From 9b25e1d1248da83fa3f39f8fe163b842ec4c4d5a Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 12 Jun 2018 07:41:45 +0100 Subject: gnu: erlang: Delete the bootstrap phase. This fails for the erlang package, as the gnu build system attempts to execute the bootstrap directory. * gnu/packages/erlang.scm (erlang)[arguments]: Delete the bootstrap phase. --- gnu/packages/erlang.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages') diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm index 0e2b7b5bcb..55e0e62478 100644 --- a/gnu/packages/erlang.scm +++ b/gnu/packages/erlang.scm @@ -89,6 +89,7 @@ (guix build gnu-build-system)) #:phases (modify-phases %standard-phases + (delete 'bootstrap) ;; The are several code fragments that embed timestamps into the ;; output. Here, we alter those fragments to use the value of ;; SOURCE_DATE_EPOCH instead. -- cgit v1.2.3 From b5453aa7c314bec95e0c25b904f3517d338577ed Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 1 Jun 2018 14:29:24 +0100 Subject: gnu: erlang: Patch occurrences of /bin/sh in the source. Previously, the elixir package would often fail to build, as running :os:cmd would fail, as /bin/sh doesn't exist when building the elixir package. These changes fix that issue. * gnu/packages/erlang.scm (erlang)[arguments]: Add new patch-/bin/sh phase to replace hardcoded references to /bin/sh with a file in the store. --- gnu/packages/erlang.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm index 55e0e62478..1c18efe9da 100644 --- a/gnu/packages/erlang.scm +++ b/gnu/packages/erlang.scm @@ -128,6 +128,29 @@ (date->string source-date-epoch "{H,Mi,S} = {~H,~M,~S},"))) #t))) + (add-after 'unpack 'patch-/bin/sh + (lambda _ + (substitute* "erts/etc/unix/run_erl.c" + (("sh = \"/bin/sh\";") + (string-append "sh = \"" + (which "sh") + "\";"))) + + (substitute* "erts/emulator/sys/unix/sys_drivers.c" + (("SHELL \"/bin/sh\"") + (string-append "SHELL \"" + (which "sh") + "\""))) + (substitute* "erts/emulator/sys/unix/erl_child_setup.c" + (("SHELL \"/bin/sh\"") + (string-append "SHELL \"" + (which "sh") + "\""))) + + (substitute* "lib/kernel/src/os.erl" + (("/bin/sh") (which "sh"))) + + #t)) (add-after 'patch-source-shebangs 'patch-source-env (lambda _ (let ((escripts -- cgit v1.2.3 From e7a25d2ae7d65f204d92f7987630eeb5c63fe659 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 1 Jun 2018 14:32:28 +0100 Subject: gnu: elixir: Enable more tests and remove patch. Previously, due to issues in the erlang package, many tests would fail, and the package would also nondeterministically fail to build. This is now fixed (by patching occurrences of /bin/sh in the erlang package), so all the tests can be run. * gnu/packages/elixir.scm (elixir)[source]: Remove patches. [arguments]: Remove the fix-or-disable-tests phase. Add a new set-home phase to set the HOME environment variable prior to running the tests. * gnu/packages/patches/elixir-disable-failing-tests.patch: Delete this file. * gnu/local.mk: Remove now deleted patch. --- gnu/local.mk | 1 - gnu/packages/elixir.scm | 36 +-- .../patches/elixir-disable-failing-tests.patch | 284 --------------------- 3 files changed, 6 insertions(+), 315 deletions(-) delete mode 100644 gnu/packages/patches/elixir-disable-failing-tests.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 7fa7e7d818..1957fb66cb 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -641,7 +641,6 @@ dist_patch_DATA = \ %D%/packages/patches/e2fsprogs-glibc-2.27.patch \ %D%/packages/patches/eigen-arm-neon-fixes.patch \ %D%/packages/patches/elfutils-tests-ptrace.patch \ - %D%/packages/patches/elixir-disable-failing-tests.patch \ %D%/packages/patches/elogind-glibc-2.27.patch \ %D%/packages/patches/einstein-build.patch \ %D%/packages/patches/emacs-browse-at-remote-cgit-gnu.patch \ diff --git a/gnu/packages/elixir.scm b/gnu/packages/elixir.scm index ceabc2a6c4..ed6bd00236 100644 --- a/gnu/packages/elixir.scm +++ b/gnu/packages/elixir.scm @@ -40,15 +40,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0acnxfwvkx1m1d0h5z051mz95n35zm468hcvc3wpmn17c15h5ihg")) - ;; FIXME: 27 tests (out of 4K) had to be disabled as - ;; they fail in the build environment. Common failures - ;; are: - ;; - Mix.Shell.cmd() fails with error 130 - ;; - The git_repo fixture cannot be found - ;; - Communication with spawned processes fails with EPIPE - ;; - Failure to copy files - (patches (search-patches "elixir-disable-failing-tests.patch")))) + "0acnxfwvkx1m1d0h5z051mz95n35zm468hcvc3wpmn17c15h5ihg")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -70,27 +62,6 @@ (("#!/usr/bin/env elixir") (string-append "#!" out "/bin/elixir")))) #t)) - (add-after 'unpack 'fix-or-disable-tests - (lambda* (#:key inputs #:allow-other-keys) - ;; Some tests require access to a home directory. - (setenv "HOME" "/tmp") - - ;; FIXME: These tests fail because the "git_repo" fixture does - ;; not exist or cannot be found. - (delete-file "lib/mix/test/mix/tasks/deps.git_test.exs") - - ;; FIXME: Mix.Shell.cmd() always fails with error code 130. - (delete-file "lib/mix/test/mix/shell_test.exs") - - ;; FIXME: - ;; disabled failing impure tests to make it build again. - ;; related discussion: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=28034#14 - (delete-file "lib/elixir/test/elixir/kernel/cli_test.exs") - (delete-file "lib/elixir/test/elixir/kernel/dialyzer_test.exs") - (delete-file "lib/iex/test/iex/helpers_test.exs") - (delete-file "lib/ex_unit/test/ex_unit/capture_io_test.exs") - - #t)) (add-before 'build 'make-current ;; The Elixir compiler checks whether or not to compile files by ;; inspecting their timestamps. When the timestamp is equal to the @@ -102,6 +73,11 @@ (utime file recent recent 0 0))) (find-files "." ".*")) #t)) + (add-before 'check 'set-home + (lambda* (#:key inputs #:allow-other-keys) + ;; Some tests require access to a home directory. + (setenv "HOME" "/tmp") + #t)) (delete 'configure)))) (inputs `(("erlang" ,erlang) diff --git a/gnu/packages/patches/elixir-disable-failing-tests.patch b/gnu/packages/patches/elixir-disable-failing-tests.patch deleted file mode 100644 index 547598b292..0000000000 --- a/gnu/packages/patches/elixir-disable-failing-tests.patch +++ /dev/null @@ -1,284 +0,0 @@ -Most of these tests fail for unknown reasons when run in the chroot -environment of a Guix build process. - -Common failures are: - - * Mix.Shell.cmd() fails with error 130 - * The git_repo fixture cannot be found - * Communication with spawned processes fails with EPIPE - * Failure to copy files - - -diff --git a/lib/elixir/test/elixir/kernel/cli_test.exs b/lib/elixir/test/elixir/kernel/cli_test.exs -index 3ffd56c..1232d19 100644 ---- a/lib/elixir/test/elixir/kernel/cli_test.exs -+++ b/lib/elixir/test/elixir/kernel/cli_test.exs -@@ -39,6 +39,7 @@ end - defmodule Kernel.CLI.OptionParsingTest do - use ExUnit.Case, async: true - -+ @tag :skip - test "properly parses paths" do - root = fixture_path("../../..") |> to_charlist - list = elixir('-pa "#{root}/*" -pz "#{root}/lib/*" -e "IO.inspect(:code.get_path, limit: :infinity)"') -@@ -57,6 +58,7 @@ end - defmodule Kernel.CLI.AtExitTest do - use ExUnit.Case, async: true - -+ @tag :skip - test "invokes at_exit callbacks" do - assert elixir(fixture_path("at_exit.exs") |> to_charlist) == - 'goodbye cruel world with status 1\n' -@@ -66,6 +68,7 @@ end - defmodule Kernel.CLI.ErrorTest do - use ExUnit.Case, async: true - -+ @tag :skip - test "properly format errors" do - assert :string.str('** (throw) 1', elixir('-e "throw 1"')) == 0 - assert :string.str('** (ErlangError) erlang error: 1', elixir('-e "error 1"')) == 0 -@@ -86,6 +89,7 @@ defmodule Kernel.CLI.CompileTest do - {:ok, [tmp_dir_path: tmp_dir_path, beam_file_path: beam_file_path, fixture: fixture]} - end - -+ @tag :skip - test "compiles code", context do - assert elixirc('#{context[:fixture]} -o #{context[:tmp_dir_path]}') == '' - assert File.regular?(context[:beam_file_path]) -@@ -96,6 +100,7 @@ defmodule Kernel.CLI.CompileTest do - Code.delete_path context[:tmp_dir_path] - end - -+ @tag :skip - test "fails on missing patterns", context do - output = elixirc('#{context[:fixture]} non_existing.ex -o #{context[:tmp_dir_path]}') - assert :string.str(output, 'non_existing.ex') > 0, "expected non_existing.ex to be mentioned" -@@ -103,6 +108,7 @@ defmodule Kernel.CLI.CompileTest do - refute File.exists?(context[:beam_file_path]), "expected the sample to not be compiled" - end - -+ @tag :skip - test "fails on missing write access to .beam file", context do - compilation_args = '#{context[:fixture]} -o #{context[:tmp_dir_path]}' - -diff --git a/lib/elixir/test/elixir/kernel/dialyzer_test.exs b/lib/elixir/test/elixir/kernel/dialyzer_test.exs -index 801d852..40fc5bc 100644 ---- a/lib/elixir/test/elixir/kernel/dialyzer_test.exs -+++ b/lib/elixir/test/elixir/kernel/dialyzer_test.exs -@@ -60,16 +60,19 @@ defmodule Kernel.DialyzerTest do - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on rewrites", context do - copy_beam! context, Dialyzer.Rewrite - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on raise", context do - copy_beam! context, Dialyzer.Raise - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on macrocallback", context do - copy_beam! context, Dialyzer.Macrocallback - copy_beam! context, Dialyzer.Macrocallback.Impl -diff --git a/lib/elixir/test/elixir/system_test.exs b/lib/elixir/test/elixir/system_test.exs -index aafa559..0f9c178 100644 ---- a/lib/elixir/test/elixir/system_test.exs -+++ b/lib/elixir/test/elixir/system_test.exs -@@ -53,7 +53,8 @@ defmodule SystemTest do - assert System.endianness in [:little, :big] - assert System.endianness == System.compiled_endianness - end -- -+ -+ @tag :skip - test "argv/0" do - list = elixir('-e "IO.inspect System.argv" -- -o opt arg1 arg2 --long-opt 10') - {args, _} = Code.eval_string list, [] -diff --git a/lib/mix/test/mix/dep_test.exs b/lib/mix/test/mix/dep_test.exs -index fff3351..d6ed1b3 100644 ---- a/lib/mix/test/mix/dep_test.exs -+++ b/lib/mix/test/mix/dep_test.exs -@@ -244,6 +244,7 @@ defmodule Mix.DepTest do - end - end - -+ @tag :skip - test "remote converger" do - deps = [{:deps_repo, "0.1.0", path: "custom/deps_repo"}, - {:git_repo, "0.2.0", git: MixTest.Case.fixture_path("git_repo")}] -@@ -301,6 +302,7 @@ defmodule Mix.DepTest do - end - end - -+ @tag :skip - test "remote converger is not invoked if deps diverge" do - deps = [{:deps_repo, "0.1.0", path: "custom/deps_repo"}, - {:git_repo, "0.2.0", git: MixTest.Case.fixture_path("git_repo"), only: :test}] - -diff --git a/lib/mix/test/mix/shell/io_test.exs b/lib/mix/test/mix/shell/io_test.exs -index 9bfb6b4..d982ef3 100644 ---- a/lib/mix/test/mix/shell/io_test.exs -+++ b/lib/mix/test/mix/shell/io_test.exs -@@ -29,6 +29,7 @@ defmodule Mix.Shell.IOTest do - assert capture_io("", fn -> refute yes?("Ok?") end) - end - -+ @tag :skip - test "runs a given command" do - assert capture_io("", fn -> assert cmd("echo hello") == 0 end) == "hello\n" - -diff --git a/lib/mix/test/mix/shell/quiet_test.exs b/lib/mix/test/mix/shell/quiet_test.exs -index 626429b..99fab35 100644 ---- a/lib/mix/test/mix/shell/quiet_test.exs -+++ b/lib/mix/test/mix/shell/quiet_test.exs -@@ -29,6 +29,7 @@ defmodule Mix.Shell.QuietTest do - assert capture_io("", fn -> refute yes?("Ok?") end) - end - -+ @tag :skip - test "runs a given command" do - assert capture_io("", fn -> assert cmd("echo hello") == 0 end) == "" - -diff --git a/lib/mix/test/mix/tasks/cmd_test.exs b/lib/mix/test/mix/tasks/cmd_test.exs -index db4bf06..4d441f7 100644 ---- a/lib/mix/test/mix/tasks/cmd_test.exs -+++ b/lib/mix/test/mix/tasks/cmd_test.exs -@@ -3,6 +3,7 @@ Code.require_file "../../test_helper.exs", __DIR__ - defmodule Mix.Tasks.CmdTest do - use MixTest.Case - -+ @tag :skip - test "runs the command for each app" do - in_fixture "umbrella_dep/deps/umbrella", fn -> - Mix.Project.in_project(:umbrella, ".", fn _ -> -diff --git a/lib/mix/test/mix/tasks/deps.tree_test.exs b/lib/mix/test/mix/tasks/deps.tree_test.exs -index 4f09ff3..c371997 100644 ---- a/lib/mix/test/mix/tasks/deps.tree_test.exs -+++ b/lib/mix/test/mix/tasks/deps.tree_test.exs -@@ -29,6 +29,7 @@ defmodule Mix.Tasks.Deps.TreeTest do - end - end - -+ @tag :skip - test "shows the dependency tree", context do - Mix.Project.push ConvergedDepsApp - -@@ -109,6 +110,7 @@ defmodule Mix.Tasks.Deps.TreeTest do - end - end - -+ @tag :skip - test "shows the dependency tree in DOT graph format", context do - Mix.Project.push ConvergedDepsApp - -diff --git a/lib/mix/test/mix/tasks/deps_test.exs b/lib/mix/test/mix/tasks/deps_test.exs -index b061777..cc45cf8 100644 ---- a/lib/mix/test/mix/tasks/deps_test.exs -+++ b/lib/mix/test/mix/tasks/deps_test.exs -@@ -96,6 +96,7 @@ - end - end - -+ @tag :skip - test "prints list of dependencies and their lock status" do - Mix.Project.push DepsApp - -@@ -409,6 +409,7 @@ defmodule Mix.Tasks.DepsTest do - end - end - -+ @tag :skip - test "fails on diverged dependencies by requirement" do - Mix.Project.push ConvergedDepsApp - -@@ -440,6 +441,7 @@ defmodule Mix.Tasks.DepsTest do - end - end - -+ @tag :skip - test "fails on diverged dependencies even when optional" do - Mix.Project.push ConvergedDepsApp - -@@ -469,6 +471,7 @@ defmodule Mix.Tasks.DepsTest do - end - end - -+ @tag :skip - test "works with converged dependencies" do - Mix.Project.push ConvergedDepsApp - -@@ -491,6 +494,7 @@ defmodule Mix.Tasks.DepsTest do - purge [GitRepo, GitRepo.Mixfile] - end - -+ @tag :skip - test "works with overridden dependencies" do - Mix.Project.push OverriddenDepsApp - -diff --git a/lib/mix/test/mix/umbrella_test.exs b/lib/mix/test/mix/umbrella_test.exs -index 69f9428..406668a 100644 ---- a/lib/mix/test/mix/umbrella_test.exs -+++ b/lib/mix/test/mix/umbrella_test.exs -@@ -98,6 +98,7 @@ defmodule Mix.UmbrellaTest do - end - end - -+ @tag :skip - test "loads umbrella child dependencies in all environments" do - in_fixture "umbrella_dep/deps/umbrella", fn -> - Mix.Project.in_project :umbrella, ".", fn _ -> - -diff --git a/lib/elixir/test/elixir/kernel/dialyzer_test.exs b/lib/elixir/test/elixir/kernel/dialyzer_test.exs -index 792222c..e90beb9 100644 ---- a/lib/elixir/test/elixir/kernel/dialyzer_test.exs -+++ b/lib/elixir/test/elixir/kernel/dialyzer_test.exs -@@ -54,6 +54,7 @@ defmodule Kernel.DialyzerTest do - {:ok, [outdir: dir, dialyzer: dialyzer]} - end - -+ @tag :skip - test "no warnings on valid remote calls", context do - copy_beam! context, Dialyzer.RemoteCall - assert_dialyze_no_warnings! context -@@ -78,11 +79,13 @@ defmodule Kernel.DialyzerTest do - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on struct update", context do - copy_beam! context, Dialyzer.StructUpdate - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on protocol calls with opaque types", context do - copy_beam! context, Dialyzer.ProtocolOpaque - copy_beam! context, Dialyzer.ProtocolOpaque.Entity -@@ -90,6 +93,7 @@ defmodule Kernel.DialyzerTest do - assert_dialyze_no_warnings! context - end - -+ @tag :skip - test "no warnings on and/2 and or/2", context do - copy_beam! context, Dialyzer.BooleanCheck - assert_dialyze_no_warnings! context - -diff --git a/Makefile b/Makefile -index 2fc4f9a..aef8366 100644 ---- a/Makefile -+++ b/Makefile -@@ -201,7 +201,7 @@ $(TEST_EBIN)/%.beam: $(TEST_ERL)/%.erl - $(Q) mkdir -p $(TEST_EBIN) - $(Q) $(ERLC) -o $(TEST_EBIN) $< - --test_elixir: test_stdlib test_ex_unit test_logger test_mix test_eex test_iex -+test_elixir: test_stdlib test_ex_unit test_logger test_eex test_iex - - test_stdlib: compile - @ echo "==> elixir (exunit)" - -- cgit v1.2.3 From 2c5f8aad9278177eb61d2e6b847058e12f1a0a10 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 24 Mar 2018 15:58:54 +0000 Subject: gnu: Add emacs-puppet-mode. * gnu/packages/emacs.scm (emacs-puppet-mode): New variable. --- gnu/packages/emacs.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 9caa01a0fd..039f52a560 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -3014,6 +3014,33 @@ This provides a basic API and common UI widgets such as popup tooltips and popup menus.") (license license:gpl3+))) +(define-public emacs-puppet-mode + (let ((commit "b3ed5057166a4f49dfa9be638523a348b55a2fd2") + (revision "1")) + (package + (name "emacs-puppet-mode") + ;; The last release, 0.3 was several years ago, and there have been many + ;; commits since + (version (git-version "0.3" revision commit)) + (source + (origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/voxpupuli/puppet-mode/" + commit "/puppet-mode.el")) + (sha256 + (base32 + "1indycxawsl0p2aqqg754f6735q3cmah9vd886rpn0ncc3ipi1xm")))) + (build-system emacs-build-system) + (home-page "https://github.com/voxpupuli/puppet-mode") + (synopsis "Emacs major mode for the Puppet configuration language") + (description + "This package provides support for the Puppet configuration language, +including syntax highlighting, indentation of expressions and statements, +linting of manifests and integration with Puppet Debugger.") + ;; Also incorporates work covered by the Apache License, Version 2.0 + (license license:gpl3+)))) + (define-public emacs-god-mode (let ((commit "6cf0807b6555eb6fcf8387a4e3b667071ef38964") (revision "1")) -- cgit v1.2.3 From f3ad05efd980ff1ce7fe7394b610952870817915 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 12 Jun 2018 02:56:19 -0400 Subject: gnu: linux-libre@4.14: Update to 4.14.49. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.49. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a42fb797c8..01eec5e9ee 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -404,8 +404,8 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.48") -(define %linux-libre-4.14-hash "011lkq30gpvbgvg2p1nw2kqkig9a3qridy678rkx3fpah0ya4rhd") +(define %linux-libre-4.14-version "4.14.49") +(define %linux-libre-4.14-hash "0p6xwgrkzccapdyrk20hsd3icad5j5grjh2n1ixflkabhbqp7cb2") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From 95d9d95a04e9d299eb85c5f9bade9caa9c3cdef6 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 12 Jun 2018 02:57:20 -0400 Subject: gnu: linux-libre: Update to 4.17.1. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.1. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 01eec5e9ee..69c81591f1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -395,8 +395,8 @@ 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 "4.17") -(define %linux-libre-hash "0abbqrq96kn97jr02mf4ahqg7hl9vhq95c1l2z0s7jqrmhv1n8pb") +(define %linux-libre-version "4.17.1") +(define %linux-libre-hash "1sxil6m17vwpaj0jg8jyrbi1mr5sjfnvhxkjaxshh6j2pdg575pw") (define-public linux-libre (make-linux-libre %linux-libre-version -- cgit v1.2.3 From 32872458a6a75f6c6a2ca5984e02863475ec323a Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Tue, 12 Jun 2018 08:26:44 +0200 Subject: gnu: wine-staging-patchset-data: Update to 3.10. * gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.10. --- gnu/packages/wine.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index bee6f0571f..ba0a60c7a2 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -223,7 +223,7 @@ integrate Windows applications into your desktop.") (define-public wine-staging-patchset-data (package (name "wine-staging-patchset-data") - (version "3.9") + (version "3.10") (source (origin (method url-fetch) @@ -232,7 +232,7 @@ integrate Windows applications into your desktop.") (file-name (string-append name "-" version ".zip")) (sha256 (base32 - "0akccqrp1ymjrra2c99f6hxlaa77jyihfs3q8x93vkgb9c0lq5xx")))) + "14rf3g9szxygbd6ypg6zbqw1h84rn8gqgrzwi607xwgh8wm59sli")))) (build-system trivial-build-system) (native-inputs `(("bash" ,bash) -- cgit v1.2.3 From 14cb7966ba4dd1f0750a4949132948ff20d95d8b Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Tue, 12 Jun 2018 08:28:23 +0200 Subject: gnu: wine-staging: Update to 3.10. * gnu/packages/wine.scm (wine-staging): Update to 3.10. --- gnu/packages/wine.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index ba0a60c7a2..6a936c7916 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -279,7 +279,7 @@ integrate Windows applications into your desktop.") (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "0ddphvlp9lsjyqc6zckinc36bggpkg925v0x2vqr8nkdjs0w5bfc")))) + "1df6g8g5nfb4ca218m78giqp3k1fmv0grv26387rbn3wkk3mql6p")))) (inputs `(("autoconf" ,autoconf) ; for autoreconf ("gtk+" ,gtk+) ("libva" ,libva) -- cgit v1.2.3 From 5b47ea9462696f59ab4530cc479ac37f528dcecf Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 10:37:52 +0300 Subject: gnu: font-gnu-unifont: Update to 11.0.01. * gnu/packages/fonts.scm (font-gnu-unifont): Update to 11.0.01. --- gnu/packages/fonts.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 031df7faa7..204f23a804 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -617,7 +617,7 @@ languages, plus Greek and Cyrillic.") (define-public font-gnu-unifont (package (name "font-gnu-unifont") - (version "10.0.07") + (version "11.0.01") (source (origin (method url-fetch) (uri (string-append @@ -625,7 +625,7 @@ languages, plus Greek and Cyrillic.") version ".tar.gz")) (sha256 (base32 - "1js8dn4v4pv8jqprsxa1fv4fs3hqhm9x4dj19fg9qgc8fx7k0v0k")))) + "1nkapra0ic4fp3lmnvfc6jly62yskhcdkwrnq29hvh3xs51ncc52")))) (build-system gnu-build-system) (outputs '("out" ; TrueType version "pcf" ; PCF (bitmap) version @@ -650,12 +650,12 @@ languages, plus Greek and Cyrillic.") (psf (string-append (assoc-ref outputs "psf") "/share/consolefonts")) (bin (assoc-ref outputs "bin"))) - (system* "make" - (string-append "PREFIX=" bin) - (string-append "TTFDEST=" ttf) - (string-append "PCFDEST=" pcf) - (string-append "CONSOLEDEST=" psf) - "install") + (invoke "make" + (string-append "PREFIX=" bin) + (string-append "TTFDEST=" ttf) + (string-append "PCFDEST=" pcf) + (string-append "CONSOLEDEST=" psf) + "install") ;; Move Texinfo file to the right place. (mkdir (string-append bin "/share/info")) (rename-file (string-append bin "/share/unifont/unifont.info.gz") -- cgit v1.2.3 From b37404740e77a4eeb465a3acd52c244dc0739b42 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 10:45:47 +0300 Subject: gnu: speedtest-cli: Update to 2.0.2. * gnu/packages/networking.scm (speedtest-cli): Update to 2.0.2. [source]: Switch to a git checkout. --- gnu/packages/networking.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 40e8f34443..e040ef339c 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1350,16 +1350,17 @@ networks.") (define-public speedtest-cli (package (name "speedtest-cli") - (version "2.0.0") + (version "2.0.2") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/sivel/speedtest-cli/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/sivel/speedtest-cli") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "16kcpba7nmszz2h0fq7qvv6src20syck2wlknaacg69kk88aybbk")))) + "0vv2z37g2kgm2dzkfa4bhri92hs0d1acxi8z66gznsl5148q7sdi")))) (build-system python-build-system) (home-page "https://github.com/sivel/speedtest-cli") (synopsis "Internet bandwidth tester") -- cgit v1.2.3 From 35a7e5742fdfad3747078d2e3bef6630f24b2b24 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 10:57:21 +0300 Subject: gnu: vim-airline: Update to 0.9. * gnu/packages/vim.scm (vim-airline): Update to 0.9. [source]: Switch to git checkout. --- gnu/packages/vim.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 76240d85f1..fd74b261c6 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -493,16 +493,17 @@ commit or run any Git arbitrary command.") (define-public vim-airline (package (name "vim-airline") - (version "0.8") + (version "0.9") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/vim-airline/vim-airline/" - "archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/vim-airline/vim-airline") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "053sfq3jmgdc5y7zbg6jrk7r2hp0raj3y3mxa2h1c1bnkb6wvcaz")))) + "0hq3304rhakx7x1v7wll7gxinmfz6561bq97qpj8jrk19rhcab75")))) (build-system gnu-build-system) (arguments `(#:tests? #f -- cgit v1.2.3 From 261348e20d25be2e8e4997ceb21811dd821df367 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 11:07:57 +0300 Subject: gnu: vim-fugitive: Update to 2.3. * gnu/packages/vim.scm (vim-fugitive): Update to 2.3. --- gnu/packages/vim.scm | 69 +++++++++++++++++++++++++--------------------------- 1 file changed, 33 insertions(+), 36 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index fd74b261c6..898a4b3533 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -450,45 +450,42 @@ trouble using them, because you do not have to remember each snippet name.") (home-page "https://github.com/Shougo/context_filetype.vim") (license license:expat)))) ; ??? check again -;; The 2.2 release was in 2015, no new releases planned. (define-public vim-fugitive - (let ((commit "de6c05720cdf74c0218218d7207f700232a5b6dc") - (revision "1")) - (package - (name "vim-fugitive") - (version (string-append "2.2-" revision "." (string-take commit 7))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/tpope/vim-fugitive.git") - (commit commit))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "0zg9vv7hirnx45vc2mwgg0xijmwwz55bssyd6cpdz71wbhrcpxxb")))) - (build-system gnu-build-system) - (arguments - '(#:tests? #f - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'build) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (vimfiles (string-append out "/share/vim/vimfiles")) - (doc (string-append vimfiles "/doc")) - (plugin (string-append vimfiles "/plugin"))) - (copy-recursively "doc" doc) - (copy-recursively "plugin" plugin) - #t)))))) - (home-page "https://github.com/tpope/vim-fugitive") - (synopsis "Vim plugin to work with Git") - (description "Vim-fugitive is a wrapper for Vim that complements the + (package + (name "vim-fugitive") + (version "2.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tpope/vim-fugitive.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17s94a8g5z0lrs7yy4nyqyvp9ykys5ws2ar3m3c0bjsn0iazd7m3")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (vimfiles (string-append out "/share/vim/vimfiles")) + (doc (string-append vimfiles "/doc")) + (plugin (string-append vimfiles "/plugin"))) + (copy-recursively "doc" doc) + (copy-recursively "plugin" plugin) + #t)))))) + (home-page "https://github.com/tpope/vim-fugitive") + (synopsis "Vim plugin to work with Git") + (description "Vim-fugitive is a wrapper for Vim that complements the command window, where you can stage and review your changes before the next commit or run any Git arbitrary command.") - (license license:vim)))) ; distributed under the same license as vim + (license license:vim))) ; distributed under the same license as vim (define-public vim-airline (package -- cgit v1.2.3 From c71cc133ecdb314fc4862739e615c08aca429746 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 11:12:33 +0300 Subject: gnu: vim-syntastic: Update to 3.9.0. * gnu/packages/vim.scm (vim-syntastic): Update to 3.9.0. [source]: Switch to git checkout. --- gnu/packages/vim.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 898a4b3533..c6906b12cf 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -573,16 +573,17 @@ and powerline symbols, etc.") (define-public vim-syntastic (package (name "vim-syntastic") - (version "3.8.0") + (version "3.9.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/vim-syntastic/syntastic/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/vim-syntastic/syntastic") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wsnd9bsp5x6yiw96h1bnd1vyxdkh130hb82kyyxydgsplx92ima")))) + "121a1mxgfng2y5zmivyyk02mca8pyw72crivf4f1q9nhn0barf57")))) (build-system gnu-build-system) (arguments `(#:tests? #f -- cgit v1.2.3 From 3d39130926c6eed89d8ed60205a4e4531f39403b Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 9 Jun 2018 18:59:37 +0800 Subject: gnu: Add libostree. * gnu/packages/package-management.scm (libostree): New variable. --- gnu/packages/package-management.scm | 59 +++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 18a848edc2..19954c3608 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Julien Lepiller ;;; Copyright © 2018 Rutger Helling +;;; Copyright © 2018 Sou Bunnbu ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,9 +27,12 @@ (define-module (gnu packages package-management) #:use-module (gnu packages) #:use-module (gnu packages acl) + #:use-module (gnu packages attr) + #:use-module (gnu packages avahi) #:use-module (gnu packages autotools) #:use-module (gnu packages backup) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages bison) #:use-module (gnu packages bootstrap) ;for 'bootstrap-guile-origin' #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -36,6 +40,7 @@ #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages databases) + #:use-module (gnu packages docbook) #:use-module (gnu packages file) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) @@ -883,3 +888,57 @@ Microsoft cabinet (.@dfn{CAB}) files.") and sign Windows@tie{}Installer (.@dfn{MSI}) files. It aims to be a solution for packaging and deployment of cross-compiled Windows applications.") (license license:lgpl2.1+))) + +(define-public libostree + (package + (name "libostree") + (version "2018.5") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/ostreedev/ostree/releases/download/v" + version "/libostree-" version ".tar.xz")) + (sha256 + (base32 + "0q82d6rvp119nx7ck7j63a591kz8vg7v465kf9ygh8kzg875l3xd")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; Don't try to use the non-existing '/var/tmp' as test + ;; directory. + (setenv "TEST_TMPDIR" (getenv "TMPDIR")) + #t))) + ;; XXX: fails with: + ;; tap-driver.sh: internal error getting exit status + ;; tap-driver.sh: fatal: I/O or internal error + #:tests? #f)) + (native-inputs + `(("attr" ,attr) ; for tests + ("bison" ,bison) + ("glib:bin" ,glib "bin") ; for 'glib-mkenums' + ("gobject-introspection" ,gobject-introspection) + ("pkg-config" ,pkg-config) + ("xsltproc" ,libxslt))) + (inputs + `(("avahi" ,avahi) + ("docbook-xml" ,docbook-xml-4.2) + ("docbook-xsl" ,docbook-xsl) + ("e2fsprogs" ,e2fsprogs) + ("fuse" ,fuse) + ("glib" ,glib) + ("gpgme" ,gpgme) + ("libarchive" ,libarchive) + ("libsoup" ,libsoup) + ("nettle" ,nettle) ; required by 'libarchive.la' + ("util-linux" ,util-linux))) + (home-page "https://ostree.readthedocs.io/en/latest/") + (synopsis "Operating system and container binary deployment and upgrades") + (description + "@code{libostree} is both a shared library and suite of command line +tools that combines a \"git-like\" model for committing and downloading +bootable filesystem trees, along with a layer for deploying them and managing +the bootloader configuration.") + (license license:lgpl2.0+))) -- cgit v1.2.3 From efdaf8def0add48e4024dfd102d8f3c1368e90c9 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 9 Jun 2018 19:00:57 +0800 Subject: gnu: Add umoci. * gnu/packages/virtualization.scm (umoci): New variable. --- gnu/packages/virtualization.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index d2419df980..db7c44b2ca 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -864,3 +864,48 @@ packaged according to the Container Initiative (OCI) format} and is a compliant implementation of the Open Container Initiative specification.") (license asl2.0))) + +(define-public umoci + (package + (name "umoci") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/openSUSE/umoci/releases/download/v" + version "/umoci.tar.xz")) + (file-name (string-append "umoci-" version ".tar.xz")) + (sha256 + (base32 + "0hg7hs4dagj2fgymm4b4s68k1v2k2093s3jg0d94j0ixhfmyg9nd")))) + (build-system go-build-system) + (arguments + '(#:import-path "github.com/openSUSE/umoci" + #:install-source? #f + #:phases + (modify-phases %standard-phases + (replace 'unpack + (lambda* (#:key source import-path #:allow-other-keys) + ;; Unpack the tarball into 'umoci' instead of "runc-${version}". + (let ((dest (string-append "src/" import-path))) + (mkdir-p dest) + (invoke "tar" "-C" (string-append "src/" import-path) + "--strip-components=1" + "-xvf" source)))) + (replace 'build + (lambda* (#:key import-path #:allow-other-keys) + (chdir (string-append "src/" import-path)) + ;; TODO: build manpages with 'go-md2man'. + (invoke "make" "SHELL=bash"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bindir (string-append out "/bin"))) + (install-file "umoci" bindir) + #t)))))) + (home-page "https://umo.ci/") + (synopsis "Tool for modifying Open Container images") + (description + "@command{umoci} is a tool that allows for high-level modification of an +Open Container Initiative (OCI) image layout and its tagged images.") + (license asl2.0))) -- cgit v1.2.3 From 7714a06943a46c6b1881e2514131c1946428d270 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 9 Jun 2018 19:01:27 +0800 Subject: gnu: Add skopeo. * gnu/packages/virtualization.scm (skopeo): New variable. --- gnu/packages/virtualization.scm | 65 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index db7c44b2ca..61f0245289 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -45,6 +45,7 @@ #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) + #:use-module (gnu packages gnupg) #:use-module (gnu packages golang) #:use-module (gnu packages gtk) #:use-module (gnu packages image) @@ -52,6 +53,7 @@ #:use-module (gnu packages linux) #:use-module (gnu packages ncurses) #:use-module (gnu packages networking) + #:use-module (gnu packages package-management) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages polkit) @@ -71,6 +73,7 @@ #:use-module (guix build-system go) #:use-module (guix build-system python) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:select (gpl2 gpl2+ gpl3+ lgpl2.1 lgpl2.1+ asl2.0)) #:use-module (guix packages) @@ -909,3 +912,65 @@ Open Container Initiative specification.") "@command{umoci} is a tool that allows for high-level modification of an Open Container Initiative (OCI) image layout and its tagged images.") (license asl2.0))) + +(define-public skopeo + (package + (name "skopeo") + (version "0.1.28") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/projectatomic/skopeo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "068nwrr3nr27alravcq1sxyhdd5jjr24213vdgn1dqva3885gbi0")))) + (build-system go-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("btrfs-progs" ,btrfs-progs) + ("eudev" ,eudev) + ("libassuan" ,libassuan) + ("libselinux" ,libselinux) + ("libostree" ,libostree) + ("lvm2" ,lvm2) + ("glib" ,glib) + ("gpgme" ,gpgme))) + (arguments + '(#:import-path "github.com/projectatomic/skopeo" + #:install-source? #f + #:phases + (modify-phases %standard-phases + (replace 'build + (lambda* (#:key import-path #:allow-other-keys) + (chdir (string-append "src/" import-path)) + ;; TODO: build manpages with 'go-md2man'. + (invoke "make" "binary-local"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (invoke "make" "install-binary" "install-completions" + (string-append "PREFIX=" out)))))))) + (home-page "https://github.com/projectatomic/skopeo") + (synopsis "Interact with container images and container image registries") + (description + "@command{skopeo} is a command line utility providing various operations +with container images and container image registries. It can: +@enumerate + +@item Copy container images between various containers image stores, +converting them as necessary. + +@item Convert a Docker schema 2 or schema 1 container image to an OCI image. + +@item Inspect a repository on a container registry without needlessly pulling +the image. + +@item Sign and verify container images. + +@item Delete container images from a remote container registry. + +@end enumerate") + (license asl2.0))) -- cgit v1.2.3 From e68e4a906f2a3ca74cf3f0ae9ddf7ad6d627b6ac Mon Sep 17 00:00:00 2001 From: Ben Sturmfels Date: Tue, 7 Nov 2017 23:37:38 +1100 Subject: gnu: fabric: Disable problematic tests. Reported by Ricardo Wurmus at . * gnu/packages/admin.scm (fabric): Add custom check phase to disable two tests. --- gnu/packages/admin.scm | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 6b8df3fb9b..6e9888cf3b 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2359,11 +2359,23 @@ Intel DRM Driver.") "13r0b0hllgf8j9rh6x1knmbgvingbdmx046aazv6vck2ll120mw1")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ; Python 2 only + `(#:python ,python-2 ; Python 2 only + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke + "nosetests" "-v" "tests/" + ;; This test hangs indefinitely when run on a single core VM + ;; (see GNU bug #26647 and Debian bug #850230). + "--exclude=test_nested_execution_with_explicit_ports" + ;; This test randomly fails in certain environments causing too + ;; much noise to be useful (see Debian bug #854686). + "--exclude=test_should_use_sentinel_for_tasks_that_errored")))))) (native-inputs - `(("python2-fudge" ,python2-fudge) - ("python2-jinja2" ,python2-jinja2) - ("python2-nose" ,python2-nose) + `(("python2-fudge" ,python2-fudge) ; Requires < 1.0 + ("python2-jinja2" ,python2-jinja2) ; Requires < 3.0 + ("python2-nose" ,python2-nose) ; Requires < 2.0 ("python2-pynacl" ,python2-pynacl) ("python2-bcrypt" ,python2-bcrypt))) (propagated-inputs -- cgit v1.2.3 From 66266d3290ec447d6f71bb78bc5cd077c808b966 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 11 Jun 2018 15:46:24 -0400 Subject: gnu: borg: Update to 1.1.6. * gnu/packages/backup.scm (borg): Update to 1.1.6. [arguments]: Remove the 'adjust-msgpack-dependency' phase because it has been adopted upstream. --- gnu/packages/backup.scm | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 444559ea80..711bd32245 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -472,13 +472,13 @@ detection, and lossless compression.") (define-public borg (package (name "borg") - (version "1.1.5") + (version "1.1.6") (source (origin (method url-fetch) (uri (pypi-uri "borgbackup" version)) (sha256 - (base32 "0gbdnq7ks46diz6y2pf6wpwkb9hy6hp3immi7jg3h7w72b3ycmj3")) + (base32 "0c09j46fi8i7klas0bh82a4whlwnajshk0izkgax6fjxr1sf9lm1")) (modules '((guix build utils))) (snippet '(begin @@ -511,17 +511,6 @@ detection, and lossless compression.") ;; HOME=/homeless-shelter. (setenv "HOME" "/tmp") #t))) - ;; Later versions of msgpack were disallowed to some warnings and lack - ;; of support for Python versions that we don't support anyways. So, - ;; it's okay to to keep using more recents versions of msgpack for - ;; Borg. Also see the note about msgpack in the list of inputs. - ;; https://github.com/borgbackup/borg/issues/3517#issuecomment-357221978 - (add-before 'build 'adjust-msgpack-dependency - (lambda _ - (substitute* "setup.py" - (("msgpack-python>=0.4.6,<0.5.0") - "msgpack-python>=0.4.6")) - #t)) ;; The tests need to be run after Borg is installed. (delete 'check) (add-after 'install 'check -- cgit v1.2.3 From feed5194b10187891ddb04c0855d02a4e31aa720 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Tue, 12 Jun 2018 20:38:01 +0800 Subject: gnu: python-urwid, python2-urwid: Update to 2.0.1. * gnu/packages/python.scm (python-urwid, python2-urwird): Update to 2.0.1. --- gnu/packages/python.scm | 32 +++----------------------------- 1 file changed, 3 insertions(+), 29 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3907fd66bd..0f28102ce0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4871,26 +4871,15 @@ computing.") (define-public python-urwid (package (name "python-urwid") - (version "1.3.1") + (version "2.0.1") (source (origin (method url-fetch) (uri (pypi-uri "urwid" version)) (sha256 (base32 - "18cnd1wdjcas08x5qwa5ayw6jsfcn33w4d9f7q3s29fy6qzc1kng")))) + "1g6cpicybvbananpjikmjk8npmjk4xvak1wjzji62wc600wkwkb4")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; Disable failing test. Bug filed upstream: - ;; https://github.com/wardi/urwid/issues/164 - ;; TODO: check again for python-urwid > 1.3.1 or python > 3.4.3. - (add-after 'unpack 'disable-failing-test - (lambda _ - (substitute* "urwid/tests/test_event_loops.py" - (("test_remove_watch_file") - "disable_remove_watch_file"))))))) (home-page "http://urwid.org") (synopsis "Console user interface library for Python") (description @@ -4899,22 +4888,7 @@ features useful for text console applications.") (license license:lgpl2.1+))) (define-public python2-urwid - (let ((python2-urwid (package-with-python2 python-urwid))) - (package - (inherit python2-urwid) - (arguments - (append - `(;; Explicitly using Python 2 is necessary due the argument list being - ;; built from only the 'delete-test_vterm.py' phase and python-urwid's - ;; package arguments, which by default assumes the use of Python 3. - #:python ,python-2 - #:phases - (modify-phases %standard-phases - ;; Disable the vterm tests because of non-deterministic failures - ;; with Python 2. See https://github.com/urwid/urwid/issues/230. - (add-after 'unpack 'delete-test_vterm.py - (delete-file "urwid/tests/test_vterm.py")))) - (package-arguments python-urwid)))))) + (package-with-python2 python-urwid)) (define-public python-urwidtrees (package -- cgit v1.2.3 From b5edc4791240d06aae07d6b8c4cb7a7b3f1937b1 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 12 Jun 2018 09:26:40 +0200 Subject: gnu: flann: Fix builds with CMake >= 3.11. * gnu/packages/patches/flann-cmake-3.11.patch: New file. * gnu/packages/maths.scm (flann)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/maths.scm | 3 +- gnu/packages/patches/flann-cmake-3.11.patch | 84 +++++++++++++++++++++++++++++ 3 files changed, 87 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/flann-cmake-3.11.