfigFromFile/") diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 3b907cafcf..7974c005c2 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -823,7 +823,7 @@ internationalized messages within program source text.") '(#:tests? #f)) ; FIXME: Tests can't find zope.event. (propagated-inputs `(("python-zope-event" ,python-zope-event) - ("python-zope-exceptions", python-zope-exceptions) + ("python-zope-exceptions" ,python-zope-exceptions) ("python-zope-interface" ,python-zope-interface))) (native-inputs `(("python-zope-testing" ,python-zope-testing) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index aef63f334b..05d3390604 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11975,7 +11975,7 @@ library.") "08if5yax1xn5yfp8p3765ccjmfcv9di7i4m5jckgnwvdsgznwkbj")))) (build-system python-build-system) (native-inputs `(("pkg-config" ,pkg-config) - ("python-cython", python-cython))) + ("python-cython" ,python-cython))) (home-page "https://github.com/aresch/rencode") (synopsis "Serialization of heterogeneous data structures") (description @@ -12158,7 +12158,7 @@ created by running @code{python setup.py develop}).") (build-system python-build-system) (propagated-inputs `(("python-tqdm" ,python-tqdm) - ("python-pkginfo", python-pkginfo) + ("python-pkginfo" ,python-pkginfo) ("python-requests" ,python-requests) ("python-requests-toolbelt" ,python-requests-toolbelt))) (home-page "https://github.com/pypa/twine") @@ -12568,7 +12568,7 @@ is the new Pyro version that is actively developed.") `(("netcdf" ,netcdf))) (propagated-inputs `(("python-numpy" ,python2-numpy-1.8) - ("python-pyro", python2-pyro))) + ("python-pyro" ,python2-pyro))) (arguments ;; ScientificPython is not compatible with Python 3 `(#:python ,python-2 @@ -12915,7 +12915,7 @@ and other tools.") #t))))) (propagated-inputs `(("python-pygments" ,python-pygments) - ("python-requests", python-requests) + ("python-requests" ,python-requests) ("python-babel" ,python-babel) ; optional, for internationalization ("python-curtsies" ,python-curtsies) ; >= 0.1.18 ("python-greenlet" ,python-greenlet) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index a8c2729ee8..d6082bd7a4 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1937,7 +1937,7 @@ different kinds of sliders, and much more.") ("libwebp" ,libwebp) ("sqlite" ,sqlite) ("fontconfig" ,fontconfig) - ("libxrender", libxrender) + ("libxrender" ,libxrender) ("qtbase" ,qtbase) ("qtdeclarative" ,qtdeclarative) ("qtmultimedia" ,qtmultimedia) diff --git a/gnu/packages/ratpoison.scm b/gnu/packages/ratpoison.scm index d630c24fd4..19321872c5 100644 --- a/gnu/packages/ratpoison.scm +++ b/gnu/packages/ratpoison.scm @@ -79,7 +79,7 @@ ("readline" ,readline) ("xextproto" ,xextproto))) (native-inputs - `(("perl",perl) + `(("perl" ,perl) ("pkg-config" ,pkg-config) ("ratpoison.desktop" ,ratpoison.desktop))) (home-page "https://www.nongnu.org/ratpoison/") diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm index 222fd5b6f1..30d18aa1c3 100644 --- a/gnu/packages/sdl.scm +++ b/gnu/packages/sdl.scm @@ -122,9 +122,9 @@ joystick, and graphics hardware.") ("fcitx" ,fcitx) ; helps with CJK input ("glib" ,glib) ("ibus" ,ibus) - ("libxkbcommon", libxkbcommon) - ("wayland", wayland) - ("wayland-protocols", wayland-protocols)) + ("libxkbcommon" ,libxkbcommon) + ("wayland" ,wayland) + ("wayland-protocols" ,wayland-protocols)) (package-inputs sdl))) (license bsd-3))) diff --git a/gnu/packages/sml.scm b/gnu/packages/sml.scm index b9bd7a7e82..1d7fd3fb51 100644 --- a/gnu/packages/sml.scm +++ b/gnu/packages/sml.scm @@ -42,7 +42,7 @@ (build-system gnu-build-system) (inputs `(("gmp" ,gmp) - ("lesstif",lesstif) + ("lesstif" ,lesstif) ("libffi" ,libffi) ("libx11" ,libx11) ("libxt" ,libxt))) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index eeae8bea41..6540a9feaf 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -128,9 +128,9 @@ configurable through a graphical wizard.") (string-append "DESTDIR=" (assoc-ref %outputs "out"))))) (inputs - `(("vte", vte-ng) - ("gtk+", gtk+) - ("ncurses", ncurses))) + `(("vte" ,vte-ng) + ("gtk+" ,gtk+) + ("ncurses" ,ncurses))) (native-inputs `(("pkg-config" ,pkg-config))) @@ -292,10 +292,10 @@ multi-seat support, a replacement for @command{mingetty}, and more.") #:phases (modify-phases %standard-phases (delete 'configure)) #:test-target "test")) - (inputs `(("ncurses", ncurses))) - (native-inputs `(("libtool", libtool) + (inputs `(("ncurses" ,ncurses))) + (native-inputs `(("libtool" ,libtool) ("perl-test-harness" ,perl-test-harness) - ("pkg-config", pkg-config))) + ("pkg-config" ,pkg-config))) (synopsis "Keyboard entry processing library for terminal-based programs") (description "Libtermkey handles all the necessary logic to recognise special keys, UTF-8 @@ -692,7 +692,7 @@ terminal or piped input.") (delete-file "tests/test_input_output.py") #t))))) (propagated-inputs - `(("python-wcwidth", python-wcwidth))) + `(("python-wcwidth" ,python-wcwidth))) (native-inputs `(("python-pytest-runner" ,python-pytest-runner) ("python-pytest" ,python-pytest))) @@ -762,7 +762,7 @@ than a terminal.") (invoke "nosetests" "-v")))))) (propagated-inputs `(("python-blessings" ,python-blessings) - ("python-wcwidth", python-wcwidth))) + ("python-wcwidth" ,python-wcwidth))) (native-inputs `(("python-mock" ,python-mock) ("python-pyte" ,python-pyte) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index f1ccab9af9..cbf077cea3 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -81,10 +81,10 @@ (list (search-path-specification (variable "VIS_PATH") (files '("share/vis"))))) - (inputs `(("lua", lua) - ("ncurses", ncurses) - ("libtermkey", libtermkey) - ("lua-lpeg", lua-lpeg) + (inputs `(("lua" ,lua) + ("ncurses" ,ncurses) + ("libtermkey" ,libtermkey) + ("lua-lpeg" ,lua-lpeg) ("tre" ,tre))) (synopsis "Vim-like text editor") (description diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 0979b4f4e7..39354f93ed 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1062,7 +1062,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.") ("waf" ,python-waf) ("wayland" ,wayland) ("wayland-protocols" ,wayland-protocols) - ("libxkbcommon", libxkbcommon) + ("libxkbcommon" ,libxkbcommon) ("youtube-dl" ,youtube-dl) ("zlib" ,zlib))) (arguments @@ -2461,7 +2461,7 @@ MPEG-2, MPEG-4, DVD (VOB)... ("libtool" ,libtool) ("pkg-config" ,pkg-config) ("zlib" ,zlib) - ("libmediainfo", libmediainfo) + ("libmediainfo" ,libmediainfo) ("libzen" ,libzen))) (build-system gnu-build-system) (arguments diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 24f7333cd8..55a92eca0d 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -747,7 +747,7 @@ Machine Protocol.") ("sdl2" ,sdl2) ("sdl2-ttf" ,sdl2-ttf) ("spice-protocol" ,spice-protocol))) - (native-inputs `(("pkg-config", pkg-config))) + (native-inputs `(("pkg-config" ,pkg-config))) (arguments `(#:tests? #f ;; No tests are available. #:phases (modify-phases %standard-phases diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index dc73ce3cad..4d981416d0 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -103,7 +103,7 @@ and for the GLSL.std.450 extended instruction set. (assoc-ref %build-inputs "spirv-headers"))))) (inputs `(("spirv-headers" ,spirv-headers))) - (native-inputs `(("pkg-config", pkg-config) + (native-inputs `(("pkg-config" ,pkg-config) ("python" ,python))) (home-page "https://github.com/KhronosGroup/SPIRV-Tools") (synopsis "API and commands for processing SPIR-V modules") @@ -190,7 +190,7 @@ interpretation of the specifications for these languages.") ("mesa" ,mesa) ("spirv-tools" ,spirv-tools) ("wayland" ,wayland))) - (native-inputs `(("pkg-config", pkg-config) + (native-inputs `(("pkg-config" ,pkg-config) ("python" ,python))) (home-page "https://github.com/KhronosGroup/Vulkan-LoaderAndValidationLayers") diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index ceb7d9b7c7..394fa7b71c 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -960,9 +960,9 @@ of people.") ; named 'stubout'". The tests can be run by replacing the check phase with ; the command "python setup.py nosetests --verbosity=3". (native-inputs `(; Required for tests: - ("python-mox3", python-mox3) - ("python-nose", python-nose))) - (propagated-inputs `(("python-numpy", python-numpy))) + ("python-mox3" ,python-mox3) + ("python-nose" ,python-nose))) + (propagated-inputs `(("python-numpy" ,python-numpy))) (home-page "https://github.com/novnc/websockify") (synopsis "WebSockets support for any application/server") (description "Websockify translates WebSockets traffic to normal socket @@ -989,7 +989,7 @@ directions.") #:tests? #f)) ; no test target (native-inputs `(("flex" ,flex))) (inputs `(("gnutls" ,gnutls) - ("libcrypt", libgcrypt))) + ("libcrypt" ,libgcrypt))) (home-page "https://www.gedanken.org.uk/software/wwwoffle/") (synopsis "Caching web proxy optimized for intermittent internet links") (description "WWWOFFLE is a proxy web server that is especially good for diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm index c6a319965a..585b8a0342 100644 --- a/gnu/packages/wget.scm +++ b/gnu/packages/wget.scm @@ -152,21 +152,21 @@ online pastebin services.") (zero? (system* "sh" "./bootstrap" "--gnulib-srcdir=gnulib" "--no-git"))))))) - (inputs `(("autoconf", autoconf) - ("automake", automake) - ("doxygen", doxygen) - ("flex", flex) - ("gettext", gettext-minimal) - ("gnutls", gnutls/dane) - ("libiconv", libiconv) - ("libidn2", libidn2) - ("libmicrohttpd", libmicrohttpd) - ("libpsl", libpsl) - ("libtool", libtool) - ("pcre2", pcre2) - ("python", python))) + (inputs `(("autoconf" ,autoconf) + ("automake" ,automake) + ("doxygen" ,doxygen) + ("flex" ,flex) + ("gettext" ,gettext-minimal) + ("gnutls" ,gnutls/dane) + ("libiconv" ,libiconv) + ("libidn2" ,libidn2) + ("libmicrohttpd" ,libmicrohttpd) + ("libpsl" ,libpsl) + ("libtool" ,libtool) + ("pcre2" ,pcre2) + ("python" ,python))) ;; TODO: Add libbrotlidec, libnghttp2. - (native-inputs `(("pkg-config", pkg-config))) + (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://gitlab.com/gnuwget/wget2") (synopsis "Successor of GNU Wget") (description "GNU Wget2 is the successor of GNU Wget, a file and recursive diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 37d36cf922..8496eb3365 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -278,8 +278,8 @@ integrate Windows applications into your desktop.") (base32 "14wf7536rkmhav9ibbvhqqkfqmbk1dckhd2679i5scizr5x290x4")))) (inputs `(("autoconf" ,autoconf) ; for autoreconf - ("gtk+", gtk+) - ("libva", libva) + ("gtk+" ,gtk+) + ("libva" ,libva) ("python" ,python) ("sdl2" ,sdl2) ("util-linux" ,util-linux) ; for hexdump diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index b38b3caa25..9bd3492413 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -710,7 +710,7 @@ experience.") ("libxdg-basedir" ,libxdg-basedir) ("libxkbcommon" ,libxkbcommon) ("lua" ,lua) - ("lua-lgi",lua-lgi) + ("lua-lgi" ,lua-lgi) ("pango" ,pango) ("startup-notification" ,startup-notification) ("xcb-util" ,xcb-util) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 07a9b390fa..4e7f2c207f 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1332,9 +1332,9 @@ XCB util-xrm module provides the following libraries: (install-file "README" doc) ;; Avoid unspecified return value. #t)))))) - (inputs `(("libx11", libx11) - ("libxext", libxext) - ("libxxf86vm", libxxf86vm))) + (inputs `(("libx11" ,libx11) + ("libxext" ,libxext) + ("libxxf86vm" ,libxxf86vm))) (synopsis "Tiny monitor calibration loader for XFree86 (or X.org)") (description "xcalib is a tiny tool to load the content of vcgt-Tags in ICC profiles to the video card's gamma ramp. It does work with most video card diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 729fa56a30..6c1d2a7796 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1415,7 +1415,7 @@ characters into a single event.") (propagated-inputs `(("perl-libxml" ,perl-libxml) ("perl-xml-filter-buffertext" ,perl-xml-filter-buffertext) - ("perl-xml-namespacesupport", perl-xml-namespacesupport) + ("perl-xml-namespacesupport" ,perl-xml-namespacesupport) ("perl-xml-sax-base" ,perl-xml-sax-base))) (home-page "http://search.cpan.org/dist/XML-SAX-Writer/") (synopsis "SAX2 XML Writer") @@ -1472,7 +1472,7 @@ It provides a flexible escaping technique and pretty printing.") ("perl-xml-sax-writer" ,perl-xml-sax-writer) ("perl-xml-simple" ,perl-xml-simple) ("perl-xml-xpathengine" ,perl-xml-xpathengine) - ("perl-test-pod", perl-test-pod) + ("perl-test-pod" ,perl-test-pod) ("perl-tree-xpathengine" ,perl-tree-xpathengine))) (home-page "http://search.cpan.org/dist/XML-Twig/") (synopsis "Perl module for processing huge XML documents in tree mode") diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 46a9a3b85f..1e4835b5c0 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5983,7 +5983,7 @@ basic eye-candy effects.") ("python2-rencode" ,python2-rencode) ("xorg-server" ,xorg-server))) (native-inputs `(("pkg-config" ,pkg-config) - ("python2-cython", python2-cython))) + ("python2-cython" ,python2-cython))) (arguments `(#:python ,python-2 ;; no full Python 3 support yet #:configure-flags '("--with-tests" From 3def739da13a166769777d0db7baba79230f64ae Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 12:23:59 +0100 Subject: [PATCH 028/110] gnu: Use the CMake build system's #:build-type key. * gnu/packages/code.scm (rtags)[arguments]: Move the CMAKE_BUILD_TYPE from #:configure-flags to #:build-type. * gnu/packages/databases.scm (apache-arrow)[arguments]: Likewise * gnu/packages/engineering.scm (kicad)[arguments]: Likewise * gnu/packages/flashing-tools.scm (heimdall)[arguments]: Likewise * gnu/packages/graphics.scm (openscenegraph)[arguments]: Likewise * gnu/packages/linux.scm (rdma-core)[arguments]: Likewise * gnu/packages/music.scm (portmidi)[arguments]: Likewise * gnu/packages/photo.scm (rawtherapee)[arguments]: Likewise * gnu/packages/rdesktop.scm (freerdp)[arguments]: Likewise * gnu/packages/serialization.scm (flatbuffers)[arguments]: Likewise * gnu/packages/web.scm (tidy-html)[arguments]: Likewise --- gnu/packages/code.scm | 4 ++-- gnu/packages/databases.scm | 4 ++-- gnu/packages/engineering.scm | 2 +- gnu/packages/flashing-tools.scm | 4 ++-- gnu/packages/graphics.scm | 13 ++++++------- gnu/packages/linux.scm | 4 ++-- gnu/packages/music.scm | 4 ++-- gnu/packages/photo.scm | 2 +- gnu/packages/rdesktop.scm | 7 ++++--- gnu/packages/serialization.scm | 8 ++++---- gnu/packages/web.scm | 6 +++--- 11 files changed, 29 insertions(+), 29 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 979c7a72b8..15fdf9d66f 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -420,9 +420,9 @@ functionality such as HTML output.") "0scjbp1z201q8njvrxqz7lk2m9b6k2rxd5q1shrng6532r7ndif2")))) (build-system cmake-build-system) (arguments - '(#:configure-flags + '(#:build-type "RelWithDebInfo" + #:configure-flags '("-DRTAGS_NO_ELISP_FILES=1" - "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_CXX_FLAGS=-std=c++11" "-DBUILD_TESTING=FALSE") #:tests? #f)) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 58da1f7a90..bcf1864775 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2771,9 +2771,9 @@ Monitor read/write activity on a mongo server (setenv "JEMALLOC_HOME" (assoc-ref %build-inputs "jemalloc")) (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson")) #t))) + #:build-type "Release" #:configure-flags - (list "-DCMAKE_BUILD_TYPE=Release" - "-DARROW_PYTHON=ON" + (list "-DARROW_PYTHON=ON" ;; Install to PREFIX/lib (the default is ;; PREFIX/lib64). diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 076d4b6094..4d45aab772 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -696,12 +696,12 @@ language.") (arguments `(#:out-of-source? #t #:tests? #f ; no tests + #:build-type "Release" #:configure-flags (list "-DKICAD_STABLE_VERSION=ON" "-DKICAD_REPO_NAME=stable" ,(string-append "-DKICAD_BUILD_VERSION=4.0-" (string-take commit 7)) - "-DCMAKE_BUILD_TYPE=Release" "-DKICAD_SKIP_BOOST=ON"; Use our system's boost library. "-DKICAD_SCRIPTING=ON" "-DKICAD_SCRIPTING_MODULES=ON" diff --git a/gnu/packages/flashing-tools.scm b/gnu/packages/flashing-tools.scm index 51b259a5cf..36c8353ee0 100644 --- a/gnu/packages/flashing-tools.scm +++ b/gnu/packages/flashing-tools.scm @@ -300,8 +300,8 @@ RK3036, RK3066, RK312X, RK3168, RK3188, RK3288, RK3368.") "1y7gwg3lipyp2zcysm2vid1qg5nwin9bxbvgzs28lz2rya4fz6sq")))) (build-system cmake-build-system) (arguments - `(#:configure-flags '("-DCMAKE_BUILD_TYPE=Release") - #:tests? #f; no tests + `(#:build-type "Release" + #:tests? #f ; no tests #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-invocations diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 8ea9c74cec..d2f1b3b0b8 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2017 Manolis Fragkiskos Ragkousis ;;; Copyright © 2017, 2018 Ben Woodcroft -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Mathieu Othacehe ;;; ;;; This file is part of GNU Guix. @@ -423,15 +423,14 @@ visual effects work for film.") (file-name (string-append name "-" version ".zip")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ;; No test target available. + `(#:tests? #f ; no test target available + ;; Without this flag, 'rd' will be added to the name of the + ;; library binaries and break linking with other programs. + #:build-type "Release" #:configure-flags (list (string-append "-DCMAKE_INSTALL_RPATH=" (assoc-ref %outputs "out") "/lib:" - (assoc-ref %outputs "out") "/lib64") - ;; We need to set this flag or otherwise 'rd' will be added - ;; to the name of the library binaries and break linking - ;; with other programs. - "-DCMAKE_BUILD_TYPE=Release"))) + (assoc-ref %outputs "out") "/lib64")))) (native-inputs `(("unzip" ,unzip))) (inputs diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a268c4db0d..b7e70249f3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3404,8 +3404,8 @@ The package provides additional NTFS tools.") ;; Upstream uses the "ninja" build system and encourage distros ;; to do the same for consistency. They also recommend using the ;; "Release" build type. - #:configure-flags (list "-GNinja" - "-DCMAKE_BUILD_TYPE=Release") + #:build-type "Release" + #:configure-flags (list "-GNinja") #:phases (modify-phases %standard-phases (replace 'build diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index c7c4913bf0..7818cfcc0b 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -1754,10 +1754,10 @@ projects.") (patches (list (search-patch "portmidi-modular-build.patch"))))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; tests cannot be linked + `(#:tests? #f ; tests cannot be linked + #:build-type "Release" ; needed to have PMALSA set #:configure-flags (list "-DPORTMIDI_ENABLE_JAVA=Off" - "-DCMAKE_BUILD_TYPE=Release" ; needed to have PMALSA set "-DPORTMIDI_ENABLE_TEST=Off"))) ; tests fail linking (inputs `(("alsa-lib" ,alsa-lib))) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 758ed3f6f1..90bc365d05 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -481,11 +481,11 @@ a complete panorama and stitch any series of overlapping pictures.") (build-system cmake-build-system) (arguments '(#:tests? #f ; no test suite + #:build-type "release" #:configure-flags (list (string-append "-DLENSFUNDBDIR=" (assoc-ref %build-inputs "lensfun") "/share/lensfun") - "-DCMAKE_BUILD_TYPE=release" ; Don't optimize the build for the host machine. See the file ; 'ProcessorTargets.cmake' in the source distribution for more ; information. diff --git a/gnu/packages/rdesktop.scm b/gnu/packages/rdesktop.scm index 1a2d0412d1..bd2b5737e9 100644 --- a/gnu/packages/rdesktop.scm +++ b/gnu/packages/rdesktop.