From 04e7b1e7f91a649dd6cf424c27d73d5d7aeae52b Mon Sep 17 00:00:00 2001 From: Christopher Lemmer Webber Date: Thu, 1 Mar 2018 11:00:30 -0600 Subject: gnu: golly: Fix source url. * gnu/packages/games.scm (golly): Fix source url. --- gnu/packages/games.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 272e9bce96..5917bbd69c 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -370,7 +370,7 @@ effects and music to make a completely free game.") (version "3.1") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/golly/golly-" + (uri (string-append "mirror://sourceforge/golly/golly/golly-" version "/golly-" version "-src.tar.gz")) (sha256 -- cgit v1.2.3 From 1debc5b9d281660a73b6ed777546213b0d9b7b32 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:11:43 +0100 Subject: gnu: ghc-uuid: Fix build. * gnu/packages/haskell.scm (ghc-uuid)[arguments]: Allow building with a newer version of QuickCheck. --- gnu/packages/haskell.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index dbb9ebc808..5c6e07a671 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -8532,6 +8532,8 @@ functions.") (base32 "09xhk42yhxvqmka0iqrv3338asncz8cap3j0ic0ps896f2581b6z")))) (build-system haskell-build-system) + (arguments + `(#:configure-flags (list "--allow-newer=QuickCheck"))) (inputs `(("ghc-cryptohash-sha1" ,ghc-cryptohash-sha1) ("ghc-cryptohash-md5" ,ghc-cryptohash-md5) ("ghc-entropy" ,ghc-entropy) -- cgit v1.2.3 From 643817e44534f58b28bb41bf75ebf7ad240e49f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Feb 2018 18:41:25 +0100 Subject: gnu: Add patchmatrix. * gnu/packages/music.scm (patchmatrix): New variable. --- gnu/packages/music.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 63b82900c0..65dfa92896 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -3726,6 +3726,34 @@ notation and includes basic support for digital audio.") (home-page "http://www.rosegardenmusic.com/") (license license:gpl2))) +(define-public patchmatrix + (package + (name "patchmatrix") + (version "0.12.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenMusicKontrollers/patchmatrix.git") + (commit version))) + (file-name (string-append "patchmatrix-" version "-checkout")) + (sha256 + (base32 + "19ivp7h5vq6r1qhmycjxzvrgg7fc4a3v5vb3n4c7afs4z3pj53zi")))) + (build-system cmake-build-system) + (arguments '(#:tests? #f)) ; no test target + (inputs + `(("jack" ,jack-1) + ("lv2" ,lv2) + ("mesa" ,mesa))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://github.com/OpenMusicKontrollers/patchmatrix") + (synopsis "Simple JACK patch bay") + (description "PatchMatrix is a patch bay for the JACK audio connection +kit. It provides a patch bay in flow matrix style for audio, MIDI, CV, and +OSC connections.") + (license license:artistic2.0))) + (define-public sorcer (package (name "sorcer") -- cgit v1.2.3 From 40a7997e63c4035a4e897f3aa3945751cca8ef3e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 1 Mar 2018 16:41:37 +0200 Subject: gnu: efl: Update to 1.20.7. * gnu/packages/enlightenment.scm (efl): Update to 1.20.7. --- gnu/packages/enlightenment.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 413bc5f102..c96c19f9f9 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Tomáš Čech ;;; Copyright © 2015 Daniel Pimentel -;;; Copyright © 2015, 2016, 2017 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2017 ng0 ;;; ;;; This file is part of GNU Guix. @@ -60,7 +60,7 @@ (define-public efl (package (name "efl") - (version "1.20.6") + (version "1.20.7") (source (origin (method url-fetch) (uri (string-append @@ -68,7 +68,7 @@ version ".tar.xz")) (sha256 (base32 - "1h9jkb1pkp2g6ld7ra9mxgblx3x5id4162ja697klx9mfjkpxijn")))) + "1zkn5ix81xck3n84dxvkjh4alwc6zj8x989d0zqi5c6ppijvgadh")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 360ea2bbd5089f1d309bb18e0890896f3a21c428 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 1 Mar 2018 22:18:23 +0200 Subject: gnu: efl: Use separate "include" output. * gnu/packages/enlightenment.scm (efl)[outputs]: Add 'include' output. --- gnu/packages/enlightenment.scm | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index c96c19f9f9..8550a89640 100644 --- a/gnu/packages/enlightenment.scm +++ b/gnu/packages/enlightenment.scm @@ -69,6 +69,8 @@ (sha256 (base32 "1zkn5ix81xck3n84dxvkjh4alwc6zj8x989d0zqi5c6ppijvgadh")))) + (outputs '("out" ; 49 MB + "include")) ; 17 MB (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From b1808932890a7f2f0d61dcfd015a644e4e5bcc16 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:15:40 +0100 Subject: gnu: r-dexseq: Update to 1.24.3. * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d036..911a2ee762 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6017,14 +6017,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj")))) + "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 99e4b11d81292d6c2cdabe8018fd8da144f84d9c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:15:50 +0100 Subject: gnu: r-shortread: Update to 1.36.1. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 911a2ee762..0b9ac7b0bf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6200,14 +6200,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "06mknlsmd4hnaxzdjapgvp2kgdnf9w103y500dsac5jgsz4vwzcz")))) + "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 22d96920d36ef87ba459dcf1db10641c5ba3ee25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:00 +0100 Subject: gnu: r-edger: Update to 3.20.9. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b9ac7b0bf..0ce038ada7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6968,13 +6968,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.8") + (version "3.20.9") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d")))) + "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eb8971b7421ccca75d540f0d7b3b4ed09f283e89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:12 +0100 Subject: gnu: r-limma: Update to 3.34.9. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0ce038ada7..e76d91c062 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7034,13 +7034,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.8") + (version "3.34.9") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw")))) + "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 535014ce605ea10b1642b065a9cf08c565ae43d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:23 +0100 Subject: gnu: r-genomicranges: Update to 1.30.3. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e76d91c062..97bbc6cf38 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7089,13 +7089,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.2") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj")))) + "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 61cbd49b305363e4965b3d14bf4b1935427138e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:35 +0100 Subject: gnu: r-topgo: Update to 2.30.1. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 97bbc6cf38..8985156e52 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7519,13 +7519,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.30.0") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1hqffz5qp7glxdvjp37005g8qk5nam3f9wpf6d1wjnzpar04f3dz")))) + "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit v1.2.3 From 6a0e13906b2832455ac6aacd02293a341c4e51fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:45 +0100 Subject: gnu: r-wgcna: Update to 1.63. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8985156e52..0b189378b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8365,14 +8365,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.62") + (version "1.63") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx")))) + "1225dqm68bynkmklnsxdqdd3zqrpzbvqwyly8ibxmk75z33xz309")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9aaf2813e2601a89c4dd3584f49f170f18b6279a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:16:57 +0100 Subject: gnu: r-scran: Update to 1.6.8. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b189378b4..e5e9192993 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10588,14 +10588,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.7") + (version "1.6.8") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb")))) + "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit v1.2.3 From 9d6f39252907e58de5d39be4ec59fb324f549bfb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:17:07 +0100 Subject: gnu: r-truncnorm: Update to 1.0-8. * gnu/packages/cran.scm (r-truncnorm): Update to 1.0-8. --- 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 e1fb1b6215..730ee8adb6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1472,14 +1472,14 @@ imputations.") (define-public r-truncnorm (package (name "r-truncnorm") - (version "1.0-7") + (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "truncnorm" version)) (sha256 (base32 - "1qac05z50618y4bw1d7yznsli1bv82s0g8h37iacrjrdkv87bmy7")))) + "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/truncnorm/") (synopsis "Truncated normal distribution") -- cgit v1.2.3 From 5e3867345588445776cc6e3e146bd35822706f8b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:17:17 +0100 Subject: gnu: r-pillar: Update to 1.2.1. * gnu/packages/cran.scm (r-pillar): Update to 1.2.1. --- 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 730ee8adb6..9279d1da83 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2139,14 +2139,14 @@ display.") (define-public r-pillar (package (name "r-pillar") - (version "1.1.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "pillar" version)) (sha256 (base32 - "1gh3j2pbbf5y4d5nyqnlr0x27jjyvjjspcccmw61airs1n6rx8jq")))) + "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd")))) (build-system r-build-system) (propagated-inputs `(("r-cli" ,r-cli) -- cgit v1.2.3 From 29c9c9c2c1dda48f51d43fc8a88d3213b5c01077 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:17:26 +0100 Subject: gnu: r-rmysql: Update to 0.10.14. * gnu/packages/databases.scm (r-rmysql): Update to 0.10.14. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 56984af6e2..b99cd3d3d5 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2042,14 +2042,14 @@ and web services platform functionality.") (define-public r-rmysql (package (name "r-rmysql") - (version "0.10.13") + (version "0.10.14") (source (origin (method url-fetch) (uri (cran-uri "RMySQL" version)) (sha256 (base32 - "1j0vr2l4s02cg2hzgr3pla96pjj4h85sxw28lidy58rg5awnsf82")))) + "01891kn263b02y6addgpy3gn5axg7m10bqbqv7dg9yx9k85am590")))) (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 744e06e7170954d98bf0f990ba45318877aaae36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:17:40 +0100 Subject: gnu: r-mass: Update to 7.3-49. * gnu/packages/statistics.scm (r-mass): Update to 7.3-49. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c1012a635b..2c5308159a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -318,14 +318,14 @@ D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") (define-public r-mass (package (name "r-mass") - (version "7.3-48") + (version "7.3-49") (source (origin (method url-fetch) (uri (cran-uri "MASS" version)) (sha256 (base32 - "02q95ba909p2gxnzfp295ipxjnv14f7bm55nicxwn2kj8hizpzqd")))) + "1yjbnj1p4z0vw84wga8q5fyqiw4n6r7pc6rdwam7vsbiamyzfcqs")))) (properties `((upstream-name . "MASS"))) (build-system r-build-system) (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") -- cgit v1.2.3 From e24ccf46f15b2a3fc0ba4cd9470aabd74b39559e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:17:53 +0100 Subject: gnu: r-rpart: Update to 4.1-13. * gnu/packages/statistics.scm (r-rpart): Update to 4.1-13. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2c5308159a..090f532232 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -554,14 +554,14 @@ single hidden layer, and for multinomial log-linear models.") (define-public r-rpart (package (name "r-rpart") - (version "4.1-12") + (version "4.1-13") (source (origin (method url-fetch) (uri (cran-uri "rpart" version)) (sha256 (base32 - "177p03w4m0qshb3sqkdyixim3f44g2an31v3vlbjmpzjvd5ff6yq")))) + "0k29qx3k3pj5sgrpg0p47yd8i811rmdakaw57bigpq1449asc4cf")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/rpart") (synopsis "Recursive partitioning and regression trees") -- cgit v1.2.3 From e3ddb563297c9707a8fc0e5c64e55915a4e842a5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:18:04 +0100 Subject: gnu: r-gdtools: Update to 0.1.7. * gnu/packages/statistics.scm (r-gdtools): Update to 0.1.7. [inputs]: Add zlib. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 090f532232..084f1a2f2c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1098,20 +1098,21 @@ agnes cluster diagrams.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.1.6") + (version "0.1.7") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "103wnc8sq0iwcnj4j14hd420d2dqdyf13s3f25icsznrlyzdkhf5")))) + "122k9spymawfnfyksxyapwq9cigydy5nrjwhrwrhy3qkax3aycf6")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) ("pkg-config" ,pkg-config))) (inputs - `(("cairo" ,cairo))) + `(("cairo" ,cairo) + ("zlib" ,zlib))) (propagated-inputs `(("r-withr" ,r-withr))) (home-page "https://cran.r-project.org/web/packages/gdtools") -- cgit v1.2.3 From 36e1202b2c47925f45317d1df99a35b0f1344627 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:18:19 +0100 Subject: gnu: r-yaml: Update to 2.1.17. * gnu/packages/statistics.scm (r-yaml): Update to 2.1.17. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 084f1a2f2c..6dc99c1b19 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1331,13 +1331,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.16") + (version "2.1.17") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm")))) + "10y6wnv2v8k396far29haqv2s82p4zm04rrsxk183wg19gb51was")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") -- cgit v1.2.3 From dafd13d5b2afa5b65fafae37088b7c023a91d767 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:18:30 +0100 Subject: gnu: r-rcpparmadillo: Update to 0.8.400.0.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.8.400.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6dc99c1b19..166cdde833 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2482,13 +2482,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.8.300.1.0") + (version "0.8.400.0.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83")))) + "11y2ksf46zw6fcz0kk70szyfn7qqxwwd33xylrxvnyb7ldmbc5yr")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From 35d12b05f0d063f9968ba4c2629ca52cceee08ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:18:47 +0100 Subject: gnu: r-rmarkdown: Update to 1.9. * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 166cdde833..d2bcf4aabd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2576,14 +2576,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.8") + (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "0q1y1qx87xp6vf9h7mfl77rqhmd01xl53l9ap9qj99bfvpabb572")))) + "0wq6kbhrkv3fhcy4hg5yyv9gdvf8gr4nsjwdifs4ih8lnn0dmdyb")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eaf0905970378dd438f3f8f705ff8e6bc3e506c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:18:58 +0100 Subject: gnu: r-tidyselect: Update to 0.2.4. * gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d2bcf4aabd..e5d448083c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3578,14 +3578,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyselect (package (name "r-tidyselect") - (version "0.2.3") + (version "0.2.4") (source (origin (method url-fetch) (uri (cran-uri "tidyselect" version)) (sha256 (base32 - "0b0w30yq30c7bwpaghp3hp0nncqwcmvrra9j58fhx9jihay3l68c")))) + "1592dbzawhd1hpsp9919l4sifyiaaj6xr7lnhsbwa6jwmmb0xcsw")))) (build-system r-build-system) (propagated-inputs `(("r-glue" ,r-glue) -- cgit v1.2.3 From bfae3f71217e867806276e0415b75ea655531461 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:19:10 +0100 Subject: gnu: r-lubridate: Update to 1.7.3. * gnu/packages/statistics.scm (r-lubridate): Update to 1.7.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e5d448083c..1c180645d4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5357,14 +5357,14 @@ is supported.") (define-public r-lubridate (package (name "r-lubridate") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "lubridate" version)) (sha256 (base32 - "0k417a1xp5gxf77ycbnx5apzpc5d25sjm83ss7wmqpbnhnr5dcav")))) + "1pzkqfiahnsdm3zx46asgn8fw43vlxvbh7r4cn70c7ffmxabzzrc")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) -- cgit v1.2.3 From b79e1fbe962c0ba9134ffb7d1250170aaeafdecf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 21:19:21 +0100 Subject: gnu: r-httpuv: Update to 1.3.6.1. * gnu/packages/web.scm (r-httpuv): Update to 1.3.6.1. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 4876918b53..e3412f60e2 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3780,13 +3780,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.3.6") + (version "1.3.6.1") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "1nzbcw1dm4l5qc9156kz95rdb8bwnpdr57wfc87w8arv7m0i40bc")))) + "11kffpki4pgh352dlwsm4lnf1dcd5vs51cnimbshadyk3jprwxdf")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/httpuv") -- cgit v1.2.3 From b672a8160755bab07fb3c13dbc43dcc26525a7b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 19 Feb 2018 20:04:06 +0100 Subject: gnu: Graft glibc to allow execution on Linux 2.6.32. * gnu/packages/patches/glibc-allow-kernel-2.6.32.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/base.scm (glibc/linux)[replacement]: New field. (glibc-2.26-patched): New variable. --- gnu/local.mk | 3 +- gnu/packages/base.scm | 11 ++++++ .../patches/glibc-allow-kernel-2.6.32.patch | 39 ++++++++++++++++++++++ 3 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/glibc-allow-kernel-2.6.32.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 3d0bd38e50..ee99882c5f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -7,7 +7,7 @@ # Copyright © 2016, 2017, 2018 Kei Kebreau # Copyright © 2016, 2017 Rene Saavedra # Copyright © 2016 Adonay "adfeno" Felipe Nogueira -# Copyright © 2016, 2017 Ricardo Wurmus +# Copyright © 2016, 2017, 2018 Ricardo Wurmus # Copyright © 2016 Ben Woodcroft # Copyright © 2016, 2017, 2018 Alex Vong # Copyright © 2016, 2017 Efraim Flashner @@ -708,6 +708,7 @@ dist_patch_DATA = \ %D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch \ + %D%/packages/patches/glibc-allow-kernel-2.6.32.patch \ %D%/packages/patches/glibc-bootstrap-system.patch \ %D%/packages/patches/glibc-ldd-x86_64.patch \ %D%/packages/patches/glibc-locales.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index b2c1d232fb..23107a823e 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017 Eric Bavier +;;; Copyright © 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -537,6 +538,7 @@ store.") ;; Note: Always use a dot after the minor version since various places rely ;; on "version-major+minor" to determine where locales are found. (version "2.26.105-g0890d5379c") + (replacement glibc-2.26-patched) (source (origin (method url-fetch) (uri (string-append "https://alpha.gnu.org/gnu/guix/mirror/" @@ -839,6 +841,15 @@ GLIBC/HURD for a Hurd host" ;; Below are old libc versions, which we use mostly to build locale data in ;; the old format (which the new libc cannot cope with.) +(define glibc-2.26-patched + (package + (inherit glibc) + (replacement #f) + (source (origin + (inherit (package-source glibc)) + (patches (cons (search-patch "glibc-allow-kernel-2.6.32.patch") + (origin-patches (package-source glibc)))))))) + (define-public glibc-2.25 (package (inherit glibc) diff --git a/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch new file mode 100644 index 0000000000..ce18b874c4 --- /dev/null +++ b/gnu/packages/patches/glibc-allow-kernel-2.6.32.patch @@ -0,0 +1,39 @@ +diff --git a/sysdeps/unix/sysv/linux/configure b/sysdeps/unix/sysv/linux/configure +index cace758c01..38fe7fe0b0 100644 +--- a/sysdeps/unix/sysv/linux/configure ++++ b/sysdeps/unix/sysv/linux/configure +@@ -69,7 +69,7 @@ fi + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for kernel header at least $minimum_kernel" >&5 + $as_echo_n "checking for kernel header at least $minimum_kernel... " >&6; } + decnum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/(\1 * 65536 + \2 * 256 + \3)/'`; +-abinum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`; ++abinum=`echo "2.6.32.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`; + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + #include +diff --git a/sysdeps/unix/sysv/linux/configure.ac b/sysdeps/unix/sysv/linux/configure.ac +index 13abda0a51..6abc12eaed 100644 +--- a/sysdeps/unix/sysv/linux/configure.ac ++++ b/sysdeps/unix/sysv/linux/configure.ac +@@ -50,7 +50,7 @@ fi + AC_MSG_CHECKING(for kernel header at least $minimum_kernel) + changequote(,)dnl + decnum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/(\1 * 65536 + \2 * 256 + \3)/'`; +-abinum=`echo "$minimum_kernel.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`; ++abinum=`echo "2.6.32.0.0.0" | sed 's/\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1,\2,\3/'`; + changequote([,])dnl + AC_TRY_COMPILE([#include + #if LINUX_VERSION_CODE < $decnum +diff --git a/sysdeps/unix/sysv/linux/dl-osinfo.h b/sysdeps/unix/sysv/linux/dl-osinfo.h +index 823cd8224d..482caaeeec 100644 +--- a/sysdeps/unix/sysv/linux/dl-osinfo.h ++++ b/sysdeps/unix/sysv/linux/dl-osinfo.h +@@ -39,7 +39,7 @@ + GLRO(dl_osversion) = version; \ + \ + /* Now we can test with the required version. */ \ +- if (__LINUX_KERNEL_VERSION > 0 && version < __LINUX_KERNEL_VERSION) \ ++ if (__LINUX_KERNEL_VERSION > 0 && version < __LINUX_KERNEL_VERSION && version != 0x020620) \ + /* Not sufficent. */ \ + FATAL ("FATAL: kernel too old\n"); \ + } \ -- cgit v1.2.3 From db317b38dc3fadf4759da8209740c616d1b599b7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 28 Feb 2018 23:54:36 +0100 Subject: gnu: dbacl: Update phase style. * gnu/packages/textutils.scm (dbacl)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/textutils.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 1417bea4e5..c9714988d6 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -508,10 +508,12 @@ in a portable way.") (add-after 'unpack 'delete-test ;; See comments about the license. (lambda _ - (delete-file "src/tests/dbacl-jap.shin"))) + (delete-file "src/tests/dbacl-jap.shin") + #t)) (add-after 'delete-sample6-and-japanese 'autoreconf (lambda _ - (zero? (system* "autoreconf" "-vif")))) + (invoke "autoreconf" "-vif") + #t)) (add-after 'unpack 'fix-test-files (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) -- cgit v1.2.3 From 7314a5475e8fe0fc7ffe17d2cc30b4ae8c5381b2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 28 Feb 2018 23:55:49 +0100 Subject: gnu: dbacl: Use HTTPS home page. * gnu/packages/textutils.scm (dbacl)[home-page]: Use HTTPS. --- gnu/packages/textutils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index c9714988d6..d75ba7766e 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -534,7 +534,7 @@ in a portable way.") ("autoconf" ,autoconf) ("automake" ,automake) ("pkg-config" ,pkg-config))) - (home-page "http://www.lbreyer.com/dbacl.html") + (home-page "https://www.lbreyer.com/dbacl.html") (synopsis "Bayesian text and email classifier") (description "dbacl is a fast Bayesian text and email classifier. It builds a variety -- cgit v1.2.3 From 4f5452ab3aaccb17a6e4e3c9b3029cd1ed408102 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 00:46:23 +0100 Subject: gnu: libftdi: Use HTTPS home page. * gnu/packages/libftdi.scm (libftdi)[home-page]: Use HTTPS. --- gnu/packages/libftdi.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/libftdi.scm b/gnu/packages/libftdi.scm index 78f849d02d..bbb98ff1f4 100644 --- a/gnu/packages/libftdi.scm +++ b/gnu/packages/libftdi.scm @@ -40,7 +40,7 @@ (build-system cmake-build-system) (propagated-inputs `(("libusb" ,libusb))) ; required by libftdi1.pc - (home-page "http://www.intra2net.com/en/developer/libftdi/") + (home-page "https://www.intra2net.com/en/developer/libftdi/") (synopsis "FTDI USB driver with bitbang mode") (description "libFTDI is a library to talk to FTDI chips: FT232BM, -- cgit v1.2.3 From 4972f9cc0a55e35e1c025190f57921f9ddcc5c36 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 00:47:18 +0100 Subject: gnu: nagios: Update to 4.3.4. * gnu/packages/monitoring.scm (nagios): Update to 4.3.4. --- gnu/packages/monitoring.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index d7a1641ad8..c5a86d02c6 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016 Ludovic Courtès ;;; Copyright © 2018 Sou Bunnbu ;;; Copyright © 2017, 2018 Ricardo Wurmus +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,7 +41,7 @@ (define-public nagios (package (name "nagios") - (version "4.2.4") + (version "4.3.4") ;; XXX: Nagios 4.2.x and later bundle a copy of AngularJS. (source (origin (method url-fetch) @@ -49,7 +50,7 @@ version "/nagios-" version ".tar.gz")) (sha256 (base32 - "0w0blbwiw0ps04b7gkyyk89qkgwsxh6gydhmggbm1kl3ar3mq1dh")) + "1wa4m952sb23dqi5w759adimsp21bkhp598rpq9dnhz3v497h2y9")) (modules '((guix build utils))) (snippet ;; Ensure reproducibility. -- cgit v1.2.3 From 57c734a628091f45cea205acfceba34d2dda3ef9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 06:50:39 +0100 Subject: gnu: liblo: Update to 0.29. * gnu/packages/audio.scm (liblo): Update to 0.29. --- gnu/packages/audio.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 1cf6441df0..a9d29345a6 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1628,14 +1628,14 @@ essential distortions.") (define-public liblo (package (name "liblo") - (version "0.28") + (version "0.29") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/liblo/liblo/" version "/liblo-" version ".tar.gz")) (sha256 (base32 - "02drgnpirvl2ihvzgsmn02agr5sj3vipzzw9vma56qlkgfvak56s")))) + "0sn0ckc1d0845mhsaa62wf7f9v0c0ykiq796a30ja5096kib9qdc")))) (build-system gnu-build-system) (arguments `(;; liblo test FAILED -- cgit v1.2.3 From 66b89ee28e1b15ff962b68e91fcd84562102fc2f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 16:29:31 +0100 Subject: gnu: python-stem: Update phase style. * gnu/packages/python.scm (python-stem)[arguments]: Substitute INVOKE for SYSTEM* and end phase with #t. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 69101c78b9..0b7ff440f0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9366,7 +9366,8 @@ etc.