From 8a49e63b2dbfe422471afb59412d16db8b31b9f0 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 9 Mar 2020 14:18:23 +0100 Subject: gnu: Add rr. * gnu/packages/debug.scm (rr): New variable. --- gnu/packages/debug.scm | 71 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 70 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 82a57d4eaa..34cc479589 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -27,19 +27,25 @@ #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages code) #:use-module (gnu packages flex) + #:use-module (gnu packages gdb) #:use-module (gnu packages glib) #:use-module (gnu packages gtk) #:use-module (gnu packages golang) - #:use-module (gnu packages code) #:use-module (gnu packages llvm) + #:use-module (gnu packages ninja) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages pretty-print) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) + #:use-module (gnu packages serialization) #:use-module (gnu packages virtualization) #:use-module (ice-9 match) #:use-module (srfi srfi-1)) @@ -406,3 +412,66 @@ the position of the variable and allows you to modify its value.") ;; The library is covered by LGPLv3 or later; the application is covered ;; by GPLv3 or later. (license (list lgpl3+ gpl3+)))) + +(define-public rr + (package + (name "rr") + (version "5.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mozilla/rr") + (commit version))) + (sha256 + (base32 + "1x6l1xsdksnhz9v50p4r7hhmr077cq20kaywqy1jzdklvkjqzf64")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + ;; The 'rr_exec_stub' is a static binary, which leads CMake to fail + ;; with: + ;; + ;; file RPATH_CHANGE could not write new RPATH: + ;; + ;; Clear CMAKE_INSTALL_RPATH to avoid that problem. + (list "-DCMAKE_INSTALL_RPATH=" + ,@(if (and (not (%current-target-system)) + (member (%current-system) + '("x86_64-linux" "aarch64-linux"))) + ;; The toolchain doesn't support '-m32'. + '("-Ddisable32bit=ON") + '())) + + ;; XXX: Most tests fail with: + ;; + ;; rr needs /proc/sys/kernel/perf_event_paranoid <= 1, but it is 2. + ;; + ;; This setting cannot be changed from the build environment, so skip + ;; the tests. + #:tests? #f + + #:phases (modify-phases %standard-phases + (add-before 'check 'set-home + (lambda _ + ;; Some tests expect 'HOME' to be set. + (setenv "HOME" (getcwd)) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("ninja" ,ninja) + ("which" ,which))) + (inputs + `(("gdb" ,gdb) + ("cpanproto" ,capnproto) + ("python" ,python) + ("python-pexpect" ,python-pexpect))) + (home-page "https://rr-project.org/") + (synopsis "Record and reply debugging framework") + (description + "rr is a lightweight tool for recording, replaying and debugging +execution of applications (trees of processes and threads). Debugging extends +GDB with very efficient reverse-execution, which in combination with standard +GDB/x86 features like hardware data watchpoints, makes debugging much more +fun.") + (license expat))) -- cgit v1.2.3 From 7e5f016cdbca09b6ee2af71e495002e7686ef6f7 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 9 Mar 2020 23:02:12 +0100 Subject: tests: zabbix: Set 'PATH' before running the scripts. This is a followup to 8b9cad01e9619f53dc5a65892ca6a09ca5de3447. * gnu/tests/monitoring.scm (run-zabbix-server-test)[test]: Set 'PATH' in MARIONETTE. --- gnu/tests/monitoring.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/tests/monitoring.scm b/gnu/tests/monitoring.scm index 14d989d79a..732fbc54d7 100644 --- a/gnu/tests/monitoring.scm +++ b/gnu/tests/monitoring.scm @@ -194,6 +194,13 @@ cat ~a | sudo -u zabbix psql zabbix; (start-service 'postgres)) marionette)) + ;; Add /run/setuid-programs to $PATH so that the scripts passed to + ;; 'system' can find 'sudo'. + (marionette-eval + '(setenv "PATH" + "/run/setuid-programs:/run/current-system/profile/bin") + marionette) + (test-eq "postgres create zabbix user" 0 (marionette-eval '(begin (system #$%psql-user-create-zabbix)) -- cgit v1.2.3 From 0e42a1643ea5a0cc4ddb81687c608ba407fdcdbb Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 9 Mar 2020 23:27:32 +0100 Subject: tests: docker-system: Increase memory requirement. The system image would no longer fit in memory, starting from commit 8c7eb58453870f380a077c7cfd8dafa97bb8e13f. * gnu/tests/docker.scm (run-docker-system-test): Set 'memory-size' to 3500. --- gnu/tests/docker.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/tests/docker.scm b/gnu/tests/docker.scm index 10882b9d1f..5ab33e1104 100644 --- a/gnu/tests/docker.scm +++ b/gnu/tests/docker.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Danny Milosavljevic -;;; Copyright © 2019 Ludovic Courtès +;;; Copyright © 2019, 2020 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -206,7 +206,7 @@ inside %DOCKER-OS." ;; load' must be able to store the whole image into memory, hence the ;; huge memory requirements. We should avoid the volatile-root setup ;; instead. - (memory-size 3000) + (memory-size 3500) (port-forwardings '()))) (define test -- cgit v1.2.3 From 827abd5deb87c1ec15112d7cde1a03a4ba4b4983 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 9 Mar 2020 23:32:44 +0100 Subject: tests: getmail: Provide a pre-initialized user account password. * gnu/tests/mail.scm (%getmail-os): Rewrite so that the "alice" account has a password. (run-getmail-test)[test]("set password for alice"): Remove. This would not work since commit 8b9cad01e9619f53dc5a65892ca6a09ca5de3447 since 'passwd' would no longer be in $PATH. --- gnu/tests/mail.scm | 96 ++++++++++++++++++++++++++++++------------------------ 1 file changed, 53 insertions(+), 43 deletions(-) (limited to 'gnu') diff --git a/gnu/tests/mail.scm b/gnu/tests/mail.scm index 023f59df10..298918b3a7 100644 --- a/gnu/tests/mail.scm +++ b/gnu/tests/mail.