From f3fda2980cd6c6cb1911c278c45e40efd81c5163 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 11:56:08 +0100 Subject: gnu: macchanger: Update to 1.7.0. * gnu/packages/networking.scm (macchanger): Update to 1.7.0. [source]: Update URI. --- gnu/packages/networking.scm | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index bf4bee2f87..395e75afa6 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -87,17 +87,22 @@ #:use-module (gnu packages xml) #:use-module (ice-9 match)) +;; The gnu.org ‘home’ for this GNU project is a directory listing with 1.6.0 as +;; the latest version. The author's git repository, mentioned in the 1.6.0 +;; README and otherwise legit-looking, contains a proper 1.7.0 release tarball +;; with many OUI updates. Use it, even though it's also several years old now. (define-public macchanger (package (name "macchanger") - (version "1.6.0") - (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/" - name "/" name "-" version ".tar.gz")) - (sha256 - (base32 - "1xsiivjjyhqcs6dyjcshrnxlgypvyfzacjz7gcjgl88xiw9lylri")))) + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/alobbs/macchanger/" + "releases/download/" version "/" + name "-" version ".tar.gz")) + (sha256 + (base32 "1gs5m0jxyprdp00w2qkbnaqm3ilkjz0q1gqdg4nzdm8g4xy73qns")))) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/macchanger/") (synopsis "Viewing and manipulating MAC addresses of network interfaces") -- cgit v1.2.3 From 98516883927f39073360adbdc5ab25e16248e297 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 11:41:01 +0100 Subject: gnu: python-betamax: Update to 0.8.1. * gnu/packages/python-web.scm (python-betamax): Update to 0.8.1. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index dce651246c..3b907cafcf 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1693,14 +1693,14 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients." (define-public python-betamax (package (name "python-betamax") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (pypi-uri "betamax" version)) (sha256 (base32 - "18f8v5gng3j773jlbbzx4rg1i4y2zw3m2l1zpmbvp8bh5a2q1i42")))) + "1hki1c2vs7adq7zr56wi6i5bhrkia4s2ywpv2c98ibnczz709w2v")))) (build-system python-build-system) (arguments '(;; Many tests fail because they require networking. -- cgit v1.2.3 From 86c9c0c11819f1e5ec6f821265a0492ddeaf83ee Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 10:24:35 +0100 Subject: gnu: webkitgtk: Update to 2.20.0. * gnu/packages/webkit.scm (webkitgtk): Update to 2.20.0. [arguments]: (Re-)disable WOFF2 web font support. --- gnu/packages/webkit.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 340221640c..99852aa0f3 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2015 David Hashe ;;; Copyright © 2015 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017, 2018 Mark H Weaver +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -54,14 +55,14 @@ (define-public webkitgtk (package (name "webkitgtk") - (version "2.18.6") + (version "2.20.0") (source (origin (method url-fetch) (uri (string-append "https://www.webkitgtk.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "0g5cpdijjv5hlrbi4i4dh97yrh5apnyvm90wpr9f84hgyk12r4ck")))) + "0g0an3pc2yz13gzpaysfgch2yp510gw1qcpk0xr8m6mx43vl1xjp")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no tests @@ -79,7 +80,12 @@ ;; included. More investigation is needed. For ;; now, we explicitly disable it to prevent an error ;; at configuration time. - "-DUSE_GSTREAMER_GL=OFF") + "-DUSE_GSTREAMER_GL=OFF" + + ;; XXX Disable WOFF2 ‘web fonts’. These were never + ;; supported in our previous builds. Enabling them + ;; requires building libwoff2 and possibly woff2dec. + "-DUSE_WOFF2=OFF") #:phases (modify-phases %standard-phases (add-after -- cgit v1.2.3 From 36b2cb029ecac75d651ea79cb98d883c3f50eae4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 10:36:44 +0100 Subject: gnu: webkitgtk: Use HTTPS for home page. * gnu/packages/webkitgtk.scm (webkitgtk)[home-page]: Use HTTPS. --- gnu/packages/webkit.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 99852aa0f3..df049e15a3 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -136,7 +136,7 @@ ("libxt" ,libxt) ("mesa" ,mesa) ("sqlite" ,sqlite))) - (home-page "http://www.webkitgtk.org/") + (home-page "https://www.webkitgtk.org/") (synopsis "Web content engine for GTK+") (description "WebKitGTK+ is a full-featured port of the WebKit rendering engine, -- cgit v1.2.3 From a76c205795a97d9126c23fa67a98bb741ac21798 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 14 Mar 2018 10:11:51 -0400 Subject: gnu: icecat: Relabel patches to reflect CVE assignments. Document the fact that we include fixes for CVE-2018-5127, CVE-2018-5129, CVE-2018-5130, CVE-2018-5144, CVE-2018-5145, and 5 out of 9 changesets for CVE-2018-5125. * gnu/packages/gnuzilla.scm (icecat)[source]: Relabel patches to reflect CVE assignments. --- gnu/packages/gnuzilla.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 323743d089..fb0d6c1592 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -420,22 +420,22 @@ security standards.") (mozilla-patch "icecat-bug-1350152.patch" "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj") (mozilla-patch "icecat-bug-1411708.patch" "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip") (mozilla-patch "icecat-bug-1375217.patch" "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv") - (mozilla-patch "icecat-bug-1261175.patch" "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v") - (mozilla-patch "icecat-bug-1433005.patch" "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk") - (mozilla-patch "icecat-bug-1434580.patch" "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r") + (mozilla-patch "icecat-CVE-2018-5145.patch" "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v") + (mozilla-patch "icecat-CVE-2018-5130.patch" "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk") + (mozilla-patch "icecat-CVE-2018-5125-pt1.patch" "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r") (mozilla-patch "icecat-bug-1426087.patch" "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n") (mozilla-patch "icecat-bug-1416307.patch" "54f2f7f93b30" "1ncjir16mqya37wgf6fy2rqki3vl433c4grjr3fypmlig6xfgg1l") - (mozilla-patch "icecat-bug-1430557.patch" "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92") - (mozilla-patch "icecat-bug-1416529.patch" "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk") - (mozilla-patch "icecat-bug-1324042.patch" "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx") - (mozilla-patch "icecat-bug-1428947.patch" "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x") + (mozilla-patch "icecat-CVE-2018-5127.patch" "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92") + (mozilla-patch "icecat-CVE-2018-5125-pt2.patch" "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk") + (mozilla-patch "icecat-CVE-2018-5125-pt3.patch" "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx") + (mozilla-patch "icecat-CVE-2018-5129.patch" "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x") (mozilla-patch "icecat-bug-1334465-pt1.patch" "f95c5b881442" "0iaddhf65jd9cycj4bw0b207n2jiqkr4q84jifzyqn4ygs75wdqd") (mozilla-patch "icecat-bug-1334465-pt2.patch" "8a4265c8fb41" "1d9zfdbrlw9wzr84b7pj7lxgy487lsx0kfd89287hjk0al8m6vrw") (mozilla-patch "icecat-bug-1398021.patch" "28855df568d8" "1kmq836gniplxpjnvq8lhbcc1aqi56al628r1mzdy94b5yb0lis3") (mozilla-patch "icecat-bug-1388020.patch" "e8ab2736499b" "0n28vcd65rxsyq3z22rfcfksryfndhm1i3g6ah3akg11jnagqf5v") - (mozilla-patch "icecat-bug-1437087.patch" "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz") - (mozilla-patch "icecat-bug-1437507.patch" "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig") - (mozilla-patch "icecat-bug-1440926.patch" "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg") + (mozilla-patch "icecat-CVE-2018-5125-pt4.patch" "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz") + (mozilla-patch "icecat-CVE-2018-5125-pt5.patch" "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig") + (mozilla-patch "icecat-CVE-2018-5144.patch" "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg") (mozilla-patch "icecat-bug-1430173-pt1.patch" "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i") (mozilla-patch "icecat-bug-1430173-pt2.patch" "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl"))) (modules '((guix build utils))) -- cgit v1.2.3 From 3328132b8740a005c243c6e9f4e339b6e40528d0 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 14 Mar 2018 10:15:21 -0400 Subject: gnu: icecat: Add more fixes from upstream mozilla-esr52. Includes fixes for CVE-2018-5131 and the remaining 4 out of 9 changesets for CVE-2018-5125. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository. --- gnu/packages/gnuzilla.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index fb0d6c1592..f7bdd17309 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -437,7 +437,15 @@ security standards.") (mozilla-patch "icecat-CVE-2018-5125-pt5.patch" "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig") (mozilla-patch "icecat-CVE-2018-5144.patch" "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg") (mozilla-patch "icecat-bug-1430173-pt1.patch" "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i") - (mozilla-patch "icecat-bug-1430173-pt2.patch" "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl"))) + (mozilla-patch "icecat-bug-1430173-pt2.patch" "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl") + (mozilla-patch "icecat-CVE-2018-5131.patch" "3102fbb97b32" "0kg0183v92gxjb9255xjwhxyd6gl77l9c0civx3040k975fybwlp") + (mozilla-patch "icecat-CVE-2018-5125-pt6.patch" "4904c0f4a645" "0lsq62ynksy1fbw0m87f1d741fyvrrp1vrznx5hx0l2p4g4frhv3") + (mozilla-patch "icecat-CVE-2018-5125-pt7.patch" "16b8073d5c30" "1dv94qqah1wjd3bxjvrkmjbb2f95d3d11zpm8mggdk52il575bwl") + (mozilla-patch "icecat-bug-1442127-pt1.patch" "f931f85b09da" "02s380w8a73g4w2wm810lbigh4z4rrlfy10ywwhv4lpkbk8xg7pr") + (mozilla-patch "icecat-bug-1442127-pt2.patch" "da5792b70f30" "116k9qja5ir9b3laazasp43f5jx59qq72nknmq5bn5v1ixya9r4l") + (mozilla-patch "icecat-CVE-2018-5125-pt8.patch" "62b831df8269" "109pn0hqn7s27580glv4z7qv1pmjzii9szvf3wkn97k5wybrzgkx") + (mozilla-patch "icecat-bug-1442504.patch" "8954ce68a364" "0bl65zw82bwqg0mmcri94pxqq6ibff7y5rclkzapb081p6yvf73q") + (mozilla-patch "icecat-CVE-2018-5125-pt9.patch" "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb"))) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 7e353a77836245074604173ab33c5ae10d244e8e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:22:43 +0200 Subject: gnu: texlive-latex-filecontents: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-filecontents)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 05a7cd834b..711ed8ea9e 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1037,6 +1037,7 @@ contain.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "filecontents")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0swkbxv8vg0yizadfnvrwjb4cj0pn34v9wm6v7wqq903fdav7k7q")))) -- cgit v1.2.3 From 24dbc6023b6b85fbf84db6b1cf3aceb3bd262104 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:23:42 +0200 Subject: gnu: texlive-generic-ifxetex: Declare a source file-name. * gnu/packages/tex.scm (texlive-generic-ifxetex)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 711ed8ea9e..4b1e709661 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1062,6 +1062,7 @@ overwrite existing files and letting you use @code{filecontents} / (source (origin (method svn-fetch) (uri (texlive-ref "generic" "ifxetex")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0w2xj7n0szavj329kds09q626szkc378p3w0sk022q0ln4ksz86d")))) -- cgit v1.2.3 From ca61c6b323d85e46130cc53a368e6f699951e821 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:24:29 +0200 Subject: gnu: texlive-generic-epsf: Declare a source file-name. * gnu/packages/tex.scm (texlive-generic-epsf)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 4b1e709661..0cb00537fa 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1091,6 +1091,7 @@ requires the e-TeX extensions to the TeX primitive set.") %texlive-tag "/Master/texmf-dist/" "/tex/generic/epsf")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "14w3j81ympyvg8hkk9i1xgr8a0gfnfsb2ki8qqsk5pa051za1xcy")))) -- cgit v1.2.3 From 88e11022db4af72a0b33a0af7c71230234ce5e17 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:25:06 +0200 Subject: gnu: texlive-latex-fancyvrb: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-fancyvrb)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 0cb00537fa..f0f0955949 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1124,6 +1124,7 @@ users, via its Plain TeX version.)") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "fancyvrb")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "03l7140y031rr14h02i4z9zqsfvrbn7wzwxbjsrjcgrk6sdr71wv")))) -- cgit v1.2.3 From f73020735cc9e7d02d1f77eeb3af1d2fae090b56 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:25:50 +0200 Subject: gnu: texlive-latex-graphics: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-graphics)[source]: Declare a source file-name. [native-inputs]: Declare a source file-name for downloaded native-inputs. --- gnu/packages/tex.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index f0f0955949..ae3c7b3abd 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1152,6 +1152,7 @@ verbatim source).") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "graphics")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "07azyn0b1s49vbdlr6dmygrminxp72ndl24j1091hiiccvrjq3xc")))) @@ -1184,6 +1185,9 @@ verbatim source).") (uri (git-reference (url "https://github.com/latex3/graphics-cfg.git") (commit "19d1238af17df376cd46333b229579b0f7f3a41f"))) + (file-name (string-append "graphics-cfg-" + (number->string %texlive-revision) + "-checkout")) (sha256 (base32 "12kbgbm52gmmgn8zajb74s8n5rvnxcfdvs3iyj8vcw5vrsw5i6mh")))) @@ -1195,6 +1199,9 @@ verbatim source).") %texlive-tag "/Master/texmf-dist/" "/tex/latex/graphics-def")) (revision %texlive-revision))) + (file-name (string-append "graphics-def-" + (number->string %texlive-revision) + "-checkout")) (sha256 (base32 "0gi4qv6378nl84s8n1yx3hjqvv7r4lza7hpbymbl5rzwgw8qrnyb")))))) -- cgit v1.2.3 From 19389bcdc23c8c111872ad6d99ef9adf4495f9b4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:30:06 +0200 Subject: gnu: texlive-latex-xcolor: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-xcolor)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index ae3c7b3abd..331e1ed80c 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1223,6 +1223,7 @@ keyval, and lscape.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "xcolor")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "01n613s7bcrd2n4jfawm0k4nn2ny3aaifp2jjfif3lz4sbv31494")))) -- cgit v1.2.3 From 7dea311973430a25eafc0ecb96d653a99659026c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:30:47 +0200 Subject: gnu: texlive-latex-oberdiek: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-oberdiek)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 331e1ed80c..2bf2948fcf 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1277,6 +1277,7 @@ pdf and HTML backends. The package is distributed with the @code{backref} and (source (origin (method svn-fetch) (uri (texlive-ref "latex" "oberdiek")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0aswvsxgsn709xmvpcg50d2xl7vcy1ckdxb9c1cligqqfjjvviqf")))) -- cgit v1.2.3 From f8340ab143b214f94c19fb010b135dbae5e01f10 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:31:22 +0200 Subject: gnu: texlive-latex-tools: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-tools)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 2bf2948fcf..11d0a1586a 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1308,6 +1308,7 @@ arrows; record information about document class(es) used; and many more.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "tools")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "052a0pch2k5zls5jlay9xxcf93rw3i60a2x28y3ip3rhbsv3xgiz")))) -- cgit v1.2.3 From a26207f8794f0cafd0ebd18ed3a6eb8aa0746202 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:32:06 +0200 Subject: gnu: texlive-latex-url: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-url)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 11d0a1586a..b8d08b4719 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1338,6 +1338,7 @@ xr, and xspace.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/url")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "184s2543cwia5l7iibhlkl1ffbncfhjpv5p56zq0c15by5sghlac")))) -- cgit v1.2.3 From f4a39a5b2fbe81e994dcf73b647db197cefd5a53 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:32:50 +0200 Subject: gnu: texlive-latex-l3kernel: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-l3kernel)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index b8d08b4719..06282b01d4 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1374,6 +1374,7 @@ of file names.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "l3kernel")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0r0wfk594j8wkdqhh21haimwsfq8x5jch4ldm21hkzk5dnmvpbg6")))) -- cgit v1.2.3 From b749aa98807b980040e478a498af9a3511b92241 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:33:25 +0200 Subject: gnu: texlive-latex-l3packages: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-l3packages)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 06282b01d4..439e7a2ec0 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1398,6 +1398,7 @@ that the LaTeX3 conventions can be used with regular LaTeX 2e packages.