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Ludovic Courtès ;;; Copyright © 2017 Thomas Danckaert +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -111,9 +112,9 @@ to remotely control a user's Windows desktop.") ("zlib" ,zlib) ("openssl" ,openssl))) (arguments - `(#:configure-flags - (list "-DCMAKE_BUILD_TYPE=RELEASE" - "-DWITH_JPEG=ON" + `(#:build-type "RELEASE" + #:configure-flags + (list "-DWITH_JPEG=ON" ,@(if (string-prefix? "x86_64" (or (%current-target-system) (%current-system))) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 3dd3a070e4..f721165751 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2017 Gregor Giesen ;;; Copyright © 2017 Frederick M. Muriithi ;;; Copyright © 2017 ng0 -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. @@ -431,10 +431,10 @@ to generate and parse. The two primary functions are @code{cbor.loads} and "0blc978wc5h91662vai24xj92c3bx56y6hzid90qva7il302jl64")))) (build-system cmake-build-system) (arguments - '(#:configure-flags + '(#:build-type "Release" + #:configure-flags (list (string-append "-DCMAKE_INSTALL_LIBDIR=" - (assoc-ref %outputs "out") "/lib") - "-DCMAKE_BUILD_TYPE=Release"))) + (assoc-ref %outputs "out") "/lib")))) (home-page "https://google.github.io/flatbuffers/") (synopsis "Memory-efficient serialization library") (description "FlatBuffers is a cross platform serialization library for C++, diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 394fa7b71c..625df2b1dc 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4971,10 +4971,10 @@ used to start services with both privileged and non-privileged port numbers.") "0n29wcgw32rhnraj9j21ibhwi0xagmmcskhbaz8ihxly7nx3p9h8")))) (build-system cmake-build-system) (outputs '("out" - "static")) ; 1.0MiB of .a files + "static")) ; 1.0MiB of .a files (arguments - `(#:tests? #f ; No tests available - #:configure-flags (list "-DCMAKE_BUILD_TYPE=Release") + `(#:tests? #f ; no tests available + #:build-type "Release" #:phases (modify-phases %standard-phases (add-after 'install 'move-static-libraries From 533808383f7fca6563aee1452f5202e0cd1b66b8 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 17 Mar 2018 20:23:33 +0000 Subject: [PATCH 029/110] services: databases: Change quote' to single-quote. In the postgresql-config-file gexp compiler. * gnu/services/databases.scm (postgresql-config-file-compiler): Change quote' to single-quote. --- gnu/services/databases.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/services/databases.scm b/gnu/services/databases.scm index 72927c4534..8ae248ebe4 100644 --- a/gnu/services/databases.scm +++ b/gnu/services/databases.scm @@ -112,7 +112,7 @@ host all all ::1/128 trust")) (match file (($ log-destination hba-file ident-file extra-config) - (define (quote' string) + (define (single-quote string) (if string (list "'" string "'") '())) @@ -124,9 +124,9 @@ host all all ::1/128 trust")) ((key . #f) '()) ((key values ...) `(,key " = " ,@values "\n"))) - `(("log_destination" ,@(quote' log-destination)) - ("hba_file" ,@(quote' hba-file)) - ("ident_file" ,@(quote' ident-file)) + `(("log_destination" ,@(single-quote log-destination)) + ("hba_file" ,@(single-quote hba-file)) + ("ident_file" ,@(single-quote ident-file)) ,@extra-config))) (gexp->derivation From fb6f35ba1d96072b22e767dec788446123acf29f Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 13 Mar 2018 18:47:41 +0000 Subject: [PATCH 030/110] gnu: Add python-prometheus-client. * gnu/packages/monitoring.scm (python-prometheus-client, python2-prometheus-client): New variables. --- gnu/packages/monitoring.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index c5a86d02c6..31ec88db81 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -28,6 +28,7 @@ #:use-module (guix build-system gnu) #:use-module (gnu packages admin) #:use-module (gnu packages base) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages django) #:use-module (gnu packages gd) @@ -262,3 +263,33 @@ and persisting them to disk using the Whisper time-series library.") two things: store numeric time-series data, and render graphs of this data on demand.") (license license:asl2.0))) + +(define-public python-prometheus-client + (package + (name "python-prometheus-client") + (version "0.1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "prometheus_client" version)) + (sha256 + (base32 + "164qzzg8q8awqk0angcm87p2sjiibaj1wgjz0xk6j0klvqi5q2mz")))) + (build-system python-build-system) + (arguments + '(;; No included tests. + #:tests? #f)) + (home-page + "https://github.com/prometheus/client_python") + (synopsis "Python client for the Prometheus monitoring system") + (description + "The @code{prometheus_client} package supports exposing metrics from +software written in Python, so that they can be scraped by a Prometheus +service. + +Metrics can be exposed through a standalone web server, or through Twisted, +WSGI and the node exporter textfile collector.") + (license license:asl2.0))) + +(define-public python2-prometheus-client + (package-with-python2 python-prometheus-client)) From 308b17f676999876bfec12841659cbfa56a652be Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Sat, 17 Mar 2018 21:55:24 +0100 Subject: [PATCH 031/110] Revert "gnu: shaderc: Use more standard keys." This reverts commit 9bc0591bc11190ac49c8ea3cf44c4903c924f6c7. This commit broke 'shaderc'. --- gnu/packages/vulkan.scm | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index 4d981416d0..bd0fb9e1ce 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -225,18 +225,11 @@ and the ICD.") "0b41inb1czxv3mciip0lfdxv19ccx2ys31fivfywjn2q8va1gd1f")))) (build-system meson-build-system) (arguments - `(#:build-type "Release" - #:configure-flags - (list "-GNinja" - "-DSHADERC_SKIP_TESTS=ON" - "-DCMAKE_INSTALL_LIBDIR=lib" - (string-append "-DCMAKE_INSTALL_PREFIX=" - (assoc-ref %outputs "out"))) - #:tests? #f ; tests don't work yet. + `(#:tests? #f ; tests don't work yet. #:phases (modify-phases %standard-phases (replace 'configure - (lambda* (#:key build-type configure-flags #:allow-other-keys) + (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) ;; Remove various lines and touch build-version.inc or ;; configuring won't work. @@ -254,8 +247,11 @@ and the ICD.") (substitute* "CMakeLists.txt" ((".*--check.*") "")) (substitute* "glslc/src/main.cc" ((".*build-version.inc.*") "\"1\"")) - (invoke "cmake" (cons build-type configure-flags)) - #t))) + (invoke "cmake" "-GNinja" "-DCMAKE_BUILD_TYPE=Release" + "-DSHADERC_SKIP_TESTS=ON" + "-DCMAKE_INSTALL_LIBDIR=lib" + (string-append "-DCMAKE_INSTALL_PREFIX=" + out))))) (add-after 'unpack 'unpack-sources (lambda* (#:key inputs #:allow-other-keys) (let ((spirv-tools-source (assoc-ref %build-inputs From 5983b78368f1033c52cc5e824115975ab0b31dff Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 17 Mar 2018 23:08:34 +0200 Subject: [PATCH 032/110] gnu: shaderc: Clean up package arguments. * gnu/packages/vulkan.scm (shaderc)[version]: Remove extra '-'. [arguments]: Remove extra 'mkdir-p' calls and refer to inputs directly. --- gnu/packages/vulkan.scm | 21 +++++++-------------- 1 file changed, 7 insertions(+), 14 deletions(-) diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm index bd0fb9e1ce..12b1f93015 100644 --- a/gnu/packages/vulkan.scm +++ b/gnu/packages/vulkan.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Rutger Helling ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -212,7 +213,7 @@ and the ICD.") (revision "1")) (package (name "shaderc") - (version (git-version "0.0.0-" revision commit)) + (version (git-version "0.0.0" revision commit)) (source (origin (method git-fetch) @@ -254,22 +255,14 @@ and the ICD.") out))))) (add-after 'unpack 'unpack-sources (lambda* (#:key inputs #:allow-other-keys) - (let ((spirv-tools-source (assoc-ref %build-inputs - "spirv-tools-source")) - (spirv-headers-source (assoc-ref %build-inputs - "spirv-headers-source")) - (glslang-source (assoc-ref %build-inputs - "glslang-source"))) - (mkdir-p "third-party/spirv-tools") - (copy-recursively spirv-tools-source - "third_party/spirv-tools") - (mkdir-p "third-party/spirv-tools/external/spirv-headers") + (let ((spirv-tools-source (assoc-ref inputs "spirv-tools-source")) + (spirv-headers-source (assoc-ref inputs "spirv-headers-source")) + (glslang-source (assoc-ref inputs "glslang-source"))) + (copy-recursively spirv-tools-source "third_party/spirv-tools") (copy-recursively spirv-headers-source (string-append "third_party/spirv-tools" "/external/spirv-headers")) - (mkdir-p "third-party/glslang") - (copy-recursively glslang-source - "third_party/glslang") + (copy-recursively glslang-source "third_party/glslang") #t)))))) (inputs `(("python" ,python))) From 3c274149688472cca4f506483b82d0b7865481b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= Date: Tue, 13 Mar 2018 22:55:10 +0100 Subject: [PATCH 033/110] gnu: java-simple-xml: Fix java8 test failures. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/patches/javas-simple-xml-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/java.scm (java-simple-xml)[source](patches): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + .../patches/java-simple-xml-fix-tests.patch | 37 +++++++++++++++++++ gnu/packages/xml.scm | 3 +- 3 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/java-simple-xml-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 788b260e5e..f27565bb29 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -789,6 +789,7 @@ dist_patch_DATA = \ %D%/packages/patches/jacal-fix-texinfo.patch \ %D%/packages/patches/java-jeromq-fix-tests.patch \ %D%/packages/patches/java-powermock-fix-java-files.patch \ + %D%/packages/patches/java-simple-xml-fix-tests.patch \ %D%/packages/patches/java-xerces-bootclasspath.patch \ %D%/packages/patches/java-xerces-build_dont_unzip.patch \ %D%/packages/patches/java-xerces-xjavac_taskdef.patch \ diff --git a/gnu/packages/patches/java-simple-xml-fix-tests.patch b/gnu/packages/patches/java-simple-xml-fix-tests.patch new file mode 100644 index 0000000000..6270b87009 --- /dev/null +++ b/gnu/packages/patches/java-simple-xml-fix-tests.patch @@ -0,0 +1,37 @@ +From b3b7a305f1278ec414500bf96c4c7a7f634c941b Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Jens=20Thee=C3=9F?= +Date: Thu, 15 Sep 2016 13:08:26 +0200 +Subject: [PATCH] Dictionary uses stable order. This fixes unit tests. + +This is upstream pull request #15: +https://github.com/ngallagher/simplexml/pull/15 +This software is unmaintained, this pull request will no get merged. +The patch is modified, to match the directory layout of the tarball. + +--- + src/main/java/org/simpleframework/xml/util/Dictionary.java | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/main/java/org/simpleframework/xml/util/Dictionary.java b/src/main/java/org/simpleframework/xml/util/Dictionary.java +index 077d2514..c7327426 100644 +--- a/src/org/simpleframework/xml/util/Dictionary.java ++++ b/src/org/simpleframework/xml/util/Dictionary.java +@@ -19,8 +19,8 @@ + package org.simpleframework.xml.util; + + import java.util.AbstractSet; +-import java.util.HashMap; + import java.util.Iterator; ++import java.util.LinkedHashMap; + + /** + * The Dictionary object represents a mapped set of entry +@@ -134,7 +134,7 @@ public T remove(String name) { + * + * @see org.simpleframework.xml.util.Entry + */ +- private static class Table extends HashMap { ++ private static class Table extends LinkedHashMap { + + /** + * Constructor for the Table object. This will diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 6c1d2a7796..212b1c8e8a 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1309,7 +1309,8 @@ SAX2 APIs.") version ".zip")) (sha256 (base32 - "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5")))) + "0w19k1awslmihpwsxwjbg89hv0vjhk4k3i0vrfchy3mqknd988y5")) + (patches (search-patches "java-simple-xml-fix-tests.patch")))) (build-system ant-build-system) (arguments `(#:build-target "build" From 985934cb218eaa44b255cfc464b11ce05f691973 Mon Sep 17 00:00:00 2001 From: Martin Castillo Date: Thu, 15 Mar 2018 23:40:58 +0100 Subject: [PATCH 034/110] services: openssh: Add 'accepted-environment' field. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/ssh.scm ()[accepted-environment]: New field. (openssh-config-file): Honor 'acccepted-environment'. * doc/guix.texi (Networking Services): Document it. Signed-off-by: Ludovic Courtès --- doc/guix.texi | 17 +++++++++++++++++ gnu/services/ssh.scm | 7 +++++++ 2 files changed, 24 insertions(+) diff --git a/doc/guix.texi b/doc/guix.texi index bcea89e07b..b768b20d6b 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -11158,6 +11158,23 @@ server. Alternately, one can specify the @command{sftp-server} command: `(("sftp" ,(file-append openssh "/libexec/sftp-server")))))) @end example +@item @code{accepted-environment} (default: @code{'()}) +List of strings describing which environment variables may be exported. + +Each string gets on its own line. See the @code{AcceptEnv} option in +@code{man sshd_config}. + +This example allows ssh-clients to export the @code{COLORTERM} variable. +It is set by terminal emulators, which support colors. You can use it in +your shell's ressource file to enable colors for the prompt and commands +if this variable is set. + +@example +(service openssh-service-type + (openssh-configuration + (accepted-environment '("COLORTERM")))) +@end example + @item @code{authorized-keys} (default: @code{'()}) @cindex authorized keys, SSH @cindex SSH authorized keys diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm index 301ba74041..f1d2be3f6b 100644 --- a/gnu/services/ssh.scm +++ b/gnu/services/ssh.scm @@ -302,6 +302,10 @@ The other options should be self-descriptive." (subsystems openssh-configuration-subsystems (default '(("sftp" "internal-sftp")))) + ;; list of strings + (accepted-environment openssh-configuration-accepted-environment + (default '())) + ;; list of user-name/file-like tuples (authorized-keys openssh-authorized-keys (default '())) @@ -430,6 +434,9 @@ of user-name/file-like tuples." (format port "AuthorizedKeysFile \ .ssh/authorized_keys .ssh/authorized_keys2 /etc/ssh/authorized_keys.d/%u\n") + (for-each (lambda (s) (format port "AcceptEnv ~a\n" s)) + '#$(openssh-configuration-accepted-environment config)) + (for-each (match-lambda ((name command) (format port "Subsystem\t~a\t~a\n" name command))) From 44dd3d579db3aa467e41d0b431029e46cae8e12d Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Fri, 16 Mar 2018 14:53:09 +0100 Subject: [PATCH 035/110] import: elpa: use https in download URLs MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/import/elpa.scm (elpa-url): Use HTTPS. Signed-off-by: Ludovic Courtès --- guix/import/elpa.