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Sou Bunnbu ;;; Copyright © 2017 Carlo Zancanaro -;;; Copyright © 2017 Ludovic Courtès +;;; Copyright © 2017, 2020 Ludovic Courtès ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2019 Christopher Baines @@ -26,8 +26,11 @@ #:use-module (gnu tests) #:use-module (gnu packages mail) #:use-module (gnu system) + #:use-module (gnu system accounts) + #:use-module (gnu system shadow) #:use-module (gnu system vm) #:use-module (gnu services) + #:use-module (gnu services base) #:use-module (gnu services getmail) #:use-module (gnu services mail) #:use-module (gnu services networking) @@ -404,43 +407,55 @@ Subject: Hello Nice to meet you!") (value (run-dovecot-test)))) (define %getmail-os - (simple-operating-system - (service dhcp-client-service-type) - (service dovecot-service-type - (dovecot-configuration - (disable-plaintext-auth? #f) - (ssl? "no") - (auth-mechanisms '("anonymous" "plain")) - (auth-anonymous-username "alice") - (mail-location - (string-append "maildir:~/Maildir" - ":INBOX=~/Maildir/INBOX" - ":LAYOUT=fs")))) - (service getmail-service-type - (list - (getmail-configuration - (name 'test) - (user "alice") - (directory "/var/lib/getmail/alice") - (idle '("TESTBOX")) - (rcfile - (getmail-configuration-file - (retriever - (getmail-retriever-configuration - (type "SimpleIMAPRetriever") - (server "localhost") - (username "alice") - (port 143) - (extra-parameters - '((password . "testpass") - (mailboxes . ("TESTBOX")))))) - (destination - (getmail-destination-configuration - (type "Maildir") - (path "/home/alice/TestMaildir/"))) - (options - (getmail-options-configuration - (read-all #f)))))))))) + (operating-system + (inherit (simple-operating-system)) + + ;; Set a password for the user account; the test needs it. + (users (cons (user-account + (name "alice") + (password (crypt "testpass" "$6$abc")) + (comment "Bob's sister") + (group "users") + (supplementary-groups '("wheel" "audio" "video"))) + %base-user-accounts)) + + (services (cons* (service dhcp-client-service-type) + (service dovecot-service-type + (dovecot-configuration + (disable-plaintext-auth? #f) + (ssl? "no") + (auth-mechanisms '("anonymous" "plain")) + (auth-anonymous-username "alice") + (mail-location + (string-append "maildir:~/Maildir" + ":INBOX=~/Maildir/INBOX" + ":LAYOUT=fs")))) + (service getmail-service-type + (list + (getmail-configuration + (name 'test) + (user "alice") + (directory "/var/lib/getmail/alice") + (idle '("TESTBOX")) + (rcfile + (getmail-configuration-file + (retriever + (getmail-retriever-configuration + (type "SimpleIMAPRetriever") + (server "localhost") + (username "alice") + (port 143) + (extra-parameters + '((password . "testpass") + (mailboxes . ("TESTBOX")))))) + (destination + (getmail-destination-configuration + (type "Maildir") + (path "/home/alice/TestMaildir/"))) + (options + (getmail-options-configuration + (read-all #f)))))))) + %base-services)))) (define (run-getmail-test) "Return a test of an OS running Getmail service." @@ -483,11 +498,6 @@ Subject: Hello Nice to meet you!") (start-service 'dovecot)) marionette)) - (test-assert "set password for alice" - (marionette-eval - '(system "echo -e \"testpass\ntestpass\" | passwd alice") - marionette)) - ;; Wait for getmail to be up and running. (test-assert "getmail-test running" (marionette-eval -- cgit v1.2.3 From 88c6a1812c76947fae7ddc27c224264d71dc4639 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:34:53 +0100 Subject: gnu: Use HTTPS for rstudio.github.io home pages. * gnu/packages/cran.scm (r-shinydashboard, r-shinythemes, r-dt) [home-page]: Use HTTPS. --- gnu/packages/cran.scm | 4 ++-- gnu/packages/statistics.scm | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 05aa746f29..6437fd46b8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -977,7 +977,7 @@ supports interactive trees, to enable rich, editable trees in Shiny.") ("r-shiny" ,r-shiny))) (native-inputs `(("uglify-js" ,uglify-js))) - (home-page "http://rstudio.github.io/shinydashboard/") + (home-page "https://rstudio.github.io/shinydashboard/") (synopsis "Create dashboards with shiny") (description "This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards.") @@ -1028,7 +1028,7 @@ well as file saving is available.") (properties `((upstream-name . "shinythemes"))) (build-system r-build-system) (propagated-inputs `(("r-shiny" ,r-shiny))) - (home-page "http://rstudio.github.io/shinythemes/") + (home-page "https://rstudio.github.io/shinythemes/") (synopsis "Themes for Shiny") (description "This package provides themes for use with Shiny. It includes several diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 13d64be498..5e614d74e1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3151,7 +3151,7 @@ using the multicore functionality of the parallel package.") ("r-jsonlite" ,r-jsonlite) ("r-magrittr" ,r-magrittr) ("r-promises" ,r-promises))) - (home-page "http://rstudio.github.io/DT") + (home-page "https://rstudio.github.io/DT") (synopsis "R wrapper of the DataTables JavaScript library") (description "This package allows for data objects in R to be rendered as HTML tables -- cgit v1.2.3 From f30444b9da293d5e0db41ed07b6162c5235a8e19 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 9 Mar 2020 21:16:04 +0100 Subject: gnu: compface: Don't use NAME in source URI. * gnu/packages/mail.scm (compface)[source]: Hard-code NAME. --- gnu/packages/mail.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 27f7820176..23d5ec697f 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1150,7 +1150,7 @@ MailCore 2.") (method url-fetch) (uri (string-append "https://ftp.heanet.ie/mirrors/" "ftp.xemacs.org/aux/" - name "-" version ".tar.gz")) + "compface-" version ".tar.gz")) (sha256 (base32 "09b89wg63hg502hsz592cd2h87wdprb1dq1k1y07n89hym2q56d6")))) -- cgit v1.2.3 From 0622403d35edcadf09357906e6c102d0ed2cf363 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:42:24 +0100 Subject: gnu: compface: Update home page. * gnu/packages/mail.scm (compface)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/mail.