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "l3packages")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "16jplkvzdysfssijq9l051nsks65c2nrarsl17k8gjhc28yznj8y")))) -- cgit v1.2.3 From 634a4a7f14eb587e5279400594be71a9c67b72cd Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:34:01 +0200 Subject: gnu: texlive-latex-fontspec: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-fontspec)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 439e7a2ec0..2fabbdeba1 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1446,6 +1446,7 @@ programming tools and kernel sup­port. Packages provided in this release are: (source (origin (method svn-fetch) (uri (texlive-ref "latex" "fontspec")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1rx43y5xmjqvc27pjdnmqwp4pcw3czcfd6nfpmzc1gnqfl1hlc0q")))) -- cgit v1.2.3 From 01d79c306ae5da6e7ed84f964f734d44f3de91ad Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:35:34 +0200 Subject: gnu: texlive-luatex-lualibs: Include version in source file-name. * gnu/packages/tex.scm (texlive-luatex-lualibs)[source]: Include version in the source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 2fabbdeba1..a64cb2a7ae 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1477,6 +1477,7 @@ the l3kernel and xparse bundles from the LaTeX 3 development team.") (uri (string-append "https://github.com/lualatex/lualibs/" "releases/download/v" version "/lualibs.zip")) + (file-name (string-append name "-" version ".zip")) (sha256 (base32 "1xx9blvrmx9hyhrl345lpai9m6xxnw997261a1ahn1bm5r2j5fqy")))) -- cgit v1.2.3 From 320c771ade32da53ec9b5131d4c3d335c21f81af Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:36:16 +0200 Subject: gnu: texlive-latex-amsmath: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-amsmath)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index a64cb2a7ae..12c8722df2 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1510,6 +1510,7 @@ this bundle for use independent of ConTeXt.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "amsmath")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "178ywjpdlv78qmfzqdyn6gy14620zjsn2q9wap76fbr9s4hw6dba")))) -- cgit v1.2.3 From 43059ed01a7123372919b4f319efb81f4bfb338b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:36:46 +0200 Subject: gnu: texlive-latex-amscls: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-amscls)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 12c8722df2..2b2961ddd7 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1539,6 +1539,7 @@ definitions.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "amscls")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0jmcr37mcdi7drczppvr6lmz5d5yd9m67ii79gp2nglg1xpw934j")))) -- cgit v1.2.3 From 8732493e75c59a03cecf92ffa028292dae6b289f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:37:16 +0200 Subject: gnu: texlive-latex-babel: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-babel)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 2b2961ddd7..78d52f592b 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1563,6 +1563,7 @@ distribution.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "babel")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1n3i5adsyy7jw0imnzrm2i8wkf73i3mjk9h3ic8cb9cd19i4r9r3")))) -- cgit v1.2.3 From 51bffe791ba26b12f30016fe8bd6446d7f388de9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:38:05 +0200 Subject: gnu: texlive-latex-cyrillic: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-cyrillic)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 78d52f592b..459d051c15 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1620,6 +1620,7 @@ for Canadian and USA text.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "cyrillic")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1mdhl35hwas68ki56qqngzar37dwv4mm64l2canihr255bz34lbv")))) -- cgit v1.2.3 From b5b10f3b3bb765e7339b844cb1b8cbc07e06c6c5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:38:57 +0200 Subject: gnu: texlive-latex-psnfss: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-psnfss)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 459d051c15..4f44b83838 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1643,6 +1643,7 @@ language that is written in a Cyrillic alphabet.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "psnfss")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1920dcq8613yzprasbg80fh4fcjcidvvl54wkx438nimyxcri7qz")))) -- cgit v1.2.3 From 681b579d6d64672307d8538be62de5e1ec1c027a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:40:33 +0200 Subject: gnu: texlive-latex-filemod: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-filemod)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 4f44b83838..ff21f3f734 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -1987,6 +1987,7 @@ without affecting the structure of the list (this works for @code{itemize} and %texlive-tag "/Master/texmf-dist/" "/tex/latex/filemod")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0vpxilfw69xv78f03g0j0zw0bw4qcn36whqp8phcq48qk1ax2kr2")))) -- cgit v1.2.3 From 23ae6e65fc7f44daff50361735b4731ba5eee70e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:41:24 +0200 Subject: gnu: texlive-latex-natbib: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-natbib)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index ff21f3f734..3e3f98ba60 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2047,6 +2047,7 @@ classes of systems.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "natbib")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0aqliq0nwblxyrzhwhv77pnmk7qh2y3prgq7z7qhwcbgz5kisld7")))) -- cgit v1.2.3 From a74ac06bb5d54a76a1288663a20a7a98010cb349 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:42:16 +0200 Subject: gnu: texlive-latex-seminar: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-seminar)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 3e3f98ba60..144f475aec 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2135,6 +2135,7 @@ re-processing.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/seminar")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0y4i651b75y6006n03x8n86bsqvjsailvvz9bhzy51dzsznqidq0")))) -- cgit v1.2.3 From 70a71d19c8711df60b57204a88132afaf71f3f35 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:42:58 +0200 Subject: gnu: texlive-latex-trimspaces: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-trimspaces)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 144f475aec..39f1ddeee1 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2159,6 +2159,7 @@ recent classes such as powerdot or beamer, both of which are tuned to (source (origin (method svn-fetch) (uri (texlive-ref "latex" "trimspaces")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0da00lb32am4g63mn96625wg48p3pj3spx79lajrk17d549apwqa")))) -- cgit v1.2.3 From 88ae1921d81ee9904dc104878f6fb651e750b24c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:44:37 +0200 Subject: gnu: texlive-tex-texinfo: Declare a source file-name. * gnu/packages/tex.scm (texlive-tex-texinfo)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 39f1ddeee1..8e0d46c404 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2507,6 +2507,7 @@ situations where longtable has problems.") %texlive-tag "/Master/texmf-dist/" "/tex/texinfo")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "09zj2w3lx0y6i2syfjjgizahf86z301dw8p37ln6syfhqhzqdz46")))) -- cgit v1.2.3 From de4eb4d1c96057d6433d943342b7ab34368b5e68 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:45:12 +0200 Subject: gnu: texlive-latex-anysize: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-anysize)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 8e0d46c404..9f57bdd861 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2571,6 +2571,7 @@ does not affect @code{\\tt}, @code{\\texttt}, etc.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/anysize")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "19khwqjlvznc955sijhww3c4zbb0053rvzwv9nz738qknq7y18vb")))) -- cgit v1.2.3 From 72d5adf4d82e6cab1034bb38a836857725020148 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:45:44 +0200 Subject: gnu: texlive-latex-appendix: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-appendix)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 9f57bdd861..8c4b9226b4 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2601,6 +2601,7 @@ considered obsolete; alternatives are the @code{typearea} package from the (source (origin (method svn-fetch) (uri (texlive-ref "latex" "appendix")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0rxfpr8vq3brwx5rc7qn91ixlp9zva4zrms8a579fqa1g5yva7vg")))) -- cgit v1.2.3 From af8aa1053a80f8333b2f5a880d8d36852fa4bdc8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:46:19 +0200 Subject: gnu: texlive-latex-changebar: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-changebar)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 8c4b9226b4..ba686a582a 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2624,6 +2624,7 @@ command.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "changebar")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1ik4m8pzfsn1grlda6fniqqfwmgj7rfxwg63jdw0p0qv002vc7ik")))) -- cgit v1.2.3 From 4439c1dedaafb1370f3f7b4adad4529f4a570872 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:46:54 +0200 Subject: gnu: texlive-latex-colortbl: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-colortbl)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index ba686a582a..805ac76c37 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2681,6 +2681,7 @@ copy-and-paste functions work properly.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "colortbl")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "190pmq8la2rq07xry8bn8z8yywzxv6fqyqaj7yjfj5rgw6x0mas8")))) -- cgit v1.2.3 From 62ee46b9a251ef9ee5e9793df451a3cf16d5c085 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:47:39 +0200 Subject: gnu: texlive-latex-fancybox: Declare a source file-name. * gnu/pacakges/tex.scm (texlive-latex-fancybox)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 805ac76c37..0a6b858e74 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2705,6 +2705,7 @@ tables to be coloured.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/fancybox")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0smmnaad2q8qwicay1frri990lv65l0k8cwzsvdsyp3jk8kp042w")))) -- cgit v1.2.3 From e89d5cf4fc51ccef65d2a559ebb2290b6e38a0c2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:49:31 +0200 Subject: gnu: texlive-latex-fancyhdr: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-fancyhdr)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 0a6b858e74..b1bca0f24f 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2740,6 +2740,7 @@ floats, center, flushleft, and flushright, lists, and pages.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/fancyhdr")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "04h430agf8aj7ziwyb46xpk95c605rjk1wzhr63m6ylipihidlgw")))) -- cgit v1.2.3 From 4fd0a59108b64d7c25537a52705fe3bbb417b89d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:50:05 +0200 Subject: gnu: texlive-latex-float: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-float)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index b1bca0f24f..0cff925f0b 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2770,6 +2770,7 @@ would automatically change the heading style in use).") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "float")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0nbl7wylkv22fcdv4p8byhhj575fli6jnqjpkhrkbv8dzwah84nq")))) -- cgit v1.2.3 From dae1d9e43627ac478ef9eb2e2f7a69fe880e40d6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:50:37 +0200 Subject: gnu: texlive-latex-footmisc: Declare a source file-name. * gnu/packages/tex.smc (texlive-latex-footmisc)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 0cff925f0b..5d5d3a6648 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2794,6 +2794,7 @@ with @code{\\floatplacement{figure}{H}}.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "footmisc")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "03x61wwql8nh6zrqiiiq3rb0x7m3pn48c606zapy19y21fybwdxs")))) -- cgit v1.2.3 From aeb135e3a1b6addb77e5149e306ac854bb60b60d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:51:09 +0200 Subject: gnu: texlive-latex-listings: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-listings)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 5d5d3a6648..5d83b5a3c0 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2818,6 +2818,7 @@ footnotes with symbols rather than numbers.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "listings")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1nsn9wp3wl12b36c0sqrim33lf33cr5wky0h4ncnw8lvqgm7h8wf")))) -- cgit v1.2.3 From aa499191b8e6672c6e45f3f6a9ab94712448940a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:51:48 +0200 Subject: gnu: texlive-latex-jknapltx: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-jknapltx)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 5d83b5a3c0..035c47a8bc 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2846,6 +2846,7 @@ styles. Support for @code{hyperref} is provided.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/jknapltx")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0m034x72f2g07icr50gacyxfb9g1lz2rmqh4kqr1qjb421x2kds9")))) -- cgit v1.2.3 From ca816eb3caa96a6cd4493c0a17a2881113b5844c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:53:50 +0200 Subject: gnu: texlive-fonts-ec: Declare a source file-name. * gnu/packages/tex.scm (texlive-fonts-ec)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 035c47a8bc..8bb172aedc 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2885,6 +2885,7 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.") %texlive-tag "/Master/texmf-dist/" "/fonts/source/jknappen/ec/")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "12av65fbz9xiashm09c9m1fj1mijxls5xspd7652ry1n5s0nixy4")))) -- cgit v1.2.3 From 6f2442a1fdb09d5982e163f1e87426ffc9f32d1d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:56:14 +0200 Subject: gnu: texlive-fonts-ec: Use 'invoke'. * gnu/packages/tex.scm (texlive-fonts-ec)[arguments]: Use 'invoke' in place of 'system*'. --- gnu/packages/tex.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 8bb172aedc..828c70df26 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2913,13 +2913,13 @@ in SGML; use maths minus in text as appropriate; simple Young tableaux.") (mkdir "build") (every (lambda (font) (format #t "building font ~a\n" font) - (zero? (system* "mf" "-progname=mf" - "-output-directory=build" - (string-append "\\" - "mode:=ljfour; " - "mag:=1; " - "batchmode; " - "input " (basename font ".mf"))))) + (invoke "mf" "-progname=mf" + "-output-directory=build" + (string-append "\\" + "mode:=ljfour; " + "mag:=1; " + "batchmode; " + "input " (basename font ".mf")))) (find-files "." "[0-9]+\\.mf$")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) -- cgit v1.2.3 From e26de9c928c996c157a3067b41836950baed7f02 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 20:59:25 +0200 Subject: gnu: texlive-fonts-rsfs: Declare a source file-name. * gnu/packages/tex.scm (texlive-fonts-rsfs)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 828c70df26..aec74912a3 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2967,6 +2967,7 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt")))) %texlive-tag "/Master/texmf-dist/" "/fonts/source/public/rsfs/")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0r12pn02r4a955prcvq0048nifh86ihlcgvw3pppqqvfngv34l5h")))) -- cgit v1.2.3 From d5fb4a3a9f202e0246e93a0a5537c72a92aa319e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:00:29 +0200 Subject: gnu: texlive-fonts-rsfs: Use 'invoke'. * gnu/packages/tex.scm (texlive-fonts-rsfs)[arguments]: Use 'invoke' in place of 'system*'. --- gnu/packages/tex.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index aec74912a3..da55e52b33 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -2995,13 +2995,13 @@ texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt")))) (mkdir "build") (every (lambda (font) (format #t "building font ~a\n" font) - (zero? (system* "mf" "-progname=mf" - "-output-directory=build" - (string-append "\\" - "mode:=ljfour; " - "mag:=1; " - "batchmode; " - "input " (basename font ".mf"))))) + (invoke "mf" "-progname=mf" + "-output-directory=build" + (string-append "\\" + "mode:=ljfour; " + "mag:=1; " + "batchmode; " + "input " (basename font ".mf")))) (find-files "." "[0-9]+\\.mf$")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) -- cgit v1.2.3 From 2678a63b23c98cc0bc0edcdad072cfecadf16032 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:02:03 +0200 Subject: gnu: texlive-latex-eso-pic: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-eso-pic)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index da55e52b33..93efc5dddc 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3037,6 +3037,7 @@ one of the packages @code{calrsfs} and @code{mathrsfs}.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "eso-pic")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1xvmms28mvvfpks9x7lfya2xhh5k8jy3qnlih1mzcnf156xnb89z")))) -- cgit v1.2.3 From 84d636431420dd8a2a4868a2fdc8549f626f7c5f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:02:42 +0200 Subject: gnu: texlive-latex-eepic: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-eepic)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 93efc5dddc..a7bed5cfaa 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3062,6 +3062,7 @@ routine, which may be used to place the output at fixed positions. The %texlive-tag "/Master/texmf-dist/" "/tex/latex/eepic")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1c68gvh021pvybg07apsd2xhq2ljbg80kq94wh71drdga3c2zqjw")))) -- cgit v1.2.3 From 6a9198046d3a0aa5bbb01bb9ab0bd7c89a936a38 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:03:36 +0200 Subject: gnu: texlive-latex-multirow: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-multirow)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index a7bed5cfaa..16f5419a0a 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3131,6 +3131,7 @@ in the form @code{key=value} are available, for example: (source (origin (method svn-fetch) (uri (texlive-ref "latex" "multirow")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0qlxy47f1f8plgch3jqfsnrdgpyz20sz46yp33i2jwvf9hvfczf0")))) -- cgit v1.2.3 From b2aef7219c754ee2fc2279230748a4fb1c2f79e1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:04:10 +0200 Subject: gnu: texlive-latex-overpic: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-overpic)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 16f5419a0a..936bcbc018 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3156,6 +3156,7 @@ entry at the \"natural\" width of its text.