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm index 45a419217c..7f76a13adb 100644 --- a/guix/import/elpa.scm +++ b/guix/import/elpa.scm @@ -69,9 +69,9 @@ NAMES (strings)." (define* (elpa-url #:optional (repo 'gnu)) "Retrun the URL of REPO." (let ((elpa-archives - '((gnu . "http://elpa.gnu.org/packages") - (melpa-stable . "http://stable.melpa.org/packages") - (melpa . "http://melpa.org/packages")))) + '((gnu . "https://elpa.gnu.org/packages") + (melpa-stable . "https://stable.melpa.org/packages") + (melpa . "https://melpa.org/packages")))) (assq-ref elpa-archives repo))) (define* (elpa-fetch-archive #:optional (repo 'gnu)) From 07d2fed2f60c43372446bee5fa2ac779e4acb0eb Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Fri, 16 Mar 2018 14:55:10 +0100 Subject: [PATCH 036/110] import: elpa: Fix typos in documentation strings MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * guix/import/elpa.scm: Fix typos in docstrings. Signed-off-by: Ludovic Courtès --- guix/import/elpa.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm index 7f76a13adb..5d3d04ee7c 100644 --- a/guix/import/elpa.scm +++ b/guix/import/elpa.scm @@ -67,7 +67,7 @@ NAMES (strings)." (string-append package-name-prefix (string-downcase name))))) (define* (elpa-url #:optional (repo 'gnu)) - "Retrun the URL of REPO." + "Retrieve the URL of REPO." (let ((elpa-archives '((gnu . "https://elpa.gnu.org/packages") (melpa-stable . "https://stable.melpa.org/packages") @@ -75,7 +75,7 @@ NAMES (strings)." (assq-ref elpa-archives repo))) (define* (elpa-fetch-archive #:optional (repo 'gnu)) - "Retrive the archive with the list of packages available from REPO." + "Retrieve the archive with the list of packages available from REPO." (let ((url (and=> (elpa-url repo) (cut string-append <> "/archive-contents")))) (if url From c217df913e00327f5c9b779fd97e222c4c22dab9 Mon Sep 17 00:00:00 2001 From: ng0 Date: Sat, 17 Mar 2018 15:57:19 +0000 Subject: [PATCH 037/110] gnu: fvwm: Add '.desktop' file. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/fvwm.scm (fvwm)[arguments]: Add new phase to create '.desktop' file. Signed-off-by: Ludovic Courtès --- gnu/packages/fvwm.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/fvwm.scm b/gnu/packages/fvwm.scm index 5ff3d5e4f2..a4c31aefc6 100644 --- a/gnu/packages/fvwm.scm +++ b/gnu/packages/fvwm.scm @@ -45,6 +45,27 @@ (base32 "0wzghjgy65pkn31rgl14fngizw7nbkzbxsfa670xmrndpmd4sr81")))) (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'install-xsession + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (xsessions (string-append out "/share/xsessions"))) + (mkdir-p xsessions) + (with-output-to-file + (string-append xsessions "/fvwm2.desktop") + (lambda _ + (format #t + "[Desktop Entry]~@ + Name=FVWM~@ + Comment=FVWM~@ + Exec=~a/bin/fvwm~@ + TryExec=~@*~a/bin/fvwm~@ + Icon=~@ + Type=Application~%" + out)))) + #t))))) (native-inputs `(("perl" ,perl) ("pkg-config" ,pkg-config) From 80f565d3137eceb479b8f7d39c26e00385dd65f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Mar 2018 23:04:30 +0100 Subject: [PATCH 038/110] gnu: datamash: Update to 1.3. * gnu/packages/datamash.scm (datamash): Update to 1.3. --- gnu/packages/datamash.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/datamash.scm b/gnu/packages/datamash.scm index 60c9ba795b..e839a1d985 100644 --- a/gnu/packages/datamash.scm +++ b/gnu/packages/datamash.scm @@ -28,7 +28,7 @@ (define-public datamash (package (name "datamash") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) @@ -36,7 +36,7 @@ version ".tar.gz")) (sha256 (base32 - "15jrv3ly0vgvwwi2qjmhi39n7wrklwifdk961wwfaxyc5jr6zm78")))) + "19jpcv4ryvbz0476d6dgpxpbjkpmih4q84wj06nslls338bm5fzf")))) (native-inputs `(("which" ,which) ;for tests ("perl" ,perl))) ;for help2man From b34ac8248205d64b4023412e61512dfefe44cb9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Mar 2018 23:20:15 +0100 Subject: [PATCH 039/110] gnu: nss-mdns: Adjust Avahi socket file name. Fixes . Regression introduced in 550f4509acf2c0f67882260414b0bb2843e07465. Reported by George myglc2 Clemmer . * gnu/packages/avahi.scm (nss-mdns)[arguments]: Remove #:configure-flags. Add #:phases. --- gnu/packages/avahi.scm | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/gnu/packages/avahi.scm b/gnu/packages/avahi.scm index 480b5e8d97..7734028dc3 100644 --- a/gnu/packages/avahi.scm +++ b/gnu/packages/avahi.scm @@ -99,10 +99,18 @@ DNS-SD (for \"DNS-Based Service Discovery\") protocols.") (method url-fetch)))))) (build-system gnu-build-system) (arguments - ;; The Avahi daemon socket is expected by src/Makefile.am to be at - ;; "$(localstatedir)/run/avahi-daemon/socket", so set $(localstatedir) - ;; appropriately. - '(#:configure-flags '("--localstatedir=/var"))) + '(#:phases (modify-phases %standard-phases + (add-after 'unpack 'set-avahi-socket-name + (lambda _ + ;; The Avahi daemon socket is expected by + ;; src/Makefile.am to be at + ;; "$(localstatedir)/run/avahi-daemon/socket", but + ;; nowadays it lives in /run/avahi-daemon/socket. + ;; Remove the "$(localstatedir)" bit. + (substitute* "src/Makefile.in" + (("\\$\\(localstatedir)/run/avahi-daemon/socket") + "/run/avahi-daemon/socket")) + #t))))) (synopsis "Multicast DNS Name Service Switch (@dfn{NSS}) plug-in") (description "Nss-mdns is a plug-in for the GNU C Library's Name Service Switch From 44efe67ed0def7b1c246e8705d23f4554b65247f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Mar 2018 23:58:22 +0100 Subject: [PATCH 040/110] gnu: guile-git: Update to 2bb9fbb. * gnu/packages/guile.scm (guile-git): Update to 2bb9fbb. --- gnu/packages/guile.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 1e8aca1acf..ddd34ae7dc 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1960,8 +1960,8 @@ is not available for Guile 2.0.") (license license:lgpl3+))) (define-public guile-git - (let ((revision "4") - (commit "951a32c56cc4d80f8836e3c7394783e69c1fcbad")) + (let ((revision "5") + (commit "2bb9fbbf93cf93496718efc85ad9394aefa21029")) (package (name "guile-git") (version (string-append "0.0-" revision "." (string-take commit 7))) @@ -1971,7 +1971,7 @@ is not available for Guile 2.0.") (uri (git-reference (url home-page) (commit commit))) (sha256 (base32 - "0qri9x73ij6g40ijs4hyhj8knxw39ydgghiafq74dp99bc8hh0qc")) + "0z3v0v89dyp35zx2h2gsq6v29lba3wbzabc5n2g4hx2fcb6q5qqy")) (file-name (git-file-name name version)))) (build-system gnu-build-system) (arguments From 95bd9f65a8ee64d17707a76aebc8720bbd961b68 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 17 Mar 2018 23:59:18 +0100 Subject: [PATCH 041/110] git: 'switch-to-ref' accepts short commit IDs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . Reported by Björn Höfling . * guix/git.scm (switch-to-ref): When REF is a commit, check the length of COMMIT and use 'object-lookup-prefix' if available. --- guix/git.scm | 40 +++++++++++++++++++++++++++++----------- 1 file changed, 29 insertions(+), 11 deletions(-) diff --git a/guix/git.scm b/guix/git.scm index fc41e2ace3..d31c35f64f 100644 --- a/guix/git.scm +++ b/guix/git.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Mathieu Othacehe +;;; Copyright © 2018 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,6 +28,8 @@ #:use-module (rnrs bytevectors) #:use-module (ice-9 match) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35) #:export (%repository-cache-directory latest-repository-commit)) @@ -94,17 +97,32 @@ create the store directory name." (define (switch-to-ref repository ref) "Switch to REPOSITORY's branch, commit or tag specified by REF." - (let* ((oid (match ref - (('branch . branch) - (reference-target - (branch-lookup repository branch BRANCH-REMOTE))) - (('commit . commit) - (string->oid commit)) - (('tag . tag) - (reference-name->oid repository - (string-append "refs/tags/" tag))))) - (obj (object-lookup repository oid))) - (reset repository obj RESET_HARD))) + (define obj + (match ref + (('branch . branch) + (let ((oid (reference-target + (branch-lookup repository branch BRANCH-REMOTE)))) + (object-lookup repository oid))) + (('commit . commit) + (let ((len (string-length commit))) + ;; 'object-lookup-prefix' appeared in Guile-Git in Mar. 2018, so we + ;; can't be sure it's available. Furthermore, 'string->oid' used to + ;; read out-of-bounds when passed a string shorter than 40 chars, + ;; which is why we delay calls to it below. + (if (< len 40) + (if (module-defined? (resolve-interface '(git object)) + 'object-lookup-prefix) + (object-lookup-prefix repository (string->oid commit) len) + (raise (condition + (&message + (message "long Git object ID is required"))))) + (object-lookup repository (string->oid commit))))) + (('tag . tag) + (let ((oid (reference-name->oid repository + (string-append "refs/tags/" tag)))) + (object-lookup repository oid))))) + + (reset repository obj RESET_HARD)) (define* (latest-repository-commit store url #:key From c4d2cffae7e8d6420dd7bd1fd19d31ddab89c101 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 25 Feb 2018 14:27:32 +0000 Subject: [PATCH 042/110] gnu: Add go-github-com-tj-docopt. * gnu/packages/golang.scm (go-github-com-tj-docopt): New variable. --- gnu/packages/golang.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 20a8c538be..92e612d34b 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2017 Sergei Trofimovich ;;; Copyright © 2017 Alex Vong ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Christopher Baines ;;; ;;; This file is part of GNU Guix. ;;; @@ -639,3 +640,27 @@ termination.") per-goroutine.") (home-page "https://github.com/jtolds/gls") (license license:expat))) + +(define-public go-github-com-tj-docopt + (package + (name "go-github-com-tj-docopt") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tj/docopt") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06h8hdg1mh3s78zqlr01g4si7k0f0g6pr7fj7lnvfg446hgc7080")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/tj/docopt")) + (synopsis "Go implementation of docopt") + (description + "This library allows the user to define a command-line interface from a +program's help message rather than specifying it programatically with +command-line parsers.") + (home-page "https://github.com/tj/docopt") + (license license:expat))) From ed0c6a768ee84fadfc88d3701fbbee982fa033a5 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 25 Feb 2018 14:28:12 +0000 Subject: [PATCH 043/110] gnu: Add go-github-com-hashicorp-hcl. * gnu/packages/golang.scm (go-github-com-hashicorp-hcl): New variable. --- gnu/packages/golang.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 92e612d34b..e0ce1032f7 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -664,3 +664,30 @@ program's help message rather than specifying it programatically with command-line parsers.") (home-page "https://github.com/tj/docopt") (license license:expat))) + +(define-public go-github-com-hashicorp-hcl + (let ((commit "23c074d0eceb2b8a5bfdbb271ab780cde70f05a8") + (revision "0")) + (package + (name "go-github-com-hashicorp-hcl") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hashicorp/hcl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0db4lpqb5m130rmfy3s3gjjf4dxllypmyrzxv6ggqhkmwmc7w4mc")))) + (build-system go-build-system) + (arguments + '(#:tests? #f + #:import-path "github.com/hashicorp/hcl")) + (synopsis "Go implementation of HashiCorp Configuration Language") + (description + "This package contains the main implementation of the @acronym{HCL, +HashiCorp Configuration Language}. HCL is designed to be a language for +expressing configuration which is easy for both humans and machines to read.") + (home-page "https://github.com/hashicorp/hcl") + (license license:mpl2.0)))) From be5ed142135e939cd23fcfe88c553fd28b32ac53 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 25 Feb 2018 14:30:46 +0000 Subject: [PATCH 044/110] gnu: Add terraform-docs. * gnu/packages/terraform.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/terraform.scm | 52 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 gnu/packages/terraform.scm diff --git a/gnu/local.mk b/gnu/local.mk index f27565bb29..dfb3073d7a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -411,6 +411,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/tcl.scm \ %D%/packages/telephony.scm \ %D%/packages/terminals.scm \ + %D%/packages/terraform.scm \ %D%/packages/texinfo.scm \ %D%/packages/tex.scm \ %D%/packages/textutils.scm \ diff --git a/gnu/packages/terraform.scm b/gnu/packages/terraform.scm new file mode 100644 index 0000000000..71b214ed0a --- /dev/null +++ b/gnu/packages/terraform.scm @@ -0,0 +1,52 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Christopher Baines +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages terraform) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system go) + #:use-module (gnu packages golang)) + +(define-public terraform-docs + (package + (name "terraform-docs") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/segmentio/terraform-docs") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xchpik32ab8m89s6jv671vswg8xhprfvh6s5md0zd36482d2nmm")))) + (build-system go-build-system) + (native-inputs + `(("go-github-com-hashicorp-hcl" ,go-github-com-hashicorp-hcl) + ("go-github-com-tj-docopt" ,go-github-com-tj-docopt))) + (arguments + '(#:import-path "github.com/segmentio/terraform-docs")) + (synopsis "Generate documentation from Terraform modules") + (description + "The @code{terraform-docs} utility can generate documentation describing +the inputs and outputs for modules of the Terraform infrastructure management +tool. These can be shown, or written to a file in JSON or Markdown formats.") + (home-page "https://github.com/segmentio/terraform-docs") + (license license:expat))) From cc4c8a576c55e8b9998538cf7c0510db2f2b982f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sat, 17 Mar 2018 21:24:57 -0400 Subject: [PATCH 045/110] gnu: icecat: Fix CVE-2018-{5146,5147}, etc. Includes fixes for CVE-2018-5146 and CVE-2018-5147. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository. --- gnu/packages/gnuzilla.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index f7bdd17309..87381ba196 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -445,7 +445,10 @@ security standards.") (mozilla-patch "icecat-bug-1442127-pt2.patch" "da5792b70f30" "116k9qja5ir9b3laazasp43f5jx59qq72nknmq5bn5v1ixya9r4l") (mozilla-patch "icecat-CVE-2018-5125-pt8.patch" "62b831df8269" "109pn0hqn7s27580glv4z7qv1pmjzii9szvf3wkn97k5wybrzgkx") (mozilla-patch "icecat-bug-1442504.patch" "8954ce68a364" "0bl65zw82bwqg0mmcri94pxqq6ibff7y5rclkzapb081p6yvf73q") - (mozilla-patch "icecat-CVE-2018-5125-pt9.patch" "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb"))) + (mozilla-patch "icecat-CVE-2018-5125-pt9.patch" "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb") + (mozilla-patch "icecat-bug-1426603.patch" "ca0b92ecedee" "0dc3mdl4a3hrq4j384zjavf3splj6blv4masign710hk7svlgbhq") + (mozilla-patch "icecat-CVE-2018-5146.patch" "494e5d5278ba" "1yb4lxjw499ppwhk31vz0vzl0cfqvj9d4jwqag7ayj53ybwsqgjr") + (mozilla-patch "icecat-CVE-2018-5147.patch" "5cd5586a2f48" "10s774pwvj6xfk3kk6ivnhp2acc8x9sqq6na8z47nkhgwl2712i5"))) (modules '((guix build utils))) (snippet '(begin From 63e07468b372e82d86087db6495ef3e1527ccb7c Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 31 Dec 2015 22:46:49 +1000 Subject: [PATCH 046/110] gnu: Add ruby-asciimath. * gnu/packages/maths.scm (ruby-asciimath): New variable. --- gnu/packages/maths.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 64fe13b9bc..51fe119712 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -53,6 +53,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system ocaml) #:use-module (guix build-system r) + #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages bison) @@ -97,6 +98,7 @@ #:use-module (gnu packages python-web) #:use-module (gnu packages qt) #:use-module (gnu packages readline) + #:use-module (gnu packages ruby) #:use-module (gnu packages tbb) #:use-module (gnu packages scheme) #:use-module (gnu packages shells) @@ -1940,6 +1942,38 @@ special functions. It uses Matlab function names where appropriate to simplify porting.") (license license:gpl3+))) +(define-public ruby-asciimath + (package + (name "ruby-asciimath") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "asciimath" version)) + (sha256 + (base32 + "1d80kiph5mc78zps7si1hv48kv4k12mzaq8jk5kb3pqpjdr72qmc")))) + (build-system ruby-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; Apply this patch + ;; https://github.com/asciidoctor/asciimath/commit/1c06fdc8086077f4785479f78b0823a4a72d7948 + (add-after 'unpack 'patch-remove-spurious-backslashes + (lambda _ + (substitute* "spec/parser_spec.rb" + (("\\\\\"") + "\""))))))) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rspec" ,ruby-rspec))) + (synopsis "AsciiMath parsing and conversion library") + (description + "A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an +easy-to-write markup language for mathematics.") + (home-page "https://github.com/asciidoctor/asciimath") + (license license:expat))) + (define-public superlu (package (name "superlu") From 34138e42ba69fa77eb6d9221a7441fa52c4d9259 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 31 Dec 2015 23:08:21 +1000 Subject: [PATCH 047/110] gnu: Add ruby-asciidoctor. * gnu/packages/ruby.scm (ruby-asciidoctor): New variable. --- gnu/packages/ruby.