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 23d5ec697f..0573e70d07 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1160,7 +1160,7 @@ MailCore 2.") (synopsis "Portrait image compressor") (description "This package takes your 48x48x1 portrait image and compresses it.") - (home-page "http://www.cs.indiana.edu/pub/faces/") + (home-page "https://legacy.cs.indiana.edu/ftp/faces/") (license (x11-style "file://README")))) (define-public claws-mail -- cgit v1.2.3 From 91fa58c73981d2a603069705f0802b1e629ee69e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:19:26 +0100 Subject: gnu: xdotool: Use HTTPS home page. * gnu/packages/xdisorg.scm (xdotool)[home-page]: Use HTTPS. --- gnu/packages/xdisorg.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm index dd05caa5f0..f46ba6714c 100644 --- a/gnu/packages/xdisorg.scm +++ b/gnu/packages/xdisorg.scm @@ -410,7 +410,7 @@ X11 (yet).") ("libxinerama" ,libxinerama) ("libxtst" ,libxtst) ("libxkbcommon" ,libxkbcommon))) - (home-page "http://www.semicomplete.com/projects/xdotool") + (home-page "https://www.semicomplete.com/projects/xdotool/") (synopsis "Fake keyboard/mouse input, window management, and more") (description "Xdotool lets you simulate keyboard input and mouse activity, move and resize windows, etc. It does this using X11's XTEST extension and -- cgit v1.2.3 From 1bcf4ba44b5f66be44aae7c075237bfd8214d81d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:49:36 +0100 Subject: gnu: iperf: Use HTTPS home page. * gnu/packages/networking.scm (iperf)[home-page]: Use HTTPS. --- gnu/packages/networking.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index eddfffd662..1840f1c0f2 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1516,7 +1516,7 @@ that block port 22.") supports tuning of various parameters related to timing, buffers and protocols (TCP, UDP, SCTP with IPv4 and IPv6). For each test it reports the bandwidth, loss, and other parameters.") - (home-page "http://software.es.net/iperf/") + (home-page "https://software.es.net/iperf/") (license (list license:bsd-3 ; Main distribution. license:ncsa ; src/{units,iperf_locale,tcp_window_size}.c license:expat ; src/{cjson,net}.[ch] -- cgit v1.2.3 From 59e884a211b2215b93827841650a588094f96951 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:37:05 +0100 Subject: gnu: polipo: Use HTTPS home page. * gnu/packages/web.scm (polipo)[home-page]: Use HTTPS. --- gnu/packages/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5a470f59b7..236dd1a506 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1381,7 +1381,7 @@ unavailable.") "CC=gcc")) ;; No 'check' target. #:tests? #f)) - (home-page "http://www.pps.univ-paris-diderot.fr/~jch/software/polipo/") + (home-page "https://www.pps.univ-paris-diderot.fr/~jch/software/polipo/") (synopsis "Small caching web proxy") (description "Polipo is a small caching web proxy (web cache, HTTP proxy, and proxy -- cgit v1.2.3 From 77dbc1c5377875e57577267e872b8c644bed0a43 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 22:46:16 +0100 Subject: gnu: slang: Use HTTPS home page. * gnu/packages/slang.scm (slang)[home-page]: Use HTTPS. --- gnu/packages/slang.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/slang.scm b/gnu/packages/slang.scm index 5a37480f67..404a4535ca 100644 --- a/gnu/packages/slang.scm +++ b/gnu/packages/slang.scm @@ -71,7 +71,7 @@ ("libpng" ,libpng) ("pcre" ,pcre) ("ncurses" ,ncurses))) - (home-page "http://www.jedsoft.org/slang/") + (home-page "https://www.jedsoft.org/slang/") (synopsis "Library for interactive applications and extensibility") (description "S-Lang is a multi-platform programmer's library designed to allow a -- cgit v1.2.3 From ef617dedd28ffa5c32cf9e0ee2482ce32aa195f4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 9 Mar 2020 22:41:01 +0100 Subject: gnu: csvkit: Update to 1.0.5. * gnu/packages/wireservice.scm (csvkit): Update to 1.0.5. [source]: Remove upstreamed patch. * gnu/packages/patches/csvkit-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/patches/csvkit-fix-tests.patch | 45 ----------------------------- gnu/packages/wireservice.scm | 8 ++--- 3 files changed, 4 insertions(+), 50 deletions(-) delete mode 100644 gnu/packages/patches/csvkit-fix-tests.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 16d7cd9529..a0e013aead 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -798,7 +798,6 @@ dist_patch_DATA = \ %D%/packages/patches/cpufrequtils-fix-aclocal.patch \ %D%/packages/patches/crawl-upgrade-saves.patch \ %D%/packages/patches/crda-optional-gcrypt.patch \ - %D%/packages/patches/csvkit-fix-tests.patch \ %D%/packages/patches/clucene-contribs-lib.patch \ %D%/packages/patches/cube-nocheck.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ diff --git a/gnu/packages/patches/csvkit-fix-tests.patch b/gnu/packages/patches/csvkit-fix-tests.patch deleted file mode 100644 index cb9ec39cb0..0000000000 --- a/gnu/packages/patches/csvkit-fix-tests.patch +++ /dev/null @@ -1,45 +0,0 @@ -diff --git a/tests/test_utilities/test_csvsql.py b/tests/test_utilities/test_csvsql.py -index e6ec4af..4f47980 100644 ---- a/tests/test_utilities/test_csvsql.py -+++ b/tests/test_utilities/test_csvsql.py -@@ -197,7 +197,7 @@ class TestCSVSQL(CSVKitTestCase, EmptyFileTests): - utility.run() - output = output_file.getvalue() - output_file.close() -- self.assertEqual(output, 'a,b,c\n1,2,3\n0,5,6\n') -+ self.assertEqual(output, 'a,b,c\n1,2.0,3.0\n0,5.0,6.0\n') - - def test_no_prefix_unique_constraint(self): - self.get_output(['--db', 'sqlite:///' + self.db_file, '--insert', 'examples/dummy.csv', '--unique-constraint', 'a']) -diff --git a/tests/test_utilities/test_sql2csv.py b/tests/test_utilities/test_sql2csv.py -index a0c3d3e..babcfd6 100644 ---- a/tests/test_utilities/test_sql2csv.py -+++ b/tests/test_utilities/test_sql2csv.py -@@ -121,23 +121,23 @@ class TestSQL2CSV(CSVKitTestCase, EmptyFileTests): - input_file.close() - - def test_unicode(self): -- expected = self.csvsql('examples/test_utf8.csv') -+ self.csvsql('examples/test_utf8.csv') - csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--query', 'select * from foo']) -- self.assertEqual(csv.strip(), expected) -+ self.assertEqual(csv.strip(), 'foo,bar,baz\n1.0,2.0,3\n4.0,5.0,ʤ') - - def test_no_header_row(self): - self.csvsql('examples/dummy.csv') - csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--no-header-row', '--query', 'select * from foo']) - - self.assertTrue('a,b,c' not in csv) -- self.assertTrue('1,2,3' in csv) -+ self.assertTrue('1,2.0,3.0' in csv) - - def test_linenumbers(self): - self.csvsql('examples/dummy.csv') - csv = self.get_output(['--db', 'sqlite:///' + self.db_file, '--linenumbers', '--query', 'select * from foo']) - - self.assertTrue('line_number,a,b,c' in csv) -- self.assertTrue('1,1,2,3' in csv) -+ self.assertTrue('1,1,2.0,3.0' in csv) - - def test_wildcard_on_sqlite(self): - self.csvsql('examples/iris.csv') diff --git a/gnu/packages/wireservice.scm b/gnu/packages/wireservice.scm index eab76970f4..0d772b54d1 100644 --- a/gnu/packages/wireservice.scm +++ b/gnu/packages/wireservice.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Pierre Langlois +;;; Copyright © 2020 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -198,17 +199,16 @@ for xls and xlsx files support to all @code{agate.Table} instances."))) (define-public csvkit (package (name "csvkit") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (pypi-uri "csvkit" version)) (sha256 (base32 - "1830lb95rh1iyi3drlwxzb6y3pqkii0qiyzd40c1kvhvaf1s6lqk")) - (patches (search-patches "csvkit-fix-tests.patch")))) + "1ffmbzk4rxnl1yhqfl58v7kvl5m9cbvjm8v7xp4mvr00sgs91lvv")))) (build-system python-build-system) (native-inputs - `(("python-psycopg2" ,python-psycopg2) ;; Used to test PostgreSQL support. + `(("python-psycopg2" ,python-psycopg2) ; to test PostgreSQL support ("python-sphinx" ,python-sphinx) ("python-sphinx-rtd-theme" ,python-sphinx-rtd-theme))) (inputs -- cgit v1.2.3 From 56451c789433e37dd0f27bff88a50bf6d3bd4136 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 10 Mar 2020 00:10:39 +0100 Subject: gnu: libinput: Note libinput-minimal inheritance. * gnu/packages/freedesktop.scm (libinput): Add a warning comment. --- gnu/packages/freedesktop.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 90956968b2..63bfdf8a97 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -179,6 +179,7 @@ freedesktop.org project.") (license license:expat))) (define-public libinput + ;; Updating this will rebuild over 700 packages through libinput-minimal. (package (name "libinput") (version "1.15.0") -- cgit v1.2.3 From b1d3e63bc2f98293efd2372fec93af9f1de62c7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 19:41:07 +0100 Subject: gnu: r-ouch: Use HTTPS home page. * gnu/packages/cran.scm (r-ouch)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 6437fd46b8..a1ad1ffb62 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9534,7 +9534,7 @@ circular variables).") "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b")))) (build-system r-build-system) (propagated-inputs `(("r-subplex" ,r-subplex))) - (home-page "http://kingaa.github.io/ouch/") + (home-page "https://kingaa.github.io/ouch/") (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses") (description "This package provides tools to fit and compare Ornstein-Uhlenbeck models -- cgit v1.2.3 From 3a18b1cc2ecc03b661a86214ba99440fd3296b19 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 19:53:05 +0100 Subject: gnu: r-knitr: Update home page. * gnu/packages/statistics.scm (r-knitr)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5e614d74e1..cd6b754425 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1414,7 +1414,7 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") ("r-stringr" ,r-stringr) ("r-xfun" ,r-xfun) ("r-yaml" ,r-yaml))) - (home-page "http://yihui.name/knitr/") + (home-page "https://yihui.org/knitr/") (synopsis "General-purpose package for dynamic report generation in R") (description "This package provides a general-purpose tool for dynamic report -- cgit v1.2.3 From b32a3e1dbfd5a3e80e24d04c0bb53aa3ada1dbd8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 20:11:24 +0100 Subject: gnu: r-varselrf: Update home page. * gnu/packages/cran.scm (r-varselrf)[home-page]: Follow (HTTPS) redirection. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a1ad1ffb62..9a323f6c6d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14319,7 +14319,7 @@ layer by layer.") (build-system r-build-system) (propagated-inputs `(("r-randomforest" ,r-randomforest))) - (home-page "http://ligarto.org/rdiaz/Software/Software.html") + (home-page "https://www.ligarto.org/rdiaz/software/software") (synopsis "Variable selection using random forests") (description "This package provides tools for the variable selection from random -- cgit v1.2.3 From b0c62de87f9bb7372cb605692022365c24491b51 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 20:30:24 +0100 Subject: gnu: r-mcmc: Use HTTPS home page. * gnu/packages/cran.scm (r-mcmc)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9a323f6c6d..77a7aab054 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -11584,7 +11584,7 @@ lasso, adaptive lasso and Ridge regression based on cross-validation.") (base32 "1i1nhdapyijvm58zx38q28zk01ndmi6smjivxk5xs2cx9b6v2av9")))) (build-system r-build-system) - (home-page "http://www.stat.umn.edu/geyer/mcmc/") + (home-page "https://www.stat.umn.edu/geyer/mcmc/") (synopsis "Markov chain Monte Carlo") (description "This package simulates continuous distributions of random vectors using -- cgit v1.2.3 From 57a2a5015b558ac885f66cf0036995b2e8e47915 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 20:37:37 +0100 Subject: gnu: r-fda: Use HTTPS home page. * gnu/packages/cran.scm (r-fda)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 77a7aab054..7e090737f5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -18003,7 +18003,7 @@ actigraphy-measured activity counts data.") (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) - (home-page "http://www.functionaldata.org") + (home-page "https://www.functionaldata.org") (synopsis "Functional data analysis") (description "These functions were developed to support functional data analysis as -- cgit v1.2.3 From 369e4e966092395d0e03e56710fa78eaf71a5ef5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:03:20 +0100 Subject: gnu: r-spams: Use HTTPS home page. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Well, it currently redirects back to HTTP… * gnu/packages/statistics.scm (r-spams)[home-page]: Use ‘HTTPS’. --- gnu/packages/statistics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cd6b754425..547450c78b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3922,7 +3922,7 @@ from within R.") (propagated-inputs `(("r-lattice" ,r-lattice) ("r-matrix" ,r-matrix))) - (home-page "http://spams-devel.gforge.inria.fr") + (home-page "https://spams-devel.gforge.inria.fr") (synopsis "Toolbox for solving sparse estimation problems") (description "SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the -- cgit v1.2.3 From 43d4eb8fc4a6074a872c80bd0b2263b98472f01a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 21:18:09 +0100 Subject: gnu: r-sparselda: Use HTTPS home page. * gnu/packages/cran.scm (r-sparselda)[home-page]: Use HTTPS. --- gnu/packages/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7e090737f5..56e86e3b74 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16892,7 +16892,7 @@ Components. The Lasso solution paths can be computed by the same function.") `(("r-elasticnet" ,r-elasticnet) ("r-mass" ,r-mass) ("r-mda" ,r-mda))) - (home-page "http://www.imm.dtu.dk/~lhc") + (home-page "https://www.imm.dtu.dk/~lkhc/") (synopsis "Sparse discriminant analysis") (description "This package performs sparse linear discriminant analysis for Gaussians -- cgit v1.2.3 From ba726ebc2d1e7df42edc061d168488791b15a497 Mon Sep 17 00:00:00 2001 From: Michael Rohleder Date: Tue, 10 Mar 2020 00:54:02 +0100 Subject: gnu: mumble: Disable statistic gathering by default. Fixes * gnu/packages/telephone.scm (mumble)[arguments]: Add phase to disable statistic gathering by default. Signed-off-by: Efraim Flashner --- gnu/packages/telephony.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/telephony.scm b/gnu/packages/telephony.scm index a645c58562..fe6c230693 100644 --- a/gnu/packages/telephony.scm +++ b/gnu/packages/telephony.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2019 Jan Wielkiewicz ;;; Copyright © 2019 Ivan Vilata i Balaguer ;;; Copyright © 2020 Brett Gilio +;;; Copyright © 2020 Michael Rohleder ;;; ;;; This file is part of GNU Guix. ;;; @@ -462,6 +463,12 @@ address of one of the participants.") (substitute* "src/mumble/TextToSpeech_unix.cpp" (("libspeechd.h") "speech-dispatcher/libspeechd.h")) #t)) + ;; disable statistic gathering by default. see + (add-before 'configure 'fix-statistic-gathering-default + (lambda _ + (substitute* "src/mumble/Settings.cpp" + (("bUsage = true;") "bUsage = false;")) + #t)) (add-before 'install 'disable-murmur-ice (lambda _ (substitute* "scripts/murmur.ini.system" -- cgit v1.2.3 From 80b2825d95c6d43b7cc96257d21e5284f4874a96 Mon Sep 17 00:00:00 2001 From: Kyle Meyer Date: Mon, 9 Mar 2020 18:29:03 -0400 Subject: gnu: git-annex: Update to 8.20200309. * gnu/packages/haskell-apps.scm (git-annex): Update to 8.20200309. Signed-off-by: Efraim Flashner --- gnu/packages/haskell-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index 521aaf5870..6005816260 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -269,14 +269,14 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}. (define-public git-annex (package (name "git-annex") - (version "8.20200226") + (version "8.20200309") (source (origin (method url-fetch) (uri (string-append "https://hackage.haskell.org/package/" "git-annex/git-annex-" version ".tar.gz")) (sha256 - (base32 "09v80ni1w9z1im79lzrnpz7xlivwna44zqpwq4axwyd17cffqi9m")))) + (base32 "1yjb01jh5rccqg44nqh4iyxmbpkcpm6m82lnw7s0s2vizj8891p5")))) (build-system haskell-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From 828996bb8a06685941408aeede4a13d42f72e952 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 10 Mar 2020 12:05:55 +0100 Subject: gnu: python-virtualenv: Propagate inputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python-xyz.scm (python-virtualenv)[inputs]: Make… [propagated-inputs]: …this. --- gnu/packages/python-xyz.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 4db272ecc7..9b4c9a1722 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -2416,7 +2416,7 @@ e.g. filters, callbacks and errbacks can all be promises.") ;; raise RuntimeError("setuptools >= 41 required to build") ("python-setuptools" ,python-setuptools) ("python-setuptools-scm" ,python-setuptools-scm))) - (inputs + (propagated-inputs `(("python-appdirs" ,python-appdirs) ("python-distlib" ,python-distlib) ("python-filelock" ,python-filelock) -- cgit v1.2.3 From e48ae0bcf9d04df86ab70d95724d2d6da4868a86 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 19 Jan 2020 01:12:50 +0100 Subject: gnu: font-dosis: Use archive.org'd URIs. * gnu/packages/fonts.scm (font-dosis)[source, home-page]: Use snapshots. --- gnu/packages/fonts.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index c302196104..5fb6bbbe18 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -1270,13 +1270,14 @@ emphasis while still being readable.") (source (origin (method url-fetch/zipbomb) - (uri (string-append "http://www.impallari.com/media/releases/dosis-" + (uri (string-append "https://web.archive.org/web/20180228233737/" + "https://www.impallari.com/media/releases/dosis-" "v" version ".zip")) (sha256 - (base32 - "1qhci68f68mf87jd69vjf9qjq3wydgw1q7ivn3amjb65ls1s0c4s")))) + (base32 "1qhci68f68mf87jd69vjf9qjq3wydgw1q7ivn3amjb65ls1s0c4s")))) (build-system font-build-system) - (home-page "http://www.impallari.com/dosis") + (home-page (string-append "https://web.archive.org/web/20180228233737/" + "https://www.impallari.com/dosis")) (synopsis "Very simple, rounded, sans serif family") (description "Dosis is a very simple, rounded, sans serif family. -- cgit v1.2.3 From fdfe65b74c8f076f2736456a0cb1a99939adda1e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:09:33 +0100 Subject: gnu: gitolite: Use HTTPS home page. * gnu/packages/version-control.scm (gitolite)[home-page]: Use HTTPS. --- gnu/packages/version-control.