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/overpic")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0m29q9qdb00558b7g2i7iw6w62n5s46yx81j8m99qkv77magk4fm")))) -- cgit v1.2.3 From 7372ce185f6d4984d7a4253e5139ec9dcb0212b7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:04:44 +0200 Subject: gnu: texlive-latex-pdfpages: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-pdfpages)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 936bcbc018..b953e7b999 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3222,6 +3222,7 @@ designed class) helps alleviate this untidiness.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "pdfpages")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "06p5smfq66559ppdnmkl3hp8534x84ywbscimsiir4gllpya3i9h")))) -- cgit v1.2.3 From 19835372a2676bac4def8021a08f6412d68554b3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:05:23 +0200 Subject: gnu: texlive-fonts-stmaryrd: Declare a source file-name. * gnu/packages/tex.scm (texlive-fonts-stmaryrd)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index b953e7b999..5d3a476d64 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3246,6 +3246,7 @@ use this package to insert PostScript files, in addition to PDF files.") (source (origin (method svn-fetch) (uri (texlive-ref "fonts" "stmaryrd")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "08pn4ca3vl6qm9l3wm5h5iyjsrg411kkm1yana329xwg2j14s9n6")))) -- cgit v1.2.3 From e1834df6b600655503ad4424e0ae24fb8d503158 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:06:00 +0200 Subject: gnu: texlive-latex-subfigure: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-subfigure)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 5d3a476d64..475300b293 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3279,6 +3279,7 @@ the whole font.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "subfigure")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "15spcl5wb7w269qd6y596vp4yi8sa5ppcx8w4z2i9kyp02r3a0yb")))) -- cgit v1.2.3 From d57e5d412849ad5016088726747cbcbdf8ea1d91 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:06:53 +0200 Subject: gnu: texlive-latex-threeparttable: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-threeparttable)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 475300b293..fa644830bc 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3335,6 +3335,7 @@ according to the natural width of the widest cell in the column.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/threeparttable")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "10vy9k150w2lviw8h22s2mcykff38xci653m5823s2vv44pwbmzq")))) -- cgit v1.2.3 From 0475e35c59eac4ad3f2efa8d8c25066dfea302f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:09:13 +0200 Subject: gnu: texlive-latex-titlesec: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-titlesec)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index fa644830bc..0973619bf5 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3543,6 +3543,7 @@ of ink traps which typify the Kurier font.") %texlive-tag "/Master/texmf-dist/" "/tex/latex/titlesec")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "04nmkhqx6jxcxx9a30zbcd5smxi5fd0cbp132bki7fnvhspnhg21")))) -- cgit v1.2.3 From de20fd6a3aedf0f2d75d02d49573477a909dca19 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:09:56 +0200 Subject: gnu: texlive-latex-lh: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-lh)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 0973619bf5..324161c4df 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3604,6 +3604,7 @@ now contains a package @code{fix-cm},f which performs the task of (source (origin (method svn-fetch) (uri (texlive-ref "latex" "lh")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "00gdiwh3sfhh1iimjhpja7lm7k4vzqzql2irgwnpz94qvh25zwi5")))) -- cgit v1.2.3 From b4bb2750ffa26d73a2f262561d28dc52d173ee71 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:10:27 +0200 Subject: gnu: texlive-metapost: Declare a source file-name. * gnu/packages/tex.scm (texlive-metapost)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 324161c4df..e7e7f19020 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3635,6 +3635,7 @@ OT2 encoded fonts, CM bright shaped fonts and Concrete shaped fonts.") %texlive-tag "/Master/texmf-dist/" "/metapost")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "03nvjddffiz796wll6axzmgfvynyciy2mqamv20qx252w71vwkwd")))) -- cgit v1.2.3 From 2cc9c011e856582e3da61d909885f03a4a7902e0 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:12:39 +0200 Subject: gnu: texlive-latex-wasysym: Declare a source file-name. * gnu/packages/tex.scm (texlive-latex-wasysym)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index e7e7f19020..5871383d09 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3719,6 +3719,7 @@ get a narrower “natural” width.") (source (origin (method svn-fetch) (uri (texlive-ref "latex" "wasysym")) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1sgwbfwjjf70g54hh93gsd9jp9nm67w6n74x9d72a56n07jbk5hv")))) -- cgit v1.2.3 From 66e765a063f17353188670a97d818db600fd8c37 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:13:34 +0200 Subject: gnu: texlive-generic-pdftex: Declare a source file-name. * gnu/packages/tex.scm (texlive-generic-pdftex)[source]: Declare a source file-name. --- gnu/packages/tex.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 5871383d09..30033e1041 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3874,6 +3874,7 @@ e-TeX.") %texlive-tag "/Master/texmf-dist/" "/tex/generic/pdftex")) (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0k68zmqzs4qvrqxdwsrawbjb14hxqjfamq649azvai0jjxdpkljd")))) -- cgit v1.2.3 From dac6095d7ecec7f9fa6e270cbe86f14636c2292d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 14 Mar 2018 21:15:14 +0200 Subject: gnu: python2-elib.intl: Declare a source file-name. * gnu/packages/python.scm (python2-elib.intl)[source]: Declare a source file-name. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 106c040bf8..135ea29706 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3806,6 +3806,7 @@ Python's distutils.") (uri (git-reference (url "https://github.com/dieterv/elib.intl.git") (commit "d09997cfef"))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0y7vzff9xgbnaay7m0va1arl6g68ncwrvbgwl7jqlclsahzzb09d")))) -- cgit v1.2.3 From dba52a2bcbbc11887df47162b4dd16b46346e362 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 21:33:18 +0100 Subject: gnu: bind: Update to 9.12.1. * gnu/packages/dns.scm (isc-bind): Update to 9.12.1. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index b0f6ddaec2..08304b0c4c 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -99,7 +99,7 @@ and BOOTP/TFTP for network booting of diskless machines.") (define-public isc-bind (package (name "bind") - (version "9.12.0") + (version "9.12.1") (source (origin (method url-fetch) (uri (string-append @@ -107,7 +107,7 @@ and BOOTP/TFTP for network booting of diskless machines.") version ".tar.gz")) (sha256 (base32 - "10iwkghl5g50b7wc17bsb9wa0dh2gd57bjlk6ynixhywz6dhx1r9")))) + "043mjcw405qa0ghm5dkhfsq35gsy279724fz3mjqpr1mbi14dr0n")))) (build-system gnu-build-system) (outputs `("out" "utils")) (inputs -- cgit v1.2.3 From 88cd7bbd3dc8ecb6b02435338eff1524ad7154ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Mar 2018 11:34:57 +0100 Subject: services: 'shepherd-service-type' now accepts a default value. * gnu/services/shepherd.scm (shepherd-service-type): Add a second form with an additional 'default' parameter. --- gnu/services/shepherd.scm | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/services/shepherd.scm b/gnu/services/shepherd.scm index f7c6983cb0..000e85eb86 100644 --- a/gnu/services/shepherd.scm +++ b/gnu/services/shepherd.scm @@ -104,14 +104,24 @@ ;; objects. (service shepherd-root-service-type '())) -(define-syntax-rule (shepherd-service-type service-name proc) - "Return a denoting a simple shepherd service--i.e., the type -for a service that extends SHEPHERD-ROOT-SERVICE-TYPE and nothing else." - (service-type - (name service-name) - (extensions - (list (service-extension shepherd-root-service-type - (compose list proc)))))) +(define-syntax shepherd-service-type + (syntax-rules () + "Return a denoting a simple shepherd service--i.e., the type +for a service that extends SHEPHERD-ROOT-SERVICE-TYPE and nothing else. When +DEFAULT is given, use it as the service's default value." + ((_ service-name proc default) + (service-type + (name service-name) + (extensions + (list (service-extension shepherd-root-service-type + (compose list proc)))) + (default-value default))) + ((_ service-name proc) + (service-type + (name service-name) + (extensions + (list (service-extension shepherd-root-service-type + (compose list proc)))))))) (define %default-imported-modules ;; Default set of modules imported for a service's consumption. -- cgit v1.2.3 From bb3062ad6290223ea24144ca8aa1f4cddac8f9be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Mar 2018 11:37:18 +0100 Subject: services: Add 'virtual-terminal'. Fixes . Suggested by Danny Milosavljevic . * gnu/services/base.scm (unicode-start): Remove. (virtual-terminal-service-type): New variable. (console-font-shepherd-services): Remove 'modules'; remove call to 'unicode-start'. Add 'virtual-terminal' to 'requirement'. (mingetty-shepherd-service, kmscon-service-type): Likewise. (%base-services): Add 'virtual-terminal-service-type'. * gnu/system/install.scm (%installation-services): Likewise. --- gnu/services/base.scm | 67 ++++++++++++++++++++++++++++---------------------- gnu/system/install.scm | 4 ++- 2 files changed, 40 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 343123a377..be1bfce578 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -62,6 +62,7 @@ %default-console-font console-font-service-type console-font-service + virtual-terminal-service-type udev-configuration udev-configuration? @@ -665,22 +666,27 @@ to add @var{device} to the kernel's entropy pool. The service will fail if "Return a service that sets the host name to @var{name}." (service host-name-service-type name)) -(define (unicode-start tty) - "Return a gexp to start Unicode support on @var{tty}." - (with-imported-modules '((guix build syscalls)) - #~(let* ((fd (open-fdes #$tty O_RDWR)) - (termios (tcgetattr fd))) - (define (set-utf8-input termios) - (set-field termios (termios-input-flags) - (logior (input-flags IUTF8) - (termios-input-flags termios)))) - - (tcsetattr fd (tcsetattr-action TCSAFLUSH) - (set-utf8-input termios)) - - ;; TODO: ioctl(fd, KDSKBMODE, K_UNICODE); - (close-fdes fd) - #t))) +(define virtual-terminal-service-type + ;; Ensure that virtual terminals run in UTF-8 mode. This is the case by + ;; default with recent Linux kernels, but this service allows us to ensure + ;; this. This service must start before any 'term-' service so that newly + ;; created terminals inherit this property. See + ;; for a discussion. + (shepherd-service-type + 'virtual-terminal + (lambda (utf8?) + (shepherd-service + (documentation "Set virtual terminals in UTF-8 module.") + (provision '(virtual-terminal)) + (requirement '(root-file-system)) + (start #~(lambda _ + (call-with-output-file + "/sys/module/vt/parameters/default_utf8" + (lambda (port) + (display 1 port))) + #t)) + (stop #~(const #f)))) + #t)) ;default to UTF-8 (define console-keymap-service-type (shepherd-service-type @@ -719,8 +725,6 @@ to add @var{device} to the kernel's entropy pool. The service will fail if (requirement (list (symbol-append 'term- (string->symbol tty)))) - (modules '((guix build syscalls) ;for 'tcsetattr' - (srfi srfi-9 gnu))) ;for 'set-field' (start #~(lambda _ ;; It could be that mingetty is not fully ready yet, ;; which we check by calling 'ttyname'. @@ -732,16 +736,18 @@ to add @var{device} to the kernel's entropy pool. The service will fail if (usleep 500) (loop (- i 1)))) - (and #$(unicode-start device) - ;; 'setfont' returns EX_OSERR (71) when an - ;; KDFONTOP ioctl fails, for example. Like - ;; systemd's vconsole support, let's not treat - ;; this as an error. - (case (status:exit-val - (system* #$(file-append kbd "/bin/setfont") - "-C" #$device #$font)) - ((0 71) #t) - (else #f))))) + ;; Assume the VT is already in UTF-8 mode, thanks to + ;; the 'virtual-terminal' service. + ;; + ;; 'setfont' returns EX_OSERR (71) when an + ;; KDFONTOP ioctl fails, for example. Like + ;; systemd's vconsole support, let's not treat + ;; this as an error. + (case (status:exit-val + (system* #$(file-append kbd "/bin/setfont") + "-C" #$device #$font)) + ((0 71) #t) + (else #f)))) (stop #~(const #t)) (respawn? #f))))) tty+font)) @@ -1093,7 +1099,7 @@ the tty to run, among other things." ;; Since the login prompt shows the host name, wait for the 'host-name' ;; service to be done. Also wait for udev essentially so that the tty ;; text is not lost in the middle of kernel messages (XXX). - (requirement '(user-processes host-name udev)) + (requirement '(user-processes host-name udev virtual-terminal)) (start #~(make-forkexec-constructor (list #$(file-append mingetty "/sbin/mingetty") @@ -2034,7 +2040,7 @@ This service is not part of @var{%base-services}." (shepherd-service (documentation "kmscon virtual terminal") - (requirement '(user-processes udev dbus-system)) + (requirement '(user-processes udev dbus-system virtual-terminal)) (provision (list (symbol-append 'term- (string->symbol virtual-terminal)))) (start #~(make-forkexec-constructor #$kmscon-command)) (stop #~(make-kill-destructor))))))) @@ -2044,6 +2050,7 @@ This service is not part of @var{%base-services}." ;; Convenience variable holding the basic services. (list (login-service) + (service virtual-terminal-service-type) (service console-font-service-type (map (lambda (tty) (cons tty %default-console-font)) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index 97f5abe0b6..920d215272 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -214,7 +214,9 @@ You have been warned. Thanks for being so brave.\x1b[0m (define bare-bones-os (load "examples/bare-bones.tmpl")) - (list (mingetty-service (mingetty-configuration + (list (service virtual-terminal-service-type) + + (mingetty-service (mingetty-configuration (tty "tty1") (auto-login "root"))) -- cgit v1.2.3 From 04953dca414788433f039e1844a6cc1c8f37be5f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 15:44:04 -0500 Subject: gnu: Add flatbuffers. * gnu/packages/serialization.scm (flatbuffers): New variable. --- gnu/packages/serialization.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 9bbac3ac22..fd61462776 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2017 Frederick M. Muriithi ;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -411,3 +412,28 @@ JSON's ability, but serializes to a binary format which is smaller and faster to generate and parse. The two primary functions are @code{cbor.loads} and @code{cbor.dumps}.") (license license:asl2.0))) + +(define-public flatbuffers + (package + (name "flatbuffers") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/google/flatbuffers/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "0blc978wc5h91662vai24xj92c3bx56y6hzid90qva7il302jl64")))) + (build-system cmake-build-system) + (arguments + '(#:configure-flags + (list (string-append "-DCMAKE_INSTALL_LIBDIR=" + (assoc-ref %outputs "out") "/lib") + "-DCMAKE_BUILD_TYPE=Release"))) + (home-page "https://google.github.io/flatbuffers/") + (synopsis "Memory-efficient serialization library") + (description "FlatBuffers is a cross platform serialization library for C++, +C#, C, Go, Java, JavaScript, PHP, and Python. It was originally created for +game development and other performance-critical applications.") + (license license:asl2.0))) -- cgit v1.2.3 From 5f3616d612273e75334a37c3c94dec490271c7a5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 15:55:24 -0500 Subject: gnu: Add python-plotly. * gnu/packages/graph.scm (python-plotly, python2-plotly): New variables. --- gnu/packages/graph.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 19c9b2269b..6a5e0e753f 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017, 2018 Ricardo Wurmus +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,7 +34,10 @@ #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages python-web) #:use-module (gnu packages statistics) + #:use-module (gnu packages time) #:use-module (gnu packages xml)) (define-public igraph @@ -199,3 +203,34 @@ objects from the @code{graph} package.") represented by horizontal lines, and edges are represented by vertical lines.") (license license:expat)))) + +(define-public python-plotly + (package + (name "python-plotly") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "plotly" version)) + (sha256 + (base32 + "0n18116jz6bl5n9cq23vabv1gcbh1x3yficdnfq55v0z4cwy0zlf")))) + (build-system python-build-system) + (arguments + '(#:tests? #f)) ; The tests are not distributed in the release + (propagated-inputs + `(("python-decorator" ,python-decorator) + ("python-nbformat" ,python-nbformat) + ("python-pytz" ,python-pytz) + ("python-requests" ,python-requests) + ("python-six" ,python-six))) + (home-page "https://plot.ly/python/") + (synopsis "Interactive plotting library for Python") + (description "Plotly's Python graphing library makes interactive, +publication-quality graphs online. Examples of how to make line plots, scatter +plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, +subplots, multiple-axes, polar charts, and bubble charts. ") + (license license:expat))) + +(define-public python2-plotly + (package-with-python2 python-plotly)) -- cgit v1.2.3 From 3d60f4265e3f89151aaf45bd238ce1c2c89790b5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:11:25 -0500 Subject: gnu: Add r-maps. * gnu/packages/geo.scm (r-maps): New variable. --- gnu/packages/geo.