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index ee5d20955c..dc2ef251de 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages java) #:use-module (gnu packages libffi) + #:use-module (gnu packages maths) #:use-module (gnu packages networking) #:use-module (gnu packages python) #:use-module (gnu packages ragel) @@ -665,6 +666,41 @@ line of code.") ;; of the Expat license. (license license:bsd-3))) +(define-public ruby-asciidoctor + (package + (name "ruby-asciidoctor") + (version "1.5.6.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "asciidoctor" version)) + (sha256 + (base32 + "1jnf9y8q5asfdzilp8vcqafrc2faj719df4yh1993mh6jd0iqdy4")))) + (build-system ruby-build-system) + (arguments + `(#:test-target "test:all" + #:phases + (modify-phases %standard-phases + (add-before 'check 'remove-circular-tests + (lambda _ + ;; Remove tests that require circular dependencies to load or pass. + (delete-file "test/invoker_test.rb") + (delete-file "test/converter_test.rb") + (delete-file "test/options_test.rb") + #t))))) + (native-inputs + `(("ruby-minitest" ,ruby-minitest) + ("ruby-nokogiri" ,ruby-nokogiri) + ("ruby-asciimath" ,ruby-asciimath) + ("ruby-coderay" ,ruby-coderay))) + (synopsis "Converter from AsciiDoc content to other formats") + (description + "Asciidoctor is a text processor and publishing toolchain for converting +AsciiDoc content to HTML5, DocBook 5 (or 4.5) and other formats.") + (home-page "http://asciidoctor.org") + (license license:expat))) + (define-public ruby-ci-reporter (package (name "ruby-ci-reporter") From 20a0f80414cc953c2a3836ded012841febd74927 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 31 Dec 2015 23:24:54 +1000 Subject: [PATCH 048/110] gnu: Add ruby-rack-test. * gnu/packages/ruby.scm (ruby-rack-test): New variable. --- gnu/packages/ruby.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index dc2ef251de..31e2e0f9eb 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3329,6 +3329,37 @@ into a single method call.") (home-page "https://rack.github.io/") (license license:expat))) +(define-public ruby-rack-test + (package + (name "ruby-rack-test") + (version "0.8.3") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "rack-test" version)) + (sha256 + (base32 + "14ij39zywvr1i9f6jsixfg4zxi2q1m1n1nydvf47f0b6sfc9mv1g")))) + (build-system ruby-build-system) + (arguments + ;; Disable tests because of circular dependencies: requires sinatra, + ;; which requires rack-protection, which requires rack-test. Instead + ;; simply require the library. + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "ruby" "-Ilib" "-r" "rack/test")))))) + (propagated-inputs + `(("ruby-rack" ,ruby-rack))) + (synopsis "Testing API for Rack applications") + (description + "Rack::Test is a small, simple testing API for Rack applications. It can +be used on its own or as a reusable starting point for Web frameworks and +testing libraries to build on.") + (home-page "https://github.com/rack-test/rack-test") + (license license:expat))) + (define-public ruby-docile (package (name "ruby-docile") From a0a7e6903ac7e6e3fb9deb3977770246f0b31dd7 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 31 Dec 2015 23:29:09 +1000 Subject: [PATCH 049/110] gnu: Add ruby-rack-protection. * gnu/packages/ruby.scm (ruby-rack-protection): New variable. --- gnu/packages/ruby.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 31e2e0f9eb..9de6a1016c 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3360,6 +3360,35 @@ testing libraries to build on.") (home-page "https://github.com/rack-test/rack-test") (license license:expat))) +(define-public ruby-rack-protection + (package + (name "ruby-rack-protection") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "rack-protection" version)) + (sha256 + (base32 + "0ywmgh7x8ljf7jfnq5hmfzki3f803waji3fcvi107w7mlyflbng7")))) + (build-system ruby-build-system) + (arguments + '(;; Tests missing from the gem + #:tests? #f)) + (propagated-inputs + `(("ruby-rack" ,ruby-rack))) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rspec" ,ruby-rspec-2) + ("ruby-rack-test" ,ruby-rack-test))) + (synopsis "Rack middleware that protects against typical web attacks") + (description "Rack middleware that can be used to protect against typical +web attacks. It can protect all Rack apps, including Rails. For instance, it +protects against cross site request forgery, cross site scripting, +clickjacking, directory traversal, session hijacking and IP spoofing.") + (home-page "https://github.com/sinatra/sinatra/tree/master/rack-protection") + (license license:expat))) + (define-public ruby-docile (package (name "ruby-docile") From 6ef85256070158b03f9c080880dc33919c46756d Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 1 Jan 2016 10:11:36 +1000 Subject: [PATCH 050/110] gnu: Add ruby-contest. * gnu/packages/ruby.scm (ruby-contest): New variable. --- gnu/packages/ruby.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 9de6a1016c..ded5645835 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3389,6 +3389,25 @@ clickjacking, directory traversal, session hijacking and IP spoofing.") (home-page "https://github.com/sinatra/sinatra/tree/master/rack-protection") (license license:expat))) +(define-public ruby-contest + (package + (name "ruby-contest") + (version "0.1.3") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "contest" version)) + (sha256 + (base32 + "1p9f2292b7b0fbrcjswvj9v01z7ig5ig52328wyqcabgb553qsdf")))) + (build-system ruby-build-system) + (synopsis "Write declarative tests using nested contexts") + (description + "Contest allows writing declarative @code{Test::Unit} tests using nested +contexts without performance penalties.") + (home-page "https://github.com/citrusbyte/contest") + (license license:expat))) + (define-public ruby-docile (package (name "ruby-docile") From c4550f7568ad2c1d6fede9a0f037ae9505b9f2f2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 1 Jan 2016 10:14:21 +1000 Subject: [PATCH 051/110] gnu: Add ruby-creole. * gnu/packages/ruby.scm (ruby-creole): New variable. --- gnu/packages/ruby.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index ded5645835..28b9bc370c 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3408,6 +3408,27 @@ contexts without performance penalties.") (home-page "https://github.com/citrusbyte/contest") (license license:expat))) +(define-public ruby-creole + (package + (name "ruby-creole") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "creole" version)) + (sha256 + (base32 + "00rcscz16idp6dx0dk5yi5i0fz593i3r6anbn5bg2q07v3i025wm")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-bacon" ,ruby-bacon))) + (synopsis "Creole markup language converter") + (description + "Creole is a lightweight markup language and this library for converting +creole to @code{HTML}.") + (home-page "https://github.com/minad/creole") + (license license:ruby))) + (define-public ruby-docile (package (name "ruby-docile") From b88502c95c15db3318587d263adebb87e863dc6f Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 1 Jan 2016 00:12:06 +1000 Subject: [PATCH 052/110] gnu: Add ruby-sporkmonger-rack-mount. * gnu/packages/ruby.scm (ruby-sporkmonger-rack-mount): New variable. --- gnu/packages/ruby.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 28b9bc370c..e4b4b96429 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -701,6 +701,37 @@ AsciiDoc content to HTML5, DocBook 5 (or 4.5) and other formats.") (home-page "http://asciidoctor.org") (license license:expat))) +(define-public ruby-sporkmonger-rack-mount + ;; Testing the addressable gem requires a newer commit than that released, so + ;; use an up to date version. + (let ((revision "1") + (commit "076aa2c47d9a4c081f1e9bcb56a826a9e72bd5c3")) + (package + (name "ruby-sporkmonger-rack-mount") + (version (git-version "0.8.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sporkmonger/rack-mount.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1scx273g3xd93424x9lxc4zyvcp2niknbw5mkz6wkivpf7xsyxdq")))) + (build-system ruby-build-system) + (arguments + ;; Tests currently fail so disable them. + ;; https://github.com/sporkmonger/rack-mount/pull/1 + `(#:tests? #f)) + (propagated-inputs `(("ruby-rack" ,ruby-rack))) + (synopsis "Stackable dynamic tree based Rack router") + (description + "@code{Rack::Mount} supports Rack's @code{X-Cascade} convention to +continue trying routes if the response returns pass. This allows multiple +routes to be nested or stacked on top of each other.") + (home-page "https://github.com/sporkmonger/rack-mount") + (license license:expat)))) + (define-public ruby-ci-reporter (package (name "ruby-ci-reporter") From d64ebebd8e91688d1f86fff72c7a133b4be09921 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 23 Dec 2015 11:42:15 +1000 Subject: [PATCH 053/110] gnu: Add ruby-erubis. * gnu/packages/ruby.scm (ruby-erubis): New variable. --- gnu/packages/ruby.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index e4b4b96429..4131529afe 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -891,6 +891,29 @@ functions.") (home-page "https://github.com/ahoward/options") (license license:ruby))) +(define-public ruby-erubis + (package + (name "ruby-erubis") + (version "2.7.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "erubis" version)) + (sha256 + (base32 + "1fj827xqjs91yqsydf0zmfyw9p4l2jz5yikg3mppz6d7fi8kyrb3")))) + (build-system ruby-build-system) + (arguments + '(#:tests? #f)) ; tests do not run properly with Ruby 2.0 + (synopsis "Implementation of embedded Ruby (eRuby)") + (description + "Erubis is a fast implementation of embedded Ruby (eRuby) with several +features such as multi-language support, auto escaping, auto trimming spaces +around @code{<% %>}, a changeable embedded pattern, and Ruby on Rails +support.") + (home-page "http://www.kuwata-lab.com/erubis/") + (license license:expat))) + (define-public ruby-orderedhash (package (name "ruby-orderedhash") From 670ee20a57a4417f34458bb489f717378077e2ae Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 5 Feb 2018 11:45:21 +0100 Subject: [PATCH 054/110] gnu: Add ruby-rake. * gnu/packages/ruby.scm (ruby-rake): New variable. --- gnu/packages/ruby.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 4131529afe..703ca37aa0 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -4911,3 +4911,24 @@ thing this library does today is convert org-mode files to HTML or Textile or Markdown.") (home-page "https://github.com/wallyqs/org-ruby") (license license:expat))) + +(define-public ruby-rake + (package + (name "ruby-rake") + (version "12.3.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "rake" version)) + (sha256 + (base32 + "190p7cs8zdn07mjj6xwwsdna3g0r98zs4crz7jh2j2q5b0nbxgjf")))) + (build-system ruby-build-system) + (native-inputs + `(("bundler" ,bundler))) + (synopsis "Rake is a Make-like program implemented in Ruby") + (description + "Rake is a Make-like program where tasks and dependencies are specified +in standard Ruby syntax.") + (home-page "https://github.com/ruby/rake") + (license license:expat))) From e218b0c8b39b5f1560ac0401181d4209ffe93119 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 30 Dec 2015 16:51:18 +1000 Subject: [PATCH 055/110] gnu: Add ruby-ruby-engine. * gnu/packages/ruby.scm (ruby-ruby-engine): New variable. --- gnu/packages/ruby.scm | 49 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 703ca37aa0..dcf4cda26a 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3716,6 +3716,55 @@ used to create both network servers and clients.") (home-page "http://rubyeventmachine.com") (license (list license:ruby license:gpl3)))) ; GPLv3 only AFAICT +(define-public ruby-ruby-engine + (package + (name "ruby-ruby-engine") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "ruby_engine" version)) + (sha256 + (base32 + "1d0sd4q50zkcqhr395wj1wpn2ql52r0fpwhzjfvi1bljml7k546v")))) + (build-system ruby-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'check 'clean-up + (lambda _ + (delete-file "Gemfile.lock") + (substitute* "ruby_engine.gemspec" + ;; Remove unnecessary imports that would entail further + ;; dependencies. + ((".*.freeze, \\[\\\"~> 10.0\\\"\\]") + "%q.freeze, [\">= 10.0\"]") + ;; Soften the rspec dependency + (("%q.freeze, \\[\\\"~> 2.4\\\"\\]") + "%q.freeze, [\">= 2.4\"]")) + (substitute* "Rakefile" + (("require 'rubygems/tasks'") "") + (("Gem::Tasks.new") "")) + ;; Remove extraneous .gem file that otherwise gets installed. + (delete-file "pkg/ruby_engine-1.0.0.gem") + #t))))) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rake" ,ruby-rake) + ("ruby-rspec" ,ruby-rspec))) + (synopsis "Simplifies checking for Ruby implementation") + (description + "@code{ruby_engine} provides an RubyEngine class that can be used to +check which implementation of Ruby is in use. It can provide the interpreter +name and provides query methods such as @{RubyEngine.mri?}.") + (home-page "https://github.com/janlelis/ruby_engine") + (license license:expat))) + (define-public ruby-turn (package (name "ruby-turn") From 72406062b9c3cdb6e9e30266f3cc31d0b2116b68 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sun, 18 Mar 2018 10:35:23 +0000 Subject: [PATCH 056/110] gnu: shotwell: Update to 0.28.0. * gnu/packages/gnome.scm (shotwell): Update to 0.28.0. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 8ce36430ee..5eea29e0b2 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4422,7 +4422,7 @@ metadata in photo and video files of various formats.") (define-public shotwell (package (name "shotwell") - (version "0.27.4") + (version "0.28.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4430,7 +4430,7 @@ metadata in photo and video files of various formats.") name "-" version ".tar.xz")) (sha256 (base32 - "0g2vphhpxrljpy9sryfsgaayix807i1i9plj9bay72dk0zphqab2")))) + "1d797nmlz9gs6ri0h65b76s40ss6ma6h6405xqx03lhg5xni3kmg")))) (build-system glib-or-gtk-build-system) (propagated-inputs `(("dconf" ,dconf))) From 14f2105dc663fcd4148b98ebd8278544f5e1813e Mon Sep 17 00:00:00 2001 From: Sohom Bhattacharjee Date: Sun, 18 Mar 2018 17:52:22 +0530 Subject: [PATCH 057/110] gnu: youtube-dl: Update to 2018.03.14. * gnu/packages/video.scm (youtube-dl): Update to 2018.03.14. Signed-off-by: Ricardo Wurmus --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 39354f93ed..5a478c5804 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1158,7 +1158,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2018.03.10") + (version "2018.03.14") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1166,7 +1166,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "1ibmz91anli1vzkgw2i3h4wf1i8arzd74730ylwcwyg3375xryjb")))) + "0j8j797gqc29fd5ra3cjvwkp8dgvigdydsj0zzjs05zccfqrj9lh")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion From e5425ed950d06f8e75697b7e8562f71704094453 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Mar 2018 22:25:54 +0100 Subject: [PATCH 058/110] import: elpa: Adjust test for HTTPS URLs. This is a followup to 44dd3d579db3aa467e41d0b431029e46cae8e12d. * tests/elpa.scm (eval-test-with-elpa): Use https. --- tests/elpa.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/elpa.scm b/tests/elpa.scm index 46c6ac2d75..e6d53c892e 100644 --- a/tests/elpa.scm +++ b/tests/elpa.scm @@ -89,7 +89,7 @@ information about package NAME. (Function 'elpa-package-info'.)" ('origin ('method 'url-fetch) ('uri ('string-append - "http://elpa.gnu.org/packages/auctex-" 'version ".tar")) + "https://elpa.gnu.org/packages/auctex-" 'version ".tar")) ('sha256 ('base32 (? string? hash))))) ('build-system 'emacs-build-system) ('home-page "http://www.gnu.org/software/auctex/") From 9bb1838c3f982dfb84ba24eb2f727cb39ee5805c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Mar 2018 22:26:34 +0100 Subject: [PATCH 059/110] import: elpa: Return 'license:gpl3+ for ELPA only. Fixes . Reported by Konrad Hinsen . * guix/import/elpa.scm (elpa-package->sexp): Add LICENSE parameter and honor it. (elpa->guix-package): Pass 'license:gpl3+ only when REPO is 'gnu. --- guix/import/elpa.scm | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/guix/import/elpa.scm b/guix/import/elpa.scm index 5d3d04ee7c..43e9eb60c9 100644 --- a/guix/import/elpa.scm +++ b/guix/import/elpa.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Federico Beffa -;;; Copyright © 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2015, 2016, 2017, 2018 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -190,7 +190,7 @@ include VERSION." url))) (_ #f)))) -(define* (elpa-package->sexp pkg) +(define* (elpa-package->sexp pkg #:optional license) "Return the `package' S-expression for the Emacs package PKG, a record of type ''." @@ -234,12 +234,17 @@ type ''." (home-page ,(elpa-package-home-page pkg)) (synopsis ,(elpa-package-synopsis pkg)) (description ,(elpa-package-description pkg)) - (license license:gpl3+)))) + (license ,license)))) (define* (elpa->guix-package name #:optional (repo 'gnu)) "Fetch the package NAME from REPO and produce a Guix package S-expression." - (let ((pkg (fetch-elpa-package name repo))) - (and=> pkg elpa-package->sexp))) + (match (fetch-elpa-package name repo) + (#f #f) + (package + ;; ELPA is known to contain only GPLv3+ code. Other repos may contain + ;; code under other license but there's no license metadata. + (let ((license (and (eq? 