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 1957fb66cb..f3da9353a3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -670,6 +670,7 @@ dist_patch_DATA = \ %D%/packages/patches/file-CVE-2017-1000249.patch \ %D%/packages/patches/findutils-localstatedir.patch \ %D%/packages/patches/findutils-test-xargs.patch \ + %D%/packages/patches/flann-cmake-3.11.patch \ %D%/packages/patches/flint-ldconfig.patch \ %D%/packages/patches/fltk-shared-lib-defines.patch \ %D%/packages/patches/fltk-xfont-on-demand.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ee5be3ed5d..208a75cbcd 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3372,7 +3372,8 @@ in finite element programs.") version "-src.zip")) (sha256 (base32 - "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")))) + "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")) + (patches (search-patches "flann-cmake-3.11.patch")))) (build-system cmake-build-system) (outputs '("out" "octave")) ;46 MiB .mex file that pulls Octave diff --git a/gnu/packages/patches/flann-cmake-3.11.patch b/gnu/packages/patches/flann-cmake-3.11.patch new file mode 100644 index 0000000000..1fb76eca0a --- /dev/null +++ b/gnu/packages/patches/flann-cmake-3.11.patch @@ -0,0 +1,84 @@ +Fixes this issue: + . +Patch from Buildroot: + . + +From fa5ec96a94646492a3f908e12905b3e48a8e800b Mon Sep 17 00:00:00 2001 +From: Romain Naour +Date: Wed, 18 Apr 2018 20:24:13 +0200 +Subject: [PATCH] src/cpp: fix cmake >= 3.11 build + +CMake < 3.11 doesn't support add_library() without any source file +(i.e add_library(foo SHARED)). But flann CMake use a trick that use +an empty string "" as source list (i.e add_library(foo SHARED "")). +This look like a bug in CMake < 3.11. + +With CMake >= 3.11, the new behaviour of add_library() break the +existing flann CMake code. + +From CMake Changelog [1]: +"add_library() and add_executable() commands can now be called without + any sources and will not complain as long as sources are added later + via the target_sources() command." + +Note: flann CMake code doesn't use target_sources() since no source file +are provided intentionally since the flann shared library is created by +linking with the flann_cpp_s static library with this line: + +target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +If you try to use "add_library(flann_cpp SHARED ${CPP_SOURCES})" (as it should +be normally done), the link fail due to already defined symbol. + +They are building the shared version using the static library "to speedup the +build time" [3] + +This issue is already reported upstream [2] with a proposed solution. + +Upstream status: Pending + +Fixes: +http://autobuild.buildroot.net/results/b2f/b2febfaf8c44ce477b3e4a5b9b976fd25e8d7454 + +[1] https://cmake.org/cmake/help/v3.11/release/3.11.html +[2] https://github.com/mariusmuja/flann/issues/369 +[3] https://github.com/mariusmuja/flann/commit/0fd62b43be2fbb0b8d791ee36290791224dc030c + +Signed-off-by: Romain Naour +--- + src/cpp/CMakeLists.txt | 4 ++-- + src/cpp/empty.cpp | 1 + + 2 files changed, 3 insertions(+), 2 deletions(-) + create mode 100644 src/cpp/empty.cpp + +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt +index b44a735..a816863 100644 +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt +@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) + endif() + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann_cpp SHARED "") ++ add_library(flann_cpp SHARED "empty.cpp") + set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +@@ -85,7 +85,7 @@ if (BUILD_C_BINDINGS) + set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann SHARED "") ++ add_library(flann SHARED "empty.cpp") + set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) + else() +diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp +new file mode 100644 +index 0000000..40a8c17 +--- /dev/null ++++ b/src/cpp/empty.cpp +@@ -0,0 +1 @@ ++/* empty */ +-- +2.14.3 -- cgit v1.2.3 From 90977eb55efa0a005c52ec41fdb0edd67f2af5cb Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 12 Jun 2018 15:01:58 +0200 Subject: gnu: guile-bytestructures: Update to 1.0.3. * gnu/packages/guile.scm (guile-bytestructures): Update to 1.0.3. (guile-git)[arguments]: Remove. The workaround for is no longer needed. --- gnu/packages/guile.scm | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index a88d24885f..4cd26cf7f2 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -1786,7 +1786,7 @@ is no support for parsing block and inline level HTML.") (define-public guile-bytestructures (package (name "guile-bytestructures") - (version "1.0.1") + (version "1.0.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/TaylanUB/scheme-bytestructures" @@ -1794,7 +1794,7 @@ is no support for parsing block and inline level HTML.") "/bytestructures-" version ".tar.gz")) (sha256 (base32 - "1lnfcy65mqj823lamy2n2vaghdz0g7mj011bgnhmd6hwpnaidnh2")))) + "0xf6s8gd3656j8k2ar6y7i62r68azawyzxhsagsk8nvldnrs1r18")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -2002,20 +2002,6 @@ is not available for Guile 2.0.") "0z1dvn0scx59pbgjkpacam7p5n7630z4qm8fazim7ixq9xv3s8wx")) (file-name (git-file-name name version)))) (build-system gnu-build-system) - (arguments - `(#:phases (modify-phases %standard-phases - ;; FIXME: On i686, bytestructures miscalculates the offset - ;; of the 'old-file' and 'new-file' fields within the - ;; '%diff-delta' structure. See - ;; . - ,@(if (string=? (%current-system) "x86_64-linux") - '() - '((add-before 'check 'skip-tests - (lambda _ - (substitute* "Makefile" - (("tests/status\\.scm") - "")) - #t))))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) -- cgit v1.2.3 From a9e7d6564b42cf62bab73eef3cf2bc99851ef379 Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 12 Jun 2018 16:11:51 +0200 Subject: gnu: multipath-tools: Fix build. (multipath-tools)[arguments]: Pass -n to gzip to avoid timestamp related warnings causing build failures. --- gnu/packages/linux.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 69c81591f1..377d46d502 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2995,7 +2995,10 @@ arrays when needed.") (let ((lvm2 (assoc-ref inputs "lvm2")) (udev (assoc-ref inputs "udev"))) (substitute* "Makefile.inc" - (("\\$\\(prefix\\)/usr") "$(prefix)")) + (("\\$\\(prefix\\)/usr") "$(prefix)") + ;; Do not save timestamp to avoid gzip "timestamp + ;; out-of-range" warnings. + (("gzip -9") "gzip -9n")) (substitute* '("kpartx/Makefile" "libmultipath/Makefile") (("/usr/include/libdevmapper.h") (string-append lvm2 "/include/libdevmapper.h")) -- cgit v1.2.3 From 6921e95ae80daad8cbd08fccaf2516298c196149 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 12 Jun 2018 19:08:32 +0300 Subject: gnu: mame: Fix renaming executable. * gnu/packages/emulators.scm (mame)[arguments]: Only rename 'mame64' to 'mame' when 'mame64' exists. --- gnu/packages/emulators.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index a7c9104683..1687c9652f 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -1235,7 +1235,8 @@ play them on systems for which they were never designed!") (find-files "keymaps" ".*LINUX\\.map"))) (let ((fonts (string-append share "/fonts"))) (install-file "uismall.bdf" fonts)) - (rename-file "mame64" "mame") + (when (file-exists? "mame64") + (rename-file "mame64" "mame")) (install-file "mame" (string-append out "/bin"))) #t)) (add-after 'install 'install-documentation -- cgit v1.2.3 From 67cb662a31988a8e9ec3a8d7bc7541d043af6347 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Mon, 11 Jun 2018 21:07:53 +0200 Subject: gnu: mes: Update to 0.15. * gnu/packages/mes.scm (mes): Update to 0.15. --- gnu/packages/mes.scm | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm index a8a19854de..8183b2b827 100644 --- a/gnu/packages/mes.scm +++ b/gnu/packages/mes.scm @@ -73,7 +73,7 @@ extensive examples, including parsers for the Javascript and C99 languages.") (let ((triplet "i686-unknown-linux-gnu")) (package (name "mes") - (version "0.14") + (version "0.15") (source (origin (method url-fetch) (uri (string-append "https://gitlab.com/janneke/mes" @@ -81,7 +81,7 @@ extensive examples, including parsers for the Javascript and C99 languages.") "/mes-" version ".tar.gz")) (sha256 (base32 - "1i23jk61iibjza2s3lka56ry4ma424g2fyk8pjd5bd1dyjd0yrzf")))) + "0kj2ywgii1795gxj6k29zxa0848h2j0ihbwlgn55wdalswl165dq")))) (build-system gnu-build-system) (supported-systems '("i686-linux" "x86_64-linux")) (propagated-inputs @@ -98,9 +98,7 @@ extensive examples, including parsers for the Javascript and C99 languages.") '()) ("perl" ,perl))) ;build-aux/gitlog-to-changelog (arguments - `(#:make-flags (list - (string-append "PREFIX=" (assoc-ref %outputs "out"))) - #:phases + `(#:phases (modify-phases %standard-phases (add-before 'install 'generate-changelog (lambda _ -- cgit v1.2.3 From bea07c7f550e0031950a333044699a1126f765fa Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 12 Jun 2018 15:12:12 -0400 Subject: gnu: python-llfuse: Update to 1.3.3. * gnu/packages/python.scm (python-llfuse, python2-llfuse): Update to 1.3.3. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0f28102ce0..88bbf3b7e5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6007,13 +6007,13 @@ should be stored on various operating systems.") (define-public python-llfuse (package (name "python-llfuse") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (pypi-uri "llfuse" version ".tar.bz2")) (sha256 (base32 - "0qxvnbz41bpvpc1vbi8qkhmpr9gj1qrrp5jdj085iqibd8l2l9cn")))) + "1rqww632y2zz71xmr6ch7yq80kvza9mhqr2z773k0d8l1lwzl575")))) (build-system python-build-system) (inputs `(("fuse" ,fuse) -- cgit v1.2.3 From 359e30c9ea8985738c3dc1057438abb7215d608b Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 30 May 2018 19:37:25 +0200 Subject: gnu: Add qtwebview. * gnu/packages/qt.scm (qtwebview): New variable. --- gnu/packages/qt.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 7d323cd2d5..107b5dff49 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017 Quiliro ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Nicolas Goaziou +;;; Copyright © 2018 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. ;;; @@ -1069,6 +1070,29 @@ between the host (QML/C++ application) and the client (HTML/JavaScript application). The transport mechanism is supported out of the box by the two popular web engines, Qt WebKit 2 and Qt WebEngine."))) +(define-public qtwebview + (package (inherit qtsvg) + (name "qtwebview") + (version "5.11.0") + (source (origin + (method url-fetch) + (uri (string-append "https://download.qt.io/official_releases/qt/" + (version-major+minor version) "/" version + "/submodules/" name "-everywhere-src-" + version ".tar.xz")) + (sha256 + (base32 + "0a89v8mj5pb7a7whyhasf4ms0n34ghfmv2qp0pyxnq56f2bsjbl4")))) + (native-inputs + `(("perl" ,perl))) + (inputs + `(("qtbase" ,qtbase) + ("qtdeclarative" ,qtdeclarative))) + (synopsis "Display web content in a QML application") + (description "Qt WebView provides a way to display web content in a QML +application without necessarily including a full web browser stack by using +native APIs where it makes sense."))) + (define-public qtlocation (package (inherit qtsvg) (name "qtlocation") -- cgit v1.2.3 From b5792b9cb8c592d4b6da76bbb2acb55cd233e715 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Wed, 30 May 2018 23:47:20 +0200 Subject: gnu: Add qtwebglplugin. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/qt.scm (qtwebglplugin): New variable. Co-authored-by: 宋文武 --- gnu/packages/qt.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 107b5dff49..a15d6453c9 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1070,6 +1070,32 @@ between the host (QML/C++ application) and the client (HTML/JavaScript application). The transport mechanism is supported out of the box by the two popular web engines, Qt WebKit 2 and Qt WebEngine."))) +(define-public qtwebglplugin + (package (inherit qtsvg) + (name "qtwebglplugin") + (version "5.11.0") + (source (origin + (method url-fetch) + (uri (string-append "https://download.qt.io/official_releases/qt/" + (version-major+minor version) "/" version + "/submodules/" name "-everywhere-src-" + version ".tar.xz")) + (sha256 + (base32 + "1al7dv7i9rg4z4p8vnipbjbbgc6113lbfjggxxap3sn6hqs986fm")))) + (native-inputs '()) + (inputs + `(("mesa" ,mesa) + ("qtbase" ,qtbase) + ("qtwebsockets" ,qtwebsockets))) + (synopsis "QPA plugin for running an application via a browser using +streamed WebGL commands") + (description "Qt back end that uses WebGL for rendering. It allows Qt +applications (with some limitations) to run in a web browser that supports +WebGL. WebGL is a JavaScript API for rendering 2D and 3D graphics within any +compatible web browser without the use of plug-ins. The API is similar to +OpenGL ES 2.0 and can be used in HTML5 canvas elements"))) + (define-public qtwebview (package (inherit qtsvg) (name "qtwebview") -- cgit v1.2.3 From 502a822dfd129fcf5acd2d35563fc4ec3785e907 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 12 Jun 2018 22:59:29 +0200 Subject: gnu: tor: Update to 0.3.3.7. * gnu/packages/tor.scm (tor): Update to 0.3.3.7. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index b18673b81b..56269dd8cf 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -47,14 +47,14 @@ (define-public tor (package (name "tor") - (version "0.3.3.6") + (version "0.3.3.7") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "1drk2h8zd05xrfpx7xn77pcxz0hs4nrq6figw56qk5gkvgv5kg4r")))) + "036ybfvldj7yfci9ipjki8smpzyxdg8c5r12bghc9yxdqh9basza")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-gcc-hardening" -- cgit v1.2.3 From 3a30ae05ae0765294525be296589356a058b66ef Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 12 Jun 2018 23:28:53 -0400 Subject: gnu: openimageio: Update to 1.7.19. * gnu/packages/graphics.scm (openimageio): Update to 1.7.19. --- gnu/packages/graphics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 439170c007..52f7ff3ba6 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -373,7 +373,7 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.") (define-public openimageio (package (name "openimageio") - (version "1.6.15") + (version "1.7.19") (source (origin (method url-fetch) (uri (string-append "https://github.com/OpenImageIO/oiio/" @@ -381,7 +381,7 @@ storage of the \"EXR\" file format for storing 16-bit floating-point images.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "144crq0205d0w5aq4iglh2rhzf54a8rv3pksy6d533b75w5d7rq7")))) + "1qlmfhvl2wva4aifyiq7c4sdy61ddl7wykwvlpfys9p701xghvj7")))) (build-system cmake-build-system) ;; FIXME: To run all tests successfully, test image sets from multiple ;; third party sources have to be present. For details see -- cgit v1.2.3 From 4b3480d62f9d98bfe7dc7b0b148312f2000d70b5 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Wed, 13 Jun 2018 08:43:23 +0200 Subject: gnu: cheese: Update to 3.28.0. * gnu/packages/gnome.scm (cheese): Update to 3.28.0. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 3a9f11bd0f..1d53af7515 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -7140,7 +7140,7 @@ photo-booth-like software, such as Cheese.") (define-public cheese (package (name "cheese") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -7148,7 +7148,7 @@ photo-booth-like software, such as Cheese.") version ".tar.xz")) (sha256 (base32 - "01f6lsp9jkhq5v2zxlghw15bca4xqavkxqkl8977r0g13p22zxcf")))) + "06da5qc5hdvwwd5vkbgbx8pjx1l3mvr07yrnnv3v1hfc3wp7l7jw")))) (arguments ;; Tests require GDK. `(#:tests? #f -- cgit v1.2.3 From 14618a1ebb8060b163acd1615c828aa2c62d0651 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Wed, 13 Jun 2018 08:46:24 +0200 Subject: gnu: vkquake: Update to 1.00.0. * gnu/packages/games.scm (vkquake): Update to 1.00.0. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index c445154b69..da8fc0b1af 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4481,7 +4481,7 @@ some graphical niceities, and numerous bug-fixes and other improvements.") (package (inherit quakespasm) (name "vkquake") - (version "0.97.3") + (version "1.00.0") (source (origin (method url-fetch) @@ -4490,7 +4490,7 @@ some graphical niceities, and numerous bug-fixes and other improvements.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1p0nh2v2ilylw62fxc5qpfcmyhs0s64w8sgh036nc6kn21kbjc0d")))) + "0bviv18jvp41jvrabgl7l5kq4n1p6p3rywij481yswawdw6l5idh")))) (arguments `(#:make-flags (let ((vulkanlib (string-append (assoc-ref %build-inputs -- cgit v1.2.3 From 0c6ade0be65ea91d62a5b4372648e711371b0f5c Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Wed, 13 Jun 2018 11:26:21 +0200 Subject: gnu: openrct2: Update to 0.2.0. * gnu/packages/games.scm (openrct2-title-sequences): New variable. * gnu/packages/games.scm (openrct2-objects): New variable. * gnu/packages/games.scm (openrct2): Update to 0.2.0. [arguments]: Add phases 'fix-usr-share-path&add-data, 'fix-gcc7 and 'get-rid-of-errors. [inputs]: Add icu4c, openrct2-objects, openrct2-title-sequences. [native-inputs]: Add gcc@7. --- gnu/packages/games.scm | 124 +++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 110 insertions(+), 14 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index da8fc0b1af..ede951fc5c 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -74,6 +74,7 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages fribidi) #:use-module (gnu packages game-development) + #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gimp) @@ -2229,10 +2230,92 @@ Transport Tycoon Deluxe.") ("opensfx" ,openttd-opensfx) ,@(package-native-inputs openttd-engine))))) +(define openrct2-title-sequences + (package + (name "openrct2-title-sequences") + (version "0.1.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/OpenRCT2/title-sequences/releases/download/v" + version "/title-sequence-v" version ".zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "0qbyxrsw8hlgaq0r5d7lx7an3idy4qbfv7yiw9byhldk763n9cfw")))) + (build-system trivial-build-system) + (native-inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("unzip" ,unzip))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (openrct2-title-sequences (string-append out + "/share/openrct2/title-sequences")) + (source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) + (copy-file source (string-append ,name "-" ,version ".zip")) + (invoke unzip (string-append ,name "-" ,version ".zip")) + (delete-file (string-append ,name "-" ,version ".zip")) + (mkdir-p openrct2-title-sequences) + (copy-recursively "." + openrct2-title-sequences) + #t)))) + (home-page "https://github.com/OpenRCT2/OpenRCT2") + (synopsis "Title sequences for OpenRCT2") + (description + "openrct2-title-sequences is a set of title sequences for OpenRCT2.") + (license license:gpl3+))) + +(define openrct2-objects + (package + (name "openrct2-objects") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/OpenRCT2/objects/releases/download/v" + version "/objects.zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "1z92afhbv13j1ig6fz0x8w9vdmfchssv16vwwhb0vj40pn1g1rwy")))) + (build-system trivial-build-system) + (native-inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("unzip" ,unzip))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (openrct2-objects (string-append out + "/share/openrct2/objects")) + (source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))) + (copy-file source (string-append ,name "-" ,version ".zip")) + (invoke unzip (string-append ,name "-" ,version ".zip")) + (delete-file (string-append ,name "-" ,version ".zip")) + (mkdir-p openrct2-objects) + (copy-recursively "." + openrct2-objects) + #t)))) + (home-page "https://github.com/OpenRCT2/OpenRCT2") + (synopsis "Objects for OpenRCT2") + (description + "openrct2-objects is a set of objects for OpenRCT2.") + (license license:gpl3+))) + (define-public openrct2 (package (name "openrct2") - (version "0.1.1") + (version "0.2.0") (source (origin (method url-fetch) @@ -2240,39 +2323,52 @@ Transport Tycoon Deluxe.") version ".tar.gz")) (sha256 (base32 - "1bahkzlf9k92cc4zs4nk4wy59323kiw8d3wm0vjps3kp7iznqyjx")) + "1yrbjra27n2xxb1x47v962lc3qi8gwm5ws4f97952nvn533zrwxz")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ;; no tests available + `(#:tests? #f ; Tests require network. #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-usr-share-paths - (lambda* (#:key make-flags outputs #:allow-other-keys) + (add-after 'unpack 'fix-usr-share-paths&add-data + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((titles (assoc-ref inputs "openrct2-title-sequences")) + (objects (assoc-ref inputs "openrct2-objects"))) ;; Fix some references to /usr/share. - (substitute* "src/openrct2/platform/linux.c" + (substitute* "src/openrct2/platform/Platform.Linux.cpp" (("/usr/share") - (string-append (assoc-ref %outputs "out") "/share"))))) - (add-after 'build 'fix-cmake-install-file + (string-append (assoc-ref %outputs "out") "/share"))) + (copy-recursively (string-append titles + "/share/openrct2/title-sequences") "data/title") + (copy-recursively (string-append objects + "/share/openrct2/objects") "data/object")))) + (add-before 'configure 'fixgcc7 + (lambda _ + (unsetenv "C_INCLUDE_PATH") + (unsetenv "CPLUS_INCLUDE_PATH") + #t)) + (add-after 'fixgcc7 'get-rid-of-errors (lambda _ - ;; The build system tries to download a file and compare hashes. - ;; Since we have no network, remove this so the install doesn't fail. - (substitute* "cmake_install.cmake" - (("EXPECTED_HASH SHA1=b587d83de508d0b104d14c599b76f8565900fce0") - ""))))))) + ;; Don't treat warnings as errors. + (substitute* "CMakeLists.txt" + (("-Werror") ""))))))) (inputs `(("curl" ,curl) ("fontconfig" ,fontconfig) ("freetype" ,freetype) + ("icu4c" ,icu4c) ("jansson" ,jansson) ("libpng" ,libpng) ("libzip" ,libzip) ("mesa" ,mesa) + ("openrct2-objects" ,openrct2-objects) + ("openrct2-title-sequences" ,openrct2-title-sequences) ("openssl" ,openssl) ("sdl2" ,sdl2) ("speexdsp" ,speexdsp) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("gcc" ,gcc-7) + ("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 -- cgit v1.2.3 From 85df1a8631014d3e0c7907ddbea53f7a6c490d6b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:39:10 +0200 Subject: gnu: Add r-ggsci. * gnu/packages/cran.scm (r-ggsci): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d4af23227..bf4c8a413f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4190,3 +4190,26 @@ generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.") ;; Unspecified version of the LGPL. (license license:lgpl3+))) + +(define-public r-ggsci + (package + (name "r-ggsci") + (version "2.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggsci" version)) + (sha256 + (base32 + "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (home-page "https://nanx.me/ggsci/") + (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2") + (description + "This package provides a collection of ggplot2 color palettes inspired by +plots in scientific journals, data visualization libraries, science fiction +movies, and TV shows.") + (license license:gpl3))) -- cgit v1.2.3 From 5219c5c585375c1b92a2320800647eae5e9e09b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:39:20 +0200 Subject: gnu: Add r-ggsignif. * gnu/packages/cran.scm (r-ggsignif): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index bf4c8a413f..ea4673eb41 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4213,3 +4213,28 @@ Sequence logos can easily be combined with other ggplot2 plots.") plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.") (license license:gpl3))) + +(define-public r-ggsignif + (package + (name "r-ggsignif") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggsignif" version)) + (sha256 + (base32 + "1rn58d7pb3axk6chiihryykrzw76adaa2yiafq4d0j6qbhax78f7")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/const-ae/ggsignif") + (synopsis "Significance brackets for ggplot2") + (description + "Enrich your ggplots with group-wise comparisons. This package provides +an easy way to indicate if two groups are significantly different. Commonly +this is shown by a bracket on top connecting the groups of interest which +itself is annotated with the level of significance. The package provides a +single layer that takes the groups for comparison and the test as arguments +and adds the annotation to the plot.") + (license license:gpl3))) -- cgit v1.2.3 From 5cbaaee83f3bbf5132288466d2febaaaad6910b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:39:31 +0200 Subject: gnu: Add r-ggpubr. * gnu/packages/cran.scm (r-ggpubr): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ea4673eb41..13b0cb251d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4238,3 +4238,37 @@ itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.") (license license:gpl3))) + +(define-public r-ggpubr + (package + (name "r-ggpubr") + (version "0.1.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggpubr" version)) + (sha256 + (base32 + "0mvw215bj887958p34f0dzlrb8mgyfcz9b5zvsschvbhamqinqna")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggsci" ,r-ggsci) + ("r-ggsignif" ,r-ggsignif) + ("r-gridextra" ,r-gridextra) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-scales" ,r-scales) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.sthda.com/english/rpkgs/ggpubr") + (synopsis "ggplot2-based publication-ready plots") + (description + "The ggplot2 package is an excellent and flexible package for elegant +data visualization in R. However the default generated plots require some +formatting before we can send them for publication. The ggpubr package +provides some easy-to-use functions for creating and customizing ggplot2-based +publication-ready plots.") + (license license:gpl2))) -- cgit v1.2.3 From 141e43bd4ee536bbfbe9ec360c9f81bc9842a9fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:39:47 +0200 Subject: gnu: Add r-ellipse. * gnu/packages/cran.scm (r-ellipse): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 13b0cb251d..232e9797b7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4272,3 +4272,26 @@ formatting before we can send them for publication. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.") (license license:gpl2))) + +(define-public r-ellipse + (package + (name "r-ellipse") + (version "0.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ellipse" version)) + (sha256 + (base32 + "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/ellipse/") + (synopsis "Functions for drawing ellipses and ellipse-like confidence regions") + (description + "This package contains various routines for drawing ellipses and +ellipse-like confidence regions, implementing the plots described in Murdoch +and Chow (1996), A graphical display of large correlation matrices, The +American Statistician 50, 178-180. There are also routines implementing the +profile plots described in Bates and Watts (1988), Nonlinear Regression +Analysis and its Applications.") + (license license:gpl2+))) -- cgit v1.2.3 From cbf6017d83e094dda7f0ed96706c15997c9b0660 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:39:55 +0200 Subject: gnu: Add r-flashclust. * gnu/packages/cran.scm (r-flashclust): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 232e9797b7..6bf278bf7d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4295,3 +4295,24 @@ American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.") (license license:gpl2+))) + +(define-public r-flashclust + (package + (name "r-flashclust") + (version "1.01-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "flashClust" version)) + (sha256 + (base32 + "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8")))) + (properties `((upstream-name . "flashClust"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/flashClust/") + (synopsis "Implementation of optimal hierarchical clustering") + (description + "This package provides a fast implementation of hierarchical +clustering.") + (license license:gpl2+))) -- cgit v1.2.3 From e83841a296ef7f25a4847aa0e02456bec774a461 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:40:17 +0200 Subject: gnu: Add r-factominer. * gnu/packages/cran.scm (r-factominer): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6bf278bf7d..f3662ef14c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4316,3 +4316,37 @@ Analysis and its Applications.") "This package provides a fast implementation of hierarchical clustering.") (license license:gpl2+))) + +(define-public r-factominer + (package + (name "r-factominer") + (version "1.41") + (source + (origin + (method url-fetch) + (uri (cran-uri "FactoMineR" version)) + (sha256 + (base32 + "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259")))) + (properties `((upstream-name . "FactoMineR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-cluster" ,r-cluster) + ("r-ellipse" ,r-ellipse) + ("r-flashclust" ,r-flashclust) + ("r-lattice" ,r-lattice) + ("r-leaps" ,r-leaps) + ("r-mass" ,r-mass) + ("r-scatterplot3d" ,r-scatterplot3d))) + (home-page "http://factominer.free.fr") + (synopsis "Multivariate exploratory data analysis and data mining") + (description + "This package provides exploratory data analysis methods to summarize, +visualize and describe datasets. The main principal component methods are +available, those with the largest potential in terms of applications: +principal component analysis (PCA) when variables are quantitative, +correspondence analysis (CA) and multiple correspondence analysis (MCA) when +variables are categorical, Multiple Factor Analysis when variables are +structured in groups, etc. and hierarchical cluster analysis.") + (license license:gpl2+))) -- cgit v1.2.3 From f22bfee9454879e0356ad79efe3a029ff72b16bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:40:31 +0200 Subject: gnu: Add r-factoextra. * gnu/packages/cran.scm (r-factoextra): New variable. --- gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f3662ef14c..c971b4d34d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4350,3 +4350,38 @@ correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.") (license license:gpl2+))) + +(define-public r-factoextra + (package + (name "r-factoextra") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "factoextra" version)) + (sha256 + (base32 + "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1")))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-cluster" ,r-cluster) + ("r-dendextend" ,r-dendextend) + ("r-factominer" ,r-factominer) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-ggrepel" ,r-ggrepel) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.sthda.com/english/rpkgs/factoextra") + (synopsis "Extract and visualize the results of multivariate data analyses") + (description + "This package provides some easy-to-use functions to extract and +visualize the output of multivariate data analyses, including +@code{PCA} (Principal Component Analysis), @cod{CA} (Correspondence Analysis), +@code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor Analysis of +Mixed Data), @code{MFA} (Multiple Factor Analysis) and +@code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R +packages. It contains also functions for simplifying some clustering analysis +steps and provides ggplot2-based elegant data visualization.") + (license license:gpl2))) -- cgit v1.2.3 From 0c9868aa5b008504b2046d824f5ae428f2bbd928 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 11:47:35 +0200 Subject: gnu: Add r-nbclust. * gnu/packages/cran.scm (r-nbclust): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c971b4d34d..90eab5c288 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4385,3 +4385,24 @@ Mixed Data), @code{MFA} (Multiple Factor Analysis) and packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") (license license:gpl2))) + +(define-public r-nbclust + (package + (name "r-nbclust") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "NbClust" version)) + (sha256 + (base32 + "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c")))) + (properties `((upstream-name . "NbClust"))) + (build-system r-build-system) + (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package") + (synopsis "Determine the best number of clusters in a data set") + (description + "NbClust provides 30 indexes for determining the optimal number of +clusters in a data set and offers the best clustering scheme from different +results to the user.") + (license license:gpl2))) -- cgit v1.2.3 From 546fc4aa552f41bec393368f6e9a9bfa2908eb9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:58:03 +0200 Subject: gnu: Add r-hdf5r. * gnu/packages/cran.scm (r-hdf5r): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 90eab5c288..60210c376d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -30,6 +30,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system r) + #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) @@ -4406,3 +4407,31 @@ steps and provides ggplot2-based elegant data visualization.") clusters in a data set and offers the best clustering scheme from different results to the user.") (license license:gpl2))) + +(define-public r-hdf5r + (package + (name "r-hdf5r") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "hdf5r" version)) + (sha256 + (base32 + "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva")))) + (build-system r-build-system) + (inputs + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) + (propagated-inputs + `(("r-bit64" ,r-bit64) + ("r-r6" ,r-r6))) + (home-page "https://hhoeflin.github.io/hdf5r") + (synopsis "Interface to the HDF5 binary data format") + (description + "HDF5 is a data model, library and file format for storing and managing +large amounts of data. This package provides a nearly feature complete, +object oriented wrapper for the HDF5 API using R6 classes. Additionally, +functionality is added so that HDF5 objects behave very similar to their +corresponding R counterparts.") + (license license:asl2.0))) -- cgit v1.2.3 From 846325a8d811a95726062f3261db00baf9f0d91e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:58:21 +0200 Subject: gnu: Add r-writexl. * gnu/packages/cran.scm (r-writexl): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 60210c376d..04a0164090 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4435,3 +4435,23 @@ object oriented wrapper for the HDF5 API using R6 classes. Additionally, functionality is added so that HDF5 objects behave very similar to their corresponding R counterparts.") (license license:asl2.0))) + +(define-public r-writexl + (package + (name "r-writexl") + (version "1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "writexl" version)) + (sha256 + (base32 + "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf")))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (home-page "https://github.com/ropensci/writexl") + (synopsis "Export data frames to xlsx format") + (description + "This package provides a data frame to xlsx exporter based on +libxlsxwriter.") + (license license:bsd-2))) -- cgit v1.2.3 From 693b4d0ba5d69c0629c16f2cf3d4303dad7997b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:58:35 +0200 Subject: gnu: r-globaloptions: Update to 0.1.0. * gnu/packages/cran.scm (r-globaloptions): Update to 0.1.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 04a0164090..61e7bb3af6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -557,14 +557,14 @@ ellipses, circles, cylinders, arrows, ...") (define-public r-globaloptions (package (name "r-globaloptions") - (version "0.0.13") + (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "GlobalOptions" version)) (sha256 (base32 - "04jvha0mafslqz5nr99xjylg9n2x31gj9v4mgyg7qcmfwpqyw3ch")))) + "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn")))) (properties `((upstream-name . "GlobalOptions"))) (build-system r-build-system) (home-page "https://github.com/jokergoo/GlobalOptions") -- cgit v1.2.3 From 7b60ab3df7d65172ca12e94b395d89f66d9ac189 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:58:49 +0200 Subject: gnu: r-circlize: Update to 0.4.4. * gnu/packages/cran.scm (r-circlize): Update to 0.4.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61e7bb3af6..aae0dee482 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -577,14 +577,14 @@ validation and filtering on the values, making options invisible or private.") (define-public r-circlize (package (name "r-circlize") - (version "0.4.3") + (version "0.4.4") (source (origin (method url-fetch) (uri (cran-uri "circlize" version)) (sha256 (base32 - "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna")))) + "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) -- cgit v1.2.3 From 5fa9be111881e7fdcd4a057f57018a7a8dabb9d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:58:59 +0200 Subject: gnu: r-getoptlong: Update to 0.1.7. * gnu/packages/cran.scm (r-getoptlong): Update to 0.1.7. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aae0dee482..10c4707465 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -682,14 +682,14 @@ compare different dendrograms to one another.") (define-public r-getoptlong (package (name "r-getoptlong") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "GetoptLong" version)) (sha256 (base32 - "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm")))) + "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr")))) (properties `((upstream-name . "GetoptLong"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From d87130cb2e5f20630ed8a39cbcce76b09f2269b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:59:09 +0200 Subject: gnu: r-sp: Update to 1.3-1. * gnu/packages/cran.scm (r-sp): Update to 1.3-1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 10c4707465..59ddfc83be 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -897,14 +897,14 @@ most popular ones.") (define-public r-sp (package (name "r-sp") - (version "1.2-7") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "sp" version)) (sha256 (base32 - "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d")))) + "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) -- cgit v1.2.3 From a151f1e60adc5210da6c93e4de5f5565bba9ba0f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:59:18 +0200 Subject: gnu: r-extremes: Update to 2.0-9. * gnu/packages/cran.scm (r-extremes): Update to 2.0-9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 59ddfc83be..be1850f689 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1010,14 +1010,14 @@ SpatialVx.") (define-public r-extremes (package (name "r-extremes") - (version "2.0-8") + (version "2.0-9") (source (origin (method url-fetch) (uri (cran-uri "extRemes" version)) (sha256 (base32 - "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm")))) + "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm")))) (properties `((upstream-name . "extRemes"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d0396c8ea1cf4fc85bb3fb5d4138091285f3afca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:59:27 +0200 Subject: gnu: r-rcpproll: Update to 0.3.0. * gnu/packages/cran.scm (r-rcpproll): Update to 0.3.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be1850f689..1e3aa8a6da 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1596,14 +1596,14 @@ Core algorithms are executed in parallel on systems supporting OpenMP.") (define-public r-rcpproll (package (name "r-rcpproll") - (version "0.2.2") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppRoll" version)) (sha256 (base32 - "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi")))) + "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb")))) (properties `((upstream-name . "RcppRoll"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2bce7795c15090c37c093f857dbe65333669426a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:59:38 +0200 Subject: gnu: r-stringdist: Update to 0.9.5.1. * gnu/packages/cran.scm (r-stringdist): Update to 0.9.5.1. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1e3aa8a6da..849c92435d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1823,14 +1823,14 @@ color labels, layout, etc.") (define-public r-stringdist (package (name "r-stringdist") - (version "0.9.4.7") + (version "0.9.5.1") (source (origin (method url-fetch) (uri (cran-uri "stringdist" version)) (sha256 (base32 - "1qg80wmcrpkba9njvgjdg15bgw7ddks40kkfh5x61as9lhchy4i4")))) + "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa")))) (build-system r-build-system) (home-page "https://github.com/markvanderloo/stringdist") (synopsis "Approximate string matching and string distance functions") -- cgit v1.2.3 From 1268a995da36c0795b0af6f06979af82d73b598f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 14:59:52 +0200 Subject: gnu: r-statnet-common: Update to 4.1.2. * gnu/packages/cran.scm (r-statnet-common): Update to 4.1.2. [propagated-inputs]: Add r-coda. --- gnu/packages/cran.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 849c92435d..c535995072 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2719,17 +2719,19 @@ supports arbitrary vertex/edge/graph attributes.") (define-public r-statnet-common (package (name "r-statnet-common") - (version "4.0.0") + (version "4.1.2") (source (origin (method url-fetch) (uri (cran-uri "statnet.common" version)) (sha256 (base32 - "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0")))) + "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd")))) (properties `((upstream-name . "statnet.common"))) (build-system r-build-system) + (propagated-inputs + `(("r-coda" ,r-coda))) (home-page "https://statnet.org") (synopsis "R scripts and utilities used by the Statnet software") (description "This package provides non-statistical utilities used by the -- cgit v1.2.3 From 8d2f8aeddf692e211f019b240ce3a8f14e0d86db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:00:19 +0200 Subject: gnu: r-extradistr: Update to 1.8.9. * gnu/packages/cran.scm (r-extradistr): Update to 1.8.9. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c535995072..d3f92232e2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2974,14 +2974,14 @@ Cryer and Kung-Sik Chan.") (define-public r-extradistr (package (name "r-extradistr") - (version "1.8.8") + (version "1.8.9") (source (origin (method url-fetch) (uri (cran-uri "extraDistr" version)) (sha256 (base32 - "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3")))) + "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p")))) (properties `((upstream-name . "extraDistr"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 014818b691c562db0ee65858bf2b08e9facedd85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:00:30 +0200 Subject: gnu: r-cubature: Update to 1.3-13. * gnu/packages/cran.scm (r-cubature): Update to 1.3-13. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d3f92232e2..712f3e8d4f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3044,14 +3044,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.3-11") + (version "1.3-13") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k")))) + "1aq0viv2d21v7iyln73973a4h113nlv8bi007qkw6z0hijzg6gz3")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) -- cgit v1.2.3 From 36dc359186f554519d859c0e83b0f97a8b9c5417 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:00:50 +0200 Subject: gnu: r-radiant-data: Update to 0.9.5. * gnu/packages/cran.scm (r-radiant-data): Update to 0.9.5. [propagated-inputs]: Remove r-plyr; add r-glue, r-plotly, r-readxl, r-rlang, and r-writexl. --- gnu/packages/cran.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 712f3e8d4f..f26abba592 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3327,14 +3327,14 @@ environment within Shiny.") (define-public r-radiant-data (package (name "r-radiant-data") - (version "0.8.1") + (version "0.9.5") (source (origin (method url-fetch) (uri (cran-uri "radiant.data" version)) (sha256 (base32 - "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1")) + "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb")) (modules '((guix build utils))) (snippet '(begin @@ -3350,6 +3350,7 @@ environment within Shiny.") ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-dt" ,r-dt) + ("r-glue" ,r-glue) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-import" ,r-import) @@ -3358,16 +3359,19 @@ environment within Shiny.") ("r-lubridate" ,r-lubridate) ("r-magrittr" ,r-magrittr) ("r-markdown" ,r-markdown) - ("r-pryr" ,r-pryr) + ("r-plotly" ,r-plotly) ("r-psych" ,r-psych) ("r-readr" ,r-readr) + ("r-readxl" ,r-readxl) + ("r-rlang" ,r-rlang) ("r-rmarkdown" ,r-rmarkdown) ("r-rstudioapi" ,r-rstudioapi) ("r-scales" ,r-scales) ("r-shiny" ,r-shiny) ("r-shinyace" ,r-shinyace) ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + ("r-tidyr" ,r-tidyr) + ("r-writexl" ,r-writexl))) (home-page "https://github.com/radiant-rstats/radiant.data") (synopsis "Data menu for Radiant: business analytics using R and Shiny") (description -- cgit v1.2.3 From fa7236f1b3464e670bc955c9b9220838d708d01e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:01:26 +0200 Subject: gnu: r-later: Update to 0.7.3. * gnu/packages/cran.scm (r-later): Update to 0.7.3. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f26abba592..14ef1ce617 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3922,14 +3922,14 @@ exchanging spatial objects with other R packages.") (define-public r-later (package (name "r-later") - (version "0.7.2") + (version "0.7.3") (source (origin (method url-fetch) (uri (cran-uri "later" version)) (sha256 (base32 - "0l5ln7sjyi2rj7bx8iamxykqlfarv05zb9882ikizppb1cr1hgyw")))) + "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) -- cgit v1.2.3 From 1df9a0cf4702763d27b804c0e489df9e15b84883 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:01:35 +0200 Subject: gnu: r-reticulate: Update to 1.8. * gnu/packages/cran.scm (r-reticulate): Update to 1.8. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14ef1ce617..b59d4b2e92 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4132,14 +4132,14 @@ obtain a better initial configuration in non-metric MDS.") (define-public r-reticulate (package (name "r-reticulate") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "reticulate" version)) (sha256 (base32 - "1ghhc4hbmwpp79ilbdbshynhs61i8sv8z6p1al04jy7ij0lcglxy")))) + "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr")))) (build-system r-build-system) (inputs `(("python" ,python))) (propagated-inputs -- cgit v1.2.3 From 0357db53c8cc5acc62dee12e85c42c817dfd6b91 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:01:48 +0200 Subject: gnu: r-rgooglemaps: Update to 1.4.2. * gnu/packages/geo.scm (r-rgooglemaps): Update to 1.4.2. --- gnu/packages/geo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 4ba09f2a90..85bb0ccf9b 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -544,14 +544,14 @@ coordinates.") (define-public r-rgooglemaps (package (name "r-rgooglemaps") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (cran-uri "RgoogleMaps" version)) (sha256 (base32 - "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq")))) + "112mdm53qx92n2m4ms02sbppckp44l1z19vy99j6gw3jrdprjydl")))) (properties `((upstream-name . "RgoogleMaps"))) (build-system r-build-system) (propagated-inputs `(("r-png" ,r-png))) -- cgit v1.2.3 From 3399dc97fcd3d19a256b58de265af808f287cb71 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:00 +0200 Subject: gnu: r-munsell: Update to 0.5.0. * gnu/packages/statistics.scm (r-munsell): Update to 0.5.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4c9f1743f0..487ee5de24 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -835,13 +835,13 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (define-public r-munsell (package (name "r-munsell") - (version "0.4.3") + (version "0.5.0") (source (origin (method url-fetch) (uri (cran-uri "munsell" version)) (sha256 - (base32 "0jdxlbjslkzaqgp058da1cgm85qvqi09wpcgpvp4hvwnmy83qz1r")))) + (base32 "16g1fzisbpqb15yh3pqf3iia4csppva5dnv1z88x9dg263xskwyh")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace))) -- cgit v1.2.3 From 26a53dd957da36c1a6ffd1c49fc8c62938059616 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:09 +0200 Subject: gnu: r-stringi: Update to 1.2.3. * gnu/packages/statistics.scm (r-stringi): Update to 1.2.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 487ee5de24..8ea2058e4c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -960,14 +960,14 @@ solution for sending email, including attachments, from within R.") (define-public r-stringi (package (name "r-stringi") - (version "1.2.2") + (version "1.2.3") (source (origin (method url-fetch) (uri (cran-uri "stringi" version)) (sha256 (base32 - "1z8yqnh3alq0xriz77vifgl27msf3av6maz07fld78m90ajb6y8r")))) + "1sgg4krw03qkz1n4dwiya0djggk7giwd0w21qlp0pfjqi0rxq6qx")))) (build-system r-build-system) (inputs `(("icu4c" ,icu4c))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From d086829d399089095bc186774aa59e04e3fea30c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:19 +0200 Subject: gnu: r-highr: Update to 0.7. * gnu/packages/statistics.scm (r-highr): Update to 0.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8ea2058e4c..09f825b589 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1289,13 +1289,13 @@ There is also a Shiny app as a user interface in this package.") (define-public r-highr (package (name "r-highr") - (version "0.6") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 - "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3")))) + "1dzknqk4x7iiiq1jkh9bqm5qcvs7mbqxbkn5955050payavabfya")))) (build-system r-build-system) (home-page "https://github.com/yihui/highr") (synopsis "Syntax highlighting for R source code") -- cgit v1.2.3 From 6221de1879b4696e57a2b57ea1eb61e005f6a29e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:31 +0200 Subject: gnu: r-rmarkdown: Update to 1.10. * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.10. [propagated-inputs]: Add r-tinytex. --- gnu/packages/statistics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 09f825b589..912f91a717 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2603,14 +2603,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb")))) + "0mh2f3k98w7pgz0ri34149s4kx5y0kfm27nwq64k0qwxd16hwd9r")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs @@ -2622,6 +2622,7 @@ certain criterion, e.g., it contains a certain regular file.") ("r-mime" ,r-mime) ("r-rprojroot" ,r-rprojroot) ("r-stringr" ,r-stringr) + ("r-tinytex" ,r-tinytex) ("r-yaml" ,r-yaml) ;; rmarkdown works with the 2.x release of Pandoc, but with degraded ;; functionality. For example, tabbed plots do not currently work with -- cgit v1.2.3 From 242ffd6c80ed50cfcaf2c583727283afeb150a10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:47 +0200 Subject: gnu: r-zoo: Update to 1.8-2. * gnu/packages/statistics.scm (r-zoo): Update to 1.8-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 912f91a717..502ff9b2f9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4223,13 +4223,13 @@ mechanism.") (define-public r-zoo (package (name "r-zoo") - (version "1.8-1") + (version "1.8-2") (source (origin (method url-fetch) (uri (cran-uri "zoo" version)) (sha256 (base32 - "16nc5jnpkf5j9vgq3pzssv7knj30mi055wj7q3sygz3l0d88hgfr")))) + "1lpwigxmi5sc23xrha4gcsccsm4yfsg0sa97y6vac3pg1lliblvx")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice))) -- cgit v1.2.3 From c812f46817b8d64797a00e706e3c715cf12aec13 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:02:58 +0200 Subject: gnu: r-rjson: Update to 0.2.20. * gnu/packages/web.scm (r-rjson): Update to 0.2.20. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d116011206..46d394f0d6 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4024,14 +4024,14 @@ objects in HTML format.") (define-public r-rjson (package (name "r-rjson") - (version "0.2.19") + (version "0.2.20") (source (origin (method url-fetch) (uri (cran-uri "rjson" version)) (sha256 (base32 - "1g29vp3gfbh73a5br68jydsrigia4vnr5avc84avgwl6353749jw")))) + "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rjson") (synopsis "JSON library for R") -- cgit v1.2.3 From 5b730eba3ea415f58deeaebaa2eae26db8802cfd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:03:10 +0200 Subject: gnu: r-biocviews: Update to 1.48.1. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e93eeb5069..b9ea410230 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6939,13 +6939,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.48.0") + (version "1.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9")))) + "1q5z6xxhjyibr165di7iyachw4gd4bdrxkd8rjkcklnngsrx1azm")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From 5b2a339e19cdce511953d13b758e6ab1210f3ba5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:03:20 +0200 Subject: gnu: r-s4vectors: Update to 0.18.3. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9ea410230..c6b6b9886f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7128,13 +7128,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.18.2") + (version "0.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5")))) + "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From 13b8dcf58965289604c8c9858094467ae0d1b0a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 15:03:31 +0200 Subject: gnu: r-seurat: Update to 2.3.2. * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2. [propagated-inputs]: Add r-hdf5r. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6b6b9886f..9aca0f808c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9705,13 +9705,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys")) + "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9755,6 +9755,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) + ("r-hdf5r" ,r-hdf5r) ("r-hmisc" ,r-hmisc) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) -- cgit v1.2.3 From 6ccd88e8cb19a439526bb8d7b3b5a2c3872c825a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 16:42:29 +0200 Subject: gnu: r-factoextra: Fix syntax error. * gnu/packages/cran.scm (r-factoextra)[description]: Fix syntax error. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b59d4b2e92..82beb7b23a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4385,9 +4385,9 @@ structured in groups, etc. and hierarchical cluster analysis.") (description "This package provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including -@code{PCA} (Principal Component Analysis), @cod{CA} (Correspondence Analysis), -@code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor Analysis of -Mixed Data), @code{MFA} (Multiple Factor Analysis) and +@code{PCA} (Principal Component Analysis), @code{CA} (Correspondence +Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor +Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.") -- cgit v1.2.3 From 935cb931b5ec850d691e27b2623c7a21e883d4b4 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 13 Jun 2018 14:34:31 -0400 Subject: gnu: emacspeak: Update to 48.0. * gnu/packages/emacs.scm (emacspeak): Update to 48.0. [arguments]: Use 'invoke'. In the 'install' phase, add additional installation directories and fix the launch script substitution. [inputs]: Add emacs and perl. [native-inputs]: Remove emacs-minimal. --- gnu/packages/emacs.scm | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 039f52a560..51a8fc7f12 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -5636,7 +5636,7 @@ highlights quasi-quoted expressions.") (define-public emacspeak (package (name "emacspeak") - (version "47.0") + (version "48.0") (source (origin (method url-fetch) @@ -5645,7 +5645,7 @@ highlights quasi-quoted expressions.") version "/emacspeak-" version ".tar.bz2")) (sha256 (base32 - "0xbcc266x752y68s3g096m161irzvsqym3axzqn8rb276a8x55n7")))) + "07imi3hji06b3r7v7v59978q76s8a7ynmxwfc9j03pgnv965lpjy")))) (build-system gnu-build-system) (arguments '(#:make-flags (list (string-append "prefix=" @@ -5653,30 +5653,35 @@ highlights quasi-quoted expressions.") #:phases (modify-phases %standard-phases (replace 'configure - (lambda _ - ;; Configure Emacspeak according to etc/install.org. - (setenv "SHELL" (which "sh")) - (zero? (system* "make" "config")))) + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lisp (string-append out + "/share/emacs/site-lisp/emacspeak"))) + (setenv "SHELL" (which "sh")) + ;; Configure Emacspeak according to etc/install.org. + (invoke "make" "config")))) (add-after 'build 'build-espeak (lambda _ - (zero? (system* "make" "espeak")))) + (invoke "make" "espeak"))) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) (lisp (string-append out "/share/emacs/site-lisp/emacspeak")) - (info (string-append out "/share/info"))) + (info (string-append out "/share/info")) + (emacs (string-append (assoc-ref inputs "emacs") + "/bin/emacs"))) ;; According to etc/install.org, the Emacspeak directory should ;; be copied to its installation destination. (for-each (lambda (file) (copy-recursively file (string-append lisp "/" file))) - '("etc" "info" "lisp" "media" "servers" "sounds" "stumpwm" - "xsl")) + '("etc" "info" "js" "lisp" "media" "scapes" "servers" "sounds" + "stumpwm" "xsl")) ;; Make sure emacspeak is loaded from the correct directory. (substitute* "etc/emacspeak.sh" - (("exec emacs.*$") - (string-append "exec emacs -l " lisp + (("exec FLAVOR.*") + (string-append "exec " emacs " -l " lisp "/lisp/emacspeak-setup.el $CL_ALL"))) ;; Install the convenient startup script. (mkdir-p bin) @@ -5695,10 +5700,11 @@ highlights quasi-quoted expressions.") #t)))) #:tests? #f)) ; no check target (inputs - `(("espeak" ,espeak) + `(("emacs" ,emacs) + ("espeak" ,espeak) + ("perl" ,perl) ("tcl" ,tcl) ("tclx" ,tclx))) - (native-inputs `(("emacs" ,emacs-minimal))) (home-page "http://emacspeak.sourceforge.net") (synopsis "Audio desktop interface for Emacs") (description -- cgit v1.2.3 From 4bf474b24302a48d5d921a02410097dba7841907 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 13 Jun 2018 21:38:18 +0200 Subject: gnu: emacs-orgalist: Update to 1.8. * gnu/packages/emacs.scm (emacs-orgalist): Update to 1.8. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 51a8fc7f12..cb4dbd7182 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4824,7 +4824,7 @@ distribution, primarily targeting Clojure users") (define-public emacs-orgalist (package (name "emacs-orgalist") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) @@ -4832,7 +4832,7 @@ distribution, primarily targeting Clojure users") "orgalist-" version ".el")) (sha256 (base32 - "13dl0l727vlny3y88gqpngcy90ly5r719s1pbmkva5gmcryb68xr")))) + "1wqwnmn08i0qkxm8b2iclvf6cydcn68h1p3h7r1kig2bdn5b8948")))) (build-system emacs-build-system) (home-page "http://elpa.gnu.org/packages/orgalist.html") (synopsis "Manage Org-like lists in non-Org buffers") -- cgit v1.2.3 From 844cc1c8f394f03b404c5bb3aee086922373490c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 13 Jun 2018 22:25:48 +0200 Subject: gnu: pigx-scrnaseq: Update to 0.0.5. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5. [inputs]: Add python-magic. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9aca0f808c..1b11c79f8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13053,7 +13053,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -13061,7 +13061,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf")))) + "0a73rilv0vnw42d5rsdq205h4f0x8j3jqv998janh4s324c6w2kj")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -13089,6 +13089,7 @@ methylation and segmentation.") ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) ("python-pandas" ,python-pandas) + ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) -- cgit v1.2.3 From 2b78360138a7043e868875137c40266bd1c75dce Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 13 Jun 2018 23:13:13 +0200 Subject: gnu: sssd: Update to 1.16.2. * gnu/packages/sssd.scm (sssd): Update to 1.16.2. [native-inputs]: Add libxml2. --- gnu/packages/sssd.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/sssd.scm b/gnu/packages/sssd.scm index 28a364ebd5..0ff94cdd24 100644 --- a/gnu/packages/sssd.scm +++ b/gnu/packages/sssd.scm @@ -81,14 +81,14 @@ fundamental object types for C.") (define-public sssd (package (name "sssd") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (string-append "http://releases.pagure.org/SSSD/sssd/" "sssd-" version ".tar.gz")) (sha256 (base32 - "0vjh1c5960wh86zjsamdjhljls7bb5fz5jpcazgzrpmga5w6ggrd")))) + "032ppk57qs1lnvz7pb7lw9ldwm9i1yagh9fzgqgn6na3bg61ynzy")))) (build-system gnu-build-system) (arguments `(#:make-flags @@ -165,6 +165,7 @@ fundamental object types for C.") `(("check" ,check) ("docbook-xsl" ,docbook-xsl) ("docbook-xml" ,docbook-xml) + ("libxml2" ,libxml2) ; for xmllint ("libxslt" ,libxslt) ("pkg-config" ,pkg-config) ("util-linux" ,util-linux))) ; for uuid.h, reqired for KCM -- cgit v1.2.3 From ff76a1e9cad607cb0b91f1e46c65aa1c87b131f6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 04:01:21 +0200 Subject: gnu: python-gnupg: Update to 0.4.3. * gnu/packages/gnupg.scm (python-gnupg): Update to 0.4.3. [arguments]: Remove obsolete substitution. --- gnu/packages/gnupg.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 42b54c1ea0..ff2efb759e 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -508,14 +508,14 @@ decrypt messages using the OpenPGP format by making use of GPGME.") (define-public python-gnupg (package (name "python-gnupg") - (version "0.3.8") + (version "0.4.3") (source (origin (method url-fetch) (uri (pypi-uri "python-gnupg" version)) (sha256 (base32 - "0nkbs9c8f30lra7ca39kg91x8cyxn0jb61vih4qky839gpbwwwiq")))) + "03dc8whhvk7ccspbk8vzfhkxli8cd9zfbss5p597g4jldgy8s59d")))) (build-system python-build-system) (arguments `(#:phases @@ -523,8 +523,6 @@ decrypt messages using the OpenPGP format by making use of GPGME.") (replace 'check (lambda _ (substitute* "test_gnupg.py" - ;; Exported keys don't have a version line! - (("del k1\\[1\\]") "#") ;; Unsure why this test fails. (("'test_search_keys'") "True") (("def test_search_keys") "def disabled__search_keys")) -- cgit v1.2.3 From b262aba7338b8e3aa97bccb91309848a553280e3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 04:02:10 +0200 Subject: gnu: python-gnupg: Return #t from phase. * gnu/packages/gnupg.scm (python-gnupg)[arguments]: Substitute INVOKE for SYSTEM*. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index ff2efb759e..ecd280f6db 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -529,8 +529,8 @@ decrypt messages using the OpenPGP format by making use of GPGME.") (setenv "USERNAME" "guixbuilder") ;; The doctests are extremely slow and sometimes time out, ;; so we disable them. - (zero? (system* "python" - "test_gnupg.py" "--no-doctests"))))))) + (invoke "python" + "test_gnupg.py" "--no-doctests")))))) (native-inputs `(("gnupg" ,gnupg-1))) (home-page "https://packages.python.org/python-gnupg/index.html") -- cgit v1.2.3 From 0b5c16c07f4cc28dc2ffa80d3b6259f10762413d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 04:30:50 +0200 Subject: Fix typo in (gnu packages gtk) header. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gtk.scm: Fix ‘Coypright’ typo. --- gnu/packages/gtk.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 41b908050d..90878ee1e9 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2015 Andy Wingo ;;; Copyright © 2015 David Hashe -;;; Coypright © 2015, 2016, 2017 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus ;;; Copyright © 2016, 2017 Efraim Flashner ;;; Copyright © 2016 Fabian Harfert ;;; Copyright © 2016 Kei Kebreau -- cgit v1.2.3 From 40c1b61aacf89c0531c0df0c7b82e05084f6517e Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Wed, 13 Jun 2018 13:26:15 +0530 Subject: gnu: Add tmate. * gnu/packages/terminals.scm (tmate): New variable. --- gnu/packages/terminals.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index 1cd00f4621..5cdc081398 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2017 Ricardo Wurmus ;;; Copyright © 2017 Petter ;;; Copyright © 2018 Hartmut Goebel +;;; Copyright © 2018 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,6 +48,7 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) + #:use-module (gnu packages libevent) #:use-module (gnu packages linux) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) @@ -55,6 +57,8 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) + #:use-module (gnu packages ssh) #:use-module (gnu packages textutils) #:use-module (gnu packages wm) #:use-module (gnu packages xdisorg) @@ -845,3 +849,33 @@ per-line fullscreen terminal rendering, and keyboard input event reporting.") (define-public python2-curtsies (package-with-python2 python-curtsies)) + +(define-public tmate + (package + (name "tmate") + (version "2.2.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/tmate-io/tmate/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "01f3hhm3x0sd6apyb1ajkjfdfvq5m2759w00yp2slr9fyicsrhnr")))) + (build-system gnu-build-system) + (inputs + `(("libevent" ,libevent) + ("libssh" ,libssh) + ("msgpack" ,msgpack) + ("ncurses" ,ncurses))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config))) + (home-page "https://tmate.io/") + (synopsis "Terminal sharing application") + (description "tmate is a terminal sharing application that allows you to +share your terminal with other users over the Internet. tmate is a fork of +tmux.") + (license license:isc))) -- cgit v1.2.3 From 0dc572380bf627863b4f9666cffa1ec50022fb1d Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 01:13:02 +0200 Subject: gnu: Add python-requests-file. * gnu/packages/python.scm (python-requests-file, python2-requests-file): New variables. --- gnu/packages/python.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 88bbf3b7e5..4b1ea91ae6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -53,6 +53,7 @@ ;;; Copyright © 2016, 2018 Tomáš Čech ;;; Copyright © 2018 Nicolas Goaziou ;;; Copyright © 2018 Oleg Pykhalov +;;; Copyright © 2018 Clément Lassieur ;;; ;;; This file is part of GNU Guix. ;;; @@ -13631,3 +13632,29 @@ introspection.") (define-public python2-fasteners (package-with-python2 python-fasteners)) + +(define-public python-requests-file + (package + (name "python-requests-file") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "requests-file" version)) + (sha256 + (base32 + "1yp2jaxg3v86pia0q512dg3hz6s9y5vzdivsgrba1kds05ial14g")))) + (build-system python-build-system) + (propagated-inputs + `(("python-requests" ,python-requests) + ("python-six" ,python-six))) + (home-page + "https://github.com/dashea/requests-file") + (synopsis "File transport adapter for Requests") + (description + "Requests-File is a transport adapter for use with the Requests Python +library to allow local filesystem access via file:// URLs.") + (license license:asl2.0))) + +(define-public python2-requests-file + (package-with-python2 python-requests-file)) -- cgit v1.2.3 From f4adbe7405fe9b0b921391b315dde79f1547b921 Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 01:02:01 +0200 Subject: gnu: Add python-tldextract. * gnu/packages/python.scm (python-tldextract, python2-tldextract): New variables. --- gnu/packages/python.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4b1ea91ae6..21201cc8d1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -13658,3 +13658,36 @@ library to allow local filesystem access via file:// URLs.") (define-public python2-requests-file (package-with-python2 python-requests-file)) + +(define-public python-tldextract + (package + (name "python-tldextract") + (version "2.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "tldextract" version)) + (sha256 + (base32 + "1d5s8v6kpsgazyahflhji1cfdcf89rv7l7z55v774bhzvcjp2y99")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-responses" ,python-responses))) + (propagated-inputs + `(("python-idna" ,python-idna) + ("python-requests" ,python-requests) + ("python-requests-file" ,python-requests-file))) + (home-page + "https://github.com/john-kurkowski/tldextract") + (synopsis + "Separate the TLD from the registered domain and subdomains of a URL") + (description + "TLDExtract accurately separates the TLD from the registered domain and +subdomains of a URL, using the Public Suffix List. By default, this includes +the public ICANN TLDs and their exceptions. It can optionally support the +Public Suffix List's private domains as well.") + (license license:bsd-3))) + +(define-public python2-tldextract + (package-with-python2 python-tldextract)) -- cgit v1.2.3 From b863b50d80f5b8b3ece01c1f7198b57e22e4edf9 Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 00:57:12 +0200 Subject: gnu: Add python-pynamecheap. * gnu/packages/python.scm (python-pynamecheap, python2-pynamecheap): New variables. --- gnu/packages/python.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 21201cc8d1..c09b006096 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -13691,3 +13691,28 @@ Public Suffix List's private domains as well.") (define-public python2-tldextract (package-with-python2 python-tldextract)) + +(define-public python-pynamecheap + (package + (name "python-pynamecheap") + (version "0.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PyNamecheap" version)) + (sha256 + (base32 + "0wkbwz208j8nfrsmzmclvxg22ymknn0mlz76wbdza9k2bx2zja6l")))) + (build-system python-build-system) + (propagated-inputs + `(("python-requests" ,python-requests))) + (home-page + "https://github.com/Bemmu/PyNamecheap") + (synopsis + "Namecheap API client in Python") + (description + "PyNamecheap is a Namecheap API client in Python.") + (license license:expat))) + +(define-public python2-pynamecheap + (package-with-python2 python-pynamecheap)) -- cgit v1.2.3 From 85d79a79e4b721e24cdfb11a90beef6d566c499a Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 00:56:23 +0200 Subject: gnu: Add python-dns-lexicon. * gnu/packages/python.scm (python-dns-lexicon, python2-dns-lexicon): New variables. --- gnu/packages/python.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c09b006096..72e8d9292d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -13716,3 +13716,36 @@ Public Suffix List's private domains as well.") (define-public python2-pynamecheap (package-with-python2 python-pynamecheap)) + +(define-public python-dns-lexicon + (package + (name "python-dns-lexicon") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dns-lexicon" version)) + (sha256 + (base32 + "0jdn3ns71bsybr7njgsqr9xlxsqh7zh6phn4ld0liazqdn2l5f6m")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ;requires internet access + (propagated-inputs + `(("python-future" ,python-future) + ("python-pynamecheap" ,python-pynamecheap) + ("python-requests" ,python-requests) + ("python-tldextract" ,python-tldextract) + ("python-urllib3" ,python-urllib3))) + (home-page "https://github.com/AnalogJ/lexicon") + (synopsis + "Manipulate DNS records on various DNS providers") + (description + "Lexicon provides a way to manipulate DNS records on multiple DNS +providers in a standardized way. It has a CLI but it can also be used as a +Python library. It was designed to be used in automation, specifically with +Let's Encrypt.") + (license license:expat))) + +(define-public python2-dns-lexicon + (package-with-python2 python-dns-lexicon)) -- cgit v1.2.3 From 03439df66fc2699b22e5786b33324e5432cfe8cf Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 13 Jun 2018 22:28:48 +0300 Subject: gnu: libgcrypt: Fix CVE-2018-0495. * gnu/packages/gnupg.scm (libgcrypt)[replacement]: New field. (libgcrypt/fixed): New package. --- gnu/packages/gnupg.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index ecd280f6db..6a0defb46f 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -108,6 +108,7 @@ Daemon and possibly more in the future.") (define-public libgcrypt (package + (replacement libgcrypt/fixed) (name "libgcrypt") (version "1.8.2") (source (origin @@ -142,6 +143,19 @@ generation.") (properties '((ftp-server . "ftp.gnupg.org") (ftp-directory . "/gcrypt/libgcrypt"))))) +(define libgcrypt/fixed + (package + (inherit libgcrypt) + (name "libgcrypt") + (version "1.8.3") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnupg/libgcrypt/libgcrypt-" + version ".tar.bz2")) + (sha256 + (base32 + "0z5gs1khzyknyfjr19k8gk4q148s6q987ya85cpn0iv70fz91v36")))))) + (define-public libassuan (package (name "libassuan") -- cgit v1.2.3 From c5a2e1ffcb029f50c4c18352cf378b61c41c625e Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 4 Jun 2018 22:31:48 +0200 Subject: build: Require Guile-SQLite3. The next commits make (sqlite3) an indirect dependency of (gnu build install), which is itself used by (guix scripts system), hence this new requirement. * configure.ac: Error out when $guix_cv_have_recent_guile_sqlite3 is false. Remove HAVE_GUILE_SQLITE3 Automake conditional. * Makefile.am (MODULES, SCM_TESTS): Remove HAVE_GUILE_SQLITE3 conditions. * doc/guix.texi (Requirements): Add Guile-SQLite3. * README: Ditto. * gnu/packages/package-management.scm (guix)[propagated-inputs]: Add GUILE-SQLITE3. [arguments]: In 'wrap-program' phase, take guile-sqlite3 into account. --- Makefile.am | 16 +++------------- README | 3 ++- configure.ac | 5 +++-- doc/guix.texi | 3 +++ gnu/packages/package-management.scm | 4 +++- 5 files changed, 14 insertions(+), 17 deletions(-) (limited to 'gnu/packages') diff --git a/Makefile.am b/Makefile.am index 0267e8fe50..f4cdba94a2 100644 --- a/Makefile.am +++ b/Makefile.am @@ -262,11 +262,7 @@ STORE_MODULES = \ guix/store/database.scm \ guix/store/deduplication.scm -if HAVE_GUILE_SQLITE3 MODULES += $(STORE_MODULES) -else -MODULES_NOT_COMPILED += $(STORE_MODULES) -endif !HAVE_GUILE_SQLITE3 # Internal modules with test suite support. dist_noinst_DATA = guix/tests.scm guix/tests/http.scm @@ -379,7 +375,9 @@ SCM_TESTS = \ tests/scripts-build.scm \ tests/containers.scm \ tests/pack.scm \ - tests/import-utils.scm + tests/import-utils.scm \ + tests/store-database.scm \ + tests/store-deduplication.scm if HAVE_GUILE_JSON @@ -391,14 +389,6 @@ SCM_TESTS += \ endif -if HAVE_GUILE_SQLITE3 - -SCM_TESTS += \ - tests/store-database.scm \ - tests/store-deduplication.scm - -endif - SH_TESTS = \ tests/guix-build.sh \ tests/guix-download.sh \ diff --git a/README b/README index 243a6c058c..e1d62763d0 100644 --- a/README +++ b/README @@ -23,7 +23,8 @@ GNU Guix currently depends on the following packages: - [[https://gnu.org/software/guile/][GNU Guile 2.2.x or 2.0.x]], version 2.0.13 or later - [[https://gnupg.org/][GNU libgcrypt]] - [[https://www.gnu.org/software/make/][GNU Make]] - - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled. + - [[https://www.gnutls.org][GnuTLS]] compiled with guile support enabled + - [[https://notabug.org/civodul/guile-sqlite3][Guile-SQLite3]] - [[https://gitlab.com/guile-git/guile-git][Guile-Git]] - [[http://www.zlib.net/][zlib]] - optionally [[https://savannah.nongnu.org/projects/guile-json/][Guile-JSON]], for the 'guix import pypi' command diff --git a/configure.ac b/configure.ac index d338bfda53..b866e91b2c 100644 --- a/configure.ac +++ b/configure.ac @@ -126,8 +126,9 @@ AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"]) dnl Guile-Sqlite3 is used by the (guix store ...) modules. GUIX_CHECK_GUILE_SQLITE3 -AM_CONDITIONAL([HAVE_GUILE_SQLITE3], - [test "x$guix_cv_have_recent_guile_sqlite3" = "xyes"]) +if test "x$guix_cv_have_recent_guile_sqlite3" != "xyes"; then + AC_MSG_ERROR([A recent Guile-SQLite3 could not be found; please install it.]) +fi dnl Make sure we have a full-fledged Guile. GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads]) diff --git a/doc/guix.texi b/doc/guix.texi index 4871bbcfe4..d86ac5044f 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -615,6 +615,9 @@ later, including 2.2.x; Guile,, gnutls-guile, GnuTLS-Guile}); @item @c FIXME: Specify a version number once a release has been made. +@uref{https://notabug.org/civodul/guile-sqlite3, Guile-SQLite3}; +@item +@c FIXME: Specify a version number once a release has been made. @uref{https://gitlab.com/guile-git/guile-git, Guile-Git}, from August 2017 or later; @item @url{http://zlib.net, zlib}; diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 19954c3608..786d2a53e9 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -213,12 +213,13 @@ (let* ((out (assoc-ref outputs "out")) (guile (assoc-ref inputs "guile")) (json (assoc-ref inputs "guile-json")) + (sqlite (assoc-ref inputs "guile-sqlite3")) (git (assoc-ref inputs "guile-git")) (bs (assoc-ref inputs "guile-bytestructures")) (ssh (assoc-ref inputs "guile-ssh")) (gnutls (assoc-ref inputs "gnutls")) - (deps (list json gnutls git bs ssh)) + (deps (list json sqlite gnutls git bs ssh)) (effective (read-line (open-pipe* OPEN_READ @@ -275,6 +276,7 @@ (propagated-inputs `(("gnutls" ,gnutls) ("guile-json" ,guile-json) + ("guile-sqlite3" ,guile-sqlite3) ("guile-ssh" ,guile-ssh) ("guile-git" ,guile-git))) -- cgit v1.2.3 From ea0a06cee2ba05451f94714a4f913db02efbe92c Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 8 Jun 2018 11:03:31 +0200 Subject: Remove 'guix-register' and its traces. * Makefile.am (SH_TESTS): Remove tests/guix-register.sh. * build-aux/pre-inst-env.in (GUIX_REGISTER): Remove. * gnu/build/install.scm (directives): Remove outdated comment. * gnu/build/vm.scm (root-partition-initializer): Update comment. * gnu/packages/package-management.scm (guix-register): Remove. * guix/config.scm.in (%sbindir, %guix-register-program): Remove. * guix/scripts/system.scm (install): Adjust docstring. * guix/self.scm (make-config.scm): Remove #:guix. Do not generate %sbindir and %guix-register-program. (specification->package): Remove "guix". * nix/guix-register/guix-register.cc: Remove. * nix/libstore/store-api.cc (decodeValidPathInfo): Remove. * nix/libstore/store-api.hh (decodeValidPathInfo): Remove declaration. * nix/local.mk (sbin_PROGRAMS, guix_register_SOURCES) (guix_register_CPPFLAGS, guix_register_LDFLAGS): Remove. * tests/guix-register.sh: Remove. --- .gitignore | 1 - Makefile.am | 7 - build-aux/pre-inst-env.in | 6 +- gnu/build/install.scm | 3 - gnu/build/vm.scm | 4 +- gnu/packages/package-management.scm | 36 ----- guix/config.scm.in | 12 +- guix/scripts/system.scm | 2 +- guix/self.scm | 21 +-- nix/guix-register/guix-register.cc | 254 ------------------------------------ nix/libstore/store-api.cc | 26 ---- nix/libstore/store-api.hh | 4 - nix/local.mk | 16 --- tests/guix-register.sh | 191 --------------------------- 14 files changed, 7 insertions(+), 576 deletions(-) delete mode 100644 nix/guix-register/guix-register.cc delete mode 100644 tests/guix-register.sh (limited to 'gnu/packages') diff --git a/.gitignore b/.gitignore index e2568ed5fe..35d50b35af 100644 --- a/.gitignore +++ b/.gitignore @@ -69,7 +69,6 @@ /etc/guix-publish.conf /etc/guix-publish.service /guix-daemon -/guix-register /guix/config.scm /libformat.a /libstore.a diff --git a/Makefile.am b/Makefile.am index f4cdba94a2..61a19b6b9e 100644 --- a/Makefile.am +++ b/Makefile.am @@ -405,13 +405,6 @@ SH_TESTS = \ tests/guix-graph.sh \ tests/guix-lint.sh -if BUILD_DAEMON - -SH_TESTS += tests/guix-register.sh - -endif BUILD_DAEMON - - TESTS = $(SCM_TESTS) $(SH_TESTS) AM_TESTS_ENVIRONMENT = abs_top_srcdir="$(abs_top_srcdir)" GUILE_AUTO_COMPILE=0 diff --git a/build-aux/pre-inst-env.in b/build-aux/pre-inst-env.in index 14315d40d4..286a81591c 100644 --- a/build-aux/pre-inst-env.in +++ b/build-aux/pre-inst-env.in @@ -1,7 +1,7 @@ #!/bin/sh # GNU Guix --- Functional package management for GNU -# Copyright © 2012, 2013, 2014, 2015, 2017 Ludovic Courtès +# Copyright © 2012, 2013, 2014, 2015, 2017, 2018 Ludovic Courtès # Copyright © 2017 Eric Bavier # # This file is part of GNU Guix. @@ -55,10 +55,6 @@ NIX_BUILD_HOOK="$abs_top_builddir/nix/scripts/offload" @BUILD_DAEMON_OFFLOAD_FALSE@# No offloading support. @BUILD_DAEMON_OFFLOAD_FALSE@unset NIX_BUILD_HOOK -# The 'guix-register' program. -GUIX_REGISTER="$abs_top_builddir/guix-register" -export GUIX_REGISTER - # The following variables need only be defined when compiling Guix # modules, but we define them to be on the safe side in case of # auto-compilation. diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 06ecb39952..5a5e703872 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -110,9 +110,6 @@ STORE." ("/var/guix/gcroots/booted-system" -> "/run/booted-system") ("/var/guix/gcroots/current-system" -> "/run/current-system") - - ;; XXX: 'guix-register' creates this symlink with a wrong target, so - ;; create it upfront to be sure. ("/var/guix/gcroots/profiles" -> "/var/guix/profiles") (directory "/bin") diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm index 803cd5996a..73d0191de7 100644 --- a/gnu/build/vm.scm +++ b/gnu/build/vm.scm @@ -346,7 +346,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation." ;; Optionally, register the inputs in the image's store. (when register-closures? (unless copy-closures? - ;; XXX: 'guix-register' wants to palpate the things it registers, so + ;; XXX: 'register-closure' wants to palpate the things it registers, so ;; bind-mount the store on the target. (mkdir-p target-store) (mount (%store-directory) target-store "" MS_BIND)) @@ -365,7 +365,7 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation." (display "populating...