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "./run_tests.py" "--unit"))))))) + (invoke "./run_tests.py" "--unit") + #t))))) (native-inputs `(("python-mock" ,python-mock) ("python-pep8" ,python-pep8) -- cgit v1.2.3 From fbb0164a5f7087a81ef5f79a4134432969f926cf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 16:30:40 +0100 Subject: gnu: privoxy: Update phase style. * gnu/packages/tor.scm (privoxy)[arguments]: Substitute INVOKE for SYSTEM* and end phase with #t. --- gnu/packages/tor.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 4a39100511..f598672d91 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -146,7 +146,8 @@ rejects UDP traffic from the application you're using.") (lambda _ ;; Unfortunately, this is not a tarball produced by ;; "make dist". - (zero? (system* "autoreconf" "-vfi"))))) + (invoke "autoreconf" "-vfi") + #t))) #:tests? #f)) (inputs `(("w3m" ,w3m) -- cgit v1.2.3 From 68e7632db052105b70704cd2c1cc42a568e9bf4a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 16:31:06 +0100 Subject: gnu: onionshare: Update phase style. * gnu/packages/tor.scm (onionshare)[arguments]: Substitute INVOKE for SYSTEM* and end phase with #t. --- gnu/packages/tor.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index f598672d91..50295da5dc 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -231,7 +231,9 @@ networks.") ;; After all the patching we run the tests after installing. ;; This is also a known issue: ;; https://github.com/micahflee/onionshare/issues/284 - (lambda _ (zero? (system* "nosetests" "test"))))))) + (lambda _ + (invoke "nosetests" "test") + #t))))) (native-inputs `(("python-nose" ,python-nose))) (inputs -- cgit v1.2.3 From a9c0a133c045f82e1084e7485c6cc65ace131fa3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 16:34:38 +0100 Subject: gnu: python-stem: Update to 1.6.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python.scm (python-stem): Update to 1.6.0. [arguments]: Add ‘fix-test-environment’ phase. --- gnu/packages/python.scm | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0b7ff440f0..126424183b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9352,18 +9352,25 @@ etc.") (define-public python-stem (package (name "python-stem") - (version "1.5.4") + (version "1.6.0") (source (origin (method url-fetch) (uri (pypi-uri "stem" version)) (sha256 (base32 - "1j7pnblrn0yr6jmxvsq6y0ihmxmj5x50jl2n2606w67f6wq16j9n")))) + "1va9p3ij7lxg6ixfsvaql06dn11l3fgpxmss1dhlvafm7sqizznp")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases + (add-before 'check 'fix-test-environment + (lambda _ + ;; Fixes: FileNotFoundError: [Errno 2] No such file or directory: + ;; '/tmp/guix-build-python-stem-1.6.0.drv-0/stem-1.6.0/.gitignore'. + (with-output-to-file ".gitignore" + (lambda _ (format #t "%"))) + #t)) (replace 'check (lambda _ (invoke "./run_tests.py" "--unit") -- cgit v1.2.3 From bb47da4a6ad012eb32a3792a9bf7337996f1c41e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 18:21:25 +0100 Subject: gnu: php: Update to 7.2.3. * gnu/packages/php.scm (php): Update to 7.2.3. --- gnu/packages/php.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index b9a5eb4bf2..1ed3dc7ce0 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 Julien Lepiller ;;; Copyright © 2016 Marius Bakke +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -52,7 +53,7 @@ (define-public php (package (name "php") - (version "7.2.1") + (version "7.2.3") (home-page "https://secure.php.net/") (source (origin (method url-fetch) @@ -60,7 +61,7 @@ name "-" version ".tar.xz")) (sha256 (base32 - "08l8zmp8wbavq6wlgx19irz59csb44jhbsr172bfsq36v8pzhv3c")) + "07v5bq5b97zdqwmig6sxqsdb50vdf04w6jzmjq5kqh9gaqdlzadk")) (modules '((guix build utils))) (snippet '(with-directory-excursion "ext" -- cgit v1.2.3 From 1ff14bf2cdc698e1aa3418a3bbea023e80075e50 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 20:34:50 +0100 Subject: gnu: sdcc: Update to 3.7.0. * gnu/packages/sdcc.scm (sdcc): Update to 3.7.0. --- gnu/packages/sdcc.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/sdcc.scm b/gnu/packages/sdcc.scm index 331425d98f..a3746537dc 100644 --- a/gnu/packages/sdcc.scm +++ b/gnu/packages/sdcc.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016 David Craven +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,7 +31,7 @@ (define-public sdcc (package (name "sdcc") - (version "3.6.0") + (version "3.7.0") (source (origin (method url-fetch) (uri (string-append @@ -38,7 +39,7 @@ "/" version "/sdcc-src-" version ".tar.bz2")) (sha256 (base32 - "0x53gh5yrrfjvlnkk29mjn8hq4v52alrsf7c8nsyzzq13sqwwpg8")))) + "13llvx0j3v5qa7qd4fh7nix4j3alpd3ccprxvx163c4q8q4lfkc5")))) (build-system gnu-build-system) (native-inputs `(("bison" ,bison) -- cgit v1.2.3 From 738aa0ca1d1b86286cf8f57620a50c4b093031b8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 20:36:09 +0100 Subject: gnu: sdcc: Fix typo in description. * gnu/packages/sdcc.scm (sdcc)[description]: Fix (upstream) typo. Add hyphens. --- gnu/packages/sdcc.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/sdcc.scm b/gnu/packages/sdcc.scm index a3746537dc..6d05470101 100644 --- a/gnu/packages/sdcc.scm +++ b/gnu/packages/sdcc.scm @@ -60,10 +60,10 @@ #t))))) (home-page "http://sdcc.sourceforge.net") (synopsis "Small devices C compiler") - (description "SDCC is a retargettable, optimizing Standard C compiler suite -that targets the Intel MCS51 based microprocessors (8031, 8032, 8051, 8052, ...), + (description "SDCC is a retargetable, optimizing Standard C compiler suite +that targets the Intel MCS51-based microprocessors (8031, 8032, 8051, 8052, ...), Maxim (formerly Dallas) DS80C390 variants, Freescale (formerly Motorola) -HC08 based (hc08, s08), Zilog Z80 based MCUs (z80, z180, gbz80, Rabbit +HC08-based (hc08, s08), Zilog Z80-based MCUs (z80, z180, gbz80, Rabbit 2000/3000, Rabbit 3000A, TLCS-90) and STMicroelectronics STM8. Work is in progress on supporting the Microchip PIC16 and PIC18 targets. It can be retargeted for other microprocessors.") -- cgit v1.2.3 From 8147d7c675e663c45d5e1ccbeebb72daeaba0b91 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Thu, 1 Mar 2018 20:34:51 +0100 Subject: gnu: php: Fix test failure. * gnu/packages/php.scm (php)[inputs]: Use gd-for-php. (gd-for-php): New private variable. * gnu/packages/patches/gd-CVE-2018-5711.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + gnu/packages/patches/gd-CVE-2018-5711.patch | 61 +++++++++++++++++++++++++++++ gnu/packages/php.scm | 17 +++++--- 3 files changed, 73 insertions(+), 6 deletions(-) create mode 100644 gnu/packages/patches/gd-CVE-2018-5711.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index ee99882c5f..ba5af56bd9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -681,6 +681,7 @@ dist_patch_DATA = \ %D%/packages/patches/gcc-6-source-date-epoch-2.patch \ %D%/packages/patches/gcr-disable-failing-tests.patch \ %D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \ + %D%/packages/patches/gd-CVE-2018-5711.patch \ %D%/packages/patches/gd-fix-tests-on-i686.patch \ %D%/packages/patches/gd-freetype-test-failure.patch \ %D%/packages/patches/gegl-CVE-2012-4433.patch \ diff --git a/gnu/packages/patches/gd-CVE-2018-5711.patch b/gnu/packages/patches/gd-CVE-2018-5711.patch new file mode 100644 index 0000000000..83b12cde63 --- /dev/null +++ b/gnu/packages/patches/gd-CVE-2018-5711.patch @@ -0,0 +1,61 @@ +This patch is adapted from commit a11f47475e6443b7f32d21f2271f28f417e2ac04 and +fixes CVE-2018-5711. + +From a11f47475e6443b7f32d21f2271f28f417e2ac04 Mon Sep 17 00:00:00 2001 +From: "Christoph M. Becker" +Date: Wed, 29 Nov 2017 19:37:38 +0100 +Subject: [PATCH] Fix #420: Potential infinite loop in gdImageCreateFromGifCtx + +Due to a signedness confusion in `GetCode_` a corrupt GIF file can +trigger an infinite loop. Furthermore we make sure that a GIF without +any palette entries is treated as invalid *after* open palette entries +have been removed. + +CVE-2018-5711 + +See also https://bugs.php.net/bug.php?id=75571. +--- + src/gd_gif_in.c | 12 ++++++------ + 1 file changed, 38 insertions(+), 6 deletions(-) + +diff --git a/src/gd_gif_in.c b/src/gd_gif_in.c +index daf26e7..0a8bd71 100644 +--- a/src/gd_gif_in.c ++++ b/src/gd_gif_in.c +@@ -335,11 +335,6 @@ terminated: + return 0; + } + +- if(!im->colorsTotal) { +- gdImageDestroy(im); +- return 0; +- } +- + /* Check for open colors at the end, so + * we can reduce colorsTotal and ultimately + * BitsPerPixel */ +@@ -351,6 +346,11 @@ terminated: + } + } + ++ if(!im->colorsTotal) { ++ gdImageDestroy(im); ++ return 0; ++ } ++ + return im; + } + +@@ -447,7 +447,7 @@ static int + GetCode_(gdIOCtx *fd, CODE_STATIC_DATA *scd, int code_size, int flag, int *ZeroDataBlockP) + { + int i, j, ret; +- unsigned char count; ++ int count; + + if(flag) { + scd->curbit = 0; + +-- +2.13.6 + diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index 1ed3dc7ce0..f3f279a533 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -50,6 +50,15 @@ #:use-module (guix build-system gnu) #:use-module ((guix licenses) #:prefix license:)) +(define gd-for-php + (package + (inherit gd) + (source (origin + (inherit (package-source gd)) + (patches (search-patches "gd-fix-tests-on-i686.patch" + "gd-freetype-test-failure.patch" + "gd-CVE-2018-5711.patch")))))) + (define-public php (package (name "php") @@ -278,11 +287,7 @@ "ext/mbstring/tests/mb_ereg_variation3.phpt" "ext/mbstring/tests/mb_ereg_replace_variation1.phpt" "ext/mbstring/tests/bug72994.phpt" - "ext/ldap/tests/ldap_set_option_error.phpt" - - ;; XXX: This is CVE-2018-5711. There is no fix yet in libgd. - ;; See https://github.com/libgd/libgd/issues/420 - "ext/gd/tests/bug75571.phpt")) + "ext/ldap/tests/ldap_set_option_error.phpt")) ;; Skip tests requiring network access. (setenv "SKIP_ONLINE_TESTS" "1") @@ -299,7 +304,7 @@ ("curl" ,curl) ("cyrus-sasl" ,cyrus-sasl) ("freetype" ,freetype) - ("gd" ,gd) + ("gd" ,gd-for-php) ("gdbm" ,gdbm) ("glibc" ,glibc) ("gmp" ,gmp) -- cgit v1.2.3 From 50266960339fb534ff65657d7718c4e853280961 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 1 Mar 2018 17:57:22 -0500 Subject: gnu: linux-libre@4.4: Update to 4.4.119. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.119. --- 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 420bdf5a47..183d27e6ca 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.118" - "0di91awl8ii1fxrfyqbpfpn134apcc98fas7yisjg87f16bn4azl" + (make-linux-libre "4.4.119" + "1cicg1yxf6rvaz8jcz8mdvnkrba9hd16pkp9mm602bzgks6s1fy9" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From 8b1f76c443ce45ca9564d5231f5ac9d31618c08a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 1 Mar 2018 17:58:04 -0500 Subject: gnu: linux-libre@4.9: Update to 4.9.85. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.85. --- 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 183d27e6ca..07c677f7ba 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.84" - "08bgdcysva2igz4rc55slyz7nbzwz5skakh5c2iahsklg343pwbw" + (make-linux-libre "4.9.85" + "17anlawvbzw6m2lrbriy7kfncdllkl7n8vjzwl2dnrgxddavd3rf" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From 433765e5994af166e986716eeccae1f7ddc961e7 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 1 Mar 2018 17:58:35 -0500 Subject: gnu: linux-libre@4.14: Update to 4.14.23. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.23. (%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 07c677f7ba..93c31da587 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 "4.14.22") -(define %linux-libre-4.14-hash "1lhswcvgl077kzsln3nxmrdbnlc3b8mphjjmkqz0f2663wa6rhcv") +(define %linux-libre-4.14-version "4.14.23") +(define %linux-libre-4.14-hash "0mz8v67zj3wn3kdjb2a781vx7nc1imi7kmlvf1h1m0f37hw0s47y") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From da525e714a96213a3258d8e8b0f7a6090c53e90e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 1 Mar 2018 17:59:21 -0500 Subject: gnu: linux-libre: Update to 4.15.7. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.15.7. (%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 93c31da587..b922989018 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 "4.15.6") -(define %linux-libre-hash "13mv6wrhwjw2wll918c1r9l872wzzanvyi8rk6gv0k6cg0f56jal") +(define %linux-libre-version "4.15.7") +(define %linux-libre-hash "1h17wc12lvva5vcm2z06cf57ywxb6i2snm9vxixw1lwibnksrb6l") (define-public linux-libre (make-linux-libre %linux-libre-version -- cgit v1.2.3 From e9802319f7df328e8deb13d576ba31732183f693 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 1 Mar 2018 19:59:55 -0500 Subject: gnu: memcached: Update to 1.5.6. * gnu/packages/databases.scm (memcached): Update to 1.5.6. --- gnu/packages/databases.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index b99cd3d3d5..19c8efc9d4 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -396,14 +396,15 @@ mapping from string keys to string values.") (define-public memcached (package (name "memcached") - (version "1.5.0") + (version "1.5.6") (source (origin (method url-fetch) (uri (string-append "https://memcached.org/files/memcached-" version ".tar.gz")) (sha256 - (base32 "0chwc0g7wfvcad36z8pf2jbgygdnm9nm1l6pwjsn3d2b089gh0f0")))) + (base32 + "00szy9d4szaixi260dcd4846zci04y0sd47ia2lzg0bxkn2ywxcn")))) (build-system gnu-build-system) (inputs `(("libevent" ,libevent) -- cgit v1.2.3 From bb17b2be49fbe50cfc44b5987f7c32fc0db1ccc5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 1 Mar 2018 18:04:43 -0500 Subject: gnu: postgresql: Update to 10.3 [fixes CVE-2018-1058]. * gnu/packages/databases.scm (postgresql): Update to 10.3. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 19c8efc9d4..1793089003 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -700,14 +700,14 @@ as a drop-in replacement of MySQL.") (define-public postgresql (package (name "postgresql") - (version "10.2") + (version "10.3") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "1bav2iyi93h866skrrlqlvsp4sfv1sfww1s305zpzffxcadh0cpy")))) + "06lkcwsf851z49zqcws5yc77s2yrbaazf2nvbk38hpp31rw6i8kf")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-uuid=e2fs") -- cgit v1.2.3 From 703a8b7dc5ff0f7150c3eec18298b53e05d2da6b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 1 Mar 2018 18:05:20 -0500 Subject: gnu: postgresql@9.6: Update to 9.6.8 [fixes CVE-2018-1058]. * gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.8. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 1793089003..ba4ad9f9b9 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -745,14 +745,14 @@ pictures, sounds, or video.") (package (inherit postgresql) (name "postgresql") - (version "9.6.6") + (version "9.6.8") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "0m417h30s18rwa7yzkqqcdb22ifpcda2fpg2cyx8bxvjp3ydz71r")))))) + "0w7bwf19wbdd3jjbjv03cnx56qka4801srcbsayk9v792awv7zga")))))) (define-public qdbm (package -- cgit v1.2.3 From 8863f2f05106c225566df1c040560f5d97af78ca Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Thu, 1 Mar 2018 22:45:25 -0500 Subject: gnu: icecat: Update to 52.6.0-gnu1. * gnu/packages/gnuzilla.scm (icecat): Update to 52.6.0-gnu1. [source]: Remove patches that are no longer needed. * gnu/packages/patches/icecat-bug-1348660-pt5.patch, gnu/packages/patches/icecat-bug-1414945.patch, gnu/packages/patches/icecat-bug-1415133.patch, gnu/packages/patches/icecat-bug-1424373-pt2.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. --- gnu/local.mk | 4 - gnu/packages/gnuzilla.scm | 117 +--- gnu/packages/patches/icecat-bug-1348660-pt5.patch | 727 ---------------------- gnu/packages/patches/icecat-bug-1414945.patch | 73 --- gnu/packages/patches/icecat-bug-1415133.patch | 40 -- gnu/packages/patches/icecat-bug-1424373-pt2.patch | 183 ------ 6 files changed, 2 insertions(+), 1142 deletions(-) delete mode 100644 gnu/packages/patches/icecat-bug-1348660-pt5.patch delete mode 100644 gnu/packages/patches/icecat-bug-1414945.patch delete mode 100644 gnu/packages/patches/icecat-bug-1415133.patch delete mode 100644 gnu/packages/patches/icecat-bug-1424373-pt2.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index ba5af56bd9..dfe3ff5fc3 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -774,10 +774,6 @@ dist_patch_DATA = \ %D%/packages/patches/hwloc-tests-without-sysfs.patch \ %D%/packages/patches/hydra-disable-darcs-test.patch \ %D%/packages/patches/icecat-avoid-bundled-libraries.patch \ - %D%/packages/patches/icecat-bug-1348660-pt5.patch \ - %D%/packages/patches/icecat-bug-1415133.patch \ - %D%/packages/patches/icecat-bug-1414945.patch \ - %D%/packages/patches/icecat-bug-1424373-pt2.patch \ %D%/packages/patches/icecat-use-system-graphite2.patch \ %D%/packages/patches/icecat-use-system-harfbuzz.patch \ %D%/packages/patches/id3lib-CVE-2007-4460.patch \ diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 8d9573fb81..e3f1bfe8c0 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -401,7 +401,7 @@ security standards.") (define-public icecat (package (name "icecat") - (version "52.3.0-gnu1") + (version "52.6.0-gnu1") (source (origin (method url-fetch) @@ -410,7 +410,7 @@ security standards.") "/" name "-" version ".tar.bz2")) (sha256 (base32 - "00jki754d6310fxj1b7dbhqj69y5igck6gqg6rgfya243nsb56k9")) + "09fn54glqg1aa93hnz5zdcy07cps09dbni2b4200azh6nang630a")) (patches (list (search-patch "icecat-avoid-bundled-libraries.patch") @@ -418,120 +418,7 @@ security standards.") (search-patch "icecat-use-system-graphite2.patch") (mozilla-patch "icecat-bug-546387.patch" "d13e3fefb76e" "1b760r0bg2ydbl585wlmajljh1nlisrwxvjws5b28a3sgjy01i6k") (mozilla-patch "icecat-bug-1350152.patch" "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj") - (mozilla-patch "icecat-bug-1388166.patch" "fbb0bdb191d5" "1y8wpj38vw1dd6f375s9i0mrk9bd8z8gz5g70p4qynfllpkn072d") - (mozilla-patch "icecat-CVE-2017-7810-pt1.patch" "fbddb5cdd3c7" "0k5nyl2z1y2rx9fwqyfj64678yv6v3pnmshgk552pbzqmaf8i1hq") - (mozilla-patch "icecat-CVE-2017-7810-pt2.patch" "76c25987a275" "095b9vwsiza9ikbnnppfcld16h75x5bxjfxc73913y04n0i42ifh") - (mozilla-patch "icecat-CVE-2017-7810-pt3.patch" "32eec29a85a5" "057simakqg56jvas1wkskg5kszn96m74nca26x08d5w7rzmbv1q2") - (mozilla-patch "icecat-bug-1373222.patch" "ecef71fa933f" "0vsymgy5j702lamvh2riahni7rdj9ba3bd6i4a2m22d638rwp1i2") - (mozilla-patch "icecat-CVE-2017-7814.patch" "68a444daf85b" "1faaadaajidzb9i00710zxdyv370hlrdg1l5rw2ymfmzbjj4jqyd") - (mozilla-patch "icecat-bug-1376825.patch" "eeeec9cafc4e" "188qf6zi9kyxb33330yia6wmrd5mdyqn5hr1cl38zy7m3akv8srh") - (mozilla-patch "icecat-bug-1385272.patch" "d68fa12fbffc" "13gh97vz9n2b7303jcvr1072iy8bghy9chvbmxzvw82prvkscavw") - (mozilla-patch "icecat-bug-1390002.patch" "c24e6fc9f689" "0aswhy5fz2f6wzd5j5gg3nqvz707ip344089h2z2chcp146vxmf4") - (mozilla-patch "icecat-CVE-2017-7810-pt4.patch" "ae110cf77596" "0gdrkfq9wy9cfcdgbj14ci86xgh2prkbz69pfy97r9igd8059syw") - (mozilla-patch "icecat-CVE-2017-7810-pt5.patch" "b8417112486d" "1hya6lccz7vm51v4f6ww072794cwzmfn9xhxmvrnqbiyspxx5fz4") - (mozilla-patch "icecat-bug-1386905.patch" "badbf4308211" "0fj1pyjqfdsbrlfykwmkzav2nvdj1f4grwq3cal9f7ay6wjnfs9b") - (mozilla-patch "icecat-CVE-2017-7810-pt6.patch" "d78675515c78" "03w5hqy40xkckbaf5bm9kdbdqvp9ffvpk9mlrc9lja6b7qa4pjhg") - (mozilla-patch "icecat-bug-1382303.patch" "f01155fe4d54" "0hnz1kvmvspg6453kydsklbvrjgzn8x3djvrym3f2xl2yinaf90d") - (mozilla-patch "icecat-bug-1393467.patch" "4eec2a60622c" "1h006mwcsagq7mz7haymwgr7fn4zj14n5lxbjcmhdqrxdvma2hjj") - (mozilla-patch "icecat-bug-1384801.patch" "9556e792f905" "0i74r807189s8i78483caiifw68cn7fs543i4cys6k3gn12dhhjy") - (mozilla-patch "icecat-CVE-2017-7823.patch" "bd284765b5bc" "1c4hss87kc4qwx30magbqczm9h7zmwirjfc8zimqbrnwv9bbsfh3") - (mozilla-patch "icecat-CVE-2017-7805.patch" "113da8d46aa4" "1vy0lw659mwixmb57mgybga152rdwqd5zj1g7nfw1zgp15pfwr75") - (mozilla-patch "icecat-bug-1376399.patch" "58a574502ca9" "1zmg91pg0s5nwngc32a4fywidvxyaayvx1h052fsv0i4cfm16l9v") - (mozilla-patch "icecat-bug-1396570.patch" "24db61862c54" "0af1jjfma042xvn0xhgims1yvb2b51nhn4m0pcfwg3fn0llmka03") - (mozilla-patch "icecat-CVE-2017-7819.patch" "1a02f11c6efe" "18a9qvdvrqw34qw3lljg6gkn358jl23lyimhmbc964023rhs36sz") - (mozilla-patch "icecat-CVE-2017-7810-pt7.patch" "002686d9536f" "065g0d759wfiaj69b1sqg7l08p2knc0q9m9hvkgwwsf0r78xcbjj") - (mozilla-patch "icecat-CVE-2017-7810-pt8.patch" "eaadb31758d8" "0b3k3la6ykac5mbp9gyqqgjbmj19vx9sl1b0wp387qar0p12nyaz") - (mozilla-patch "icecat-bug-1368269.patch" "0cff5e66e0f4" "0jb0wqi7c0ih4441s1908j6gv18v4inh7k2w47h3c9nhz4rgyrw7") - (mozilla-patch "icecat-CVE-2017-7793.patch" "6ff3c82962f0" "0bw82034kdmrpznigbavzzsiybzrw8giyf8v0z2cxf6mwl72bf9k") - (mozilla-patch "icecat-bug-1400399.patch" "d6f78b1349b7" "0i3gwr2al3xl65yfa3nimvy8dp0jzpx21f6bjw18xwn7zkkh9j54") - (mozilla-patch "icecat-bug-1400721.patch" "285cde398833" "0a1i32zl30wfyw7zkqj595s94n6wdlg5c495m0910pd05pjg3qam") - (mozilla-patch "icecat-CVE-2017-7826-pt01.patch" "98b3988592a6" "03wy173lj6mvmh5q92brf596h8676h0zasgqfnndpvsmsiaih120") - (mozilla-patch "icecat-CVE-2017-7826-pt02.patch" "47590f0c274b" "0zsys6dcyhfb4a8k2dhsls7425jg6r1ijlrsn1lc5smwyf62zx5v") - (mozilla-patch "icecat-CVE-2017-7826-pt03.patch" "55b435cbbb55" "1gcasaqrxa13a55v05bkxl3d1md829kpfhqiaws83wn08x28l0my") - (mozilla-patch "icecat-CVE-2017-7826-pt04.patch" "8549cf2dab3e" "168gs32ncavaj9xn4gwhh9i01cbpnhgx9yn333apsrc1gwknpvsr") - (mozilla-patch "icecat-CVE-2017-7826-pt05.patch" "349acf56ff49" "1vwn87rdryfjsn809pl50xmr82q98gz3vz9h6clkd905vbd9rwz7") - (mozilla-patch "icecat-CVE-2017-7826-pt06.patch" "3af5bf8bdea0" "07az28dnpxr36j7i3llxkrlkrmg0bwk4f3sm75x1f0r1v5575p3p") - (mozilla-patch "icecat-CVE-2017-7826-pt07.patch" "592df6088926" "1gy27idik4b6wcg4szww08cmpcljssja8wql6w1d807h7ni65lr7") - (mozilla-patch "icecat-CVE-2017-7826-pt08.patch" "77a2d4610275" "13ysbwflnysj4rs45ibckd621s0vyg1s8dvannlvanvrz1g72zcz") - (mozilla-patch "icecat-CVE-2017-7826-pt09.patch" "2b30335d0b95" "0hs5cwickvfw7r5dn7y148jgr2b21hl613qp83k56634d0y64qwp") - (mozilla-patch "icecat-CVE-2017-7826-pt10.patch" "d6f008f95598" "0xclxrbg7pv8pa2j15p0gy9c8sigy2i9j0kvazl5fbyg6jsg3xgd") - (mozilla-patch "icecat-CVE-2017-7826-pt11.patch" "ab9b51cd75ac" "08jy3rbkyh934aw261ls0s87947d2mhss7xqk1xfdir9crij2g27") - (mozilla-patch "icecat-bug-1343147-pt1.patch" "971d6345bc3a" "13791cvc51i991i5qyz6gp94vwzwkx479bnr8fsf8dw7z72wrsch") - (mozilla-patch "icecat-bug-1343147-pt2.patch" "60df7db06669" "0r372g1zksvkzyz0qpq0mp30frilgsfxxx2xida8xc08wgxp5lh9") - (mozilla-patch "icecat-CVE-2017-7826-pt12.patch" "df49c25e6e4c" "0j77xbkxpflqf4jlccrv61vq0jgp4lfn8kb0zw1lswp3cyd6ml4i") - (mozilla-patch "icecat-CVE-2017-7826-pt13.patch" "3b899f872623" "01zjcpm8yp4s8yf4mj1bzq01aylmi69kd8qv0rrcl9hmj4g3pzr2") - (mozilla-patch "icecat-CVE-2017-7826-pt14.patch" "3d6d558ae6a6" "17wynknvs5wi7m9g5vn43rjmivbg1l6pnv8jymz1ccidy27qgdqi") - (mozilla-patch "icecat-CVE-2017-7826-pt15.patch" "8426754b7130" "0bbm2294bkvld55rdbpsc8b82ljqdcxpbg6cwdzvwfhqayl2pnqm") - (mozilla-patch "icecat-CVE-2017-7828-pt1.patch" "5ddd5d2aa769" "12z5i8h6qwjb1h1fvp2426bgsnsxx539d8k2is9x1q4133356niy") - (mozilla-patch "icecat-CVE-2017-7826-pt16.patch" "dd068f4e132a" "17qy9c1vfkz3pj6y8qmqbic73wrangsbdlylk2s54nbzhhp9cj1g") - (mozilla-patch "icecat-CVE-2017-7826-pt17.patch" "e6bd533b57e9" "1mmqav9yhxd0j47yffcdykaqjibfwjsk0jn0f44099s87y8qn9zy") - (mozilla-patch "icecat-CVE-2017-7826-pt18.patch" "2a87fb6b9c07" "0z0scw4y1vqhqkbw1ag14g8xrif14l95x7fd50q2sw425lli29lc") - (mozilla-patch "icecat-bug-1404910.patch" "5007f2472f64" "0ns1l4yipwbb52sps2xzg30qd1rkpwykxq4chjg3wllhmcxbvvpw") - (mozilla-patch "icecat-CVE-2017-7830.patch" "04e3b5c1f0b2" "0nmv3jnx94ykxg64xkiwc8kx4df8zw7y5yzjnxz1sll2v88b9hmf") - (mozilla-patch "icecat-CVE-2017-7828-pt2.patch" "2f48c03d9b3f" "16qdy3rahmkhsjnzqjcgzg1a4k7czd40m04gs9i75cd88kbripri") - (mozilla-patch "icecat-bug-1348660-pt1.patch" "a352bfcbaf55" "1j3kxnhci9fh3lj8rizbcfv8xzn5kikxwpfy8a091d51sdn20873") - (mozilla-patch "icecat-bug-1348660-pt2.patch" "57f43e2ab9b5" "1jva4y79zb85npak3mddrx5rsf4mxczb314kcr8yhlkwqv0nx5sp") - (mozilla-patch "icecat-bug-1348660-pt3.patch" "917d65bb8896" "0k29y8i96lanqjjm6vybg0s6gjbk1mz5bfnga6aj1g0hnb7c3s8d") - (mozilla-patch "icecat-bug-1348660-pt4.patch" "28934912eede" "1mhxw26050l3d09n8w912a86df87afcshvsk9k1k375anfk0927x") - (search-patch "icecat-bug-1348660-pt5.patch") - (mozilla-patch "icecat-bug-1348660-pt6.patch" "556ff3bfb9fc" "0kckjc8jp885xfaiwx2b9qnk1plqjhi0mwhjjcmfajvh3l3mrl8h") - (mozilla-patch "icecat-bug-1350564.patch" "2abf26abb2a2" "0axdzp9g9k74wpkwrsdx263h01sv9bd3rarhhl68xnvc7n6i45lx") - (mozilla-patch "icecat-bug-1404787.patch" "8335e1d7b140" "17d7kb8ginzflhdkrbi60vh2b907spbzmvwih7a595gqpihmnqqn") - (mozilla-patch "icecat-CVE-2017-7826-pt19.patch" "de336078d36b" "0gyzbap8hr1iywk0x2x0h7z7zp7q89hi56h8c03vvc7771dkvjkf") - (mozilla-patch "icecat-bug-1047098-pt1.patch" "088577f0c46e" "0y3sz6kx07ls7jsvhqhhrl6v69a94wqvv3lz7hnplah23y06h17z") - (mozilla-patch "icecat-bug-1047098-pt2.patch" "c7e3abf74023" "11dcjzx56v4yb2dvm23j2g86q8yva2hc69lmb7s5w18l6ygwwhzr") - (mozilla-patch "icecat-bug-1047098-pt3.patch" "36bd15d14c5a" "0cb3l3hpsgk674f08kfamxhqfga3ah5v904gpxq9ag006vzd2cxz") - (mozilla-patch "icecat-bug-1404105.patch" "2909ba991f31" "126vssj57dc800347f075wlnjzcwamnxxmgxl9w78jpb0hj9gf16") - (search-patch "icecat-bug-1415133.patch") - (mozilla-patch "icecat-bug-1355576.patch" "cf34a0574e58" "1z7sa1d12hypgivm5xxn32s58afpjcij97jvnafcgnfvxywrgr1m") - (mozilla-patch "icecat-CVE-2017-7843.patch" "f6216ea8b8fc" "0jnhdkj0ch9mj01mzlvhjgf8zsxlbg6m7yvpq99qr7xmg0pzbgwl") - (mozilla-patch "icecat-bug-1413741.patch" "4e00ce2897c4" "0k95vi31glia2i03djidkc0gkwp9qldy34fz1rxcj56a1iphbq7w") - (mozilla-patch "icecat-CVE-2018-5089-pt01.patch" "92d450811409" "0xsvggnr0y65nd52nkbjvpcbs5nd84pvbayk5vinbx1mnk2wh2vy") - (mozilla-patch "icecat-CVE-2018-5089-pt02.patch" "7eba7d14704a" "1vi17qmjzh3kji14iz370kvs4425asgp93ns2chf5ldlq5b9196g") - (mozilla-patch "icecat-CVE-2018-5089-pt03.patch" "457d023c167e" "11g8hg8yp20lsn52dx1ym8r4yjsnsmx0h182d6nbl6ab9wp7d1m9") - (mozilla-patch "icecat-CVE-2018-5089-pt04.patch" "5e7b16213198" "14c4x6c3mygf8p77n9bia5rndjpngbvik1r1ylk97k3ggy4fj6zh") - (mozilla-patch "icecat-CVE-2018-5102.patch" "0712b6cbbdc8" "0rllsq6ckpms7g9k6qky1gr5rz1gav4widrha6w1s9f88cbrqgk5") - (mozilla-patch "icecat-CVE-2018-5089-pt05.patch" "084c427ccf99" "0sjdy2iang09a9g6liavpjgry04dp6smjgj0y7lp5lfqijdr8q2d") - (mozilla-patch "icecat-CVE-2018-5089-pt06.patch" "1bfb3d8d4510" "0c2dcxj74ijs6qf9sqcbj8w998hblic66vy41818z7xnw46j5j1j") - (mozilla-patch "icecat-bug-1414425.patch" "5623e01e63a8" "08dn3v96bsb61hy3wfxz43fhn1mk9vlm5ydvdjgi3wiqadvacgzs") - (mozilla-patch "icecat-CVE-2018-5089-pt07.patch" "14a389d40329" "0f4gbak5bd2walxrxs3myig28v9lhvplf3a1nws1a4ajx80slzq1") - (mozilla-patch "icecat-bug-1415441.patch" "7339297cddb7" "017lbw0mn5rwzb2abfw6qrk07m3r96vwbj81cmqvdfnmprcjni5j") - (mozilla-patch "icecat-CVE-2018-5096.patch" "aa55d4cdaee5" "1l3qwjfx0jsbbw2dg8bsnx7k47zibamgswndq0d1bchnmary62aw") - (mozilla-patch "icecat-bug-1382358.patch" "762f4e53889a" "0n61zrb6rz9bhhdsqs5ziwaiy81pq52c76p9qmi9hrxbn24ism1k") - (mozilla-patch "icecat-CVE-2018-5089-pt08.patch" "0152d097672f" "16ybg718calvciv00kil8s97lhh11hj6gx0acf73r44xfkvm8nfg") - (search-patch "icecat-bug-1414945.patch") - (mozilla-patch "icecat-CVE-2018-5089-pt09.patch" "079356ed5317" "107c0b93g2k743wvhwz2ps3j6p09qld7d0raljijv5y5n8q4wp92") - (mozilla-patch "icecat-CVE-2018-5089-pt10.patch" "93e4994a892c" "00r2qxw3619529vy9d04dl9kcziqy3fv3iawgy9svzygyx1kj5wx") - (mozilla-patch "icecat-CVE-2018-5089-pt11.patch" "f8a6e1864832" "1wbxn0v50637yjg8b8675k01x9cyx95jpjxpyqfaa97762qkznba") - (mozilla-patch "icecat-CVE-2018-5089-pt12.patch" "0cc1c9068714" "1qmqpi14zs7c95k3c7396gpp6apb622k0mgv553kw4rr81nj1yac") - (mozilla-patch "icecat-CVE-2018-5095.patch" "ce6f3fb2bf58" "1b1msb5d5jsgrqa2hkbsrm0n54qdmx1b2bf65v44v17appa03lra") - (mozilla-patch "icecat-CVE-2018-5103.patch" "6b4d3c5d5e51" "074p93dhwr1ckhypkjpblnmg9hg44a9030g1glqffi9dyn3iq3k4") - (mozilla-patch "icecat-bug-1411745.patch" "1a510ee578a0" "1imb7glh2m1zwvvpvr4k4iddms5byqzr35j7kv3y5is77aiwl4z5") (mozilla-patch "icecat-bug-1411708.patch" "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip") - (mozilla-patch "icecat-CVE-2018-5091.patch" "bc166be85bb4" "0w1lrjzfrfflaw4l6sfi3ir81iyi9gyfck5g41dwp0jc1b59jzvg") - (mozilla-patch "icecat-CVE-2018-5089-pt13.patch" "66cfc3c4047d" "05j8ic4lv2d2ygr6d62rkdlfyg2rpljalwrkkhllinw2dfi3n15b") - (mozilla-patch "icecat-CVE-2018-5098.patch" "3236ffdf0ced" "1kvk4qyslaj1ldgs1wpxnf79zajcihzcd1zvbrg990i3hgyn3gk3") - (mozilla-patch "icecat-bug-1424373-pt1.patch" "320032aaa068" "1ch282qibprz1q0f2imvynh4sg7gads6sf3ayhjcd62zjncpgyz7") - (search-patch "icecat-bug-1424373-pt2.patch") - (mozilla-patch "icecat-CVE-2018-5089-pt14.patch" "c2945f1249eb" "18p0344w6grpyfiz8dczfw977p0qy37iqv95whgnrjli2ab51kji") - (mozilla-patch "icecat-CVE-2018-5117-pt1.patch" "263165eacc54" "0518xnd9f4qkn7l0z73kldm9dr33y6hf054ril4f8r2j8s9fy33i") - (mozilla-patch "icecat-CVE-2018-5117-pt2.patch" "58e87d9cc44e" "0j9qwjm25bmhw0sj426yl4fqaa6zknf5cjk0yisdd3895652n5i4") - (mozilla-patch "icecat-CVE-2018-5089-pt15.patch" "aa4b11615431" "0whfvwaj3dmk89ah2kbv7zz7a8ckqa0xajf5fl12bgl7q8c8ndnm") - (mozilla-patch "icecat-CVE-2018-5104.patch" "66761c5bfbe1" "076128pxc7ik1zq2v0d5m6vd7nls2030jzdc4w0ggy8hd5yyb8g9") - (mozilla-patch "icecat-bug-1408631.patch" "6f5c8df1925d" "1hgr18p5dwhlsan6jxlj3ay7cbfyywk40bpbnjc8gqmq6y25cn48") - (mozilla-patch "icecat-bug-1422735.patch" "b88ef76f5687" "0rzpxfrhddc0238rq3r1b02j95g0rdplk1fjmk85m51xvggh9086") - (mozilla-patch "icecat-bug-1261963.patch" "d0c98f5b6c12" "1z9jn19hnwjand9c0ifc39gq71nz17jjqy2s5fqr2z06y8qys62h") - (mozilla-patch "icecat-CVE-2018-5089-pt16.patch" "f7865afb1fe6" "0i7ydmcr1g0ih3myyxaxjq6wfg3rvq5j4893kjqksqihfqrkzs4j") - (mozilla-patch "icecat-CVE-2018-5097.patch" "9fb7614319df" "1xirahk06w8pyw4pdh64f4pg3qcb7c8x8frrmad2895fagy14g4k") - (mozilla-patch "icecat-mitigate-spectre.patch" "81d6465bd7c2" "1za5l249pb5x7f283vrimy0ankjzvwa99hfql3v4fm5a4grjkj9n") - (mozilla-patch "icecat-CVE-2018-5089-pt17.patch" "5f753161df25" "1k2mpwagz08wzxfzwy2b4a0pz0hkhdqby6n11i7pasx3ary670km") - (mozilla-patch "icecat-CVE-2018-5099.patch" "b95d654de120" "1cv7nz2gsyjjigw6wv4xagh8q6bcg0971md8b6xjvz5m26aynlaw") - (mozilla-patch "icecat-bug-1408631.patch" "3b1faddc0e5f" "0817x5mrdyjj0gc9yi19m6d78d18ypc9nbld64d2axhc8v9bz3xf") - (mozilla-patch "icecat-glibc-2.26.patch" "57d4fae4dffe" "1sv7kp7m4i7n31ny8k7cpjsrqpxh5y5jm27sh2cgpj7fhi5kqsj2") - (mozilla-patch "icecat-CVE-2018-5089-pt18.patch" "fe271a2b9503" "11wr8mdxw01dlmzkq55hf0qd52cwmx4vk96cff66d4kkl1dbj6qn") - (mozilla-patch "icecat-CVE-2018-5089-pt19.patch" "410da936a1e8" "14dvaysz0svlh50kdabjhd2s5avz6p93sbyqhwik5rlvcg5ax5zp") - (mozilla-patch "icecat-CVE-2018-5089-pt20.patch" "8368a9a379e3" "0fqq01ms7m4kb9b10n8gy5n9n4x43crz2gn1r6c4ny52wzgm3j6f") - (mozilla-patch "icecat-CVE-2018-5089-pt21.patch" "a7c8e85285e2" "1caa2w5r8rqb1qrk4mgf2vw1k592idvqmgs8qfz2dp2744kk6z98") (mozilla-patch "icecat-bug-1375217.patch" "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv") (mozilla-patch "icecat-bug-1261175.patch" "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v") (mozilla-patch "icecat-bug-1433005.patch" "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk") diff --git a/gnu/packages/patches/icecat-bug-1348660-pt5.patch b/gnu/packages/patches/icecat-bug-1348660-pt5.patch deleted file mode 100644 index b0bede3b38..0000000000 --- a/gnu/packages/patches/icecat-bug-1348660-pt5.patch +++ /dev/null @@ -1,727 +0,0 @@ -This is a subset of the following changeset from upstream: - https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/5e07bd37ac61 - -This excludes all test code from that changeset, including a GIT binary patch -that is not supported by Guix's patch-and-repack mechanism. - -# HG changeset patch -# User Jan Varga -# Date 1490181244 -3600 -# Node ID 5e07bd37ac6162f218dfe03ed83b5dcca9653b68 -# Parent 28934912eede9e14895baf4af7575ca9639f59ee -Bug 1348660 - Part 5: Implement a method to retrieve usage data for all origins at once. r=btseng, a=lizzard - -diff --git a/dom/quota/ActorsChild.cpp b/dom/quota/ActorsChild.cpp ---- a/dom/quota/ActorsChild.cpp -+++ b/dom/quota/ActorsChild.cpp -@@ -137,16 +137,52 @@ QuotaUsageRequestChild::HandleResponse(n - AssertIsOnOwningThread(); - MOZ_ASSERT(NS_FAILED(aResponse)); - MOZ_ASSERT(mRequest); - - mRequest->SetError(aResponse); - } - - void -+QuotaUsageRequestChild::HandleResponse(const nsTArray& aResponse) -+{ -+ AssertIsOnOwningThread(); -+ MOZ_ASSERT(mRequest); -+ -+ RefPtr variant = new nsVariant(); -+ -+ if (aResponse.IsEmpty()) { -+ variant->SetAsEmptyArray(); -+ } else { -+ nsTArray> usageResults; -+ -+ const uint32_t count = aResponse.Length(); -+ -+ usageResults.SetCapacity(count); -+ -+ for (uint32_t index = 0; index < count; index++) { -+ auto& originUsage = aResponse[index]; -+ -+ RefPtr usageResult = new UsageResult(originUsage.origin(), -+ originUsage.persisted(), -+ originUsage.usage()); -+ -+ usageResults.AppendElement(usageResult.forget()); -+ } -+ -+ variant->SetAsArray(nsIDataType::VTYPE_INTERFACE_IS, -+ &NS_GET_IID(nsIQuotaUsageResult), -+ usageResults.Length(), -+ static_cast(usageResults.Elements())); -+ } -+ -+ mRequest->SetResult(variant); -+} -+ -+void - QuotaUsageRequestChild::HandleResponse(const OriginUsageResponse& aResponse) - { - AssertIsOnOwningThread(); - MOZ_ASSERT(mRequest); - - RefPtr result = - new OriginUsageResult(aResponse.usage(), - aResponse.fileUsage(), -@@ -177,16 +213,20 @@ QuotaUsageRequestChild::Recv__delete__(c - AssertIsOnOwningThread(); - MOZ_ASSERT(mRequest); - - switch (aResponse.type()) { - case UsageRequestResponse::Tnsresult: - HandleResponse(aResponse.get_nsresult()); - break; - -+ case UsageRequestResponse::TAllUsageResponse: -+ HandleResponse(aResponse.get_AllUsageResponse().originUsages()); -+ break; -+ - case UsageRequestResponse::TOriginUsageResponse: - HandleResponse(aResponse.get_OriginUsageResponse()); - break; - - default: - MOZ_CRASH("Unknown response type!"); - } - -diff --git a/dom/quota/ActorsChild.h b/dom/quota/ActorsChild.h ---- a/dom/quota/ActorsChild.h -+++ b/dom/quota/ActorsChild.h -@@ -93,16 +93,19 @@ private: - - // Only destroyed by QuotaChild. - ~QuotaUsageRequestChild(); - - void - HandleResponse(nsresult aResponse); - - void -+ HandleResponse(const nsTArray& aResponse); -+ -+ void - HandleResponse(const OriginUsageResponse& aResponse); - - // IPDL methods are only called by IPDL. - virtual void - ActorDestroy(ActorDestroyReason aWhy) override; - - virtual bool - Recv__delete__(const UsageRequestResponse& aResponse) override; -diff --git a/dom/quota/ActorsParent.cpp b/dom/quota/ActorsParent.cpp ---- a/dom/quota/ActorsParent.cpp -+++ b/dom/quota/ActorsParent.cpp -@@ -1039,16 +1039,42 @@ private: - // IPDL methods. - void - ActorDestroy(ActorDestroyReason aWhy) override; - - bool - RecvCancel() override; - }; - -+class GetUsageOp final -+ : public QuotaUsageRequestBase -+{ -+ nsTArray mOriginUsages; -+ nsDataHashtable mOriginUsagesIndex; -+ -+ bool mGetAll; -+ -+public: -+ explicit GetUsageOp(const UsageRequestParams& aParams); -+ -+private: -+ ~GetUsageOp() -+ { } -+ -+ nsresult -+ TraverseRepository(QuotaManager* aQuotaManager, -+ PersistenceType aPersistenceType); -+ -+ nsresult -+ DoDirectoryWork(QuotaManager* aQuotaManager) override; -+ -+ void -+ GetResponse(UsageRequestResponse& aResponse) override; -+}; -+ - class GetOriginUsageOp final - : public QuotaUsageRequestBase - { - // If mGetGroupUsage is false, we use mUsageInfo to record the origin usage - // and the file usage. Otherwise, we use it to record the group usage and the - // limit. - UsageInfo mUsageInfo; - -@@ -5693,16 +5719,20 @@ PQuotaUsageRequestParent* - Quota::AllocPQuotaUsageRequestParent(const UsageRequestParams& aParams) - { - AssertIsOnBackgroundThread(); - MOZ_ASSERT(aParams.type() != UsageRequestParams::T__None); - - RefPtr actor; - - switch (aParams.type()) { -+ case UsageRequestParams::TAllUsageParams: -+ actor = new GetUsageOp(aParams); -+ break; -+ - case UsageRequestParams::TOriginUsageParams: - actor = new GetOriginUsageOp(aParams); - break; - - default: - MOZ_CRASH("Should never get here!"); - } - -@@ -6033,16 +6063,189 @@ QuotaUsageRequestBase::RecvCancel() - if (mCanceled.exchange(true)) { - NS_WARNING("Canceled more than once?!"); - return false; - } - - return true; - } - -+GetUsageOp::GetUsageOp(const UsageRequestParams& aParams) -+ : mGetAll(aParams.get_AllUsageParams().getAll()) -+{ -+ AssertIsOnOwningThread(); -+ MOZ_ASSERT(aParams.type() == UsageRequestParams::TAllUsageParams); -+} -+ -+nsresult -+GetUsageOp::TraverseRepository(QuotaManager* aQuotaManager, -+ PersistenceType aPersistenceType) -+{ -+ AssertIsOnIOThread(); -+ MOZ_ASSERT(aQuotaManager); -+ -+ nsresult rv; -+ -+ nsCOMPtr directory = -+ do_CreateInstance(NS_LOCAL_FILE_CONTRACTID, &rv); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ rv = directory->InitWithPath(aQuotaManager->GetStoragePath(aPersistenceType)); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ bool exists; -+ rv = directory->Exists(&exists); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ if (!exists) { -+ return NS_OK; -+ } -+ -+ nsCOMPtr entries; -+ rv = directory->GetDirectoryEntries(getter_AddRefs(entries)); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ bool persistent = aPersistenceType == PERSISTENCE_TYPE_PERSISTENT; -+ -+ bool hasMore; -+ while (NS_SUCCEEDED((rv = entries->HasMoreElements(&hasMore))) && -+ hasMore && !mCanceled) { -+ nsCOMPtr entry; -+ rv = entries->GetNext(getter_AddRefs(entry)); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ nsCOMPtr originDir = do_QueryInterface(entry); -+ MOZ_ASSERT(originDir); -+ -+ bool isDirectory; -+ rv = originDir->IsDirectory(&isDirectory); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ if (!isDirectory) { -+ nsString leafName; -+ rv = originDir->GetLeafName(leafName); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ if (!leafName.EqualsLiteral(DSSTORE_FILE_NAME)) { -+ QM_WARNING("Something (%s) in the repository that doesn't belong!", -+ NS_ConvertUTF16toUTF8(leafName).get()); -+ } -+ continue; -+ } -+ -+ int64_t timestamp; -+ nsCString suffix; -+ nsCString group; -+ nsCString origin; -+ bool isApp; -+ rv = aQuotaManager->GetDirectoryMetadata2WithRestore(originDir, -+ persistent, -+ ×tamp, -+ suffix, -+ group, -+ origin, -+ &isApp); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ if (!mGetAll && -+ aQuotaManager->IsOriginWhitelistedForPersistentStorage(origin)) { -+ continue; -+ } -+ -+ OriginUsage* originUsage; -+ -+ // We can't store pointers to OriginUsage objects in the hashtable -+ // since AppendElement() reallocates its internal array buffer as number -+ // of elements grows. -+ uint32_t index; -+ if (mOriginUsagesIndex.Get(origin, &index)) { -+ originUsage = &mOriginUsages[index]; -+ } else { -+ index = mOriginUsages.Length(); -+ -+ originUsage = mOriginUsages.AppendElement(); -+ -+ originUsage->origin() = origin; -+ originUsage->persisted() = false; -+ originUsage->usage() = 0; -+ -+ mOriginUsagesIndex.Put(origin, index); -+ } -+ -+ UsageInfo usageInfo; -+ rv = GetUsageForOrigin(aQuotaManager, -+ aPersistenceType, -+ group, -+ origin, -+ isApp, -+ &usageInfo); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ originUsage->usage() = originUsage->usage() + usageInfo.TotalUsage(); -+ } -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ return NS_OK; -+} -+ -+nsresult -+GetUsageOp::DoDirectoryWork(QuotaManager* aQuotaManager) -+{ -+ AssertIsOnIOThread(); -+ -+ PROFILER_LABEL("Quota", "GetUsageOp::DoDirectoryWork", -+ js::ProfileEntry::Category::OTHER); -+ -+ nsresult rv; -+ -+ for (const PersistenceType type : kAllPersistenceTypes) { -+ rv = TraverseRepository(aQuotaManager, type); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ } -+ -+ return NS_OK; -+} -+ -+void -+GetUsageOp::GetResponse(UsageRequestResponse& aResponse) -+{ -+ AssertIsOnOwningThread(); -+ -+ aResponse = AllUsageResponse(); -+ -+ if (!mOriginUsages.IsEmpty()) { -+ nsTArray& originUsages = -+ aResponse.get_AllUsageResponse().originUsages(); -+ -+ mOriginUsages.SwapElements(originUsages); -+ } -+} -+ - GetOriginUsageOp::GetOriginUsageOp(const UsageRequestParams& aParams) - : mParams(aParams.get_OriginUsageParams()) - , mGetGroupUsage(aParams.get_OriginUsageParams().getGroupUsage()) - { - AssertIsOnOwningThread(); - MOZ_ASSERT(aParams.type() == UsageRequestParams::TOriginUsageParams); - } - -diff --git a/dom/quota/PQuota.ipdl b/dom/quota/PQuota.ipdl ---- a/dom/quota/PQuota.ipdl -+++ b/dom/quota/PQuota.ipdl -@@ -12,24 +12,30 @@ include "mozilla/dom/quota/Serialization - - using mozilla::dom::quota::PersistenceType - from "mozilla/dom/quota/PersistenceType.h"; - - namespace mozilla { - namespace dom { - namespace quota { - -+struct AllUsageParams -+{ -+ bool getAll; -+}; -+ - struct OriginUsageParams - { - PrincipalInfo principalInfo; - bool getGroupUsage; - }; - - union UsageRequestParams - { -+ AllUsageParams; - OriginUsageParams; - }; - - struct ClearOriginParams - { - PrincipalInfo principalInfo; - PersistenceType persistenceType; - bool persistenceTypeIsExplicit; -diff --git a/dom/quota/PQuotaUsageRequest.ipdl b/dom/quota/PQuotaUsageRequest.ipdl ---- a/dom/quota/PQuotaUsageRequest.ipdl -+++ b/dom/quota/PQuotaUsageRequest.ipdl -@@ -3,26 +3,39 @@ - * You can obtain one at http://mozilla.org/MPL/2.0/. */ - - include protocol PQuota; - - namespace mozilla { - namespace dom { - namespace quota { - -+struct OriginUsage -+{ -+ nsCString origin; -+ bool persisted; -+ uint64_t usage; -+}; -+ -+struct AllUsageResponse -+{ -+ OriginUsage[] originUsages; -+}; -+ - struct OriginUsageResponse - { - uint64_t usage; - uint64_t fileUsage; - uint64_t limit; - }; - - union UsageRequestResponse - { - nsresult; -+ AllUsageResponse; - OriginUsageResponse; - }; - - protocol PQuotaUsageRequest - { - manager PQuota; - - parent: -diff --git a/dom/quota/QuotaManagerService.cpp b/dom/quota/QuotaManagerService.cpp ---- a/dom/quota/QuotaManagerService.cpp -+++ b/dom/quota/QuotaManagerService.cpp -@@ -490,16 +490,41 @@ QuotaManagerService::RemoveIdleObserver( - - NS_IMPL_ADDREF(QuotaManagerService) - NS_IMPL_RELEASE_WITH_DESTROY(QuotaManagerService, Destroy()) - NS_IMPL_QUERY_INTERFACE(QuotaManagerService, - nsIQuotaManagerService, - nsIObserver) - - NS_IMETHODIMP -+QuotaManagerService::GetUsage(nsIQuotaUsageCallback* aCallback, -+ bool aGetAll, -+ nsIQuotaUsageRequest** _retval) -+{ -+ MOZ_ASSERT(NS_IsMainThread()); -+ MOZ_ASSERT(aCallback); -+ -+ RefPtr request = new UsageRequest(aCallback); -+ -+ AllUsageParams params; -+ -+ params.getAll() = aGetAll; -+ -+ nsAutoPtr info(new UsageRequestInfo(request, params)); -+ -+ nsresult rv = InitiateRequest(info); -+ if (NS_WARN_IF(NS_FAILED(rv))) { -+ return rv; -+ } -+ -+ request.forget(_retval); -+ return NS_OK; -+} -+ -+NS_IMETHODIMP - QuotaManagerService::GetUsageForPrincipal(nsIPrincipal* aPrincipal, - nsIQuotaUsageCallback* aCallback, - bool aGetGroupUsage, - nsIQuotaUsageRequest** _retval) - { - MOZ_ASSERT(NS_IsMainThread()); - MOZ_ASSERT(aPrincipal); - MOZ_ASSERT(aCallback); -diff --git a/dom/quota/QuotaRequests.cpp b/dom/quota/QuotaRequests.cpp ---- a/dom/quota/QuotaRequests.cpp -+++ b/dom/quota/QuotaRequests.cpp -@@ -86,16 +86,25 @@ RequestBase::GetResultCode(nsresult* aRe - if (!mHaveResultOrErrorCode) { - return NS_ERROR_FAILURE; - } - - *aResultCode = mResultCode; - return NS_OK; - } - -+UsageRequest::UsageRequest(nsIQuotaUsageCallback* aCallback) -+ : mCallback(aCallback) -+ , mBackgroundActor(nullptr) -+ , mCanceled(false) -+{ -+ AssertIsOnOwningThread(); -+ MOZ_ASSERT(aCallback); -+} -+ - UsageRequest::UsageRequest(nsIPrincipal* aPrincipal, - nsIQuotaUsageCallback* aCallback) - : RequestBase(aPrincipal) - , mCallback(aCallback) - , mBackgroundActor(nullptr) - , mCanceled(false) - { - AssertIsOnOwningThread(); -diff --git a/dom/quota/QuotaRequests.h b/dom/quota/QuotaRequests.h ---- a/dom/quota/QuotaRequests.h -+++ b/dom/quota/QuotaRequests.h -@@ -73,16 +73,18 @@ class UsageRequest final - - nsCOMPtr mResult; - - QuotaUsageRequestChild* mBackgroundActor; - - bool mCanceled; - - public: -+ explicit UsageRequest(nsIQuotaUsageCallback* aCallback); -+ - UsageRequest(nsIPrincipal* aPrincipal, - nsIQuotaUsageCallback* aCallback); - - void - SetBackgroundActor(QuotaUsageRequestChild* aBackgroundActor); - - void - ClearBackgroundActor() -diff --git a/dom/quota/QuotaResults.cpp b/dom/quota/QuotaResults.cpp ---- a/dom/quota/QuotaResults.cpp -+++ b/dom/quota/QuotaResults.cpp -@@ -5,16 +5,53 @@ - * file, You can obtain one at http://mozilla.org/MPL/2.0/. */ - - #include "QuotaResults.h" - - namespace mozilla { - namespace dom { - namespace quota { - -+UsageResult::UsageResult(const nsACString& aOrigin, -+ bool aPersisted, -+ uint64_t aUsage) -+ : mOrigin(aOrigin) -+ , mUsage(aUsage) -+ , mPersisted(aPersisted) -+{ -+} -+ -+NS_IMPL_ISUPPORTS(UsageResult, -+ nsIQuotaUsageResult) -+ -+NS_IMETHODIMP -+UsageResult::GetOrigin(nsACString& aOrigin) -+{ -+ aOrigin = mOrigin; -+ return NS_OK; -+} -+ -+NS_IMETHODIMP -+UsageResult::GetPersisted(bool* aPersisted) -+{ -+ MOZ_ASSERT(aPersisted); -+ -+ *aPersisted = mPersisted; -+ return NS_OK; -+} -+ -+NS_IMETHODIMP -+UsageResult::GetUsage(uint64_t* aUsage) -+{ -+ MOZ_ASSERT(aUsage); -+ -+ *aUsage = mUsage; -+ return NS_OK; -+} -+ - OriginUsageResult::OriginUsageResult(uint64_t aUsage, - uint64_t aFileUsage, - uint64_t aLimit) - : mUsage(aUsage) - , mFileUsage(aFileUsage) - , mLimit(aLimit) - { - } -diff --git a/dom/quota/QuotaResults.h b/dom/quota/QuotaResults.h ---- a/dom/quota/QuotaResults.h -+++ b/dom/quota/QuotaResults.h -@@ -8,16 +8,36 @@ - #define mozilla_dom_quota_QuotaResults_h - - #include "nsIQuotaResults.h" - - namespace mozilla { - namespace dom { - namespace quota { - -+class UsageResult -+ : public nsIQuotaUsageResult -+{ -+ nsCString mOrigin; -+ uint64_t mUsage; -+ bool mPersisted; -+ -+public: -+ UsageResult(const nsACString& aOrigin, -+ bool aPersisted, -+ uint64_t aUsage); -+ -+private: -+ virtual ~UsageResult() -+ { } -+ -+ NS_DECL_ISUPPORTS -+ NS_DECL_NSIQUOTAUSAGERESULT -+}; -+ - class OriginUsageResult - : public nsIQuotaOriginUsageResult - { - uint64_t mUsage; - uint64_t mFileUsage; - uint64_t mLimit; - - public: -diff --git a/dom/quota/nsIQuotaManagerService.idl b/dom/quota/nsIQuotaManagerService.idl ---- a/dom/quota/nsIQuotaManagerService.idl -+++ b/dom/quota/nsIQuotaManagerService.idl -@@ -10,16 +10,31 @@ interface nsIPrincipal; - interface nsIQuotaRequest; - interface nsIQuotaUsageCallback; - interface nsIQuotaUsageRequest; - - [scriptable, builtinclass, uuid(1b3d0a38-8151-4cf9-89fa-4f92c2ef0e7e)] - interface nsIQuotaManagerService : nsISupports - { - /** -+ * Schedules an asynchronous callback that will inspect all origins and -+ * return the total amount of disk space being used by storages for each -+ * origin separately. -+ * -+ * @param aCallback -+ * The callback that will be called when the usage is available. -+ * @param aGetAll -+ * An optional boolean to indicate inspection of all origins, -+ * including internal ones. -+ */ -+ [must_use] nsIQuotaUsageRequest -+ getUsage(in nsIQuotaUsageCallback aCallback, -+ [optional] in boolean aGetAll); -+ -+ /** - * Schedules an asynchronous callback that will return the total amount of - * disk space being used by storages for the given origin. - * - * @param aPrincipal - * A principal for the origin whose usage is being queried. - * @param aCallback - * The callback that will be called when the usage is available. - * @param aGetGroupUsage -diff --git a/dom/quota/nsIQuotaRequests.idl b/dom/quota/nsIQuotaRequests.idl ---- a/dom/quota/nsIQuotaRequests.idl -+++ b/dom/quota/nsIQuotaRequests.idl -@@ -18,16 +18,17 @@ interface nsIQuotaRequestBase : nsISuppo - - [must_use] readonly attribute nsresult resultCode; - }; - - [scriptable, uuid(166e28e6-cf6d-4927-a6d7-b51bca9d3469)] - interface nsIQuotaUsageRequest : nsIQuotaRequestBase - { - // The result can contain one of these types: -+ // array of nsIQuotaUsageResult - // nsIQuotaOriginUsageResult - [must_use] readonly attribute nsIVariant result; - - attribute nsIQuotaUsageCallback callback; - - [must_use] void - cancel(); - }; -diff --git a/dom/quota/nsIQuotaResults.idl b/dom/quota/nsIQuotaResults.idl ---- a/dom/quota/nsIQuotaResults.idl -+++ b/dom/quota/nsIQuotaResults.idl -@@ -1,16 +1,26 @@ - /* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */ - /* vim: set ts=2 et sw=2 tw=80: */ - /* This Source Code Form is subject to the terms of the Mozilla Public - * License, v. 2.0. If a copy of the MPL was not distributed with this - * file, You can obtain one at http://mozilla.org/MPL/2.0/. */ - - #include "nsISupports.idl" - -+[scriptable, function, uuid(d8c9328b-9aa8-4f5d-90e6-482de4a6d5b8)] -+interface nsIQuotaUsageResult : nsISupports -+{ -+ readonly attribute ACString origin; -+ -+ readonly attribute boolean persisted; -+ -+ readonly attribute unsigned long long usage; -+}; -+ - [scriptable, function, uuid(96df03d2-116a-493f-bb0b-118c212a6b32)] - interface nsIQuotaOriginUsageResult : nsISupports - { - readonly attribute unsigned long long usage; - - readonly attribute unsigned long long fileUsage; - - readonly attribute unsigned long long limit; - diff --git a/gnu/packages/patches/icecat-bug-1414945.patch b/gnu/packages/patches/icecat-bug-1414945.patch deleted file mode 100644 index 3638ace1c4..0000000000 --- a/gnu/packages/patches/icecat-bug-1414945.patch +++ /dev/null @@ -1,73 +0,0 @@ -Based on: - https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/d303b3bb88c3 - -Adapted to apply cleanly to IceCat. - -# HG changeset patch -# User Philip Chimento -# Date 1510012155 28800 -# Node ID d303b3bb88c3345d3a089901e2b6fe883d148e44 -# Parent 0152d097672f7e99504815cf7b06d9f303419fba -Bug 1414945 - Don't use TimeDuration in static initializer. r=jandem, a=ritu - -On Darwin this would cause a race between two static initializers. - -diff --git a/js/src/shell/js.cpp b/js/src/shell/js.cpp ---- a/js/src/shell/js.cpp -+++ b/js/src/shell/js.cpp -@@ -138,17 +138,17 @@ static const size_t gMaxStackSize = 2 * - #else - static const size_t gMaxStackSize = 128 * sizeof(size_t) * 1024; - #endif - - /* - * Limit the timeout to 30 minutes to prevent an overflow on platfoms - * that represent the time internally in microseconds using 32-bit int. - */ --static const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(1800.0); -+static const double MAX_TIMEOUT_SECONDS = 1800.0; - - // SharedArrayBuffer and Atomics settings track IceCat. Choose a custom setting - // with --shared-memory={on,off}. - #ifndef RELEASE_OR_BETA - # define SHARED_MEMORY_DEFAULT 1 - #else - # define SHARED_MEMORY_DEFAULT 0 - #endif -@@ -3518,16 +3518,17 @@ Sleep_fn(JSContext* cx, unsigned argc, V - if (!ToNumber(cx, args[0], &t_secs)) - return false; - if (mozilla::IsNaN(t_secs)) { - JS_ReportErrorASCII(cx, "sleep interval is not a number"); - return false; - } - - duration = TimeDuration::FromSeconds(Max(0.0, t_secs)); -+ const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(MAX_TIMEOUT_SECONDS); - if (duration > MAX_TIMEOUT_INTERVAL) { - JS_ReportErrorASCII(cx, "Excessive sleep interval"); - return false; - } - } - { - LockGuard guard(sc->watchdogLock); - TimeStamp toWakeup = TimeStamp::Now() + duration; -@@ -3675,16 +3676,17 @@ CancelExecution(JSContext* cx) - - static bool - SetTimeoutValue(JSContext* cx, double t) - { - if (mozilla::IsNaN(t)) { - JS_ReportErrorASCII(cx, "timeout is not a number"); - return false; - } -+ const TimeDuration MAX_TIMEOUT_INTERVAL = TimeDuration::FromSeconds(MAX_TIMEOUT_SECONDS); - if (TimeDuration::FromSeconds(t) > MAX_TIMEOUT_INTERVAL) { - JS_ReportErrorASCII(cx, "Excessive timeout value"); - return false; - } - GetShellContext(cx)->timeoutInterval = t; - if (!ScheduleWatchdog(cx, t)) { - JS_ReportErrorASCII(cx, "Failed to create the watchdog"); - return false; - diff --git a/gnu/packages/patches/icecat-bug-1415133.patch b/gnu/packages/patches/icecat-bug-1415133.patch deleted file mode 100644 index 4e322d21fb..0000000000 --- a/gnu/packages/patches/icecat-bug-1415133.patch +++ /dev/null @@ -1,40 +0,0 @@ -Based on: - https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/22fe3ff3f923 - -Adapted to apply cleanly to IceCat. - -# HG changeset patch -# User Marco Bonardo -# Date 1510052455 -3600 -# Node ID 22fe3ff3f92358596521f7155ddc512006022207 -# Parent 2909ba991f3134f9fbf4859cf08582f1c9845594 -Bug 1415133 - Downgrades from 55+ to ESR lose bookmarks. r=past a=lizzard - -MozReview-Commit-ID: 44Rw7m1FP4h - -diff --git