'gnu repo) 'license:gpl3+))) + (elpa-package->sexp package license))))) ;;; From 17cdd3d0fe1987d0272f2c3496123be1ef772d6b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Mar 2018 22:33:41 +0100 Subject: [PATCH 060/110] tests: elpa: Don't actually download files. * tests/elpa.scm (eval-test-with-elpa): Mock 'url-fetch'. --- tests/elpa.scm | 43 +++++++++++++++++++++++++------------------ 1 file changed, 25 insertions(+), 18 deletions(-) diff --git a/tests/elpa.scm b/tests/elpa.scm index e6d53c892e..44e3914f2e 100644 --- a/tests/elpa.scm +++ b/tests/elpa.scm @@ -81,24 +81,31 @@ information about package NAME. (Function 'elpa-package-info'.)" auctex-readme-mock url))) (_ #f))))) - (match (elpa->guix-package pkg) - (('package - ('name "emacs-auctex") - ('version "11.88.6") - ('source - ('origin - ('method 'url-fetch) - ('uri ('string-append - "https://elpa.gnu.org/packages/auctex-" 'version ".tar")) - ('sha256 ('base32 (? string? hash))))) - ('build-system 'emacs-build-system) - ('home-page "http://www.gnu.org/software/auctex/") - ('synopsis "Integrated environment for *TeX*") - ('description (? string?)) - ('license 'license:gpl3+)) - #t) - (x - (pk 'fail x #f))))) + (mock + ((guix build download) url-fetch + (lambda (url file . _) + (call-with-output-file file + (lambda (port) + (display "fake tarball" port))))) + + (match (elpa->guix-package pkg) + (('package + ('name "emacs-auctex") + ('version "11.88.6") + ('source + ('origin + ('method 'url-fetch) + ('uri ('string-append + "https://elpa.gnu.org/packages/auctex-" 'version ".tar")) + ('sha256 ('base32 (? string? hash))))) + ('build-system 'emacs-build-system) + ('home-page "http://www.gnu.org/software/auctex/") + ('synopsis "Integrated environment for *TeX*") + ('description (? string?)) + ('license 'license:gpl3+)) + #t) + (x + (pk 'fail x #f)))))) (test-assert "elpa->guix-package test 1" (eval-test-with-elpa "auctex")) From 248db51c7ee2ef68653fbfe34b17d1cc905e10a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 14 Mar 2018 10:51:32 +0100 Subject: [PATCH 061/110] vm: Display a backtrace upon error by default. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass #:on-error to 'base-initrd'. --- gnu/system/vm.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index ae8780d2e1..594ba66ff4 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -144,6 +144,7 @@ made available under the /xchg CIFS share." (initrd (if initrd ; use the default initrd? (return initrd) (base-initrd %linux-vm-file-systems + #:on-error 'backtrace #:linux linux #:linux-modules %base-initrd-modules #:qemu-networking? #t)))) From a57df67b5932c7f458d4a31a82a477634d6af1a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 14 Mar 2018 23:09:57 +0100 Subject: [PATCH 062/110] linux-modules: Add 'current-kernel-directory'. * gnu/build/linux-modules.scm (current-kernel-directory): New procedure. (current-alias-file): Use it. --- gnu/build/linux-modules.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index 4fe673cca2..3dd60f434f 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -357,12 +357,15 @@ and each module is a module name like \"snd_hda_intel\"." (() ;empty line (loop aliases))))))) -(define (current-alias-file) - "Return the absolute file name of the default 'modules.alias' file." +(define (current-kernel-directory) + "Return the directory of the currently running Linux kernel." (string-append (or (getenv "LINUX_MODULE_DIRECTORY") "/run/booted-system/kernel/lib/modules") - "/" (utsname:release (uname)) - "/" "modules.alias")) + "/" (utsname:release (uname)))) + +(define (current-alias-file) + "Return the absolute file name of the default 'modules.alias' file." + (string-append (current-kernel-directory) "/modules.alias")) (define* (known-module-aliases #:optional (alias-file (current-alias-file))) "Return the list of alias/module pairs read from ALIAS-FILE. Each alias is From 675e81a082b47aec7b3c2caa950953edb7c01c1e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Mar 2018 18:26:12 +0100 Subject: [PATCH 063/110] linux-modules: 'load-linux-module*' honors BLACK-LIST in recursive calls. * gnu/build/linux-modules.scm (load-linux-module*): Pass BLACK-LIST in recursive call. --- gnu/build/linux-modules.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index 3dd60f434f..e97c9c95f1 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -206,7 +206,9 @@ appears in BLACK-LIST are not loaded." (define (load-dependencies file) (let ((dependencies (module-dependencies file))) - (every (cut load-linux-module* <> #:lookup-module lookup-module) + (every (cut load-linux-module* <> + #:lookup-module lookup-module + #:black-list black-list) (map lookup-module dependencies)))) (and (not (black-listed? (file-name->module-name file))) From e914b398af11f909e88a8bc85eeebb0768aacd54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 16 Mar 2018 23:35:07 +0100 Subject: [PATCH 064/110] glob: Support square brackets in patterns. * guix/glob.scm (wildcard-indices): Remove. (parse-bracket): New procedure. (compile-glob-pattern): Rewrite. Support square brackets for sets and ranges. (glob-match?): Support sets and ranges. * tests/glob.scm (test-compile-glob-pattern) (test-glob-match): New macros. Use them to rewrite the existing tests, and add new tests. --- guix/glob.scm | 95 +++++++++++++++++++++++++++++++------------------- tests/glob.scm | 67 ++++++++++++++++++++--------------- 2 files changed, 99 insertions(+), 63 deletions(-) diff --git a/guix/glob.scm b/guix/glob.scm index 4fc5173ac0..29c335ca1d 100644 --- a/guix/glob.scm +++ b/guix/glob.scm @@ -25,20 +25,17 @@ ;;; ;;; This is a minimal implementation of "glob patterns" (info "(libc) ;;; Globbbing"). It is currently limited to simple patterns and does not -;;; support braces and square brackets, for instance. +;;; support braces, for instance. ;;; ;;; Code: -(define (wildcard-indices str) - "Return the list of indices in STR where wildcards can be found." - (let loop ((index 0) - (result '())) - (if (= index (string-length str)) - (reverse result) - (loop (+ 1 index) - (case (string-ref str index) - ((#\? #\*) (cons index result)) - (else result)))))) +(define (parse-bracket chars) + "Parse CHARS, a list of characters that extracted from a '[...]' sequence." + (match chars + ((start #\- end) + `(range ,start ,end)) + (lst + `(set ,@lst)))) (define (compile-glob-pattern str) "Return an sexp that represents the compiled form of STR, a glob pattern @@ -48,29 +45,43 @@ such as \"foo*\" or \"foo??bar\"." (((? string? str)) str) (x x))) - (let loop ((index 0) - (indices (wildcard-indices str)) + (define (cons-string chars lst) + (match chars + (() lst) + (_ (cons (list->string (reverse chars)) lst)))) + + (let loop ((chars (string->list str)) + (pending '()) + (brackets 0) (result '())) - (match indices + (match chars (() - (flatten (cond ((zero? index) - (list str)) - ((= index (string-length str)) - (reverse result)) - (else - (reverse (cons (string-drop str index) - result)))))) - ((wildcard-index . rest) - (let ((wildcard (match (string-ref str wildcard-index) + (flatten (reverse (if (null? pending) + result + (cons-string pending result))))) + (((and chr (or #\? #\*)) . rest) + (let ((wildcard (match chr (#\? '?) (#\* '*)))) - (match (substring str index wildcard-index) - ("" (loop (+ 1 wildcard-index) - rest - (cons wildcard result))) - (str (loop (+ 1 wildcard-index) - rest - (cons* wildcard str result))))))))) + (if (zero? brackets) + (loop rest '() 0 + (cons* wildcard (cons-string pending result))) + (loop rest (cons chr pending) brackets result)))) + ((#\[ . rest) + (if (zero? brackets) + (loop rest '() (+ 1 brackets) + (cons-string pending result)) + (loop rest (cons #\[ pending) (+ 1 brackets) result))) + ((#\] . rest) + (cond ((zero? brackets) + (error "unexpected closing bracket" str)) + ((= 1 brackets) + (loop rest '() 0 + (cons (parse-bracket (reverse pending)) result))) + (else + (loop rest (cons #\] pending) (- brackets 1) result)))) + ((chr . rest) + (loop rest (cons chr pending) brackets result))))) (define (glob-match? pattern str) "Return true if STR matches PATTERN, a compiled glob pattern as returned by @@ -78,11 +89,12 @@ such as \"foo*\" or \"foo??bar\"." (let loop ((pattern pattern) (str str)) (match pattern - ((? string? literal) (string=? literal str)) - (((? string? one)) (string=? one str)) - (('*) #t) - (('?) (= 1 (string-length str))) - (() #t) + ((? string? literal) + (string=? literal str)) + (() + (string-null? str)) + (('*) + #t) (('* suffix . rest) (match (string-contains str suffix) (#f #f) @@ -92,6 +104,19 @@ such as \"foo*\" or \"foo??bar\"." (('? . rest) (and (>= (string-length str) 1) (loop rest (string-drop str 1)))) + ((('range start end) . rest) + (and (>= (string-length str) 1) + (let ((chr (string-ref str 0))) + (and (char-set-contains? (ucs-range->char-set + (char->integer start) + (+ 1 (char->integer end))) + chr) + (loop rest (string-drop str 1)))))) + ((('set . chars) . rest) + (and (>= (string-length str) 1) + (let ((chr (string-ref str 0))) + (and (char-set-contains? (list->char-set chars) chr) + (loop rest (string-drop str 1)))))) ((prefix . rest) (and (string-prefix? prefix str) (loop rest (string-drop str (string-length prefix)))))))) diff --git a/tests/glob.scm b/tests/glob.scm index 033eeb10fe..71e2d3fce0 100644 --- a/tests/glob.scm +++ b/tests/glob.scm @@ -23,36 +23,47 @@ (test-begin "glob") -(test-equal "compile-glob-pattern, no wildcards" - "foo" - (compile-glob-pattern "foo")) +(define-syntax test-compile-glob-pattern + (syntax-rules (=>) + ((_ pattern => result rest ...) + (begin + (test-equal (format #f "compile-glob-pattern, ~s" pattern) + result + (compile-glob-pattern pattern)) + (test-compile-glob-pattern rest ...))) + ((_) + #t))) -(test-equal "compile-glob-pattern, Kleene star" - '("foo" * "bar") - (compile-glob-pattern "foo*bar")) +(define-syntax test-glob-match + (syntax-rules (matches and not) + ((_ (pattern-string matches strings ... (and not others ...)) rest ...) + (begin + (test-assert (format #f "glob-match? ~s" pattern-string) + (let ((pattern (compile-glob-pattern pattern-string))) + (and (glob-match? pattern strings) ... + (not (glob-match? pattern others)) ...))) + (test-glob-match rest ...))) + ((_) + #t))) -(test-equal "compile-glob-pattern, question mark" - '(? "foo" *) - (compile-glob-pattern "?foo*")) +(test-compile-glob-pattern + "foo" => "foo" + "?foo*" => '(? "foo" *) + "foo[1-5]" => '("foo" (range #\1 #\5)) + "foo[abc]bar" => '("foo" (set #\a #\b #\c) "bar") + "foo[a[b]c]bar" => '("foo" (set #\a #\[ #\b #\] #\c) "bar") + "[123]x" => '((set #\1 #\2 #\3) "x") + "[a-z]" => '((range #\a #\z))) -(test-assert "literal match" - (let ((pattern (compile-glob-pattern "foo"))) - (and (glob-match? pattern "foo") - (not (glob-match? pattern "foobar")) - (not (glob-match? pattern "barfoo"))))) - -(test-assert "trailing star" - (let ((pattern (compile-glob-pattern "foo*"))) - (and (glob-match? pattern "foo") - (glob-match? pattern "foobar") - (not (glob-match? pattern "xfoo"))))) - -(test-assert "question marks" - (let ((pattern (compile-glob-pattern "foo??bar"))) - (and (glob-match? pattern "fooxxbar") - (glob-match? pattern "fooZZbar") - (not (glob-match? pattern "foobar")) - (not (glob-match? pattern "fooxxxbar")) - (not (glob-match? pattern "fooxxbarzz"))))) +(test-glob-match + ("foo" matches "foo" (and not "foobar" "barfoo")) + ("foo*" matches "foo" "foobar" (and not "xfoo")) + ("foo??bar" matches "fooxxbar" "fooZZbar" + (and not "foobar" "fooxxxbar" "fooxxbarzz")) + ("foo?" matches "foox" (and not "fooxx")) + ("ab[0-9]c" matches "ab0c" "ab7c" "ab9c" + (and not "ab-c" "ab00c" "ab3")) + ("ab[cdefg]" matches "abc" "abd" "abg" + (and not "abh" "abcd" "ab["))) (test-end "glob") From 71e08fde28fa335bdba2ec2150fd6663390bba5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sun, 18 Mar 2018 22:54:34 +0100 Subject: [PATCH 065/110] glob: Add an extra glob pattern compilation stage. * guix/glob.scm (compile-glob-pattern): Rename to... (string->sglob): ... this. (compile-sglob, string->compiled-sglob): New procedures. (glob-match?): Replace '?, 'range, and 'set with a single clause. * tests/glob.scm (test-compile-glob-pattern): Rename to... (test-string->sglob): ... this. Adjust accordingly. (test-glob-match): Use 'string->compiled-sglob' instead of 'compile-glob-pattern'. * gnu/build/linux-modules.scm (read-module-aliases): Use 'string->compiled-sglob' instead of 'compile-glob-pattern'. --- gnu/build/linux-modules.scm | 4 +-- guix/glob.scm | 51 ++++++++++++++++++++++++------------- tests/glob.scm | 12 ++++----- 3 files changed, 41 insertions(+), 26 deletions(-) diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index e97c9c95f1..87d2e98edf 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -329,7 +329,7 @@ The modules corresponding to these aliases can then be found using list of alias/module pairs where each alias is a glob pattern as like the result of: - (compile-glob-pattern \"scsi:t-0x01*\") + (string->compiled-sglob \"scsi:t-0x01*\") and each module is a module name like \"snd_hda_intel\"." (define (comment? str) @@ -354,7 +354,7 @@ and each module is a module name like \"snd_hda_intel\"." (line (match (tokenize line) (("alias" alias module) - (loop (alist-cons (compile-glob-pattern alias) module + (loop (alist-cons (string->compiled-sglob alias) module aliases))) (() ;empty line (loop aliases))))))) diff --git a/guix/glob.scm b/guix/glob.scm index 29c335ca1d..a9fc744802 100644 --- a/guix/glob.scm +++ b/guix/glob.scm @@ -18,7 +18,9 @@ (define-module (guix glob) #:use-module (ice-9 match) - #:export (compile-glob-pattern + #:export (string->sglob + compile-sglob + string->compiled-sglob glob-match?)) ;;; Commentary: @@ -37,9 +39,9 @@ (lst `(set ,@lst)))) -(define (compile-glob-pattern str) - "Return an sexp that represents the compiled form of STR, a glob pattern -such as \"foo*\" or \"foo??bar\"." +(define (string->sglob str) + "Return an sexp, called an \"sglob\", that represents the compiled form of +STR, a glob pattern such as \"foo*\" or \"foo??bar\"." (define flatten (match-lambda (((? string? str)) str) @@ -83,9 +85,33 @@ such as \"foo*\" or \"foo??bar\"." ((chr . rest) (loop rest (cons chr pending) brackets result))))) +(define (compile-sglob sglob) + "Compile SGLOB into a more efficient representation." + (if (string? sglob) + sglob + (let loop ((sglob sglob) + (result '())) + (match sglob + (() + (reverse result)) + (('? . rest) + (loop rest (cons char-set:full result))) + ((('range start end) . rest) + (loop rest (cons (ucs-range->char-set + (char->integer start) + (+ 1 (char->integer end))) + result))) + ((('set . chars) . rest) + (loop rest (cons (list->char-set chars) result))) + ((head . rest) + (loop rest (cons head result))))))) + +(define string->compiled-sglob + (compose compile-sglob string->sglob)) + (define (glob-match? pattern str) "Return true if STR matches PATTERN, a compiled glob pattern as returned by -'compile-glob-pattern'." +'compile-sglob'." (let loop ((pattern pattern) (str str)) (match pattern @@ -101,21 +127,10 @@ such as \"foo*\" or \"foo??bar\"." (index (loop rest (string-drop str (+ index (string-length suffix))))))) - (('? . rest) - (and (>= (string-length str) 1) - (loop rest (string-drop str 1)))) - ((('range start end) . rest) + (((? char-set? cs) . rest) (and (>= (string-length str) 1) (let ((chr (string-ref str 0))) - (and (char-set-contains? (ucs-range->char-set - (char->integer start) - (+ 1 (char->integer end))) - chr) - (loop rest (string-drop str 1)))))) - ((('set . chars) . rest) - (and (>= (string-length str) 1) - (let ((chr (string-ref str 0))) - (and (char-set-contains? (list->char-set chars) chr) + (and (char-set-contains? cs chr) (loop rest (string-drop str 1)))))) ((prefix . rest) (and (string-prefix? prefix str) diff --git a/tests/glob.scm b/tests/glob.scm index 71e2d3fce0..3134069789 100644 --- a/tests/glob.scm +++ b/tests/glob.scm @@ -23,14 +23,14 @@ (test-begin "glob") -(define-syntax test-compile-glob-pattern +(define-syntax test-string->sglob (syntax-rules (=>) ((_ pattern => result rest ...) (begin - (test-equal (format #f "compile-glob-pattern, ~s" pattern) + (test-equal (format #f "string->sglob, ~s" pattern) result - (compile-glob-pattern pattern)) - (test-compile-glob-pattern rest ...))) + (string->sglob pattern)) + (test-string->sglob rest ...))) ((_) #t))) @@ -39,14 +39,14 @@ ((_ (pattern-string matches strings ... (and not others ...)) rest ...) (begin (test-assert (format #f "glob-match? ~s" pattern-string) - (let ((pattern (compile-glob-pattern pattern-string))) + (let ((pattern (string->compiled-sglob pattern-string))) (and (glob-match? pattern strings) ... (not (glob-match? pattern others)) ...))) (test-glob-match rest ...))) ((_) #t))) -(test-compile-glob-pattern +(test-string->sglob "foo" => "foo" "?foo*" => '(? "foo" *) "foo[1-5]" => '("foo" (range #\1 #\5)) From 109b2f7c93f15a3ee9eb705584c384dcf13862f4 Mon Sep 17 00:00:00 2001 From: Vijayalakshmi Vedantham Date: Mon, 19 Mar 2018 00:39:05 +0530 Subject: [PATCH 066/110] gnu: Add r-abbyyr. * gnu/packages/cran.scm (r-abbyyr): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 717fa7fdfa..b54ddc6b55 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; Copyright © 2017 Raoul Bonnal +;;; Copyright © 2018 Vijayalakshmi Vedantham ;;; ;;; This file is part of GNU Guix. ;;; @@ -59,6 +60,36 @@ diversification and macroevolution, computing distances from DNA sequences, and several other tools.") (license license:gpl2+))) +(define-public r-abbyyr + (package + (name "r-abbyyr") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "abbyyR" version)) + (sha256 + (base32 + "1s8zf18sh0s89vk3dl09fzrq50csmmfvmsanf5vfkv9n5lx6pklg")))) + (properties `((upstream-name . "abbyyR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-httr" ,r-httr) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-readr" ,r-readr) + ("r-xml" ,r-xml))) + (home-page "https://github.com/soodoku/abbyyR") + (synopsis "Access to Abbyy Optical Character Recognition (OCR) API") + (description + "This package provides tools to get text from images of text using Abbyy +Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily +OCR images, barcodes, forms, documents with machine readable zones, e.g. +passports and get the results in a variety of formats including plain text and +XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.") + (license license:expat))) + (define-public r-colorspace (package (name "r-colorspace") From be95bcf0887dc7d90177fda20cab56c6e248dcfa Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Thu, 15 Mar 2018 23:25:01 -0500 Subject: [PATCH 067/110] git-download: Fix recursive checkouts. * guix/git-download.scm (git-fetch): Fix match on INPUTS, which may contain package outputs. --- guix/git-download.