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 9014cc3206..3af196bed3 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Ricardo Wurmus ;;; Copyright © 2018 Arun Isaac +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +27,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (guix build-system scons) + #:use-module (guix build-system r) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -490,3 +492,22 @@ development.") construct common SQL queries, or craft your own SQL queries.") (home-page "https://www.gaia-gis.it/fossil/spatialite_gui/index") (license license:gpl3+))) + +(define-public r-maps + (package + (name "r-maps") + (version "3.2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "maps" version)) + (sha256 + (base32 + "0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/maps") + (synopsis "Draw geographical maps") + (description "This package provies an R module for display of maps. +Projection code and larger maps are in separate packages ('mapproj' and +'mapdata').") + (license license:gpl2))) -- cgit v1.2.3 From ebc4bd5b54260082a2897669668144467b856198 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:24:09 -0500 Subject: gnu: Add r-mapproj. * gnu/packages/geo.scm (r-mapproj): New variable. --- gnu/packages/geo.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 3af196bed3..e58342d62e 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -511,3 +511,25 @@ development.") Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').") (license license:gpl2))) + +(define-public r-mapproj + (package + (name "r-mapproj") + (version "1.2-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "mapproj" version)) + (sha256 + (base32 + "0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk")))) + (build-system r-build-system) + (propagated-inputs `(("r-maps" ,r-maps))) + (home-page "https://cran.r-project.org/web/packages/mapproj") + (synopsis "Map projection in R") + (description "This package converts latitude/longitude into projected +coordinates.") + (license (list license:gpl2 ; The R interface + (license:non-copyleft ; The C code + "https://www.gnu.org/licenses/license-list.en.html#lucent102" + "Lucent Public License Version 1.02"))))) -- cgit v1.2.3 From 9ddf42099b398d107467bc42bb495a20f502925f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:31:41 -0500 Subject: gnu: Add Rgooglemaps. * gnu/packages/geo.scm (r-rgooglemaps): New variable. --- gnu/packages/geo.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index e58342d62e..b6b185e5cb 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -533,3 +533,25 @@ coordinates.") (license:non-copyleft ; The C code "https://www.gnu.org/licenses/license-list.en.html#lucent102" "Lucent Public License Version 1.02"))))) + +(define-public r-rgooglemaps + (package + (name "r-rgooglemaps") + (version "1.4.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "RgoogleMaps" version)) + (sha256 + (base32 + "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq")))) + (properties `((upstream-name . "RgoogleMaps"))) + (build-system r-build-system) + (propagated-inputs `(("r-png" ,r-png))) + (home-page "https://cran.r-project.org/web/packages/RgoogleMaps") + (synopsis "Use Google Maps in R") + (description "This package serves two purposes: (i) Provide a comfortable R +interface to query the Google server for static maps, and (ii) Use the map as a +background image to overlay plots within R. This requires proper coordinate +scaling.") + (license license:gpl2+))) -- cgit v1.2.3 From 24fb9a55918655cada3bd3cb070aaf02f382e109 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:42:13 -0500 Subject: gnu: Add r-geosphere. * gnu/packages/geo.scm (r-geosphere): New variable. --- gnu/packages/geo.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index b6b185e5cb..29d8265eb8 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -37,6 +37,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) + #:use-module (gnu packages cran) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gtk) @@ -555,3 +556,23 @@ interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.") (license license:gpl2+))) + +(define-public r-geosphere + (package + (name "r-geosphere") + (version "1.5-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "geosphere" version)) + (sha256 + (base32 + "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx")))) + (build-system r-build-system) + (propagated-inputs `(("r-sp" ,r-sp))) + (home-page "https://cran.r-project.org/web/packages/geosphere") + (synopsis "Spherical trigonometry") + (description "This package computes spherical trigonometry for geographic +applications. That is, compute distances and related measures for angular +(longitude/latitude) locations.") + (license license:gpl3+))) -- cgit v1.2.3 From 41835f947e84b99d2b8aa5e32c68db2016c7437a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:47:57 -0500 Subject: gnu: Add r-subplex. gnu/packages/maths.scm (r-subplex): New variable. --- gnu/packages/maths.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f9e5d2c3a2..5382260f3c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Dave Love ;;; Copyright © 2018 Jan Nieuwenhuizen +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -3754,3 +3755,25 @@ specifications. Also, state spaces can be manipulated, visualised and analysed.") (home-page "http://mcrl2.org") (license license:boost1.0))) + +(define-public r-subplex + (package + (name "r-subplex") + (version "1.5-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "subplex" version)) + (sha256 + (base32 + "1v9xrnkapnq7v1jbhlg32ignklzf2vn8rqpayc8pzk8wvz53r33g")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://cran.r-project.org/web/packages/subplex") + (synopsis "Unconstrained optimization using the subplex algorithm") + (description "This package implements the Subplex optimization algorithm. +It solves unconstrained optimization problems using a simplex method on +subspaces. The method is well suited for optimizing objective functions that +are noisy or are discontinuous at the solution.") + (license license:gpl3+))) -- cgit v1.2.3 From 799ad71bfc05f084d595ee11b608745a9c56eb10 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 16:55:07 -0500 Subject: gnu: Add r-desolve. * gnu/packages/maths.scm (r-desolve): New variable. --- gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5382260f3c..b372ad9874 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3777,3 +3777,32 @@ It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.") (license license:gpl3+))) + +(define-public r-desolve + (package + (name "r-desolve") + (version "1.20") + (source + (origin + (method url-fetch) + (uri (cran-uri "deSolve" version)) + (sha256 + (base32 + "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan")))) + (properties `((upstream-name . "deSolve"))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "https://desolve.r-forge.r-project.org/") + (synopsis "Solvers for initial value problems of differential equations") + (description "This package provides functions that solve initial +value problems of a system of first-order ordinary differential equations (ODE), +of partial differential equations (PDE), of differential algebraic equations +(DAE), and of delay differential equations. The functions provide an interface +to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, +to the FORTRAN functions dvode and daspk and a C-implementation of solvers of +the Runge-Kutta family with fixed or variable time steps. The package contains +routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial +differential equations (PDE) that have been converted to ODEs by numerical +differencing.") + (license license:gpl2+))) -- cgit v1.2.3 From 32cbbac11a8d8d656ed795865d88a6eeb3877dbe Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 17:06:26 -0500 Subject: gnu: Add Diversitree. * gnu/packages/bioinformatics.scm (r-diversitree): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 567dd2c24b..3d754bfbfa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9,6 +9,7 @@ ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Arun Isaac +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -12855,3 +12856,34 @@ data of bisulfite experiments; it produces reports on aggregate methylation and coverage and can be used to produce information on differential methylation and segmentation.") (license license:gpl3+))) + +(define-public r-diversitree + (package + (name "r-diversitree") + (version "0.9-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "diversitree" version)) + (sha256 + (base32 + "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-desolve" ,r-desolve) + ("r-rcpp" ,r-rcpp) + ("r-suplex" ,r-subplex))) + (home-page "https://www.zoology.ubc.ca/prog/diversitree") + (synopsis "Comparative 'phylogenetic' analyses of diversification") + (description "This package contains a number of comparative \"phylogenetic\" +methods, mostly focusing on analysing diversification and character evolution. +Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) +and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and +Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods +include Markov models of discrete and continuous trait evolution and constant +rate speciation and extinction.") + (license license:gpl2+))) -- cgit v1.2.3 From da4dde610984c3ddb1baf2a92fe6e838cb0720c6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 17:10:29 -0500 Subject: gnu: Add r-jpeg. * gnu/packages/image.scm (r-jpeg): New variable. --- gnu/packages/image.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index b576c508ec..caafb2ea70 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Hartmut Goebel ;;; Copyright © 2017 Julien Lepiller +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -1293,3 +1294,23 @@ Features: @item Upload to Imgur. @end itemize\n") (license license:gpl3+))) + +(define-public r-jpeg + (package + (name "r-jpeg") + (version "0.1-8") + (source + (origin + (method url-fetch) + (uri (cran-uri "jpeg" version)) + (sha256 + (base32 + "05hawv5qcb82ljc1l2nchx1wah8mq2k2kfkhpzyww554ngzbwcnh")))) + (build-system r-build-system) + (inputs `(("libjpeg" ,libjpeg))) + (home-page "http://www.rforge.net/jpeg/") + (synopsis "Read and write JPEG images with R") + (description "This package provides a way to read, write and display bitmap +images stored in the JPEG format with R. It can read and write both files and +in-memory raw vectors.") + (license license:gpl2+))) -- cgit v1.2.3 From 5b19776e055c7033f72fd7291711294cc276ab1f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 17:23:38 -0500 Subject: gnu: Add r-ggmap. * gnu/packages/geo.scm (r-ggmap): New variable. --- gnu/packages/geo.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index 29d8265eb8..9c7c071db0 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -45,6 +45,8 @@ #:use-module (gnu packages icu4c) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages statistics) + #:use-module (gnu packages web) #:use-module (gnu packages webkit) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xml)) @@ -576,3 +578,36 @@ scaling.") applications. That is, compute distances and related measures for angular (longitude/latitude) locations.") (license license:gpl3+))) + +(define-public r-ggmap + (package + (name "r-ggmap") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "ggmap" version)) + (sha256 + (base32 + "0mssb09w818jv58h7mly9y181pzv22sgcd4a079cfpq04bs0wigw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-geosphere" ,r-geosphere) + ("r-ggplot2" ,r-ggplot2) + ("r-jpeg" ,r-jpeg) + ("r-mapproj" ,r-mapproj) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-proto" ,r-proto) + ("r-reshape2" ,r-reshape2) + ("r-rgooglemaps" ,r-rgooglemaps) + ("r-rjson" ,r-rjson) + ("r-scales" ,r-scales))) + (home-page "https://github.com/dkahle/ggmap") + (synopsis "Spatial visualization with ggplot2") + (description "This package provides a collection of functions to visualize +spatial data and models on top of static maps from various online sources (e.g +Google Maps and Stamen Maps). It includes tools common to those tasks, +including functions for geolocation and routing.") + (license license:gpl2))) -- cgit v1.2.3 From 9f1c0e03ecfe6453f57ba9d9344dcf97c257799b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 17 Feb 2018 17:29:53 -0500 Subject: gnu: Add r-feather. * gnu/packages/serialization.scm (r-feather): New variable. --- gnu/packages/serialization.scm | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index fd61462776..0c07a6384c 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -33,17 +33,20 @@ #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) + #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages cran) #:use-module (gnu packages documentation) #:use-module (gnu packages lua) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages perl) - #:use-module (guix build-system python)) + #:use-module (gnu packages statistics)) (define-public cereal (package @@ -437,3 +440,25 @@ to generate and parse. The two primary functions are @code{cbor.loads} and C#, C, Go, Java, JavaScript, PHP, and Python. It was originally created for game development and other performance-critical applications.") (license license:asl2.0))) + +(define-public r-feather + (package + (name "r-feather") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "feather" version)) + (sha256 + (base32 + "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-hms" ,r-hms) + ("r-rcpp" ,r-rcpp) + ("r-tibble" ,r-tibble))) + (home-page "https://github.com/wesm/feather") + (synopsis "R Bindings to the Feather API") + (description "Read and write feather files, a lightweight binary columnar +daa store designed for maximum speed.") + (license license:asl2.0))) -- cgit v1.2.3 From 2ed0ef2fb794de28036616c4b29e9617f0ca9425 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Feb 2018 12:18:31 -0500 Subject: gnu: Add google-brotli. * gnu/packages/compression.scm (google-brotli): New variable. --- gnu/packages/compression.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 86efe2a40e..05442024f6 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -21,6 +21,7 @@ ;;; Copyright © 2017 Petter ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2018 Rutger Helling +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -2111,3 +2112,46 @@ single-member files which can't be decompressed in parallel.") (description "innoextract allows extracting Inno Setup installers under non-Windows systems without running the actual installer using wine.") (license license:zlib))) + +(define-public google-brotli + (package + (name "google-brotli") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/google/brotli/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "08kl9gww2058p1p7j9xqmcmrabcfihhj3fq984d7fi3bchb2mky2")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'rename-static-libraries + ;; The build tools put a 'static' suffix on the static libraries, but + ;; other applications don't know how to find these. + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref %outputs "out") "/lib/"))) + (rename-file (string-append lib "libbrotlicommon-static.a") + (string-append lib "libbrotlicommon.a")) + (rename-file (string-append lib "libbrotlidec-static.a") + (string-append lib "libbrotlidec.a")) + (rename-file (string-append lib "libbrotlienc-static.a") + (string-append lib "libbrotlienc.a")) + #t)))) + #:configure-flags + (list ;; Defaults to "lib64" on 64-bit archs. + (string-append "-DCMAKE_INSTALL_LIBDIR=" + (assoc-ref %outputs "out") "/lib")))) + (home-page "https://github.com/google/brotli") + (synopsis "General-purpose lossless compression") + (description "This package provides the reference implementation of Brotli, +a generic-purpose lossless compression algorithm that compresses data using a +combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd +order context modeling, with a compression ratio comparable to the best +currently available general-purpose compression methods. It is similar in speed +with @code{deflate} but offers more dense compression. + +The specification of the Brotli Compressed Data Format is defined in RFC 7932.") + (license license:expat))) -- cgit v1.2.3 From dae7661a0da9b5a081fb2097cb5e431ad0b8443c Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Feb 2018 12:19:33 -0500 Subject: gnu: Add apache-arrow. * gnu/packages/databases.scm (apache-arrow): New variable. --- gnu/packages/databases.scm | 74 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 87f65404f8..f2e5622731 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -31,6 +31,7 @@ ;;; Copyright © 2015, 2017 Ricardo Wurmus ;;; Copyright © 2017 Kristofer Buffington ;;; Copyright © 2018 Amirouche Boubekki +;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; ;;; This file is part of GNU Guix. ;;; @@ -58,6 +59,7 @@ #:use-module (gnu packages bison) #:use-module (gnu packages boost) #:use-module (gnu packages check) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) @@ -92,6 +94,7 @@ #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages valgrind) + #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -2738,3 +2741,74 @@ Replay oplog entries between MongoDB servers Monitor read/write activity on a mongo server @end table") (license license:asl2.0))) + +(define-public apache-arrow + (package + (name "apache-arrow") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/apache/arrow") + (commit (string-append "apache-arrow-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'enter-source-directory + (lambda _ (chdir "cpp") #t)) + (add-after 'unpack 'set-env + (lambda _ + (setenv "BOOST_ROOT" (assoc-ref %build-inputs "boost")) + (setenv "BROTLI_HOME" (assoc-ref %build-inputs "brotli")) + (setenv "FLATBUFFERS_HOME" (assoc-ref %build-inputs "flatbuffers")) + (setenv "JEMALLOC_HOME" (assoc-ref %build-inputs "jemalloc")) + (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson")) + #t))) + #:configure-flags + (list "-DCMAKE_BUILD_TYPE=Release" + "-DARROW_PYTHON=ON" + + ;; Install to PREFIX/lib (the default is + ;; PREFIX/lib64). + (string-append "-DCMAKE_INSTALL_LIBDIR=" + (assoc-ref %outputs "out") + "/lib") + + ;; XXX These Guix package offer static + ;; libraries that are not position independent, + ;; and ld fails to link them into the arrow .so + "-DARROW_WITH_SNAPPY=OFF" + "-DARROW_WITH_ZLIB=OFF" + "-DARROW_WITH_ZSTD=OFF" + "-DARROW_WITH_LZ4=OFF" + + ;; Building the tests forces on all the + ;; optional features and the use of static + ;; libraries. + "-DARROW_BUILD_TESTS=OFF" + "-DARROW_BUILD_STATIC=OFF"))) + (inputs + `(("boost" ,boost) + ("rapidjson" ,rapidjson) + ("brotli" ,google-brotli) + ("flatbuffers" ,flatbuffers) + ;; Arrow is not yet compatible with jemalloc >= 5: + ;; https://issues.apache.org/jira/browse/ARROW-1141 + ("jemalloc" ,jemalloc-4.5.0) + ("python-3" ,python) + ("python-numpy" ,python-numpy))) + (home-page "https://arrow.apache.org/") + (synopsis "Columnar in-memory analytics") + (description "Apache Arrow is a columnar in-memory analytics layer +designed to accelerate big data. It houses a set of canonical in-memory +representations of flat and hierarchical data along with multiple +language-bindings for structure manipulation. It also provides IPC and common +algorithm implementations.") + (license license:asl2.0))) -- cgit v1.2.3 From 5e5ac7102c2d28676ab1b756862ba9c02cd3ba2f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Feb 2018 12:23:03 -0500 Subject: gnu: Add python-pyarrow. * gnu/packages/databases.scm (python-pyarrow, python2-pyarrow): New variables. --- gnu/packages/databases.