a/toolkit/components/places/Database.cpp b/toolkit/components/places/Database.cpp ---- a/toolkit/components/places/Database.cpp -+++ b/toolkit/components/places/Database.cpp -@@ -761,16 +761,21 @@ Database::InitSchema(bool* aDatabaseMigr - // 2. implement a method that performs upgrade to your version from the - // previous one. - // - // NOTE: The downgrade process is pretty much complicated by the fact old - // versions cannot know what a new version is going to implement. - // The only thing we will do for downgrades is setting back the schema - // version, so that next upgrades will run again the migration step. - -+ if (currentSchemaVersion > 36) { -+ // These versions are not downgradable. -+ return NS_ERROR_FILE_CORRUPTED; -+ } -+ - if (currentSchemaVersion < DATABASE_SCHEMA_VERSION) { - *aDatabaseMigrated = true; - - if (currentSchemaVersion < 11) { - // These are versions older than IceCat 4 that are not supported - // anymore. In this case it's safer to just replace the database. - return NS_ERROR_FILE_CORRUPTED; - } - diff --git a/gnu/packages/patches/icecat-bug-1424373-pt2.patch b/gnu/packages/patches/icecat-bug-1424373-pt2.patch deleted file mode 100644 index cdc7226bd3..0000000000 --- a/gnu/packages/patches/icecat-bug-1424373-pt2.patch +++ /dev/null @@ -1,183 +0,0 @@ -Based on: - https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/19ea736e7e3d - -Adapted to apply cleanly to IceCat. - -# HG changeset patch -# User Mike Conley -# Date 1513892173 18000 -# Node ID 19ea736e7e3d20555ee6633b9d7803c1225979e1 -# Parent 320032aaa06899f5585dcd0288059e5342118714 -Bug 1424373 - Rename crash report submission pref. r=Mossop a=jcristau - -diff --git a/browser/app/profile/icecat.js b/browser/app/profile/icecat.js ---- a/browser/app/profile/icecat.js -+++ b/browser/app/profile/icecat.js -@@ -1557,15 +1557,15 @@ pref("browser.crashReports.unsubmittedCh - pref("browser.crashReports.unsubmittedCheck.enabled", false); - #endif - - // chancesUntilSuppress is how many times we'll show the unsubmitted - // crash report notification across different days and shutdown - // without a user choice before we suppress the notification for - // some number of days. - pref("browser.crashReports.unsubmittedCheck.chancesUntilSuppress", 4); --pref("browser.crashReports.unsubmittedCheck.autoSubmit", false); -+pref("browser.crashReports.unsubmittedCheck.autoSubmit2", false); - - #ifdef NIGHTLY_BUILD - // Enable the (fairly costly) client/server validation on nightly only. The other prefs - // controlling validation are located in /services/sync/services-sync.js - pref("services.sync.validation.enabled", true); - #endif -diff --git a/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js b/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js ---- a/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js -+++ b/browser/base/content/test/tabcrashed/browser_autoSubmitRequest.js -@@ -1,12 +1,12 @@ - "use strict"; - - const PAGE = "data:text/html,A%20regular,%20everyday,%20normal%20page."; --const AUTOSUBMIT_PREF = "browser.crashReports.unsubmittedCheck.autoSubmit"; -+const AUTOSUBMIT_PREF = "browser.crashReports.unsubmittedCheck.autoSubmit2"; - - const {TabStateFlusher} = - Cu.import("resource:///modules/sessionstore/TabStateFlusher.jsm", {}); - - // On debug builds, crashing tabs results in much thinking, which - // slows down the test and results in intermittent test timeouts, - // so we'll pump up the expected timeout for this test. - requestLongerTimeout(2); -diff --git a/browser/components/preferences/in-content/advanced.xul b/browser/components/preferences/in-content/advanced.xul ---- a/browser/components/preferences/in-content/advanced.xul -+++ b/browser/components/preferences/in-content/advanced.xul -@@ -51,18 +51,18 @@ - #ifdef MOZ_TELEMETRY_REPORTING - - #endif - - - #ifdef MOZ_CRASHREPORTER -- - #endif - - - - - - - #endif - #ifdef MOZ_CRASHREPORTER - - - - - - - - -diff --git a/browser/components/sessionstore/test/browser_background_tab_crash.js b/browser/components/sessionstore/test/browser_background_tab_crash.js ---- a/browser/components/sessionstore/test/browser_background_tab_crash.js -+++ b/browser/components/sessionstore/test/browser_background_tab_crash.js -@@ -142,17 +142,17 @@ add_task(function* test_background_crash - /** - * Tests that if a content process crashes taking down only - * background tabs, and the user is configured to send backlogged - * crash reports automatically, that the tab crashed page is not - * shown. - */ - add_task(function* test_background_crash_autosubmit_backlogged() { - yield SpecialPowers.pushPrefEnv({ -- set: [["browser.crashReports.unsubmittedCheck.autoSubmit", true]], -+ set: [["browser.crashReports.unsubmittedCheck.autoSubmit2", true]], - }); - - yield setupBackgroundTabs(function*([tab1, tab2]) { - // Let's crash one of those background tabs now... - yield crashBackgroundTabs([tab1, tab2]); - - // Selecting the first tab should restore it. - let tabRestored = promiseTabRestored(tab1); -diff --git a/browser/modules/ContentCrashHandlers.jsm b/browser/modules/ContentCrashHandlers.jsm ---- a/browser/modules/ContentCrashHandlers.jsm -+++ b/browser/modules/ContentCrashHandlers.jsm -@@ -865,21 +865,21 @@ this.UnsubmittedCrashHandler = { - return nb.appendNotification(message, notificationID, - "chrome://browser/skin/tab-crashed.svg", - nb.PRIORITY_INFO_HIGH, buttons, - eventCallback); - }, - - get autoSubmit() { - return Services.prefs -- .getBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit"); -+ .getBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit2"); - }, - - set autoSubmit(val) { -- Services.prefs.setBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit", -+ Services.prefs.setBoolPref("browser.crashReports.unsubmittedCheck.autoSubmit2", - val); - }, - - /** - * Attempt to submit reports to the crash report server. Each - * report will have the "SubmittedFromInfobar" extra key set - * to true. - * -diff --git a/browser/modules/test/browser_UnsubmittedCrashHandler.js b/browser/modules/test/browser_UnsubmittedCrashHandler.js ---- a/browser/modules/test/browser_UnsubmittedCrashHandler.js -+++ b/browser/modules/test/browser_UnsubmittedCrashHandler.js -@@ -344,17 +344,17 @@ add_task(function* test_can_submit_sever - clearPendingCrashReports(); - }); - - /** - * Tests that choosing "Send Always" flips the autoSubmit pref - * and sends the pending crash reports. - */ - add_task(function* test_can_submit_always() { -- let pref = "browser.crashReports.unsubmittedCheck.autoSubmit"; -+ let pref = "browser.crashReports.unsubmittedCheck.autoSubmit2"; - Assert.equal(Services.prefs.getBoolPref(pref), false, - "We should not be auto-submitting by default"); - - let reportIDs = yield createPendingCrashReports(1); - let notification = - yield UnsubmittedCrashHandler.checkForUnsubmittedCrashReports(); - Assert.ok(notification, "There should be a notification"); - -@@ -388,17 +388,17 @@ add_task(function* test_can_submit_alway - - /** - * Tests that if the user has chosen to automatically send - * crash reports that no notification is displayed to the - * user. - */ - add_task(function* test_can_auto_submit() { - yield SpecialPowers.pushPrefEnv({ set: [ -- ["browser.crashReports.unsubmittedCheck.autoSubmit", true], -+ ["browser.crashReports.unsubmittedCheck.autoSubmit2", true], - ]}); - - let reportIDs = yield createPendingCrashReports(3); - let promiseReports = waitForSubmittedReports(reportIDs); - let notification = - yield UnsubmittedCrashHandler.checkForUnsubmittedCrashReports(); - Assert.equal(notification, null, "There should be no notification"); - info("Waiting on reports to be received."); - -- cgit v1.2.3 From 99654a1685005ef757b33bb7be2fbb8021c2a481 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 2 Mar 2018 00:04:24 -0500 Subject: gnu: icecat: Add more fixes from upstream mozilla-esr52. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr52 repository. --- gnu/packages/gnuzilla.scm | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index e3f1bfe8c0..457a8fbcdc 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -423,7 +423,21 @@ security standards.") (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-bug-1426087.patch" "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n"))) + (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-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-bug-1430173-pt1.patch" "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i") + (mozilla-patch "icecat-bug-1430173-pt2.patch" "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl"))) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 8661ad27435695ef1fbd05f6d9a01330520a3b2e Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 16 Feb 2018 18:51:16 +0100 Subject: linux-modules: Add 'device-module-aliases' and related procedures. * gnu/build/linux-modules.scm (readlink*, stat->device-major) (stat->device-minor): New procedures. (%not-slash): New variable. (read-uevent, device-module-aliases, read-module-aliases) (current-alias-file, known-module-aliases, matching-modules): New procedures. --- gnu/build/linux-modules.scm | 159 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 158 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index 115a17c64e..4a6d4ff089 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -19,6 +19,7 @@ (define-module (gnu build linux-modules) #:use-module (guix elf) + #:use-module (guix glob) #:use-module (guix build syscalls) #:use-module (rnrs io ports) #:use-module (rnrs bytevectors) @@ -26,6 +27,7 @@ #:use-module (srfi srfi-26) #:use-module (ice-9 vlist) #:use-module (ice-9 match) + #:use-module (ice-9 rdelim) #:export (dot-ko ensure-dot-ko module-dependencies @@ -34,7 +36,11 @@ module-loaded? load-linux-module* - current-module-debugging-port)) + current-module-debugging-port + + device-module-aliases + known-module-aliases + matching-modules)) ;;; Commentary: ;;; @@ -213,4 +219,155 @@ appears in BLACK-LIST are not loaded." (or (and recursive? (= EEXIST (system-error-errno args))) (apply throw args))))))) + +;;; +;;; Device modules. +;;; + +;; Copied from (guix utils). FIXME: Factorize. +(define (readlink* file) + "Call 'readlink' until the result is not a symlink." + (define %max-symlink-depth 50) + + (let loop ((file file) + (depth 0)) + (define (absolute target) + (if (absolute-file-name? target) + target + (string-append (dirname file) "/" target))) + + (if (>= depth %max-symlink-depth) + file + (call-with-values + (lambda () + (catch 'system-error + (lambda () + (values #t (readlink file))) + (lambda args + (let ((errno (system-error-errno args))) + (if (or (= errno EINVAL)) + (values #f file) + (apply throw args)))))) + (lambda (success? target) + (if success? + (loop (absolute target) (+ depth 1)) + file)))))) + +;; See 'major' and 'minor' in . + +(define (stat->device-major st) + (ash (logand #xfff00 (stat:rdev st)) -8)) + +(define (stat->device-minor st) + (logand #xff (stat:rdev st))) + +(define %not-slash + (char-set-complement (char-set #\/))) + +(define (read-uevent port) + "Read a /sys 'uevent' file from PORT and return an alist where each car is a +key such as 'MAJOR or 'DEVTYPE and each cdr is the corresponding value." + (let loop ((result '())) + (match (read-line port) + ((? eof-object?) + (reverse result)) + (line + (loop (cons (key=value->pair line) result)))))) + +(define (device-module-aliases device) + "Return the list of module aliases required by DEVICE, a /dev file name, as +in this example: + + (device-module-aliases \"/dev/sda\") + => (\"scsi:t-0x00\" \"pci:v00008086d00009D03sv0000103Csd000080FAbc01sc06i01\") + +The modules corresponding to these aliases can then be found using +'matching-modules'." + ;; The approach is adapted from + ;; . + (let* ((st (stat device)) + (type (stat:type st)) + (major (stat->device-major st)) + (minor (stat->device-minor st)) + (sys-name (string-append "/sys/dev/" + (case type + ((block-special) "block") + ((char-special) "char") + (else (symbol->string type))) + "/" (number->string major) ":" + (number->string minor))) + (directory (canonicalize-path (readlink* sys-name)))) + (let loop ((components (string-tokenize directory %not-slash)) + (aliases '())) + (match components + (("sys" "devices" _) + (reverse aliases)) + ((head ... _) + (let ((uevent (string-append (string-join components "/" 'prefix) + "/uevent"))) + (if (file-exists? uevent) + (let ((props (call-with-input-file uevent read-uevent))) + (match (assq-ref props 'MODALIAS) + (#f (loop head aliases)) + (alias (loop head (cons alias aliases))))) + (loop head aliases)))))))) + +(define (read-module-aliases port) + "Read from PORT data in the Linux 'modules.alias' file format. Return a +list of alias/module pairs where each alias is a glob pattern as like the +result of: + + (compile-glob-pattern \"scsi:t-0x01*\") + +and each module is a module name like \"snd_hda_intel\"." + (define (comment? str) + (string-prefix? "#" str)) + + (define (tokenize str) + ;; Lines have the form "alias ALIAS MODULE", where ALIAS can contain + ;; whitespace. This is why we don't use 'string-tokenize'. + (let* ((str (string-trim-both str)) + (left (string-index str #\space)) + (right (string-rindex str #\space))) + (list (string-take str left) + (string-trim-both (substring str left right)) + (string-trim-both (string-drop str right))))) + + (let loop ((aliases '())) + (match (read-line port) + ((? eof-object?) + (reverse aliases)) + ((? comment?) + (loop aliases)) + (line + (match (tokenize line) + (("alias" alias module) + (loop (alist-cons (compile-glob-pattern alias) module + aliases))) + (() ;empty line + (loop aliases))))))) + +(define (current-alias-file) + "Return the absolute file name of the default 'modules.alias' file." + (string-append (or (getenv "LINUX_MODULE_DIRECTORY") + "/run/booted-system/kernel/lib/modules") + "/" (utsname:release (uname)) + "/" "modules.alias")) + +(define* (known-module-aliases #:optional (alias-file (current-alias-file))) + "Return the list of alias/module pairs read from ALIAS-FILE. Each alias is +actually a pattern." + (call-with-input-file alias-file read-module-aliases)) + +(define* (matching-modules alias + #:optional (known-aliases (known-module-aliases))) + "Return the list of modules that match ALIAS according to KNOWN-ALIASES. +ALIAS is a string like \"scsi:t-0x00\" as returned by +'device-module-aliases'." + (filter-map (match-lambda + ((pattern . module) + (and (glob-match? pattern alias) + module))) + known-aliases)) + ;;; linux-modules.scm ends here -- cgit v1.2.3 From 615a89e3101b1a512008a3ca3239035674c7d098 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 27 Feb 2018 11:16:37 +0100 Subject: linux-initrd: Separate file system module logic. * gnu/system/linux-initrd.scm (vhash, lookup-procedure): New macros. (file-system-type-modules, file-system-modules): New procedures. (base-initrd)[cifs-modules, virtio-9p-modules]: Remove. [file-system-type-predicate]: Remove. Use 'file-system-modules' instead of 'find' + 'file-system-type-predicate'. --- gnu/system/linux-initrd.scm | 60 +++++++++++++++++++++++++++------------------ 1 file changed, 36 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 330438bce4..830445ac83 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -39,6 +39,7 @@ #:use-module (gnu system mapped-devices) #:use-module (ice-9 match) #:use-module (ice-9 regex) + #:use-module (ice-9 vlist) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:export (expression->initrd @@ -242,6 +243,40 @@ FILE-SYSTEMS." (list btrfs-progs/static) '()))) +(define-syntax vhash ;TODO: factorize + (syntax-rules (=>) + "Build a vhash with the given key/value mappings." + ((_) + vlist-null) + ((_ (key others ... => value) rest ...) + (vhash-cons key value + (vhash (others ... => value) rest ...))) + ((_ (=> value) rest ...) + (vhash rest ...)))) + +(define-syntax lookup-procedure + (syntax-rules (else) + "Return a procedure that lookups keys in the given dictionary." + ((_ mapping ... (else default)) + (let ((table (vhash mapping ...))) + (lambda (key) + (match (vhash-assoc key table) + (#f default) + (value value))))))) + +(define file-system-type-modules + ;; Given a file system type, return the list of modules it needs. + (lookup-procedure ("cifs" => '("md4" "ecb" "cifs")) + ("9p" => '("9p" "9pnet_virtio")) + ("btrfs" => '("btrfs")) + ("iso9660" => '("isofs")) + (else '()))) + +(define (file-system-modules file-systems) + "Return the list of Linux modules needed to mount FILE-SYSTEMS." + (append-map (compose file-system-type-modules file-system-type) + file-systems)) + (define* (base-initrd file-systems #:key (linux linux-libre) @@ -272,18 +307,6 @@ loaded at boot time in the order in which they appear." '("virtio_pci" "virtio_balloon" "virtio_blk" "virtio_net" "virtio_console")) - (define cifs-modules - ;; Modules needed to mount CIFS file systems. - '("md4" "ecb" "cifs")) - - (define virtio-9p-modules - ;; Modules for the 9p paravirtualized file system. - '("9p" "9pnet_virtio")) - - (define (file-system-type-predicate type) - (lambda (fs) - (string=? (file-system-type fs) type))) - (define linux-modules ;; Modules added to the initrd and loaded from the initrd. `("ahci" ;for SATA controllers @@ -298,18 +321,7 @@ loaded at boot time in the order in which they appear." ,@(if (or virtio? qemu-networking?) virtio-modules '()) - ,@(if (find (file-system-type-predicate "cifs") file-systems) - cifs-modules - '()) - ,@(if (find (file-system-type-predicate "9p") file-systems) - virtio-9p-modules - '()) - ,@(if (find (file-system-type-predicate "btrfs") file-systems) - '("btrfs") - '()) - ,@(if (find (file-system-type-predicate "iso9660") file-systems) - '("isofs") - '()) + ,@(file-system-modules file-systems) ,@(if volatile-root? '("overlay") '()) -- cgit v1.2.3 From bc499b113a598c0e7863da9887a4133472985713 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 27 Feb 2018 11:42:09 +0100 Subject: system: Add 'initrd-modules' field. * gnu/system.scm ()[initrd-modules]: New field. (operating-system-initrd-file): Pass #:linux-modules to 'make-initrd'. * gnu/system/linux-initrd.scm (default-initrd-modules): New procedure. (%base-initrd-modules): New macro. (base-initrd): Add #:linux-modules and honor it. * gnu/system/install.scm (embedded-installation-os): Use 'initrd-modules' instead of 'initrd'. * gnu/tests/install.scm (%raid-root-os): Likewise. * doc/guix.texi (operating-system Reference): Add 'initrd-modules'. (Initial RAM Disk): Document it. Adjust example to not use #:extra-modules. --- doc/guix.texi | 40 ++++++++++++++++++++++++++++++++-------- gnu/system.scm | 7 +++++++ gnu/system/install.scm | 7 ++----- gnu/system/linux-initrd.scm | 34 ++++++++++++++++++++++------------ gnu/tests/install.scm | 11 +++++------ 5 files changed, 68 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index d35ce0e26b..70e53b3825 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -8889,11 +8889,16 @@ the command-line of the kernel---e.g., @code{("console=ttyS0")}. @item @code{bootloader} The system bootloader configuration object. @xref{Bootloader Configuration}. -@item @code{initrd} (default: @code{base-initrd}) +@item @code{initrd-modules} (default: @code{%base-initrd-modules}) @cindex initrd @cindex initial RAM disk -A two-argument monadic procedure that returns an initial RAM disk for -the Linux kernel. @xref{Initial RAM Disk}. +The list of Linux kernel modules that need to be available in the +initial RAM disk. @xref{Initial RAM Disk}. + +@item @code{initrd} (default: @code{base-initrd}) +A monadic procedure that returns an initial RAM disk for the Linux +kernel. This field is provided to support low-level customization and +should rarely be needed for casual use. @xref{Initial RAM Disk}. @item @code{firmware} (default: @var{%base-firmware}) @cindex firmware @@ -19768,7 +19773,27 @@ root file system as well as an initialization script. The latter is responsible for mounting the real root file system, and for loading any kernel modules that may be needed to achieve that. -The @code{initrd} field of an @code{operating-system} declaration allows +The @code{initrd-modules} field of an @code{operating-system} +declaration allows you to specify Linux-libre kernel modules that must +be available in the initrd. In particular, this is where you would list +modules needed to actually drive the hard disk where your root partition +is---although the default value of @code{initrd-modules} should cover +most use cases. For example, assuming you need the @code{megaraid_sas} +module in addition to the default modules to be able to access your root +file system, you would write: + +@example +(operating-system + ;; @dots{} + (initrd-modules (cons "megaraid_sas" %base-initrd-modules))) +@end example + +@defvr {Scheme Variable} %base-initrd-modules +This is the list of kernel modules included in the initrd by default. +@end defvr + +Furthermore, if you need lower-level customization, the @code{initrd} +field of an @code{operating-system} declaration allows you to specify which initrd you would like to use. The @code{(gnu system linux-initrd)} module provides three ways to build an initrd: the high-level @code{base-initrd} procedure and the low-level @@ -19781,11 +19806,10 @@ system declaration like this: @example (initrd (lambda (file-systems . rest) - ;; Create a standard initrd that has modules "foo.ko" - ;; and "bar.ko", as well as their dependencies, in - ;; addition to the modules available by default. + ;; Create a standard initrd but set up networking + ;; with the parameters QEMU expects by default. (apply base-initrd file-systems - #:extra-modules '("foo" "bar") + #:qemu-networking? #t rest))) @end example diff --git a/gnu/system.scm b/gnu/system.scm index 71beee8259..1bcc1e1384 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -74,6 +74,7 @@ operating-system-kernel operating-system-kernel-file operating-system-kernel-arguments + operating-system-initrd-modules operating-system-initrd operating-system-users operating-system-groups @@ -154,6 +155,10 @@ booted from ROOT-DEVICE" (initrd operating-system-initrd ; (list fs) -> M derivation (default base-initrd)) + (initrd-modules operating-system-initrd-modules ; list of strings + (thunked) ; it's system-dependent + (default %base-initrd-modules)) + (firmware operating-system-firmware ; list of packages (default %base-firmware)) @@ -846,6 +851,8 @@ hardware-related operations as necessary when booting a Linux container." (mlet %store-monad ((initrd (make-initrd boot-file-systems #:linux (operating-system-kernel os) + #:linux-modules + (operating-system-initrd-modules os) #:mapped-devices mapped-devices))) (return (file-append initrd "/initrd")))) diff --git a/gnu/system/install.scm b/gnu/system/install.scm index b61660b4b9..37c591ec3a 100644 --- a/gnu/system/install.scm +++ b/gnu/system/install.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2017 Marius Bakke @@ -396,10 +396,7 @@ The bootloader BOOTLOADER is installed to BOOTLOADER-TARGET." (kernel-arguments (cons (string-append "console=" tty) (operating-system-user-kernel-arguments installation-os))) - (initrd (lambda (fs . rest) - (apply base-initrd fs - #:extra-modules extra-modules - rest))))) + (initrd-modules (append extra-modules %base-initrd-modules)))) (define beaglebone-black-installation-os (embedded-installation-os u-boot-beaglebone-black-bootloader diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 830445ac83..e7f97bb88d 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -43,6 +43,7 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:export (expression->initrd + %base-initrd-modules raw-initrd file-system-packages base-initrd)) @@ -277,14 +278,31 @@ FILE-SYSTEMS." (append-map (compose file-system-type-modules file-system-type) file-systems)) +(define* (default-initrd-modules #:optional (system (%current-system))) + "Return the list of modules included in the initrd by default." + `("ahci" ;for SATA controllers + "usb-storage" "uas" ;for the installation image etc. + "usbhid" "hid-generic" "hid-apple" ;keyboards during early boot + "dm-crypt" "xts" "serpent_generic" "wp512" ;for encrypted root partitions + "nls_iso8859-1" ;for `mkfs.fat`, et.al + ,@(if (string-match "^(x86_64|i[3-6]86)-" system) + '("pata_acpi" "pata_atiixp" ;for ATA controllers + "isci") ;for SAS controllers like Intel C602 + '()))) + +(define-syntax %base-initrd-modules + ;; This more closely matches our naming convention. + (identifier-syntax (default-initrd-modules))) + (define* (base-initrd file-systems #:key (linux linux-libre) + (linux-modules '()) (mapped-devices '()) qemu-networking? volatile-root? (virtio? #t) - (extra-modules '()) + (extra-modules '()) ;deprecated (on-error 'debug)) "Return a monadic derivation that builds a generic initrd, with kernel modules taken from LINUX. FILE-SYSTEMS is a list of file-systems to be @@ -307,17 +325,9 @@ loaded at boot time in the order in which they appear." '("virtio_pci" "virtio_balloon" "virtio_blk" "virtio_net" "virtio_console")) - (define linux-modules + (define linux-modules* ;; Modules added to the initrd and loaded from the initrd. - `("ahci" ;for SATA controllers - "usb-storage" "uas" ;for the installation image etc. - "usbhid" "hid-generic" "hid-apple" ;keyboards during early boot - "dm-crypt" "xts" "serpent_generic" "wp512" ;for encrypted root partitions - "nls_iso8859-1" ;for `mkfs.fat`, et.al - ,@(if (string-match "^(x86_64|i[3-6]86)-" (%current-system)) - '("pata_acpi" "pata_atiixp" ;for ATA controllers - "isci") ;for SAS controllers like Intel C602 - '()) + `(,@linux-modules ,@(if (or virtio? qemu-networking?) virtio-modules '()) @@ -332,7 +342,7 @@ loaded at boot time in the order in which they appear." (raw-initrd file-systems #:linux linux - #:linux-modules linux-modules + #:linux-modules linux-modules* #:mapped-devices mapped-devices #:helper-packages helper-packages #:qemu-networking? qemu-networking? diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm index 3ac4a579da..e3bb1b46af 100644 --- a/gnu/tests/install.scm +++ b/gnu/tests/install.