\n") (populate-root-file-system system-directory target) - ;; 'guix-register' resets timestamps and everything, so no need to do it + ;; 'register-closure' resets timestamps and everything, so no need to do it ;; once more in that case. (unless register-closures? (reset-timestamps target)))) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 786d2a53e9..24cf3ad015 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -294,42 +294,6 @@ the Nix package manager.") ;; Alias for backward compatibility. (define-public guix-devel guix) -(define-public guix-register - ;; This package is for internal consumption: it allows us to quickly build - ;; the 'guix-register' program, which is referred to by (guix config). - ;; TODO: Remove this hack when 'guix-register' has been superseded by Scheme - ;; code. - (package - (inherit guix) - (properties `((hidden? . #t))) - (name "guix-register") - - ;; Use a minimum set of dependencies. - (native-inputs - (fold alist-delete (package-native-inputs guix) - '("po4a" "graphviz" "help2man"))) - (propagated-inputs - `(("gnutls" ,gnutls) - ("guile-git" ,guile-git))) - - (arguments - (substitute-keyword-arguments (package-arguments guix) - ((#:tests? #f #f) - #f) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (replace 'build - (lambda _ - (invoke "make" "nix/libstore/schema.sql.hh") - (invoke "make" "-j" (number->string - (parallel-job-count)) - "guix-register"))) - (delete 'copy-bootstrap-guile) - (replace 'install - (lambda _ - (invoke "make" "install-sbinPROGRAMS"))) - (delete 'wrap-program))))))) - (define-public guile2.0-guix (package (inherit guix) diff --git a/guix/config.scm.in b/guix/config.scm.in index aeea81bd3f..4490112e07 100644 --- a/guix/config.scm.in +++ b/guix/config.scm.in @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès +;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2018 Ludovic Courtès ;;; Copyright © 2017 Caleb Ristvedt ;;; ;;; This file is part of GNU Guix. @@ -26,13 +26,11 @@ %storedir %localstatedir %sysconfdir - %sbindir %store-directory %state-directory %store-database-directory %config-directory - %guix-register-program %system %libgcrypt @@ -70,9 +68,6 @@ (define %sysconfdir "@guix_sysconfdir@") -(define %sbindir - "@guix_sbindir@") - (define %store-directory (or (and=> (getenv "NIX_STORE_DIR") canonicalize-path) %storedir)) @@ -91,11 +86,6 @@ (or (getenv "GUIX_CONFIGURATION_DIRECTORY") (string-append %sysconfdir "/guix"))) -(define %guix-register-program - ;; The 'guix-register' program. - (or (getenv "GUIX_REGISTER") - (string-append %sbindir "/guix-register"))) - (define %system "@guix_system@") diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 9112177bfb..727f1ac55f 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -198,7 +198,7 @@ TARGET, and register them." bootcfg bootcfg-file) "Copy the closure of BOOTCFG, which includes the output of OS-DRV, to directory TARGET. TARGET must be an absolute directory name since that's what -'guix-register' expects. +'register-path' expects. When INSTALL-BOOTLOADER? is true, install bootloader using BOOTCFG." (define (maybe-copy to-copy) diff --git a/guix/self.scm b/guix/self.scm index ed3f31cdbc..3023ae379b 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -89,8 +89,6 @@ GUILE-VERSION (\"2.0\" or \"2.2\"), or #f if none of the packages matches." ("gzip" (ref '(gnu packages compression) 'gzip)) ("bzip2" (ref '(gnu packages compression) 'bzip2)) ("xz" (ref '(gnu packages compression) 'xz)) - ("guix" (ref '(gnu packages package-management) - 'guix-register)) ("guile2.0-json" (ref '(gnu packages guile) 'guile2.0-json)) ("guile2.0-ssh" (ref '(gnu packages ssh) 'guile2.0-ssh)) ("guile2.0-git" (ref '(gnu packages guile) 'guile2.0-git)) @@ -565,7 +563,6 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the #:gzip gzip #:bzip2 bzip2 #:xz xz - #:guix guix #:package-name %guix-package-name #:package-version @@ -630,8 +627,7 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the (define %dependency-variables ;; (guix config) variables corresponding to dependencies. - '(%libgcrypt %libz %xz %gzip %bzip2 %nix-instantiate - %sbindir %guix-register-program)) + '(%libgcrypt %libz %xz %gzip %bzip2 %nix-instantiate)) (define %persona-variables ;; (guix config) variables that define Guix's persona. @@ -653,7 +649,7 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the (stringstring (car name+value1)) (symbol->string (car name+value2)))))) -(define* (make-config.scm #:key libgcrypt zlib gzip xz bzip2 guix +(define* (make-config.scm #:key libgcrypt zlib gzip xz bzip2 (package-name "GNU Guix") (package-version "0") (bug-report-address "bug-guix@gnu.org") @@ -669,8 +665,6 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the %guix-version %guix-bug-report-address %guix-home-page-url - %sbindir - %guix-register-program %libgcrypt %libz %gzip @@ -688,17 +682,6 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the (define %guix-bug-report-address #$bug-report-address) (define %guix-home-page-url #$home-page-url) - (define %sbindir - ;; This is used to define '%guix-register-program'. - ;; TODO: Use a derivation that builds nothing but the - ;; C++ part. - #+(and guix (file-append guix "/sbin"))) - - (define %guix-register-program - (or (getenv "GUIX_REGISTER") - (and %sbindir - (string-append %sbindir "/guix-register")))) - (define %gzip #+(and gzip (file-append gzip "/bin/gzip"))) (define %bzip2 diff --git a/nix/guix-register/guix-register.cc b/nix/guix-register/guix-register.cc deleted file mode 100644 index 16dae62b3d..0000000000 --- a/nix/guix-register/guix-register.cc +++ /dev/null @@ -1,254 +0,0 @@ -/* GNU Guix --- Functional package management for GNU - Copyright (C) 2013, 2014, 2015 Ludovic Courtès - Copyright (C) 2007, 2008, 2009, 2010, 2011, 2012, - 2013 Eelco Dolstra - - 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 . */ - -/* This file derives from the implementation of 'nix-store - --register-validity', by Eelco Dolstra, as found in the Nix package - manager's src/nix-store/nix-store.cc. */ - -#include - -#include -#include - -#include -#include -#include -#include - -#include -#include - -using namespace nix; - -/* Input stream where we read closure descriptions. */ -static std::istream *input = &std::cin; - - - -/* Command-line options. */ - -const char *argp_program_version = - "guix-register (" PACKAGE_NAME ") " PACKAGE_VERSION; -const char *argp_program_bug_address = PACKAGE_BUGREPORT; - -static char doc[] = -"guix-register -- register a closure as valid in a store\ -\v\ -This program is used internally when populating a store with data \ -from an existing store. It updates the new store's database with \ -information about which store files are valid, and what their \ -references are."; - -#define GUIX_OPT_STATE_DIRECTORY 1 -#define GUIX_OPT_DEDUPLICATE 2 - -static const struct argp_option options[] = - { - { "prefix", 'p', "DIRECTORY", 0, - "Open the store that lies under DIRECTORY" }, - { "state-directory", GUIX_OPT_STATE_DIRECTORY, "DIRECTORY", 0, - "Use DIRECTORY as the state directory of the target store" }, - { "no-deduplication", GUIX_OPT_DEDUPLICATE, 0, 0, - "Disable automatic deduplication of registered store items" }, - { 0, 0, 0, 0, 0 } - }; - - -/* Prefix of the store being populated. */ -static std::string prefix; - -/* Whether to deduplicate the registered store items. */ -static bool deduplication = true; - -/* Parse a single option. */ -static error_t -parse_opt (int key, char *arg, struct argp_state *state) -{ - switch (key) - { - case 'p': - { - prefix = canonPath (arg); - settings.nixStore = prefix + NIX_STORE_DIR; - settings.nixDataDir = prefix + NIX_DATA_DIR; - settings.nixLogDir = prefix + NIX_LOG_DIR; - settings.nixStateDir = prefix + NIX_STATE_DIR; - settings.nixDBPath = settings.nixStateDir + "/db"; - break; - } - - case GUIX_OPT_STATE_DIRECTORY: - { - string state_dir = canonPath (arg); - - settings.nixStateDir = state_dir; - settings.nixDBPath = state_dir + "/db"; - break; - } - - case GUIX_OPT_DEDUPLICATE: - deduplication = false; - break; - - case ARGP_KEY_ARG: - { - std::ifstream *file; - - if (state->arg_num >= 2) - /* Too many arguments. */ - argp_usage (state); - - file = new std::ifstream (); - file->open (arg); - - input = file; - } - break; - - default: - return (error_t) ARGP_ERR_UNKNOWN; - } - - return (error_t) 0; -} - -/* Argument parsing. */ -static struct argp argp = { options, parse_opt, 0, doc }; - - -/* Read from INPUT the description of a closure, and register it as valid in - STORE. The expected format on INPUT is that used by #:references-graphs: - - FILE - DERIVER - NUMBER-OF-REFERENCES - REF1 - ... - REFN - - This is really meant as an internal format. */ -static void -register_validity (LocalStore *store, std::istream &input, - bool optimize = true, - bool reregister = true, bool hashGiven = false, - bool canonicalise = true) -{ - ValidPathInfos infos; - - while (1) - { - ValidPathInfo info = decodeValidPathInfo (input, hashGiven); - if (info.path == "") - break; - - if (!prefix.empty ()) - { - /* Rewrite the input to refer to the final name, as if we were in a - chroot under PREFIX. */ - std::string final_prefix (NIX_STORE_DIR "/"); - info.path = final_prefix + baseNameOf (info.path); - } - - /* Keep its real path to canonicalize it and compute its hash. */ - std::string real_path; - real_path = prefix + "/" + settings.nixStore + "/" + baseNameOf (info.path); - - if (!store->isValidPath (info.path) || reregister) - { - /* !!! races */ - if (canonicalise) - canonicalisePathMetaData (real_path, -1); - - if (!hashGiven) - { - HashResult hash = hashPath (htSHA256, real_path); - info.hash = hash.first; - info.narSize = hash.second; - } - infos.push_back (info); - } - } - - store->registerValidPaths (infos); - - /* XXX: When PREFIX is non-empty, store->linksDir points to the original - store's '.links' directory, which means 'optimisePath' would try to link - to that instead of linking to the target store. Thus, disable - deduplication in this case. */ - if (optimize) - { - /* Make sure deduplication is enabled. */ - settings.autoOptimiseStore = true; - - std::string store_dir = settings.nixStore; - - /* 'optimisePath' creates temporary links under 'settings.nixStore' and - this must be the real target store, under PREFIX, to avoid - cross-device links. Thus, temporarily switch the value of - 'settings.nixStore'. */ - settings.nixStore = prefix + store_dir; - for (auto&& i: infos) - store->optimisePath (prefix + i.path); - settings.nixStore = store_dir; - } -} - - -int -main (int argc, char *argv[]) -{ - /* Initialize libgcrypt, which is indirectly used. */ - if (!gcry_check_version (GCRYPT_VERSION)) - { - fprintf (stderr, "error: libgcrypt version mismatch\n"); - exit (EXIT_FAILURE); - } - - /* Tell Libgcrypt that initialization has completed, as per the Libgcrypt - 1.6.0 manual (although this does not appear to be strictly needed.) */ - gcry_control (GCRYCTL_INITIALIZATION_FINISHED, 0); - - /* Honor the environment variables, and initialize the settings. */ - settings.processEnvironment (); - - try - { - argp_parse (&argp, argc, argv, 0, 0, 0); - - /* Instantiate the store. This creates any missing directories among - 'settings.nixStore', 'settings.nixDBPath', etc. */ - LocalStore store; - - if (!prefix.empty ()) - /* Under the --prefix tree, the final name of the store will be - NIX_STORE_DIR. Set it here so that the database uses file names - prefixed by NIX_STORE_DIR and not PREFIX + NIX_STORE_DIR. */ - settings.nixStore = NIX_STORE_DIR; - - register_validity (&store, *input, deduplication); - } - catch (std::exception &e) - { - fprintf (stderr, "error: %s\n", e.what ()); - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} diff --git a/nix/libstore/store-api.cc b/nix/libstore/store-api.cc index 6742d2ed49..9e07c67e97 100644 --- a/nix/libstore/store-api.cc +++ b/nix/libstore/store-api.cc @@ -226,32 +226,6 @@ string StoreAPI::makeValidityRegistration(const PathSet & paths, return s; } - -ValidPathInfo decodeValidPathInfo(std::istream & str, bool hashGiven) -{ - ValidPathInfo info; - getline(str, info.path); - if (str.eof()) { info.path = ""; return info; } - if (hashGiven) { - string s; - getline(str, s); - info.hash = parseHash(htSHA256, s); - getline(str, s); - if (!string2Int(s, info.narSize)) throw Error("number expected"); - } - getline(str, info.deriver); - string s; int n; - getline(str, s); - if (!string2Int(s, n)) throw Error("number expected"); - while (n--) { - getline(str, s); - info.references.insert(s); - } - if (!str || str.eof()) throw Error("missing input"); - return info; -} - - string showPaths(const PathSet & paths) { string s; diff --git a/nix/libstore/store-api.hh b/nix/libstore/store-api.hh index e957cedebc..2d9dcbd573 100644 --- a/nix/libstore/store-api.hh +++ b/nix/libstore/store-api.hh @@ -371,10 +371,6 @@ std::shared_ptr openStore(bool reserveSpace = true); string showPaths(const PathSet & paths); -ValidPathInfo decodeValidPathInfo(std::istream & str, - bool hashGiven = false); - - /* Export multiple paths in the format expected by ‘nix-store --import’. */ void exportPaths(StoreAPI & store, const Paths & paths, diff --git a/nix/local.mk b/nix/local.mk index b4c6ba61a4..140c78df37 100644 --- a/nix/local.mk +++ b/nix/local.mk @@ -120,7 +120,6 @@ libstore_a_CXXFLAGS = $(AM_CXXFLAGS) \ $(SQLITE3_CFLAGS) $(LIBGCRYPT_CFLAGS) bin_PROGRAMS = guix-daemon -sbin_PROGRAMS = guix-register guix_daemon_SOURCES = \ %D%/nix-daemon/nix-daemon.cc \ @@ -138,24 +137,9 @@ guix_daemon_LDADD = \ guix_daemon_headers = \ %D%/nix-daemon/shared.hh - -guix_register_SOURCES = \ - %D%/guix-register/guix-register.cc - -guix_register_CPPFLAGS = \ - $(libutil_a_CPPFLAGS) \ - $(libstore_a_CPPFLAGS) \ - -I$(top_srcdir)/%D%/libstore - -# XXX: Should we start using shared libs? -guix_register_LDADD = \ - libstore.a libutil.a libformat.a -lz \ - $(SQLITE3_LIBS) $(LIBGCRYPT_LIBS) - if HAVE_LIBBZ2 guix_daemon_LDADD += -lbz2 -guix_register_LDADD += -lbz2 endif HAVE_LIBBZ2 diff --git a/tests/guix-register.sh b/tests/guix-register.sh deleted file mode 100644 index 521735b8a4..0000000000 --- a/tests/guix-register.sh +++ /dev/null @@ -1,191 +0,0 @@ -# GNU Guix --- Functional package management for GNU -# Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès -# -# 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 . - -# -# Test the 'guix-register' command-line utility. -# - -guix-register --version - -new_store="t-register-$$" -closure="t-register-closure-$$" -rm -rf "$new_store" - -exit_hook=":" -trap "chmod -R +w $new_store ; rm -rf $new_store $closure ; \$exit_hook" EXIT - -# -# Registering items in the current store---i.e., without '--prefix'. -# - -new_file="$NIX_STORE_DIR/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-guix-register-$$" -echo "Fake store file to test registration." > "$new_file" - -# Register the file with zero references and no deriver. -guix-register < "$new_file2" -guix-register <> "$closure" < Date: Thu, 14 Jun 2018 12:50:10 +0200 Subject: gnu: pigx-bsseq: Update to 0.0.9. * gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1b11c79f8a..56fae09d93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12986,7 +12986,7 @@ in an easily configurable manner.") (define-public pigx-bsseq (package (name "pigx-bsseq") - (version "0.0.8") + (version "0.0.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/" @@ -12994,7 +12994,7 @@ in an easily configurable manner.") "/pigx_bsseq-" version ".tar.gz")) (sha256 (base32 - "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y")))) + "0j1dfjk8m1p1h6d5yw63scjlbx56z8gixmbw626w1vcyblg0frmz")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 53131eab2d97a5a2ce43b6f0c7fe47536dbcca84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Jun 2018 13:50:21 +0200 Subject: gnu: Add minimap2. * gnu/packages/bioinformatics.scm (minimap2): New variable. --- gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56fae09d93..a210319243 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13247,3 +13247,62 @@ rate speciation and extinction.") junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.") (license license:gpl3+)))) + +(define-public minimap2 + (package + (name "minimap2") + (version "2.10") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/lh3/minimap2/" + "releases/download/v" version "/" + "minimap2-" version ".tar.bz2")) + (sha256 + (base32 + "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:make-flags + (list "CC=gcc" + (let ((system ,(or (%current-target-system) + (%current-system)))) + (cond + ((string-prefix? "x86_64" system) + "all") + ((or (string-prefix? "armhf" system) + (string-prefix? "aarch64" system)) + "arm_neon=1") + (_ "sse2only=1")))) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (man (string-append out "/share/man/man1"))) + (install-file "minimap2" bin) + (mkdir-p man) + (install-file "minimap2.1" man)) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://lh3.github.io/minimap2/") + (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences") + (description "Minimap2 is a versatile sequence alignment program that +aligns DNA or mRNA sequences against a large reference database. Typical use +cases include: + +@enumerate +@item mapping PacBio or Oxford Nanopore genomic reads to the human genome; +@item finding overlaps between long reads with error rate up to ~15%; +@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA + reads against a reference genome; +@item aligning Illumina single- or paired-end reads; +@item assembly-to-assembly alignment; +@item full-genome alignment between two closely related species with + divergence below ~15%. +@end enumerate\n") + (license license:expat))) -- cgit v1.2.3 From f715f102e076872d560ea2c12a9618f99ef1f707 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Jun 2018 15:41:09 +0200 Subject: gnu: fio: Update to 3.7. * gnu/packages/benchmark.scm (fio): Update to 3.7. --- gnu/packages/benchmark.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/benchmark.scm b/gnu/packages/benchmark.scm index ebc8bdb5f2..be3662798b 100644 --- a/gnu/packages/benchmark.scm +++ b/gnu/packages/benchmark.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017 Marius Bakke ;;; Copyright © 2017 Dave Love ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -34,15 +35,14 @@ (define-public fio (package (name "fio") - (version "3.6") + (version "3.7") (source (origin (method url-fetch) - (uri (string-append - "http://brick.kernel.dk/snaps/" - "fio-" version ".tar.bz2")) + (uri (string-append "http://brick.kernel.dk/snaps/" + "fio-" version ".tar.gz")) (sha256 (base32 - "1d2jibp1b2dq97f22wj6pcjl7gbd2kmhfggj2c7q3j8v9axjqsh2")))) + "0rw9jf2ikm19lq4jizavdvvp3vfvlm3annq7jsxl2y5nf1pi2qr7")))) (build-system gnu-build-system) (arguments '(#:test-target "test" -- cgit v1.2.3 From ab6f400531f735c867cb85021790b487fad235f9 Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 17:12:14 +0200 Subject: gnu: password-store: Update to 1.7.2. * gnu/packages/password-utils.scm (password-store): Update to 1.7.2. [source]: Remove 'password-store-gnupg-compat.patch'. * gnu/packages/patches/password-store-gnupg-compat.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/password-utils.scm | 5 ++-- .../patches/password-store-gnupg-compat.patch | 28 ---------------------- 3 files changed, 2 insertions(+), 32 deletions(-) delete mode 100644 gnu/packages/patches/password-store-gnupg-compat.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index f3da9353a3..59e983ae58 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -983,7 +983,6 @@ dist_patch_DATA = \ %D%/packages/patches/p7zip-CVE-2016-9296.patch \ %D%/packages/patches/p7zip-CVE-2017-17969.patch \ %D%/packages/patches/p7zip-remove-unused-code.patch \ - %D%/packages/patches/password-store-gnupg-compat.patch \ %D%/packages/patches/patchelf-page-size.patch \ %D%/packages/patches/patchelf-rework-for-arm.patch \ %D%/packages/patches/patchutils-xfail-gendiff-tests.patch \ diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 497963af63..9ac30420b7 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -358,7 +358,7 @@ any X11 window.") (define-public password-store (package (name "password-store") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri @@ -366,8 +366,7 @@ any X11 window.") name "-" version ".tar.xz")) (sha256 (base32 - "0scqkpll2q8jhzcgcsh9kqz0gwdpvynivqjmmbzax2irjfaiklpn")) - (patches (search-patches "password-store-gnupg-compat.patch")))) + "1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27")))) (build-system gnu-build-system) (arguments '(#:phases diff --git a/gnu/packages/patches/password-store-gnupg-compat.patch b/gnu/packages/patches/password-store-gnupg-compat.patch deleted file mode 100644 index 75c6362021..0000000000 --- a/gnu/packages/patches/password-store-gnupg-compat.patch +++ /dev/null @@ -1,28 +0,0 @@ -Copied from upstream mailing list: -https://lists.zx2c4.com/pipermail/password-store/2018-February/003216.html. - -From 9b0c86159d754cc88dd3642564eed527153dfb7f Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= -Date: Sat, 24 Feb 2018 12:05:46 +0100 -Subject: [PATCH] tests: fix compatibility with GnuPG 2.2.5 - ---- - tests/t0300-reencryption.sh | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/tests/t0300-reencryption.sh b/tests/t0300-reencryption.sh -index 6d5811d..6d15364 100755 ---- a/tests/t0300-reencryption.sh -+++ b/tests/t0300-reencryption.sh -@@ -10,7 +10,7 @@ canonicalize_gpg_keys() { - $GPG --list-keys --with-colons "$@" | sed -n 's/sub:[^:]*:[^:]*:[^:]*:\([^:]*\):[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[a-zA-Z]*e[a-zA-Z]*:.*/\1/p' | LC_ALL=C sort -u - } - gpg_keys_from_encrypted_file() { -- $GPG -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$1" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u -+ $GPG -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$1" 2>&1 | grep "public key is" | cut -d ' ' -f 5 | LC_ALL=C sort -u - } - gpg_keys_from_group() { - local output="$($GPG --list-config --with-colons | sed -n "s/^cfg:group:$1:\\(.*\\)/\\1/p" | head -n 1)" --- -2.16.2 - -- cgit v1.2.3 From 43fa239717e575ef38ded135055ea09716180b0b Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Thu, 14 Jun 2018 17:17:38 +0200 Subject: gnu: emacs-password-store: Update to 1.7.2. * gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.2. [propagated-inputs]: Add emacs-with-editor. --- gnu/packages/emacs.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index cb4dbd7182..02e7791705 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7950,7 +7950,7 @@ close, copy, cut, paste, undo, redo.") (define-public emacs-password-store (package (name "emacs-password-store") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri @@ -7958,7 +7958,7 @@ close, copy, cut, paste, undo, redo.") "password-store-" version ".tar.xz")) (sha256 (base32 - "0scqkpll2q8jhzcgcsh9kqz0gwdpvynivqjmmbzax2irjfaiklpn")))) + "1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27")))) (build-system emacs-build-system) (arguments `(#:phases @@ -7973,6 +7973,7 @@ close, copy, cut, paste, undo, redo.") (propagated-inputs `(("emacs-f" ,emacs-f) ("emacs-s" ,emacs-s) + ("emacs-with-editor" ,emacs-with-editor) ("password-store" ,password-store))) (home-page "https://git.zx2c4.com/password-store/tree/contrib/emacs") (synopsis "Password store (pass) support for Emacs") -- cgit v1.2.3 From ecbac51a0c132b1b1369e2693516a0638b7a076c Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Thu, 14 Jun 2018 18:09:55 +0200 Subject: gnu: openrct2: Downgrade to 0.1.1. * gnu/packages/games.scm (openrct2): Downgrade to 0.1.1 due to audio not working on 0.1.2+. Needs fixing before upgrade. [arguments]: Add "-DDOWNLOAD_TITLE_SEQUENCES=OFF" configure-flag. Remove 'fixgcc7 and 'get-rid-of-errors phases. [native-inputs]: Remove gcc@7. --- gnu/packages/games.scm | 26 ++++++++------------------ 1 file changed, 8 insertions(+), 18 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index ede951fc5c..7d6d2e8c4a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -74,7 +74,6 @@ #:use-module (gnu packages freedesktop) #:use-module (gnu packages fribidi) #:use-module (gnu packages game-development) - #:use-module (gnu packages gcc) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gimp) @@ -2315,7 +2314,7 @@ Transport Tycoon Deluxe.") (define-public openrct2 (package (name "openrct2") - (version "0.2.0") + (version "0.1.1") (source (origin (method url-fetch) @@ -2323,11 +2322,12 @@ Transport Tycoon Deluxe.") version ".tar.gz")) (sha256 (base32 - "1yrbjra27n2xxb1x47v962lc3qi8gwm5ws4f97952nvn533zrwxz")) + "1bahkzlf9k92cc4zs4nk4wy59323kiw8d3wm0vjps3kp7iznqyjx")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; Tests require network. + `(#:configure-flags '("-DDOWNLOAD_TITLE_SEQUENCES=OFF") + #:tests? #f ; Tests require network. #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-usr-share-paths&add-data @@ -2335,23 +2335,14 @@ Transport Tycoon Deluxe.") (let ((titles (assoc-ref inputs "openrct2-title-sequences")) (objects (assoc-ref inputs "openrct2-objects"))) ;; Fix some references to /usr/share. - (substitute* "src/openrct2/platform/Platform.Linux.cpp" + ;; Change to Platform.Linux.cpp on 0.1.2+ + (substitute* "src/openrct2/platform/linux.c" (("/usr/share") (string-append (assoc-ref %outputs "out") "/share"))) (copy-recursively (string-append titles "/share/openrct2/title-sequences") "data/title") (copy-recursively (string-append objects - "/share/openrct2/objects") "data/object")))) - (add-before 'configure 'fixgcc7 - (lambda _ - (unsetenv "C_INCLUDE_PATH") - (unsetenv "CPLUS_INCLUDE_PATH") - #t)) - (add-after 'fixgcc7 'get-rid-of-errors - (lambda _ - ;; Don't treat warnings as errors. - (substitute* "CMakeLists.txt" - (("-Werror") ""))))))) + "/share/openrct2/objects") "data/object"))))))) (inputs `(("curl" ,curl) ("fontconfig" ,fontconfig) ("freetype" ,freetype) @@ -2367,8 +2358,7 @@ Transport Tycoon Deluxe.") ("speexdsp" ,speexdsp) ("zlib" ,zlib))) (native-inputs - `(("gcc" ,gcc-7) - ("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 -- cgit v1.2.3 From 1ba7a62362d332f1c059222ce177217860e5437d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 16:42:05 +0200 Subject: gnu: python-nose-timer: Update to 0.7.2. * gnu/packages/check.scm (python-nose-timer): Update to 0.7.2. [source]: Remove patch... * gnu/packages/patches/python-nose-timer-drop-ordereddict.patch: ...delete file... * gnu/local.mk (dist_patch_DATA): ...and remove it. --- gnu/local.mk | 1 - gnu/packages/check.scm | 9 +---- .../python-nose-timer-drop-ordereddict.patch | 44 ---------------------- 3 files changed, 2 insertions(+), 52 deletions(-) delete mode 100644 gnu/packages/patches/python-nose-timer-drop-ordereddict.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 59e983ae58..bfe8a9ee7e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1050,7 +1050,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch \ %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \ %D%/packages/patches/python-networkx2-reproducible-build.patch \ - %D%/packages/patches/python-nose-timer-drop-ordereddict.patch \ %D%/packages/patches/python-pillow-fix-failing-tests.patch \ %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \ %D%/packages/patches/python-scikit-learn-fix-test-non-determinism.patch \ diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 3e959bde92..44e38c55c8 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1902,19 +1902,14 @@ create data based on random numbers and yet remain repeatable.") (define-public python-nose-timer (package (name "python-nose-timer") - (version "0.7.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (pypi-uri "nose-timer" version)) - (patches - (search-patches - ;; This patch will not be needed in the next version. - ;; It is taken from the master branch. - "python-nose-timer-drop-ordereddict.patch")) (sha256 (base32 - "1s32ymsnby8lz2qk55ifj9zi50dqcg6swnj5cz2rmwxg2jsslsxp")))) + "0ywg223p528014z5s0vzck74r4xyw3kvcp2casfnc85dkvir1zj7")))) (build-system python-build-system) (propagated-inputs `(("python-nose" ,python-nose) diff --git a/gnu/packages/patches/python-nose-timer-drop-ordereddict.patch b/gnu/packages/patches/python-nose-timer-drop-ordereddict.patch deleted file mode 100644 index e1e71a332a..0000000000 --- a/gnu/packages/patches/python-nose-timer-drop-ordereddict.patch +++ /dev/null @@ -1,44 +0,0 @@ -From 700076019b5aff72aac7651cc830aaef21ee9a47 Mon Sep 17 00:00:00 2001 -From: jakirkham -Date: Fri, 7 Jul 2017 05:57:56 -0400 -Subject: [PATCH] Drop ordereddict requirement (#84) - -* Drop ordereddict requirement - -As Python 2.7 is the minimum Python supported, every version of Python -should have `ordereddict` preincluded in the standard library one way or -another. So we can drop this dependency and just handle the differences -between Python 2 and Python 3. ---- - nosetimer/plugin.py | 5 +---- - setup.py | 1 - - 2 files changed, 1 insertion(+), 5 deletions(-) - -diff --git a/nosetimer/plugin.py b/nosetimer/plugin.py -index ef28e11..d093a51 100644 ---- a/nosetimer/plugin.py -+++ b/nosetimer/plugin.py -@@ -12,10 +12,7 @@ - except ImportError: - import queue as Queue - --try: -- from collections import OrderedDict --except ImportError: -- from ordereddict import OrderedDict -+from collections import OrderedDict - - - # define constants -diff --git a/setup.py b/setup.py -index 6a55b82..d249325 100755 ---- a/setup.py -+++ b/setup.py -@@ -27,7 +27,6 @@ - install_requires=[ - 'nose', - 'termcolor', -- 'ordereddict', - ], - license='MIT', - entry_points={ -- cgit v1.2.3 From f71619648ce0ca6c2e070c7b59e803538656eed4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 17:14:38 +0200 Subject: gnu: perl-dbi: Update to 1.641. * gnu/packages/databases.scm (perl-dbi): Update to 1.641. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index e853b62fdf..d240b75ad6 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1107,7 +1107,7 @@ extremely small.") (define-public perl-dbi (package (name "perl-dbi") - (version "1.637") + (version "1.641") (source (origin (method url-fetch) (uri (string-append @@ -1115,7 +1115,7 @@ extremely small.") version ".tar.gz")) (sha256 (base32 - "1ikbsb6sb0bd2m1dqknl4vx7ikmnd41y0xq8np1l40g8jcjp2mr5")))) + "1hf2x29bnqf2x1v4bdhji802z7n2mbg7h1amv8gdkqyhrlrfa2am")))) (build-system perl-build-system) (synopsis "Database independent interface for Perl") (description "This package provides an database interface for Perl.") -- cgit v1.2.3 From 6dd5f2ea634107625831fbd36fb313df5c3c79d6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 17:14:51 +0200 Subject: gnu: qrencode: Update to 4.0.2. * gnu/packages/aidc.scm (qrencode): Update to 4.0.2. --- gnu/packages/aidc.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/aidc.scm b/gnu/packages/aidc.scm index 4615b346d6..64d26548c4 100644 --- a/gnu/packages/aidc.scm +++ b/gnu/packages/aidc.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014 John Darringon ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Hartmut Goebel +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -51,7 +52,7 @@ formats.") (define-public qrencode (package (name "qrencode") - (version "4.0.0") + (version "4.0.2") (source (origin (method url-fetch) (uri (string-append @@ -59,7 +60,7 @@ formats.") ".tar.bz2")) (sha256 (base32 - "02vx69fl52jbcrmnydsaxcmy6nxqm9jyxzd7hr07s491d7hka069")))) + "1d2q5d3v8g3hsi3h5jq4n177bjhf3kawms09immw7p187f6jgjy9")))) (build-system gnu-build-system) (inputs `(("libpng" ,libpng))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From d518261f05f81d49d64d2b1a44cde904bcc1cada Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 17:43:40 +0200 Subject: gnu: cppcheck: Update to 1.84. * gnu/packages/check.scm (cppcheck): Update to 1.84. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 44e38c55c8..b414cc147e 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -293,13 +293,13 @@ format.") (define-public cppcheck (package (name "cppcheck") - (version "1.83") + (version "1.84") (source (origin (method url-fetch) (uri (string-append "https://github.com/danmar/cppcheck/archive/" version ".tar.gz")) (sha256 - (base32 "15ghxwmyy09cd9mi008k4jn09c441j86qyaa4dz0is7f5dv5cdkx")) + (base32 "1ibz07dgs1dpfb8bmjh3qsma37wl5p6s6b4qlv5ccpshj4yjk9ma")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (home-page "http://cppcheck.sourceforge.net") -- cgit v1.2.3 From 19611b7a0aeb108512576efab63da4bdafd49890 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 18:23:36 +0200 Subject: gnu: python-freezegun: Return #t from phase. * gnu/packages/check.scm (python-freezegun)[arguments]: Substitute INVOKE for SYSTEM*. --- gnu/packages/check.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index b414cc147e..17fbcc68f9 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1948,7 +1948,7 @@ create data based on random numbers and yet remain repeatable.") ;; package does not include the Makefile. (replace 'check (lambda _ - (zero? (system* "nosetests" "./tests/"))))))) + (invoke "nosetests" "./tests/")))))) (home-page "https://github.com/spulec/freezegun") (synopsis "Test utility for mocking the datetime module") (description -- cgit v1.2.3 From ef0d765605087442ee4f919e2cfda27739f7b3b3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 18:23:58 +0200 Subject: gnu: python-freezegun: Update to 0.3.10. * gnu/packages/check.scm (python-freezegun): Update to 0.3.10. --- gnu/packages/check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 17fbcc68f9..42b90bc2b2 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -1925,14 +1925,14 @@ create data based on random numbers and yet remain repeatable.") (define-public python-freezegun (package (name "python-freezegun") - (version "0.3.9") + (version "0.3.10") (source (origin (method url-fetch) (uri (pypi-uri "freezegun" version)) (sha256 (base32 - "1vhf3kgdy7gpy70n3bxa3y1n6aza316137md97z8p5k0gz6wqg3q")))) + "08m6b42yxb9hk5lv747v9n2qsxyadmkb0k6yg0gxdanwap0slg3h")))) (build-system python-build-system) (native-inputs `(("python-mock" ,python-mock) -- cgit v1.2.3 From b6c675c693d21345f4b0589563f914c79f957846 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 15:34:47 -0400 Subject: gnu: GnuPG 1.4: Update to 1.4.23. * gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.23. [source]: Remove patch. * gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/gnupg.scm | 5 +-- .../patches/gnupg-1.4-CVE-2018-12020.patch | 50 ---------------------- 3 files changed, 2 insertions(+), 54 deletions(-) delete mode 100644 gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index bfe8a9ee7e..01e0718723 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -744,7 +744,6 @@ dist_patch_DATA = \ %D%/packages/patches/gnome-todo-libical-compat.patch \ %D%/packages/patches/gnome-tweak-tool-search-paths.patch \ %D%/packages/patches/gnucash-price-quotes-perl.patch \ - %D%/packages/patches/gnupg-1.4-CVE-2018-12020.patch \ %D%/packages/patches/gnutls-skip-trust-store-test.patch \ %D%/packages/patches/gnutls-skip-pkgconfig-test.patch \ %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \ diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 6a0defb46f..da0c33565a 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -363,15 +363,14 @@ libskba (working with X.509 certificates and CMS data).") (define-public gnupg-1 (package (inherit gnupg) - (version "1.4.22") + (version "1.4.23") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) - (patches (search-patches "gnupg-1.4-CVE-2018-12020.patch")) (sha256 (base32 - "1d1hz4szh1kvwhsw7w2zxa6q5ndrk3qy6hj289l1b8k3xi5s554m")))) + "1fkq4sqldvf6a25mm2qz95swv1qjg464736091w51djiwqbjyin9")))) (native-inputs '()) (inputs `(("zlib" ,zlib) diff --git a/gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch b/gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch deleted file mode 100644 index 306d4d348b..0000000000 --- a/gnu/packages/patches/gnupg-1.4-CVE-2018-12020.patch +++ /dev/null @@ -1,50 +0,0 @@ -Fix CVE-2018-12020: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-12020 -https://lists.gnupg.org/pipermail/gnupg-announce/2018q2/000425.html - -Patch copied from upstream source repository: - -https://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=2326851c60793653069494379b16d84e4c10a0ac - -From 2326851c60793653069494379b16d84e4c10a0ac Mon Sep 17 00:00:00 2001 -From: Werner Koch -Date: Fri, 8 Jun 2018 10:45:21 +0200 -Subject: [PATCH] gpg: Sanitize diagnostic with the original file name. - -* g10/mainproc.c (proc_plaintext): Sanitize verbose output. --- - -This fixes a forgotten sanitation of user supplied data in a verbose -mode diagnostic. The mention CVE is about using this to inject -status-fd lines into the stderr output. Other harm good as well be -done. Note that GPGME based applications are not affected because -GPGME does not fold status output into stderr. - -CVE-id: CVE-2018-12020 -GnuPG-bug-id: 4012 -(cherry picked from commit 13f135c7a252cc46cff96e75968d92b6dc8dce1b) ---- - g10/mainproc.c | 6 +++++- - 1 file changed, 5 insertions(+), 1 deletion(-) - -diff --git a/g10/mainproc.c b/g10/mainproc.c -index 33a654b34..ffa7ef6d8 100644 ---- a/g10/mainproc.c -+++ b/g10/mainproc.c -@@ -638,7 +638,11 @@ proc_plaintext( CTX c, PACKET *pkt ) - if( pt->namelen == 8 && !memcmp( pt->name, "_CONSOLE", 8 ) ) - log_info(_("NOTE: sender requested \"for-your-eyes-only\"\n")); - else if( opt.verbose ) -- log_info(_("original file name='%.*s'\n"), pt->namelen, pt->name); -+ { -+ char *tmp = make_printable_string (pt->name, pt->namelen, 0); -+ log_info (_("original file name='%.*s'\n"), (int)strlen (tmp), tmp); -+ xfree (tmp); -+ } - free_md_filter_context( &c->mfx ); - c->mfx.md = md_open( 0, 0); - /* fixme: we may need to push the textfilter if we have sigclass 1 --- -2.17.1 - -- cgit v1.2.3 From 44d1b9569b47f563a3b38b09c9c348c2ce60b1ec Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 15:45:29 -0400 Subject: gnu: python-click-log: Update to 0.3.2. * gnu/packages/python.scm (python-click-log): Update to 0.3.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 72e8d9292d..7bb918605c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7260,13 +7260,13 @@ applications.") (define-public python-click-log (package (name "python-click-log") - (version "0.2.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (pypi-uri "click-log" version)) (sha256 (base32 - "1r1x85023cslb2pwldd089jjk573mk3w78cnashs77wrx7yz8fj9")))) + "091i03bhxyzsdbc6kilxhivfda2f8ymz3b33xa6cj5kbzjiirz8n")))) (build-system python-build-system) (propagated-inputs `(("python-click" ,python-click))) -- cgit v1.2.3 From a4bae9af009df2e3cd1fb96941084e0af137d366 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 15:45:59 -0400 Subject: gnu: vdirsyncer: Update to 0.6.6. * gnu/packages/dav.scm (vdirsyncer): Update to 0.6.6. [arguments]: Simplify the man-page building. --- gnu/packages/dav.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm index 0c6c62d5a3..9d0479b1e1 100644 --- a/gnu/packages/dav.scm +++ b/gnu/packages/dav.scm @@ -57,13 +57,13 @@ clients.") (define-public vdirsyncer (package (name "vdirsyncer") - (version "0.16.4") + (version "0.16.6") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "03wva48bgv1ad3df6plc9b8xxh6k8bcaxrhlzwh81c9mzn5bspzv")))) + "07iqq5c53cfrb5xnmam1rsl683hc3rykmdak896n2gm81r361c66")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -76,7 +76,6 @@ clients.") (zero? (system* "make" "test")))) (add-after 'install 'manpage (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) (zero? (system* "make" "--directory=docs/" "man")) (install-file "docs/_build/man/vdirsyncer.1" -- cgit v1.2.3 From e3173fe18e836cea124e90ca85c76b495cd48e4d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 15:55:26 -0400 Subject: gnu: botan: Update to 2.6.0 [fixes CVE-2018-{9127,9860}]. * gnu/packages/crypto.scm (botan): Update to 2.6.0. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 929fbb5bc2..105760afa3 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -713,14 +713,14 @@ SHA256, SHA512, SHA3, AICH, ED2K, Tiger, DC++ TTH, BitTorrent BTIH, GOST R (define-public botan (package (name "botan") - (version "2.5.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (string-append "https://botan.randombit.net/releases/" "Botan-" version ".tgz")) (sha256 (base32 - "06zvwknhwfrkdvq2sybqbqhnd2d4nq2cszlnsddql13z7vh1z8xq")))) + "1iawmymmnp5j2mcjj70slivn6bgg8gbpppldc1rjqw5sbdan3wn1")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit v1.2.3 From 0effadcad538241e0cd4ae49a7dececfbb3a8782 Mon Sep 17 00:00:00 2001 From: Gábor Boskovits Date: Thu, 14 Jun 2018 22:40:01 +0200 Subject: gnu: libressl: Update to 2.7.4 [fixes CVE-2018-{0495,0732}]. * gnu/packages/tls.scm (libressl): Update to 2.7.4. Signed-off-by: Leo Famulari --- gnu/packages/tls.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index a934a50878..9e6aac81b6 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -459,14 +459,14 @@ required structures.") (define-public libressl (package (name "libressl") - (version "2.7.3") + (version "2.7.4") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/LibreSSL/" name "-" version ".tar.gz")) (sha256 (base32 - "1597kj9jy3jyw52ys19sd4blg2gkam5q0rqdxbnrnvnyw67hviqn")))) + "19kxa5i97q7p6rrps9qm0nd8zqhdjvzx02j72400c73cl2nryfhy")))) (build-system gnu-build-system) (arguments ;; Do as if 'getentropy' was missing since older Linux kernels lack it -- cgit v1.2.3 From baed923682802b7281bd68274f080d2bb55d3eff Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 14 Jun 2018 21:59:23 +0200 Subject: self: Add 'guix-daemon' to the result. * gnu/packages/package-management.scm (guix-daemon): New variable. * guix/self.scm (whole-package): Add #:daemon and honor it. (compiled-guix): Pass #:daemon to 'whole-package'. --- gnu/packages/package-management.scm | 47 +++++++++++++++++++++++++++++++++++++ guix/self.scm | 15 +++++++++++- 2 files changed, 61 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 24cf3ad015..6d99cddc0d 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -294,6 +294,53 @@ the Nix package manager.") ;; Alias for backward compatibility. (define-public guix-devel guix) +(define-public guix-daemon + ;; This package is for internal consumption: it allows us to quickly build + ;; the 'guix-daemon' program and use that in (guix self), used by 'guix + ;; pull'. + (package + (inherit guix) + (properties `((hidden? . #t))) + (name "guix-daemon") + + ;; Use a minimum set of dependencies. + (native-inputs + (fold alist-delete (package-native-inputs guix) + '("po4a" "graphviz" "help2man"))) + (inputs + `(("gnutls" ,gnutls) + ("guile-git" ,guile-git) + ,@(package-inputs guix))) + (propagated-inputs '()) + + (arguments + (substitute-keyword-arguments (package-arguments guix) + ((#:tests? #f #f) + #f) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (replace 'build + (lambda _ + (invoke "make" "nix/libstore/schema.sql.hh") + (invoke "make" "-j" (number->string + (parallel-job-count)) + "guix-daemon"))) + (delete 'copy-bootstrap-guile) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (invoke "make" "install-binPROGRAMS" + "install-nodist_pkglibexecSCRIPTS") + + ;; We need to tell 'guix-daemon' which 'guix' command to use. + ;; Here we use a questionable hack where we hard-code + ;; "~root/.config", which could be wrong (XXX). + (let ((out (assoc-ref outputs "out"))) + (substitute* (find-files (string-append out "/libexec")) + (("exec \".