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f2e5622731..ab8729bde0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2812,3 +2812,49 @@ representations of flat and hierarchical data along with multiple language-bindings for structure manipulation. It also provides IPC and common algorithm implementations.") (license license:asl2.0))) + +(define-public python-pyarrow + (package + (name "python-pyarrow") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/apache/arrow") + (commit (string-append "apache-arrow-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1x7sdd8lbs3nfqjql1pcgbkjc19bls56zmgjayshkmablvlc4dy3")))) + (build-system python-build-system) + (arguments + '(#:tests? #f ; XXX Test failures related to missing libhdfs, libhdfs3, + ; and "Unsupported numpy type 22". + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-source-directory + (lambda _ (chdir "python") #t)) + (add-after 'unpack 'set-env + (lambda _ + (setenv "ARROW_HOME" (assoc-ref %build-inputs "apache-arrow")) + #t))))) + (propagated-inputs + `(("apache-arrow" ,apache-arrow) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-six" ,python-six))) + (native-inputs + `(("cmake" ,cmake) + ("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://arrow.apache.org/docs/python/") + (synopsis "Python bindings for Apache Arrow") + (description "This library provides a Pythonic API wrapper for the reference +Arrow C++ implementation, along with tools for interoperability with pandas, +NumPy, and other traditional Python scientific computing packages.") + (license license:asl2.0))) + +(define-public python2-pyarrow + (package-with-python2 python-pyarrow)) -- cgit v1.2.3 From 8d4f34d6c9667c82f1dc136f54954fb4ccef81b1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 21 Feb 2018 12:25:17 -0500 Subject: gnu: Add python-feather-format. * gnu/packages/serialization.scm (python-feather-format, python2-feather-format): New variables. --- gnu/packages/serialization.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 0c07a6384c..3dd3a070e4 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) + #:use-module (gnu packages databases) #:use-module (gnu packages documentation) #:use-module (gnu packages lua) #:use-module (gnu packages pkg-config) @@ -462,3 +463,27 @@ game development and other performance-critical applications.") (description "Read and write feather files, a lightweight binary columnar daa store designed for maximum speed.") (license license:asl2.0))) + +(define-public python-feather-format + (package + (name "python-feather-format") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "feather-format" version)) + (sha256 + (base32 + "1adivm5w5ji4qv7hq7942vqlk8l2wgw87bdlsia771z14z3zp857")))) + (build-system python-build-system) + (propagated-inputs + `(("python-pandas" ,python-pandas) + ("python-pyarrow" ,python-pyarrow))) + (home-page "https://github.com/wesm/feather") + (synopsis "Python wrapper to the Feather file format") + (description "This package provides a Python wrapper library to the +Apache Arrow-based Feather binary columnar serialization data frame format.") + (license license:asl2.0))) + +(define-public python2-feather-format + (package-with-python2 python-feather-format)) -- cgit v1.2.3 From 71f9ca53e58de6ecd4d1dcbc7647990ac4685665 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 15 Mar 2018 11:45:04 -0400 Subject: gnu: certbot: Update to 0.22.0. * gnu/packages/tls.scm (certbot, python-acme): Update to 0.22.0. --- gnu/packages/tls.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 45f5255665..bd86b2e0d9 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -512,13 +512,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.21.1") + (version "0.22.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "02x6f37ddldaxrxzh2wjw8wmzqchxb7gl5i4i4daysas9yzqlvi9")))) + "1s2zamyb99zdyga3c75xxgnj0z2hixw8wv24v1l4p49fncnxab2a")))) (build-system python-build-system) (arguments `(#:phases @@ -567,7 +567,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "1sn4wqkp6kjj9p8maf4jnjwwvb083hgakm9i10rk9273nnqfkj76")))) + "1cyb3lhxrw7ghyhrl2wc95vqhdaxz6n4pai66c573gcly7c7sc7f")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) -- cgit v1.2.3 From 20ecede9690cb7f75bc8fee60619a4adf82ba4d5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 15 Mar 2018 11:31:31 -0400 Subject: gnu: shadow: Fix CVE-2018-7169. * gnu/packages/patches/shadow-CVE-2018-7169.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/admin.scm (shadow)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/admin.scm | 1 + gnu/packages/patches/shadow-CVE-2018-7169.patch | 191 ++++++++++++++++++++++++ 3 files changed, 193 insertions(+) create mode 100644 gnu/packages/patches/shadow-CVE-2018-7169.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 165b830673..69e4d2b7b5 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1082,6 +1082,7 @@ dist_patch_DATA = \ %D%/packages/patches/scotch-test-threading.patch \ %D%/packages/patches/sdl-libx11-1.6.patch \ %D%/packages/patches/seq24-rename-mutex.patch \ + %D%/packages/patches/shadow-CVE-2018-7169.patch \ %D%/packages/patches/shepherd-close-fds.patch \ %D%/packages/patches/shepherd-herd-status-sorted.patch \ %D%/packages/patches/shishi-fix-libgcrypt-detection.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index ad31bc498f..d6f4a5fabc 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -360,6 +360,7 @@ hostname.") (uri (string-append "https://github.com/shadow-maint/shadow/releases/" "download/" version "/shadow-" version ".tar.xz")) + (patches (search-patches "shadow-CVE-2018-7169.patch")) (sha256 (base32 "0hdpai78n63l3v3fgr3kkiqzhd0awrpfnnzz4mf7lmxdh61qb37w")))) diff --git a/gnu/packages/patches/shadow-CVE-2018-7169.patch b/gnu/packages/patches/shadow-CVE-2018-7169.patch new file mode 100644 index 0000000000..eeae5b9b71 --- /dev/null +++ b/gnu/packages/patches/shadow-CVE-2018-7169.patch @@ -0,0 +1,191 @@ +Fix CVE-2018-7169: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7169 + +Patch copied from upstream source repository: + +https://github.com/shadow-maint/shadow/commit/fb28c99b8a66ff2605c5cb96abc0a4d975f92de0 + +From fb28c99b8a66ff2605c5cb96abc0a4d975f92de0 Mon Sep 17 00:00:00 2001 +From: Aleksa Sarai +Date: Thu, 15 Feb 2018 23:49:40 +1100 +Subject: [PATCH] newgidmap: enforce setgroups=deny if self-mapping a group + +This is necessary to match the kernel-side policy of "self-mapping in a +user namespace is fine, but you cannot drop groups" -- a policy that was +created in order to stop user namespaces from allowing trivial privilege +escalation by dropping supplementary groups that were "blacklisted" from +certain paths. + +This is the simplest fix for the underlying issue, and effectively makes +it so that unless a user has a valid mapping set in /etc/subgid (which +only administrators can modify) -- and they are currently trying to use +that mapping -- then /proc/$pid/setgroups will be set to deny. This +workaround is only partial, because ideally it should be possible to set +an "allow_setgroups" or "deny_setgroups" flag in /etc/subgid to allow +administrators to further restrict newgidmap(1). + +We also don't write anything in the "allow" case because "allow" is the +default, and users may have already written "deny" even if they +technically are allowed to use setgroups. And we don't write anything if +the setgroups policy is already "deny". + +Ref: https://bugs.launchpad.net/ubuntu/+source/shadow/+bug/1729357 +Fixes: CVE-2018-7169 +Reported-by: Craig Furman +Signed-off-by: Aleksa Sarai +--- + src/newgidmap.c | 89 +++++++++++++++++++++++++++++++++++++++++++++++++++------ + 1 file changed, 80 insertions(+), 9 deletions(-) + +diff --git a/src/newgidmap.c b/src/newgidmap.c +index b1e33513..59a2e75c 100644 +--- a/src/newgidmap.c ++++ b/src/newgidmap.c +@@ -46,32 +46,37 @@ + */ + const char *Prog; + +-static bool verify_range(struct passwd *pw, struct map_range *range) ++ ++static bool verify_range(struct passwd *pw, struct map_range *range, bool *allow_setgroups) + { + /* An empty range is invalid */ + if (range->count == 0) + return false; + +- /* Test /etc/subgid */ +- if (have_sub_gids(pw->pw_name, range->lower, range->count)) ++ /* Test /etc/subgid. If the mapping is valid then we allow setgroups. */ ++ if (have_sub_gids(pw->pw_name, range->lower, range->count)) { ++ *allow_setgroups = true; + return true; ++ } + +- /* Allow a process to map its own gid */ +- if ((range->count == 1) && (pw->pw_gid == range->lower)) ++ /* Allow a process to map its own gid. */ ++ if ((range->count == 1) && (pw->pw_gid == range->lower)) { ++ /* noop -- if setgroups is enabled already we won't disable it. */ + return true; ++ } + + return false; + } + + static void verify_ranges(struct passwd *pw, int ranges, +- struct map_range *mappings) ++ struct map_range *mappings, bool *allow_setgroups) + { + struct map_range *mapping; + int idx; + + mapping = mappings; + for (idx = 0; idx < ranges; idx++, mapping++) { +- if (!verify_range(pw, mapping)) { ++ if (!verify_range(pw, mapping, allow_setgroups)) { + fprintf(stderr, _( "%s: gid range [%lu-%lu) -> [%lu-%lu) not allowed\n"), + Prog, + mapping->upper, +@@ -89,6 +94,70 @@ static void usage(void) + exit(EXIT_FAILURE); + } + ++void write_setgroups(int proc_dir_fd, bool allow_setgroups) ++{ ++ int setgroups_fd; ++ char *policy, policy_buffer[4096]; ++ ++ /* ++ * Default is "deny", and any "allow" will out-rank a "deny". We don't ++ * forcefully write an "allow" here because the process we are writing ++ * mappings for may have already set themselves to "deny" (and "allow" ++ * is the default anyway). So allow_setgroups == true is a noop. ++ */ ++ policy = "deny\n"; ++ if (allow_setgroups) ++ return; ++ ++ setgroups_fd = openat(proc_dir_fd, "setgroups", O_RDWR|O_CLOEXEC); ++ if (setgroups_fd < 0) { ++ /* ++ * If it's an ENOENT then we are on too old a kernel for the setgroups ++ * code to exist. Emit a warning and bail on this. ++ */ ++ if (ENOENT == errno) { ++ fprintf(stderr, _("%s: kernel doesn't support setgroups restrictions\n"), Prog); ++ goto out; ++ } ++ fprintf(stderr, _("%s: couldn't open process setgroups: %s\n"), ++ Prog, ++ strerror(errno)); ++ exit(EXIT_FAILURE); ++ } ++ ++ /* ++ * Check whether the policy is already what we want. /proc/self/setgroups ++ * is write-once, so attempting to write after it's already written to will ++ * fail. ++ */ ++ if (read(setgroups_fd, policy_buffer, sizeof(policy_buffer)) < 0) { ++ fprintf(stderr, _("%s: failed to read setgroups: %s\n"), ++ Prog, ++ strerror(errno)); ++ exit(EXIT_FAILURE); ++ } ++ if (!strncmp(policy_buffer, policy, strlen(policy))) ++ goto out; ++ ++ /* Write the policy. */ ++ if (lseek(setgroups_fd, 0, SEEK_SET) < 0) { ++ fprintf(stderr, _("%s: failed to seek setgroups: %s\n"), ++ Prog, ++ strerror(errno)); ++ exit(EXIT_FAILURE); ++ } ++ if (dprintf(setgroups_fd, "%s", policy) < 0) { ++ fprintf(stderr, _("%s: failed to setgroups %s policy: %s\n"), ++ Prog, ++ policy, ++ strerror(errno)); ++ exit(EXIT_FAILURE); ++ } ++ ++out: ++ close(setgroups_fd); ++} ++ + /* + * newgidmap - Set the gid_map for the specified process + */ +@@ -103,6 +172,7 @@ int main(int argc, char **argv) + struct stat st; + struct passwd *pw; + int written; ++ bool allow_setgroups = false; + + Prog = Basename (argv[0]); + +@@ -145,7 +215,7 @@ int main(int argc, char **argv) + (unsigned long) getuid ())); + return EXIT_FAILURE; + } +- ++ + /* Get the effective uid and effective gid of the target process */ + if (fstat(proc_dir_fd, &st) < 0) { + fprintf(stderr, _("%s: Could not stat directory for target %u\n"), +@@ -177,8 +247,9 @@ int main(int argc, char **argv) + if (!mappings) + usage(); + +- verify_ranges(pw, ranges, mappings); ++ verify_ranges(pw, ranges, mappings, &allow_setgroups); + ++ write_setgroups(proc_dir_fd, allow_setgroups); + write_mapping(proc_dir_fd, ranges, mappings, "gid_map"); + sub_gid_close(); + +-- +2.16.2 + -- cgit v1.2.3 From b9d020056d7e5a63d1c0f81c513bfd73c790390e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 14 Mar 2018 21:35:14 +0100 Subject: gnu: bind: Use INVOKE. * gnu/packages/dns.scm (isc-bind)[arguments]: Substitute INVOKE for SYSTEM* and end phase with an explicit #t. --- gnu/packages/dns.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 08304b0c4c..d093b0d9b5 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -149,7 +149,8 @@ and BOOTP/TFTP for network booting of diskless machines.") ;; (system "bin/tests/system/ifconfig.sh up"))) (replace 'check (lambda _ - (zero? (system* "make" "force-test"))))))) + (invoke "make" "force-test") + #t))))) (synopsis "An implementation of the Domain Name System") (description "BIND is an implementation of the @dfn{Domain Name System} (DNS) protocols for the Internet. It is a reference implementation of those -- cgit v1.2.3 From cd75b642d983000717e8b73b6402b1f67d1343a6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 12 Mar 2018 04:45:14 +0100 Subject: gnu: perl-lingua-en-inflect-phrase: Update to 0.20. * gnu/packages/language.scm (perl-lingua-en-inflect-phrase): Update to 0.20. --- gnu/packages/language.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm index 237c4bc18d..36368b594e 100644 --- a/gnu/packages/language.scm +++ b/gnu/packages/language.scm @@ -98,7 +98,7 @@ converting a word to singular or plural.") (define-public perl-lingua-en-inflect-phrase (package (name "perl-lingua-en-inflect-phrase") - (version "0.18") + (version "0.20") (source (origin (method url-fetch) @@ -106,7 +106,7 @@ converting a word to singular or plural.") "Lingua-EN-Inflect-Phrase-" version ".tar.gz")) (sha256 (base32 - "19prg6pkgnznrc82ymdkdi3l9schg815axjig7adca5yqa7mn2i9")))) + "1a6y1l2pjim2242wcpgz066di4pbzfgsjjdl7vg5a5wzm48qj1am")))) (build-system perl-build-system) (native-inputs `(("perl-test-nowarnings" ,perl-test-nowarnings))) -- cgit v1.2.3 From 97c794942af813965e1f0113023d1fae234d7c1a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 12 Mar 2018 04:45:52 +0100 Subject: gnu: perl-string-toidentifier-en: Update to 0.12. * gnu/packages/language.scm (perl-string-toidentifier-en): Update to 0.12. --- gnu/packages/language.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm index 36368b594e..cf85c510f1 100644 --- a/gnu/packages/language.scm +++ b/gnu/packages/language.scm @@ -365,7 +365,7 @@ stemmer at http://snowball.sourceforge.net.") (define-public perl-string-toidentifier-en (package (name "perl-string-toidentifier-en") - (version "0.11") + (version "0.12") (source (origin (method url-fetch) @@ -373,7 +373,7 @@ stemmer at http://snowball.sourceforge.net.") "String-ToIdentifier-EN-" version ".tar.gz")) (sha256 (base32 - "1bawghkgkkx7j3avnrj5sg3vix1z5564ks6wf9az3jc2knh8s5nh")))) + "12nw7h2yiybhdw0vnnpc7bif8ylhsn6kqf6s39dsrf9h54iq9yrs")))) (build-system perl-build-system) (propagated-inputs `(("perl-lingua-en-inflect-phrase" ,perl-lingua-en-inflect-phrase) -- cgit v1.2.3 From 96b4f5adc2569c708acb48dbdcce0f578f22660d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 00:01:24 +0100 Subject: gnu: autoconf-archive: Update to 2018.03.13. * gnu/packages/autotools.scm (autoconf-archive): Update to 2018.03.13. --- gnu/packages/autotools.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm index 9394ee014f..0f4ecc4ab6 100644 --- a/gnu/packages/autotools.scm +++ b/gnu/packages/autotools.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2016 David Thompson ;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Efraim Flashner +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -202,7 +203,7 @@ exec ~a --no-auto-compile \"$0\" \"$@\" (define-public autoconf-archive (package (name "autoconf-archive") - (version "2017.09.28") + (version "2018.03.13") (source (origin (method url-fetch) @@ -210,7 +211,7 @@ exec ~a --no-auto-compile \"$0\" \"$@\" version ".tar.xz")) (sha256 (base32 - "00gsh9hkrgg291my98plkrwlcpxkfrpq64pglf18kciqbf2bb7sw")))) + "0ng1lvpijf3kv7w7nb1shqs23vp0398yicyvkf9lsk56kw6zjxb1")))) (build-system gnu-build-system) (home-page "https://www.gnu.org/software/autoconf-archive/") (synopsis "Collection of freely reusable Autoconf macros") -- cgit v1.2.3 From 1a7cc9efcd4fd9485195e511ac6c5974d9ba9682 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 00:08:28 +0100 Subject: gnu: cifs-utils: Update to 6.8. * gnu/packages/samba.scm (cifs-utils): Update to 6.8. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index d7ae5715ff..3b1c2d4885 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -50,14 +50,14 @@ (define-public cifs-utils (package (name "cifs-utils") - (version "6.7") + (version "6.8") (source (origin (method url-fetch) (uri (string-append "https://download.samba.org/pub/linux-cifs/" name "/" name "-" version ".tar.bz2")) (sha256 (base32 - "1ayghnkryy1n1zm5dyvyyr7n3807nsm6glfcbbki5c2a8w91dwmj")))) + "0ygz3pagjpaj5ky11hzh4byyymb7fpmqiqkprn11zwj31h2zdlg7")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) -- cgit v1.2.3 From 47653b39332977e899e756305d6378c322c0c52c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 00:17:26 +0100 Subject: gnu: octave: Update to 4.2.2. * gnu/packages/maths.scm (octave): Update to 4.2.2. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b372ad9874..64fe13b9bc 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1308,7 +1308,7 @@ can solve two kinds of problems: (define-public octave (package (name "octave") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) @@ -1316,7 +1316,7 @@ can solve two kinds of problems: version ".tar.lz")) (sha256 (base32 - "09zhhch79jw3ynw39vizx0i2cbd2bjz3sp38pjdzraqrbivpwp92")))) + "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) -- cgit v1.2.3 From 8027f84d8fd43d1165c02758962669f66e2a96f2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 02:46:54 +0100 Subject: gnu: acpica: Update to 20180313. * gnu/packages/admin.scm (acpica): Update to 20180313. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index d6f4a5fabc..9befa845e5 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1206,7 +1206,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).") (define-public acpica (package (name "acpica") - (version "20180209") + (version "20180313") (source (origin (method url-fetch) (uri (string-append @@ -1214,7 +1214,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).") version ".tar.gz")) (sha256 (base32 - "04hyc5s9iiyiznvspx7q73r6ns98d51wrv8zfvqbqv52gqq8hzdh")))) + "16galaadmr37q2pvk2gyxrm8d1xldzk31djfxfq9v1c9yq4i425h")))) (build-system gnu-build-system) (native-inputs `(("flex" ,flex) ("bison" ,bison))) -- cgit v1.2.3 From 5ade82bbb8c768861d8dc6f12d07b661e6f92f73 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 04:03:27 +0100 Subject: gnu: r-scatterplot3d: Update to 0.3-41. * gnu/packages/cran.scm (r-scatterplot3d): Update to 0.3-41. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b7126518c1..9b045c122f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1809,14 +1809,14 @@ statistics, etc.") (define-public r-scatterplot3d (package (name "r-scatterplot3d") - (version "0.3-40") + (version "0.3-41") (source (origin (method url-fetch) (uri (cran-uri "scatterplot3d" version)) (sha256 (base32 - "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2")))) + "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/scatterplot3d/") (synopsis "3D scatter plot") -- cgit v1.2.3 From 7c9b7c5c6db7d236bc9c97446ba360618ada3308 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 04:04:18 +0100 Subject: gnu: xdg-user-dirs: Update to 0.17. * gnu/packages/freedesktop.scm (xdg-user-dirs): Update to 0.17. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 3c83e668b0..366fcecea2 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -1087,13 +1087,13 @@ update-desktop-database: updates the database containing a cache of MIME types (define-public xdg-user-dirs (package (name "xdg-user-dirs") - (version "0.16") + (version "0.17") (source (origin (method url-fetch) (uri (string-append "http://user-dirs.freedesktop.org/releases/" name "-" version ".tar.gz")) (sha256 - (base32 "1rp3c94hxjlfsryvwajklynfnrcvxplhwnjqc7395l89i0nb83vp")))) + (base32 "13216b8rfkzak5k6bvpx6jvqv3cnbgpijnjwj8a8d3kq4cl0a1ra")))) (build-system gnu-build-system) (native-inputs `(("gettext" ,gettext-minimal) -- cgit v1.2.3 From 7b8d3a5e1ee0431c1c9a4e0ac72852502c89d016 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 04:06:44 +0100 Subject: gnu: gtksourceview: Update to 3.24.7. * gnu/packages/gtk.scm (gtksourceview): Update to 3.24.7. --- gnu/packages/gtk.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 0e98a7c9d5..f0f49bbce5 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -385,7 +385,7 @@ printing and other features typical of a source code editor.") (define-public gtksourceview (package (name "gtksourceview") - (version "3.24.6") + (version "3.24.7") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -393,7 +393,7 @@ printing and other features typical of a source code editor.") name "-" version ".tar.xz")) (sha256 (base32 - "1261fwjpwn3qizmvjns9z3k3a264j3ql5anyvmisfwywpkzbv9ks")))) + "1rp8zspwyw3mmdgccsas3pa6v7s0hqjaaglg6n4kcls7ccx0vhm5")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit v1.2.3 From d87d3f963e604bc5a128adfebc45f208d4cbfb67 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 19:00:27 +0100 Subject: gnu: libisofs: Update to 1.4.8. * gnu/packages/cdrom.scm (libisofs): Update to 1.4.8. --- gnu/packages/cdrom.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 672064db12..6a2f853029 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -720,14 +720,14 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.") (define-public libisofs (package (name "libisofs") - (version "1.4.6") + (version "1.4.8") (source (origin (method url-fetch) (uri (string-append "http://files.libburnia-project.org/releases/" "libisofs-" version ".tar.gz")) (sha256 (base32 - "02m5g6lbmmkh2xc5xzq5zaf3ma6v31gls66aj886b3cq9qw0paql")))) + "0scvqb72qq24wcg814p1iw1dknldl21hr1hxsc1wy9vc6vgyk7fw")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) -- cgit v1.2.3 From 2773c244b1a814b2a80d415744b31f0031fb87ad Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 19:01:10 +0100 Subject: gnu: libisofs: Fix description typos. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/cdrom.scm (libisofs)[description]: Spell ‘file system’ as ‘file system’. --- gnu/packages/cdrom.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index 6a2f853029..e38242fb44 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -737,11 +737,11 @@ DVD-RW, DVD-R, DVD-R/DL, BD-R, and BD-RE.") (home-page "https://dev.lovelyhq.com/libburnia/libisofs") (synopsis "Library to create ISO 9660 images") (description - "Libisofs creates ISO 9660 (also known as ECMA-119) filesystem images + "Libisofs creates ISO 9660 (also known as ECMA-119) file system images which can either be written to POSIX file objects or handed over to libburn for being written directly to optical media. It can read metadata of ISO 9660 filesystems, manipulate them, and use them -to produce new complete filesystem images or add-on images to be appended -to the read filesystem image. +to produce new complete file system images or add-on images to be appended +to the read file system image. Supported extensions to ISO 9660 are Rock Ridge, Joliet, AAIP, zisofs.") (license gpl2+))) -- cgit v1.2.3 From 896bbb035678e994a602a2ea78b16aa5871e8e59 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 19:11:07 +0100 Subject: gnu: libburn: Update to 1.4.8. * gnu/packages/cdrom.scm (libburn): Update to 1.4.8. --- gnu/packages/cdrom.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm index e38242fb44..2e51544b05 100644 --- a/gnu/packages/cdrom.scm +++ b/gnu/packages/cdrom.scm @@ -698,14 +698,14 @@ laid out on the image.") (define-public libburn (package (name "libburn") - (version "1.4.6") + (version "1.4.8") (source (origin (method url-fetch) (uri (string-append "http://files.libburnia-project.org/releases/" "libburn-" version ".tar.gz")) (sha256 (base32 - "0wbh49s3az3sfpai09z1zdgynq7wnwrk31v5589033274nmzldlx")))) + "19lxnzn8bz70glrrrn2hs43gf5g7gfbcka9rcbckhv1pb7is509y")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From fdae9718a1016b02562f38380a903261d1dd39ed Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 19:49:49 +0100 Subject: gnu: intel-gpu-tools: Update to 1.22. * gnu/packages/admin.scm (intel-gpu-tools): Update to 1.22. [inputs]: Add eudev. --- gnu/packages/admin.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9befa845e5..3f13210a60 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2199,7 +2199,7 @@ buffers.") (define-public intel-gpu-tools (package (name "intel-gpu-tools") - (version "1.21") + (version "1.22") (source (origin (method url-fetch) (uri (string-append "https://cgit.freedesktop.org/xorg/app/" @@ -2207,7 +2207,7 @@ buffers.") "intel-gpu-tools-" version ".tar.gz")) (sha256 (base32 - "1xfy4cgimyyn5qixlrfkadgnl9qwbk30vw8k80g8vjnrcc4hx986")))) + "1jx5w5fr6jp67rcrlp5v79cn8kp9n0wgd5pbfgzamlah5cx6j3yd")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; many of the tests try to load kernel modules @@ -2219,7 +2219,8 @@ buffers.") (setenv "NOCONFIGURE" "1") (invoke "sh" "autogen.sh")))))) (inputs - `(("util-macros" ,util-macros) + `(("eudev" ,eudev) + ("util-macros" ,util-macros) ("libdrm" ,libdrm) ("libpciaccess" ,libpciaccess) ("kmod" ,kmod) -- cgit v1.2.3 From 35edaa22aafc01496a60a7a242a94844d5618167 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 20:12:57 +0100 Subject: gnu: you-get: Update to 0.4.1040. * gnu/packages/video.scm (you-get): Update to 0.4.1040. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 6c9769d9fa..0979b4f4e7 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1276,7 +1276,7 @@ other site that youtube-dl supports.") (define-public you-get (package (name "you-get") - (version "0.4.1025") + (version "0.4.1040") (source (origin (method url-fetch) (uri (string-append @@ -1285,7 +1285,7 @@ other site that youtube-dl supports.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "10103jw1gzar85jlajzl9wslk08vw21n26hkhfcz5bvkm9lxxs2c")))) + "0257p9bn426rv0cjk2j5hsx6cg7dz5gpjwlqq0sy1axa47phis46")))) (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg))) ; for multi-part and >=1080p videos -- cgit v1.2.3 From 0ab5aa056d4fdfb53de24ad416d978a5220e313d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 15 Mar 2018 20:13:29 +0100 Subject: gnu: dmenu: Update to 4.8. * gnu/packages/suckless.scm (dmenu): Update to 4.8. --- gnu/packages/suckless.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/suckless.scm b/gnu/packages/suckless.scm index c343b42274..eadc8409c2 100644 --- a/gnu/packages/suckless.scm +++ b/gnu/packages/suckless.scm @@ -138,14 +138,14 @@ optimising the environment for the application in use and the task performed.") (define-public dmenu (package (name "dmenu") - (version "4.7") + (version "4.8") (source (origin (method url-fetch) (uri (string-append "https://dl.suckless.org/tools/dmenu-" version ".tar.gz")) (sha256 (base32 - "1fgph549i0yw62x02jhfc8qmqk2rnzcnm46bxq6jig1cvkw3amm7")))) + "0qfvfrj10xlwd9hkvb57wshryan65bl6423h0qhiw1h76rf5lqgy")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests -- cgit v1.2.3 From e1d0f2aa87b8045aacb821c2406ecdfa832c7473 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Mar 2018 16:30:41 +0100 Subject: vm: Use 'invoke' instead of 'system*'. * gnu/build/vm.scm (load-in-linux-vm, initialize-partition-table) (create-ext-file-system, create-fat-file-system) (install-efi, make-iso9660-image): Use 'invoke' instead of (unless (zero? (system* ...)) (error ...)). --- gnu/build/vm.scm | 105 +++++++++++++++++++++++++------------------------------ 1 file changed, 47 insertions(+), 58 deletions(-) (limited to 'gnu') diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm index fe003ea458..7817507269 100644 --- a/gnu/build/vm.scm +++ b/gnu/build/vm.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 © 2016 Christopher Allan Webber ;;; Copyright © 2016, 2017 Leo Famulari ;;; Copyright © 2017 Mathieu Othacehe @@ -121,10 +121,8 @@ the #:references-graphs parameter of 'derivation'." (format #t "creating ~a image of ~,2f MiB...~%" disk-image-format (/ disk-image-size (expt 2 20))) (force-output) - (unless (zero? (system* "qemu-img" "create" "-f" disk-image-format - output - (number->string disk-image-size))) - (error "qemu-img failed"))) + (invoke "qemu-img" "create" "-f" disk-image-format output + (number->string disk-image-size))) (mkdir "xchg") @@ -136,31 +134,29 @@ the #:references-graphs parameter of 'derivation'." graph-files)) (_ #f)) - (unless (zero? - (apply system* qemu "-nographic" "-no-reboot" - "-m" (number->string memory-size) - "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" - "-device" "virtio-rng-pci,rng=guixsd-vm-rng" - "-virtfs" - (string-append "local,id=store_dev,path=" - (%store-directory) - ",security_model=none,mount_tag=store") - "-virtfs" - (string-append "local,id=xchg_dev,path=xchg" - ",security_model=none,mount_tag=xchg") - "-kernel" linux - "-initrd" initrd - "-append" (string-append "console=ttyS0 --load=" - builder) - (append - (if make-disk-image? - `("-device" "virtio-blk,drive=myhd" - "-drive" ,(string-append "if=none,file=" output - ",format=" disk-image-format - ",id=myhd")) - '()) - arch-specific-flags))) - (error "qemu failed" qemu)) + (apply invoke qemu "-nographic" "-no-reboot" + "-m" (number->string memory-size) + "-object" "rng-random,filename=/dev/urandom,id=guixsd-vm-rng" + "-device" "virtio-rng-pci,rng=guixsd-vm-rng" + "-virtfs" + (string-append "local,id=store_dev,path=" + (%store-directory) + ",security_model=none,mount_tag=store") + "-virtfs" + (string-append "local,id=xchg_dev,path=xchg" + ",security_model=none,mount_tag=xchg") + "-kernel" linux + "-initrd" initrd + "-append" (string-append "console=ttyS0 --load=" + builder) + (append + (if make-disk-image? + `("-device" "virtio-blk,drive=myhd" + "-drive" ,(string-append "if=none,file=" output + ",format=" disk-image-format + ",id=myhd")) + '()) + arch-specific-flags)) ;; When MAKE-DISK-IMAGE? is true, the image is in OUTPUT already. (unless make-disk-image? @@ -240,10 +236,9 @@ actual /dev name based on DEVICE." partition-size) partitions) ", ")) - (unless (zero? (apply system* "parted" "--script" - device "mklabel" label-type - (options partitions offset))) - (error "failed to create partition table")) + (apply invoke "parted" "--script" + device "mklabel" label-type + (options partitions offset)) ;; Set the 'device' field of each partition. (reverse @@ -265,15 +260,14 @@ actual /dev name based on DEVICE." "Create an ext-family file system of TYPE on PARTITION. If LABEL is true, use that as the volume name. If UUID is true, use it as the partition UUID." (format #t "creating ~a partition...\n" type) - (unless (zero? (apply system* (string-append "mkfs." type) - "-F" partition - `(,@(if label - `("-L" ,label) - '()) - ,@(if uuid - `("-U" ,(uuid->string uuid)) - '())))) - (error "failed to create partition"))) + (apply invoke (string-append "mkfs." type) + "-F" partition + `(,@(if label + `("-L" ,label) + '()) + ,@(if uuid + `("-U" ,(uuid->string uuid)) + '())))) (define* (create-fat-file-system partition #:key label uuid) @@ -282,11 +276,8 @@ will be determined based on file system size. If LABEL is true, use that as the volume name." ;; FIXME: UUID is ignored! (format #t "creating FAT partition...\n") - (unless (zero? (apply system* "mkfs.fat" partition - (if label - `("-n" ,label) - '()))) - (error "failed to create FAT partition"))) + (apply invoke "mkfs.fat" partition + (if label `("-n" ,label) '()))) (define* (format-partition partition type #:key label uuid) @@ -388,12 +379,11 @@ SYSTEM-DIRECTORY is the name of the directory of the 'system' derivation." (setenv "TMPDIR" esp) (mkdir-p efi-directory) - (unless (zero? (system* grub-mkstandalone "-O" (car efi-targets) - "-o" (string-append efi-directory "/" - (cdr efi-targets)) - ;; Graft the configuration file onto the image. - (string-append "boot/grub/grub.cfg=" config-file))) - (error "failed to create GRUB EFI image")))) + (invoke grub-mkstandalone "-O" (car efi-targets) + "-o" (string-append efi-directory "/" + (cdr efi-targets)) + ;; Graft the configuration file onto the image. + (string-append "boot/grub/grub.cfg=" config-file)))) (define* (make-iso9660-image grub config-file os-drv target #:key (volume-id "GuixSD_image") (volume-uuid #f) @@ -416,8 +406,8 @@ GRUB configuration and OS-DRV as the stuff in it." #:deduplicate? #f)) closures)) - (unless (zero? (apply system* - `(,grub-mkrescue "-o" ,target + (apply invoke + `(,grub-mkrescue "-o" ,target ,(string-append "boot/grub/grub.cfg=" config-file) ,(string-append "gnu/store=" os-drv "/..") "etc=/tmp/root/etc" @@ -435,8 +425,7 @@ GRUB configuration and OS-DRV as the stuff in it." (not (char=? #\- value))) (iso9660-uuid->string volume-uuid))) - `())))) - (error "failed to create ISO9660 image")))) + `()))))) (define* (initialize-hard-disk device #:key -- cgit v1.2.3 From dab03baa0a4d857edf8c5752e5dd8ecaab8862a7 Mon Sep 17 00:00:00 2001 From: Diego Nicola Barbato Date: Thu, 15 Mar 2018 02:19:51 +0100 Subject: gnu: qtox: Wrap executable and fix misplaced comma (unquote). MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/messaging.scm (qtox)[arguments]: Add phase "wrap-executable". [inputs]: Fix misplaced comma (unquote). Signed-off-by: Ludovic Courtès --- gnu/packages/messaging.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index b6323c39b2..ae489e1586 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -874,10 +874,18 @@ instant messenger with audio and video chat capabilities.") (("__DATE__") "\"\"") (("__TIME__") "\"\"") (("TIMESTAMP") "\"\"")) - #t))))) + #t)) + ;; Ensure that icons are found at runtime. + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/qtox") + `("QT_PLUGIN_PATH" prefix + ,(list (string-append (assoc-ref inputs "qtsvg") + "/lib/qt5/plugins/")))))))))) (inputs `(("ffmpeg" ,ffmpeg) - ("filteraudio", filteraudio) + ("filteraudio" ,filteraudio) ("glib" ,glib) ("gtk+" ,gtk+-2) ("libsodium" ,libsodium) -- cgit v1.2.3 From 9c7e17fd61826506a06b2bf737ebd8bbcd0ce2b5 Mon Sep 17 00:00:00 2001 From: Alex ter Weele Date: Wed, 7 Mar 2018 18:28:24 -0600 Subject: gnu: Add ghc-aeson-1.1.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/idris.scm (ghc-aeson-1.1.2.0): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/idris.