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017 Ludovic Courtès +;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. @@ -565,11 +565,10 @@ where /gnu lives on a separate partition.") (bootloader grub-bootloader) (target "/dev/vdb"))) (kernel-arguments '("console=ttyS0")) - (initrd (lambda (file-systems . rest) - ;; Add a kernel module for RAID-0 (aka. "stripe"). - (apply base-initrd file-systems - #:extra-modules '("raid0") - rest))) + + ;; Add a kernel module for RAID-0 (aka. "stripe"). + (initrd-modules (cons "raid0" %base-initrd-modules)) + (mapped-devices (list (mapped-device (source (list "/dev/vda2" "/dev/vda3")) (target "/dev/md0") -- cgit v1.2.3 From 424cea8083a4cee63290c80235aed61bd12affb1 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 27 Feb 2018 14:55:43 +0100 Subject: guix system: Check for the lack of modules in the initrd. * guix/scripts/system.scm (check-mapped-devices): Take an OS instead of a list of . Pass #:needed-for-boot? and #:initrd-modules to CHECK. (check-initrd-modules): New procedure. (perform-action): Move 'check-mapped-devices' call first. Add call to 'check-initrd-modules'. * gnu/system/mapped-devices.scm (check-device-initrd-modules): New procedure. (check-luks-device): Add #:initrd-modules and #:needed-for-boot?. Use them to call 'check-device-initrd-modules'. --- gnu/system/mapped-devices.scm | 53 +++++++++++++++++++++++++--------- guix/scripts/system.scm | 67 ++++++++++++++++++++++++++++++++++++------- 2 files changed, 96 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm index dbeb0d3436..5ceb5e658c 100644 --- a/gnu/system/mapped-devices.scm +++ b/gnu/system/mapped-devices.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2017 Mark H Weaver ;;; @@ -30,9 +30,12 @@ #:use-module (gnu services shepherd) #: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) #:autoload (gnu packages cryptsetup) (cryptsetup-static) #:autoload (gnu packages linux) (mdadm-static) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) #:use-module (ice-9 match) @@ -151,19 +154,43 @@ #~(zero? (system* #$(file-append cryptsetup-static "/sbin/cryptsetup") "close" #$target))) -(define (check-luks-device md) +(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." + (let ((modules (delete-duplicates + (append-map matching-modules + (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))) + (&error-location + (location (source-properties->location location)))))))) + +(define* (check-luks-device md #:key + needed-for-boot? + (initrd-modules '()) + #:allow-other-keys + #:rest rest) "Ensure the source of MD is valid." - (let ((source (mapped-device-source md))) - (or (not (uuid? source)) - (not (zero? (getuid))) - (find-partition-by-luks-uuid (uuid-bytevector source)) - (raise (condition - (&message - (message (format #f (G_ "no LUKS partition with UUID '~a'") - (uuid->string source)))) - (&error-location - (location (source-properties->location - (mapped-device-location md))))))))) + (let ((source (mapped-device-source md)) + (location (mapped-device-location md))) + (or (not (zero? (getuid))) + (if (uuid? source) + (match (find-partition-by-luks-uuid (uuid-bytevector source)) + (#f + (raise (condition + (&message + (message (format #f (G_ "no LUKS partition with UUID '~a'") + (uuid->string source)))) + (&error-location + (location (source-properties->location + (mapped-device-location md))))))) + ((? string? device) + (check-device-initrd-modules device initrd-modules location))) + (check-device-initrd-modules source initrd-modules location))))) (define luks-device-mapping ;; The type of LUKS mapped devices. diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 999ffb010b..ff322ec785 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -41,6 +41,10 @@ #:use-module (gnu build install) #:autoload (gnu build file-systems) (find-partition-by-label find-partition-by-uuid) + #:autoload (gnu build linux-modules) + (device-module-aliases matching-modules) + #:autoload (gnu system linux-initrd) + (base-initrd default-initrd-modules) #:use-module (gnu system) #:use-module (gnu bootloader) #:use-module (gnu system file-systems) @@ -624,21 +628,61 @@ any, are available. Raise an error if they're not." ;; Better be safe than sorry. (exit 1)))) -(define (check-mapped-devices mapped-devices) +(define (check-mapped-devices os) "Check that each of MAPPED-DEVICES is valid according to the 'check' procedure of its type." + (define boot-mapped-devices + (operating-system-boot-mapped-devices os)) + + (define (needed-for-boot? md) + (memq md boot-mapped-devices)) + + (define initrd-modules + (operating-system-initrd-modules os)) + (for-each (lambda (md) (let ((check (mapped-device-kind-check (mapped-device-type md)))) ;; We expect CHECK to raise an exception with a detailed - ;; '&message' if something goes wrong, but handle the case - ;; where it just returns #f. - (unless (check md) - (leave (G_ "~a: invalid '~a' mapped device~%") - (location->string - (source-properties->location - (mapped-device-location md))))))) - mapped-devices)) + ;; '&message' if something goes wrong. + (check md + #:needed-for-boot? (needed-for-boot? md) + #:initrd-modules initrd-modules))) + (operating-system-mapped-devices os))) + +(define (check-initrd-modules os) + "Check that modules needed by 'needed-for-boot' file systems in OS are +available in the initrd. Note that mapped devices are responsible for +checking this by themselves in their 'check' procedure." + (define (file-system-/dev fs) + (let ((device (file-system-device fs))) + (match (file-system-title fs) + ('device device) + ('uuid (find-partition-by-uuid device)) + ('label (find-partition-by-label device))))) + + (define (check-device device location) + (let ((modules (delete-duplicates + (append-map matching-modules + (device-module-aliases device))))) + (unless (every (cute member <> (operating-system-initrd-modules os)) + modules) + (raise (condition + (&message + (message (format #f (G_ "you need these modules \ +in the initrd for ~a:~{ ~a~}") + device modules))) + (&error-location (location location))))))) + + (define file-systems + (filter file-system-needed-for-boot? + (operating-system-file-systems os))) + + (for-each (lambda (fs) + (check-device (file-system-/dev fs) + (source-properties->location + (file-system-location fs)))) + file-systems)) ;;; @@ -730,9 +774,10 @@ output when building a system derivation, such as a disk image." ;; instantiating a broken configuration. Assume that we can only check if ;; running as root. (when (memq action '(init reconfigure)) + (check-mapped-devices os) (when (zero? (getuid)) - (check-file-system-availability (operating-system-file-systems os))) - (check-mapped-devices (operating-system-mapped-devices os))) + (check-file-system-availability (operating-system-file-systems os)) + (check-initrd-modules os))) (mlet* %store-monad ((sys (system-derivation-for-action os action -- cgit v1.2.3 From 1a6fb8dac1a9d7ae6d1a9b07bb0df6e4b606cb87 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:54:26 +0100 Subject: gnu: python-flask-babel: Update to 0.11.2. * gnu/packages/python-web.scm (python-flask-babel): Update to 0.11.2. --- 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 47fc5cd63a..18022ecd5e 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -138,14 +138,14 @@ between a web browser and web server.") (define-public python-flask-babel (package (name "python-flask-babel") - (version "0.11.1") + (version "0.11.2") (source (origin (method url-fetch) (uri (pypi-uri "Flask-Babel" version)) (sha256 (base32 - "16b80cipdba9xj3jlaiaq6wgrgpjb70w3j01jjy9hbp4k71kd6yj")))) + "0ff9n165vhf1nhv6807ckhpp224jw7k7sd7jz5kfh3sbpl85gmy0")))) (build-system python-build-system) (propagated-inputs `(("python-flask" ,python-flask) -- cgit v1.2.3 From 3c5658c596d570b4f2381de9ee9abd87a292a35b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:55:45 +0100 Subject: gnu: python-cssutils: Update to 1.0.2. * gnu/packages/python-web.scm (python-cssutils): Update to 1.0.2. --- gnu/packages/python-web.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 18022ecd5e..dd14446b09 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -332,19 +332,19 @@ for clients and servers.") (define-public python-cssutils (package (name "python-cssutils") - (version "1.0.1") + (version "1.0.2") (source (origin (method url-fetch) (uri (pypi-uri "cssutils" version)) (sha256 (base32 - "0qwha9x1wml2qmipbcz03gndnlwhzrjdvw9i09si247a90l8p8fq")))) + "1bxchrbqzapwijap0yhlxdil1w9bmwvgx77aizlkhc2mcxjg1z52")))) (build-system python-build-system) (native-inputs - `(("unzip" ,unzip))) ; for unpacking the source + `(("unzip" ,unzip))) ; for unpacking the source (arguments - `(#:tests? #f)) ;tests require python-pbr < 1.7.0 + `(#:tests? #f)) ; tests require python-pbr < 1.7.0 (home-page "http://cthedot.de/cssutils/") (synopsis "CSS Cascading Style Sheets library for Python") -- cgit v1.2.3 From 6f21aca728cdfd32fb8f64b4805425d297b31429 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:58:49 +0100 Subject: gnu: python-ndg-httpsclient: Update to 0.4.4. * gnu/packages/python-web.scm (python-ndg-httpsclient): Update to 0.4.4. --- 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 dd14446b09..513a455967 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -956,13 +956,13 @@ facilities for defining, registering and looking up components.") (define-public python-ndg-httpsclient (package (name "python-ndg-httpsclient") - (version "0.4.2") + (version "0.4.4") (source (origin (method url-fetch) (uri (pypi-uri "ndg_httpsclient" version)) (sha256 (base32 - "1b5qirv46v4dpnmfqviwq42mdwfcby4dxmz0i41wad2337pqf2aq")))) + "0sl5ak1r1xil9ms0a9fh9fm6ncml65kgnjpjfic9dhnaimwx997v")))) (build-system python-build-system) (arguments '(;; The tests appear to require networking. -- cgit v1.2.3 From e46dd02d99fccabecd59bf8bd3664a67e24053c0 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:00:52 +0100 Subject: gnu: python-webtest: Update to 2.0.29. * gnu/packages/python-web.scm (python-webtest): Update to 2.0.29. --- 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 513a455967..8f5827cd2c 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1306,14 +1306,14 @@ file.") (define-public python-webtest (package (name "python-webtest") - (version "2.0.20") + (version "2.0.29") (source (origin (method url-fetch) (uri (pypi-uri "WebTest" version)) (sha256 (base32 - "0bv0qhdjakdsdgj4sk21gnpp8xp8bga4x03p6gjb83ihrsb7n4xv")))) + "0bcj1ica5lnmj5zbvk46x28kgphcsgh7sfnwjmn0cr94mhawrg6v")))) (build-system python-build-system) (arguments `(;; Unfortunately we have to disable tests! -- cgit v1.2.3 From bda82eff18c97c773b4f503932c1df0f04086c2c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:04:35 +0100 Subject: gnu: python-s3transfer: Update to 0.1.13. * gnu/packages/python-web.scm (python-s3transfer): Update to 0.1.13. --- 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 8f5827cd2c..769b3dea51 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1700,13 +1700,13 @@ Betamax.") (define-public python-s3transfer (package (name "python-s3transfer") - (version "0.1.11") + (version "0.1.13") (source (origin (method url-fetch) (uri (pypi-uri "s3transfer" version)) (sha256 (base32 - "0yfrfnf404cxzn3iswibqjxklsl0b1lwgqiml6pwiqj79a7zbwbn")))) + "1harvyn1s8v54n1w5h7c0lg4bgjh68aylhg28s8n174q53h1ip4h")))) (build-system python-build-system) (arguments `(#:phases -- cgit v1.2.3 From 05075433a2b8661200a6f40fc1319414a9e44b7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:09:24 +0100 Subject: gnu: python-htmlmin: Update to 0.1.12. * gnu/packages/python-web.scm (python-htmlmin): Update to 0.1.12. --- gnu/packages/python-web.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 769b3dea51..ed3d2ec57b 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -1877,16 +1877,16 @@ specs from your Flask-Restful projects.") (define-public python-htmlmin (package (name "python-htmlmin") - (version "0.1.10") + (version "0.1.12") (source (origin (method url-fetch) (uri (pypi-uri "htmlmin" version)) (sha256 (base32 - "0qxa93j3p1ak32qh8d9kshqv8v3z0hkc13dwbhp5cn7sn3xmsp6a")))) + "0y51xhabw6x8jk8k93xl8vznshpz3jb6l28075r5sjip613fzhah")))) (arguments - `(#:tests? #f)) ;htmlmin has no tests + `(#:tests? #f)) ; no tests (build-system python-build-system) (home-page "https://htmlmin.readthedocs.org/en/latest/") (synopsis "HTML minifier") -- cgit v1.2.3 From 6a192184ecd0b1e99d59cfd115475ff9cb6de866 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:09:50 +0100 Subject: gnu: python-flask-script: Update to 2.0.6. * gnu/packages/python-web.scm (python-flask-script): Update to 2.0.6. --- 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 ed3d2ec57b..9dc0650230 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -2081,14 +2081,14 @@ this it tries to be opinion-free and very extendable.") (define-public python-flask-script (package (name "python-flask-script") - (version "2.0.5") + (version "2.0.6") (source (origin (method url-fetch) (uri (pypi-uri "Flask-Script" version)) (sha256 (base32 - "0zqh2yq8zk7m9b4xw1ryqmrljkdigfb3hk5155a3b5hkfnn6xxyf")))) + "0r8w2v89nj6b9p91p495cga5m72a673l2wc0hp0zqk05j4yrc9b4")))) (build-system python-build-system) (propagated-inputs `(("python-flask" ,python-flask) -- cgit v1.2.3 From 12adfdf0b6fe84346f2a578a341ae8537ac0606f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 04:39:51 +0100 Subject: gnu: Update (gnu packages python-web) phase styles. * gnu/packages/python-web.scm (python-openid, python-terminado) (python-geventhttpclient, python-cachecontrol, python-webencodings) (python-s3transfer)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/python-web.scm | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 9dc0650230..3ab7dafa42 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -254,7 +254,8 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "py.test" "-v" "webencodings/tests.py"))))))) + (invoke "py.test" "-v" "webencodings/tests.py") + #t))))) (native-inputs `(("python-pytest" ,python-pytest))) (home-page "https://github.com/SimonSapin/python-webencodings") @@ -295,7 +296,8 @@ is Python’s.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "./admin/runtests"))))))) + (invoke "./admin/runtests") + #t))))) (properties `((python2-variant . ,(delay python2-openid)))) (propagated-inputs `(("python-defusedxml" ,python-defusedxml))) @@ -451,7 +453,8 @@ teams extension for python-openid.") ;; (lambda _ ;; ;; 'setup.py test' hits an AssertionError on BSD-specific ;; ;; "tornado/platform/kqueue.py". This is the supported method: - ;; (zero? (system* "python" "-m" "tornado.test"))))) + ;; (invoke- "python" "-m" "tornado.test") + ;; #t))) #:tests? #f)) (native-inputs `(("python-certifi" ,python-certifi))) @@ -522,7 +525,8 @@ web framework, either via the basic or digest authentication schemes.") (modify-phases %standard-phases (replace 'check (lambda _ - (zero? (system* "nosetests"))))))) + (invoke "nosetests") + #t))))) (home-page "https://github.com/takluyver/terminado") (synopsis "Terminals served to term.js using Tornado websockets") (description "This package provides a Tornado websocket backend for the @@ -1519,7 +1523,8 @@ library.") (add-after 'install 'check (lambda* (#:key inputs outputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) - (zero? (system* "py.test" "src/geventhttpclient/tests" "-v"))))))) + (invoke "py.test" "src/geventhttpclient/tests" "-v") + #t))))) (native-inputs `(("python-pytest" ,python-pytest))) (propagated-inputs @@ -1629,7 +1634,8 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients." (setenv "PYTHONPATH" (string-append (getcwd) "/build/lib:" (getenv "PYTHONPATH"))) - (zero? (system* "py.test" "-vv"))))))) + (invoke "py.test" "-vv") + #t))))) (native-inputs `(("python-pytest" ,python-pytest) ("python-redis" ,python-redis) @@ -1715,7 +1721,8 @@ Betamax.") (lambda _ ;; 7 of the 'integration' tests require network access or login ;; credentials. - (zero? (system* "nosetests" "--exclude=integration"))))))) + (invoke "nosetests" "--exclude=integration") + #t))))) (native-inputs `(("python-docutils" ,python-docutils) ("python-mock" ,python-mock) @@ -1831,7 +1838,8 @@ transfers.") ;; (modify-phases %standard-phases ;; (replace 'check ;; (lambda _ - ;; (zero? (system* "nosetests"))))))) + ;; (invoke "nosetests") + ;; #t))))) (propagated-inputs `(("python-aniso8601" ,python-aniso8601) ("python-flask" ,python-flask) -- cgit v1.2.3 From bb5c35820448ef9b83b59a49e94b73ae2d8f7052 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:18:52 +0100 Subject: gnu: b43-tools: Update to 0.0.0-1.27892ef. * gnu/packages/firmware.scm (b43-tools): Update to 0.0.0-1.27892ef. [version]: Use our standard versioning scheme. --- gnu/packages/firmware.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 12595dc31c..5f82f7c31a 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2017 David Craven ;;; Copyright © 2017 Efraim Flashner +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -94,11 +95,11 @@ Linux-libre.") (license (license:non-copyleft "http://directory.fsf.org/wiki/License:ClearBSD")))) (define-public b43-tools - (let ((commit "8dce53297966b31b6c70a7a03c2433978dd9f288") - (rev "1")) + (let ((commit "27892ef741e7f1d08cb939744f8b8f5dac7b04ae") + (revision "1")) (package (name "b43-tools") - (version (string-append "20140625-" rev "." (string-take commit 7))) + (version (git-version "0.0.0" revision commit)) (source (origin (method git-fetch) @@ -108,7 +109,7 @@ Linux-libre.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "08k7sdr9jagm43r2zv4h03j86klhkblpk73p12444a3vzg1gy1lv")))) + "1wgmj4d65izbhprwb5bcwimc2ryv19b9066lqzy4sa5m6wncm9cn")))) (build-system gnu-build-system) (native-inputs `(("flex" ,flex) @@ -117,11 +118,11 @@ Linux-libre.") `(#:modules ((srfi srfi-1) (guix build gnu-build-system) (guix build utils)) - #:tests? #f ;no tests + #:tests? #f ; no tests #:phases (let ((subdirs '("assembler" "disassembler"))) (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (add-before 'build 'patch-/bin/true (lambda _ (substitute* (find-files "." "Makefile") -- cgit v1.2.3 From 315c89f5ba89e18bd365846a62944820a8760b83 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:19:27 +0100 Subject: gnu: b43-tools: Update phase style. * gnu/packages/firmware.scm (b43-tools)[arguments]: Substitute INVOKE for SYSTEM* and FOR-EACH for EVERY, and end phases with #t. --- gnu/packages/firmware.scm | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 5f82f7c31a..d9d0c2910c 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -130,19 +130,20 @@ Linux-libre.") #t)) (replace 'build (lambda _ - (every (lambda (dir) - (zero? (system* "make" "-C" dir "CC=gcc"))) - subdirs))) + (for-each (lambda (dir) + (invoke "make" "-C" dir "CC=gcc")) + subdirs) + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (mkdir-p (string-append out "/bin")) - (every (lambda (dir) - (zero? - (system* "make" "-C" dir - (string-append "PREFIX=" out) - "install"))) - subdirs)))))))) + (for-each (lambda (dir) + (invoke "make" "-C" dir + (string-append "PREFIX=" out) + "install")) + subdirs) + #t))))))) (home-page "http://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools") (synopsis "Collection of tools for the b43 wireless driver") -- cgit v1.2.3 From 3ebf12ea0e380e3619618701b58564cf9423517c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:24:33 +0100 Subject: gnu: b43-tools: Use HTTPS home page. * gnu/packages/firmware.scm (b43-tools)[home-page]: Use HTTPS. --- gnu/packages/firmware.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index d9d0c2910c..6a96f7a1f5 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -145,7 +145,7 @@ Linux-libre.") subdirs) #t))))))) (home-page - "http://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools") + "https://bues.ch/cms/hacking/misc.html#linux_b43_driver_firmware_tools") (synopsis "Collection of tools for the b43 wireless driver") (description "The b43 firmware tools is a collection of firmware extractor, -- cgit v1.2.3 From 0dae492195a0d6e54ed76e43902541bab4ead2e3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 22:51:19 +0100 Subject: gnu: ovmf: Use HTTPS home page. * gnu/packages/firmware.scm (ovmf)[home-page]: Use HTTPS. --- gnu/packages/firmware.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 6a96f7a1f5..1579ba472f 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -301,7 +301,7 @@ coreboot.") '())) #t))))) (supported-systems '("x86_64-linux" "i686-linux")) - (home-page "http://www.tianocore.org") + (home-page "https://www.tianocore.org") (synopsis "UEFI firmware for QEMU") (description "OVMF is an EDK II based project to enable UEFI support for Virtual Machines. OVMF contains a sample UEFI firmware for QEMU and KVM.") -- cgit v1.2.3 From f563d1990466e067e7c73eab553fe1ee20a44ffe Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:06:41 +0100 Subject: gnu: ovmf: Update phase style. * gnu/packages/firmware.scm (ovmf): Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/firmware.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 1579ba472f..0e1539cf66 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -261,7 +261,7 @@ coreboot.") (setenv "WORKSPACE" cwd) (setenv "EDK_TOOLS_PATH" tools) (setenv "PATH" (string-append (getenv "PATH") ":" bin)) - (system* "bash" "edksetup.sh" "BaseTools") + (invoke "bash" "edksetup.sh" "BaseTools") (substitute* "Conf/target.txt" (("^TARGET[ ]*=.*$") "TARGET = RELEASE\n") (("^TOOL_CHAIN_TAG[ ]*=.*$") "TOOL_CHAIN_TAG = GCC49\n") @@ -270,14 +270,16 @@ coreboot.") (number->string (parallel-job-count))))) ;; Build build support. (setenv "BUILD_CC" "gcc") - (zero? (system* "make" "-C" (string-append tools "/Source/C")))))) + (invoke "make" "-C" (string-append tools "/Source/C")) + #t))) (add-after 'build 'build-ia32 (lambda _ (substitute* "Conf/target.txt" (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = IA32\n") (("^ACTIVE_PLATFORM[ ]*=.*$") "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgIa32.dsc\n")) - (zero? (system* "build")))) + (invoke "build") + #t)) ,@(if (string=? "x86_64-linux" (%current-system)) '((add-after 'build 'build-x64 (lambda _ @@ -285,7 +287,8 @@ coreboot.") (("^TARGET_ARCH[ ]*=.*$") "TARGET_ARCH = X64\n") (("^ACTIVE_PLATFORM[ ]*=.*$") "ACTIVE_PLATFORM = OvmfPkg/OvmfPkgX64.dsc\n")) - (zero? (system* "build"))))) + (invoke "build") + #t))) '()) (delete 'build) (replace 'install -- cgit v1.2.3 From 65a3c342b0e53a23509ad479cb5140f09dd008bd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:48:09 +0100 Subject: gnu: ath9k-htc-firmware: Use INSTALL-FILE. * gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Substitute INSTALL-FILE for COPY-FILE with MKDIR-P. --- gnu/packages/firmware.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index 0e1539cf66..da7430b063 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -71,11 +71,8 @@ (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (fw-dir (string-append out "/lib/firmware"))) - (mkdir-p fw-dir) (for-each (lambda (file) - (copy-file file - (string-append fw-dir "/" - (basename file)))) + (install-file file fw-dir)) (find-files "." "\\.fw$")) #t)))) #:tests? #f)) -- cgit v1.2.3 From f136c8f23d6dc0b52540456d50187f3417afb5e3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 1 Mar 2018 23:50:57 +0100 Subject: gnu: gnome-mpv: Update to 0.14. * gnu/packages/video.scm (gnome-mpv): Update to 0.14. --- 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 8190b0ffc1..e4e71e9dcc 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1091,7 +1091,7 @@ projects while introducing many more.") (define-public gnome-mpv (package (name "gnome-mpv") - (version "0.13") + (version "0.14") (source (origin (method url-fetch) @@ -1100,7 +1100,7 @@ projects while introducing many more.") ".tar.xz")) (sha256 (base32 - "1w944ymyssgfcjiczrq4saig90crw9b9hhdsnchfbjsw173qi8n5")))) + "03kjwd5jq0i5ajnvhjwf5019bjjaa16xkdrhdkiz1k58ipjvvj93")))) (native-inputs `(("intltool" ,intltool) ("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 5c0f68e84491b03332e0f070f43c54effac3c64f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:22:09 +0100 Subject: gnu: fossil: Update phase style. * gnu/packages/version-control.scm (fossil)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/version-control.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 6c05ab59db..05f50869a3 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1643,14 +1643,15 @@ repository\" with git-annex.") #:phases (modify-phases %standard-phases (replace 'configure (lambda* (#:key outputs (configure-flags '()) - #:allow-other-keys) + #:allow-other-keys) ;; The 'configure' script is not an autoconf script and ;; chokes on unrecognized options. - (zero? (apply system* - "./configure" - (string-append "--prefix=" - (assoc-ref outputs "out")) - configure-flags)))) + (apply invoke + "./configure" + (string-append "--prefix=" + (assoc-ref outputs "out")) + configure-flags) + #t)) (add-before 'check 'test-setup (lambda _ (setenv "USER" "guix") -- cgit v1.2.3 From 2c1cc27f8fffa3fbce8cf75cd45ea3ec2f8f4ee5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:28:48 +0100 Subject: gnu: fortify-headers: Update to 0.9. * gnu/packages/suckless.scm (fortify-headers): Update to 0.9. --- 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 8a5f158878..c343b42274 100644 --- a/gnu/packages/suckless.scm +++ b/gnu/packages/suckless.scm @@ -564,7 +564,7 @@ environment variable.") (define-public fortify-headers (package (name "fortify-headers") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) @@ -572,7 +572,7 @@ environment variable.") name "-" version ".tar.gz")) (sha256 (base32 - "1cacdczpjb49c4i1168g541wnl3i3gbpv2m2wbnmw5wddlyhgkdg")))) + "1z517ajy34l2k5lz2gvhbmia9xjgagffi4s22azqxnlmgb1g2xfg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; No tests -- cgit v1.2.3 From d338321ddbd8545ff711254abc5d80c5b8cb3698 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 00:33:37 +0100 Subject: gnu: qscintilla: Use HTTPS home page. * gnu/packages/qt.scm (qscintilla)[home-page]: Use HTTPS. --- gnu/packages/qt.