*/bin/guix\"") + "exec ~root/.config/current/bin/guix")) + #t))) + (delete 'wrap-program))))))) + (define-public guile2.0-guix (package (inherit guix) diff --git a/guix/self.scm b/guix/self.scm index 3023ae379b..1306df46f5 100644 --- a/guix/self.scm +++ b/guix/self.scm @@ -385,7 +385,7 @@ load path." (define* (whole-package name modules dependencies #:key (guile-version (effective-version)) - info + info daemon (command (guix-command modules #:dependencies dependencies #:guile-version guile-version))) @@ -401,6 +401,10 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the (symlink #$command (string-append #$output "/bin/guix")) + (when #$daemon + (symlink (string-append #$daemon "/bin/guix-daemon") + (string-append #$output "/bin/guix-daemon"))) + (let ((modules (string-append #$output "/share/guile/site/" (effective-version))) @@ -611,6 +615,15 @@ the modules, and DEPENDENCIES, a list of packages depended on. COMMAND is the #:guile-version guile-version))) (whole-package name built-modules dependencies #:command command + + ;; Include 'guix-daemon'. XXX: Here we inject an + ;; older snapshot of guix-daemon, but that's a good + ;; enough approximation for now. + #:daemon (module-ref (resolve-interface + '(gnu packages + package-management)) + 'guix-daemon) + #:info (info-manual source) #:guile-version guile-version))) ((= 0 pull-version) -- cgit v1.2.3 From 112c2c010b2e84691302bdc174d9a4825dc6ca24 Mon Sep 17 00:00:00 2001 From: Fis Trivial Date: Tue, 12 Jun 2018 10:01:16 +0000 Subject: gnu: Add lightgbm. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/machine-learning.scm (lightgbm): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/machine-learning.scm | 47 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 15e4d45749..cda5c1e2c8 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -47,6 +47,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) #:use-module (gnu packages ocaml) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) @@ -786,3 +787,49 @@ main intended application of Autograd is gradient-based optimization.") (define-public python2-autograd (package-with-python2 python-autograd)) + +(define-public lightgbm + (package + (name "lightgbm") + (version "2.0.12") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/Microsoft/LightGBM/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1")) + (file-name (string-append name "-" version ".tar.gz")))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-nose" ,python-nose))) + (inputs + `(("openmpi" ,openmpi))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (arguments + `(#:configure-flags + '("-DUSE_MPI=ON") + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key outputs #:allow-other-keys) + (with-directory-excursion ,(string-append "../LightGBM-" version) + (invoke "pytest" "tests/c_api_test/test_.py"))))))) + (build-system cmake-build-system) + (home-page "https://github.com/Microsoft/LightGBM") + (synopsis "Gradient boosting framework based on decision tree algorithms") + (description "LightGBM is a gradient boosting framework that uses tree +based learning algorithms. It is designed to be distributed and efficient with +the following advantages: + +@itemize +@item Faster training speed and higher efficiency +@item Lower memory usage +@item Better accuracy +@item Parallel and GPU learning supported (not enabled in this package) +@item Capable of handling large-scale data +@end itemize\n") + (license license:expat))) -- cgit v1.2.3 From a8fb82a8ab772b5cb0c93063fc02563423230c46 Mon Sep 17 00:00:00 2001 From: Fis Trivial Date: Tue, 12 Jun 2018 10:02:15 +0000 Subject: gnu: Add vowpal-wabbit. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/machine-learning.scm (vowpal-wabbit): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/machine-learning.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index cda5c1e2c8..59e38bb88e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -833,3 +833,32 @@ the following advantages: @item Capable of handling large-scale data @end itemize\n") (license license:expat))) + +(define-public vowpal-wabbit + ;; Language bindings not included. + (package + (name "vowpal-wabbit") + (version "8.5.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/JohnLangford/vowpal_wabbit/archive/" + version ".tar.gz")) + (sha256 + (base32 + "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr")) + (file-name (string-append name "-" version ".tar.gz")))) + (inputs + `(("boost" ,boost) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags + (list (string-append "--with-boost=" + (assoc-ref %build-inputs "boost"))))) + (build-system gnu-build-system) + (home-page "https://github.com/JohnLangford/vowpal_wabbit") + (synopsis "Fast machine learning library for online learning") + (description "Vowpal Wabbit is a machine learning system with techniques +such as online, hashing, allreduce, reductions, learning2search, active, and +interactive learning.") + (license license:bsd-3))) -- cgit v1.2.3 From 565af91acc66404ad7bc9ef3b9f6f5a2ca4460b5 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Thu, 14 Jun 2018 11:02:53 +0200 Subject: gnu: emacs-racket-mode: Update and bug fix. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (emacs-racket-mode): Update and bug fix. - Update to the current commit - Bug fix: include Racket files in addition to Emacs Lisp files Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 02e7791705..4999dda55b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -9968,11 +9968,11 @@ perform regression test for packages that provide font-lock rules.") (license license:gpl3+)))) (define-public emacs-racket-mode - (let ((commit "33877b1bb24faea68842e0396bd5718b84e47451") + (let ((commit "48f0cb99d3b2ca6066249546d2063d85437251c1") (revision "1")) (package (name "emacs-racket-mode") - (version (string-append "0.0.1" "-" revision "." + (version (string-append "0.0.2" "-" revision "." (string-take commit 7))) (source (origin @@ -9983,8 +9983,10 @@ perform regression test for packages that provide font-lock rules.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0681mzwx08zwbh8qg3s26jw1jn4fw2ljp1akxqkhy08sxhafqvb1")))) + "0fxky8xj639bjhiab9way9daqda22301b7w85vm4b4ydgjgnc59x")))) (build-system emacs-build-system) + (arguments + `(#:include '("\\.el$" "\\.rkt$"))) (propagated-inputs `(("emacs-faceup" ,emacs-faceup) ("emacs-s" ,emacs-s))) -- cgit v1.2.3 From 96fd9a0e622b1afd470efa5b47fcfb38ca65105e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 17:38:45 -0400 Subject: gnu: Go 1.9: Update to 1.9.7. * gnu/packages/golang.scm (go-1.9): Update to 1.9.7. --- gnu/packages/golang.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 1d8e80c8fe..1d13b69963 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -215,7 +215,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (package (inherit go-1.4) (name "go") - (version "1.9.6") + (version "1.9.7") (source (origin (method url-fetch) @@ -223,7 +223,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") name version ".src.tar.gz")) (sha256 (base32 - "0a2qkvzr0g5cbd66wi7b6r40qyp9p55y0zz2j5qg1xsqwsdhbx1n")))) + "08kpy874x0rx43zpyv5kwd8xj2ma91xm33i0ka2v1v788px18a2q")))) (arguments (substitute-keyword-arguments (package-arguments go-1.4) ((#:phases phases) -- cgit v1.2.3 From 9297fc61cc4eb7b78210f68dfa7396f525d619a1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 17:39:30 -0400 Subject: gnu: Go 1.10: Update to 1.10.3. * gnu/packages/golang.scm (go-1.10): Update to 1.10.3. --- gnu/packages/golang.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 1d13b69963..a83cdcde83 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -384,7 +384,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (package (inherit go-1.9) (name "go") - (version "1.10.2") + (version "1.10.3") (source (origin (method url-fetch) @@ -392,7 +392,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") name version ".src.tar.gz")) (sha256 (base32 - "1gcqbac3wbhbcr0ri9zgfj6qkqbwf9fn116a0a7fvn4wdff60r32")))) + "1wjmw65nfkkzz084695gdgn13sbjcaafy2y5370d214pdk31qysn")))) (arguments (substitute-keyword-arguments (package-arguments go-1.9) ((#:phases phases) -- cgit v1.2.3 From b494bbe466419dcac9f415c1152131f012b9555e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 17:55:40 -0400 Subject: gnu: certbot, python-acme: Update to 0.25.1. * gnu/packages/tls.scm (certbot): Update 0.25.1. (python-acme): Update to 0.25.1. [native-inputs]: Add python-pytest. [propagated-inputs]: Add python-requests-toolbelt. --- gnu/packages/tls.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 9e6aac81b6..c81197b812 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -503,13 +503,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.24.0") + (version "0.25.1") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "1jq1nlly5146k08dw31fc1pw78plya5jswznnd512c08giif0mfn")))) + "0d177dhy8a7472pz9v4blrlk02d8fp6s52li7z8v3dv97pvz7da7")))) (build-system python-build-system) (arguments `(#:phases @@ -528,6 +528,7 @@ netcat implementation that supports TLS.") ;; TODO: Add optional inputs for testing. (native-inputs `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) ;; For documentation ("python-sphinx" ,python-sphinx) ("python-sphinxcontrib-programoutput" ,python-sphinxcontrib-programoutput) @@ -537,6 +538,7 @@ netcat implementation that supports TLS.") `(("python-josepy" ,python-josepy) ("python-six" ,python-six) ("python-requests" ,python-requests) + ("python-requests-toolbelt" ,python-requests-toolbelt) ("python-pytz" ,python-pytz) ("python-pyrfc3339" ,python-pyrfc3339) ("python-pyasn1" ,python-pyasn1) @@ -558,7 +560,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "0w3dbz74rpabjnc3l3ybnzjdypbr65lsjqf9yn243b5kid9d8wm0")))) + "0kp56gwn1bnlrag9qidhm1i5ifdp5z6y1ravh3yimfrkc4cfa8sw")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) -- cgit v1.2.3 From bb15b581f74dbf4f06425e3ef0aae1863adca377 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:24:23 +0200 Subject: gnu: Add r-bayseq. * gnu/packages/bioconductor.scm (r-bayseq): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed35b4c61a..3dba9cbab4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -371,3 +371,29 @@ filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.") (license license:gpl2+))) + +(define-public r-bayseq + (package + (name "r-bayseq") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "baySeq" version)) + (sha256 + (base32 + "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg")))) + (properties `((upstream-name . "baySeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-edger" ,r-edger) + ("r-genomicranges" ,r-genomicranges))) + (home-page "https://bioconductor.org/packages/baySeq/") + (synopsis "Bayesian analysis of differential expression patterns in count data") + (description + "This package identifies differential expression in high-throughput count +data, such as that derived from next-generation sequencing machines, +calculating estimated posterior likelihoods of differential expression (or +more complex hypotheses) via empirical Bayesian methods.") + (license license:gpl3))) -- cgit v1.2.3 From dfac7eb9170ae3b93ca2c179c13b33bc1ae7023d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:26:48 +0200 Subject: gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3-masked. * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3-masked): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3dba9cbab4..7685cee9e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -61,6 +61,41 @@ melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked + (package + (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") + (version "1.3.99") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Dmelanogaster.UCSC.dm3.masked_" + version ".tar.gz")) + (sha256 + (base32 + "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) + (properties + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-dmelanogaster-ucsc-dm3" + ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") + (synopsis "Full masked genome sequences for Fly") + (description + "This package provides full masked genome sequences for Drosophila +melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in +Biostrings objects. The sequences are the same as in +BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following +masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of +intra-contig ambiguities (AMB mask), (3) the mask of repeats from +RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats +Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 6fbd759b132d65825bfeb47ac66a957bde38c770 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:27:10 +0200 Subject: gnu: Add r-bsgenome-hsapiens-ucsc-hg19-masked. * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19-masked): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7685cee9e5..e1a1ba1963 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -96,6 +96,41 @@ RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(define-public r-bsgenome-hsapiens-ucsc-hg19-masked + (package + (name "r-bsgenome-hsapiens-ucsc-hg19-masked") + (version "1.3.99") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Hsapiens.UCSC.hg19.masked_" + version ".tar.gz")) + (sha256 + (base32 + "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) + (properties + `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" + ,r-bsgenome-hsapiens-ucsc-hg19))) + (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") + (synopsis "Full masked genome sequences for Homo sapiens") + (description + "This package provides full genome sequences for Homo sapiens (Human) as +provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The +sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of +them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS +mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of +repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem +Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by +default.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 2bece692a685d4a4e823cf908898a2aceaadc6c2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:27:29 +0200 Subject: gnu: Add r-bsgenome-mmusculus-ucsc-mm9-masked. * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked): New variable. --- gnu/packages/bioconductor.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e1a1ba1963..e962ad523e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -131,6 +131,41 @@ Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(define-public r-bsgenome-mmusculus-ucsc-mm9-masked + (package + (name "r-bsgenome-mmusculus-ucsc-mm9-masked") + (version "1.3.99") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Mmusculus.UCSC.mm9.masked_" + version ".tar.gz")) + (sha256 + (base32 + "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) + (properties + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-mmusculus-ucsc-mm9" + ,r-bsgenome-mmusculus-ucsc-mm9))) + (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") + (synopsis "Full masked genome sequences for Mouse") + (description + "This package provides full genome sequences for Mus musculus (Mouse) as +provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The +sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of +them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS +mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of +repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem +Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by +default." ) + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") -- cgit v1.2.3 From 609f4ad12fb37e256d6bb2b89cb2c1a8b30bd28c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:36:15 +0200 Subject: gnu: Add r-chipcomp. * gnu/packages/bioconductor.scm (r-chipcomp): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e962ad523e..93d68c2a5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -502,3 +502,37 @@ data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.") (license license:gpl3))) + +(define-public r-chipcomp + (package + (name "r-chipcomp") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChIPComp" version)) + (sha256 + (base32 + "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs")))) + (properties `((upstream-name . "ChIPComp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/ChIPComp") + (synopsis "Quantitative comparison of multiple ChIP-seq datasets") + (description + "ChIPComp implements a statistical method for quantitative comparison of +multiple ChIP-seq datasets. It detects differentially bound sharp binding +sites across multiple conditions considering matching control in ChIP-seq +datasets.") + ;; Any version of the GPL. + (license license:gpl3+))) -- cgit v1.2.3 From 0490f9de88edef1947c6e047701a86bf1b37a506 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:38:17 +0200 Subject: gnu: Add r-riboprofiling. * gnu/packages/bioconductor.scm (r-riboprofiling): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93d68c2a5f..8dbbb74b3f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -536,3 +536,42 @@ sites across multiple conditions considering matching control in ChIP-seq datasets.") ;; Any version of the GPL. (license license:gpl3+))) + +(define-public r-riboprofiling + (package + (name "r-riboprofiling") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RiboProfiling" version)) + (sha256 + (base32 + "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0")))) + (properties `((upstream-name . "RiboProfiling"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-sqldf" ,r-sqldf))) + (home-page "https://bioconductor.org/packages/RiboProfiling/") + (synopsis "Ribosome profiling data analysis") + (description "Starting with a BAM file, this package provides the +necessary functions for quality assessment, read start position recalibration, +the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting +of count data: pairs, log fold-change, codon frequency and coverage +assessment, principal component analysis on codon coverage.") + (license license:gpl3))) -- cgit v1.2.3 From 6ffdfe6a0121f6e9e6029ef16d1653afc49628d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 07:38:27 +0200 Subject: gnu: Add r-riboseqr. * gnu/packages/bioconductor.scm (r-riboseqr): New variable. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8dbbb74b3f..634493d136 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -575,3 +575,31 @@ the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.") (license license:gpl3))) + +(define-public r-riboseqr + (package + (name "r-riboseqr") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "riboSeqR" version)) + (sha256 + (base32 + "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn")))) + (properties `((upstream-name . "riboSeqR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-bayseq" ,r-bayseq) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-seqlogo" ,r-seqlogo))) + (home-page "https://bioconductor.org/packages/riboSeqR/") + (synopsis "Analysis of sequencing data from ribosome profiling experiments") + (description + "This package provides plotting functions, frameshift detection and +parsing of genetic sequencing data from ribosome profiling experiments.") + (license license:gpl3))) -- cgit v1.2.3 From 056402220e54d6942a622331c8a66e983e7d7356 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Fri, 15 Jun 2018 09:09:39 +0200 Subject: gnu: innoextract: Update to 1.7. * gnu/packages/compression.scm (innoextract): Update to 1.7. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 2984e854ce..8f062049a6 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2111,7 +2111,7 @@ single-member files which can't be decompressed in parallel.") (define-public innoextract (package (name "innoextract") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) @@ -2119,7 +2119,7 @@ single-member files which can't be decompressed in parallel.") version ".tar.gz")) (sha256 (base32 - "08sp5vbfjvq1irhhraqkn5m2x1z209r4axhx7laf1adcw30ccapi")) + "0khwi9f0q0h6xfbixrrc1rfpgj0b7ajwilq7yhmxnn5lpc807f6x")) (file-name (string-append name "-" version ".tar.gz")))) (build-system cmake-build-system) (arguments -- cgit v1.2.3 From a32279ffb68a23458177bf6a9b9cae5abea59e2e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 08:21:01 +0200 Subject: gnu: Add r-interactionset. * gnu/packages/bioconductor.scm (r-interactionset): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 634493d136..771f6a46d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -603,3 +603,35 @@ assessment, principal component analysis on codon coverage.") "This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) + +(define-public r-interactionset + (package + (name "r-interactionset") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "InteractionSet" version)) + (sha256 + (base32 + "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n")))) + (properties + `((upstream-name . "InteractionSet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/InteractionSet") + (synopsis "Base classes for storing genomic interaction data") + (description + "This packages provides the @code{GInteractions}, +@code{InteractionSet} and @code{ContactMatrix} objects and associated methods +for storing and manipulating genomic interaction data from Hi-C and ChIA-PET +experiments.") + (license license:gpl3))) -- cgit v1.2.3 From cf9a29b24c990aeadb673d233b3ca686249b2b10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 15 Jun 2018 08:21:17 +0200 Subject: gnu: Add r-genomicinteractions. * gnu/packages/bioconductor.scm (r-genomicinteractions): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 771f6a46d1..a6a8216ccb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -24,10 +24,11 @@ #:use-module (guix download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) - #:use-module (gnu packages statistics) - #:use-module (gnu packages bioinformatics)) + #:use-module (gnu packages graph) + #:use-module (gnu packages statistics)) (define-public r-bsgenome-dmelanogaster-ucsc-dm6 (package @@ -635,3 +636,42 @@ parsing of genetic sequencing data from ribosome profiling experiments.") for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.") (license license:gpl3))) + +(define-public r-genomicinteractions + (package + (name "r-genomicinteractions") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicInteractions" version)) + (sha256 + (base32 + "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q")))) + (properties + `((upstream-name . "GenomicInteractions"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gviz" ,r-gviz) + ("r-igraph" ,r-igraph) + ("r-interactionset" ,r-interactionset) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") + (synopsis "R package for handling genomic interaction data") + (description + "This R package provides tools for handling genomic interaction data, +such as ChIA-PET/Hi-C, annotating genomic features with interaction +information and producing various plots and statistics.") + (license license:gpl3))) -- cgit v1.2.3 From abde01f27dc3fb9ec53897c4d9ee36cbca0a8949 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Fri, 15 Jun 2018 09:16:22 +0200 Subject: gnu: neofetch: Update to 4.0.2. * gnu/packages/admin.scm (neofetch): Update to 4.0.2. --- gnu/packages/admin.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 6e9888cf3b..cf459bfbc6 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2017, 2018 Marius Bakke ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2018 Pierre-Antoine Rouby +;;; Copyright © 2018 Rutger Helling ;;; ;;; This file is part of GNU Guix. ;;; @@ -2395,7 +2396,7 @@ tool for remote execution and deployment.") (define-public neofetch (package (name "neofetch") - (version "3.4.0") + (version "4.0.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/dylanaraps/neofetch/" @@ -2403,7 +2404,7 @@ tool for remote execution and deployment.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "18rhamy910ig03rr55y9x5i6pf78yj9xc6jpm6nfh3gqja7340rb")))) + "014hlbzs6j4b669b64hnq8vc5knwiv9ncw9m9d193p9jsybxpm1w")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests -- cgit v1.2.3 From 752ff6e9aa3a3e03415059b6d5de24b25ce169ce Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 20:53:06 +0200 Subject: gnu: r-cubature: Update to 1.4. * gnu/packages/cran.scm (r-cubature): Update to 1.4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 82beb7b23a..aa5bdc958d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3044,14 +3044,14 @@ applied econometric analysis.") (define-public r-cubature (package (name "r-cubature") - (version "1.3-13") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "cubature" version)) (sha256 (base32 - "1aq0viv2d21v7iyln73973a4h113nlv8bi007qkw6z0hijzg6gz3")))) + "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp))) -- cgit v1.2.3 From beb2d4be84f6d632c77cf9d1c9698b1fde015c1c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 21:02:26 +0200 Subject: gnu: nickle: Update to 2.81. * gnu/packages/nickle.scm (nickle): Update to 2.81. --- gnu/packages/nickle.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/nickle.scm b/gnu/packages/nickle.scm index 4c2269635b..860c111f43 100644 --- a/gnu/packages/nickle.scm +++ b/gnu/packages/nickle.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Nils Gillmann +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,14 +28,14 @@ (define-public nickle (package (name "nickle") - (version "2.77") + (version "2.81") (source (origin (method url-fetch) (uri (string-append "https://nickle.org/release/nickle-" version ".tar.gz")) (sha256 (base32 - "0rhij7cn1zkn8wzxyjkamz9fs262zyg80p6v6i864hdalg4plpm3")))) + "1daqsflnqqgfkq6w6dknbm42avz70f5qxn7qidvgp472i4a37acr")))) (build-system gnu-build-system) (native-inputs `(("readline" ,readline))) -- cgit v1.2.3 From 50632f0a8dd69c81bdaffb382f54d8ac62c87c9c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 21:36:14 +0200 Subject: gnu: perl-xml-atom: Propagate inputs. * gnu/packages/xml.scm (perl-xml-atom)[inputs]: Rename to... [propagated-inputs]: ...this, and... [native-inputs]: ...remove duplicate packages from here. --- gnu/packages/xml.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 5c31a9e669..0f6b5dc9bc 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -263,13 +263,11 @@ the @code{Graph} class and write it out in a specific file format.") (getenv "PERL5LIB"))) #t))))) (native-inputs - `(("perl-datetime" ,perl-datetime) - ;; TODO package: perl-datetime-format-atom - ("perl-html-tagset" ,perl-html-tagset) + ;; TODO package: perl-datetime-format-atom + `(("perl-html-tagset" ,perl-html-tagset) ("perl-module-build-tiny" ,perl-module-build-tiny) - ("perl-module-install" ,perl-module-install) - ("perl-xml-xpath" ,perl-xml-xpath))) - (inputs + ("perl-module-install" ,perl-module-install))) + (propagated-inputs `(("perl-class-data-inheritable" ,perl-class-data-inheritable) ("perl-datetime" ,perl-datetime) ("perl-datetime-timezone" ,perl-datetime-timezone) -- cgit v1.2.3 From 9332d70602357c9dfd7a699ed43eab009b7981e4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 22:36:33 +0200 Subject: gnu: perl-xml-xpath: Propagate inputs. * gnu/packages/xml.scm (perl-xml-xpath)[inputs]: Rename this... [propagated-inputs]: ...to this. --- gnu/packages/xml.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 0f6b5dc9bc..b9661f91d1 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -824,7 +824,7 @@ RSS 0.91, RSS 1.0, RSS 2.0, Atom") (build-system perl-build-system) (native-inputs `(("perl-path-tiny" ,perl-path-tiny))) - (inputs + (propagated-inputs `(("perl-xml-parser" ,perl-xml-parser))) (home-page "http://search.cpan.org/dist/XML-XPath") (synopsis "Parse and evaluate XPath statements") -- cgit v1.2.3 From 26d66a518c0e5d17999065dda6787da7889832bf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 22:36:46 +0200 Subject: gnu: perl-xml-xpath: Update to 1.42. * gnu/packages/xml.scm (perl-xml-xpath): Update to 1.42. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index b9661f91d1..d9cc4c36ad 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -813,14 +813,14 @@ RSS 0.91, RSS 1.0, RSS 2.0, Atom") (define-public perl-xml-xpath (package (name "perl-xml-xpath") - (version "1.40") + (version "1.42") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/MA/MANWAR/" "XML-XPath-" version ".tar.gz")) (sha256 (base32 - "07pa0bl42jka8mj7jshjynx8vpfh8b4cdyiv4zlkqvkqz98nzxib")))) + "04mm91kxav598ax7nlg81dhnvanwvg6bkf30l0cgkmga5iyccsly")))) (build-system perl-build-system) (native-inputs `(("perl-path-tiny" ,perl-path-tiny))) -- cgit v1.2.3 From 657bed34f4b5de3863fa815dabd94ba40bd4dec7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 23:43:56 +0200 Subject: gnu: fcitx: Use HTTPS home page. * gnu/packages/fcitx.scm (fcitx)[home-page]: Use HTTPS. --- gnu/packages/fcitx.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fcitx.scm b/gnu/packages/fcitx.scm index fc55df14a6..6dd7797aa4 100644 --- a/gnu/packages/fcitx.scm +++ b/gnu/packages/fcitx.scm @@ -78,7 +78,7 @@ ("libxkbfile" ,libxkbfile) ("libxml2" ,libxml2) ("xkeyboard-config" ,xkeyboard-config))) - (home-page "http://fcitx-im.org") + (home-page "https://fcitx-im.org") (synopsis "Input method framework") (description "Fcitx is an input method framework with extension support. It has -- cgit v1.2.3 From 50ca5fb332ebb524da405dcdb8d202adcabc1f75 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 14 Jun 2018 23:44:54 +0200 Subject: gnu: fcitx: Update to 4.2.9.6. * gnu/packages/fcitx.scm (fcitx): Update to 4.2.9.6. [native-inputs]: Add extra-cmake-modules. --- gnu/packages/fcitx.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fcitx.scm b/gnu/packages/fcitx.scm index 6dd7797aa4..8225d253ac 100644 --- a/gnu/packages/fcitx.scm +++ b/gnu/packages/fcitx.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Sou Bunnbu +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,14 +36,14 @@ (define-public fcitx (package (name "fcitx") - (version "4.2.8.6") + (version "4.2.9.6") (source (origin (method url-fetch) (uri (string-append "http://download.fcitx-im.org/fcitx/" name "-" version "_dict.tar.xz")) (sha256 (base32 - "15ymd42kg920ri0f8fymq3i68g8k1kgpmdlnk9jf5fvnz6g4w0wi")))) + "0hyrh3v82a32ylnlvzrp6cmq56x4p1a42q5xc6njmmj2msxm34x5")))) (build-system cmake-build-system) (outputs '("out" "gtk2" "gtk3")) (arguments @@ -65,7 +66,12 @@ "-DENABLE_QT_IM_MODULE=OFF"))) (native-inputs `(("doxygen" ,doxygen) - ("glib:bin" ,glib "bin") ; for glib-genmarshal + ("extra-cmake-modules" + ;; XXX: We can't simply #:use-module due to a cycle somewhere. + ,(module-ref + (resolve-interface '(gnu packages kde-frameworks)) + 'extra-cmake-modules)) + ("glib:bin" ,glib "bin") ; for glib-genmarshal ("pkg-config" ,pkg-config))) (inputs `(("dbus" ,dbus) -- cgit v1.2.3 From 914c6f621ec55086431b027ccb1ff0e7f3744b56 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 00:04:35 +0200 Subject: gnu: fcitx-configtool: Update to 0.4.10. * gnu/packages/fcitx.scm (fcitx-configtool): Update to 0.4.10. --- gnu/packages/fcitx.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/fcitx.scm b/gnu/packages/fcitx.scm index 8225d253ac..bcd5f12dd1 100644 --- a/gnu/packages/fcitx.scm +++ b/gnu/packages/fcitx.scm @@ -95,14 +95,14 @@ built-in.") (define-public fcitx-configtool (package (name "fcitx-configtool") - (version "0.4.8") + (version "0.4.10") (source (origin (method url-fetch) (uri (string-append "https://download.fcitx-im.org/fcitx-configtool/" name "-" version ".tar.xz")) (sha256 (base32 - "1vaim0namw58bfafbvws1vgd4010p19zwqfbx6bd1zi5sgchdg0f")))) + "1yyi9jhkwn49lx9a47k1zbvwgazv4y4z72gnqgzdpgdzfrlrgi5w")))) (build-system cmake-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From d21fb90a2797af99f23f899acdcc6f018ac4c833 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 01:22:31 +0200 Subject: gnu: perl-xml-libxml-simple: Update to 0.99. * gnu/packages/xml.scm (perl-xml-libxml-simple): Update to 0.99. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index d9cc4c36ad..9112d0273f 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -416,14 +416,14 @@ XML parser and the high performance DOM implementation.") (define-public perl-xml-libxml-simple (package (name "perl-xml-libxml-simple") - (version "0.97") + (version "0.99") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/" "XML-LibXML-Simple-" version ".tar.gz")) (sha256 (base32 - "1g8nlk3zdz2cclxf7azvsb3jfxmvy6ml8wmj774k4qjqcsqmzk0w")))) + "0i4ybiqdnvnbfxqslw2y392kvy7i752dl8n99bqiqv5kzk4lbzhl")))) (build-system perl-build-system) (propagated-inputs `(("perl-file-slurp-tiny" ,perl-file-slurp-tiny) -- cgit v1.2.3 From 5bc4188ffd0c6166373fef60e78ddd9b2c7a8c7a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 01:46:13 +0200 Subject: gnu: gource: Update to 0.49. * gnu/packages/version-control.scm (gource): Update to 0.49. --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5487298929..378a6fcf09 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1911,7 +1911,7 @@ network protocols, and core version control algorithms.") (define-public gource (package (name "gource") - (version "0.48") + (version "0.49") (source (origin (method url-fetch) (uri (string-append @@ -1919,7 +1919,7 @@ network protocols, and core version control algorithms.") "/gource-" version "/gource-" version ".tar.gz")) (sha256 (base32 - "04qxcm05qiyr9rg2kv6abfy7kkzqr8ziw4iyp1d14lniv93m61dp")))) + "12hf5ipcsp9dxsqn84n4kr63xaiskrnf5a084wr29qk171lj7pd9")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From 0ce92d74a285b82ab3b8d559242a85c03c198e42 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 01:48:48 +0200 Subject: gnu: python-pyrfc3339: Update to 1.1. * gnu/packages/time.scm (python-pyrfc3339): Update to 1.1. --- gnu/packages/time.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/time.scm b/gnu/packages/time.scm index a2f8a80704..fc831ab6cc 100644 --- a/gnu/packages/time.scm +++ b/gnu/packages/time.scm @@ -287,14 +287,14 @@ value (in fractional seconds) of a clock which never goes backwards.") (define-public python-pyrfc3339 (package (name "python-pyrfc3339") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (pypi-uri "pyRFC3339" version)) (sha256 (base32 - "0dgm4l9y8jiax5cp6yxjd2i27cq8h33sh81n1wfbmnmqb32cdywd")))) + "06jv7ar7lpvvk0dixzwdr3wgm0g1lipxs429s2z7knwwa7hwpf41")))) (build-system python-build-system) (propagated-inputs `(("python-pytz" ,python-pytz))) -- cgit v1.2.3 From 52d5b73fc40184bbb4e2a188fa61e6fcdaad5a97 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 02:17:27 +0200 Subject: gnu: spice-protocol: Update to 0.12.14. * gnu/packages/spice.scm (spice-protocol): Update to 0.12.14. --- gnu/packages/spice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index 38d4a3a6bd..a648634646 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -128,7 +128,7 @@ system to use the host GPU to accelerate 3D rendering.") (define-public spice-protocol (package (name "spice-protocol") - (version "0.12.13") + (version "0.12.14") (source (origin (method url-fetch) (uri (string-append @@ -136,7 +136,7 @@ system to use the host GPU to accelerate 3D rendering.") "spice-protocol-" version ".tar.bz2")) (sha256 (base32 - "0cwrgkp558mblcf4vrhacb3iizz12khsrrl82w38w9nj0ar13vl9")))) + "170ckpgazvqv7hxy209myg67pqnd6c0gvr4ysbqgsfch6320nd90")))) (build-system gnu-build-system) (synopsis "Protocol headers for the SPICE protocol") (description "SPICE (the Simple Protocol for Independent Computing -- cgit v1.2.3 From 14b0c49670241c0703c120eebc8a7252ce55cad4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 02:42:51 +0200 Subject: gnu: f2fs-tools: Update to 1.10.0. * gnu/packages/linux.scm (f2fs-tools): Update to 1.10.0. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 377d46d502..8be3634b0e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3367,7 +3367,7 @@ disks and SD cards. This package provides the userland utilities.") (package (inherit f2fs-tools-1.7) (name "f2fs-tools") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (string-append @@ -3375,7 +3375,7 @@ disks and SD cards. This package provides the userland utilities.") "/f2fs-tools.git/snapshot/" name "-" version ".tar.gz")) (sha256 (base32 - "1bir9ladb58ijlcvrjrq1fb1xv5ys50zdjaq0yzliib0apsyrnyl")))) + "05ikaim0qq3dx9x3sp43ralwz43r3b0viv62n99kabp0vf3b0hg8")))) (inputs `(("libuuid" ,util-linux))))) -- cgit v1.2.3 From a756fa5ac06ad9934c6efcb9c5fe881834e94e52 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 02:50:58 +0200 Subject: gnu: light: Update to 1.1. * gnu/packages/linux.scm (light): Update to 1.1. [source]: Switch to GIT-FETCH. --- gnu/packages/linux.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8be3634b0e..dbf3ab3507 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4036,23 +4036,23 @@ monitoring tools for Linux. These include @code{mpstat}, @code{iostat}, (define-public light (package (name "light") - (version "1.0") + (version "1.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/haikarainen/" name - "/archive/v" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/haikarainen/light") + (commit version))) (sha256 (base32 - "0r5gn6c0jcxknzybl6059dplxv46dpahchqq4gymrs7z8bp0hilp")) - (file-name (string-append name "-" version ".tar.gz")))) + "1qra8yzsga29bxlvq63v1db071a1xdji7i60p4kzrciidm1206js")))) (build-system gnu-build-system) (arguments - '(#:tests? #f ; no tests + '(#:tests? #f ; no tests #:make-flags (list "CC=gcc" (string-append "PREFIX=" %output)) #:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (add-after 'unpack 'patch-makefile (lambda _ (substitute* "Makefile" (("chown") "#"))))))) -- cgit v1.2.3 From d41a5f826dcc4ec86a30f401711201a5650bc72e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 02:51:39 +0200 Subject: gnu: light: Return #t from phase. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (light)[arguments]: End ‘patch-makefile’ phase with #t. --- gnu/packages/linux.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index dbf3ab3507..5bcb95139c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4055,7 +4055,8 @@ monitoring tools for Linux. These include @code{mpstat}, @code{iostat}, (delete 'configure) ; no configure script (add-after 'unpack 'patch-makefile (lambda _ - (substitute* "Makefile" (("chown") "#"))))))) + (substitute* "Makefile" (("chown") "#")) + #t))))) (native-inputs `(("help2man" ,help2man))) (home-page "https://haikarainen.github.io/light") -- cgit v1.2.3 From ad21323c9649ebedca831d88a2f01aea76f62127 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 15 Jun 2018 02:57:08 +0200 Subject: gnu: cpuid: Update to 20180519. * gnu/packages/linux.scm (cpuid): Update to 20180519. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5bcb95139c..9938af99b8 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -4409,14 +4409,14 @@ available in the kernel Linux.") (define-public cpuid (package (name "cpuid") - (version "20180419") + (version "20180519") (source (origin (method url-fetch) (uri (string-append "http://www.etallen.com/cpuid/cpuid-" version ".src.tar.gz")) (sha256 (base32 - "0cnxj72pjalsszhn862r6shw64zbrkw0k3mm36fn93bivswjnj12")))) + "16pzwyifc9glpk1hm6bqb5d1a7cw0qnqiamh5sbvqg7j6sz26y4n")))) (build-system gnu-build-system) (arguments '(#:make-flags '("CC=gcc") -- cgit v1.2.3 From 0017e55f892828f7a4d29a50f06e5146270ab8cb Mon Sep 17 00:00:00 2001 From: fis Date: Tue, 12 Jun 2018 18:10:19 +0800 Subject: gnu: Add shadowsocks. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (shadowsocks): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/networking.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index e040ef339c..5cdfec3431 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1902,3 +1902,36 @@ eight bytes) tools low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach.") (license license:boost1.0))) + +(define-public shadowsocks + ;; There are some security fixes after the last release. + (let* ((commit "e332ec93e9c90f1cbee676b022bf2c5d5b7b1239") + (revision "0") + (version (git-version "2.8.2" revision commit))) + (package + (name "shadowsocks") + (version version) + (home-page "https://github.com/shadowsocks/shadowsocks") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (sha256 + (base32 + "1idd9b4f2pnhcpk1bh030hqg5zq25gkwxd53xi3c0cj242w7sp2j")) + (file-name (git-file-name name version)))) + (build-system python-build-system) + (synopsis "Fast tunnel proxy that helps you bypass firewalls") + (description + "This package is a fast tunnel proxy that helps you bypass firewalls. + +Features: +@itemize +@item TCP & UDP support +@item User management API +@item TCP Fast Open +@item Workers and graceful restart +@item Destination IP blacklist +@end itemize") + (license license:asl2.0)))) -- cgit v1.2.3 From 4ce4fc501035a8ef461e10d5f3df6ea3a63c7572 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 15 Jun 2018 09:52:42 +0200 Subject: system: Add os-with-u-boot. * gnu/system/install.scm (os-with-u-boot): New procedure. * gnu/packages/bootloaders.scm (make-u-boot-package): Export. * doc/guix.texi (Building the Installation Image for ARM Boards): New subsection. --- doc/guix.texi | 16 ++++++++++++++++ gnu/packages/bootloaders.scm | 2 +- gnu/system/install.scm | 16 +++++++++++++++- 3 files changed, 32 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/doc/guix.texi b/doc/guix.texi index d86ac5044f..a90af34f80 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8881,6 +8881,22 @@ Have a look at @file{gnu/system/install.scm} in the source tree, and see also @ref{Invoking guix system} for more information about the installation image. +@subsection Building the Installation Image for ARM Boards + +Many ARM boards require a specific variant of the +@uref{http://www.denx.de/wiki/U-Boot/, U-Boot} bootloader. + +If you build a disk image and the bootloader is not available otherwise +(on another boot drive etc), it's advisable to build an image that +includes the bootloader, specifically: + +@example +guix system disk-image --system=armhf-linux -e '((@@ (gnu system install) os-with-u-boot) (@@ (gnu system install) installation-os) "A20-OLinuXino-Lime2")' +@end example + +@code{A20-OLinuXino-Lime2} is the name of the board. If you specify an invalid +board, a list of possible boards will be printed. + @node System Configuration @section System Configuration diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index a86c73731e..c58fe07423 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -439,7 +439,7 @@ def test_ctrl_c")) also initializes the boards (RAM etc). This package provides its board-independent tools."))) -(define (make-u-boot-package board triplet) +(define-public (make-u-boot-package board triplet) "Returns a u-boot package for BOARD cross-compiled for TRIPLET." (let ((same-arch? (if (string-prefix? (%current-system) (gnu-triplet->nix-system triplet)) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 35f4ba9c24..6a3ae1947b 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -54,7 +54,8 @@ novena-installation-os pine64-plus-installation-os rk3399-puma-installation-os - wandboard-installation-os)) + wandboard-installation-os + os-with-u-boot)) ;;; Commentary: ;;; @@ -386,6 +387,19 @@ You have been warned. Thanks for being so brave.