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm index 6eb940c9d5..ae90676d5c 100644 --- a/gnu/packages/idris.scm +++ b/gnu/packages/idris.scm @@ -30,6 +30,20 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages)) +(define ghc-aeson-1.1.2.0 + (package (inherit ghc-aeson) + (version "1.1.2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://hackage.haskell.org/package/aeson/aeson-" + version + ".tar.gz")) + (sha256 + (base32 + "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p")))))) + (define-public idris (package (name "idris") -- cgit v1.2.3 From 78dc985bee57eaaa45cb9b38c93c8ac4148e908d Mon Sep 17 00:00:00 2001 From: Alex ter Weele Date: Wed, 7 Mar 2018 18:29:23 -0600 Subject: gnu: Add ghc-trifecta-1.6.2.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/idris.scm (ghc-trifecta-1.6.2.1): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/idris.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm index ae90676d5c..b67fcbccfa 100644 --- a/gnu/packages/idris.scm +++ b/gnu/packages/idris.scm @@ -44,6 +44,19 @@ (base32 "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p")))))) +(define ghc-trifecta-1.6.2.1 + (package (inherit ghc-trifecta) + (version "1.6.2.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://hackage.haskell.org/package/trifecta/" + "trifecta-" version ".tar.gz")) + (sha256 + (base32 + "1rgv62dlmm4vkdymx5rw5jg3w8ifpzg1745rvs1m4kzdx16p5cxs")))))) + (define-public idris (package (name "idris") -- cgit v1.2.3 From 866b19086e7f294261e694b228ff05ffb129296c Mon Sep 17 00:00:00 2001 From: Alex ter Weele Date: Wed, 7 Mar 2018 18:31:22 -0600 Subject: gnu: Add ghc-cheapskate-0.1.0.5. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/idris.scm (ghc-cheapskate-0.1.0.5): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/idris.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm index b67fcbccfa..c103055f50 100644 --- a/gnu/packages/idris.scm +++ b/gnu/packages/idris.scm @@ -57,6 +57,25 @@ (base32 "1rgv62dlmm4vkdymx5rw5jg3w8ifpzg1745rvs1m4kzdx16p5cxs")))))) +;; ghc-cheapskate appeared too new. This follows LTS Haskell. +(define ghc-cheapskate-0.1.0.5 + (package + (inherit ghc-cheapskate) + (version "0.1.0.5") + (source + (origin + (method url-fetch) + (uri (string-append + "https://hackage.haskell.org/package/cheapskate/cheapskate-" + version + ".tar.gz")) + (sha256 + (base32 + "0cpsmfx5z2xykg71sv8j7pl8ga6pzyjnjdb9bxn00vcpqkzvfqvs")))) + (arguments + ;; LTS Haskell says data-default >=0.5 && <0.8 + `(#:configure-flags (list "--allow-newer=data-default"))))) + (define-public idris (package (name "idris") -- cgit v1.2.3 From d661ed521eedf4663c57e5d96e409a32a52113e0 Mon Sep 17 00:00:00 2001 From: Alex ter Weele Date: Wed, 7 Mar 2018 18:32:19 -0600 Subject: gnu: idris: Provide the right versions of dependencies. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Previously it would fail to build. See . * gnu/packages/idris.scm (idris)[inputs]: alphebetize ghc-vector-binary-instances and ghc-async. Use ghc-aeson-1.1.2.0, ghc-cheapskate-0.1.0.5, and ghc-trifecta-1.6.2.1. Remove ghc-aeson, ghc-cheapskate, ghc-parsers, ghc-tasty, ghc-tasty-golden, ghc-tasty-rerun, ghc-trifecta, and ghc-zlib. Signed-off-by: Ludovic Courtès --- gnu/packages/idris.scm | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm index c103055f50..79f89d6f54 100644 --- a/gnu/packages/idris.scm +++ b/gnu/packages/idris.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Paul van der Walt ;;; Copyright © 2016, 2017 David Craven +;;; Copyright © 2018 Alex ter Weele ;;; ;;; This file is part of GNU Guix. ;;; @@ -92,15 +93,15 @@ (inputs `(("gmp" ,gmp) ("ncurses" ,ncurses) - ("ghc-aeson" ,ghc-aeson) - ("ghc-async" ,ghc-async) + ("ghc-aeson" ,ghc-aeson-1.1.2.0) ("ghc-annotated-wl-pprint" ,ghc-annotated-wl-pprint) ("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint) + ("ghc-async" ,ghc-async) ("ghc-base64-bytestring" ,ghc-base64-bytestring) ("ghc-blaze-html" ,ghc-blaze-html) ("ghc-blaze-markup" ,ghc-blaze-markup) - ("ghc-cheapskate" ,ghc-cheapskate) + ("ghc-cheapskate" ,ghc-cheapskate-0.1.0.5) ("ghc-code-page" ,ghc-code-page) ("ghc-fingertree" ,ghc-fingertree) ("ghc-fsnotify" ,ghc-fsnotify) @@ -108,23 +109,18 @@ ("ghc-mtl" ,ghc-mtl) ("ghc-network" ,ghc-network) ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-parsers" ,ghc-parsers) ("ghc-regex-tdfa" ,ghc-regex-tdfa) ("ghc-safe" ,ghc-safe) ("ghc-split" ,ghc-split) - ("ghc-tasty" ,ghc-tasty) - ("ghc-tasty-golden" ,ghc-tasty-golden) - ("ghc-tasty-rerun" ,ghc-tasty-rerun) ("ghc-terminal-size" ,ghc-terminal-size) ("ghc-text" ,ghc-text) - ("ghc-trifecta" ,ghc-trifecta) + ("ghc-trifecta" ,ghc-trifecta-1.6.2.1) ("ghc-uniplate" ,ghc-uniplate) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-utf8-string" ,ghc-utf8-string) - ("ghc-vector-binary-instances" ,ghc-vector-binary-instances) ("ghc-vector" ,ghc-vector) - ("ghc-zip-archive" ,ghc-zip-archive) - ("ghc-zlib" ,ghc-zlib))) + ("ghc-vector-binary-instances" ,ghc-vector-binary-instances) + ("ghc-zip-archive" ,ghc-zip-archive))) (arguments `(#:tests? #f ; FIXME: Test suite doesn't run in a sandbox. #:configure-flags -- cgit v1.2.3 From 8ab10c19d72caab7459034a6e72b0117d7c5cec8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 15 Mar 2018 23:41:31 +0100 Subject: linux-initrd: Move 'check-device-initrd-modules' elsewhere. This mostly reverts ca23693d280de5c4031058da4d3041d830080484, which introduced a circular dependency between (gnu system linux-initrd) and (gnu system mapped-devices). Reported by Eric Bavier. * gnu/system/linux-initrd.scm (check-device-initrd-modules): Move to... * gnu/system/mapped-devices.scm (check-device-initrd-modules): ... here. * po/guix/POTFILES.in: Adjust accordingly. --- gnu/system/linux-initrd.scm | 46 +--------------------------------------- gnu/system/mapped-devices.scm | 49 +++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 48 insertions(+), 47 deletions(-) (limited to 'gnu') diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 410484390c..e0cb59c009 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -24,7 +24,6 @@ #:use-module (guix store) #:use-module (guix gexp) #:use-module (guix utils) - #:use-module (guix i18n) #:use-module ((guix store) #:select (%store-prefix)) #:use-module ((guix derivations) @@ -38,22 +37,16 @@ #:select (%guile-static-stripped)) #:use-module (gnu system file-systems) #:use-module (gnu system mapped-devices) - #:autoload (gnu build linux-modules) - (device-module-aliases matching-modules known-module-aliases) #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module (ice-9 vlist) - #:use-module (ice-9 format) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) - #:use-module (srfi srfi-34) - #:use-module (srfi srfi-35) #:export (expression->initrd %base-initrd-modules raw-initrd file-system-packages - base-initrd - check-device-initrd-modules)) + base-initrd)) ;;; Commentary: @@ -350,41 +343,4 @@ loaded at boot time in the order in which they appear." #:volatile-root? volatile-root? #:on-error on-error)) -(define (check-device-initrd-modules device linux-modules location) - "Raise an error if DEVICE needs modules beyond LINUX-MODULES to operate. -DEVICE must be a \"/dev\" file name." - (define aliases - ;; Attempt to load 'modules.alias' from the current kernel, assuming we're - ;; on GuixSD, and assuming that corresponds to the kernel we'll be - ;; installing. Skip the whole thing if that file cannot be read. - (catch 'system-error - (lambda () - (known-module-aliases)) - (const #f))) - - (when aliases - (let ((modules (delete-duplicates - (append-map (cut matching-modules <> aliases) - (device-module-aliases device))))) - (unless (every (cute member <> linux-modules) modules) - (raise (condition - (&message - (message (format #f (G_ "you may need these modules \ -in the initrd for ~a:~{ ~a~}") - device modules))) - (&fix-hint - (hint (format #f (G_ "Try adding them to the -@code{initrd-modules} field of your @code{operating-system} declaration, along -these lines: - -@example - (operating-system - ;; @dots{} - (initrd-modules (append (list~{ ~s~}) - %base-initrd-modules))) -@end example\n") - modules))) - (&error-location - (location (source-properties->location location))))))))) - ;;; linux-initrd.scm ends here diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm index e6ac635231..279d521cac 100644 --- a/gnu/system/mapped-devices.scm +++ b/gnu/system/mapped-devices.scm @@ -25,13 +25,14 @@ #:use-module (guix i18n) #:use-module ((guix utils) #:select (source-properties->location + &fix-hint &error-location)) #:use-module (gnu services) #:use-module (gnu services shepherd) #:use-module (gnu system uuid) - #:use-module ((gnu system linux-initrd) - #:select (check-device-initrd-modules)) #:autoload (gnu build file-systems) (find-partition-by-luks-uuid) + #:autoload (gnu build linux-modules) + (device-module-aliases matching-modules) #:autoload (gnu packages cryptsetup) (cryptsetup-static) #:autoload (gnu packages linux) (mdadm-static) #:use-module (srfi srfi-1) @@ -55,6 +56,8 @@ device-mapping-service-type device-mapping-service + check-device-initrd-modules ;XXX: needs a better place + luks-device-mapping raid-device-mapping)) @@ -106,6 +109,48 @@ "Return a service that sets up @var{mapped-device}." (service device-mapping-service-type mapped-device)) + +;;; +;;; Static checks. +;;; + +(define (check-device-initrd-modules device linux-modules location) + "Raise an error if DEVICE needs modules beyond LINUX-MODULES to operate. +DEVICE must be a \"/dev\" file name." + (define aliases + ;; Attempt to load 'modules.alias' from the current kernel, assuming we're + ;; on GuixSD, and assuming that corresponds to the kernel we'll be + ;; installing. Skip the whole thing if that file cannot be read. + (catch 'system-error + (lambda () + (known-module-aliases)) + (const #f))) + + (when aliases + (let ((modules (delete-duplicates + (append-map (cut matching-modules <> aliases) + (device-module-aliases device))))) + (unless (every (cute member <> linux-modules) modules) + (raise (condition + (&message + (message (format #f (G_ "you may need these modules \ +in the initrd for ~a:~{ ~a~}") + device modules))) + (&fix-hint + (hint (format #f (G_ "Try adding them to the +@code{initrd-modules} field of your @code{operating-system} declaration, along +these lines: + +@example + (operating-system + ;; @dots{} + (initrd-modules (append (list~{ ~s~}) + %base-initrd-modules))) +@end example\n") + modules))) + (&error-location + (location (source-properties->location location))))))))) + ;;; ;;; Common device mappings. -- cgit v1.2.3 From 570d79c8df49142a6b0a5bf6fcd120177459563a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 15 Mar 2018 19:16:25 -0400 Subject: gnu: linux-libre@4.14: Update to 4.14.27. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.27. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index b81cb55d6b..0b609e1d21 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -392,8 +392,8 @@ It has been modified to remove all non-free binary blobs.") %linux-compatible-systems #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.26") -(define %linux-libre-4.14-hash "1m2zr17wpasg5riysbaa4g5i492jzr93py2jm088ki818s4a9cm3") +(define %linux-libre-4.14-version "4.14.27") +(define %linux-libre-4.14-hash "0mgkka9niyd0lj4qliy4v7jjh9lg1a5jwlv60yw7z0s4k7ajyyrp") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From 8e4ce402693d6f6fb5bbb26d7907595948669350 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 15 Mar 2018 19:17:22 -0400 Subject: gnu: linux-libre: Update to 4.15.10. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.10. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 0b609e1d21..bd6f005719 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -383,8 +383,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.15.9") -(define %linux-libre-hash "13lcard7i6w2c1cf9rfhvmq79xk4qp2p1c1920mfi69l20yvm572") +(define %linux-libre-version "4.15.10") +(define %linux-libre-hash "10fp8jmy0fxq8l01m1nnagpq1hznl9jmhcwknk8izjmdcb5snq6c") (define-public linux-libre (make-linux-libre %linux-libre-version -- cgit v1.2.3 From 3e5783e2920dfd78f10e0e3b160fb310c6c810ca Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 15 Mar 2018 23:08:02 -0400 Subject: linux-initrd: Autoload known-module-aliases, again. Fixes a regression introduced in 8ab10c19d72caab7459034a6e72b0117d7c5cec8. * gnu/system/mapped-devices.scm: Autoload 'known-module-aliases'. --- gnu/system/mapped-devices.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm index 279d521cac..a2cca0a93b 100644 --- a/gnu/system/mapped-devices.scm +++ b/gnu/system/mapped-devices.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Andreas Enge -;;; Copyright © 2017 Mark H Weaver +;;; Copyright © 2017, 2018 Mark H Weaver ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,7 +32,7 @@ #:use-module (gnu system uuid) #:autoload (gnu build file-systems) (find-partition-by-luks-uuid) #:autoload (gnu build linux-modules) - (device-module-aliases matching-modules) + (device-module-aliases matching-modules known-module-aliases) #:autoload (gnu packages cryptsetup) (cryptsetup-static) #:autoload (gnu packages linux) (mdadm-static) #:use-module (srfi srfi-1) -- cgit v1.2.3 From b44437c5499c7eeb66c396bc1541fa4dcc4faf76 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Mar 2018 09:59:04 +0100 Subject: gnu: kentutils: Build with mariadb. * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with mariadb. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3d754bfbfa..989e963c57 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11420,7 +11420,7 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) - ("mysql" ,mysql) + ("mariadb" ,mariadb) ("openssl" ,openssl))) (home-page "http://genome.cse.ucsc.edu/index.html") (synopsis "Assorted bioinformatics utilities") -- cgit v1.2.3 From 46264c73a6364e0510cbe6841a135da5d7f29dfa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Mar 2018 10:59:17 +0100 Subject: gnu: Add pigx-scrnaseq. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable. --- gnu/packages/bioinformatics.scm | 77 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 989e963c57..1b49cfdfbf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12857,6 +12857,83 @@ and coverage and can be used to produce information on differential methylation and segmentation.") (license license:gpl3+))) +(define-public pigx-scrnaseq + (package + (name "pigx-scrnaseq") + (version "0.0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" + "releases/download/v" version + "/pigx_scrnaseq-" version ".tar.gz")) + (sha256 + (base32 + "03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard") + "/share/java/picard.jar") + (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools") + "/share/java/dropseq.jar")) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executable + ;; Make sure the executable finds all R modules. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-program (string-append out "/bin/pigx-scrnaseq") + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) + `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) + #t))))) + (inputs + `(("dropseq-tools" ,dropseq-tools) + ("fastqc" ,fastqc) + ("java-picard" ,java-picard) + ("java" ,icedtea-8) + ("python-wrapper" ,python-wrapper) + ("python-pyyaml" ,python-pyyaml) + ("python-pandas" ,python-pandas) + ("python-numpy" ,python-numpy) + ("python-loompy" ,python-loompy) + ("ghc-pandoc" ,ghc-pandoc) + ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) + ("snakemake" ,snakemake) + ("star" ,star) + ("r-minimal" ,r-minimal) + ("r-argparser" ,r-argparser) + ("r-cowplot" ,r-cowplot) + ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dplyr" ,r-dplyr) + ("r-dropbead" ,r-dropbead) + ("r-dt" ,r-dt) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hdf5array" ,r-hdf5array) + ("r-pheatmap" ,r-pheatmap) + ("r-rmarkdown" ,r-rmarkdown) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-rtsne" ,r-rtsne) + ("r-scater" ,r-scater) + ("r-scran" ,r-scran) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-stringr" ,r-stringr) + ("r-yaml" ,r-yaml))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") + (description "PiGX scRNAseq is an analysis pipeline for preprocessing and +quality control for single cell RNA sequencing experiments. The inputs are +read files from the sequencing experiment, and a configuration file which +describes the experiment. It produces processed files for downstream analysis +and interactive quality reports. The pipeline is designed to work with UMI +based methods.") + (license license:gpl3+))) + (define-public r-diversitree (package (name "r-diversitree") -- cgit v1.2.3 From 22d628148ce857b620f5b8e48dc7cabe004313c5 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Fri, 16 Mar 2018 13:11:09 +0100 Subject: gnu: Add emacs-exec-path-from-shell. * gnu/packages/emacs.scm (emacs-exec-path-from-shell): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index c2c162c75c..fbdde863c7 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7361,3 +7361,28 @@ highlighting and indentation support.") @uref{https://www.terraform.io/, Terraform} configuration files. Most of the functionality is inherited from @code{hcl-mode}.") (license license:gpl3+))) + +(define-public emacs-exec-path-from-shell + (package + (name "emacs-exec-path-from-shell") + (version "1.11") + (source + (origin + (method url-fetch) + (uri (string-append + "https://stable.melpa.org/packages/exec-path-from-shell-" + version ".el")) + (sha256 + (base32 + "03qjgb81cq1l3j54lvlf98r75vmmgd06mj6qh5wa6mz4xzp4w26r")))) + (build-system emacs-build-system) + (home-page "https://github.com/purcell/exec-path-from-shell") + (synopsis "Get environment variables such as @var{PATH} from the shell") + (description + "This library allows the user to set Emacs @var{exec-path} and @var{PATH} +from the shell @var{PATH}, so that @code{shell-command}, @code{compile} and +the like work as expected on systems on which Emacs is not guaranteed to +inherit a login shell's environment variables. It also allows other +environment variables to be retrieved from the shell, so that Emacs will see +the same values you get in a terminal.") + (license license:gpl3+))) -- cgit v1.2.3 From 5d818b3557cc3b546d5bd0639359c14c7c0ab685 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Fri, 16 Mar 2018 13:10:28 +0100 Subject: gnu: Add emacs-deft. * gnu/packages/emacs.scm (emacs-deft): New variable. Signed-off-by: Oleg Pykhalov --- gnu/packages/emacs.