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 4c4249bb90..a8c2729ee8 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -1735,7 +1735,7 @@ contain over 620 classes.") (string-append out "/lib/qt$${QT_MAJOR_VERSION}"))) (invoke "qmake"))))))) (native-inputs `(("qtbase" ,qtbase))) - (home-page "http://www.riverbankcomputing.co.uk/software/qscintilla/intro") + (home-page "https://www.riverbankcomputing.co.uk/software/qscintilla/intro") (synopsis "Qt port of the Scintilla C++ editor control") (description "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control. QScintilla includes features especially useful when editing -- cgit v1.2.3 From 467834d5505473dc853677be4ca7d151e28fd669 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:14:53 +0100 Subject: gnu: ghc-abstract-deque: Fix typos in description. * gnu/packages/haskell.scm (ghc-abstract-deque)[description]: Fix typos. --- gnu/packages/haskell.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 5c6e07a671..3ff78047db 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -8181,12 +8181,12 @@ Background: There exists a feature space for queues that extends between: @itemize @item Simple, single-ended, non-concurrent, bounded queues -@item Double-ended, threadsafe, growable queues with important points -inbetween (such as the queues used for work-stealing). +@item Double-ended, thread-safe, growable queues with important points +in between (such as the queues used for work stealing). @end itemize This package includes an interface for Deques that allows the programmer -to use a single API for all of the above, while using the type-system to +to use a single API for all of the above, while using the type system to select an efficient implementation given the requirements (using type families). This package also includes a simple reference implementation based on -- cgit v1.2.3 From 3a5c02777d6a51620d8cb8afa01602bc669bbfea Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:40:20 +0100 Subject: gnu: highlight: Update to 3.42. * gnu/packages/pretty-print.scm (highlight): Update to 3.42. --- gnu/packages/pretty-print.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm index 2f61de8994..e8baefa1d4 100644 --- a/gnu/packages/pretty-print.scm +++ b/gnu/packages/pretty-print.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2016 Ricardo Wurmus ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017 Ludovic Courtès -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -242,7 +242,7 @@ seen in a terminal.") (define-public highlight (package (name "highlight") - (version "3.33") + (version "3.42") (source (origin (method url-fetch) @@ -250,10 +250,10 @@ seen in a terminal.") version ".tar.bz2")) (sha256 (base32 - "0g2whi6pxl640795vymikm82a1my841jmh7fiqzbrjpc9wsk1db4")))) + "07iihzy8ckzdrxqd6bzbij4hy4mmlixibjnjviqfihd0hh1q30m5")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no tests + `(#:tests? #f ; no tests #:make-flags (let ((confdir (string-append %output "/share/highlight/config/"))) (list (string-append "PREFIX=" %output) @@ -261,7 +261,7 @@ seen in a terminal.") (string-append "conf_dir=" confdir))) #:phases (modify-phases %standard-phases - (delete 'configure) + (delete 'configure) ; no configure script (add-after 'unpack 'fix-search-for-lua (lambda _ (substitute* "src/makefile" -- cgit v1.2.3 From 6e48fbb19a420ea0be1d922ebdce36d7beb0240f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 01:41:40 +0100 Subject: gnu: highlight: Don't hard-code Lua version. * gnu/packages/pretty-print.scm (highlight)[arguments]: Construct the Lua prefix programatically instead of hard-coding it. --- gnu/packages/pretty-print.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/pretty-print.scm b/gnu/packages/pretty-print.scm index e8baefa1d4..6edfba95cc 100644 --- a/gnu/packages/pretty-print.scm +++ b/gnu/packages/pretty-print.scm @@ -27,6 +27,7 @@ #:use-module (guix download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix utils) #:use-module (gnu packages) #:use-module (gnu packages ghostscript) #:use-module (gnu packages groff) @@ -266,7 +267,8 @@ seen in a terminal.") (lambda _ (substitute* "src/makefile" (("(pkg-config.*)lua" _ prefix) - (string-append prefix "lua-5.3"))) + (string-append prefix "lua-" ,(version-major+minor + (package-version lua))))) #t))))) (inputs `(("lua" ,lua) -- cgit v1.2.3 From dc8584d2b17f75bdf653b977e29821fb5692d7b2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 02:24:23 +0100 Subject: gnu: perl-test-harness: Update to 3.41. * gnu/packages/perl-check.scm (perl-test-harness): Update to 3.41. --- gnu/packages/perl-check.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index 110ba45d3d..6464385327 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -529,7 +529,7 @@ contents of a file is equal to a particular string.") (define-public perl-test-harness (package (name "perl-test-harness") - (version "3.39") + (version "3.41") (source (origin (method url-fetch) @@ -537,7 +537,7 @@ contents of a file is equal to a particular string.") "Test-Harness-" version ".tar.gz")) (sha256 (base32 - "0chiqnzmna2mglm37nzxvn9qhq2j31iwz3i9isqjs7bf3k449gb9")))) + "0cgdgzywvscbvb9i0dmd2ls5jwqlnf2z6hx4f4lljpvdjd59v3m8")))) (build-system perl-build-system) (arguments `(#:phases -- cgit v1.2.3 From defe0282c29cbc9bdb774ebdf8095a02c4aaea98 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 02:30:53 +0100 Subject: gnu: perl-mozilla-ca: Update to 20180117. * gnu/packages/perl.scm (perl-mozilla-ca): Update to 20180117. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 556d8d31b4..e44d5c3f0f 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -6008,7 +6008,7 @@ of data.") (define-public perl-mozilla-ca (package (name "perl-mozilla-ca") - (version "20160104") + (version "20180117") (source (origin (method url-fetch) @@ -6016,7 +6016,7 @@ of data.") version ".tar.gz")) (sha256 (base32 - "0aizn08lrdrgjz9vagkjmw2c7sxn46fzz521v9dbcqii4jd0d9r7")))) + "01p4ykyilk1639dxgjaa2n7rz1f0zbqxkq11yc9n6xcz26z9zk7j")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Mozilla-CA/") (synopsis "Mozilla's CA cert bundle in PEM format") -- cgit v1.2.3 From 139ecdee8e592c515eea8cff4b918f0655196b4c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 02:43:54 +0100 Subject: gnu: delta: Remove redundant code. * gnu/packages/debug.scm (delta)[arguments]: Remove unneeded MKDIR-P calls. --- gnu/packages/debug.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 2354f0fbb9..6b566b0097 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -66,8 +66,6 @@ (bin (string-append out "/bin")) (doc (string-append out "/share/doc/delta-" ,version))) (begin - (mkdir-p bin) - (mkdir-p doc) (for-each (lambda (h) (install-file h doc)) `("License.txt" ,@(find-files "www" ".*\\.html"))) @@ -75,7 +73,7 @@ (install-file b bin)) `("delta" "multidelta" "topformflat")))) #t)) - (delete 'configure)))) + (delete 'configure)))) ; no configure script (home-page "http://delta.tigris.org/") (synopsis "Heuristical file minimizer") (description -- cgit v1.2.3 From a40f732bb6a8fc2f22d5931efad428a7cbdbe609 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 04:35:08 +0100 Subject: gnu: python-webencodings: Fix typo in description. * gnu/packages/python-web.scm (python-webencodings)[description]: Fix typo. --- gnu/packages/python-web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 3ab7dafa42..d9721f1375 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -265,7 +265,7 @@ C, yielding parse times that can be a thirtieth of the html5lib parse times.") something like @code{Content-Type: text/html; charset=latin1}, tools need to use a particular set of aliases for encoding labels as well as some overriding rules. For example, @code{US-ASCII} and @code{iso-8859-1} on -the web are actually aliases for @code{windows-1252}, and an @code{UTF-8} +the web are actually aliases for @code{windows-1252}, and a @code{UTF-8} or @code{UTF-16} BOM takes precedence over any other encoding declaration. The WHATWG @url{https://encoding.spec.whatwg.org/,Encoding} standard defines all such details so that implementations do not have to -- cgit v1.2.3 From 5658b4ce693637123375ccf594c3b4557b643224 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 05:01:16 +0100 Subject: gnu: zerofree: Update to 1.1.1. * gnu/packages/linux.scm (zerofree): Update to 1.1.1. --- 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 b922989018..b4d81943e1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -873,7 +873,7 @@ ext3 or ext4 partition.") (define-public zerofree (package (name "zerofree") - (version "1.1.0") + (version "1.1.1") (home-page "https://frippery.org/uml/") (source (origin (method url-fetch) @@ -881,7 +881,7 @@ ext3 or ext4 partition.") ".tgz")) (sha256 (base32 - "059g29x5r1xj6wcj4xj85l8w6qrxyl86yqbybjqqz6nxz4falxzf")))) + "0rrqfa5z103ws89vi8kfvbks1cfs74ix6n1wb6vs582vnmhwhswm")))) (build-system gnu-build-system) (arguments '(#:phases -- cgit v1.2.3 From 6fda93e6c8aa25c2b482a0502be9d39335ed2172 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 05:16:00 +0100 Subject: gnu: libpsl: Update to 0.20.1. * gnu/packages/web.scm (libpsl): Update to 0.20.1. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e3412f60e2..f9b7e3f70f 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -799,7 +799,7 @@ for efficient socket-like bidirectional reliable communication channels.") (define-public libpsl (package (name "libpsl") - (version "0.20.0") + (version "0.20.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/rockdaboot/libpsl/" @@ -807,7 +807,7 @@ for efficient socket-like bidirectional reliable communication channels.") "/libpsl-" version ".tar.gz")) (sha256 (base32 - "0rsjm6mb71nnj6ikr2dq5qmny314v3j7m07zz1i7m6v8hxxm98i7")))) + "17r18y25ka2ck2ykfidbg4a7jpyzmkqwrzplgqjp7mwd2l9rc6cm")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From b01a1b34f2345e66e2ba4b647fca75e7951567d6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 05:16:27 +0100 Subject: gnu: nghttp2: Update to 1.31.0. * gnu/packages/web.scm (nghttp2): Update to 1.31.0. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index f9b7e3f70f..760f4ef2ab 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -6350,7 +6350,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") (define-public nghttp2 (package (name "nghttp2") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) @@ -6359,7 +6359,7 @@ derivation by David Revoy from the original MonsterID by Andreas Gohr.") name "-" version ".tar.xz")) (sha256 (base32 - "1b2j7il0wp8hi4jl3cah7fkshmg29cchdski9cw74gx5496gp6h8")))) + "1ivs74v9sa2sds3dq0s7vn9bkmhr2hgwyg1an1rah3agqwnkqmrn")))) (build-system gnu-build-system) (outputs (list "out" "lib")) ; only libnghttp2 -- cgit v1.2.3 From 5f4565b18fa0bdb0388265c9e97e284826327c3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 22:21:00 +0100 Subject: gnu: Add r-network. * gnu/packages/cran.scm (r-network): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9279d1da83..211d292397 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2225,3 +2225,23 @@ meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") (license license:gpl2))) + +(define-public r-network + (package + (name "r-network") + (version "1.13.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "network" version)) + (sha256 + (base32 + "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s")))) + (build-system r-build-system) + (home-page "http://statnet.org/") + (synopsis "Classes for relational data") + (description + "This package provides tools to create and modify network objects. The +@code{network} class can represent a range of relational data types, and +supports arbitrary vertex/edge/graph attributes.") + (license license:gpl2+))) -- cgit v1.2.3 From 07a2f34d5c8342b88530f8cb968090eccd0da91c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 22:22:20 +0100 Subject: gnu: Add r-statnet-common. * gnu/packages/cran.scm (r-statnet-common): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 211d292397..e06eb60e94 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2245,3 +2245,23 @@ published results; and a routine for graphical display.") @code{network} class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.") (license license:gpl2+))) + +(define-public r-statnet-common + (package + (name "r-statnet-common") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "statnet.common" version)) + (sha256 + (base32 + "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0")))) + (properties + `((upstream-name . "statnet.common"))) + (build-system r-build-system) + (home-page "http://www.statnet.org") + (synopsis "R scripts and utilities used by the Statnet software") + (description "This package provides non-statistical utilities used by the +software developed by the Statnet Project.") + (license license:gpl3))) -- cgit v1.2.3 From 1088744d8748a4ed81accdacab95eb397de0f23b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 22:22:32 +0100 Subject: gnu: Add r-sna. * gnu/packages/cran.scm (r-sna): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e06eb60e94..2e229e9e0f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2265,3 +2265,27 @@ supports arbitrary vertex/edge/graph attributes.") (description "This package provides non-statistical utilities used by the software developed by the Statnet Project.") (license license:gpl3))) + +(define-public r-sna + (package + (name "r-sna") + (version "2.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "sna" version)) + (sha256 + (base32 + "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-network" ,r-network) + ("r-statnet-common" ,r-statnet-common))) + (home-page "http://www.statnet.org") + (synopsis "Tools for social network analysis") + (description + "This package provides a range of tools for social network analysis, +including node and graph-level indices, structural distance and covariance +methods, structural equivalence detection, network regression, random graph +generation, and 2D/3D network visualization.") + (license license:gpl2+))) -- cgit v1.2.3 From 4e35c4290ef64e8fba376f9c3d9754757ebf89da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 22:22:54 +0100 Subject: gnu: Add r-rbiofabric. * gnu/packages/graph.scm (r-rbiofabric): New variable. --- gnu/packages/graph.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 70df77b5d2..19c9b2269b 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Ricardo Wurmus +;;; Copyright © 2017, 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,6 +18,7 @@ (define-module (gnu packages graph) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix packages) #:use-module (guix build-system gnu) #:use-module (guix build-system python) @@ -172,3 +173,29 @@ model.") "This package interfaces R with the graphviz library for plotting R graph objects from the @code{graph} package.") (license license:epl1.0))) + +(define-public r-rbiofabric + (let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac") + (revision "1")) + (package + (name "r-rbiofabric") + (version (string-append "0.3-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wjrl/RBioFabric.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z")))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph))) + (home-page "http://www.biofabric.org/") + (synopsis "BioFabric network visualization") + (description "This package provides an implementation of the function +@code{bioFabric} for creating scalable network digrams where nodes are +represented by horizontal lines, and edges are represented by vertical +lines.") + (license license:expat)))) -- cgit v1.2.3 From 93c21ddc8620ec1e6930b85161cdbc89fc459f02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 22:55:10 +0100 Subject: gnu: Add r-ttr. * gnu/packages/cran.scm (r-ttr): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 2e229e9e0f..63f1405472 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2289,3 +2289,28 @@ including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.") (license license:gpl2+))) + +(define-public r-ttr + (package + (name "r-ttr") + (version "0.23-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "TTR" version)) + (sha256 + (base32 + "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1")))) + (properties `((upstream-name . "TTR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "https://github.com/joshuaulrich/TTR") + (synopsis "Technical trading rules") + (description + "This package provides functions and data to construct technical trading +rules with R.") + (license license:gpl2))) -- cgit v1.2.3 From 0b64332c74fa09d768349c05b0db6bd309962781 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:03:10 +0100 Subject: gnu: Add r-leaps. * gnu/packages/cran.scm (r-leaps): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 63f1405472..4f54b40149 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2314,3 +2314,23 @@ generation, and 2D/3D network visualization.") "This package provides functions and data to construct technical trading rules with R.") (license license:gpl2))) + +(define-public r-leaps + (package + (name "r-leaps") + (version "3.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "leaps" version)) + (sha256 + (base32 + "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m")))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/leaps/") + (synopsis "Regression subset selection") + (description + "This package provides tools for regression subset selection, including +exhaustive search.") + (license license:gpl2+))) -- cgit v1.2.3 From d3cb62e58d99a23a9154a9b03fdffa496c36d337 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:05:02 +0100 Subject: gnu: Add r-splus2r. * gnu/packages/cran.scm (r-splus2r): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4f54b40149..b0dcaccbdd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2334,3 +2334,25 @@ rules with R.") "This package provides tools for regression subset selection, including exhaustive search.") (license license:gpl2+))) + +(define-public r-splus2r + (package + (name "r-splus2r") + (version "1.2-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "splus2R" version)) + (sha256 + (base32 + "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz")))) + (properties `((upstream-name . "splus2R"))) + (build-system r-build-system) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/splus2R/") + (synopsis "Supplemental S-PLUS functionality in R") + (description + "Currently there are many functions in S-PLUS that are missing in R. To +facilitate the conversion of S-PLUS packages to R packages, this package +provides some missing S-PLUS functionality in R.") + (license license:gpl2))) -- cgit v1.2.3 From 034ac9d67a3cbb4cf0976ff1c796a35f6a73cb2f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:05:14 +0100 Subject: gnu: Add r-ifultools. * gnu/packages/cran.scm (r-ifultools): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b0dcaccbdd..613ed130d3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2356,3 +2356,24 @@ exhaustive search.") facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.") (license license:gpl2))) + +(define-public r-ifultools + (package + (name "r-ifultools") + (version "2.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "ifultools" version)) + (sha256 + (base32 + "0pv2msaa1rmj8csxdclzi2jwg9pfdvh87blj9j3xa3myisglq092")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-splus2r" ,r-splus2r))) + (home-page "http://cran.r-project.org/web/packages/ifultools/") + (synopsis "Insightful research tools") + (description "This package provides C code used by the wmtsa, fractal, and +sapa R packages.") + (license license:gpl2))) -- cgit v1.2.3 From 0be7effefa4aaa39a2312b9b57d8bed5811e4069 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:05:35 +0100 Subject: gnu: Add r-sapa. * gnu/packages/cran.scm (r-sapa): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 613ed130d3..1f76dac57c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2377,3 +2377,25 @@ provides some missing S-PLUS functionality in R.") (description "This package provides C code used by the wmtsa, fractal, and sapa R packages.") (license license:gpl2))) + +(define-public r-sapa + (package + (name "r-sapa") + (version "2.0-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "sapa" version)) + (sha256 + (base32 + "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ifultools" ,r-ifultools) + ("r-splus2r" ,r-splus2r))) + (home-page "http://cran.r-project.org/web/packages/sapa/") + (synopsis "Spectral analysis for physical applications") + (description "This package provides software for the book Spectral +Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, +Cambridge University Press, 1993.") + (license license:gpl2))) -- cgit v1.2.3 From dceb159206e8336f855d768a83c2da6b9dd95982 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:05:43 +0100 Subject: gnu: Add r-quantmod. * gnu/packages/cran.scm (r-quantmod): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1f76dac57c..8c811269f3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2399,3 +2399,27 @@ sapa R packages.") Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.") (license license:gpl2))) + +(define-public r-quantmod + (package + (name "r-quantmod") + (version "0.4-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "quantmod" version)) + (sha256 + (base32 + "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-curl" ,r-curl) + ("r-ttr" ,r-ttr) + ("r-xts" ,r-xts) + ("r-zoo" ,r-zoo))) + (home-page "http://cran.r-project.org/web/packages/quantmod/") + (synopsis "Quantitative financial modelling framework") + (description "This package provides a quantitative financial modelling +framework to allow users to specify, build, trade, and analyse quantitative +financial trading strategies.") + (license license:gpl3))) -- cgit v1.2.3 From b6dc3255386a61de6abe5fa26afd760a3e8573a0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:05:52 +0100 Subject: gnu: Add r-tseries. * gnu/packages/cran.scm (r-tseries): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8c811269f3..e9d243d992 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2423,3 +2423,28 @@ Cambridge University Press, 1993.") framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.") (license license:gpl3))) + +(define-public r-tseries + (package + (name "r-tseries") + (version "0.10-43") + (source + (origin + (method url-fetch) + (uri (cran-uri "tseries" version)) + (sha256 + (base32 + "1yjxhj7l1p2przczl6frggfcr5iwda9lbcsmh0y75gbbbps14yf2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-quadprog" ,r-quadprog) + ("r-quantmod" ,r-quantmod) + ("r-zoo" ,r-zoo))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/tseries/") + (synopsis "Time series analysis and computational finance") + (description + "This package provides functions relating to time series analysis and +computational finance.") + (license license:gpl2))) -- cgit v1.2.3 From a2c079a780b8a8c552577eb43f6d855e7fede2c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:00 +0100 Subject: gnu: Add r-wmtsa. * gnu/packages/cran.scm (r-wmtsa): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e9d243d992..b6610cb93f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2448,3 +2448,27 @@ financial trading strategies.") "This package provides functions relating to time series analysis and computational finance.") (license license:gpl2))) + +(define-public r-wmtsa + (package + (name "r-wmtsa") + (version "2.0-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "wmtsa" version)) + (sha256 + (base32 + "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ifultools" ,r-ifultools) + ("r-mass" ,r-mass) + ("r-splus2r" ,r-splus2r))) + (home-page "http://cran.r-project.org/web/packages/wmtsa/") + (synopsis "Wavelet methods for time series analysis") + (description + "This package provides software to accompany the book \"Wavelet Methods +for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge +University Press, 2000.") + (license license:gpl2))) -- cgit v1.2.3 From 4993a02ad70b3fb152bfb2b9f91ab9fc590220f4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:10 +0100 Subject: gnu: Add r-tsa. * gnu/packages/cran.scm (r-tsa): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b6610cb93f..750e82ad60 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2472,3 +2472,29 @@ computational finance.") for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge University Press, 2000.") (license license:gpl2))) + +(define-public r-tsa + (package + (name "r-tsa") + (version "1.01") + (source + (origin + (method url-fetch) + (uri (cran-uri "TSA" version)) + (sha256 + (base32 + "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx")))) + (properties `((upstream-name . "TSA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-leaps" ,r-leaps) + ("r-locfit" ,r-locfit) + ("r-mgcv" ,r-mgcv) + ("r-tseries" ,r-tseries))) + (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm") + (synopsis "Time series analysis") + (description + "This package contains R functions and datasets detailed in the book +\"Time Series Analysis with Applications in R (second edition)\" by Jonathan +Cryer and Kung-Sik Chan.") + (license license:gpl2+))) -- cgit v1.2.3 From 19da7fe314629e894ef201fdf8ca10ca4555b6b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:17 +0100 Subject: gnu: Add r-extradistr. * gnu/packages/cran.scm (r-extradistr): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 750e82ad60..5d1f24aa08 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2498,3 +2498,26 @@ University Press, 2000.") \"Time Series Analysis with Applications in R (second edition)\" by Jonathan Cryer and Kung-Sik Chan.") (license license:gpl2+))) + +(define-public r-extradistr + (package + (name "r-extradistr") + (version "1.8.8") + (source + (origin + (method url-fetch) + (uri (cran-uri "extraDistr" version)) + (sha256 + (base32 + "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3")))) + (properties `((upstream-name . "extraDistr"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/twolodzko/extraDistr") + (synopsis "Additional univariate and multivariate distributions") + (description + "This package implements density, distribution functions, quantile +functions and random generation functions for a large number of univariate and +multivariate distributions.") + (license license:gpl2))) -- cgit v1.2.3 From 5b25bc55dc6e23936719e2748b5d9445ce9eea97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:26 +0100 Subject: gnu: Add r-fractal. * gnu/packages/cran.scm (r-fractal): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 5d1f24aa08..d4aeb26171 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2521,3 +2521,29 @@ Cryer and Kung-Sik Chan.") functions and random generation functions for a large number of univariate and multivariate distributions.") (license license:gpl2))) + +(define-public r-fractal + (package + (name "r-fractal") + (version "2.0-4") + (source + (origin + (method url-fetch) + (uri (cran-uri "fractal" version)) + (sha256 + (base32 + "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ifultools" ,r-ifultools) + ("r-mass" ,r-mass) + ("r-sapa" ,r-sapa) + ("r-scatterplot3d" ,r-scatterplot3d) + ("r-splus2r" ,r-splus2r) + ("r-wmtsa" ,r-wmtsa))) + (home-page "http://cran.r-project.org/web/packages/fractal/") + (synopsis "Fractal time series modeling and analysis") + (description + "This package provides tools for stochastic fractal and deterministic +chaotic time series analysis.") + (license license:gpl2))) -- cgit v1.2.3 From 6615a364212ac7e731ecf0e9357317257f7114de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:33 +0100 Subject: gnu: Add r-urca. * gnu/packages/cran.scm (r-urca): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d4aeb26171..1c8b9ba521 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2547,3 +2547,24 @@ multivariate distributions.") "This package provides tools for stochastic fractal and deterministic chaotic time series analysis.") (license license:gpl2))) + +(define-public r-urca + (package + (name "r-urca") + (version "1.3-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "urca" version)) + (sha256 + (base32 + "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732")))) + (build-system r-build-system) + (propagated-inputs `(("r-nlme" ,r-nlme))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/urca/") + (synopsis "Unit root and cointegration tests for time series data") + (description + "This package provides unit root and cointegration tests encountered in +applied econometric analysis.") + (license license:gpl2+))) -- cgit v1.2.3 From d32e57248954d20ef892ee9fbc3bae9afa1299d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:41 +0100 Subject: gnu: Add r-cubature. * gnu/packages/cran.scm (r-cubature): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c8b9ba521..f7b657bc3a 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2568,3 +2568,28 @@ chaotic time series analysis.") "This package provides unit root and cointegration tests encountered in applied econometric analysis.") (license license:gpl2+))) + +(define-public r-cubature + (package + (name "r-cubature") + (version "1.3-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "cubature" version)) + (sha256 + (base32 + "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/bnaras/cubature") + (synopsis "Adaptive multivariate integration over hypercubes") + (description + "This package is an R wrapper around the cubature C library for adaptive +multivariate integration over hypercubes. This version provides both +@code{hcubature} and @code{pcubature} routines in addition to a vector +interface.") + ;; The included cubature C library is released under GPLv2+, but the + ;; wrapper declares the license to be GPLv3+. + (license (list license:gpl2+ license:gpl3+)))) -- cgit v1.2.3 From 7531ee842c19c481b3e4785b36cf6558b054e6b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:50 +0100 Subject: gnu: Add r-trend. * gnu/packages/cran.scm (r-trend): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f7b657bc3a..ce676334c6 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2593,3 +2593,34 @@ interface.") ;; The included cubature C library is released under GPLv2+, but the ;; wrapper declares the license to be GPLv3+. (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-trend + (package + (name "r-trend") + (version "1.1.