\x1b[0m nvi ;:wq! %base-packages)))) +(define* (os-with-u-boot os board #:key (bootloader-target "/dev/mmcblk0") + (triplet "arm-linux-gnueabihf")) + "Given OS, amend it with the u-boot bootloader for BOARD, +installed to BOOTLOADER-TARGET (a drive), compiled for TRIPLET. + +If you want a serial console, make sure to specify one in your +operating-system's kernel-arguments (\"console=ttyS0\" or similar)." + (operating-system (inherit os) + (bootloader (bootloader-configuration + (bootloader (bootloader (inherit u-boot-bootloader) + (package (make-u-boot-package board triplet)))) + (target bootloader-target))))) + (define* (embedded-installation-os bootloader bootloader-target tty #:key (extra-modules '())) "Return an installation os for embedded systems. -- cgit v1.2.3 From a7c8716928a240ba2c36d360e4ffeb447671fa6b Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 15 Jun 2018 13:48:51 +0200 Subject: gnu: grub: Fix build on i686. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes . * gnu/packages/bootloaders.scm (grub)[native-inputs]: Add "ld-wrapper" and "binutils". Co-authored-by: Ludovic Courtès --- gnu/packages/bootloaders.scm | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index c58fe07423..eb1e433ba7 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2015, 2018 Mark H Weaver ;;; Copyright © 2015 Leo Famulari ;;; Copyright © 2016 Jan Nieuwenhuizen @@ -61,7 +61,8 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (srfi srfi-1) - #:use-module (srfi srfi-26)) + #:use-module (srfi srfi-26) + #:use-module (ice-9 regex)) (define unifont ;; GNU Unifont, . @@ -144,6 +145,22 @@ ("texinfo" ,texinfo) ("help2man" ,help2man) + ;; XXX: When building GRUB 2.02 on 32-bit x86, we need a binutils + ;; capable of assembling 64-bit instructions. However, our default + ;; binutils on 32-bit x86 is not 64-bit capable. + ,@(if (string-match "^i[3456]86-" (%current-system)) + (let ((binutils (package/inherit + binutils + (name "binutils-i386") + (arguments + (substitute-keyword-arguments (package-arguments binutils) + ((#:configure-flags flags ''()) + `(cons "--enable-64-bit-bfd" ,flags))))))) + `(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper-i386" + #:binutils binutils)) + ("binutils" ,binutils))) + '()) + ;; Dependencies for the test suite. The "real" QEMU is needed here, ;; because several targets are used. ("parted" ,parted) -- cgit v1.2.3 From 12e530ba63ad848d3d3194f09e8b54b693d74896 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 14 Jun 2018 16:49:21 -0400 Subject: gnu: BIND: Fix CVE-2018-5738. * gnu/packages/patches/bind-CVE-2018-5738.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/dns.scm (isc-bind)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/dns.scm | 2 + gnu/packages/patches/bind-CVE-2018-5738.patch | 100 ++++++++++++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 gnu/packages/patches/bind-CVE-2018-5738.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 01e0718723..4d2cefdbde 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -581,6 +581,7 @@ dist_patch_DATA = \ %D%/packages/patches/azr3.patch \ %D%/packages/patches/bash-completion-directories.patch \ %D%/packages/patches/bazaar-CVE-2017-14176.patch \ + %D%/packages/patches/bind-CVE-2018-5738.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blast+-fix-makefile.patch \ %D%/packages/patches/boost-fix-icu-build.patch \ diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 0b8d8be574..4fce4b34ba 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -50,6 +50,7 @@ #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xml) + #:use-module (gnu packages) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) @@ -104,6 +105,7 @@ and BOOTP/TFTP for network booting of diskless machines.") (uri (string-append "ftp://ftp.isc.org/isc/bind9/" version "/" name "-" version ".tar.gz")) + (patches (search-patches "bind-CVE-2018-5738.patch")) (sha256 (base32 "0a9dvyg1dk7vpqn9gz7p5jas3bz7z22bjd66b98g1qk16i2w7rqd")))) diff --git a/gnu/packages/patches/bind-CVE-2018-5738.patch b/gnu/packages/patches/bind-CVE-2018-5738.patch new file mode 100644 index 0000000000..ddef014651 --- /dev/null +++ b/gnu/packages/patches/bind-CVE-2018-5738.patch @@ -0,0 +1,100 @@ +Fix CVE-2018-5738: + +https://kb.isc.org/article/AA-01616/0/CVE-2018-5738 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-5738 + +diff --git a/bin/named/server.c b/bin/named/server.c +index f63554e..847c4ff 100644 +--- a/bin/named/server.c ++++ b/bin/named/server.c +@@ -3725,10 +3725,6 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist, + CHECKM(named_config_getport(config, &port), "port"); + dns_view_setdstport(view, port); + +- CHECK(configure_view_acl(vconfig, config, named_g_config, +- "allow-query", NULL, actx, +- named_g_mctx, &view->queryacl)); +- + /* + * Make the list of response policy zone names for a view that + * is used for real lookups and so cares about hints. +@@ -4692,21 +4688,35 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist, + "allow-query-cache-on", NULL, actx, + named_g_mctx, &view->cacheonacl)); + /* +- * Set "allow-query-cache", "allow-recursion", and +- * "allow-recursion-on" acls if configured in named.conf. +- * (Ignore the global defaults for now, because these ACLs +- * can inherit from each other when only some of them set at +- * the options/view level.) ++ * Set the "allow-query", "allow-query-cache", "allow-recursion", ++ * and "allow-recursion-on" ACLs if configured in named.conf, but ++ * NOT from the global defaults. This is done by leaving the third ++ * argument to configure_view_acl() NULL. ++ * ++ * We ignore the global defaults here because these ACLs ++ * can inherit from each other. If any are still unset after ++ * applying the inheritance rules, we'll look up the defaults at ++ * that time. + */ +- CHECK(configure_view_acl(vconfig, config, NULL, "allow-query-cache", +- NULL, actx, named_g_mctx, &view->cacheacl)); ++ ++ /* named.conf only */ ++ CHECK(configure_view_acl(vconfig, config, NULL, ++ "allow-query", NULL, actx, ++ named_g_mctx, &view->queryacl)); ++ ++ /* named.conf only */ ++ CHECK(configure_view_acl(vconfig, config, NULL, ++ "allow-query-cache", NULL, actx, ++ named_g_mctx, &view->cacheacl)); + + if (strcmp(view->name, "_bind") != 0 && + view->rdclass != dns_rdataclass_chaos) + { ++ /* named.conf only */ + CHECK(configure_view_acl(vconfig, config, NULL, + "allow-recursion", NULL, actx, + named_g_mctx, &view->recursionacl)); ++ /* named.conf only */ + CHECK(configure_view_acl(vconfig, config, NULL, + "allow-recursion-on", NULL, actx, + named_g_mctx, &view->recursiononacl)); +@@ -4744,18 +4754,21 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist, + * the global config. + */ + if (view->recursionacl == NULL) { ++ /* global default only */ + CHECK(configure_view_acl(NULL, NULL, named_g_config, + "allow-recursion", NULL, + actx, named_g_mctx, + &view->recursionacl)); + } + if (view->recursiononacl == NULL) { ++ /* global default only */ + CHECK(configure_view_acl(NULL, NULL, named_g_config, + "allow-recursion-on", NULL, + actx, named_g_mctx, + &view->recursiononacl)); + } + if (view->cacheacl == NULL) { ++ /* global default only */ + CHECK(configure_view_acl(NULL, NULL, named_g_config, + "allow-query-cache", NULL, + actx, named_g_mctx, +@@ -4769,6 +4782,14 @@ configure_view(dns_view_t *view, dns_viewlist_t *viewlist, + CHECK(dns_acl_none(mctx, &view->cacheacl)); + } + ++ if (view->queryacl == NULL) { ++ /* global default only */ ++ CHECK(configure_view_acl(NULL, NULL, named_g_config, ++ "allow-query", NULL, ++ actx, named_g_mctx, ++ &view->queryacl)); ++ } ++ + /* + * Ignore case when compressing responses to the specified + * clients. This causes case not always to be preserved, -- cgit v1.2.3 From 901bcb7815e6df702ee385dfa8fc6cd72c293869 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 16 Jun 2018 12:08:02 +0200 Subject: gnu: pigx-chipseq: Update to 0.0.16. * gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a210319243..42bc67e808 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12906,7 +12906,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.15") + (version "0.0.16") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12914,7 +12914,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg")))) + "0s53840z53pih0jkllmcfb2la7c36zxmf229fshhyq8n6a2hgr8f")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network -- cgit v1.2.3 From c099f6a716c035253816344ad24e364d14dc8ba0 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 10 Jun 2018 13:02:59 +0200 Subject: gnu: java-eclipse-jetty-security-9.2: Ignore test error. * gnu/packages/web.scm (java-eclipse-jetty-security-9.2)[arguments]: Ignore one failing test. --- gnu/packages/web.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 46d394f0d6..fe6aa5cdcb 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6117,6 +6117,11 @@ infrastructure"))) (inherit java-eclipse-jetty-security) (version (package-version java-eclipse-jetty-util-9.2)) (source (package-source java-eclipse-jetty-util-9.2)) + (arguments + `(#:test-exclude + ;; This test fails. + (list "**/ConstraintTest.*") + ,@(package-arguments java-eclipse-jetty-security))) (inputs `(("util" ,java-eclipse-jetty-util-9.2) ("http" ,java-eclipse-jetty-http-9.2) -- cgit v1.2.3 From f69a1d04a1bbcedcf55d3d8ac45e2d957311e9f5 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 12:58:23 +0100 Subject: gnu: Add java-eclipse-jetty-xml. * gnu/packages/web.scm (java-eclipse-jetty-xml): New variable. --- gnu/packages/web.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index fe6aa5cdcb..a1e63130b9 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6187,6 +6187,27 @@ container."))) ("server" ,java-eclipse-jetty-server-9.2) ,@(package-inputs java-eclipse-jetty-util-9.2))))) +(define-public java-eclipse-jetty-xml + (package + (inherit java-eclipse-jetty-util) + (name "java-eclipse-jetty-xml") + (arguments + `(#:jar-name "eclipse-jetty-xml.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + #:tests? #f; most tests require network + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + (chdir "jetty-xml") + #t))))) + (inputs + `(("java-eclipse-jetty-util" ,java-eclipse-jetty-util))) + (native-inputs + `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io) + ,@(package-native-inputs java-eclipse-jetty-util))))) + (define-public java-jsoup (package (name "java-jsoup") -- cgit v1.2.3 From 38b57575c1d6aabfe61259bf970a60d807dcd678 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 12:59:28 +0100 Subject: gnu. Add java-eclipse-jetty-xml-9.2. * gnu/packages/web.scm (java-eclipse-jetty-xml-9.2): New variable. --- gnu/packages/web.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index a1e63130b9..9cc8bdeda9 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6208,6 +6208,29 @@ container."))) `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io) ,@(package-native-inputs java-eclipse-jetty-util))))) +(define-public java-eclipse-jetty-xml-9.2 + (package + (inherit java-eclipse-jetty-xml) + (version (package-version java-eclipse-jetty-util-9.2)) + (source (package-source java-eclipse-jetty-util-9.2)) + (arguments + `(#:jar-name "eclipse-jetty-xml.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + #:tests? #f; most tests require network + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + (chdir "jetty-xml") + #t))))) + (inputs + `(("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2) + ,@(package-inputs java-eclipse-jetty-util-9.2))) + (native-inputs + `(("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2) + ,@(package-native-inputs java-eclipse-jetty-util-9.2))))) + (define-public java-jsoup (package (name "java-jsoup") -- cgit v1.2.3 From d736511864e3f77c61009ede81c40bdf45ccde8d Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 13:00:06 +0100 Subject: gnu: Add java-eclipse-jetty-webapp. * gnu/packages/web.scm (java-eclipse-jetty-webapp): New variable. --- gnu/packages/web.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 9cc8bdeda9..6414c147d5 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6231,6 +6231,34 @@ container."))) `(("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2) ,@(package-native-inputs java-eclipse-jetty-util-9.2))))) +(define-public java-eclipse-jetty-webapp + (package + (inherit java-eclipse-jetty-util) + (name "java-eclipse-jetty-webapp") + (arguments + `(#:jar-name "eclipse-jetty-webapp.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + ;; One test fails + #:test-exclude (list "**/WebAppContextTest.java") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + (chdir "jetty-webapp") + #t))))) + (inputs + `(("java-eclipse-jetty-util" ,java-eclipse-jetty-util) + ("java-eclipse-jetty-http" ,java-eclipse-jetty-http) + ("java-eclipse-jetty-server" ,java-eclipse-jetty-server) + ("java-eclipse-jetty-servlet" ,java-eclipse-jetty-servlet) + ("java-eclipse-jetty-security" ,java-eclipse-jetty-security) + ("java-eclipse-jetty-xml" ,java-eclipse-jetty-xml) + ("java-tomcat" ,java-tomcat))) + (native-inputs + `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io) + ,@(package-native-inputs java-eclipse-jetty-util))))) + (define-public java-jsoup (package (name "java-jsoup") -- cgit v1.2.3 From 087583a7dbe6c9da526f39a691ed8eef8b097bb1 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 13:00:43 +0100 Subject: gnu: Add java-eclipse-jetty-webapp-9.2. * gnu/packages/web.scm (java-eclipse-jetty-webapp-9.2): New variable. --- gnu/packages/web.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 6414c147d5..19058de2d3 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6259,6 +6259,35 @@ container."))) `(("java-eclipse-jetty-io" ,java-eclipse-jetty-io) ,@(package-native-inputs java-eclipse-jetty-util))))) +(define-public java-eclipse-jetty-webapp-9.2 + (package + (inherit java-eclipse-jetty-webapp) + (version (package-version java-eclipse-jetty-util-9.2)) + (source (package-source java-eclipse-jetty-util-9.2)) + (arguments + `(#:jar-name "eclipse-jetty-webapp.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + #:test-exclude (list "**/WebAppContextTest.java") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + (chdir "jetty-webapp") + #t))))) + (inputs + `(("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2) + ("java-eclipse-jetty-http-9.2" ,java-eclipse-jetty-http-9.2) + ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2) + ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2) + ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2) + ("java-eclipse-jetty-xml-9.2" ,java-eclipse-jetty-xml-9.2) + ("java-tomcat" ,java-tomcat) + ,@(package-inputs java-eclipse-jetty-util-9.2))) + (native-inputs + `(("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2) + ,@(package-native-inputs java-eclipse-jetty-util-9.2))))) + (define-public java-jsoup (package (name "java-jsoup") -- cgit v1.2.3 From 7d65489ffe27276d9d373374190bbeedd8a9c6da Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 13:03:50 +0100 Subject: gnu: Add java-plexus-cli. * gnu/packages/java.scm (java-plexus-cli): New variable. --- gnu/packages/java.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 678cbee188..115b0b498b 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -3262,6 +3262,39 @@ Compiler component."))) This component decrypts a string passed to it.") (license license:asl2.0))) +(define-public java-plexus-cli + (package + (name "java-plexus-cli") + (version "1.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sonatype/plexus-cli") + (commit "a776afa6bca84e5107bedb69440329cdb24ed645"))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0xjrlay605rypv3zd7y24vlwf0039bil3n2cqw54r1ddpysq46vx")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "plexus-cli.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + #:test-dir "src/test")) + (inputs + `(("java-commons-cli" ,java-commons-cli) + ("java-plexus-container-default" ,java-plexus-container-default) + ("java-plexus-classworlds" ,java-plexus-classworlds))) + (native-inputs + `(("java-plexus-utils" ,java-plexus-utils) + ("java-junit" ,java-junit) + ("java-guava" ,java-guava))) + (home-page "https://codehaus-plexus.github.io/plexus-cli") + (synopsis "CLI building library for plexus") + (description "This package is a library to help creating CLI around +Plexus components.") + (license license:asl2.0))) + (define-public java-sisu-build-api (package (name "java-sisu-build-api") -- cgit v1.2.3 From ab621bf142d2803e4a6b8c79df715d204e0bfb47 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 13:15:33 +0100 Subject: gnu: Add java-qdox. * gnu/packages/java.scm (java-qdox): New variable. --- gnu/packages/java.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 115b0b498b..b4b1eedd2e 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -10186,3 +10186,32 @@ This module can be assimilated to a significantly improved version of log4j. Moreover, @code{logback-classic} natively implements the slf4j API so that you can readily switch back and forth between logback and other logging frameworks such as log4j or @code{java.util.logging} (JUL)."))) + +(define-public java-qdox + (package + (name "java-qdox") + ; Newer version exists, but this version is required by java-plexus-component-metadata + (version "2.0-M2") + (source (origin + (method url-fetch) + ;; 2.0-M4, -M5 at https://github.com/paul-hammant/qdox + ;; Older releases at https://github.com/codehaus/qdox/ + ;; Note: The release at maven is pre-generated. The release at + ;; github requires jflex. + (uri (string-append "http://central.maven.org/maven2/" + "com/thoughtworks/qdox/qdox/" version + "/qdox-" version "-sources.jar")) + (sha256 + (base32 + "10xxrcaicq6axszcr2jpygisa4ch4sinyx5q7kqqxv4lknrmxp5x")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "qdox.jar" + #:tests? #f)); no tests + (home-page "http://qdox.codehaus.org/") + (synopsis "Parse definitions from Java source files") + (description "QDox is a high speed, small footprint parser for extracting +class/interface/method definitions from source files complete with JavaDoc +@code{@@tags}. It is designed to be used by active code generators or +documentation tools.") + (license license:asl2.0))) -- cgit v1.2.3 From 8f5caf936623e32158f2996da8c2cb2017048415 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:25:45 +0100 Subject: gnu: Add maven-plugin-api. * gnu/packages/maven.scm (maven-plugin-api): New variable. --- gnu/packages/maven.scm | 53 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 473847c044..65903b9c12 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -562,3 +562,56 @@ so really just plain objects."))) ("java-guava" ,java-guava) ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) ("java-javax-inject" ,java-javax-inject))))) + +(define-public maven-plugin-api + (package + (inherit maven-artifact) + (name "maven-plugin-api") + (arguments + `(#:jar-name "maven-plugin-api.jar" + #:source-dir "maven-plugin-api/src/main/java" + #:jdk ,icedtea-8 + #:test-dir "maven-plugin-api/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'generate-models + (lambda* (#:key inputs #:allow-other-keys) + (define (modello-single-mode file version mode) + (invoke "java" "org.codehaus.modello.ModelloCli" + file mode "maven-plugin-api/src/main/java" version + "false" "true")) + (let ((file "maven-plugin-api/src/main/mdo/lifecycle.mdo")) + (modello-single-mode file "1.0.0" "java") + (modello-single-mode file "1.0.0" "xpp3-reader") + (modello-single-mode file "1.0.0" "xpp3-writer")) + #t))))) + (inputs + `(("maven-artifact" ,maven-artifact) + ("maven-model" ,maven-model) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("guice" ,java-guice) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("sisu-inject" ,java-eclipse-sisu-inject) + ("javax-inject" ,java-javax-inject) + ("utils" ,java-plexus-utils))) + (native-inputs + `(("modello" ,java-modello-core) + ;; for modello: + ("classworlds" ,java-plexus-classworlds) + ("guava" ,java-guava) + ("xbean" ,java-geronimo-xbean-reflect) + ("build-api" ,java-sisu-build-api) + ;; modello plugins: + ("java" ,java-modello-plugins-java) + ("xml" ,java-modello-plugins-xml) + ("xpp3" ,java-modello-plugins-xpp3) + ;; for tests + ("java-junit" ,java-junit))) + (description "Apache Maven is a software project management and comprehension +tool. This package contains strictly the API for plugins -- composed of goals +implemented by Mojos -- development. + +A plugin is described in a @file{META-INF/maven/plugin.xml} plugin descriptor, +generally generated from plugin sources using maven-plugin-plugin."))) -- cgit v1.2.3 From 7a42f0586910418c72d4df3abecc5ded6b3aa309 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:27:50 +0100 Subject: gnu: Add maven-core-bootstrap. --- gnu/packages/maven.scm | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 65903b9c12..59cee90785 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -615,3 +615,85 @@ implemented by Mojos -- development. A plugin is described in a @file{META-INF/maven/plugin.xml} plugin descriptor, generally generated from plugin sources using maven-plugin-plugin."))) + +(define maven-core-bootstrap + (package + (inherit maven-artifact) + (name "maven-core") + (arguments + `(#:jar-name "maven-core.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + ;; Tests need maven-compat, which requires maven-core + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + ;; Required for generating components.xml in maven-core + (chdir "maven-core") + #t)) + (add-before 'build 'copy-resources + (lambda _ + (mkdir-p "build/classes/") + (copy-recursively "src/main/resources" "build/classes") + #t)) + (add-before 'build 'generate-sisu-named + (lambda _ + (mkdir-p "build/classes/META-INF/sisu") + (chmod "../sisu.sh" #o755) + (invoke "../sisu.sh" "src/main/java" + "build/classes/META-INF/sisu/javax.inject.Named") + #t)) + (add-before 'build 'generate-models + (lambda* (#:key inputs #:allow-other-keys) + (define (modello-single-mode file version mode) + (invoke "java" "org.codehaus.modello.ModelloCli" + file mode "src/main/java" version + "false" "true")) + (let ((file "src/main/mdo/toolchains.mdo")) + (modello-single-mode file "1.1.0" "java") + (modello-single-mode file "1.1.0" "xpp3-reader") + (modello-single-mode file "1.1.0" "xpp3-writer")) + #t))))) + (inputs + `(("maven-artifact" ,maven-artifact) + ("maven-resolver-provider" ,maven-resolver-provider) + ("maven-builder-support" ,maven-builder-support) + ("maven-model" ,maven-model) + ("maven-model-builder" ,maven-model-builder) + ("maven-settings" ,maven-settings) + ("maven-settings-builder" ,maven-settings-builder) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-repository-metadata" ,maven-repository-metadata) + ("maven-shared-utils" ,maven-shared-utils) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-plexus-utils" ,java-plexus-utils) + ("java-commons-lang3" ,java-commons-lang3) + ("java-guava" ,java-guava) + ("java-guice" ,java-guice) + ("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi) + ("maven-resolver-util" ,maven-resolver-util) + ("maven-resolver-impl" ,maven-resolver-impl) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-javax-inject" ,java-javax-inject) + ("java-plexus-classworld" ,java-plexus-classworlds))) + (native-inputs + `(("java-modello-core" ,java-modello-core) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ("java-sisu-build-api" ,java-sisu-build-api) + ("java-modello-plugins-java" ,java-modello-plugins-java) + ("java-modello-plugins-xml" ,java-modello-plugins-xml) + ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3) + ;; tests + ("java-junit" ,java-junit) + ("java-mockito-1" ,java-mockito-1) + ("java-commons-jxpath" ,java-commons-jxpath))) + (description "Apache Maven is a software project management and comprehension +tool. This package contains the maven core classes managing the whole build +process."))) -- cgit v1.2.3 From a59d5f3542cc2c0b327f6c2bb84ba8a82be04c57 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:31:01 +0100 Subject: gnu: Add maven-plugin-annotations. * gnu/packages/maven.scm (maven-plugin-annotations): New variable. --- gnu/packages/maven.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 59cee90785..09fab71108 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -230,6 +230,30 @@ plexus-utils in Maven. It is not a 100% API compatible replacement but a replacement with improvements.") (license license:asl2.0))) +(define-public maven-plugin-annotations + (package + (name "maven-plugin-annotations") + (version "3.5") + (source (origin + (method url-fetch) + (uri (string-append "https://archive.apache.org/dist/maven/" + "plugin-tools/maven-plugin-tools-" version + "-source-release.zip")) + (sha256 (base32 "1ryqhs62j5pas93brhf5dsnvp99hxbvssf681yj5rk3r9h24hqm2")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "maven-plugin-annotations.jar" + #:source-dir "maven-plugin-annotations/src/main/java" + #:tests? #f)) + (inputs + `(("maven-artifact" ,maven-artifact))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://maven.apache.org/plugin-tools/maven-plugin-annotations/") + (synopsis "Java 5 annotations to use in Mojos") + (description "This package contains Java 5 annotations for use in Mojos.") + (license license:asl2.0))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From 9f25cba65af3f71b429fe3e2ddba5becc07a66f1 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:33:01 +0100 Subject: gnu: Add java-plexus-component-metadata. * gnu/packages/maven.scm (java-plexus-component-metadata): New variable. --- gnu/packages/maven.scm | 48 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 47 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 09fab71108..8b69f16314 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -24,7 +24,53 @@ #:use-module (guix build-system ant) #:use-module (gnu packages) #:use-module (gnu packages compression) - #:use-module (gnu packages java)) + #:use-module (gnu packages java) + #:use-module (gnu packages xml)) + +(define-public java-plexus-component-metadata + (package + (inherit java-plexus-container-default) + (name "java-plexus-component-metadata") + (arguments + `(#:jar-name "plexus-component-metadata.jar" + #:source-dir "src/main/java" + #:test-dir "src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir + (lambda _ + (chdir "plexus-component-metadata") + #t)) + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "src/main/resources" + "build/classes/") + #t))))) + (inputs + `(("java-plexus-container-default" ,java-plexus-container-default) + ("java-plexu-component-annotations" ,java-plexus-component-annotations) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-cli" ,java-plexus-cli) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-plugin-annotations" ,maven-plugin-annotations) + ("maven-core-bootstrap" ,maven-core-bootstrap) + ("maven-model" ,maven-model) + ("java-commons-cli" ,java-commons-cli) + ("java-qdox" ,java-qdox) + ("java-jdom2" ,java-jdom2) + ("java-asm" ,java-asm))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-guava" ,java-guava) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect))) + (synopsis "Inversion-of-control container for Maven") + (description "The Plexus project provides a full software stack for creating +and executing software projects. Based on the Plexus container, the +applications can utilise component-oriented programming to build modular, +reusable components that can easily be assembled and reused. This package +provides the Maven plugin generating the component metadata."))) (define-public maven-resolver-api (package -- cgit v1.2.3 From b822544cfeb450e8fd4ead86fd0a7451db9ac859 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:34:46 +0100 Subject: gnu: Add maven-core. * gnu/packages/maven.scm (maven-core): New variable. --- gnu/packages/maven.scm | 72 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 8b69f16314..aa6c196a2b 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -767,3 +767,75 @@ generally generated from plugin sources using maven-plugin-plugin."))) (description "Apache Maven is a software project management and comprehension tool. This package contains the maven core classes managing the whole build process."))) + +(define-public maven-core + (package + (inherit maven-core-bootstrap) + (arguments + (substitute-keyword-arguments (package-arguments maven-core-bootstrap) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'build 'modify-metainf + (lambda _ + (substitute* "build.xml" + (("message=\"\"") "message=\"Implementation-Version: 3.5.3\n\"")) + #t)) + (add-before 'build 'add-maven-files + (lambda _ + (mkdir-p "build/classes/META-INF/maven/org.apache.maven/maven-core") + (copy-file "pom.xml" + "build/classes/META-INF/maven/org.apache.maven/maven-core/pom.xml") + (with-output-to-file "build/classes/META-INF/maven/org.apache.maven/maven-core/pom.properties" + (lambda _ + (format #t "version=~a~% +groupId=org.apache.maven~% +artifactId=maven-core" ,(package-version maven-core-bootstrap)))) + #t)) + (add-after 'build 'generate-metadata + (lambda _ + (define (components file) + (let ((sxml (with-input-from-file file + (lambda _ (xml->sxml (current-input-port) + #:trim-whitespace? #t))))) + ;; Select the list of s inside the + ;; and . + ((@ (ice-9 match) match) sxml + (('*TOP* + ('*PI* foo ...) + ('component-set + ('components x ...))) x)))) + (use-modules (sxml simple)) + (delete-file "build/classes/META-INF/plexus/components.xml") + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes") + "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli" + "--source" "build/classes/META-INF/plexus" + "--output" "build/classes/META-INF/plexus/components.t.xml" + "--classes" "build/classes" + "--descriptors" "build/classes") + ;; Now we merge all other components from hand-written xml + (let ((generated-xml (components "build/classes/META-INF/plexus/components.t.xml")) + (components-xml (components "src/main/resources/META-INF/plexus/components.xml")) + (default-bindings-xml (components "src/main/resources/META-INF/plexus/default-bindings.xml")) + (artifact-handlers-xml (components "src/main/resources/META-INF/plexus/artifact-handlers.xml"))) + (with-output-to-file "build/classes/META-INF/plexus/components.xml" + (lambda _ + (display "\n") + (sxml->xml + `(component-set + (components + ,@(append generated-xml components-xml + default-bindings-xml + artifact-handlers-xml))))))) + #t)) + (add-after 'generate-metadata 'rebuild + (lambda _ + (invoke "ant" "jar") + #t)))))) + (native-inputs + `(("java-plexus-component-metadata" ,java-plexus-component-metadata) + ("java-commons-cli" ,java-commons-cli) + ("java-plexus-cli" ,java-plexus-cli) + ("java-jdom2" ,java-jdom2) + ("java-qdox" ,java-qdox) + ("maven-core-boot" ,maven-core-bootstrap) + ,@(package-native-inputs maven-core-bootstrap))))) -- cgit v1.2.3 From e2c7d32995aa204f68e9c00f06e7885f425a1379 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:36:16 +0100 Subject: gnu: Add maven-embedder. * gnu/packages/maven.scm (maven-embedder): New variable. --- gnu/packages/maven.scm | 93 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index aa6c196a2b..8ee44dd8d6 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -839,3 +839,96 @@ artifactId=maven-core" ,(package-version maven-core-bootstrap)))) ("java-qdox" ,java-qdox) ("maven-core-boot" ,maven-core-bootstrap) ,@(package-native-inputs maven-core-bootstrap))))) + +(define-public maven-embedder + (package + (inherit maven-artifact) + (name "maven-embedder") + (arguments + `(#:jar-name "maven-embedder.jar" + #:source-dir "maven-embedder/src/main/java" + #:test-dir "maven-embedder/src/test" + #:test-exclude (list "**/MavenCliTest.java") + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'build 'generate-sisu-named + (lambda _ + (mkdir-p "build/classes/META-INF/sisu") + (chmod "sisu.sh" #o755) + (invoke "./sisu.sh" "maven-embedder/src/main/java" + "build/classes/META-INF/sisu/javax.inject.Named") + #t)) + (add-before 'build 'generate-models + (lambda* (#:key inputs #:allow-other-keys) + (define (modello-single-mode file version mode) + (invoke "java" "org.codehaus.modello.ModelloCli" + file mode "maven-embedder/src/main/java" version + "false" "true")) + (let ((file "maven-embedder/src/main/mdo/core-extensions.mdo")) + (modello-single-mode file "1.0.0" "java") + (modello-single-mode file "1.0.0" "xpp3-reader") + (modello-single-mode file "1.0.0" "xpp3-writer")) + #t)) + (add-before 'check 'fix-test-paths + (lambda _ + (substitute* "maven-embedder/src/test/java/org/apache/maven/cli/CLIManagerDocumentationTest.java" + (("target/test-classes") "build/test-classes")) + #t)) + (add-before 'check 'fix-test-compilation + (lambda _ + ;; Tests are in the java/ subdir. Other subdirectories contain + ;; additional test plugins, with duplicate classes, so we can't + ;; compile them. Also, they are meant to be built with maven, to + ;; test its build process. + (substitute* "build.xml" + (("srcdir=\"maven-embedder/src/test\"") + "srcdir=\"maven-embedder/src/test/java\"")) + #t))))) + (inputs + `(("maven-core" ,maven-core) + ("maven-artifact" ,maven-artifact) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-builder-support" ,maven-builder-support) + ("maven-model" ,maven-model) + ("maven-model-builder" ,maven-model-builder) + ("maven-settings" ,maven-settings) + ("maven-settings-builder" ,maven-settings-builder) + ("maven-shared-utils" ,maven-shared-utils) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-plexus-util" ,java-plexus-utils) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-plexus-cipher" ,java-plexus-cipher) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher) + ("maven-resolevr-util" ,maven-resolver-util) + ("maven-resolevr-api" ,maven-resolver-api) + ("java-logback-core" ,java-logback-core) + ("java-logback-classic" ,java-logback-classic) + ("java-commons-cli" ,java-commons-cli) + ("java-commons-io" ,java-commons-io) + ("java-commons-lang3" ,java-commons-lang3) + ("java-guava" ,java-guava) + ("java-guice" ,java-guice) + ("java-javax-inject" ,java-javax-inject) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple))) + (native-inputs + `(("java-modello-core" ,java-modello-core) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ("java-sisu-build-api" ,java-sisu-build-api) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("java-modello-plugins-java" ,java-modello-plugins-java) + ("java-modello-plugins-xml" ,java-modello-plugins-xml) + ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3) + ;; tests + ("java-junit" ,java-junit) + ("java-objenesis" ,java-objenesis) + ("java-mockito-1" ,java-mockito-1) + ("java-hamcrest-core" ,java-hamcrest-core))) + (description "Apache Maven is a software project management and comprehension +tool. This package contains a Maven embeddable component, with CLI and +logging support."))) -- cgit v1.2.3 From ff7a0fcff34b3ba686342f31c5b45b5782470562 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:38:46 +0100 Subject: gnu: Add maven-wagon-provider-api. * gnu/packages/maven.scm (maven-wagon-provider-api): New variable. --- gnu/packages/maven.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 8ee44dd8d6..a5cda7e000 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -300,6 +300,32 @@ replacement with improvements.") (description "This package contains Java 5 annotations for use in Mojos.") (license license:asl2.0))) +(define-public maven-wagon-provider-api + (package + (name "maven-wagon-provider-api") + (version "3.0.0") + (source (origin + (method url-fetch) + (uri (string-append "https://archive.apache.org/dist/maven/wagon/" + "wagon-" version "-source-release.zip")) + (sha256 (base32 "1qb0q4m7vmf290xp3fnfdi3pwl3hkskia5g3z2v82q1ch3y2knqv")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "maven-wagon-provider-api.jar" + #:source-dir "wagon-provider-api/src/main/java" + #:test-dir "wagon-provider-api/src/test")) + (inputs + `(("java-plexus-utils" ,java-plexus-utils))) + (native-inputs + `(("unzip" ,unzip) + ("java-junit" ,java-junit) + ("java-easymock" ,java-easymock))) + (home-page "https://maven.apache.org/wagon") + (synopsis "Transport abstraction for Maven") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code.") + (license license:asl2.0))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From f216a9f99a57905d7beed9595cfb2124a6cf27e4 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:40:18 +0100 Subject: gnu: Add maven-wagon-provider-test. * gnu/packages/maven.scm (maven-wagon-provider-test): New variable. --- gnu/packages/maven.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index a5cda7e000..e282a9a8c2 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -25,6 +25,7 @@ #:use-module (gnu packages) #:use-module (gnu packages compression) #:use-module (gnu packages java) + #:use-module (gnu packages web) #:use-module (gnu packages xml)) (define-public java-plexus-component-metadata @@ -326,6 +327,30 @@ replacement with improvements.") artifact and repository handling code.") (license license:asl2.0))) +(define-public maven-wagon-provider-test + (package + (inherit maven-wagon-provider-api) + (name "maven-wagon-provider-test") + (arguments + `(#:jar-name "maven-wagon-provider-test.jar" + #:source-dir "wagon-provider-test/src/main/java" + #:tests? #f; no tests + #:jdk ,icedtea-8)) + (inputs + `(("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-container-default" ,java-plexus-container-default) + ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2) + ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2) + ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2) + ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2) + ("java-slf4j-api" ,java-slf4j-api) + ("java-tomcat" ,java-tomcat) + ("maven-wagon-provider-api" ,maven-wagon-provider-api))) + (synopsis "Test classes from maven-wagon") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code. This package contains common test +classes used in multiple maven-wagon components."))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From 0d1b3b39bcb6672ee056e1f0c671992f398260ca Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:41:06 +0100 Subject: gnu: Add maven-wagon-file. * gnu/packages/maven.scm (maven-wagon-file): New variable. --- gnu/packages/maven.scm | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index e282a9a8c2..2ee8dc0e30 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -351,6 +351,71 @@ artifact and repository handling code.") artifact and repository handling code. This package contains common test classes used in multiple maven-wagon components."))) +(define-public maven-wagon-file + (package + (inherit maven-wagon-provider-api) + (name "maven-wagon-file") + (arguments + `(#:jar-name "maven-wagon-file.jar" + #:source-dir "wagon-providers/wagon-file/src/main/java" + #:test-dir "wagon-providers/wagon-file/src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'check 'fix-paths + (lambda _ + ;; Tests assume they are run by maven, which copies test resources + ;; to target. Our ant-build-system does the same, but with the + ;; build directory. + (substitute* "wagon-providers/wagon-file/src/test/java/org/apache/maven/wagon/providers/file/FileWagonTest.java" + (("target") "build")) + #t)) + (add-after 'build 'generate-metadata + (lambda _ + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes") + "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli" + "--source" "wagon-providers/wagon-file/src/main/java" + "--output" "build/classes/META-INF/plexus/components.xml" + "--classes" "build/classes" + "--descriptors" "build/classes/META-INF") + #t)) + (add-after 'generate-metadata 'rebuild + (lambda _ + (invoke "ant" "jar") + #t))))) + (inputs + `(("java-plexus-utils" ,java-plexus-utils) + ("maven-wagon-provider-api" ,maven-wagon-provider-api))) + (native-inputs + `(("maven-wagon-provider-test" ,maven-wagon-provider-test) + ("java-plexus-component-metadata" ,java-plexus-component-metadata) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-guava" ,java-guava) + ("java-guice" ,java-guice) + ("java-javax-inject" ,java-javax-inject) + ("java-cglib" ,java-cglib) + ("java-slf4j-api" ,java-slf4j-api) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-cli" ,java-plexus-cli) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-plugin-annotations" ,maven-plugin-annotations) + ("maven-core" ,maven-core) + ("maven-model" ,maven-model) + ("java-commons-cli" ,java-commons-cli) + ("java-qdox" ,java-qdox) + ("java-jdom2" ,java-jdom2) + ("java-asm" ,java-asm) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ,@(package-native-inputs maven-wagon-provider-api))) + (synopsis "Wagon provider that gets and puts artifacts using the file system") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code. It uses providers, that are tools to +manage artifacts and deployment. This package contains the file provider which +gets and puts artifacts using the file system."))