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index fbdde863c7..a6c674dfb2 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7386,3 +7386,23 @@ inherit a login shell's environment variables. It also allows other environment variables to be retrieved from the shell, so that Emacs will see the same values you get in a terminal.") (license license:gpl3+))) + +(define-public emacs-deft + (package + (name "emacs-deft") + (version "0.8") + (source + (origin + (method url-fetch) + (uri (string-append "https://stable.melpa.org/packages/deft-" + version ".el")) + (sha256 + (base32 + "1vb9cjxskc7c0yyf9pvxy1fzypg1vrcgwnjz0m3hslinsgdyig58")))) + (build-system emacs-build-system) + (home-page "https://jblevins.org/projects/deft/") + (synopsis "Quickly browse, filter, and edit plain text notes") + (description + "Deft is an Emacs mode for quickly browsing, filtering, and editing +directories of plain text notes, inspired by Notational Velocity.") + (license license:bsd-3))) -- cgit v1.2.3 From 77166eb758ff565837db9e9a26d34ba9aaa16281 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 15 Mar 2018 13:57:48 -0400 Subject: gnu: util-linux: Fix CVE-2018-7738. * gnu/packages/patches/util-linux-CVE-2018-7738.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/linux.scm (util-linux)[replacement]: New field. (util-linux/fixed): New variable. --- gnu/local.mk | 1 + gnu/packages/linux.scm | 10 +++++ .../patches/util-linux-CVE-2018-7738.patch | 49 ++++++++++++++++++++++ 3 files changed, 60 insertions(+) create mode 100644 gnu/packages/patches/util-linux-CVE-2018-7738.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 69e4d2b7b5..788b260e5e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1135,6 +1135,7 @@ dist_patch_DATA = \ %D%/packages/patches/unzip-overflow-long-fsize.patch \ %D%/packages/patches/unzip-remove-build-date.patch \ %D%/packages/patches/ustr-fix-build-with-gcc-5.patch \ + %D%/packages/patches/util-linux-CVE-2018-7738.patch \ %D%/packages/patches/util-linux-tests.patch \ %D%/packages/patches/upower-builddir.patch \ %D%/packages/patches/valgrind-enable-arm.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bd6f005719..df6d7468ac 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -547,6 +547,7 @@ providing the system administrator with some help in common tasks.") (define-public util-linux (package (name "util-linux") + (replacement util-linux/fixed) (version "2.31") (source (origin (method url-fetch) @@ -634,6 +635,15 @@ block devices, UUIDs, TTYs, and many other tools.") (license (list license:gpl3+ license:gpl2+ license:gpl2 license:lgpl2.0+ license:bsd-4 license:public-domain)))) +(define util-linux/fixed + (package + (inherit util-linux) + (source + (origin + (inherit (package-source util-linux)) + (patches (append (origin-patches (package-source util-linux)) + (search-patches "util-linux-CVE-2018-7738.patch"))))))) + (define-public ddate (package (name "ddate") diff --git a/gnu/packages/patches/util-linux-CVE-2018-7738.patch b/gnu/packages/patches/util-linux-CVE-2018-7738.patch new file mode 100644 index 0000000000..080e2f56ba --- /dev/null +++ b/gnu/packages/patches/util-linux-CVE-2018-7738.patch @@ -0,0 +1,49 @@ +Fix CVE-2018-7738: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-7738 + +Patch copied from upstream source repository: + +https://github.com/karelzak/util-linux/commit/75f03badd7ed9f1dd951863d75e756883d3acc55 + +From 75f03badd7ed9f1dd951863d75e756883d3acc55 Mon Sep 17 00:00:00 2001 +From: Karel Zak +Date: Thu, 16 Nov 2017 16:27:32 +0100 +Subject: [PATCH] bash-completion: (umount) use findmnt, escape a space in + paths + + # mount /dev/sdc1 /mnt/test/foo\ bar + # umount + +has to return "/mnt/test/foo\ bar". + +Changes: + + * don't use mount | awk output, we have findmnt + * force compgen use \n as entries separator + +Addresses: https://github.com/karelzak/util-linux/issues/539 +Signed-off-by: Karel Zak +--- + bash-completion/umount | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) + +diff --git a/bash-completion/umount b/bash-completion/umount +index d76cb9fff..98c90d61a 100644 +--- a/bash-completion/umount ++++ b/bash-completion/umount +@@ -40,9 +40,10 @@ _umount_module() + return 0 + ;; + esac +- local DEVS_MPOINTS +- DEVS_MPOINTS="$(mount | awk '{print $1, $3}')" +- COMPREPLY=( $(compgen -W "$DEVS_MPOINTS" -- $cur) ) +- return 0 ++ ++ local oldifs=$IFS ++ IFS=$'\n' ++ COMPREPLY=( $( compgen -W '$(findmnt -lno TARGET | sed "s/\([[:blank:]]\)/\\\\\1/g")' -- "$cur" ) ) ++ IFS=$oldifs + } + complete -F _umount_module umount -- cgit v1.2.3 From fe52a215e53514d1857131e3a75104a081e415b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Mar 2018 15:03:02 +0100 Subject: gnu: pigx-rnaseq: Disable memory hungry test. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to disable a memory hungry test. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1b49cfdfbf..fa4a4957b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12677,6 +12677,13 @@ once. This package provides tools to perform Drop-seq analyses.") `(#:parallel-tests? #f ; not supported #:phases (modify-phases %standard-phases + ;; "test.sh" runs STAR, which requires excessive amounts of memory. + (add-after 'unpack 'disable-resource-intensive-test + (lambda _ + (substitute* "Makefile.in" + (("(^ tests/test_trim_galore/test.sh).*" _ m) m) + (("^ test.sh") "")) + #t)) (add-after 'install 'wrap-executable ;; Make sure the executable finds all R modules. (lambda* (#:key inputs outputs #:allow-other-keys) -- cgit v1.2.3 From c1c9cc664b600b1de7557e44a67471ef1556f793 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 16 Mar 2018 15:40:01 +0100 Subject: gnu: Add pigx. * gnu/packages/bioinformatics.scm (pigx): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa4a4957b7..78754793a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12941,6 +12941,42 @@ and interactive quality reports. The pipeline is designed to work with UMI based methods.") (license license:gpl3+))) +(define-public pigx + (package + (name "pigx") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BIMSBbioinfo/pigx/" + "releases/download/v" version + "/pigx-" version ".tar.gz")) + (sha256 + (base32 + "1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf")))) + (build-system gnu-build-system) + (inputs + `(("python" ,python) + ("pigx-bsseq" ,pigx-bsseq) + ("pigx-chipseq" ,pigx-chipseq) + ("pigx-rnaseq" ,pigx-rnaseq) + ("pigx-scrnaseq" ,pigx-scrnaseq))) + (home-page "http://bioinformatics.mdc-berlin.de/pigx/") + (synopsis "Analysis pipelines for genomics") + (description "PiGx is a collection of genomics pipelines. It includes the +following pipelines: + +@itemize +@item PiGx BSseq for raw fastq read data of bisulfite experiments +@item PiGx RNAseq for RNAseq samples +@item PiGx scRNAseq for single cell dropseq analysis +@item PiGx ChIPseq for reads from ChIPseq experiments +@end itemize + +All pipelines are easily configured with a simple sample sheet and a +descriptive settings file. The result is a set of comprehensive, interactive +HTML reports with interesting findings about your samples.") + (license license:gpl3+))) + (define-public r-diversitree (package (name "r-diversitree") -- cgit v1.2.3 From 7f6485e70c9c5f1a35e81dc746a45c68f9319618 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 15 Mar 2018 14:14:17 -0400 Subject: gnu: icedtea@2: Update to 2.6.13 [security fixes]. Fixes CVE-2018-{2579,2588,2599,2602,2603,2618,2629,2633,2634,2637,2641,2663, 2677,2678}. * gnu/packages/java.scm (icedtea-7): Update to 2.6.13. --- gnu/packages/java.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 521293da48..6782eaf5e6 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1074,7 +1074,7 @@ bootstrapping purposes.") (license license:gpl2+))) (define-public icedtea-7 - (let* ((version "2.6.12") + (let* ((version "2.6.13") (drop (lambda (name hash) (origin (method url-fetch) @@ -1092,7 +1092,7 @@ bootstrapping purposes.") version ".tar.xz")) (sha256 (base32 - "0s0zh0mj1sab99kb516lsgq3859vsc951phc565gwix4l5g9zppk")) + "1w331rdqx1dcx2xb0fmjmrkdc71xqn20fxsgw8by4xhiblh88khh")) (modules '((guix build utils))) (snippet '(substitute* "Makefile.in" @@ -1502,25 +1502,25 @@ bootstrapping purposes.") (native-inputs `(("openjdk-src" ,(drop "openjdk" - "15qf3nfidgnigh2zny6djfp8bhfwjnwk9i06mxs2jbq6na953ql2")) + "0l34ikyf62hbzlf9032alzkkqvf7bpmckz4gvirvph755w7gka8l")) ("corba-drop" ,(drop "corba" - "1phvn8fyl5mw2n2sn97f17nm442k75xsz2023bfw4h66ywzkqhqy")) + "050gv2jbg1pi6qkn8w18bwpbklfa5b0kymjvan9pncddbj8m84fz")) ("jaxp-drop" ,(drop "jaxp" - "0j4ms6lmnfa2cwfh9yfqdfg1bnn3fc40ay4x6k8zqa8yvspik5w5")) + "1k6yldwnxfzdg5926r1nlfv8d1r1j7rlp2nkz6gqh05vgyamnfhl")) ("jaxws-drop" ,(drop "jaxws" - "09sddj73k7n29s39hvdk14r130mvlknbxkpd2w58f34sq5sgpdrg")) + "110j7jlz47x2gg6f7653x12mssan5kvj9l9h1m1c8c92drfxbqyk")) ("jdk-drop" ,(drop "jdk" - "0q896zz8wyswmksy225q1k27nz3v3l27052dcvvpv20ryykz8yp7")) + "0d1mca38ksxvdskp9im3pp7fdijhj1n3lwq9w13r9s4v3qyskgdd")) ("langtools-drop" ,(drop "langtools" - "0niicyfccim4a9is4akh87jd7wbl8jrazdaab957mcv9l1x3bnqc")) + "0nq5236fzxn3p6x8cgncl56mzcmsj07q9gymysnws4c8byc6n0qj")) ("hotspot-drop" ,(drop "hotspot" - "1jw42qhbm3wfavk39304m53lmqipcllrvjqiab2f42mjs10i8gfx")) + "17bdv39n4lh8l5737c96f3xgamx4y305m067p01cywgp7zaddqws")) ("ant" ,ant-bootstrap) ("attr" ,attr) ("coreutils" ,coreutils) -- cgit v1.2.3 From 1d97d8ffd8531696b1a651419aa9e106b09bb615 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 15 Mar 2018 14:16:45 -0400 Subject: gnu: icedtea@3: Update to 3.7.0 [security fixes]. Fixes CVE-2018-{2579,2582,2588,2599,2602,2603,2618,2629,2633,2634,2637,2641, 2663,2677,2678}. * gnu/packages/java.scm (icedtea-8): Update to 3.7.0. --- gnu/packages/java.scm | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 6782eaf5e6..5771366f66 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -1570,7 +1570,7 @@ IcedTea build harness.") (license license:gpl2+)))) (define-public icedtea-8 - (let* ((version "3.6.0") + (let* ((version "3.7.0") (drop (lambda (name hash) (origin (method url-fetch) @@ -1579,7 +1579,7 @@ IcedTea build harness.") "/icedtea8/" version "/" name ".tar.xz")) (sha256 (base32 hash)))))) (package (inherit icedtea-7) - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (string-append @@ -1587,7 +1587,7 @@ IcedTea build harness.") version ".tar.xz")) (sha256 (base32 - "0zj192zrrxqh6j1ywc3399gk2ycay9w8pvzcvvr2kvdkb37ak86h")) + "09yqzn8rpccs7cyv89hhy5zlznpgqw5x3jz0w1ccp0cz1vgs8l5w")) (modules '((guix build utils))) (snippet '(begin @@ -1689,34 +1689,34 @@ new Date();")) `(("jdk" ,icedtea-7 "jdk") ("openjdk-src" ,(drop "openjdk" - "0mqxh81kq05z4wydkik0yrr81ibf84xmwsdcw9n2gfrzs4f5jxnb")) + "1mj6xgmw31i6qd30qi9dmv7160fbcfq5ikz1jwjihdg2793il19p")) ("aarch32-drop" ,(drop "aarch32" - "0b207g2n6kn510zf5vwh58bsxgqrmkvrna4p20r74v9cwcwx83n2")) + "1wb8k5zm40zld0986dvmlh5xh3gyixbg9h26sl662zy92amhmyyg")) ("corba-drop" ,(drop "corba" - "0qinc1q4w01nkr9klhfyd8caxvyrrfxjrz32nd7kgyja2bj8x7dd")) + "11ma4zz0599cy70xd219v7a8vin7p96xrhhz3wsaw6cjhkzpagah")) ("jaxp-drop" ,(drop "jaxp" - "07azrp3g86vk2laybmr5xfn0yrljkxs0rlm1q48385br225bgdxi")) + "14m1y0z0fbm5z5zjw3vnq85py8dma84bi3f9cw8rhdyc6skk8q4i")) ("jaxws-drop" ,(drop "jaxws" - "018fd2hq57zp3pq06wlxy5pabqcyk36xi8hk0d6xk3a90wsjvyik")) + "09andnm6xaasnp963hgx42yiflifiljp9z7z85jrfyc5z8a5whmf")) ("jdk-drop" ,(drop "jdk" - "0vs488kq5j2cc6kplc78jbhfxwq4fn06l34xrbq4d6y17777arg8")) + "0s6lcpc0zckz2fnq98aqf28nz9y3wbi41a3kyaqqa2abwbkm1zwl")) ("langtools-drop" ,(drop "langtools" - "04f6d1wvck5jrpvrcw5gsbzxnihcry9zrf1v85czdm959q21zv9c")) + "15wizy123vhk40chl1b4p552jf2pw2hdww0myf11qab425axz4nw")) ("hotspot-drop" ,(drop "hotspot" - "1mfgpzyr6zzy9klf8nn3z6d41fydb9ghpfpqzjq3cl95axfbdl1g")) + "1ciz1w9j0kz7s1dxdhyqq71nla9icyz6qvn0b9z2zgkklqa98qmm")) ("nashorn-drop" ,(drop "nashorn" - "1a26cmzbs50gkh4rmmmxls7zljx62vfp1wq02gsfd5jqs4xvlibj")) + "19pzl3ppaw8j6r5cnyp8qiw3hxijh3hdc46l39g5yfhdl4pr4hpa")) ("shenandoah-drop" ,(drop "shenandoah" - "11hmn9mwmvryfddcanzx3qffjm8bbiv18nwv3iy9cswrvxjy010f")) + "0k33anxdzw1icn072wynfmmdjhsv50hay0j1sfkfxny12rb3vgdy")) ,@(fold alist-delete (package-native-inputs icedtea-7) '("jdk" "openjdk-src" "corba-drop" "jaxp-drop" "jaxws-drop" "jdk-drop" "langtools-drop" "hotspot-drop"))))))) -- cgit v1.2.3 From fe1b04df2f9dc2eb35b2bd70dd0651553384f97c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Mar 2018 19:27:43 +0100 Subject: gnu: libvorbis: Replace with 1.3.6 [fixes CVE-2018-5146]. * gnu/packages/xiph.scm (libvorbis)[replacement]: New field. (libvorbis-1.3.6): New public variable. --- gnu/packages/xiph.scm | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm index a8e7833990..2e922d2a95 100644 --- a/gnu/packages/xiph.scm +++ b/gnu/packages/xiph.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2014 Mark H Weaver ;;; Copyright © 2015 Paul van der Walt ;;; Copyright © 2015, 2016, 2017 Efraim Flashner -;;; Copyright © 2017 Marius Bakke +;;; Copyright © 2017, 2018 Marius Bakke ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -81,6 +81,7 @@ periodic timestamps for seeking.") (package (name "libvorbis") (version "1.3.5") + (replacement libvorbis-1.3.6) (source (origin (method url-fetch) (uri (string-append "http://downloads.xiph.org/releases/vorbis/" @@ -105,6 +106,18 @@ polyphonic) audio and music at fixed and variable bitrates from 16 to "See COPYING in the distribution.")) (home-page "https://xiph.org/vorbis/"))) +;; For CVE-2018-5146. +(define-public libvorbis-1.3.6 + (package/inherit libvorbis + (version "1.3.6") + (source (origin + (method url-fetch) + (uri (string-append "http://downloads.xiph.org/releases/vorbis/" + "libvorbis-" version ".tar.xz")) + (sha256 + (base32 + "05dlzjkdpv46zb837wysxqyn8l636x3dw8v8ymlrwz2fg1dbn05g")))))) + (define libtheora (package (name "libtheora") -- cgit v1.2.3 From 593681f613816a046ea3c0dd17b11d72bb8275ec Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Tue, 13 Mar 2018 21:16:51 +0100 Subject: gnu: Add python2-libadalang. * gnu/packages/ada.scm (python2-libadalang): New variable. --- gnu/packages/ada.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm index d6cd1e9787..d60723edfa 100644 --- a/gnu/packages/ada.scm +++ b/gnu/packages/ada.scm @@ -59,3 +59,43 @@ specification in our Python DSL and Langkit will generate for you an Ada library with bindings for the C and Python programming languages.") (home-page "https://github.com/AdaCore/langkit/") (license license:gpl3+)))) ; and gcc runtime library exception + +(define-public python2-libadalang + (let ((commit "9b205e9bacdd50a68117727332e16fbef5f6ac49") + (revision "0")) + (package + (name "python2-libadalang") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/AdaCore/libadalang.git") + (commit commit))) + (sha256 + (base32 + "06hsnzj2syqpq2yhg1bb0zil7ydbyqkdmkjbf8j9b5sdgkyh5xrp")) + (file-name (string-append name "-" version "-checkout")))) + (build-system python-build-system) + (native-inputs + `(("python2-langkit" ,python2-langkit) + ("python2-quex" ,python2-quex-0.67.3))) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'build + (lambda _ + (invoke "python2" "ada/manage.py" "generate") + (invoke "python2" "ada/manage.py" "build"))) + (replace 'check + (lambda _ + (invoke "python2" "ada/manage.py" "test"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (invoke "python2" "ada/manage.py" "install" out))))))) + (synopsis "Semantic Analysis for Ada in Python") + (description "@code{libadalang} provides a high-performance semantic +engine for the Ada programming language.") + (home-page "https://github.com/AdaCore/libadalang") + (license license:gpl3)))) ; and gcc runtime gcc lib exception -- cgit v1.2.3 From 363be0c6db8f70be8f1b17a6003fa949c3d7104a Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 16 Mar 2018 22:59:28 +0100 Subject: vm: Pass "-append ..." only once. * gnu/build/vm.scm (load-in-linux-vm): Pass "-append ..." only once. --- gnu/build/vm.scm | 2 -- 1 file changed, 2 deletions(-) (limited to 'gnu') diff --git a/gnu/build/vm.scm b/gnu/build/vm.scm index 7817507269..7f6801b9dd 100644 --- a/gnu/build/vm.scm +++ b/gnu/build/vm.scm @@ -147,8 +147,6 @@ the #:references-graphs parameter of 'derivation'." ",security_model=none,mount_tag=xchg") "-kernel" linux "-initrd" initrd - "-append" (string-append "console=ttyS0 --load=" - builder) (append (if make-disk-image? `("-device" "virtio-blk,drive=myhd" -- cgit v1.2.3 From 68376f6c88865066ffa196937b4c41076d6e1044 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Sat, 17 Mar 2018 04:58:18 +0530 Subject: gnu: inkscape: Build with potrace support. From Inkscape 0.92, potrace is required for the Paintbucket and Trace Bitmap tools. * gnu/packages/inkscape.scm (inkscape)[inputs]: Add potrace. --- gnu/packages/inkscape.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm index 1e98369ea3..ffd5f60b38 100644 --- a/gnu/packages/inkscape.scm +++ b/gnu/packages/inkscape.scm @@ -68,6 +68,7 @@ ("libgc" ,libgc) ("freetype" ,freetype) ("popt" ,popt) + ("potrace" ,potrace) ("python" ,python-2) ("lcms" ,lcms) ("boost" ,boost))) -- cgit v1.2.3 From 9f375a4c0f55238614e047448c8e878b9829f918 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sat, 17 Mar 2018 00:42:15 -0400 Subject: gnu: intel-gpu-tools: Supported only on x86_64-linux and i686-linux. * gnu/packages/admin.scm (intel-gpu-tools)[supported-systems]: New field. --- gnu/packages/admin.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 3f13210a60..8f48e42fec 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2244,6 +2244,7 @@ changes, and many require complicated build procedures or specific testing environments to get useful results. Therefore, Intel GPU Tools includes low-level tools and tests specifically for development and testing of the Intel DRM Driver.") + (supported-systems '("i686-linux" "x86_64-linux")) (license license:expat))) (define-public fabric -- cgit v1.2.3