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 74f26c03f9..5ea3dc415c 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1310,7 +1310,7 @@ also walk each side of a merge and test those changes individually.") (propagated-inputs `(("git" ,git) ("openssh" ,openssh))) - (home-page "http://gitolite.com") + (home-page "https://gitolite.com") (synopsis "Git access control layer") (description "Gitolite is an access control layer on top of Git, providing fine access -- cgit v1.2.3 From 680e803d6659dd0a9dcf8e14678a8e2e938d7a6e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:10:10 +0100 Subject: gnu: xmobar: Use HTTPS home page. * gnu/packages/wm.scm (xmobar)[home-page]: Use HTTPS. --- gnu/packages/wm.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 8193975555..f9b6ef9880 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -730,7 +730,7 @@ tiled on several screens.") (substitute* "test/Xmobar/Plugins/Monitors/AlsaSpec.hs" (("/bin/bash") (which "bash"))) #t))))) - (home-page "http://xmobar.org") + (home-page "https://xmobar.org") (synopsis "Minimalistic text based status bar") (description "@code{xmobar} is a lightweight, text-based, status bar written in -- cgit v1.2.3 From 76fcbb788798ce294e29afd8f46b8580c6cd20a8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:12:46 +0100 Subject: gnu: ode: Use HTTPS home page. * gnu/packages/game-development.scm (ode)[home-page]: Use HTTPS. --- gnu/packages/game-development.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 262633760b..7638a545ca 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -2078,7 +2078,7 @@ a.k.a. XenoCollide) as described in Game Programming Gems 7.") `(("glu" ,glu) ("libccd" ,libccd) ("mesa" ,mesa))) - (home-page "http://www.ode.org/") + (home-page "https://www.ode.org/") (synopsis "High performance library for simulating rigid body dynamics") (description "ODE is a high performance library for simulating rigid body dynamics. It is fully featured, stable, mature and -- cgit v1.2.3 From 75c33c888abacc477589fa8aa96c03a8cfbb39e3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 18 Jan 2020 23:08:57 +0100 Subject: gnu: mars: Fix home page. * gnu/packages/games.scm (mars)[home-page]: Use working domain & HTTPS. --- gnu/packages/games.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 322e309591..fa802c79fe 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -2054,7 +2054,7 @@ for common mesh file formats, and collision detection.") ("fribidi" ,fribidi) ("taglib" ,taglib) ("sfml" ,sfml))) - (home-page "http://marsshooter.org") + (home-page "http://mars-game.sourceforge.net/") (synopsis "2D space shooter") (description "M.A.R.S. is a 2D space shooter with pretty visual effects and -- cgit v1.2.3 From fc3aa1138575a7b270da91d68b9be22cf37310ae Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 15 Feb 2020 15:14:33 +0100 Subject: gnu: monero: Update to 0.15.0.5. * gnu/packages/finance.scm (monero): Update to 0.15.0.5. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 8e12f684e0..edd513b4d9 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -495,7 +495,7 @@ other machines/servers. Electroncash does not download the Bitcoin Cash blockch ;; the system's dynamically linked library. (package (name "monero") - (version "0.15.0.1") + (version "0.15.0.5") (source (origin (method git-fetch) @@ -516,7 +516,7 @@ other machines/servers. Electroncash does not download the Bitcoin Cash blockch #t)) (sha256 (base32 - "0sypa235lf2bbib4b71xpaw39h9304slgsvnsz8wmy9fq1zx009m")))) + "06zzwa0y8ic6x3y2fy501788r51p4klanyvmm76ywrwf087njlkv")))) (build-system cmake-build-system) (native-inputs `(("doxygen" ,doxygen) -- cgit v1.2.3 From 06c8638830c991a24a731e95fd1c599da095d034 Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Sat, 15 Feb 2020 15:14:33 +0100 Subject: gnu: monero-gui: Update to 0.15.0.4. * gnu/packages/finance.scm (monero-gui): Update to 0.15.0.4. --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index edd513b4d9..5143b500ee 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -614,7 +614,7 @@ the Monero command line client and daemon.") (define-public monero-gui (package (name "monero-gui") - (version "0.15.0.3") + (version "0.15.0.4") (source (origin (method git-fetch) @@ -624,7 +624,7 @@ the Monero command line client and daemon.") (file-name (git-file-name name version)) (sha256 (base32 - "1v2mk6qp7dfdj4j4cilxp0s0phfwwnmjvpvjrz6jzzlpvbnavkr0")))) + "12m5fgnxkr11q2arx1m5ccpxqm5ljcvm6l547dwqn297zs5jim4z")))) (build-system qt-build-system) (native-inputs `(("pkg-config" ,pkg-config) -- cgit v1.2.3 From 49a221151cca3a29b0bf50e9087137204326b3da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 Mar 2020 15:13:05 +0100 Subject: gnu: Add r-ppcor. * gnu/packages/cran.scm (r-ppcor): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 56e86e3b74..f6be0d387b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20727,3 +20727,26 @@ Encyclopedia of Integer Sequences} (OEIS) in the function help page.") lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.") (license license:expat))) + +(define-public r-ppcor + (package + (name "r-ppcor") + (version "1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ppcor" version)) + (sha256 + (base32 + "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a")))) + (properties `((upstream-name . "ppcor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/ppcor/") + (synopsis "Partial and semi-partial correlation") + (description + "This package provides users not only with a function to readily +calculate the higher-order partial and semi-partial correlations but also with +statistics and p-values of the correlation coefficients.") + (license license:gpl2))) -- cgit v1.2.3 From 0e20e2c3871075a8fa117e2139f9ac494e08f0de Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 10 Mar 2020 16:20:02 +0100 Subject: gnu: emacs-xr: Update to 1.18. * gnu/packages/emacs-xyz.scm (emacs-xr): Update to 1.18. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 984613e54e..d45814379b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -972,13 +972,13 @@ in certain cases. It also enables recursion for anonymous functions.") (define-public emacs-xr (package (name "emacs-xr") - (version "1.17") + (version "1.18") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/xr-" version ".tar")) (sha256 - (base32 "0kicy15hww85kf7vii1j4yypa9z44d5vbpm65vwb6fzz0lv639zm")))) + (base32 "1nq9pj47sxgpkw97c2xrkhgcwh3zsfd2a22qiqbl4i9zf2l9yy91")))) (build-system emacs-build-system) (home-page "https://elpa.gnu.org/packages/xr.html") (synopsis "Convert string regexp to rx notation") -- cgit v1.2.3 From 98619142b8c54287136216d0008871f9170a1808 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 9 Mar 2020 17:31:00 +0100 Subject: gnu: guile-next: Update to 3.0.1 with bug-fix for crash. * gnu/packages/guile.scm (guile-3.0): Update to 3.0.1 with "guile-3.0-crash.patch". * gnu/packages/patches/guile-3.0-crash.patch: New file. * gnu/local.mk (dist_patch_DATA): Use it. --- gnu/local.mk | 1 + gnu/packages/guile.scm | 8 ++++++-- gnu/packages/patches/guile-3.0-crash.patch | 17 +++++++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/guile-3.0-crash.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index a0e013aead..99baddea92 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -977,6 +977,7 @@ dist_patch_DATA = \ %D%/packages/patches/guile-1.8-cpp-4.5.patch \ %D%/packages/patches/guile-2.2-default-utf8.patch \ %D%/packages/patches/guile-2.2-skip-oom-test.patch \ + %D%/packages/patches/guile-3.0-crash.patch \ %D%/packages/patches/guile-default-utf8.patch \ %D%/packages/patches/guile-gdbm-ffi-support-gdbm-1.14.patch \ %D%/packages/patches/guile-linux-syscalls.patch \ diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 3116f3c30a..1d9d93d774 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -292,14 +292,18 @@ without requiring the source code to be rewritten.") (package (inherit guile-2.2) (name "guile-next") ;to be renamed to "guile" - (version "3.0.0") + (version "3.0.1") (source (origin (inherit (package-source guile-2.2)) (uri (string-append "mirror://gnu/guile/guile-" version ".tar.xz")) (sha256 (base32 - "0x8ca6q1qdmk29lh12gj6ngvgn7kp79w42rxfgwrpxm9jmjqs4y9")))) + "1jakps3127h8g69ixgb4zwc8v2g29dmwql1vi3pwg30kzp8fm5nn")) + (patches + (append (search-patches "guile-3.0-crash.patch") + (origin-patches (package-source guile-2.2)))))) + (arguments (substitute-keyword-arguments (package-arguments guile-2.2) ;; XXX: On ARMv7, work around by disabling diff --git a/gnu/packages/patches/guile-3.0-crash.patch b/gnu/packages/patches/guile-3.0-crash.patch new file mode 100644 index 0000000000..510834ab57 --- /dev/null +++ b/gnu/packages/patches/guile-3.0-crash.patch @@ -0,0 +1,17 @@ +Fix crash due to: . + +diff --git a/libguile/struct.c b/libguile/struct.c +index 3dbcc71d4..ddcbe46d2 100644 +--- a/libguile/struct.c ++++ b/libguile/struct.c +@@ -139,7 +139,9 @@ set_vtable_access_fields (SCM vtable) + nfields = len / 2; + + bitmask_size = (nfields + 31U) / 32U; +- unboxed_fields = scm_gc_malloc_pointerless (bitmask_size, "unboxed fields"); ++ unboxed_fields = ++ scm_gc_malloc_pointerless (bitmask_size * sizeof (*unboxed_fields), ++ "unboxed fields"); + memset (unboxed_fields, 0, bitmask_size * sizeof(*unboxed_fields)); + + /* Update FLAGS according to LAYOUT. */ -- cgit v1.2.3 From 09844816c77caaa60f4149f99a34733966724627 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 10 Mar 2020 15:21:48 +0100 Subject: vm: Compute UUIDs truly deterministically. This is a followup to 1540075c790dfaeff52c93392f2fc63b9e23b77e. The mistake had no effect on prior Guile versions but it's visible since Guile 3.0.1 and the fix for . * gnu/system/vm.scm (operating-system-uuid): Hash a list of 'file-system-digest' values, not the 'file-system-type' procedure. --- gnu/system/vm.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 03a511cdde..d1c131ecb4 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès ;;; Copyright © 2016 Christopher Allan Webber ;;; Copyright © 2016, 2017 Leo Famulari ;;; Copyright © 2017 Mathieu Othacehe @@ -629,7 +629,8 @@ TYPE (one of 'iso9660 or 'dce). Return a UUID object." 'iso9660)) (bytevector->uuid (uint-list->bytevector - (list (hash file-system-type + (list (hash (map file-system-digest + (operating-system-file-systems os)) (- (expt 2 32) 1)) (hash (operating-system-host-name os) (- (expt 2 32) 1)) -- cgit v1.2.3 From c90c0bd53865dd76b5fa3a8a1cd42eea5a565e7a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 9 Mar 2020 14:48:21 -0400 Subject: gnu: icecat: Update to 68.6.0-guix0-preview1 [security fixes]. Includes fixes for CVE-2019-20503, CVE-2020-6805, CVE-2020-6806, CVE-2020-6807, CVE-2020-6811, CVE-2020-6812, and CVE-2020-6814. * gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update. (icecat-source): Update gnuzilla commit, base version, and hashes. * gnu/packages/patches/icecat-makeicecat.patch: Adapt to new version. --- gnu/packages/gnuzilla.scm | 12 ++++++------ gnu/packages/patches/icecat-makeicecat.patch | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index fea50625b6..c69a4e7e03 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -554,8 +554,8 @@ from forcing GEXP-PROMISE." #:system system #:guile-for-build guile))) -(define %icecat-version "68.5.0-guix0-preview1") -(define %icecat-build-id "20200211000000") ;must be of the form YYYYMMDDhhmmss +(define %icecat-version "68.6.0-guix0-preview1") +(define %icecat-build-id "20200309000000") ;must be of the form YYYYMMDDhhmmss ;; 'icecat-source' is a "computed" origin that generates an IceCat tarball ;; from the corresponding upstream Firefox ESR tarball, using the 'makeicecat' @@ -577,11 +577,11 @@ from forcing GEXP-PROMISE." "firefox-" upstream-firefox-version ".source.tar.xz")) (sha256 (base32 - "1ld6jinnln0si6p8qy93v5nzd21ckhl266vz425lwqipibwq9rsj")))) + "17qwfq9hwra8jarawy8k2sqfa6hdhwa9qk84ndr6gjvmxcy22a14")))) - (upstream-icecat-base-version "68.5.0") ; maybe older than base-version + (upstream-icecat-base-version "68.6.0") ; maybe older than base-version ;;(gnuzilla-commit (string-append "v" upstream-icecat-base-version)) - (gnuzilla-commit "2dc3c0bed6f8a41a8426ae66db92729af5c27c70") + (gnuzilla-commit "9dcb24d885eae5973eb2245b532b158c685d707a") (gnuzilla-source (origin (method git-fetch) @@ -593,7 +593,7 @@ from forcing GEXP-PROMISE." (string-take gnuzilla-commit 8))) (sha256 (base32 - "1xwr1xjs4j2i6skm8hknh37gzsd6r396n0lchbwlahig7w6z506y")))) + "1y3jmh055vmx44gsjgwxvwv3zcyvz8pc5mhgrwkzm0ybbwpp2pqi")))) (makeicecat-patch (local-file (search-patch "icecat-makeicecat.patch")))) diff --git a/gnu/packages/patches/icecat-makeicecat.patch b/gnu/packages/patches/icecat-makeicecat.patch index beaddf9437..a90d7fdee8 100644 --- a/gnu/packages/patches/icecat-makeicecat.patch +++ b/gnu/packages/patches/icecat-makeicecat.patch @@ -25,7 +25,7 @@ index 8be2362..48716f2 100755 -wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc -gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353 -gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc --echo -n 52e784f98a37624e8b207f1b23289c2c88f66dd923798cae891a586a6d94a6d1 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c - +-echo -n 2428213ceb75cb6772b3044d9c14870d1ae5b0161379aeb29248650e13761c9f firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c - - -echo Extracting Firefox tarball -tar -xf firefox-${FFVERSION}esr.source.tar.xz @@ -37,7 +37,7 @@ index 8be2362..48716f2 100755 +# wget -N https://ftp.mozilla.org/pub/mozilla.org/firefox/releases/${FFVERSION}esr/source/firefox-${FFVERSION}esr.source.tar.xz.asc +# gpg --recv-keys --keyserver keyserver.ubuntu.com 14F26682D0916CDD81E37B6D61B7B526D98F0353 +# gpg --verify firefox-${FFVERSION}esr.source.tar.xz.asc -+# echo -n 52e784f98a37624e8b207f1b23289c2c88f66dd923798cae891a586a6d94a6d1 firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c - ++# echo -n 2428213ceb75cb6772b3044d9c14870d1ae5b0161379aeb29248650e13761c9f firefox-${FFVERSION}esr.source.tar.xz |sha256sum -c - +# +# echo Extracting Firefox tarball +# tar -xf firefox-${FFVERSION}esr.source.tar.xz -- cgit v1.2.3 From 79093034b9103393a7edc90c8dce45ab1acea3f3 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 10 Mar 2020 19:46:58 +0100 Subject: gnu: guix: Update to 0984481. * gnu/packages/package-management.scm (guix): Update to 0984481. --- gnu/packages/package-management.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 23a0b2b4e8..b0457ba87a 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -110,8 +110,8 @@ ;; Note: the 'update-guix-package.scm' script expects this definition to ;; start precisely like this. (let ((version "1.0.1") - (commit "c2f9ea2b502a617bb69227d5f858eee9d4288a6a") - (revision 14)) + (commit "09844816c77caaa60f4149f99a34733966724627") + (revision 15)) (package (name "guix") @@ -127,7 +127,7 @@ (commit commit))) (sha256 (base32 - "0hg6yrqlzqiv4gmk9liqar6m9qhhn66q75jsmh86awjwq4qmvyab")) + "1fciffls6cw9zz13vig5x37r73qxc0irzyh0caimciddlksvabf7")) (file-name (string-append "guix-" version "-checkout")))) (build-system gnu-build-system) (arguments -- cgit v1.2.3 From 944e3502b133fc0e84e257c60ac36bdff9fcffd4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 10 Mar 2020 20:26:17 +0100 Subject: gnu: mercurial: Enable more tests. * gnu/packages/version-control.scm (mercurial)[arguments]: Add phase 'patch-tests'. Do not remove patched tests in the 'check' phase. --- gnu/packages/version-control.scm | 32 ++++++++++++++++++++++---------- 1 file changed, 22 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 5ea3dc415c..c289e43d94 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1332,27 +1332,39 @@ control to Git repositories.") (arguments `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* '("tests/test-extdiff.t" + "tests/test-logtoprocess.t" + "tests/test-patchbomb.t" + "tests/test-run-tests.t" + "tests/test-transplant.t") + (("/bin/sh") + (which "sh"))) + #t)) (replace 'check (lambda* (#:key tests? #:allow-other-keys) (with-directory-excursion "tests" ;; The following tests are known to fail. - (for-each (lambda (file) - (delete-file file)) - '("test-extdiff.t" + (for-each delete-file + '(;; XXX: This test calls 'run-tests.py --with-hg= + ;; `which hg`' and fails because there is no hg on + ;; PATH from before (that's why we are building it!)? "test-hghave.t" + + ;; FIXME: Why does this fail in the build container, but + ;; not in 'guix environment -C' (even without /bin/sh)? + "test-nointerrupt.t" + + ;; TODO: the fqaddr() call fails in the build + ;; container, causing these server tests to fail. "test-hgwebdir.t" "test-http-branchmap.t" - "test-logtoprocess.t" - "test-merge-combination.t" - "test-nointerrupt.t" - "test-patchbomb.t" "test-pull-bundle.t" "test-push-http.t" - "test-run-tests.t" "test-serve.t" "test-subrepo-deep-nested-change.t" - "test-subrepo-recursion.t" - "test-transplant.t")) + "test-subrepo-recursion.t")) (when tests? (invoke "./run-tests.py" ;; ‘make check’ does not respect ‘-j’. -- cgit v1.2.3 From 90799c35bd9cadaf7c28be5ea6e41ec692d5b4a4 Mon Sep 17 00:00:00 2001 From: Carl Dong Date: Tue, 10 Mar 2020 15:19:42 -0400 Subject: gnu: bitcoin-core: Update to 0.19.1. * gnu/packages/finance.scm (bitcoin-core): Update to 0.19.1. Co-Authored-By: fanquake --- gnu/packages/finance.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index 5143b500ee..89a7ffe956 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -97,7 +97,7 @@ (define-public bitcoin-core (package (name "bitcoin-core") - (version "0.19.0.1") + (version "0.19.1") (source (origin (method url-fetch) (uri @@ -105,7 +105,7 @@ version "/bitcoin-" version ".tar.gz")) (sha256 (base32 - "1172dl4b8h2a80ilk9sfgbl8yi55k6hs4b1m07nic2ls4irgkjbs")))) + "1h3w7brc18145np920vy7j5ms5hym59hvr40swdjx34fbdaisngj")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) -- cgit v1.2.3