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From 53360e488dcfd7d7ef7aac743509b8773fd5b59f Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:42:12 +0100 Subject: gnu: Add maven-wagon-tck-http. * gnu/packages/maven.scm (maven-wagon-tck-http): New variable. --- gnu/packages/maven.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 2ee8dc0e30..005d9b9249 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -416,6 +416,33 @@ artifact and repository handling code. It uses providers, that are tools to manage artifacts and deployment. This package contains the file provider which gets and puts artifacts using the file system."))) +(define-public maven-wagon-tck-http + (package + (inherit maven-wagon-provider-api) + (name "maven-wagon-tck-http") + (arguments + `(#:jar-name "maven-wagon-tck-http.jar" + #:source-dir "wagon-tcks/wagon-tck-http/src/main/java" + #:tests? #f; no tests + #:jdk ,icedtea-8)) + (inputs + `(("java-plexus-util" ,java-plexus-utils) + ("maven-wagon-provider-api" ,maven-wagon-provider-api) + ("java-tomcat" ,java-tomcat) + ("java-slf4j-api" ,java-slf4j-api) + ("java-commons-codec" ,java-commons-codec) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2) + ("java-eclipse-jetty-webapp-9.2" ,java-eclipse-jetty-webapp-9.2) + ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2) + ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2) + ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2))) + (synopsis "Wagon HTTP Test Compatibility Kit") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code. This package contains the HTTP +Test Compatibility Kit."))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From c3f5ec6ec7a3495c4ce4c2f713698c8ce7882967 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:43:50 +0100 Subject: gnu: Add maven-wagon-http-shared. * gnu/packages/maven.scm (maven-wagon-http-shared): New variable. --- gnu/packages/maven.scm | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 005d9b9249..2b7c15aba2 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -443,6 +443,67 @@ gets and puts artifacts using the file system."))) artifact and repository handling code. This package contains the HTTP Test Compatibility Kit."))) +(define-public maven-wagon-http-shared + (package + (inherit maven-wagon-provider-api) + (name "maven-wagon-http-shared") + (arguments + `(#:jar-name "maven-wagon-http-shared.jar" + #:source-dir "wagon-providers/wagon-http-shared/src/main/java" + #:test-dir "wagon-providers/wagon-http-shared/src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'build 'generate-metadata + (lambda _ + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes") + "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli" + "--source" "wagon-providers/wagon-http-shared/src/main/java" + "--output" "build/classes/META-INF/plexus/components.xml" + "--classes" "build/classes" + "--descriptors" "build/classes/META-INF") + #t)) + (add-after 'generate-metadata 'rebuild + (lambda _ + (invoke "ant" "jar") + #t))))) + (inputs + `(("java-plexus-utils" ,java-plexus-utils) + ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient) + ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore) + ("java-commons-io" ,java-commons-io) + ("java-jsoup" ,java-jsoup) + ("maven-wagon-provider-api" ,maven-wagon-provider-api))) + (native-inputs + `(("maven-wagon-provider-test" ,maven-wagon-provider-test) + ("java-plexus-component-metadata" ,java-plexus-component-metadata) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-guava" ,java-guava) + ("java-guice" ,java-guice) + ("java-javax-inject" ,java-javax-inject) + ("java-cglib" ,java-cglib) + ("java-slf4j-api" ,java-slf4j-api) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-cli" ,java-plexus-cli) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-plugin-annotations" ,maven-plugin-annotations) + ("maven-core" ,maven-core) + ("maven-model" ,maven-model) + ("java-commons-cli" ,java-commons-cli) + ("java-qdox" ,java-qdox) + ("java-jdom2" ,java-jdom2) + ("java-asm" ,java-asm) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ,@(package-native-inputs maven-wagon-provider-api))) + (synopsis "Shared Library for wagon providers supporting HTTP.") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code. It uses providers, that are tools to +manage artifacts and deployment. This package contains a shared library for +wagon providers supporting HTTP."))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From aa06dd0f7d0dedd68b26eaadccef30a916bd7dc8 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:45:06 +0100 Subject: gnu: Add maven-wagon-http. * gnu/packages/maven.scm (maven-wagon-http): New variable. --- gnu/packages/maven.scm | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 2b7c15aba2..85591ce4ad 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -504,6 +504,90 @@ artifact and repository handling code. It uses providers, that are tools to manage artifacts and deployment. This package contains a shared library for wagon providers supporting HTTP."))) +(define-public maven-wagon-http + (package + (inherit maven-wagon-provider-api) + (name "maven-wagon-http") + (arguments + `(#:jar-name "maven-wagon-http.jar" + #:source-dir "wagon-providers/wagon-http/src/main/java" + #:test-dir "wagon-providers/wagon-http/src/test" + #:test-exclude (list + "**/Abstract*.java" + ;; FIXME: javax.net.ssl.SSLHandshakeException: + ;; sun.security.validator.ValidatorException: + ;; PKIX path building failed: + ;; sun.security.provider.certpath.SunCertPathBuilderException: + ;; unable to find valid certification path to requested target + "**/HttpsWagonPreemptiveTest.java" + "**/HttpsWagonTest.java" + ;; Injection errors + "**/TckTest.java") + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (install-file "wagon-providers/wagon-http/src/main/resources/META-INF/plexus/components.xml" + "build/classes/META-INF/plexus") + #t)) + (add-before 'check 'fix-resource-path + (lambda _ + (substitute* '("wagon-providers/wagon-http/src/test/java/org/apache/maven/wagon/providers/http/HttpsWagonPreemptiveTest.java" + "wagon-providers/wagon-http/src/test/java/org/apache/maven/wagon/providers/http/HttpsWagonTest.java") + (("src/test") "wagon-providers/wagon-http/src/test")) + #t))))) + (inputs + `(("java-plexus-utils" ,java-plexus-utils) + ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient) + ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore) + ("maven-wagon-http-shared" ,maven-wagon-http-shared) + ("maven-wagon-tck-http" ,maven-wagon-tck-http) + ("maven-wagon-provider-api" ,maven-wagon-provider-api))) + (native-inputs + `(("maven-wagon-provider-test" ,maven-wagon-provider-test) + ("java-plexus-component-metadata" ,java-plexus-component-metadata) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-plexus-container-default" ,java-plexus-container-default) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-guava" ,java-guava) + ("java-guice" ,java-guice) + ("java-inject" ,java-javax-inject) + ("java-cglib" ,java-cglib) + ("java-slf4j-api" ,java-slf4j-api) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-cli" ,java-plexus-cli) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-plugin-annotations" ,maven-plugin-annotations) + ("maven-core" ,maven-core) + ("maven-model" ,maven-model) + ("java-commons-cli" ,java-commons-cli) + ("java-qdox" ,java-qdox) + ("java-jdom2" ,java-jdom2) + ("java-asm" ,java-asm) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ("java-tomcat" ,java-tomcat) + ("java-eclipse-jetty-util-9.2" ,java-eclipse-jetty-util-9.2) + ("java-eclipse-jetty-io-9.2" ,java-eclipse-jetty-io-9.2) + ("java-eclipse-jetty-http-9.2" ,java-eclipse-jetty-http-9.2) + ("java-eclipse-jetty-server-9.2" ,java-eclipse-jetty-server-9.2) + ("java-eclipse-jetty-servlet-9.2" ,java-eclipse-jetty-servlet-9.2) + ("java-eclipse-jetty-security-9.2" ,java-eclipse-jetty-security-9.2) + ("java-hamcrest-core" ,java-hamcrest-core) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-codec" ,java-commons-codec) + ("java-commons-io" ,java-commons-io) + ("java-jsoup" ,java-jsoup) + ("java-slf4j-simple" ,java-slf4j-simple) + ,@(package-native-inputs maven-wagon-provider-api))) + (synopsis "Wagon provider that gets and puts artifacts through HTTP(S)") + (description "Maven Wagon is a transport abstraction that is used in Maven's +artifact and repository handling code. It uses providers, that are tools to +manage artifacts and deployment. This package contains a Wagon provider that +gets and puts artifacts through HTTP(S) using Apache HttpClient-4.x."))) + (define-public maven-artifact (package (name "maven-artifact") -- cgit v1.2.3 From 19126bba4e54211c2bf61f67c98cd08e5f455409 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:47:17 +0100 Subject: gnu: Add maven-resolver-transport-wagon. * gnu/packages/maven.scm (maven-resolver-transport-wagon): New variable. --- gnu/packages/maven.scm | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 83 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 85591ce4ad..9a152c3194 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -237,6 +237,89 @@ for repositories using URI-based layouts."))) ("java-hamcrest-core" ,java-hamcrest-core) ("maven-resolver-test-util" ,maven-resolver-test-util))))) +(define-public maven-resolver-transport-wagon + (package + (inherit maven-resolver-api) + (name "maven-resolver-transport-wagon") + (arguments + `(#:jar-name "maven-resolver-transport-wagon.jar" + #:source-dir "maven-resolver-transport-wagon/src/main/java" + #:test-dir "maven-resolver-transport-wagon/src/test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-before 'build 'generate-sisu + (lambda _ + (mkdir-p "build/classes/META-INF/sisu") + (with-output-to-file "build/classes/META-INF/sisu/javax.inject.Named" + (lambda _ + (display "org.eclipse.aether.transport.wagon.WagonTransporterFactory\n"))) + #t)) + (add-before 'build 'generate-components.xml + (lambda _ + (mkdir-p "build/classes/META-INF/plexus") + (with-output-to-file "build/classes/META-INF/plexus/components.xml" + (lambda _ + (display + (string-append + " + + + + org.eclipse.aether.transport.wagon.WagonConfigurator + plexus + org.eclipse.aether.internal.transport.wagon.PlexusWagonConfigurator + + false + + + org.codehaus.plexus.PlexusContainer + + container + + + + + org.eclipse.aether.transport.wagon.WagonProvider + plexus + org.eclipse.aether.internal.transport.wagon.PlexusWagonProvider + + false + + + org.codehaus.plexus.PlexusContainer + + container + + + + +\n")))) + #t))))) + (inputs + `(("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi) + ("maven-resolver-util" ,maven-resolver-util) + ("java-javax-inject" ,java-javax-inject) + ("mavne-wagon-provider-api" ,maven-wagon-provider-api) + ("java-plexus-component-annotation" ,java-plexus-component-annotations) + ("java-plexus-classworld" ,java-plexus-classworlds) + ("java-plexus-plexus-util" ,java-plexus-utils) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core) + ("maven-resolver-test-util" ,maven-resolver-test-util) + ("java-guava" ,java-guava) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("java-aopalliance" ,java-aopalliance) + ("java-guice" ,java-guice))) + (synopsis "Transport implementation for Maven") + (description "This package contains a transport implementation based on +Maven Wagon, for use in Maven."))) + (define-public maven-shared-utils (package (name "maven-shared-utils") -- cgit v1.2.3 From 0c1e98eb92470b4ec595a4f15d62786dedf5d1e6 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:48:27 +0100 Subject: gnu: Add maven-compat. * gnu/packages/maven.scm (maven-compat): New variable. --- gnu/packages/maven.scm | 117 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 117 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 9a152c3194..2e920f9b44 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -1303,3 +1303,120 @@ artifactId=maven-core" ,(package-version maven-core-bootstrap)))) (description "Apache Maven is a software project management and comprehension tool. This package contains a Maven embeddable component, with CLI and logging support."))) + +(define-public maven-compat + (package + (inherit maven-artifact) + (name "maven-compat") + (arguments + `(#:jar-name "maven-compat.jar" + #:source-dir "src/main/java" + #:jdk ,icedtea-8 + #:test-dir "src/test" + #:phases + (modify-phases %standard-phases + ;; Tests assume we're in this directory + (add-before 'configure 'chdir + (lambda _ + (chdir "maven-compat") + #t)) + (add-before 'build 'generate-models + (lambda* (#:key inputs #:allow-other-keys) + (define (modello-single-mode file version mode) + (invoke "java" "org.codehaus.modello.ModelloCli" + file mode "src/main/java" version + "false" "true")) + (let ((file "src/main/mdo/profiles.mdo")) + (modello-single-mode file "1.0.0" "java") + (modello-single-mode file "1.0.0" "xpp3-reader") + (modello-single-mode file "1.0.0" "xpp3-writer")) + (let ((file "src/main/mdo/paramdoc.mdo")) + (modello-single-mode file "1.0.0" "java") + (modello-single-mode file "1.0.0" "xpp3-reader") + (modello-single-mode file "1.0.0" "xpp3-writer")) + #t)) + (add-after 'build 'generate-metadata + (lambda _ + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") ":build/classes") + "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli" + "--source" "src/main/java" + "--output" "build/classes/META-INF/plexus/components.xml" + "--classes" "build/classes" + "--descriptors" "build/classes/META-INF") + #t)) + (add-before 'check 'build-tests + (lambda _ + (invoke "ant" "compile-tests") + #t)) + (add-after 'build-tests 'generate-test-metadata + (lambda _ + (invoke "java" "-cp" (string-append (getenv "CLASSPATH") + ":build/classes" + ":build/test-classes") + "org.codehaus.plexus.metadata.PlexusMetadataGeneratorCli" + "--source" "src/test/java" + "--output" "build/test-classes/META-INF/plexus/components.xml" + "--classes" "build/test-classes" + "--descriptors" "build/test-classes/META-INF") + #t)) + (add-after 'generate-metadata 'rebuild + (lambda _ + (invoke "ant" "jar") + #t))))) + (inputs + `(("maven-artifact" ,maven-artifact) + ("maven-repository-metadata" ,maven-repository-metadata) + ("maven-builder-support" ,maven-builder-support) + ("maven-model" ,maven-model) + ("maven-model-builder" ,maven-model-builder) + ("maven-settings" ,maven-settings) + ("maven-settings-builder" ,maven-settings-builder) + ("maven-core" ,maven-core) + ("maven-wagon-provider-api" ,maven-wagon-provider-api) + ("maven-wagon-file" ,maven-wagon-file) + ("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-util" ,maven-resolver-util) + ("maven-resolver-spi" ,maven-resolver-spi) + ("java-plexus-interpolation" ,java-plexus-interpolation))) + (native-inputs + `(("java-modello-core" ,java-modello-core) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-plexus-classworlds" ,java-plexus-classworlds) + ("java-geronimo-xbean-reflect" ,java-geronimo-xbean-reflect) + ("java-sisu-build-api" ,java-sisu-build-api) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-exclispe-sisu-inject" ,java-eclipse-sisu-inject) + ("java-javax-inject" ,java-javax-inject) + ("java-guice" ,java-guice) + ("java-guava" ,java-guava) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("java-modello-plugins-java" ,java-modello-plugins-java) + ("java-modello-plugins-xml" ,java-modello-plugins-xml) + ("java-modello-plugins-xpp3" ,java-modello-plugins-xpp3) + ;; metadata + ("java-plexus-component-metadata" ,java-plexus-component-metadata) + ("java-commons-cli" ,java-commons-cli) + ("java-plexus-cli" ,java-plexus-cli) + ("java-jdom2" ,java-jdom2) + ("maven-plugin-api" ,maven-plugin-api) + ("java-qdox" ,java-qdox) + ;; tests + ("java-plexus-cipher" ,java-plexus-cipher) + ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher) + ("java-jsr250", java-jsr250) + ("java-cdi-api" ,java-cdi-api) + ("java-junit" ,java-junit) + ("maven-resolver-impl" ,maven-resolver-impl) + ("maven-resolver-connector-basic" ,maven-resolver-connector-basic) + ("maven-resolver-transport-wagon" ,maven-resolver-transport-wagon) + ("java-commons-lang3" ,java-commons-lang3) + ("java-aop" ,java-aopalliance) + ("maven-resolver-provider" ,maven-resolver-provider) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ,@(package-inputs java-slf4j-api))) + (description "Apache Maven is a software project management and comprehension +tool. This package contains Maven2 classes maintained as compatibility +layer for plugins that need to keep Maven2 compatibility."))) -- cgit v1.2.3 From 8c2c105c12e7cc21bc6f27592550bb7132884955 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 17 Mar 2018 16:49:27 +0100 Subject: gnu: Add maven. * gnu/packages/maven.scm (maven): New variable. --- gnu/packages/maven.scm | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 2e920f9b44..070bd7131c 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -1420,3 +1420,91 @@ logging support."))) (description "Apache Maven is a software project management and comprehension tool. This package contains Maven2 classes maintained as compatibility layer for plugins that need to keep Maven2 compatibility."))) + +(define-public maven + (package + (inherit maven-artifact) + (name "maven") + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'build + (lambda _ + (substitute* "apache-maven/src/bin/mvn" + (("cygwin=false;") + (string-append + "CLASSPATH=" (getenv "CLASSPATH") "\n" + "cygwin=false;")) + (("-classpath.*") "-classpath ${CLASSPATH} \\\n")) + #t)) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/")) + (conf (string-append (assoc-ref outputs "out") "/conf/"))) + (mkdir-p (string-append (assoc-ref outputs "out") "/lib")) + (for-each (lambda (file) + (install-file (string-append "apache-maven/src/bin/" file) + bin) + (chmod (string-append bin file) #o755)) + '("mvn" "mvnDebug" "mvnyjp")) + (install-file "apache-maven/src/bin/m2.conf" bin) + (copy-recursively "apache-maven/src/conf" conf)) + #t))))) + (inputs + `(("java-plexus-classworlds" ,java-plexus-classworlds) + ("maven-artifact" ,maven-artifact) + ("maven-embedder" ,maven-embedder) + ("maven-core" ,maven-core) + ("maven-compat" ,maven-compat) + ("maven-builder-support" ,maven-builder-support) + ("maven-model" ,maven-model) + ("maven-model-builder" ,maven-model-builder) + ("maven-settings" ,maven-settings) + ("maven-settings-builder" ,maven-settings-builder) + ("maven-plugin-api" ,maven-plugin-api) + ("maven-repository-metadata", maven-repository-metadata) + ("maven-shared-utils" ,maven-shared-utils) + ("maven-resolver-api" ,maven-resolver-api) + ("maven-resolver-spi" ,maven-resolver-spi) + ("maven-resolver-util" ,maven-resolver-util) + ("maven-resolver-impl" ,maven-resolver-impl) + ("maven-resolver-connector-basic" ,maven-resolver-connector-basic) + ("maven-resolver-provider" ,maven-resolver-provider) + ("maven-resolver-transport-wagon" ,maven-resolver-transport-wagon) + ("maven-wagon-provider-api" ,maven-wagon-provider-api) + ("maven-wagon-file" ,maven-wagon-file) + ("maven-wagon-http" ,maven-wagon-http) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-httpcomponents-httpclient" ,java-httpcomponents-httpclient) + ("java-httpcomponents-httpcore" ,java-httpcomponents-httpcore) + ("maven-wagon-http-shared" ,maven-wagon-http-shared) + ("maven-wagon-tck-http" ,maven-wagon-tck-http) + ("java-eclipse-sisu-plexus" ,java-eclipse-sisu-plexus) + ("java-guice" ,java-guice) + ("java-aopalliance" ,java-aopalliance) + ("java-cglib" ,java-cglib) + ("java-asm" ,java-asm) + ("java-eclipse-sisu-inject" ,java-eclipse-sisu-inject) + ("java-javax-inject" ,java-javax-inject) + ("java-plexus-component-annotations" ,java-plexus-component-annotations) + ("java-plexus-utils" ,java-plexus-utils) + ("java-plexus-interpolation" ,java-plexus-interpolation) + ("java-plexus-sec-dispatcher" ,java-plexus-sec-dispatcher) + ("java-plexus-cipher" ,java-plexus-cipher) + ("java-guava" ,java-guava) + ("java-jansi" ,java-jansi) + ("java-jsr250" ,java-jsr250) + ("java-cdi-api" ,java-cdi-api) + ("java-commons-cli" ,java-commons-cli) + ("java-commons-io" ,java-commons-io) + ("java-commons-lang3" ,java-commons-lang3) + ("java-slf4j-api" ,java-slf4j-api) + ;; TODO: replace with maven-slf4j-provider + ("java-slf4j-simple" ,java-slf4j-simple))) + (description "Apache Maven is a software project management and comprehension +tool. Based on the concept of a project object model: builds, dependency +management, documentation creation, site publication, and distribution +publication are all controlled from the @file{pom.xml} declarative file. Maven +can be extended by plugins to utilise a number of other development tools for +reporting or the build process."))) -- cgit v1.2.3 From 697a9d0d06bde87dec4a684be46f39eb9b485190 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sat, 16 Jun 2018 14:09:40 +0200 Subject: gnu: groovy: Add groovy-xml to the closure. * gnu/packages/groovy.scm (groovy)[inputs]: Add groovy-xml. [arguments]: Add groovy-xml to the list of classes available for class loading. --- gnu/packages/groovy.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu/packages') diff --git a/gnu/packages/groovy.scm b/gnu/packages/groovy.scm index 512f9c9edb..aaa524b1ba 100644 --- a/gnu/packages/groovy.scm +++ b/gnu/packages/groovy.scm @@ -1107,7 +1107,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST)."))) "groovy-jmx" "groovy-json" "groovy-jsr223" "groovy-nio" "groovy-servlet" "groovy-sql" "groovy-swing" "groovy-templates" "groovy-testng" - "java-commons-cli" "java-asm" + "groovy-xml" "java-commons-cli" "java-asm" "java-classpathx-servletapi" "java-xstream" "java-jansi" "java-jline-2")) ;; antlr.jar is present twice in antlr2. Symlink doesn't like @@ -1140,6 +1140,7 @@ and modify groovy's @dfn{Abstract Syntax Tree} (AST)."))) ("groovy-swing" ,groovy-swing) ("groovy-templates" ,groovy-templates) ("groovy-testng" ,groovy-testng) + ("groovy-xml" ,groovy-xml) ("java-commons-cli" ,java-commons-cli) ("java-asm" ,java-asm) ("java-classpathx-servletapi" ,java-classpathx-servletapi) -- cgit v1.2.3 From 806f599c5bc630362359809e66ee8d6f275580c3 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sat, 16 Jun 2018 20:51:49 +0800 Subject: gnu: wesnoth: Update to 1.14.3. * gnu/packages/games.scm (wesnoth): Update to 1.14.3. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 7d6d2e8c4a..e5d5765ff3 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1822,7 +1822,7 @@ falling, themeable graphics and sounds, and replays.") (define-public wesnoth (package (name "wesnoth") - (version "1.14.1") + (version "1.14.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-" @@ -1831,7 +1831,7 @@ falling, themeable graphics and sounds, and replays.") name "-" version ".tar.bz2")) (sha256 (base32 - "1mzrnbv71b4s41c5x8clhb53l8lidiwzny1hl828228pvys5bxkb")))) + "06648041nr77sgzr7jpmcn37cma3hp41qynp50xzddx28l17zwg9")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no check target -- cgit v1.2.3 From e8b3a15849e513dd0421eeae5077b57e7f56043b Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Fri, 15 Jun 2018 03:00:25 +0200 Subject: gnu: Add dehydrated. * gnu/packages/tls.scm (dehydrated): New variable. --- gnu/packages/tls.scm | 71 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index c81197b812..35134025b8 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2017, 2018 Marius Bakke ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Rutger Helling +;;; Copyright © 2018 Clément Lassieur ;;; ;;; This file is part of GNU Guix. ;;; @@ -38,10 +39,14 @@ #:use-module (guix build-system python) #:use-module (guix build-system cmake) #:use-module (guix build-system haskell) + #:use-module (guix build-system trivial) #:use-module (gnu packages compression) #:use-module (gnu packages) + #:use-module (gnu packages bash) #:use-module (gnu packages check) + #:use-module (gnu packages curl) #:use-module (gnu packages dns) + #:use-module (gnu packages gawk) #:use-module (gnu packages guile) #:use-module (gnu packages haskell) #:use-module (gnu packages haskell-check) @@ -875,3 +880,69 @@ implement the SSL3.0, TLS1.0, TLS1.1 and TLS1.2 protocol, and support RSA and Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many extensions.") (license license:bsd-3))) + +(define-public dehydrated + (package + (name "dehydrated") + (version "0.6.2") + (source (origin + (method url-fetch/tarbomb) + (uri (string-append + "https://github.com/lukas2511/dehydrated/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "03p80yj6bnzjc6dkp5hb9wpplmlrla8n5src71cnzw4rj53q8cqn")) + (file-name (string-append name "-" version ".tar.gz")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((source (assoc-ref %build-inputs "source")) + (out (assoc-ref %outputs "out")) + (bin (string-append out "/bin")) + (bash (in-vicinity (assoc-ref %build-inputs "bash") "bin"))) + (mkdir-p bin) + (with-directory-excursion bin + (copy-file + (in-vicinity source (string-append "/dehydrated-" ,version + "/dehydrated")) + (in-vicinity bin "dehydrated")) + (patch-shebang "dehydrated" (list bash)) + + ;; Do not try to write in the store. + (substitute* "dehydrated" + (("SCRIPTDIR=\"\\$.*\"") "SCRIPTDIR=~/.dehydrated")) + + (setenv "PATH" bash) + (wrap-program "dehydrated" + `("PATH" ":" prefix + ,(map (lambda (dir) + (string-append dir "/bin")) + (map (lambda (input) + (assoc-ref %build-inputs input)) + '("coreutils" + "curl" + "diffutils" + "gawk" + "grep" + "openssl" + "sed")))))) + #t)))) + (inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("curl" ,curl) + ("diffutils" ,diffutils) + ("gawk" ,gawk) + ("grep" ,grep) + ("openssl" ,openssl) + ("sed" ,sed))) + (home-page "https://dehydrated.io/") + (synopsis "Let's Encrypt/ACME client implemented as a shell script") + (description "Dehydrated is a client for signing certificates with an +ACME-server (currently only provided by Let's Encrypt) implemented as a +relatively simple Bash script.") + (license license:expat))) -- cgit v1.2.3 From f77886c1c5f3c2bf33b78391cea5c4e5b2c05948 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Wed, 13 Jun 2018 22:17:05 +0300 Subject: gnu: Add restic. * gnu/packages/backup.scm (restic): New variable. --- gnu/packages/backup.scm | 112 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 112 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 711bd32245..85764b073e 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2017 Christopher Allan Webber ;;; Copyright © 2017 Rutger Helling ;;; Copyright © 2018 Mark H Weaver +;;; Copyright © 2018 Oleg Pykhalov ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,6 +33,7 @@ #:use-module (guix download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system go) #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages acl) @@ -45,6 +47,7 @@ #:use-module (gnu packages ftp) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) + #:use-module (gnu packages golang) #:use-module (gnu packages gperf) #:use-module (gnu packages guile) #:use-module (gnu packages linux) @@ -822,3 +825,112 @@ file systems with unattended creation and expiration. A dirvish backup vault is like a time machine for your data. ") (license (license:fsf-free "file://COPYING" "Open Software License 2.0")))) + +(define-public restic ; bundled / vendored dependencies + (package + (name "restic") + (version "0.9.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/restic/restic/releases/download/" + "v" version "/restic-" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "15f0rsm2lxk4lmn4773q28g49p68pqyyx0ccp7r556asan73p79m")))) + (build-system go-build-system) + (arguments + `(#:import-path "github.com/restic/restic" + #:unpack-path "github.com/restic" + ;; We don't need to install the source code for end-user applications. + #:install-source? #f + #:phases + (modify-phases %standard-phases + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion (string-append + "src/github.com/restic/restic-" + ,version) + (invoke "go" "run" "build.go")))) + + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (src (string-append "src/github.com/restic/restic-" + ,version))) + (install-file (string-append src "/restic") + (string-append out "/bin")) + #t))) + + (add-after 'install 'install-docs + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (man "/share/man") + (man-section (string-append man "/man")) + (src (string-append "src/github.com/restic/restic-" + ,version "/doc/man/"))) + ;; Install all the man pages to "out". + (for-each + (lambda (file) + (install-file file + (string-append out man-section + (string-take-right file 1)))) + (find-files src "\\.[1-9]")) + #t))) + + (add-after 'install-docs 'install-shell-completion + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (etc (string-append out "/etc")) + (share (string-append out "/share"))) + (for-each + (lambda (shell) + (let* ((shell-name (symbol->string shell)) + (dir (string-append "etc/completion/" shell-name))) + (mkdir-p dir) + (invoke (string-append bin "/restic") "generate" + (string-append "--" shell-name "-completion") + (string-append dir "/" + (case shell + ((bash) "restic") + ((zsh) "_restic")))))) + '(bash zsh)) + (with-directory-excursion "etc/completion" + (install-file "bash/restic" + (string-append etc "/bash_completion.d")) + (install-file "zsh/_restic" + (string-append share "/zsh/site-functions"))) + #t)))))) + (home-page "https://restic.net/") + (synopsis "Backup program with multiple revisions, encryption and more") + (description "Restic is a program that does backups right and was designed +with the following principles in mind: + +@itemize +@item Easy: Doing backups should be a frictionless process, otherwise you +might be tempted to skip it. Restic should be easy to configure and use, so +that, in the event of a data loss, you can just restore it. Likewise, +restoring data should not be complicated. + +@item Fast: Backing up your data with restic should only be limited by your +network or hard disk bandwidth so that you can backup your files every day. +Nobody does backups if it takes too much time. Restoring backups should only +transfer data that is needed for the files that are to be restored, so that +this process is also fast. + +@item Verifiable: Much more important than backup is restore, so restic +enables you to easily verify that all data can be restored. @item Secure: +Restic uses cryptography to guarantee confidentiality and integrity of your +data. The location the backup data is stored is assumed not to be a trusted +environment (e.g. a shared space where others like system administrators are +able to access your backups). Restic is built to secure your data against +such attackers. + +@item Efficient: With the growth of data, additional snapshots should only +take the storage of the actual increment. Even more, duplicate data should be +de-duplicated before it is actually written to the storage back end to save +precious backup space. +@end itemize") + (license license:bsd-2))) -- cgit v1.2.3 From cdbcfc113bfc02e58bdf6ec42c545c479681602f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 6 Jun 2018 17:19:18 +0200 Subject: gnu: linux-libre: Fix build on AArch64. * gnu/packages/patches/binutils-aarch64-symbol-relocation.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/base.scm (binutils/fixed): New public variable. * gnu/packages/linux.scm (make-linux-libre)[native-inputs]: On aarch64, define new ld-wrapper with the above binutils and use it. --- gnu/local.mk | 1 + gnu/packages/base.scm | 11 +++++++ gnu/packages/linux.scm | 6 ++++ .../binutils-aarch64-symbol-relocation.patch | 36 ++++++++++++++++++++++ 4 files changed, 54 insertions(+) create mode 100644 gnu/packages/patches/binutils-aarch64-symbol-relocation.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 4d2cefdbde..d02f07031f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -582,6 +582,7 @@ dist_patch_DATA = \ %D%/packages/patches/bash-completion-directories.patch \ %D%/packages/patches/bazaar-CVE-2017-14176.patch \ %D%/packages/patches/bind-CVE-2018-5738.patch \ + %D%/packages/patches/binutils-aarch64-symbol-relocation.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/blast+-fix-makefile.patch \ %D%/packages/patches/boost-fix-icu-build.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 6d9f019857..fef6002b3c 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -480,6 +480,17 @@ included.") (license gpl3+) (home-page "https://www.gnu.org/software/binutils/"))) +(define-public binutils/fixed + ;; TODO: Incorporate this in binutils during the next rebuild cycle. + (hidden-package + (package + (inherit binutils) + (source (origin + (inherit (package-source binutils)) + (patches (append (origin-patches (package-source binutils)) + (search-patches + "binutils-aarch64-symbol-relocation.patch")))))))) + (define* (make-ld-wrapper name #:key (target (const #f)) binutils diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 9938af99b8..4ed418d6a9 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -295,6 +295,12 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (or (%current-target-system) (%current-system))) ((or "x86_64" "i386") `(("gcc" ,gcc-7))) + ("arm64" + ;; Work around a binutils 2.30 bug where some kernel symbols would + ;; be incorrectly marked as relocatable: + ;; . + `(("ld-wrapper" ,(make-ld-wrapper "ld-wrapper" + #:binutils binutils/fixed)))) (_ '())) ,@(match (and configuration-file diff --git a/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch b/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch new file mode 100644 index 0000000000..fbd596862b --- /dev/null +++ b/gnu/packages/patches/binutils-aarch64-symbol-relocation.patch @@ -0,0 +1,36 @@ +Fix a regression in Binutils 2.30 where some symbols are incorrectly assumed +to be addresses: + +https://sourceware.org/bugzilla/show_bug.cgi?id=22764 + +Patch taken from upstream (with ChangeLog entries and tests omitted): + +https://sourceware.org/git/gitweb.cgi?p=binutils-gdb.git;a=commitdiff;h=279b2f94168ee91e02ccd070d27c983fc001fe12 + +diff --git a/bfd/elfnn-aarch64.c b/bfd/elfnn-aarch64.c +index af448f9..2737773 100644 +--- a/bfd/elfnn-aarch64.c ++++ b/bfd/elfnn-aarch64.c +@@ -7189,10 +7189,19 @@ elfNN_aarch64_check_relocs (bfd *abfd, struct bfd_link_info *info, + #if ARCH_SIZE == 64 + case BFD_RELOC_AARCH64_32: + #endif +- if (bfd_link_pic (info) +- && (sec->flags & SEC_ALLOC) != 0 +- && (sec->flags & SEC_READONLY) != 0) ++ if (bfd_link_pic (info) && (sec->flags & SEC_ALLOC) != 0) + { ++ if (h != NULL ++ /* This is an absolute symbol. It represents a value instead ++ of an address. */ ++ && ((h->root.type == bfd_link_hash_defined ++ && bfd_is_abs_section (h->root.u.def.section)) ++ /* This is an undefined symbol. */ ++ || h->root.type == bfd_link_hash_undefined)) ++ break; ++ ++ /* For local symbols, defined global symbols in a non-ABS section, ++ it is assumed that the value is an address. */ + int howto_index = bfd_r_type - BFD_RELOC_AARCH64_RELOC_START; + _bfd_error_handler + /* xgettext:c-format */ -- cgit v1.2.3 From 7727f91f44a2ef9fd6dabfa3d191914852583a12 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 12 Jun 2018 00:56:05 +0200 Subject: gnu: openal: Update to 0.18.2. * gnu/packages/audio.scm (openal): Update to 0.18.2. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index d8dc1e3134..0664545e4a 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1890,7 +1890,7 @@ lv2-c++-tools.") (define-public openal (package (name "openal") - (version "1.17.2") + (version "1.18.2") (source (origin (method url-fetch) (uri (string-append @@ -1898,7 +1898,7 @@ lv2-c++-tools.") version ".tar.bz2")) (sha256 (base32 - "051k5fy8pk4fd9ha3qaqcv08xwbks09xl5qs4ijqq2qz5xaghhd3")))) + "10kydm8701a2kppiss9sdidn1820cmzhqgx1b2bsa5dsgzic32lz")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; no check target -- cgit v1.2.3 From 57b1dba116741584e7360a94d1df593b5b130f55 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 12 Jun 2018 11:01:40 +0200 Subject: gnu: libedit: Update to 20180525-3.1. * gnu/packages/libedit.scm (libedit): Update to 20180525-3.1. --- gnu/packages/libedit.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/libedit.scm b/gnu/packages/libedit.scm index 9f6f1d05ce..095749e868 100644 --- a/gnu/packages/libedit.scm +++ b/gnu/packages/libedit.scm @@ -28,7 +28,7 @@ (define-public libedit (package (name "libedit") - (version "20170329-3.1") + (version "20180525-3.1") (source (origin (method url-fetch) @@ -36,7 +36,7 @@ "/" name "-" version ".tar.gz")) (sha256 (base32 - "1gnlgl0x8g9ky59s70nriy5gv47676d1s4ypvbv8y11apl7xkwli")))) + "05iicng4kag5hxdc7adbyj1gm3qbmvcc33m9cyx5gys0s67yl6y4")))) (build-system gnu-build-system) (inputs `(("ncurses" ,ncurses))) -- cgit v1.2.3 From 406c83f78d4c7851743bb0f82a9de02c8afa63f3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 12 Jun 2018 11:24:29 +0200 Subject: gnu: perl: Fix CVE-2018-12015. * gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. * gnu/packages/perl.scm (perl-5.26.2)[source](patches): Use it. --- gnu/local.mk | 1 + .../patches/perl-archive-tar-CVE-2018-12015.patch | 36 ++++++++++++++++++++++ gnu/packages/perl.scm | 2 ++ 3 files changed, 39 insertions(+) create mode 100644 gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index d02f07031f..a1bebe0dfa 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -989,6 +989,7 @@ dist_patch_DATA = \ %D%/packages/patches/patchutils-xfail-gendiff-tests.patch \ %D%/packages/patches/patch-hurd-path-max.patch \ %D%/packages/patches/perf-gcc-ice.patch \ + %D%/packages/patches/perl-archive-tar-CVE-2018-12015.patch \ %D%/packages/patches/perl-file-path-CVE-2017-6512.patch \ %D%/packages/patches/perl-autosplit-default-time.patch \ %D%/packages/patches/perl-dbd-mysql-CVE-2017-10788.patch \ diff --git a/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch b/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch new file mode 100644 index 0000000000..6460cf5855 --- /dev/null +++ b/gnu/packages/patches/perl-archive-tar-CVE-2018-12015.patch @@ -0,0 +1,36 @@ +Fix CVE-2018-12015: + +https://security-tracker.debian.org/tracker/CVE-2018-12015 +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-12015 +https://rt.cpan.org/Ticket/Display.html?id=125523 + +Patch taken from this upstream commit and adapted to apply to +the bundled copy in the Perl distribution: + +https://github.com/jib/archive-tar-new/commit/ae65651eab053fc6dc4590dbb863a268215c1fc5 + +diff --git a/cpan/Archive-Tar/lib/Archive/Tar.pm b/cpan/Archive-Tar/lib/Archive/Tar.pm +index 6244369..a83975f 100644 +--- a/cpan/Archive-Tar/lib/Archive/Tar.pm ++++ b/cpan/Archive-Tar/lib/Archive/Tar.pm +@@ -845,6 +845,20 @@ sub _extract_file { + return; + } + ++ ### If a file system already contains a block device with the same name as ++ ### the being extracted regular file, we would write the file's content ++ ### to the block device. So remove the existing file (block device) now. ++ ### If an archive contains multiple same-named entries, the last one ++ ### should replace the previous ones. So remove the old file now. ++ ### If the old entry is a symlink to a file outside of the CWD, the new ++ ### entry would create a file there. This is CVE-2018-12015 ++ ### . ++ if (-l $full || -e _) { ++ if (!unlink $full) { ++ $self->_error( qq[Could not remove old file '$full': $!] ); ++ return; ++ } ++ } + if( length $entry->type && $entry->is_file ) { + my $fh = IO::File->new; + $fh->open( $full, '>' ) or ( diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 2d2bb62a78..93b1a3f672 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -170,6 +170,8 @@ (inherit (package-source perl)) (uri (string-append "mirror://cpan/src/5.0/perl-" version ".tar.gz")) + (patches (append (origin-patches (package-source perl)) + (search-patches "perl-archive-tar-CVE-2018-12015.patch"))) (sha256 (base32 "03gpnxx1g6hvlh0v4aqx00580h787sfywp1vlvw64q2xcbm9qbsp")))))) -- cgit v1.2.3 From 259341cf93de80533d212cb73e5e652aa4bc716c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 12 Jun 2018 19:51:23 +0200 Subject: gnu: ldb: Fix build on 32-bit systems. * guix/utils.scm (target-64bit?): New procedure. * gnu/packages/samba.scm (ldb)[inputs]: Only add LMDB on 64-bit systems. [arguments]: Make #:tests? conditional on LMDB availability. --- gnu/packages/samba.scm | 9 +++++++-- guix/utils.scm | 6 ++++++ 2 files changed, 13 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index abbfdd83c4..e10f00a83b 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -362,7 +362,10 @@ many event types, including timers, signals, and the classic file descriptor eve #t)))) (build-system gnu-build-system) (arguments - '(#:phases + '(;; LMDB is only supported on 64-bit systems, yet the test suite + ;; requires it. + #:tests? (assoc-ref %build-inputs "lmdb") + #:phases (modify-phases %standard-phases (replace 'configure ;; ldb use a custom configuration script that runs waf. @@ -382,7 +385,9 @@ many event types, including timers, signals, and the classic file descriptor eve `(("talloc" ,talloc) ("tdb" ,tdb))) (inputs - `(("lmdb" ,lmdb) + `(,@(if (target-64bit?) + `(("lmdb" ,lmdb)) + '()) ("popt" ,popt) ("tevent" ,tevent))) (synopsis "LDAP-like embedded database") diff --git a/guix/utils.scm b/guix/utils.scm index e9efea5866..a5de9605e7 100644 --- a/guix/utils.scm +++ b/guix/utils.