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/git-download.scm b/guix/git-download.scm index 731e549b38..33f102bc6c 100644 --- a/guix/git-download.scm +++ b/guix/git-download.scm @@ -109,7 +109,7 @@ HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f." ;; grep, etc. to be in $PATH. (set-path-environment-variable "PATH" '("bin") (match '#+inputs - (((names dirs) ...) + (((names dirs outputs ...) ...) dirs))) (or (git-fetch (getenv "git url") (getenv "git commit") From 8c6117ee2250f2629bc25fae84a7cfd837250780 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:43:06 +0100 Subject: [PATCH 068/110] gnu: Add ghc-pandoc-citeproc-with-pandoc-1. * gnu/packages/haskell.scm (ghc-pandoc-citeproc-with-pandoc-1): New variable. --- gnu/packages/haskell.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 9c59f56139..d00bbea7b5 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -6396,6 +6396,19 @@ and also has a mode for converting bibliographic databases a YAML format suitable for inclusion in pandoc YAML metadata.") (license license:bsd-3))) +(define-public ghc-pandoc-citeproc-with-pandoc-1 + (let ((for-pandoc-1 + (package-input-rewriting + `((,ghc-aeson . ,ghc-aeson-for-pandoc-1) + (,ghc-yaml . ,ghc-yaml-for-pandoc-1) + (,ghc-texmath . ,ghc-texmath-for-pandoc-1) + (,ghc-pandoc-types . ,ghc-pandoc-types-for-pandoc-1) + (,ghc-hslua . ,ghc-hslua-for-pandoc-1) + (,ghc-skylighting . ,ghc-skylighting-for-pandoc-1) + (,ghc-doctemplates . ,ghc-doctemplates-for-pandoc-1) + (,ghc-pandoc . ,ghc-pandoc-1))))) + (for-pandoc-1 ghc-pandoc-citeproc))) + (define-public ghc-union-find (package (name "ghc-union-find") From 1a29fc3ff95a6e5155607893a45e39ba75c1b806 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:43:28 +0100 Subject: [PATCH 069/110] gnu: pigx-rnaseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78754793a5..3672241aac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12720,8 +12720,8 @@ once. This package provides tools to perform Drop-seq analyses.") ("r-rtracklayer" ,r-rtracklayer) ("r-rjson" ,r-rjson) ("salmon" ,salmon) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml))) (home-page "http://bioinformatics.mdc-berlin.de/pigx/") From fd757a8f21252044f8180ed69de1cd82ef1857f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:44:32 +0100 Subject: [PATCH 070/110] gnu: pigx-chipseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3672241aac..59cd1bdee8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12778,8 +12778,8 @@ expression report comparing samples in an easily configurable manner.") ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) From 9dcb4d22a4ed004db02f4443b697caf5f29531e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:44:55 +0100 Subject: [PATCH 071/110] gnu: pigx-bsseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 59cd1bdee8..1c9965ac10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12845,8 +12845,8 @@ in an easily configurable manner.") ("r-bookdown" ,r-bookdown) ("r-ggplot2" ,r-ggplot2) ("r-ggbio" ,r-ggbio) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("snakemake" ,snakemake) From 2915221bcba0ee152b9d1910ec2462f2d5ebf8e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:45:17 +0100 Subject: [PATCH 072/110] gnu: pigx-scrnaseq: Use pandoc-1. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc with ghc-pandoc-1, and ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c9965ac10..91f5d617eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12903,8 +12903,8 @@ methylation and segmentation.") ("python-pandas" ,python-pandas) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) - ("ghc-pandoc" ,ghc-pandoc) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("ghc-pandoc" ,ghc-pandoc-1) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("snakemake" ,snakemake) ("star" ,star) ("r-minimal" ,r-minimal) From 32b7ccf9b4c490613395d5f8ad06334c797e47e0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 10:45:40 +0100 Subject: [PATCH 073/110] gnu: pigx-chipseq: Update to 0.0.8. * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8. [inputs]: Add python-magic, python-xlrd, and trim-galore. [arguments]: Disable tests. --- gnu/packages/bioinformatics.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 91f5d617eb..80f1437f22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12737,7 +12737,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.2") + (version "0.0.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12745,10 +12745,11 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5")))) + "1plw0bz0b7flj0g9irbn8n520005lmajkiq5flpizzapsl0a0r9g")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:tests? #f ; parts of the tests rely on access to the network + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-executable ;; Make sure the executable finds all R modules. @@ -12773,8 +12774,11 @@ expression report comparing samples in an easily configurable manner.") ("r-ggplot2" ,r-ggplot2) ("r-plotly" ,r-plotly) ("python-wrapper" ,python-wrapper) + ("python-magic" ,python-magic) ("python-pyyaml" ,python-pyyaml) + ("python-xlrd" ,python-xlrd) ("snakemake" ,snakemake) + ("trim-galore" ,trim-galore) ("macs" ,macs) ("multiqc" ,multiqc) ("perl" ,perl) From 9760061315e9a8966427b7eb593dcf86e6fec2ca Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 19 Mar 2018 14:21:20 +0200 Subject: [PATCH 074/110] gnu: tilda: Update to 1.4.1. * gnu/packages/terminals.scm (tilda): Update to 1.4.1. [arguments]: Rename 'autogen phase to 'bootstrap. Clean up 'bootstrap phase. --- gnu/packages/terminals.scm | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 6540a9feaf..6f3453670c 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 Mckinley Olsen ;;; Copyright © 2016, 2017 Alex Griffin ;;; Copyright © 2016 David Craven @@ -65,22 +65,21 @@ (define-public tilda (package (name "tilda") - (version "1.3.3") + (version "1.4.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/lanoxx/tilda/archive/" "tilda-" version ".tar.gz")) (sha256 (base32 - "1cc4qbg1m3i04lj5p6i6xbd0zvy1320pxdgmjhz5p3j95ibsbfki")))) + "0w2hry2bqcqrkik4l100b1a9jlsih6sq8zwhfpl8zzfq20i00lfs")))) (build-system glib-or-gtk-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-before 'patch-source-shebangs 'autogen - (lambda _ ; Avoid running ./configure. - (substitute* "autogen.sh" - (("^.*\\$srcdir/configure.*") "")) - (zero? (system* "sh" "autogen.sh"))))))) + '(#:phases (modify-phases %standard-phases + (add-before 'patch-source-shebangs 'bootstrap + (lambda _ + (setenv "NOCONFIGURE" "true") + (invoke "sh" "autogen.sh")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) From bae598d6c9f22d61f47f1e0ff988a8f70c46f6a6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 19:03:56 +0100 Subject: [PATCH 075/110] gnu: r-withr: Update to 2.1.2. * gnu/packages/statistics.scm (r-withr): Update to 2.1.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8afccb0737..19a05ea10b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2358,13 +2358,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "2.1.1") + (version "2.1.2") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "17pbllxv18gf1mli9mm5px4wzp364907a4wrl20r1y5q8qwawpxx")))) + "11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1")))) (build-system r-build-system) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") From 207e4d2705d4fc49caceb7ddbdf29d389824d925 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 19:41:33 +0100 Subject: [PATCH 076/110] gnu: python-oslo.i18n: Update to 3.20.0. * gnu/packages/openstack.scm (python-oslo.i18n): Update to 3.20.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index c1380a1af5..e58b07c2af 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -452,14 +452,14 @@ pipeline and used by various modules such as logging.") (define-public python-oslo.i18n (package (name "python-oslo.i18n") - (version "3.19.0") + (version "3.20.0") (source (origin (method url-fetch) (uri (pypi-uri "oslo.i18n" version)) (sha256 (base32 - "18lbfq55cqrbmwm5p6vci9mkjfzr0zwz54ax3ysa463wba5m84cp")))) + "0kjcdw4bk3mi4vqmqwhhq053kxbbbj05si6nwxd1pzx33z067ky3")))) (build-system python-build-system) (propagated-inputs `(("python-babel" ,python-babel) From ad1976285960800f76b38a1ece8dbfa2ad2436b6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 19:41:51 +0100 Subject: [PATCH 077/110] gnu: python-oslo.utils: Update to 3.36.0. * gnu/packages/openstack.scm (python-oslo.utils): Update to 3.36.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index e58b07c2af..5875562aa1 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -680,14 +680,14 @@ and better support for mocking results.") (define-public python-oslo.utils (package (name "python-oslo.utils") - (version "3.35.0") + (version "3.36.0") (source (origin (method url-fetch) (uri (pypi-uri "oslo.utils" version)) (sha256 (base32 - "1ai9yyasyh1563khsri6ryk6iqdprmyiashg377m9h4nmv700ybx")))) + "0zvm31qdvqywxppqdjwbxxsqaga3dg4slpvbbmqqm9ig4n78mhay")))) (build-system python-build-system) (propagated-inputs `(("python-debtcollector" ,python-debtcollector) From 0f7514580b1ec8e42062651be0a2a64aa437b473 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 18:58:40 +0100 Subject: [PATCH 078/110] gnu: enlightenment: Update to 0.22.2. * gnu/packages/enlightenment.scm (enlightenment): Update to 0.22.2. --- gnu/packages/enlightenment.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index a0bf841415..c04493a192 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015 Daniel Pimentel ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2017 ng0 +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -258,7 +259,7 @@ Libraries with some extra bells and whistles.") (define-public enlightenment (package (name "enlightenment") - (version "0.22.1") + (version "0.22.2") (source (origin (method url-fetch) (uri @@ -266,7 +267,7 @@ Libraries with some extra bells and whistles.") name "/" name "-" version ".tar.xz")) (sha256 (base32 - "1q57fz57d0b26z06m1wiq7c1sniwh885b0vs02mk4jgwva46nyr0")))) + "0b33w75s4w7xmz9cv8dyp8vy2gcffnrvjys20fhcpw26abw1wn2d")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--enable-mount-eeze") From 12c069dbcfe1f38d2f1ba5206c1f862dd075f277 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 21:03:44 +0100 Subject: [PATCH 079/110] gnu: perl-file-basedir: Update to 0.08. * gnu/packages/freedesktop.scm (perl-file-basedir): Update to 0.08. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index f673c4bf34..981303545a 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1131,7 +1131,7 @@ manually by a user.") (define-public perl-file-basedir (package (name "perl-file-basedir") - (version "0.07") + (version "0.08") (source (origin (method url-fetch) @@ -1139,7 +1139,7 @@ manually by a user.") "File-BaseDir-" version ".tar.gz")) (sha256 (base32 - "0aq8d4hsaxqibp36f773y6dfck7zd82v85sp8vhi6pjkg3pmf2hj")))) + "1qq5ag9zffx8zc5i9b4z03ar80pqj4drgk3vjdlyfapjwb9zqrf0")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build) From 86ce44c503cdabe6f8b177e6e66b585e89cb84dd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 19:39:48 +0100 Subject: [PATCH 080/110] gnu: libtirpc: Always return #t from phases. * gnu/packages/onc-rpc.scm (libtirpc)[arguments]: End phase with #t. --- gnu/packages/onc-rpc.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/onc-rpc.scm b/gnu/packages/onc-rpc.scm index 03d51d9517..b2f13fb111 100644 --- a/gnu/packages/onc-rpc.scm +++ b/gnu/packages/onc-rpc.scm @@ -59,7 +59,8 @@ ;; Remove the dangling symlinks since it breaks the ;; 'patch-source-shebangs' file tree traversal. - (delete-file "INSTALL")))))) + (delete-file "INSTALL") + #t))))) (inputs `(("mit-krb5" ,mit-krb5))) (home-page "https://sourceforge.net/projects/libtirpc/") (synopsis "Transport-independent Sun/ONC RPC implementation") From eaa69a7996c8250100a20e65dd5e8ce9b3141439 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 17 Mar 2018 19:40:48 +0100 Subject: [PATCH 081/110] gnu: libtirpc: Update to 1.0.3. * gnu/packages/onc-rpc.scm (libtirpc): Update to 1.0.3. [source]: Remove patch. * gnu/packages/patches/libtirpc-missing-headers.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/onc-rpc.scm | 5 +-- .../patches/libtirpc-missing-headers.patch | 40 ------------------- 3 files changed, 2 insertions(+), 44 deletions(-) delete mode 100644 gnu/packages/patches/libtirpc-missing-headers.patch diff --git a/gnu/local.mk b/gnu/local.mk index dfb3073d7a..490f07b9de 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -865,7 +865,6 @@ dist_patch_DATA = \ %D%/packages/patches/libtasn1-CVE-2017-10790.patch \ %D%/packages/patches/libtasn1-CVE-2018-6003.patch \ %D%/packages/patches/libtheora-config-guess.patch \ - %D%/packages/patches/libtirpc-missing-headers.patch \ %D%/packages/patches/libtiff-CVE-2017-9935.patch \ %D%/packages/patches/libtiff-CVE-2017-18013.patch \ %D%/packages/patches/libtool-skip-tests2.patch \ diff --git a/gnu/packages/onc-rpc.scm b/gnu/packages/onc-rpc.scm index b2f13fb111..44400ebe57 100644 --- a/gnu/packages/onc-rpc.scm +++ b/gnu/packages/onc-rpc.scm @@ -33,16 +33,15 @@ (define-public libtirpc (package (name "libtirpc") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/libtirpc/libtirpc/" version "/libtirpc-" version ".tar.bz2")) - (patches (search-patches "libtirpc-missing-headers.patch")) (sha256 (base32 - "1xchbxy0xql7yl7z4n1icj8r7dmly46i22fvm00vdjq64zlmqg3j")))) + "0ppxl3k3nsz0qdakq844i2kj4fvh9h937lhx26bgmpmxq67sghw6")))) (build-system gnu-build-system) (arguments `(#:phases diff --git a/gnu/packages/patches/libtirpc-missing-headers.patch b/gnu/packages/patches/libtirpc-missing-headers.patch deleted file mode 100644 index 5a96711820..0000000000 --- a/gnu/packages/patches/libtirpc-missing-headers.patch +++ /dev/null @@ -1,40 +0,0 @@ -Fix compilation failure with glibc 2.26 caused by missing type -declarations: - ------- -xdr_sizeof.c: In function ‘x_inline’: -xdr_sizeof.c:93:13: error: ‘uintptr_t’ undeclared (first use in this function) - if (len < (uintptr_t)xdrs->x_base) { ------- - -Patch copied from upstream source repository: - -http://git.linux-nfs.org/?p=steved/libtirpc.git;a=commit;h=acb9a37977cf0a9630eac74af9adebf35e38e719 - -From acb9a37977cf0a9630eac74af9adebf35e38e719 Mon Sep 17 00:00:00 2001 -From: Thorsten Kukuk -Date: Tue, 14 Nov 2017 10:39:08 -0500 -Subject: [PATCH] Include stdint.h from xdr_sizeof.c to avoid missing - declaration errors. - -Signed-off-by: Thorsten Kukuk -Signed-off-by: Steve Dickson ---- - src/xdr_sizeof.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/src/xdr_sizeof.c b/src/xdr_sizeof.c -index d23fbd1..79d6707 100644 ---- a/src/xdr_sizeof.c -+++ b/src/xdr_sizeof.c -@@ -39,6 +39,7 @@ - #include - #include - #include -+#include - #include "un-namespace.h" - - /* ARGSUSED */ --- -1.8.3.1 - From 39c6af47741f04e07693ccd4de8cc13456bafcfb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 14:41:47 +0100 Subject: [PATCH 082/110] gnu: hdparm: Update to 9.55. * gnu/packages/linux.scm (hdparm): Update to 9.55. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b7e70249f3..b586c29d0e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2540,14 +2540,14 @@ thanks to the use of namespaces.") (define-public hdparm (package (name "hdparm") - (version "9.54") + (version "9.55") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/" name "/" name "/" name "-" version ".tar.gz")) (sha256 (base32 - "0ghnhdj7wfw6acfyhdawpfa5n9kvkvzgi1fw6i7sghgbjx5nhyjd")))) + "1ivdvrzimaayiq03by8mcq0mhmdljndj06h012zkdpw34irnpixm")))) (build-system gnu-build-system) (arguments `(#:make-flags (let ((out (assoc-ref %outputs "out"))) From 504be7db587d5ba2f5d777b45920f3f1229b7243 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 14:43:23 +0100 Subject: [PATCH 083/110] gnu: bash-completion: Update to 2.8. * gnu/packages/bash.scm (bash-completion): Update to 2.8. * gnu/packages/patches/bash-completion-directories.patch: Update context. --- gnu/packages/bash.scm | 5 +++-- gnu/packages/patches/bash-completion-directories.patch | 8 ++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bash.scm b/gnu/packages/bash.scm index b8b0ae58f6..b98ffe1c12 100644 --- a/gnu/packages/bash.scm +++ b/gnu/packages/bash.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2015, 2017 Leo Famulari ;;; Copyright © 2016, 2017 Efraim Flashner +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -263,7 +264,7 @@ without modification.") (define-public bash-completion (package (name "bash-completion") - (version "2.7") + (version "2.8") (source (origin (method url-fetch) (uri (string-append @@ -271,7 +272,7 @@ without modification.") version "/" name "-" version ".tar.xz")) (sha256 (base32 - "07j484vb3k90f4989xh1g1x99g01akrp69p3dml4lza27wnqkfj1")) + "0kgmflrr1ga9wfk770vmakna3nj46ylb5ky9ipd0v2k9ymq5a7y0")) (patches (search-patches "bash-completion-directories.patch")))) (build-system gnu-build-system) diff --git a/gnu/packages/patches/bash-completion-directories.patch b/gnu/packages/patches/bash-completion-directories.patch index 351a8e02fb..164096f16c 100644 --- a/gnu/packages/patches/bash-completion-directories.patch +++ b/gnu/packages/patches/bash-completion-directories.patch @@ -8,9 +8,9 @@ directory, but also in the user's profile and in the system profile. This is what this patch does. ---- a/bash_completion 2016-08-03 10:23:02.356782287 +0200 -+++ b/bash_completion 2016-08-03 10:27:50.120140403 +0200 -@@ -1960,7 +1960,13 @@ +--- a/bash_completion ++++ b/bash_completion +@@ -2016,7 +2016,13 @@ complete -F _minimal '' __load_completion() { @@ -22,6 +22,6 @@ This is what this patch does. + "/run/current-system/profile/etc/bash_completion.d/$base" + ${BASH_COMPLETION_USER_DIR:-${XDG_DATA_HOME:-$HOME/.local/share}/bash-completion}/completions ) + - local OIFS=$IFS IFS=: dir cmd="$1" compfile + local OIFS=$IFS IFS=: dir cmd="${1##*/}" compfile for dir in ${XDG_DATA_DIRS:-/usr/local/share:/usr/share}; do dirs+=( $dir/bash-completion/completions ) From d93a1c276b85944198da8395b2d46e06d8a24665 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 11:51:35 +0100 Subject: [PATCH 084/110] gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1. * gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 80f1437f22..c6f9b8f347 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8434,7 +8434,7 @@ paired-end data.") ("r-testthat" ,r-testthat) ;; During vignette building knitr checks that "pandoc-citeproc" ;; is in the PATH. - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc))) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1))) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-biomart" ,r-biomart) From d8f08c85adc18c103e99a706db98e046a5c1c94b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 16:55:08 +0100 Subject: [PATCH 085/110] gnu: pigx: Update to 0.0.2. * gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6f9b8f347..1e1f0e5dad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12948,7 +12948,7 @@ based methods.") (define-public pigx (package (name "pigx") - (version "0.0.1") + (version "0.0.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" @@ -12956,7 +12956,7 @@ based methods.") "/pigx-" version ".tar.gz")) (sha256 (base32 - "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) + "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8")))) (build-system gnu-build-system) (inputs `(("python" ,python) From 6969ad0eddfb237bfee31fb62ada6a239f5af055 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Mar 2018 12:20:22 -0400 Subject: [PATCH 086/110] gnu: python-pynacl: Update to 1.2.0. * gnu/packages/python-crypto.scm (python-pynacl): Update to 1.2.0. [native-inputs]: Add python-hypothesis. --- gnu/packages/python-crypto.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 3734b6ba10..e94ca305ee 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -556,7 +556,7 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (define-public python-pynacl (package (name "python-pynacl") - (version "1.1.2") + (version "1.2.0") (source (origin (method url-fetch) @@ -566,7 +566,7 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (snippet '(delete-file-recursively "src/libsodium")) (sha256 (base32 - "135gz0020fqx8fbr9izpwyq49aww202nkqacq0cw61xz99sjpx9j")))) + "01vjq0pxyw1mxaqy013hzs8nknmvg3kpzlzmh69jxznyipgvria5")))) (build-system python-build-system) (arguments `(#:phases @@ -576,7 +576,8 @@ PKCS#8, PKCS#12, PKCS#5, X.509 and TSP.") (setenv "SODIUM_INSTALL" "system") #t))))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-hypothesis" ,python-hypothesis) + ("python-pytest" ,python-pytest))) (propagated-inputs `(("python-cffi" ,python-cffi) ("python-six" ,python-six) From 9687d4042a986b5ef140a5b9a8103b07a08eda10 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Mar 2018 12:17:24 -0400 Subject: [PATCH 087/110] gnu: python-paramiko: Update to 2.1.5. * gnu/packages/python-crypto.scm (python-paramiko, python2-paramiko): Update to 2.1.5. --- gnu/packages/python-crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index e94ca305ee..e8cbacc4ec 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -122,14 +122,14 @@ John the Ripper).") (define-public python-paramiko (package (name "python-paramiko") - (version "2.1.2") + (version "2.1.5") (source (origin (method url-fetch) (uri (pypi-uri "paramiko" version)) (sha256 (base32 - "04734n0wy3hxk6rij4fr29in5jmr70nxpc7pqi2ksbjysfz4kbjz")))) + "1pf0zxzhgyy4avby3ajg5hp18b0d8iirbkdfw53z0h6w611bp0wk")))) (build-system python-build-system) (arguments '(#:phases From 203631d9adf4d7c2d3dd10aa35cc4c8b5b7c347f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 19 Mar 2018 21:44:50 +0200 Subject: [PATCH 088/110] patchelf: Use 'https' for source uri. * gnu/packages/elf.scm (patchelf)[source]: Use 'https' for source uri. --- gnu/packages/elf.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/elf.scm b/gnu/packages/elf.scm index 8fb568b841..576f649c2d 100644 --- a/gnu/packages/elf.scm +++ b/gnu/packages/elf.scm @@ -108,7 +108,7 @@ Executable and Linkable Format (@dfn{ELF}). This includes @command{ld}, (source (origin (method url-fetch) (uri (string-append - "http://nixos.org/releases/patchelf/patchelf-" + "https://nixos.org/releases/patchelf/patchelf-" version "/patchelf-" version ".tar.bz2")) (sha256 From 51237011bfa1da1374fbd84581e337d6b54a5fc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 20:39:53 +0100 Subject: [PATCH 089/110] gnu: pigx-scrnaseq: Update to 0.0.3. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3. [inputs]: Add coreutils and perl. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e1f0e5dad..a6dcc63bf3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12871,7 +12871,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.2") + (version "0.0.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12879,7 +12879,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) + "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -12898,7 +12898,9 @@ methylation and segmentation.") `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) #t))))) (inputs - `(("dropseq-tools" ,dropseq-tools) + `(("coreutils" ,coreutils) + ("perl" ,perl) + ("dropseq-tools" ,dropseq-tools) ("fastqc" ,fastqc) ("java-picard" ,java-picard) ("java" ,icedtea-8) From 096589035ed154b6ecb4619ca8cdde208be1b8da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 20:53:27 +0100 Subject: [PATCH 090/110] gnu: bismark: Fix references to gunzip. * gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to gunzip executable. [inputs]: Add gzip. --- gnu/packages/bioinformatics.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6dcc63bf3..af994c6a89 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11514,7 +11514,7 @@ Browser.") (delete 'configure) (delete 'build) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin")) (docdir (string-append (assoc-ref outputs "out") @@ -11537,7 +11537,16 @@ Browser.") scripts) (for-each (lambda (file) (install-file file docdir)) docs) + ;; Fix references to gunzip + (substitute* (map (lambda (file) + (string-append bin "/" file)) + scripts) + (("\"gunzip -c") + (string-append "\"" (assoc-ref inputs "gzip") + "/bin/gunzip -c"))) #t)))))) + (inputs + `(("gzip" ,gzip))) (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") (synopsis "Map bisulfite treated sequence reads and analyze methylation") (description "Bismark is a program to map bisulfite treated sequencing From 9dbdc830f6fbf95127d2845603ca8b23a4e40982 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Mar 2018 21:03:07 +0100 Subject: [PATCH 091/110] gnu: pigx-bsseq: Update to 0.0.7. * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7. [inputs]: Add coreutils, sed, and grep. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af994c6a89..c1f9e66a53 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12816,7 +12816,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.5") + (version "0.0.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -12824,7 +12824,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp")))) + "0pw797gxx6x1n56lyrvglj7q5hqq4ylfqkvlcrzq1z3j5lxcyl69")))) (build-system gnu-build-system) (arguments `(#:phases @@ -12848,7 +12848,10 @@ in an easily configurable manner.") (native-inputs `(("tzdata" ,tzdata))) (inputs - `(("r-minimal" ,r-minimal) + `(("coreutils" ,coreutils) + ("sed" ,sed) + ("grep" ,grep) + ("r-minimal" ,r-minimal) ("r-annotationhub" ,r-annotationhub) ("r-dt" ,r-dt) ("r-genomation" ,r-genomation) From 8d0d14479d0df0fba8d19b92fe7925ea02ec185b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 18:13:21 +0100 Subject: [PATCH 092/110] gnu: perl-math-random-secure: Fix typo. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/crypto.scm (perl-math-random-secure)[description]: Fix the spelling of ‘millennia’. --- gnu/packages/crypto.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 7716205947..84a3b7876f 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -576,7 +576,7 @@ cryptographically-secure replacement for Perl's built-in @code{rand} function. @item No matter how many numbers you see generated by the random number generator, you cannot guess the future numbers, and you cannot guess the seed. @item There are so many possible seeds that it would take decades, centuries, -or millenia for an attacker to try them all. +or millennia for an attacker to try them all. @item The seed comes from a source that generates relatively strong random data on your platform, so the seed itself will be as random as possible. @end enumerate\n") From fa3fff430bf3da50ea5e1fdbb2d4fef4cfb0fc23 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 19:06:33 +0100 Subject: [PATCH 093/110] gnu: perl-xml-simple: Update to 2.25. * gnu/packages/xml.scm (perl-xml-simple): Update to 2.25. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 212b1c8e8a..46db9c9f47 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -560,7 +560,7 @@ callback.") (define-public perl-xml-simple (package (name "perl-xml-simple") - (version "2.22") + (version "2.25") (source (origin (method url-fetch) (uri (string-append @@ -568,7 +568,7 @@ callback.") version ".tar.gz")) (sha256 (base32 - "0jgbk30jizafpl7078jhw1di1yh08gf8d85dsvjllr595vr0widr")))) + "1y6vh328zrh085d40852v4ij2l4g0amxykswxd1nfhd2pspds7sk")))) (build-system perl-build-system) (propagated-inputs `(("perl-xml-parser" ,perl-xml-parser) From 1d9b041c2efe5f903980381bc3ceeae4048d1fd1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 19:06:53 +0100 Subject: [PATCH 094/110] gnu: perl-xml-compile-soap: Update to 3.24. * gnu/packages/xml.scm (perl-xml-compile-soap): Update to 3.24. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 46db9c9f47..ab7b9bf986 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -707,14 +707,14 @@ a schema.") (define-public perl-xml-compile-soap (package (name "perl-xml-compile-soap") - (version "3.21") + (version "3.24") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/" "XML-Compile-SOAP-" version ".tar.gz")) (sha256 (base32 - "0rxidh7kjyhnw2y789bqbwccnp8n0m3xskn524y9c752s64qpjcz")))) + "0pkcph562l2ij7rlwlvm58v6y062qsbydfpaz2qnph2ixqy0xfd1")))) (build-system perl-build-system) (propagated-inputs `(("perl-file-slurp-tiny" ,perl-file-slurp-tiny) From 901012356511eda3744703d81bbd08d863624219 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 22:06:24 +0100 Subject: [PATCH 095/110] gnu: weechat: Update to 2.1. * gnu/packages/irc.scm (weechat): Update to 2.1. --- gnu/packages/irc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index bad27dacb6..22ac3c662a 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -155,14 +155,14 @@ SILC and ICB protocols via plugins.") (define-public weechat (package (name "weechat") - (version "2.0.1") + (version "2.1") (source (origin (method url-fetch) (uri (string-append "https://weechat.org/files/src/weechat-" version ".tar.xz")) (sha256 (base32 - "1l854dramvn9vfba7jpazkjwm4k4i5pshq58vjv6z2mxmcp5hhv9")) + "0f7d2vdbxc5kgjl7lkamnbxvidgxwa8f9j3nr9fd4gr4z0gzi86d")) (patches (search-patches "weechat-python.patch")))) (build-system cmake-build-system) (native-inputs From 75abeb73e387f3a8cf81e97ec24b2a70a58aaf04 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 19 Mar 2018 18:00:37 -0400 Subject: [PATCH 096/110] gnu: linux-libre@4.4: Update to 4.4.122. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.122. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b586c29d0e..2bbde3a308 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.121" - "1d7djrhiib0ds9ssjkali6b5w6rzap4zgj5hf9jq1jmqpp54jkm4" + (make-linux-libre "4.4.122" + "1ayilv7474vsif3jpb723jbcy4kymv1fpdr96c1g743bad1wkqqq" %intel-compatible-systems #:configuration-file kernel-config)) From cc367c7c7a000899b136f6ae6285ff81866a597e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 19 Mar 2018 18:01:12 -0400 Subject: [PATCH 097/110] gnu: linux-libre@4.9: Update to 4.9.88. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.88. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2bbde3a308..18fc48c4b0 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.87" - "1p8phvmxp04npzqzqcfmv8k9l5l65s7vpjcakdm0fxfkzvnswsp6" + (make-linux-libre "4.9.88" + "0qlhd8xw3g00i7krpfndkwxzjszk067h26qsxxsszvxyx2s6gp4x" %intel-compatible-systems #:configuration-file kernel-config)) From dd07a549d09af86db326b724e00da0c1a71b39fd Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 19 Mar 2018 18:01:49 -0400 Subject: [PATCH 098/110] gnu: linux-libre@4.14: Update to 4.14.28. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.28. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 18fc48c4b0..50ab0c6cc3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.27") -(define %linux-libre-4.14-hash "0mgkka9niyd0lj4qliy4v7jjh9lg1a5jwlv60yw7z0s4k7ajyyrp") +(define %linux-libre-4.14-version "4.14.28") +(define %linux-libre-4.14-hash "0xg3zsm1yjsvxir8sz7zliz8gcc8d45xh23qyiszl75cfqjl36l3") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From f88028c432c3b90fee4ddd89030a30b19d54324b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 19 Mar 2018 18:02:29 -0400 Subject: [PATCH 099/110] gnu: linux-libre: Update to 4.15.11. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.11. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 50ab0c6cc3..90cf887527 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.15.10") -(define %linux-libre-hash "10fp8jmy0fxq8l01m1nnagpq1hznl9jmhcwknk8izjmdcb5snq6c") +(define %linux-libre-version "4.15.11") +(define %linux-libre-hash "0nrsmw7x5nsc3906dfvfakkibv8pv09r1sf5ckzbkcbkwpyq62h8") (define-public linux-libre (make-linux-libre %linux-libre-version From cfbf6de18cc70d2e385feb5f61f9363f18e78ddf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 19 Mar 2018 23:16:48 +0100 Subject: [PATCH 100/110] gnu: mcron: Update to 1.1 and deprecate "mcron2". * gnu/packages/guile.scm (mcron): Update to 1.1. [native-inputs]: Add TZDATA-FOR-TESTS. [arguments]: New field. (mcron2): Define using 'deprecated-package'. * gnu/services/mcron.scm: Replace 'mcron2' with 'mcron'. * doc/guix.texi (Scheduled Job Execution): Likewise. * gnu/tests/base.scm (%mcron-os): Remove comment about mcron2. --- doc/guix.texi | 4 +- gnu/packages/guile.scm | 116 ++++++++++++++++------------------------- gnu/services/mcron.scm | 8 +-- gnu/tests/base.scm | 4 +- 4 files changed, 53 insertions(+), 79 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index b768b20d6b..4de8e9cb5a 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10479,7 +10479,7 @@ gexps to introduce job definitions that are passed to mcron for more information on mcron job specifications. Below is the reference of the mcron service. -@deffn {Scheme Procedure} mcron-service @var{jobs} [#:mcron @var{mcron2}] +@deffn {Scheme Procedure} mcron-service @var{jobs} [#:mcron @var{mcron}] Return an mcron service running @var{mcron} that schedules @var{jobs}, a list of gexps denoting mcron job specifications. @@ -10504,7 +10504,7 @@ mcron jobs to run. Data type representing the configuration of mcron. @table @asis -@item @code{mcron} (default: @var{mcron2}) +@item @code{mcron} (default: @var{mcron}) The mcron package to use. @item @code{jobs} diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index ddd34ae7dc..33ef822b16 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -662,18 +662,51 @@ library.") (define-public mcron (package (name "mcron") - (version "1.0.8") + (version "1.1") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/mcron/mcron-" - version ".tar.gz")) - (sha256 - (base32 - "0zparwgf01jgl1x53ik71ghabldq6zz18ha4dscps1i0qrzgap1b")) - (patches (search-patches "mcron-install.patch")))) + (method url-fetch) + (uri (string-append "mirror://gnu/mcron/mcron-" + version ".tar.gz")) + (sha256 + (base32 + "1f547sqqfbp0k02sqk4ivwx8y9mx8l0rrx1c9rrj033av073h6xq")))) (build-system gnu-build-system) - (native-inputs `(("pkg-config" ,pkg-config))) - (inputs `(("ed" ,ed) ("which" ,which) ("guile" ,guile-2.0))) + (arguments + '(#:phases (modify-phases %standard-phases + (add-before 'check 'set-timezone + (lambda* (#:key inputs #:allow-other-keys) + ;; 'tests/schedule.sh' expects to be running in UTC+1. + (let ((tzdata (assoc-ref inputs "tzdata"))) + (setenv "TZDIR" + (string-append tzdata + "/share/zoneinfo")) + (setenv "TZ" "UTC+1") + #t))) + (add-before 'check 'disable-schedule-test + (lambda _ + ;; But! As it turns out, that test additionally relies + ;; on non-deterministic behavior; see + ;; . + (substitute* "tests/schedule.sh" + (("mkdir cron") "exit 77\n")) + #t)) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + ;; By default mcron doesn't have its own modules in the + ;; search path, so the 'mcron' command fails to start. + (let* ((output (assoc-ref outputs "out")) + (modules (string-append output + "/share/guile/site/2.2")) + (go (string-append output + "/lib/guile/2.2/site-ccache"))) + (wrap-program (string-append output "/bin/mcron") + `("GUILE_LOAD_PATH" ":" prefix + (,modules)) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,go))) + #t)))))) + (native-inputs `(("pkg-config" ,pkg-config) + ("tzdata" ,tzdata-for-tests))) + (inputs `(("ed" ,ed) ("which" ,which) ("guile" ,guile-2.2))) (home-page "https://www.gnu.org/software/mcron/") (synopsis "Run jobs at scheduled times") (description @@ -684,67 +717,8 @@ format is also supported.") (license license:gpl3+))) (define-public mcron2 - ;; This is mthl's mcron development branch, not yet merged in mcron. - (let ((commit "31baff1a5187d8ddc89324cbe42dbeffc309c962")) - (package - (inherit mcron) - (name "mcron2") - (version (string-append (package-version mcron) "-0." - (string-take commit 7))) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://notabug.org/mthl/mcron/") - (commit commit))) - (sha256 - (base32 - "1h5wxy997hxi718hpx419c23q09939kbxrjbbq54lv0cgw1bb63z")) - (file-name (string-append name "-" version "-checkout")))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("pkg-config" ,pkg-config) - ("texinfo" ,texinfo) - ("help2man" ,help2man))) - (inputs - `(("guile-2.2" ,guile-2.2) - ,@(srfi-1:alist-delete "guile" (package-inputs mcron)))) - (arguments - `(#:modules ((ice-9 match) (ice-9 ftw) - ,@%gnu-build-system-modules) - ;; When building the targets in parallel, help2man tries to generate - ;; the manpage from ./cron --help before it is built, which fails. - #:parallel-build? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-guile-2.2 - (lambda _ - (substitute* "configure.ac" - (("PKG_CHECK_MODULES\\(\\[GUILE\\],.*$") - "PKG_CHECK_MODULES([GUILE], [guile-2.2])\n") - (("guile/site/2.0") - "guile/site/2.2")) - #t)) - (add-after 'use-guile-2.2 'bootstrap - (lambda _ - (invoke "autoreconf" "-vfi"))) - (add-after 'install 'wrap-mcron - (lambda* (#:key outputs #:allow-other-keys) - ;; Wrap the 'mcron' command to refer to the right - ;; modules. - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (site (string-append - out "/share/guile/site"))) - (match (scandir site) - (("." ".." version) - (let ((modules (string-append site "/" version))) - (wrap-program (string-append bin "/mcron") - `("GUILE_LOAD_PATH" ":" prefix - (,modules)) - `("GUILE_LOAD_COMPILED_PATH" ":" prefix - (,modules))) - #t)))))))))))) + ;; This was mthl's mcron development branch, and it became mcron 1.1. + (deprecated-package "mcron2" mcron)) (define-public guile-ics (package diff --git a/gnu/services/mcron.scm b/gnu/services/mcron.scm index b6cb8bc726..5bee02a587 100644 --- a/gnu/services/mcron.scm +++ b/gnu/services/mcron.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -20,7 +20,7 @@ #:use-module (gnu services) #:use-module (gnu services base) #:use-module (gnu services shepherd) - #:autoload (gnu packages guile) (mcron2) + #:autoload (gnu packages guile) (mcron) #:use-module (guix records) #:use-module (guix gexp) #:use-module (srfi srfi-1) @@ -53,7 +53,7 @@ make-mcron-configuration mcron-configuration? (mcron mcron-configuration-mcron ;package - (default mcron2)) + (default mcron)) (jobs mcron-configuration-jobs ;list of (default '()))) @@ -100,7 +100,7 @@ jobs))))) (default-value (mcron-configuration)))) ;empty job list -(define* (mcron-service jobs #:optional (mcron mcron2)) +(define* (mcron-service jobs #:optional (mcron mcron)) "Return an mcron service running @var{mcron} that schedules @var{jobs}, a list of gexps denoting mcron job specifications. diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm index 378c7ff021..63d2789cc5 100644 --- a/gnu/tests/base.scm +++ b/gnu/tests/base.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -477,7 +477,7 @@ in a loop. See .") (define %mcron-os ;; System with an mcron service, with one mcron job for "root" and one mcron - ;; job for an unprivileged user (note: #:user is an 'mcron2' thing.) + ;; job for an unprivileged user. (let ((job1 #~(job next-second-from (lambda () (call-with-output-file "witness" From d41ad1d553f255edaad55ab26330746913ba473d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 19 Mar 2018 18:55:50 -0400 Subject: [PATCH 101/110] gnu: uwsgi: Update to 2.0.17 [fixes CVE-2018-7490]. * gnu/packages/web.scm (uwsgi): Update to 2.0.17. [source]: Use HTTPS URL. --- gnu/packages/web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 625df2b1dc..d04e5310bf 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4053,14 +4053,14 @@ a pure C99 library.") (define-public uwsgi (package (name "uwsgi") - (version "2.0.15") + (version "2.0.17") (source (origin (method url-fetch) - (uri (string-append "http://projects.unbit.it/downloads/uwsgi-" + (uri (string-append "https://projects.unbit.it/downloads/uwsgi-" version ".tar.gz")) (sha256 (base32 - "1zvj28wp3c1hacpd4c6ra5ilwvvfq3l8y6gn8i7mnncpddlzjbjp")))) + "1wlbaairsmhp6bx5wv282q9pgh6w7w6yrb8vxjznfaxrinsfkhix")))) (build-system gnu-build-system) (outputs '("out" "python")) (arguments From 712be306a810cb1eb493926da9721e49af56e63c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 00:27:07 +0100 Subject: [PATCH 102/110] gnu: rofi: Update to 1.5.1. * gnu/packages/xdisorg.scm (rofi): Update to 1.5.1. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 4e7f2c207f..93cc57a176 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -1101,7 +1101,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.") (define-public rofi (package (name "rofi") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/DaveDavenport/rofi/" @@ -1109,7 +1109,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.") version "/rofi-" version ".tar.xz")) (sha256 (base32 - "0li2hl55sxzdpbxxiwgxsvkhyy6bh8qd2j1r8xh8y6q8a318zsz9")))) + "10r1jd3h5i22pdr619hmvxv6dhzf9i13j50c28g7yffdggx8ncjg")))) (build-system gnu-build-system) (inputs `(("pango" ,pango) From 3f986ff657a8ea4f46dc0312df7ff0eeeb98c6ee Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 00:56:04 +0100 Subject: [PATCH 103/110] gnu: zziplib: Update to 0.13.69. * gnu/packages/compression.scm (zziplib): Update to 0.13.69. [home-page]: Use new GitHub home. [source](uri): Adjust accordingly. [arguments]: Remove. --- gnu/packages/compression.scm | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index f92239d505..071aecb0f8 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1807,16 +1807,15 @@ recreates the stored directory structure by default.") (define-public zziplib (package (name "zziplib") - (version "0.13.68") + (version "0.13.69") + (home-page "https://github.com/gdraheim/zziplib") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/zziplib/zziplib13/" - version "/zziplib-" - version ".tar.bz2")) + (uri (string-append home-page "/archive/v" version ".tar.gz")) (sha256 (base32 - "1s0wz1hf2q4qxcp4lkg4rzpbz2814xagmvlyicqdj0ww0cvxv036")))) + "0i052a7shww0fzsxrdp3rd7g4mbzx7324a8ysbc0br7frpblcql4")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -1826,12 +1825,6 @@ recreates the stored directory structure by default.") ;; http://forums.gentoo.org/viewtopic-t-863161-start-0.html ("python" ,python-2) ("zip" ,zip))) ; to create test files - (arguments - ;; XXX: "make check" is broken, and the alternative (test/zziptests.py) - ;; requires network access. See - ;; and . - `(#:tests? #f)) - (home-page "http://zziplib.sourceforge.net/") (synopsis "Library for accessing zip files") (description "ZZipLib is a library based on zlib for accessing zip files.") From 0d729c5b141142981d4f18173fca5e3a1a6ee415 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 01:02:13 +0100 Subject: [PATCH 104/110] gnu: zziplib: Correct license. * gnu/packages/compression.scm (zziplib)[license]: Add MPL1.1. --- gnu/packages/compression.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 071aecb0f8..26decfaf84 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1828,7 +1828,9 @@ recreates the stored directory structure by default.") (synopsis "Library for accessing zip files") (description "ZZipLib is a library based on zlib for accessing zip files.") - (license license:lgpl2.0+))) + ;; zziplib is dual licensed under LGPL2.0+ and MPL1.1. Some example source + ;; files carry the Zlib license; see "docs/copying.html" for details. + (license (list license:lgpl2.0+ license:mpl1.1)))) (define-public perl-archive-zip (package From 264cb77646778f6bb7bca7d4bd4b8712a485b448 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 01:09:16 +0100 Subject: [PATCH 105/110] gnu: imagemagick: Update to 6.9.9-39. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-39. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index d798833742..d3cc656f11 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -47,14 +47,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.9-37") + (version "6.9.9-39") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "1hmfw0jcpc3s3gz9zrzjy9amyrfz6gzzjdsyaw3xw994aq9qf4lq")))) + "0cgrvfg8722cdv2y0hw2f7xhzdfmfiqc1348l71ki38dg4b0q4sn")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch") From c9838530d3d508754167fef6e93b5a88909ddce8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 01:24:48 +0100 Subject: [PATCH 106/110] gnu: imlib2: Update to 1.5.1. * gnu/packages/image.scm (imlib2): Update to 1.5.1. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index caafb2ea70..e0f6794247 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -634,7 +634,7 @@ compose, and analyze GIF images.") (define-public imlib2 (package (name "imlib2") - (version "1.5.0") + (version "1.5.1") (source (origin (method url-fetch) (uri (string-append @@ -642,7 +642,7 @@ compose, and analyze GIF images.") "/imlib2-" version ".tar.bz2")) (sha256 (base32 - "0kg28b5wp886hiy12v7abdybrvlymb7g3nvg0ysn2y8h883s5w8m")))) + "1bms2iwmvnvpz5jqq3r52glarqkafif47zbh1ykz8hw85d2mfkps")))) (build-system gnu-build-system) (native-inputs `(("pkgconfig" ,pkg-config))) From 818e6d9704ccccfe72ce26331ff646d5beb1efd5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 01:25:10 +0100 Subject: [PATCH 107/110] gnu: python-cryptography: Update to 2.2. * gnu/packages/python-crypto.scm (python-cryptography-vectors, python-cryptography): Update to 2.2. --- gnu/packages/python-crypto.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index e8cbacc4ec..3fbaf1c3c4 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -281,14 +281,14 @@ is used by the Requests library to verify HTTPS requests.") (define-public python-cryptography-vectors (package (name "python-cryptography-vectors") - (version "2.1.4") + (version "2.2") (source (origin (method url-fetch) (uri (pypi-uri "cryptography_vectors" version)) (sha256 (base32 - "1jm5c33qaz297sf99kz9kw8xi792ap9m6bwf0dfylls8z3rv9i3q")))) + "03cpmi5azvipphmva7dxv8k3w7ffblvn5452rs5r6smdhxyiqq6g")))) (build-system python-build-system) (home-page "https://github.com/pyca/cryptography") (synopsis "Test vectors for the cryptography package") @@ -303,14 +303,14 @@ is used by the Requests library to verify HTTPS requests.") (define-public python-cryptography (package (name "python-cryptography") - (version "2.1.4") + (version "2.2") (source (origin (method url-fetch) (uri (pypi-uri "cryptography" version)) (sha256 (base32 - "14aj5ipbj1w5kba2hv6323954pachhflfrjhhmkjwssv3hvngng4")))) + "0j2gwr4qxvskip77z4n9nqvr4vi243n3bzij18ay4drc6sg2g87m")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) From a3e2b72ca900fe14e552a85816d77ad7d0b20b33 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 20 Mar 2018 01:40:07 +0100 Subject: [PATCH 108/110] gnu: certbot: Update to 0.22.1. * gnu/packages/tls.scm (python-acme, certbot): Update to 0.22.1. --- gnu/packages/tls.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index bd86b2e0d9..299ac85dc9 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -512,13 +512,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.22.0") + (version "0.22.1") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "1s2zamyb99zdyga3c75xxgnj0z2hixw8wv24v1l4p49fncnxab2a")))) + "0cbw062xmaqhmdb5d04d2xs9aacmq1i7yvnd37gw1d71qgxlnmsz")))) (build-system python-build-system) (arguments `(#:phases @@ -567,7 +567,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "1cyb3lhxrw7ghyhrl2wc95vqhdaxz6n4pai66c573gcly7c7sc7f")))) + "1d9abvlwi2d4d991dakds7jyrzxcsqkl13sd0clkriav9cdqwhv4")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) From 4e6c51d4eb203578524d2910f17934aa643fc779 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 22:58:48 +0100 Subject: [PATCH 109/110] gnu: dnsmasq: Update to 2.79. * gnu/packages/dns.scm (dnsmasq): Update to 2.79. --- gnu/packages/dns.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index d093b0d9b5..e76dd5cfe7 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -59,7 +59,7 @@ (define-public dnsmasq (package (name "dnsmasq") - (version "2.78") + (version "2.79") (source (origin (method url-fetch) (uri (string-append @@ -67,7 +67,7 @@ version ".tar.xz")) (sha256 (base32 - "0ar5h5v3kas2qx2wgy5iqin15gc4jhqrqs067xacgc3lii1rz549")))) + "07w6cw706yyahwvbvslhkrbjf2ynv567cgy9pal8bz8lrbsp9bbq")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -79,8 +79,7 @@ #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) "CC=gcc" "COPTS=\"-DHAVE_DBUS\"") - ;; No 'check' target. - #:tests? #f)) + #:tests? #f)) ; no ‘check’ target (home-page "http://www.thekelleys.org.uk/dnsmasq/doc.html") (synopsis "Small caching DNS proxy and DHCP/TFTP server") (description From c657716ede8932da356635802534aa13205a6ecd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 19 Mar 2018 23:00:01 +0100 Subject: [PATCH 110/110] gnu: dnsmasq: Fix description typos. * gnu/packages/dns.scm (dnsmasq)[description]: Fix some typos. --- gnu/packages/dns.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index e76dd5cfe7..bd61784ebd 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -83,11 +83,11 @@ (home-page "http://www.thekelleys.org.uk/dnsmasq/doc.html") (synopsis "Small caching DNS proxy and DHCP/TFTP server") (description - "Dnsmasq is a lightweight DNS forwarder and DHCP server. It is designed -to provide DNS and optionally, DHCP, to a small network. It can serve the + "Dnsmasq is a light-weight DNS forwarder and DHCP server. It is designed +to provide DNS and, optionally, DHCP to a small network. It can serve the names of local machines which are not in the global DNS. The DHCP server integrates with the DNS server and allows machines with DHCP-allocated -addresses to appear in the DNS with names configured either in each host or in +addresses to appear in the DNS with names configured either on each host or in a central configuration file. Dnsmasq supports static and dynamic DHCP leases and BOOTP/TFTP for network booting of diskless machines.") ;; Source files only say GPL2 and GPL3 are allowed.