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2015 David Thompson ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017 Mathieu Othacehe +;;; Copyright © 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -77,6 +78,7 @@ package-name->name+version target-mingw? target-arm32? + target-64bit? version-compare version>? version>=? @@ -474,6 +476,10 @@ a character other than '@'." (define (target-arm32?) (string-prefix? "arm" (or (%current-target-system) (%current-system)))) +(define (target-64bit?) + (let ((system (or (%current-target-system) (%current-system)))) + (any (cut string-prefix? <> system) '("x86_64" "aarch64" "mips64" "ppc64")))) + (define version-compare (let ((strverscmp (let ((sym (or (dynamic-func "strverscmp" (dynamic-link)) -- cgit v1.2.3 From 30e26b6af3cb4a6dc88bccaa2ead0ba5500e7e46 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Jun 2018 18:48:11 +0200 Subject: gnu: ffmpeg: Update to 4.0.1. * gnu/packages/video.scm (ffmpeg): Update to 4.0.1. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 8cd7a3d57c..e31238243f 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -606,14 +606,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).") (define-public ffmpeg (package (name "ffmpeg") - (version "4.0") + (version "4.0.1") (source (origin (method url-fetch) (uri (string-append "https://ffmpeg.org/releases/ffmpeg-" version ".tar.xz")) (sha256 (base32 - "0gx4ngnhi5glmxh38603qy5n6vq8bl1cr4sqd1xff95i82pmv57d")))) + "1vn04n0n46zdxq14cma3w8ml2ckh5jxwlybsc4xmvcqdqq0mqpv0")))) (build-system gnu-build-system) (inputs `(("fontconfig" ,fontconfig) -- cgit v1.2.3 From ec8cdd0ec6d8fffed5494b5765ddf9490b6f4db1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Jun 2018 18:50:22 +0200 Subject: gnu: maim: Update to 5.5.2. * gnu/packages/xdisorg.scm (maim): Update to 5.5.2. --- gnu/packages/xdisorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index 57200d803c..bbc413a130 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -530,7 +530,7 @@ selection's dimensions to stdout.") (define-public maim (package (name "maim") - (version "5.5.1") + (version "5.5.2") (source (origin (method url-fetch) (uri (string-append @@ -539,7 +539,7 @@ selection's dimensions to stdout.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1dvw0axnr9hhjg6zdcq9lwvaq0x7vrzlz00p8n3hj25qzsi4z5as")))) + "14zdhsx1cndg5m8wbv1rqmza7wgknwfj5h0knzxg3p2jkjw66i95")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no "check" target -- cgit v1.2.3 From 4c0df1a8705287d60498261e1cd59a6eaf100aa5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Jun 2018 18:51:43 +0200 Subject: gnu: offlineimap: Update to 7.2.1. * gnu/packages/mail.scm (offlineimap): Update to 7.2.1. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 57edc6f535..77e81acff4 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -491,7 +491,7 @@ and corrections. It is based on a Bayesian filter.") (define-public offlineimap (package (name "offlineimap") - (version "7.2.0") + (version "7.2.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/OfflineIMAP/offlineimap/" @@ -499,7 +499,7 @@ and corrections. It is based on a Bayesian filter.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i7pzm1vrj98jcyn1ygsg1yp0gqlsssnc25451icvivysvdwdj5n")))) + "1022xf2w1xax4vx4kzhlfbhaf0b72wkpvrcscvs4q8qk2ja68h8x")))) (build-system python-build-system) (native-inputs `(("asciidoc" ,asciidoc))) -- cgit v1.2.3 From ed2ae0dc7f44d884ed1329cba457f5479cafd2ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 16 Jun 2018 18:54:14 +0200 Subject: gnu: strace: Update to 4.23. * gnu/packages/linux.scm (strace): Update to 4.23. [source]: Remove obsolete patch. * gnu/packages/patches/strace-kernel-4.16.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/linux.scm | 5 +- gnu/packages/patches/strace-kernel-4.16.patch | 92 --------------------------- 3 files changed, 2 insertions(+), 96 deletions(-) delete mode 100644 gnu/packages/patches/strace-kernel-4.16.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index a1bebe0dfa..3aad334a11 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1112,7 +1112,6 @@ dist_patch_DATA = \ %D%/packages/patches/slim-login.patch \ %D%/packages/patches/sooperlooper-build-with-wx-30.patch \ %D%/packages/patches/steghide-fixes.patch \ - %D%/packages/patches/strace-kernel-4.16.patch \ %D%/packages/patches/superlu-dist-scotchmetis.patch \ %D%/packages/patches/swish-e-search.patch \ %D%/packages/patches/swish-e-format-security.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 4ed418d6a9..60cd80ec04 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -920,16 +920,15 @@ Zerofree requires the file system to be unmounted or mounted read-only.") (define-public strace (package (name "strace") - (version "4.22") + (version "4.23") (home-page "https://strace.io") (source (origin (method url-fetch) (uri (string-append home-page "/files/" version "/strace-" version ".tar.xz")) - (patches (search-patches "strace-kernel-4.16.patch")) (sha256 (base32 - "17dkpnsjxmys1ydidm9wcvc3wscsz44fmlxw3dclspn9cj9d1306")))) + "1bcsq2gbpcb81ayryvn56a6kjx42fc21la6qgds35n0xbybacq3q")))) (build-system gnu-build-system) (arguments '(#:phases diff --git a/gnu/packages/patches/strace-kernel-4.16.patch b/gnu/packages/patches/strace-kernel-4.16.patch deleted file mode 100644 index e86d3be439..0000000000 --- a/gnu/packages/patches/strace-kernel-4.16.patch +++ /dev/null @@ -1,92 +0,0 @@ -Fix test failure when using Linux-Libre >= 4.16. - -Taken from upstream: -https://github.com/strace/strace/commit/bcff87c31c0f27c678a43d6b7f67dab363a974fa - -From bcff87c31c0f27c678a43d6b7f67dab363a974fa Mon Sep 17 00:00:00 2001 -From: Masatake YAMATO -Date: Wed, 2 May 2018 17:11:07 +0900 -Subject: [PATCH] tests/ioctl_kvm_run.c: handle cpuid at the end of vcpu dentry - -Since Linux 4.16, kernel appends the cpuid as suffix to the entry -for a kvm vcpu in /proc/$pid/fd like: - - anon_inode:kvm-vcpu:0 - -That was - - anon_inode:kvm-vcpu - -This kernel change causes the test case failure on newer kernels. -Update the test to deal with the new name as well as the old one. - -* tests/ioctl_kvm_run.c: Include unistd.h for using readlink(2). -(vcpu_dev_should_have_cpuid): New function for detecting whether -a proc entry for given fd has the cpuid suffix or not. -(main): Trim vcpu_dev to remove the cpuid suffix if needed. -(vcpu_dev): Remove const modifier. ---- - tests/ioctl_kvm_run.c | 29 ++++++++++++++++++++++++++++- - 1 file changed, 28 insertions(+), 1 deletion(-) - -diff --git a/tests/ioctl_kvm_run.c b/tests/ioctl_kvm_run.c -index 179461430..e1bef5796 100644 ---- a/tests/ioctl_kvm_run.c -+++ b/tests/ioctl_kvm_run.c -@@ -40,6 +40,7 @@ - # include - # include - # include -+# include - # include - - static int -@@ -56,7 +57,7 @@ kvm_ioctl(int fd, unsigned long cmd, const char *cmd_str, void *arg) - - static const char dev[] = "/dev/kvm"; - static const char vm_dev[] = "anon_inode:kvm-vm"; --static const char vcpu_dev[] = "anon_inode:kvm-vcpu"; -+static char vcpu_dev[] = "anon_inode:kvm-vcpu:0"; - static size_t page_size; - - extern const char code[]; -@@ -165,6 +166,23 @@ run_kvm(const int vcpu_fd, struct kvm_run *const run, const size_t mmap_size, - } - } - -+static int -+vcpu_dev_should_have_cpuid(int fd) -+{ -+ int r = 0; -+ char *filename = NULL; -+ char buf[sizeof(vcpu_dev)]; -+ -+ if (asprintf(&filename, "/proc/%d/fd/%d", getpid(), fd) < 0) -+ error_msg_and_fail("asprintf"); -+ -+ if (readlink(filename, buf, sizeof(buf)) == sizeof(buf) - 1 -+ && (memcmp(buf, vcpu_dev, sizeof(buf) - 1) == 0)) -+ r = 1; -+ free(filename); -+ return r; -+} -+ - int - main(void) - { -@@ -208,6 +226,15 @@ main(void) - (unsigned long) page_size, (unsigned long) page_size, mem); - - int vcpu_fd = KVM_IOCTL(vm_fd, KVM_CREATE_VCPU, NULL); -+ if (!vcpu_dev_should_have_cpuid(vcpu_fd)) -+ /* -+ * This is an older kernel that doesn't place a cpuid -+ * at the end of the dentry associated with vcpu_fd. -+ * Trim the cpuid part of vcpu_dev like: -+ * "anon_inode:kvm-vcpu:0" -> "anon_inode:kvm-vcpu" -+ */ -+ vcpu_dev[strlen (vcpu_dev) - 2] = '\0'; -+ - printf("ioctl(%d<%s>, KVM_CREATE_VCPU, 0) = %d<%s>\n", - vm_fd, vm_dev, vcpu_fd, vcpu_dev); - -- cgit v1.2.3 From a14de83213a8d4fe6befced5a3dcf05e40fe4513 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 16 Jun 2018 16:54:53 +0200 Subject: gnu: upx: Fix CVE-2017-15056. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/patches/upx-protect-against-bad-crafted-input.patch: New file. * gnu/packages/compression.scm (upx)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/compression.scm | 8 +- gnu/packages/patches/upx-fix-CVE-2017-15056.patch | 96 +++++++++++++++++++++++ 3 files changed, 104 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/upx-fix-CVE-2017-15056.patch (limited to 'gnu/packages') diff --git a/gnu/local.mk b/gnu/local.mk index 3aad334a11..2856186595 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1157,6 +1157,7 @@ dist_patch_DATA = \ %D%/packages/patches/ustr-fix-build-with-gcc-5.patch \ %D%/packages/patches/util-linux-tests.patch \ %D%/packages/patches/upower-builddir.patch \ + %D%/packages/patches/upx-fix-CVE-2017-15056.patch \ %D%/packages/patches/valgrind-enable-arm.patch \ %D%/packages/patches/valgrind-glibc-compat.patch \ %D%/packages/patches/vinagre-revert-1.patch \ diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 8f062049a6..9cb0917dae 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -2209,7 +2209,8 @@ decompression is a little bit slower.") version "/" name "-" version "-src.tar.xz")) (sha256 (base32 - "08anybdliqsbsl6x835iwzljahnm9i7v26icdjkcv33xmk6p5vw1")))) + "08anybdliqsbsl6x835iwzljahnm9i7v26icdjkcv33xmk6p5vw1")) + (patches (search-patches "upx-fix-CVE-2017-15056.patch")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) ("ucl" ,ucl))) @@ -2241,6 +2242,11 @@ decompression is a little bit slower.") #t)) ))) (home-page "https://upx.github.io/") + ;; CVE-2017-16869 is about Mach-O files which is not of a big concern for Guix. + ;; See https://github.com/upx/upx/issues/146 and + ;; https://nvd.nist.gov/vuln/detail?vulnId=CVE-2017-16869. + ;; The issue will be fixed after version 3.94. + (properties `((lint-hidden-cve . ("CVE-2017-16869")))) (synopsis "Compression tool for executables") (description "The Ultimate Packer for eXecutables (UPX) is an executable file diff --git a/gnu/packages/patches/upx-fix-CVE-2017-15056.patch b/gnu/packages/patches/upx-fix-CVE-2017-15056.patch new file mode 100644 index 0000000000..525980e73e --- /dev/null +++ b/gnu/packages/patches/upx-fix-CVE-2017-15056.patch @@ -0,0 +1,96 @@ +From 3e0c2966dffb5dadb512a476ef4be3d0cc51c2be Mon Sep 17 00:00:00 2001 +From: Pierre Neidhardt +Date: Sat, 16 Jun 2018 16:35:00 +0200 +Subject: [PATCH] Protect against bad crafted input + +Also check for wrap-around when checking oversize involving e_shoff and e_shnum. + +raised by https://github.com/upx/upx/pull/190 + modified: p_lx_elf.cpp +--- + src/p_lx_elf.cpp | 30 ++++++++++++++++++++++++++++++ + 1 file changed, 30 insertions(+) + +diff --git a/src/p_lx_elf.cpp b/src/p_lx_elf.cpp +index 822a7652..41e805ee 100644 +--- a/src/p_lx_elf.cpp ++++ b/src/p_lx_elf.cpp +@@ -235,8 +235,17 @@ PackLinuxElf32::PackLinuxElf32help1(InputFile *f) + sz_phdrs = 0; + return; + } ++ if (0==e_phnum) throwCantUnpack("0==e_phnum"); + e_phoff = get_te32(&ehdri.e_phoff); ++ unsigned const last_Phdr = e_phoff + e_phnum * sizeof(Elf32_Phdr); ++ if (last_Phdr < e_phoff || (unsigned long)file_size < last_Phdr) { ++ throwCantUnpack("bad e_phoff"); ++ } + e_shoff = get_te32(&ehdri.e_shoff); ++ unsigned const last_Shdr = e_shoff + e_shnum * sizeof(Elf32_Shdr); ++ if (last_Shdr < e_shoff || (unsigned long)file_size < last_Shdr) { ++ throwCantUnpack("bad e_shoff"); ++ } + sz_phdrs = e_phnum * e_phentsize; + + if (f && Elf32_Ehdr::ET_DYN!=e_type) { +@@ -599,8 +608,17 @@ PackLinuxElf64::PackLinuxElf64help1(InputFile *f) + sz_phdrs = 0; + return; + } ++ if (0==e_phnum) throwCantUnpack("0==e_phnum"); + e_phoff = get_te64(&ehdri.e_phoff); ++ upx_uint64_t const last_Phdr = e_phoff + e_phnum * sizeof(Elf64_Phdr); ++ if (last_Phdr < e_phoff || (unsigned long)file_size < last_Phdr) { ++ throwCantUnpack("bad e_phoff"); ++ } + e_shoff = get_te64(&ehdri.e_shoff); ++ upx_uint64_t const last_Shdr = e_shoff + e_shnum * sizeof(Elf64_Shdr); ++ if (last_Shdr < e_shoff || (unsigned long)file_size < last_Shdr) { ++ throwCantUnpack("bad e_shoff"); ++ } + sz_phdrs = e_phnum * e_phentsize; + + if (f && Elf64_Ehdr::ET_DYN!=e_type) { +@@ -3763,6 +3781,9 @@ void PackLinuxElf64::pack4(OutputFile *fo, Filter &ft) + + void PackLinuxElf64::unpack(OutputFile *fo) + { ++ if (e_phoff != sizeof(Elf64_Ehdr)) {// Phdrs not contiguous with Ehdr ++ throwCantUnpack("bad e_phoff"); ++ } + unsigned const c_phnum = get_te16(&ehdri.e_phnum); + upx_uint64_t old_data_off = 0; + upx_uint64_t old_data_len = 0; +@@ -3828,6 +3849,9 @@ void PackLinuxElf64::unpack(OutputFile *fo) + unsigned total_out = 0; + unsigned c_adler = upx_adler32(NULL, 0); + unsigned u_adler = upx_adler32(NULL, 0); ++ if ((MAX_ELF_HDR - sizeof(Elf64_Ehdr))/sizeof(Elf64_Phdr) < u_phnum) { ++ throwCantUnpack("bad compressed e_phnum"); ++ } + + // Packed ET_EXE has no PT_DYNAMIC. + // Packed ET_DYN has original PT_DYNAMIC for info needed by rtld. +@@ -4383,6 +4407,9 @@ Elf64_Sym const *PackLinuxElf64::elf_lookup(char const *name) const + + void PackLinuxElf32::unpack(OutputFile *fo) + { ++ if (e_phoff != sizeof(Elf32_Ehdr)) {// Phdrs not contiguous with Ehdr ++ throwCantUnpack("bad e_phoff"); ++ } + unsigned const c_phnum = get_te16(&ehdri.e_phnum); + unsigned old_data_off = 0; + unsigned old_data_len = 0; +@@ -4449,6 +4476,9 @@ void PackLinuxElf32::unpack(OutputFile *fo) + unsigned total_out = 0; + unsigned c_adler = upx_adler32(NULL, 0); + unsigned u_adler = upx_adler32(NULL, 0); ++ if ((MAX_ELF_HDR - sizeof(Elf32_Ehdr))/sizeof(Elf32_Phdr) < u_phnum) { ++ throwCantUnpack("bad compressed e_phnum"); ++ } + + // Packed ET_EXE has no PT_DYNAMIC. + // Packed ET_DYN has original PT_DYNAMIC for info needed by rtld. +-- +2.17.0 + -- cgit v1.2.3 From 3348e9f371da1ff7d73e09af28e150d0653568a5 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 16 Jun 2018 23:50:49 +0200 Subject: gnu: emacs-fish-completion: Don't propagate inputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (emacs-fish-completion)[propagated-inputs]: Remove fish [inputs]: Add fish. [arguments]: New field. Signed-off-by: Ludovic Courtès --- gnu/packages/emacs.scm | 55 +++++++++++++++++++++++++++++++------------------- 1 file changed, 34 insertions(+), 21 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 4999dda55b..88134ea4e7 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -10843,26 +10843,39 @@ Org-mode. It features: (license license:gpl3+)))) (define-public emacs-fish-completion - (package - (name "emacs-fish-completion") - (version "20180329") - (source - (origin - (method url-fetch) - (uri (string-append - "https://github.com/Ambrevar/emacs-fish-completion/archive/" - "3e3ed1f19fa778b7c35ad88e033dce5a6b1fc153" - ".tar.gz")) - (sha256 - (base32 - "16329py7fvid0bap1qhqxhdc68m9qqy1p8gc2bhng81zhm5a5zsm")))) - (build-system emacs-build-system) - (propagated-inputs `(("fish" ,fish))) - (home-page - "https://github.com/Ambrevar/emacs-fish-completion") - (synopsis "Fish completion for Emacs pcomplete") - (description - "This package provides completion for the Fish shell to pcomplete (used + (let ((commit "bac15fda1392a891070574dfe5d2d50b10831e8b")) + (package + (name "emacs-fish-completion") + (version (git-version "20180616" "1" commit)) + (source + (origin + (method url-fetch) + (uri (string-append + "https://gitlab.com/Ambrevar/emacs-fish-completion/repository/" + "archive.tar.gz?ref=" + commit)) + (sha256 + (base32 + "093qzdrbkl7dhjk16zq8i13kh1phyigkblcfrbgbrxjqd2ndrfdi")))) + (build-system emacs-build-system) + (inputs `(("fish" ,fish))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((fish (assoc-ref inputs "fish"))) + ;; Specify the absolute file names of the various + ;; programs so that everything works out-of-the-box. + (emacs-substitute-variables + "fish-completion.el" + ("fish-completion-command" + (string-append fish "/bin/fish"))))))))) + (home-page + "https://gitlab.com/Ambrevar/emacs-fish-completion") + (synopsis "Fish completion for Emacs pcomplete") + (description + "This package provides completion for the Fish shell to pcomplete (used by shell and Eshell). You can set it up globally with: @example @@ -10877,7 +10890,7 @@ shell/Eshell mode hook. The package @code{emacs-bash-completion} is an optional dependency: if available, @code{fish-completion-complete} can be configured to fall back on bash to further try completing. See @code{fish-completion-fallback-on-bash-p}.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public emacs-gif-screencast (let ((commit "825e606950ec842304bf75cf85baef707b853b03")) -- cgit v1.2.3 From 6710206881bfc8364aaf0bd1f9c33bc0a2a0ebde Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 17 Jun 2018 00:28:35 +0200 Subject: gnu: magit: Update to 2.13.0. * gnu/packages/emacs.scm (magit): Update to 2.13.0. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 88134ea4e7..3b2c41c5d8 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -436,7 +436,7 @@ on stdout instead of using a socket as the Emacsclient does.") (define-public magit (package (name "magit") - (version "2.12.1") + (version "2.13.0") (source (origin (method url-fetch) (uri (string-append @@ -444,7 +444,7 @@ on stdout instead of using a socket as the Emacsclient does.") version "/" name "-" version ".tar.gz")) (sha256 (base32 - "1czzknmhzbggcv3bxl5amvfpp0zrkdwl1x05qarsq6qakvc85xy3")))) + "1ygaah3dd3nxpyd17297xgvdcgr7pgzzwlmpnmchki0kiwgg3sbc")))) (build-system gnu-build-system) (native-inputs `(("texinfo" ,texinfo) ("emacs" ,emacs-minimal))) -- cgit v1.2.3 From 554eaae4a068c58ac401a22b97f1c1967052b68a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 17 Jun 2018 00:29:51 +0200 Subject: gnu: diffoscope: Update to 96. * gnu/packages/package-management.scm (diffoscope): Update to 96. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 6d99cddc0d..a9485a7e7a 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -546,13 +546,13 @@ transactions from C or Python.") (define-public diffoscope (package (name "diffoscope") - (version "95") + (version "96") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "0aksxxivxli6l3fylxgl771hw0h7l8x35l76cmj0d12zgx54w0a1")))) + "1x66f2x8miy3giff14higpcs70c0zb5d3gj6yn8ac6p183sngl72")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From f3a34b9de8e15f237a33fae0e035b004cff2e80f Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 17 Jun 2018 01:25:35 +0200 Subject: gnu: gsl: Update to 2.5. * gnu/packages/maths.scm (gsl): Update to 2.5. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 208a75cbcd..ee9d84d1c3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -294,14 +294,14 @@ semiconductors.") (define-public gsl (package (name "gsl") - (version "2.4") + (version "2.5") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/gsl/gsl-" version ".tar.gz")) (sha256 (base32 - "16yfs5n444s03np1naj6yp1fsysd42kdscxzkg0k2yvfjixx0ijd")) + "1395y9hlhqadn5g9j8q22224fds5sd92jxi9czfavjj24myasq04")) (patches (search-patches "gsl-test-i686.patch")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From f82fe68f996e1bde63c03e1e130ea36604dee2fd Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 11:09:01 -0400 Subject: gnu: Add perl-x11-protocol-other. * gnu/packages/xorg.scm (perl-x11-protocol-other): New variable. --- gnu/packages/xorg.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 54001187da..86906074f6 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2017, 2018 Rutger Helling ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; @@ -5855,6 +5856,34 @@ perl programs to display windows and graphics on X11 servers.") ;; for details)." (license license:perl-license))) +(define-public perl-x11-protocol-other + (package + (name "perl-x11-protocol-other") + (version "30") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/K/KR/KRYDE/X11-Protocol-Other-" + version ".tar.gz")) + (sha256 + (base32 + "1mambi57cdkj82wiw1l8y2f70a60qsamdas0165hlj10drryfgrj")))) + (build-system perl-build-system) + (native-inputs + `(("perl-encode-hanextra" ,perl-encode-hanextra) + ("perl-module-util" ,perl-module-util))) + (propagated-inputs + `(("perl-x11-protocol" ,perl-x11-protocol))) + (home-page "http://search.cpan.org/dist/X11-Protocol-Other/") + (synopsis "Miscellaneous helpers for @code{X11::Protocol} connections") + (description + "@code{X11::Protocol::Other} contains window manager related functions for +use by client programs, as per the @dfn{ICCCM} (Inter-Client Communication +Conventions Manual) and some of the @dfn{EWMH} +(Extended Window Manager Hints).") + (license license:gpl3+))) + (define-public xcompmgr (package (name "xcompmgr") -- cgit v1.2.3 From b2d5b00d42803f48d7dc5fd1432c03287ed1d34e Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 11:26:30 -0400 Subject: gnu: Add perl-cpan-changes. * gnu/packages/perl.scm (perl-cpan-changes): New variable. --- gnu/packages/perl.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 93b1a3f672..813aeecf9c 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2017 Christopher Allan Webber ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Pierre Neidhardt +;;; Copyright © 2018 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; @@ -1524,6 +1525,27 @@ provides a means of converting those data streams back into into binary data.") (license perl-license))) +(define-public perl-cpan-changes + (package + (name "perl-cpan-changes") + (version "0.400002") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/H/HA/HAARG/CPAN-Changes-" + version ".tar.gz")) + (sha256 + (base32 + "13dy78amkhwg278sv5im0ylyskhxpfivyl2aissqqih71nlxxvh1")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/CPAN-Changes/") + (synopsis "Read and write @file{Changes} files") + (description + "@code{CPAN::Changes} helps users programmatically read and write +@file{Changes} files that conform to a common specification.") + (license perl-license))) + (define-public perl-cpan-meta-check (package (name "perl-cpan-meta-check") -- cgit v1.2.3 From 048657cccdac3042f994253153aa3c1d6ebc0130 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 20:00:44 -0400 Subject: gnu: Add perl-module-manifest. * gnu/packages/perl.scm (perl-module-manifest): New variable. --- gnu/packages/perl.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 813aeecf9c..4974d7e9d8 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -5237,6 +5237,36 @@ strictly correct manner with ExtUtils::MakeMaker, and will run on any Perl installation version 5.005 or newer.") (license (package-license perl)))) +(define-public perl-module-manifest + (package + (name "perl-module-manifest") + (version "1.09") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/E/ET/ETHER/Module-Manifest-" + version ".tar.gz")) + (sha256 + (base32 + "16skpm804a19gsgxzn1wba3lmvc7cx5q8ly4srpyd82yy47zi5d3")))) + (build-system perl-build-system) + (native-inputs + `(("perl-test-exception" ,perl-test-exception) + ("perl-test-warn" ,perl-test-warn))) + (propagated-inputs + `(("perl-params-util" ,perl-params-util))) + (home-page "http://search.cpan.org/dist/Module-Manifest/") + (synopsis "Parse and examine a Perl distribution @file{MANIFEST} file") + (description + "@code{Module::Manifest} is a simple utility module created originally for +use in @code{Module::Inspector}. + +It can load a @file{MANIFEST} file that comes in a Perl distribution tarball, +examine the contents, and perform some simple tasks. It can also load the +@file{MANIFEST.SKIP} file and check that.") + (license perl-license))) + (define-public perl-module-pluggable (package (name "perl-module-pluggable") -- cgit v1.2.3 From 52b1551bff9befe12c13bfe7c9f2d0fa5810b455 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 20:19:10 -0400 Subject: gnu: Add perl-test-distmanifest. * gnu/packages/perl-check.scm (perl-test-distmanifest): New variable. --- gnu/packages/perl-check.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index a1be996e04..4cac6dcd9e 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Pierre Neidhardt +;;; Copyright © 2018 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; @@ -364,6 +365,30 @@ modified or tested with this API, making it simple to test both individual files, as well as to verify that there are no missing or unknown files.") (license perl-license))) +(define-public perl-test-distmanifest + (package + (name "perl-test-distmanifest") + (version "1.014") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/E/ET/ETHER/Test-DistManifest-" + version ".tar.gz")) + (sha256 + (base32 "1ifpff5simjslabwy7ac6kdylv4c0b5b39fgpwf9ha16yh6w49ix")))) + (build-system perl-build-system) + (native-inputs + `(("perl-module-build" ,perl-module-build))) + (propagated-inputs + `(("perl-module-manifest" ,perl-module-manifest))) + (home-page "https://github.com/jawnsy/Test-DistManifest") + (synopsis "Author test that validates a package @file{MANIFEST}") + (description + "@code{Test::DistManifest} provides a simple method of testing that a +@file{MANIFEST} file matches its distribution.") + (license perl-license))) + (define-public perl-test-eol (package (name "perl-test-eol") -- cgit v1.2.3 From 32315df9c70587bbf5d2fd414c9dd2def7b7685a Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 21:07:26 -0400 Subject: gnu: Add perl-file-finder. * gnu/packages/perl.scm (perl-file-finder): New variable. --- gnu/packages/perl.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 4974d7e9d8..7d5c834d67 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -9530,6 +9530,38 @@ File::Find replacement in Perl.") interface to File::Find::Object.") (license (package-license perl)))) +(define-public perl-file-finder + (package + (name "perl-file-finder") + (version "0.53") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/M/ME/MERLYN/File-Finder-" + version ".tar.gz")) + (sha256 + (base32 + "0x3a2xgzrka73lcmmwalq2mmpzxa7s6pm01ahxf677ksqsdc3jrf")))) + (build-system perl-build-system) + (propagated-inputs + `(("perl-text-glob" ,perl-text-glob))) + (home-page "http://search.cpan.org/dist/File-Finder/") + (synopsis "Wrapper for @code{File::Find} ala @code{find(1)}") + (description + "@code{File::Find} is great, but constructing the wanted routine can +sometimes be a pain. @code{File::Finder} provides a wanted-writer, using +syntax that is directly mappable to the @code{find(1)} command's syntax. + +A @code{File::Finder} object contains a hash of @code{File::Find} options, and +a series of steps that mimic find's predicates. Initially, a +@code{File::Finder} object has no steps. Each step method clones the previous +object's options and steps, and then adds the new step, returning the new +object. In this manner, an object can be grown, step by step, by chaining +method calls. Furthermore, a partial sequence can be created and held, and +used as the head of many different sequences.") + (license perl-license))) + (define-public perl-font-ttf (package (name "perl-font-ttf") -- cgit v1.2.3 From 0943b0b534e9ef6b30fd1d805d46b52f53dbac6c Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 21:10:19 -0400 Subject: gnu: Add perl-test-perltidy. * gnu/packages/perl-check.scm (perl-test-perltidy): New variable. --- gnu/packages/perl-check.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages') diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 4cac6dcd9e..89a761f0a7 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -1165,6 +1165,32 @@ a minimum of effort.") ;; "Under the same license as Perl itself" (license perl-license))) +(define-public perl-test-perltidy + (package + (name "perl-test-perltidy") + (version "20130104") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/L/LA/LARRYL/Test-PerlTidy-" + version ".tar.gz")) + (sha256 + (base32 + "1j5rsb4km9rzcbd1ljavj8vm42bmilji40v2jj2k87l1ykrxj59z")))) + (build-system perl-build-system) + (propagated-inputs + `(("perl-file-finder" ,perl-file-finder) + ("perl-file-slurp" ,perl-file-slurp) + ("perltidy" ,perltidy) + ("perl-text-diff" ,perl-text-diff))) + (home-page "http://search.cpan.org/dist/Test-PerlTidy/") + (synopsis "Check that all your Perl files are tidy") + (description + "Using @code{Test::PerlTidy}, any file ending in .pl, .pm, .t or .PL will +cause a test fail unless it is exactly as @code{perltidy} would like it to be.") + (license perl-license))) + (define-public perl-test-trap (package (name "perl-test-trap") -- cgit v1.2.3 From 469e82715e7701f0f3ee8ae519bc2126bdda0b3b Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 21:32:10 -0400 Subject: gnu: perltidy: Update to 20180220. * gnu/packages/perl.scm (perltidy): Update to 20180220. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 7d5c834d67..afbe5979db 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -8515,14 +8515,14 @@ as exceptions to standard program flow.") (define-public perltidy (package (name "perltidy") - (version "20160302") + (version "20180220") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/perltidy/" version "/Perl-Tidy-" version ".tar.gz")) (sha256 (base32 - "19yw63yh5s3pq7k3nkw6nsamg5b8vvwyhgbizslgxg0mqgc4xl3d")))) + "0w1k5ffcrpx0fm9jgprrwy0290k6cmy7dyk83s61063migi3r5z9")))) (build-system perl-build-system) (home-page "http://perltidy.sourceforge.net/") (synopsis "Perl script tidier") -- cgit v1.2.3 From c5829179caeca969d02fb83d86a29b1012761e92 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 15 Jun 2018 22:02:32 -0400 Subject: gnu: clusterssh: Update to 4.13.2. * gnu/packages/admin.scm (clusterssh): Update to 4.13.2. [build-system]: Switch to perl-build-system. [arguments]: Remove 'set-load-paths' phase. [inputs]: Remove perl. [native-inputs]: Add perl-cpan-changes, perl-file-slurp, perl-file-which, perl-module-build, perl-readonly, perl-test-differences, perl-test-distmanifest, perl-test-perltidy, perl-test-pod, perl-test-pod-coverage, perl-test-trap and perltidy. [propagated-inputs]: Add perl-exception-class, perl-try-tiny and perl-x11-protocol-other. --- gnu/packages/admin.scm | 55 +++++++++++++++++++++++--------------------------- 1 file changed, 25 insertions(+), 30 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index cf459bfbc6..d1bc004410 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -823,41 +823,36 @@ by bandwidth they use.") (define-public clusterssh (package (name "clusterssh") - (version "3.28") + (version "4.13.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/clusterssh/" - "1.%20ClusterSSH%20Series%203/" version - "/clusterssh-" version ".tar.gz")) + "2.%20ClusterSSH%20Series%204/" + "App-ClusterSSH-v" version ".tar.gz")) (sha256 (base32 - "1bwggpvaj2al5blg1ynapviv2kpydffpzq2zkhi81najnvzc1rr7")))) - (build-system gnu-build-system) - (inputs `(("perl" ,perl))) - (propagated-inputs `(("xterm" ,xterm) - ("perl-tk" ,perl-tk) - ("perl-x11-protocol" ,perl-x11-protocol))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'install 'set-load-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Put the perl-tk and perl-x11-protocol modules in the perl inc - ;; path for PROG - (let* ((out (assoc-ref outputs "out")) - (prog (string-append out "/bin/cssh")) - (perl-ver ,(package-version perl)) - (x11-inc (string-append - (assoc-ref inputs "perl-x11-protocol") - "/lib/perl5/site_perl/" perl-ver)) - (tk-inc (string-append - (assoc-ref inputs "perl-tk") - "/lib/perl5/site_perl/" perl-ver - "/x86_64-linux"))) - (wrap-program - prog - `("PERL5LIB" ":" prefix (,x11-inc ,tk-inc)))) - #t))))) + "0rmk2p3f2wz1h092anidjclh212rv3gxyk0c641qk3frlrjnw6mp")))) + (build-system perl-build-system) + (native-inputs + `(("perl-cpan-changes" ,perl-cpan-changes) + ("perl-file-slurp" ,perl-file-slurp) + ("perl-file-which" ,perl-file-which) + ("perl-module-build" ,perl-module-build) + ("perl-readonly" ,perl-readonly) + ("perl-test-differences" ,perl-test-differences) + ("perl-test-distmanifest" ,perl-test-distmanifest) + ("perl-test-perltidy" ,perl-test-perltidy) + ("perl-test-pod" ,perl-test-pod) + ("perl-test-pod-coverage" ,perl-test-pod-coverage) + ("perl-test-trap" ,perl-test-trap) + ("perltidy" ,perltidy))) + (propagated-inputs + `(("xterm" ,xterm) + ("perl-exception-class" ,perl-exception-class) + ("perl-tk" ,perl-tk) + ("perl-try-tiny" ,perl-try-tiny) + ("perl-x11-protocol" ,perl-x11-protocol) + ("perl-x11-protocol-other" ,perl-x11-protocol-other))) ;; The clusterssh.sourceforge.net address requires login to view (home-page "https://sourceforge.net/projects/clusterssh/") (synopsis "Secure concurrent multi-server terminal control") -- cgit v1.2.3 From 33f61dc1b5e14f8a2e3dfb3fb48102bda0fd6b13 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sun, 17 Jun 2018 20:23:42 +0800 Subject: gnu: Remove Mr. Rescue. It's not compatible with love-11.1. * gnu/packages/game.scm (mrrescue): Remove variable. --- gnu/packages/games.scm | 47 ----------------------------------------------- 1 file changed, 47 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index e5d5765ff3..06ac1b80bb 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3252,53 +3252,6 @@ application that locks the keyboard and mouse and instead displays bright colors, pictures, and sounds.") (license license:gpl3+))) -(define-public mrrescue - (package - (name "mrrescue") - (version "1.02e") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/SimonLarsen/mrrescue/releases/" - "download/" version "/" name version ".love")) - (file-name (string-append name "-" version ".love")) - (sha256 - (base32 - "0jwzbwkgp1l5ia6c7s760gmdirbsncp6nfqp7vqdqsfb63la9gl2")))) - (build-system trivial-build-system) - (arguments - '(#:modules ((guix build utils)) - #:builder - (begin - (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (bindir (string-append out "/bin")) - (prog (string-append bindir "/mrrescue")) - (source (assoc-ref %build-inputs "source")) - (bash (string-append (assoc-ref %build-inputs "bash") - "/bin/bash")) - (love (string-append (assoc-ref %build-inputs "love") - "/bin/love"))) - (mkdir-p bindir) - (with-output-to-file prog - (lambda () - (format #t "#!~a~%" bash) - (format #t "exec -a mrrescue \"~a\" \"~a\"~%" love source))) - (chmod prog #o755) - #t)))) - (inputs - `(("bash" ,bash) - ("love" ,love))) - (home-page "http://tangramgames.dk/games/mrrescue") - (synopsis "Arcade-style fire fighting game") - (description - "Mr. Rescue is an arcade styled 2d action game centered around evacuating -civilians from burning buildings. The game features fast paced fire -extinguishing action, intense boss battles, a catchy soundtrack and lots of -throwing people around in pseudo-randomly generated buildings.") - (license (list license:zlib ; for source code - license:cc-by-sa3.0)))) ; for graphics and music assets - (define-public hyperrogue (package (name "hyperrogue") -- cgit v1.2.3 From b4eae997fe5b928f179c34d281e9f2c3eccd3670 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 16 Jun 2018 00:53:11 +0530 Subject: gnu: texlive-bin: Use absolute path to ghostscript executable "gs". * gnu/packages/tex.scm (texlive-bin)[arguments]: Rename fix-unix-detection phase to configure-ghostscript-executable. Replace "gs" in epstopdf.pl with the absolute path to "gs" in the store. --- gnu/packages/tex.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index b6bc9dda62..b290644aac 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -176,14 +176,17 @@ (string-prefix? "mips64" s)))) #:phases (modify-phases %standard-phases - (add-after 'unpack 'fix-unix-detection + (add-after 'unpack 'configure-ghostscript-executable ;; ps2eps.pl uses the "gswin32c" ghostscript executable on Windows, ;; and the "gs" ghostscript executable on Unix. It detects Unix by ;; checking for the existence of the /usr/bin directory. Since ;; GuixSD does not have /usr/bin, it is also detected as Windows. - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (substitute* "utils/ps2eps/ps2eps-src/bin/ps2eps.pl" (("gswin32c") "gs")) + (substitute* "texk/texlive/linked_scripts/epstopdf/epstopdf.pl" + (("\"gs\"") + (string-append "\"" (assoc-ref inputs "ghostscript") "/bin/gs\""))) #t)) (add-after 'install 'postint (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) -- cgit v1.2.3 From 47de00af16168a5ff751cf28ea6e91dd3eb05aa8 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Wed, 6 Jun 2018 11:47:30 +0200 Subject: gnu: encfs: Update to 1.9.5. * gnu/packages/crypto.scm (encfs): Update to 1.9.5. [source](snippet): Adjust paths. Remove two bundled libraries. [native-inputs]: Add googletest-source. [arguments]: Add 'unpack-googletest' and 'make-unittests' phases. Signed-off-by: Kei Kebreau --- gnu/packages/crypto.scm | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 105760afa3..338db04f53 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages attr) #:use-module (gnu packages autotools) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cryptsetup) #:use-module (gnu packages databases) @@ -217,7 +218,7 @@ communication.") (define-public encfs (package (name "encfs") - (version "1.9.1") + (version "1.9.5") (source (origin (method url-fetch) @@ -226,13 +227,13 @@ communication.") version "/encfs-" version ".tar.gz")) (sha256 (base32 - "1906254dg5hwljh0h4gyrw09ms3b57dlhjfzhfzffv50yzpkl837")) + "0qzxavvv20577bxvly8s7d3y7bqasqclc2mllp0ddfncjm9z02a7")) (modules '((guix build utils))) ;; Remove bundled dependencies in favour of proper inputs. (snippet '(begin (for-each delete-file-recursively - (find-files "internal" "^tinyxml2-[0-9]" - #:directories? #t)) + '("vendor/github.com/leethomason/tinyxml2" + "vendor/github.com/google/googletest")) #t)))) (build-system cmake-build-system) (native-inputs @@ -240,6 +241,7 @@ communication.") ;; Test dependencies. ("expect" ,expect) + ("googletest-source" ,(package-source googletest)) ("perl" ,perl))) (inputs `(("attr" ,attr) @@ -247,7 +249,18 @@ communication.") ("openssl" ,openssl) ("tinyxml2" ,tinyxml2))) (arguments - `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF"))) + `(#:configure-flags (list "-DUSE_INTERNAL_TINYXML=OFF") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-googletest + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "vendor/github.com/google/googletest") + (invoke "tar" "xvf" (assoc-ref inputs "googletest-source") + "-C" "vendor/github.com/google/googletest" + "--strip-components=1"))) + (add-before 'check 'make-unittests + (lambda _ + (invoke "make" "unittests")))))) (home-page "https://vgough.github.io/encfs") (synopsis "Encrypted virtual file system") (description -- cgit v1.2.3 From 021d6296d8ae3d88e8ba6229bf0c0e764adeb8b9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Jun 2018 03:37:14 -0400 Subject: gnu: linux-libre@4.4: Update to 4.4.138. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.138. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 60cd80ec04..8c1e8e2f5c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -426,8 +426,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.136" - "0bc278l9arl8bb2gvcg02x57h66b4r8iaan3r4kzqbmkfspkl2gi" + (make-linux-libre "4.4.138" + "1030ra5gn24qmx8lsnhr6kfnfm60avzs23r81dl7mvzr5dci8vsl" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From d5ce3594f60a3641520c5243836f806c983882bc Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Jun 2018 03:38:11 -0400 Subject: gnu: linux-libre@4.9: Update to 4.9.109. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.109. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 8c1e8e2f5c..2bf0aba249 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -420,8 +420,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.107" - "0560sy53l42wi1jidwdbhjaa9p6kf46snk2hfcjk9f0ciiiiz5gi" + (make-linux-libre "4.9.109" + "1i27fmlr0b05n4qri2vxdbg0qddwk1clyaramwbl3w0w10k63qkc" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From 3b682b2ba79a04af89e8537523fbedb96e0a7bec Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Jun 2018 03:38:50 -0400 Subject: gnu: linux-libre@4.14: Update to 4.14.50. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.50. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2bf0aba249..fac0f876c1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -410,8 +410,8 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.49") -(define %linux-libre-4.14-hash "0p6xwgrkzccapdyrk20hsd3icad5j5grjh2n1ixflkabhbqp7cb2") +(define %linux-libre-4.14-version "4.14.50") +(define %linux-libre-4.14-hash "19k7s33dyykm2vh1zpxxh3qrbjcx2p2md2r8s8z5mbv8yaldgvmj") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From d06352d9dcd139c9a4f053d7dd70cc8dd79d074f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Jun 2018 03:39:51 -0400 Subject: gnu: linux-libre: Update to 4.17.2. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.17.2. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index fac0f876c1..7e81f6387e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -401,8 +401,8 @@ 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 "4.17.1") -(define %linux-libre-hash "1sxil6m17vwpaj0jg8jyrbi1mr5sjfnvhxkjaxshh6j2pdg575pw") +(define %linux-libre-version "4.17.2") +(define %linux-libre-hash "0xkswi9vhbzi466pqvyli7glkvdyxhphn8yjg69kpw37rpw8ix5l") (define-public linux-libre (make-linux-libre %linux-libre-version -- cgit v1.2.3