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "trend" version)) + (sha256 + (base32 + "06yifqbsvxbmk5gld4z2nnyhf59v8ks5xjwacmb25mv9r6bn388b")))) + (build-system r-build-system) + (propagated-inputs + `(("r-extradistr" ,r-extradistr))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/trend/") + (synopsis "Non-parametric trend tests and change-point detection") + (description + "The analysis of environmental data often requires the detection of +trends and change-points. This package includes tests for trend +detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) +Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite) +Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman +correlation trend test), change-point detection (Lanzante's test procedures, +Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal +Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency +Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two +sample Robust Rank-Order Distributional Test.") + (license license:gpl3))) -- cgit v1.2.3 From f96eda90d5b015057dfd28d4ef7466dbae4bc3f5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:06:57 +0100 Subject: gnu: Add r-expm. * gnu/packages/cran.scm (r-expm): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index ce676334c6..e7efab78ec 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2624,3 +2624,24 @@ Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two sample Robust Rank-Order Distributional Test.") (license license:gpl3))) + +(define-public r-expm + (package + (name "r-expm") + (version "0.999-2") + (source + (origin + (method url-fetch) + (uri (cran-uri "expm" version)) + (sha256 + (base32 + "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q")))) + (build-system r-build-system) + (propagated-inputs `(("r-matrix" ,r-matrix))) + (native-inputs `(("gfortran" ,gfortran))) + (home-page "http://r-forge.r-project.org/projects/expm/") + (synopsis "Tools for matrix exponentials and related quantities") + (description + "This package provides tools for the computation of the matrix +exponential, logarithm, square root, and related quantities.") + (license license:gpl2+))) -- cgit v1.2.3 From 68b6a67e94a2c4e57444b0aa3714910d0ad0190b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:07:04 +0100 Subject: gnu: Add r-complexplus. * gnu/packages/cran.scm (r-complexplus): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e7efab78ec..a82700fb38 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2645,3 +2645,25 @@ sample Robust Rank-Order Distributional Test.") "This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.") (license license:gpl2+))) + +(define-public r-complexplus + (package + (name "r-complexplus") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "complexplus" version)) + (sha256 + (base32 + "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx")))) + (build-system r-build-system) + (propagated-inputs + `(("r-expm" ,r-expm) + ("r-matrix" ,r-matrix))) + (home-page "http://cran.r-project.org/web/packages/complexplus/") + (synopsis "Functions of complex or real variables") + (description + "This package extends several functions to the complex domain, including +the matrix exponential and logarithm, and the determinant.") + (license license:gpl2))) -- cgit v1.2.3 From 7b81a7eabf71ccf989d2b3e33ff7d1801b848558 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:07:12 +0100 Subject: gnu: Add r-phontools. * gnu/packages/cran.scm (r-phontools): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a82700fb38..d20635b91b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2667,3 +2667,25 @@ exponential, logarithm, square root, and related quantities.") "This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.") (license license:gpl2))) + +(define-public r-phontools + (package + (name "r-phontools") + (version "0.2-2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "phonTools" version)) + (sha256 + (base32 + "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7")))) + (properties `((upstream-name . "phonTools"))) + (build-system r-build-system) + (home-page "http://www.santiagobarreda.com/rscripts.html") + (synopsis "Tools for phonetic and acoustic analyses") + (description + "This package contains tools for the organization, display, and analysis +of the sorts of data frequently encountered in phonetics research and +experimentation, including the easy creation of IPA vowel plots, and the +creation and manipulation of WAVE audio files.") + (license license:bsd-2))) -- cgit v1.2.3 From d976454c6b65264eb1be6b69852a69fe5f6cf6e1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:07:20 +0100 Subject: gnu: Add r-np. * gnu/packages/cran.scm (r-np): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d20635b91b..14351e6ae0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2689,3 +2689,27 @@ of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the creation and manipulation of WAVE audio files.") (license license:bsd-2))) + +(define-public r-np + (package + (name "r-np") + (version "0.60-6") + (source + (origin + (method url-fetch) + (uri (cran-uri "np" version)) + (sha256 + (base32 + "1y72x5j9j9mcgcy2xizk31gl843hfkngxdn8s4qw7yhw2qj79hsr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) + ("r-cubature" ,r-cubature) + ("r-quantreg" ,r-quantreg))) + (home-page "https://github.com/JeffreyRacine/R-Package-np") + (synopsis "Non-parametric kernel smoothing methods for mixed data types") + (description "This package provides non-parametric (and semi-parametric) +kernel methods that seamlessly handle a mix of continuous, unordered, and +ordered factor data types.") + ;; Any version of the GPL. + (license license:gpl3+))) -- cgit v1.2.3 From 2a112be09aebb3da15958e58fb677e3fa76e2bd8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:07:26 +0100 Subject: gnu: Add r-powerplus. * gnu/packages/cran.scm (r-powerplus): New variable. --- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 14351e6ae0..7433a561ad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2713,3 +2713,28 @@ kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types.") ;; Any version of the GPL. (license license:gpl3+))) + +(define-public r-powerplus + (package + (name "r-powerplus") + (version "3.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "powerplus" version)) + (sha256 + (base32 + "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-complexplus" ,r-complexplus) + ("r-expm" ,r-expm) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-phontools" ,r-phontools))) + (home-page "http://cran.r-project.org/web/packages/powerplus/") + (synopsis "Exponentiation operations") + (description + "This package provides tools for the computation of matrix and scalar +exponentiation.") + (license license:gpl2))) -- cgit v1.2.3 From fa5965990d583cd9d87f7abc07d1874616cd262b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:24:57 +0100 Subject: gnu: Add r-hpar. * gnu/packages/bioconductor.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 gnu/packages/bioconductor.scm (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index dfe3ff5fc3..9684d949f6 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -76,6 +76,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/bash.scm \ %D%/packages/bdw-gc.scm \ %D%/packages/benchmark.scm \ + %D%/packages/bioconductor.scm \ %D%/packages/bioinformatics.scm \ %D%/packages/bittorrent.scm \ %D%/packages/bison.scm \ diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm new file mode 100644 index 0000000000..f557dce8e5 --- /dev/null +++ b/gnu/packages/bioconductor.scm @@ -0,0 +1,42 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2018 Ricardo Wurmus +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages bioconductor) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix build-system r) + #:use-module (gnu packages)) + +(define-public r-hpar + (package + (name "r-hpar") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "hpar" version)) + (sha256 + (base32 + "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8")))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/hpar/") + (synopsis "Human Protein Atlas in R") + (description "This package provides a simple interface to and data from +the Human Protein Atlas project.") + (license license:artistic2.0))) -- cgit v1.2.3 From 62a4b952c041d5643f1a1ef05450dd8fb59e9bbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:43:55 +0100 Subject: gnu: python-xopen: Update to 0.3.2. * gnu/packages/python.scm (python-xopen): Update to 0.3.2. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 126424183b..5f701701a4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2014, 2015 Federico Beffa ;;; Copyright © 2015 Omar Radwan ;;; Copyright © 2015 Pierre-Antoine Rault -;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2015, 2016 Christopher Allan Webber ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2015, 2016 David Thompson @@ -10173,14 +10173,14 @@ network.") (define-public python-xopen (package (name "python-xopen") - (version "0.1.1") + (version "0.3.2") (source (origin (method url-fetch) (uri (pypi-uri "xopen" version)) (sha256 (base32 - "1wx6mylzcsyhjl19ycb83qq6iqpmr927lz62njfsar6ldsj0qcni")) + "0bzjmn3rl1cd3d2q39cjwnkhaspk2b0hfj3rl64pclm44ihg5fb6")) (file-name (string-append name "-" version ".tar.gz")))) (build-system python-build-system) (home-page "https://github.com/marcelm/xopen/") -- cgit v1.2.3 From 3ede1550e8310a8a544c1fb0f7f372c60c00bbe0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 2 Mar 2018 23:44:16 +0100 Subject: gnu: cutadapt: Update to 1.16. * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16. [source]: Fetch via git. [arguments]: Remove. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/bioinformatics.scm | 32 ++++++++------------------------ 1 file changed, 8 insertions(+), 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e5e9192993..e13f1b369f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1854,38 +1854,22 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (define-public cutadapt (package (name "cutadapt") - (version "1.14") + (version "1.16") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/marcelm/cutadapt/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/marcelm/cutadapt.git") + (commit (string-append "v" version)))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "16gbpiwy4m48vq2h5wqar3i8vr6vcj9gcl2qvqim19x6ya9dp8kd")))) + "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; The tests must be run after installation. - (delete 'check) - (add-after 'install 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (setenv "PYTHONPATH" - (string-append - (getenv "PYTHONPATH") - ":" (assoc-ref outputs "out") - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) - (zero? (system* "nosetests" "-P" "tests"))))))) (inputs `(("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose))) + ("python-pytest" ,python-pytest))) (home-page "https://cutadapt.readthedocs.io/en/stable/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description -- cgit v1.2.3 From 3cb3a4e6e5c8252829a4ef9fd3d0f897c0c5e53f Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 3 Mar 2018 00:04:17 +0100 Subject: linux-initrd: 'file-system-modules' returns the right module list. Fixes a bug whereby, for an "iso9660" file system, it would return '("iso9660" "isofs"), i.e., both the key and the value. Reported by Danny Milosavljevic at . * gnu/system/linux-initrd.scm (lookup-procedure): 'vhash-assoc' returns a key/value pair; match it. --- gnu/system/linux-initrd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index e7f97bb88d..7a7592bf0a 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -262,8 +262,8 @@ FILE-SYSTEMS." (let ((table (vhash mapping ...))) (lambda (key) (match (vhash-assoc key table) - (#f default) - (value value))))))) + (#f default) + ((key . value) value))))))) (define file-system-type-modules ;; Given a file system type, return the list of modules it needs. -- cgit v1.2.3 From 5a3716aebfa3a967165499589f044514dc1d98d7 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 3 Mar 2018 01:25:15 +0100 Subject: vm: Add missing modules to the 'expression->derivation-in-linux-vm' initrd. Fixes a regression introduced in bc499b113a598c0e7863da9887a4133472985713, whereby the default initrd used by 'expression->derivation-in-linux-vm' would lack all the usual modules: virtio, nls_iso8859-1, etc. * gnu/system/vm.scm (expression->derivation-in-linux-vm): Pass #:linux-modules to 'base-initrd'. --- gnu/system/vm.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 345cecedd8..db29fd5ce9 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -143,6 +143,7 @@ made available under the /xchg CIFS share." (return initrd) (base-initrd %linux-vm-file-systems #:linux linux + #:linux-modules %base-initrd-modules #:virtio? #t #:qemu-networking? #t)))) -- cgit v1.2.3 From f850e0da8e56b8e38b0a6c49f4c0618f16c8c572 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 3 Mar 2018 01:29:18 +0100 Subject: system: beaglebone-black: Use 'initrd-modules'. * gnu/system/examples/beaglebone-black.tmpl: Use 'initrd-modules' instead of 'initrd'. --- gnu/system/examples/beaglebone-black.tmpl | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/system/examples/beaglebone-black.tmpl b/gnu/system/examples/beaglebone-black.tmpl index 4b090e0fb7..97201330c7 100644 --- a/gnu/system/examples/beaglebone-black.tmpl +++ b/gnu/system/examples/beaglebone-black.tmpl @@ -15,11 +15,10 @@ (bootloader (bootloader-configuration (bootloader u-boot-beaglebone-black-bootloader) (target "/dev/mmcblk1"))) - (initrd (lambda (fs . rest) - (apply base-initrd fs - ;; This module is required to mount the sd card. - #:extra-modules (list "omap_hsmmc") - rest))) + + ;; This module is required to mount the SD card. + (initrd-modules (cons "omap_hsmmc" %base-initrd-modules)) + (file-systems (cons (file-system (device "my-root") (title 'label) -- cgit v1.2.3 From eac026e5c80caae88a6cef317a46007dca343578 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 3 Mar 2018 09:33:34 +0100 Subject: linux-initrd: Add virtio modules to '%base-initrd-modules'. Fixes a regression in installation tests, whereby 'guix system init' would report that virtio modules are missing for the target devices. In practice virtio modules were always available since 'base-initrd' was always called with #:virtio? #t. This commit simply moves them to '%base-initrd-modules' so that 'guix system' knows they're available. Reported by Danny Milosavljevic at . * gnu/system/linux-initrd.scm (default-initrd-modules): Add virtio modules. (base-initrd): Remove #:virtio? and 'virtio-modules'. * gnu/system/vm.scm (expression->derivation-in-linux-vm) (system-qemu-image, virtualized-operating-system): Remove uses of #:virtio?. * doc/guix.texi (Initial RAM Disk): Update 'base-initrd' doc. --- doc/guix.texi | 18 +++++++++--------- gnu/system/linux-initrd.scm | 26 ++++++++++---------------- gnu/system/vm.scm | 9 +-------- 3 files changed, 20 insertions(+), 33 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 70e53b3825..50438f7cb4 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -19893,18 +19893,18 @@ to it are lost. @deffn {Monadic Procedure} base-initrd @var{file-systems} @ [#:mapped-devices '()] [#:qemu-networking? #f] [#:volatile-root? #f]@ - [#:virtio? #t] [#:extra-modules '()] -Return a monadic derivation that builds a generic initrd. @var{file-systems} is -a list of file systems to be mounted by the initrd like for @code{raw-initrd}. -@var{mapped-devices}, @var{qemu-networking?} and @var{volatile-root?} -also behaves as in @code{raw-initrd}. + [#:linux-modules '()] +Return a monadic derivation that builds a generic initrd, with kernel +modules taken from @var{linux}. @var{file-systems} is a list of file-systems to be +mounted by the initrd, possibly in addition to the root file system specified +on the kernel command line via @code{--root}. @var{mapped-devices} is a list of device +mappings to realize before @var{file-systems} are mounted. -When @var{virtio?} is true, load additional modules so that the -initrd can be used as a QEMU guest with para-virtualized I/O drivers. +@var{qemu-networking?} and @var{volatile-root?} behaves as in @code{raw-initrd}. The initrd is automatically populated with all the kernel modules necessary -for @var{file-systems} and for the given options. However, additional kernel -modules can be listed in @var{extra-modules}. They will be added to the initrd, and +for @var{file-systems} and for the given options. Additional kernel +modules can be listed in @var{linux-modules}. They will be added to the initrd, and loaded at boot time in the order in which they appear. @end deffn diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 7a7592bf0a..e0cb59c009 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -280,6 +280,11 @@ FILE-SYSTEMS." (define* (default-initrd-modules #:optional (system (%current-system))) "Return the list of modules included in the initrd by default." + (define virtio-modules + ;; Modules for Linux para-virtualized devices, for use in QEMU guests. + '("virtio_pci" "virtio_balloon" "virtio_blk" "virtio_net" + "virtio_console")) + `("ahci" ;for SATA controllers "usb-storage" "uas" ;for the installation image etc. "usbhid" "hid-generic" "hid-apple" ;keyboards during early boot @@ -288,7 +293,9 @@ FILE-SYSTEMS." ,@(if (string-match "^(x86_64|i[3-6]86)-" system) '("pata_acpi" "pata_atiixp" ;for ATA controllers "isci") ;for SAS controllers like Intel C602 - '()))) + '()) + + ,@virtio-modules)) (define-syntax %base-initrd-modules ;; This more closely matches our naming convention. @@ -301,7 +308,6 @@ FILE-SYSTEMS." (mapped-devices '()) qemu-networking? volatile-root? - (virtio? #t) (extra-modules '()) ;deprecated (on-error 'debug)) "Return a monadic derivation that builds a generic initrd, with kernel @@ -312,25 +318,13 @@ mappings to realize before FILE-SYSTEMS are mounted. QEMU-NETWORKING? and VOLATILE-ROOT? behaves as in raw-initrd. -When VIRTIO? is true, load additional modules so the initrd can -be used as a QEMU guest with the root file system on a para-virtualized block -device. - The initrd is automatically populated with all the kernel modules necessary -for FILE-SYSTEMS and for the given options. However, additional kernel -modules can be listed in EXTRA-MODULES. They will be added to the initrd, and +for FILE-SYSTEMS and for the given options. Additional kernel +modules can be listed in LINUX-MODULES. They will be added to the initrd, and loaded at boot time in the order in which they appear." - (define virtio-modules - ;; Modules for Linux para-virtualized devices, for use in QEMU guests. - '("virtio_pci" "virtio_balloon" "virtio_blk" "virtio_net" - "virtio_console")) - (define linux-modules* ;; Modules added to the initrd and loaded from the initrd. `(,@linux-modules - ,@(if (or virtio? qemu-networking?) - virtio-modules - '()) ,@(file-system-modules file-systems) ,@(if volatile-root? '("overlay") diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index db29fd5ce9..91ff32ce9a 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -144,7 +144,6 @@ made available under the /xchg CIFS share." (base-initrd %linux-vm-file-systems #:linux linux #:linux-modules %base-initrd-modules - #:virtio? #t #:qemu-networking? #t)))) (define builder @@ -513,12 +512,7 @@ of the GNU system as described by OS." (let ((os (operating-system (inherit os) - ;; Use an initrd with the whole QEMU shebang. - (initrd (lambda (file-systems . rest) - (apply (operating-system-initrd os) - file-systems - #:virtio? #t - rest))) + ;; Assume we have an initrd with the whole QEMU shebang. ;; Force our own root file system. Refer to it by UUID so that ;; it works regardless of how the image is used ("qemu -hda", @@ -615,7 +609,6 @@ environment with the store shared with the host. MAPPINGS is a list of (apply (operating-system-initrd os) file-systems #:volatile-root? #t - #:virtio? #t rest))) ;; Disable swap. -- cgit v1.2.3 From 081d143d3b20c6d06039d31454ac16b5108ec22a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Mar 2018 10:39:17 +0100 Subject: gnu: r-performanceanalytics: Update to 1.5.2. * gnu/packages/cran.scm (r-performanceanalytics): Update to 1.5.2. [propagated-inputs]: Add r-quadprog. [native-inputs]: Remove gfortran. --- gnu/packages/cran.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7433a561ad..f8d17e1ad2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1637,21 +1637,21 @@ simplifying cross-class interoperability.") (define-public r-performanceanalytics (package (name "r-performanceanalytics") - (version "1.4.3541") + (version "1.5.2") (source (origin (method url-fetch) (uri (cran-uri "PerformanceAnalytics" version)) (sha256 (base32 - "1czchsccsbdfjw743j6rm101q2q01pggyl8zmlva213pwm86zb3v")))) + "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6")))) (properties `((upstream-name . "PerformanceAnalytics"))) (build-system r-build-system) (propagated-inputs - `(("r-xts" ,r-xts) + `(("r-quadprog" ,r-quadprog) + ("r-xts" ,r-xts) ("r-zoo" ,r-zoo))) - (native-inputs `(("gfortran" ,gfortran))) (home-page "http://r-forge.r-project.org/projects/returnanalytics/") (synopsis "Econometric tools for performance and risk analysis") (description "This is a collection of econometric functions for -- cgit v1.2.3 From fac40f38fed5e219d28a1b41135ec5961a28993f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Mar 2018 10:39:55 +0100 Subject: gnu: r-dbi: Update to 0.8. * gnu/packages/statistics.scm (r-dbi): Update to 0.8. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1c180645d4..620edfa9fb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1188,13 +1188,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5")))) + "16nf8flxr5vdz8yrpprfbzydy3ajixkp9hc8ibd9n7r9nc29waym")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") -- cgit v1.2.3 From ec8b3d48ff7f73f772e4e254c58f118935070189 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 3 Mar 2018 10:40:05 +0100 Subject: gnu: r-httpuv: Update to 1.3.6.2. * gnu/packages/web.scm (r-httpuv): Update to 1.3.6.2. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 760f4ef2ab..23bcc5fb1c 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3780,13 +3780,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.3.6.1") + (version "1.3.6.2") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "11kffpki4pgh352dlwsm4lnf1dcd5vs51cnimbshadyk3jprwxdf")))) + "0h3hkw575b211bxma23inbq1565wkhiapgasd539h219apqs534f")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/httpuv") -- cgit v1.2.3 From f4009ade25b5e7b72db10df089894928b75fde7d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 22:19:08 +0100 Subject: gnu: sdl2: Update to 2.0.8. * gnu/packages/sdl.scm (sdl2): Update to 2.0.8. --- gnu/packages/sdl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm index c56e5d94c8..222fd5b6f1 100644 --- a/gnu/packages/sdl.scm +++ b/gnu/packages/sdl.scm @@ -99,7 +99,7 @@ joystick, and graphics hardware.") (define-public sdl2 (package (inherit sdl) (name "sdl2") - (version "2.0.7") + (version "2.0.8") (source (origin (method url-fetch) (uri @@ -107,7 +107,7 @@ joystick, and graphics hardware.") version ".tar.gz")) (sha256 (base32 - "0pjdpxla5kh1w1b0shxrx97a116vyy31njxi0jhyvqhk8d6cfdgf")))) + "1v4js1gkr75hzbxzhwzzif0sf9g07234sd23x1vdaqc661bprizd")))) (arguments (substitute-keyword-arguments (package-arguments sdl) ((#:configure-flags flags) -- cgit v1.2.3 From 74a2f8ff1fc61e759afd71f2503dd9a9365c9226 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 22:36:23 +0100 Subject: gnu: hdparm: Update to 9.54. * gnu/packages/linux.scm (hdparm): Update to 9.54. --- 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 b4d81943e1..0b544dd61f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2530,14 +2530,14 @@ thanks to the use of namespaces.") (define-public hdparm (package (name "hdparm") - (version "9.53") + (version "9.54") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/" name "/" name "/" name "-" version ".tar.gz")) (sha256 (base32 - "1rb5086gp4l1h1fn2nk10ziqxjxigsd0c1zczahwc5k9vy8zawr6")))) + "0ghnhdj7wfw6acfyhdawpfa5n9kvkvzgi1fw6i7sghgbjx5nhyjd")))) (build-system gnu-build-system) (arguments `(#:make-flags (let ((out (assoc-ref %outputs "out"))) -- cgit v1.2.3 From 83a9003c5d6560d3a7873f1be43f5e2d57b2b0a1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 22:40:45 +0100 Subject: gnu: libseccomp: Update to 2.3.3. * gnu/packages/linux.scm (libseccomp): Update to 2.3.3. --- 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 0b544dd61f..1f9e084e85 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3717,7 +3717,7 @@ of flash storage.") (define-public libseccomp (package (name "libseccomp") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/seccomp/libseccomp/" @@ -3725,7 +3725,7 @@ of flash storage.") "/libseccomp-" version ".tar.gz")) (sha256 (base32 - "18dwfxzsw3agiy2dxbflrkhmjgvlji0wwkk636nabh2ng41qrp1x")))) + "0mdiyfljrkfl50q1m3ws8yfcyfjwf1zgkvcva8ffcwncji18zhkz")))) (build-system gnu-build-system) (native-inputs `(("which" ,which))) -- cgit v1.2.3 From dbefd3ff72debf27e59abaecbbf0dd94a879f829 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 9 Feb 2018 00:02:45 +0100 Subject: gnu: wv: Edit description. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Wv is still unmaintained – this just makes it more obvious. * gnu/packages/wv.scm (wv)[description]: Mention the product versions in addition to internal file format ones. Align more closely with the upstream description. --- gnu/packages/wv.scm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/wv.scm b/gnu/packages/wv.scm index 12201faa3a..866cfee222 100644 --- a/gnu/packages/wv.scm +++ b/gnu/packages/wv.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Marek Benc ;;; Copyright © 2017 Leo Famulari +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -52,11 +53,12 @@ ("pkg-config" ,pkg-config))) (synopsis "Microsoft Word conversion library and utilities") (description - "wv converts Word 2,6,7,8,9 files to HTML and LaTeX. The Word 2 -conversion is still incomplete (no formatting), but it will do a passable job -extracting the text, which is what you probably want anyway. + "wv converts files written by Word 2000, 97, 95, and 6 (known internally as +Word 9, 8, 7, and 6) to HTML or LaTeX. Word 2 documents can still be converted +to plain text but will lack formatting. -libwv can be used as a library by third party programs, AbiWord uses it as its -word importer, and KWord may use it in the future.") +Othe programs can use wv as a library to convert Word documents to other +formats. AbiWord uses it as its Word importer, and KWord uses concepts and +code from wv in theirs.") (home-page "http://wvware.sourceforge.net/") (license license:gpl2+))) -- cgit v1.2.3 From 9d13f82da88c5832444534270801da0ee813a397 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 22:39:35 +0100 Subject: gnu: sslh: Update to 1.19c. * gnu/packages/networking.scm (sslh): Update to 1.19c. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index cd3f4f124b..5816474370 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1031,7 +1031,7 @@ library remains flexible, portable, and easily embeddable.") (define-public sslh (package (name "sslh") - (version "1.19b") + (version "1.19c") (source (origin (method url-fetch) (uri (string-append "https://github.com/yrutschle/sslh/archive/v" @@ -1039,7 +1039,7 @@ library remains flexible, portable, and easily embeddable.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0p0zfy5ifzj7508zqidgkf8g43frm7l5xcs5s6v7132lypcsbd4k")))) + "0pd8hifa9h0rm7vms3k6ic1k29xigrlv2idc5wgcafmb1v1243di")))) (build-system gnu-build-system) (native-inputs `(;; Test dependencies. -- cgit v1.2.3 From e6d30cf7552502b59c2996b5b1d530c38b88c4f7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 2 Mar 2018 17:38:28 +0100 Subject: gnu: conky: Remove redundant MKDIR-P. * gnu/packages/conky.scm (conky)[arguments]: Remove redundant MKDIR-P. --- gnu/packages/conky.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/conky.scm b/gnu/packages/conky.scm index 22a0427b9a..0da9f8438b 100644 --- a/gnu/packages/conky.scm +++ b/gnu/packages/conky.scm @@ -60,8 +60,8 @@ #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) (install-file "src/conky" bin)) #t))))) (inputs -- cgit v1.2.3 From 75377c6c485f5dc93d42f59fe39eb7c12fe75da6 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 3 Mar 2018 02:50:09 +0100 Subject: gnu: quagga: Update to 1.2.4. * gnu/packages/networking.scm (quagga): Update to 1.2.4. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5816474370..d4c9d40d7a 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1403,14 +1403,14 @@ does not use SSH and requires a pre-shared symmetric key.") (define-public quagga (package (name "quagga") - (version "1.2.3") + (version "1.2.4") (source (origin (method url-fetch) (uri (string-append "mirror://savannah/quagga/quagga-" version ".tar.gz")) (sha256 (base32 - "0cddxip9gd579parx64n6d7iq937ikrb8qxgvjxjm406l43hjb7f")) + "1lsksqxij5f1llqn86pkygrf5672kvrqn1kvxghi169hqf1c0r73")) (patches (search-patches "quagga-reproducible-build.patch")))) (build-system gnu-build-system) -- cgit v1.2.3 From add928d35fb7a182662ecfdf261cc6a4c98b3c67 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 3 Mar 2018 11:56:23 +0100 Subject: gnu: ghc-refact: Fix typo in description. * gnu/packages/haskell.scm (ghc-refact)[description]: Fix typo. --- gnu/packages/haskell.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 3ff78047db..e7401e5cf4 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -1072,7 +1072,7 @@ patterns as per the HaRP extension as well as HSX-style embedded XML syntax.") (synopsis "Specify refactorings to perform with apply-refact") (description "This library provides a datatype which can be interpreted by -@code{apply-refact}. It exists as a seperate library so that applications can +@code{apply-refact}. It exists as a separate library so that applications can specify refactorings without depending on GHC.") (license license:bsd-3))) -- cgit v1.2.3 From 433dc74611b0338ae15c7a7dc344a802c5667a34 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Mon, 9 Oct 2017 06:57:26 +0100 Subject: gnu: networking: Add czmq. * gnu/packages/networking.scm (czmq): New variable. --- gnu/packages/networking.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index d4c9d40d7a..3c18620bd2 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -267,6 +267,42 @@ filtering (subscriptions), seamless access to multiple transport protocols and more.") (license license:lgpl3+))) +(define-public czmq + (package + (name "czmq") + (version "4.1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/zeromq/" name + "/releases/download/v" version + "/" name "-" version ".tar.gz")) + (sha256 + (base32 + "04gwf61rijwm6b2wblwv8gky1gdrbfmg1d19hf72kdc691ds7vrv")))) + (build-system gnu-build-system) + (arguments + '(;; TODO Tests fail for some reason: + ;; * zauth: OK + ;; * zbeacon: OK (skipping test, no UDP broadcasting) + ;; E: (czmq_selftest) 18-02-24 16:25:52 No broadcast interface found, (ZSYS_INTERFACE=lo) + ;; make[2]: *** [Makefile:2245: check-local] Segmentation fault + ;; make[2]: Leaving directory '/tmp/guix-build-czmq-4.1.0.drv-0/czmq-4.1.0' + ;; make[1]: *** [Makefile:2032: check-am] Error 2 + ;; make[1]: Leaving directory '/tmp/guix-build-czmq-4.1.0.drv-0/czmq-4.1.0' + ;; make: *** [Makefile:1588: check-recursive] Error 1 + ;; phase `check' failed after 19.4 seconds + #:tests? #f + #:configure-flags '("--enable-drafts"))) + (inputs + `(("zeromq" ,zeromq))) + (home-page "http://zeromq.org") + (synopsis "High-level C bindings for ØMQ") + (description + "czmq provides bindings for the ØMQ core API that hides the differences +between different versions of ØMQ.") + (license license:mpl2.0))) + (define-public librdkafka (package (name "librdkafka") -- cgit v1.2.3 From cf646acf96d0567bea124dc8ea2a0782ad3f4e8d Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:00:49 +0100 Subject: gnu: Add ruby-mocha-on-bacon. * gnu/packages/ruby.scm (ruby-mocha-on-bacon): New variable. --- gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index b15e1a2717..5ba140e01d 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1502,6 +1502,30 @@ allows mocking and stubbing of methods on real (non-mock) classes.") (home-page "http://gofreerange.com/mocha/docs") (license license:expat))) +(define-public ruby-mocha-on-bacon + (package + (name "ruby-mocha-on-bacon") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "mocha-on-bacon" version)) + (sha256 + (base32 + "1h49b33rq889hn8x3wp9byczl91va16jh1w4d2wyy4yj23icdrcp")))) + (build-system ruby-build-system) + (arguments + ;; rubygems.org release missing tests + '(#:tests? #f)) + (propagated-inputs `(("ruby-mocha" ,ruby-mocha))) + (synopsis "Mocha adapter for Bacon") + (description + "This package provides a Mocha adapter for Bacon, allowing you to use the +Mocha stubbing and mocking library with Bacon, a small RSpec clone.") + (home-page + "https://github.com/alloy/mocha-on-bacon") + (license license:expat))) + (define-public ruby-net-ssh (package (name "ruby-net-ssh") -- cgit v1.2.3 From a8d2bf3cab8ba5472620c1fb8d68c02836a04f1b Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:00:21 +0100 Subject: gnu: Add ruby-bacon-bits. * gnu/packages/ruby.scm (ruby-bacon-bits): New variable. --- gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 5ba140e01d..31a97f0b74 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1094,6 +1094,30 @@ features.") (home-page "https://github.com/chneukirchen/bacon") (license license:expat))) +(define-public ruby-bacon-bits + (package + (name "ruby-bacon-bits") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bacon-bits" version)) + (sha256 + (base32 + "1ghpj8ja94lhi8rgi872hqk4fd2amz2k7g9znd64z5dj7v6l0dmx")))) + (build-system ruby-build-system) + (arguments + ;; No tests + '(#:tests? #f)) + (propagated-inputs `(("ruby-bacon" ,ruby-bacon))) + (synopsis "Extensions to Bacon, for disabling tests, before and after +blocks and more") + (description + "This extends the bacon testing framework with useful extensions to +disable tests, have before and after blocks that run once and more.") + (home-page "https://github.com/cldwalker/bacon-bits") + (license license:expat))) + (define-public ruby-connection-pool (package (name "ruby-connection-pool") -- cgit v1.2.3 From afdb437c82ddc0d8c6cb64b934129bcab8169a48 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:02:19 +0100 Subject: gnu: Add ruby-bond. * gnu/packages/ruby.scm (ruby-bond): New variable. --- gnu/packages/ruby.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 31a97f0b74..456afb3f54 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1361,6 +1361,34 @@ as a base class when writing classes that depend upon (home-page "https://github.com/masover/blankslate") (license license:expat))) +(define-public ruby-bond + (package + (name "ruby-bond") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bond" version)) + (sha256 + (base32 + "1r19ifc4skyl2gxnifrxa5jvbbay9fb2in79ppgv02b6n4bhsw90")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-bacon" ,ruby-bacon) + ("ruby-bacon-bits" ,ruby-bacon-bits) + ("ruby-mocha-on-bacon" ,ruby-mocha-on-bacon))) + (synopsis "Bond can provide custom autocompletion for arguments, methods +and more") + (description + "Bond can autocomplete argument(s) to methods, uniquely completing per +module, per method and per argument. Bond provides a configuration system and +a DSL for creating custom completions and completion rules. Bond can also +load completions that ship with gems. Bond is able to offer more than irb's +completion since it uses the full line of input when completing as opposed to +irb's last-word approach.") + (home-page "http://tagaholic.me/bond/") + (license license:expat))) + (define-public ruby-instantiator (package (name "ruby-instantiator") -- cgit v1.2.3 From fe5dd5f44659139b7327a3cf887dbb03741e4e42 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:07:45 +0100 Subject: gnu: Add ruby-czmq-ffi-gen. * gnu/packages/ruby.scm (ruby-czmq-ffi-gen): New variable. --- gnu/packages/ruby.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 456afb3f54..a9725af81e 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -36,6 +36,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages java) #:use-module (gnu packages libffi) + #:use-module (gnu packages networking) #:use-module (gnu packages python) #:use-module (gnu packages ragel) #:use-module (gnu packages tls) @@ -635,6 +636,46 @@ format.") (home-page "https://github.com/nicksieger/ci_reporter") (license license:expat))) +(define-public ruby-czmq-ffi-gen + (package + (name "ruby-czmq-ffi-gen") + (version "0.13.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "czmq-ffi-gen" version)) + (sha256 + (base32 + "1yf719dmf4mwks1hqdsy6i5kzfvlsha69sfnhb2fr2cgk2snbys3")))) + (build-system ruby-build-system) + (arguments + '(#:tests? #f ;; Tests are not included in the release on rubygems.org + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-lib_dirs + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/czmq-ffi-gen/czmq/ffi.rb" + (("lib\\_dirs = \\[.*\\]") + (string-append "lib_dirs = ['" + (assoc-ref inputs "czmq") "/lib" + "']"))) + (substitute* "lib/czmq-ffi-gen/libzmq.rb" + (("lib\\_dirs = \\[.*\\]") + (string-append "lib_dirs = ['" + (assoc-ref inputs "zeromq") "/lib" + "']")))))))) + (inputs + `(("zeromq" ,zeromq) + ("czmq" ,czmq))) + (propagated-inputs `(("ruby-ffi" ,ruby-ffi))) + (synopsis "Low-level Ruby bindings for CZMQ (generated using zproject)") + (description + "These Ruby bindings are not intended to be directly used, but rather +used by higher level bindings like those provided by CZTop.") + (home-page + "https://github.com/paddor/czmq-ffi-gen") + (license license:isc))) + (define-public ruby-saikuro-treemap (package (name "ruby-saikuro-treemap") -- cgit v1.2.3 From d0afff263c546fa7ef132b09ef04af7d178cd2ae Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:08:09 +0100 Subject: gnu: Add ruby-cztop. * gnu/packages/ruby.scm (ruby-cztop): New variable. --- gnu/packages/ruby.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index a9725af81e..f94ac54001 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -676,6 +676,44 @@ used by higher level bindings like those provided by CZTop.") "https://github.com/paddor/czmq-ffi-gen") (license license:isc))) +(define-public ruby-cztop + (package + (name "ruby-cztop") + (version "0.12.2") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "cztop" version)) + (sha256 + (base32 + "0yqbpaiw5d7f271d73lyrsh8xpx6n4zi6xqwfgi00dacxrq3s3fa")))) + (build-system ruby-build-system) + (arguments + '(#:test-target "spec" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-lib_paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/cztop/poller/zmq.rb" + (("lib\\_paths = \\[.*\\]") + (string-append "lib_paths = ['" + (assoc-ref inputs "zeromq") "/lib" + "']")))))))) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rspec" ,ruby-rspec))) + (inputs + `(("zeromq" ,zeromq))) + (propagated-inputs + `(("ruby-czmq-ffi-gen" ,ruby-czmq-ffi-gen))) + (synopsis "CZMQ Ruby bindings") + (description + "CZMQ Ruby bindings, based on the generated low-level FFI bindings of +CZMQ. The focus of of CZTop is on being easy to use and providing first class +support for security mechanisms.") + (home-page "https://github.com/paddor/cztop") + (license license:isc))) + (define-public ruby-saikuro-treemap (package (name "ruby-saikuro-treemap") -- cgit v1.2.3 From b03eb6acb45cf6c0672e309204f5a92ce5fd88ce Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:09:18 +0100 Subject: gnu: Add ruby-data_uri. * gnu/packages/ruby.scm (ruby-data_uri): New variable. --- gnu/packages/ruby.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index f94ac54001..47cb8eea8c 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1965,6 +1965,26 @@ run as a daemon and to be controlled by simple start/stop/restart commands.") (home-page "https://github.com/thuehlinger/daemons") (license license:expat))) +(define-public ruby-data_uri + (package + (name "ruby-data_uri") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "data_uri" version)) + (sha256 + (base32 + "0fzkxgdxrlbfl4537y3n9mjxbm28kir639gcw3x47ffchwsgdcky")))) + (build-system ruby-build-system) + (synopsis "URI class for parsing data URIs") + (description + "Data @acronym{URI, universal resource idenfitier}s allow resources to be +embedded inside a URI. The URI::Data class provides support for parsing these +URIs using the normal URI.parse method.") + (home-page "https://github.com/dball/data_uri") + (license license:expat))) + (define-public ruby-git (package (name "ruby-git") -- cgit v1.2.3 From 8279b1d3b11ac3e0ad3d94b515695e6d7f2c3511 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:09:45 +0100 Subject: gnu: Add ruby-mimemagic. * gnu/packages/ruby.scm (ruby-mimemagic): New variable. --- gnu/packages/ruby.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 47cb8eea8c..3d914d1c46 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3503,6 +3503,33 @@ that TURN is no longer being maintained.") (home-page "http://rubygems.org/gems/turn") (license license:expat))) +(define-public ruby-mimemagic + (package + (name "ruby-mimemagic") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "mimemagic" version)) + (sha256 + (base32 + "00ibc1mhvdfyfyl103xwb45621nwyqxf124cni5hyfhag0fn1c3q")))) + (build-system ruby-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This phase breaks the tests, as it patches some of the test data. + (delete 'patch-source-shebangs)))) + (native-inputs + `(("ruby-bacon" ,ruby-bacon))) + (synopsis "Ruby library for MIME detection by extension or content") + (description + "@acronym{MIME, Multipurpose Internet Mail Extensions} detection by +extension or content, using the freedesktop.org.xml shared-mime-info +database.") + (home-page "https://github.com/minad/mimemagic") + (license license:expat))) + (define-public ruby-mime-types-data (package (name "ruby-mime-types-data") -- cgit v1.2.3 From 62b138caf55f8090e0ad8e04296dc0f98a4fd212 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Tue, 10 Oct 2017 20:07:20 +0100 Subject: gnu: Add ruby-iruby. * gnu/packages/ruby.scm (ruby-iruby): New variable. --- gnu/packages/ruby.scm | 56 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 3d914d1c46..ee5d20955c 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -281,6 +281,62 @@ an extensible architecture with a swappable backend.") (home-page "https://github.com/svenfuchs/i18n") (license license:expat))) +(define-public ruby-iruby + (package + (name "ruby-iruby") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "iruby" version)) + (sha256 + (base32 + "1wdf2c0x8y6cya0n3y0p3p7b1sxkb2fdavdn2k58rf4rs37s7rzn")))) + (build-system ruby-build-system) + (arguments + ;; TODO: Tests currently fail. + ;; + ;; Finished in 1.764405s, 1.1335 runs/s, 5.1009 assertions/s. + ;; + ;; 1) Failure: + ;; IntegrationTest#test_interaction [/tmp/guix-build-ruby-iruby-0.3.drv-0/gem/test/integration_test.rb:25]: + ;; In [ expected + ;; + ;; 2 runs, 9 assertions, 1 failures, 0 errors, 0 skips + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-ipython + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/iruby/command.rb" + (("version = `") + (string-append + "version = `" + (assoc-ref inputs "python-ipython") + "/bin/")) + (("Kernel\\.exec\\('") + (string-append + "Kernel.exec('" + (assoc-ref inputs "python-ipython") + "/bin/"))) + #t))))) + (inputs + `(("python-ipython" ,python-ipython))) + (propagated-inputs + `(("ruby-bond" ,ruby-bond) + ("ruby-data_uri" ,ruby-data_uri) + ("ruby-mimemagic" ,ruby-mimemagic) + ("ruby-multi-json" ,ruby-multi-json) + ("ruby-cztop" ,ruby-cztop) + ;; Optional inputs + ("ruby-pry" ,ruby-pry))) + (synopsis "Ruby kernel for Jupyter/IPython") + (description + "This package provides a Ruby kernel for Jupyter/IPython frontends (e.g. +notebook).") + (home-page "https://github.com/SciRuby/iruby") + (license license:expat))) + ;; RSpec is the dominant testing library for Ruby projects. Even RSpec's ;; dependencies use RSpec for their test suites! To avoid these circular ;; dependencies, we disable tests for all of the RSpec-related packages. -- cgit v1.2.3 From 0645da3fe3112a3568e646babf524bd9439ffb8e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 3 Mar 2018 14:06:43 +0100 Subject: gnu: grammalecte: Update to 0.6.2. * gnu/packages/dictionaries.scm (grammalecte): Update to 0.6.2. [arguments]: Remove. --- gnu/packages/dictionaries.scm | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm index 25e4613170..1c1d6247a7 100644 --- a/gnu/packages/dictionaries.scm +++ b/gnu/packages/dictionaries.scm @@ -211,7 +211,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.") (define-public grammalecte (package (name "grammalecte") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch/zipbomb) @@ -219,20 +219,8 @@ It comes with a German-English dictionary with approximately 270,000 entries.") "Grammalecte-fr-v" version ".zip")) (sha256 (base32 - "0bl342i7nqbg8swk3fxashg9liyp3jdnix59pndhy41cpm1xln4i")))) + "0pvblclvbxbfgmq0cvmpmzpf6bi6r41arndwprl7ab9kci9hi8j2")))) (build-system python-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-setup.py - ;; FIXME: "setup.py" contains a typo in 0.6.1 release. The - ;; issue was reported and fixed upstream - ;; (https://dicollecte.org/thread.php?prj=fr&t=674). This - ;; phase can be removed in next release. - (lambda _ - (substitute* "setup.py" - (("server_options\\.") "grammalecte-server-options.")) - #t))))) (home-page "https://www.dicollecte.org") (synopsis "French spelling and grammar checker") (description "Grammalecte is a grammar checker dedicated to the French -- cgit v1.2.3 From 5e332c57d1dd7f0326a25763634d90b272b8d821 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 3 Mar 2018 14:21:20 +0100 Subject: gnu: wireshark: Update to 2.4.5. * gnu/packages/networking.scm (wireshark): Update to 2.4.5. --- gnu/packages/networking.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 3c18620bd2..bf4bee2f87 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Raimon Grau ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2016 John Darrington -;;; Copyright © 2016, 2017 Nicolas Goaziou +;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2016, 2017 ng0 ;;; Copyright © 2016, 2017 Arun Isaac @@ -534,7 +534,7 @@ of the same name.") (define-public wireshark (package (name "wireshark") - (version "2.4.4") + (version "2.4.5") (source (origin (method url-fetch) @@ -542,7 +542,7 @@ of the same name.") version ".tar.xz")) (sha256 (base32 - "0n3g28hrhifnchlz4av0blq4ykm4zaxwwxbzdm9wsba27677b6h4")))) + "1mvgy67rvnwj2kbc43s4il81jvz5ai0bx2j3j2js7x50zclyrcmk")))) (build-system gnu-build-system) (inputs `(("c-ares" ,c-ares) ("glib" ,glib) -- cgit v1.2.3 From fb547c3429c32081d68f6f78d7fdfc95a4851348 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 3 Mar 2018 14:23:17 +0100 Subject: gnu: dictionaries: Add copyright line. * gnu/packages/dictionaries.scm: Add copyright line. --- gnu/packages/dictionaries.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm index 1c1d6247a7..3f50070ef7 100644 --- a/gnu/packages/dictionaries.scm +++ b/gnu/packages/dictionaries.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014, 2015, 2016 Ludovic Courtès ;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 Sou Bunnbu +;;; Copyright © 2017, 2018 Nicolas Goaziou ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. -- cgit v1.2.3 From bdcf0e6fd484a54240a98ddf8b6fa433c1b9bd6c Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Mon, 26 Feb 2018 01:12:24 +0100 Subject: services: messaging: Prosody config supports file-like objects. * doc/guix.texi (Messaging Services): Update accordingly. * gnu/services/configuration.scm (serialize-configuration, serialize-maybe-stem, serialize-package): Return strings or string-valued gexps (these procedures were only used for their side-effects). * gnu/services/messaging.scm (serialize-field, serialize-field-list, enclose-quotes, serialize-raw-content, serialize-ssl-configuration, serialize-virtualhost-configuration-list, serialize-int-component-configuration-list, serialize-ext-component-configuration-list, serialize-virtualhost-configuration, serialize-int-component-configuration, serialize-ext-component-configuration, serialize-prosody-configuration): Return strings or string-valued gexps and stop printing. (prosody-activation): Use SERIALIZE-PROSODY-CONFIGURATION's return value with MIXED-TEXT-FILE instead of using its output with PLAIN-FILE. (serialize-non-negative-integer, serialize-non-negative-integer-list): Convert numbers to strings. (file-object?, serialize-file-object, file-object-list?, serialize-file-object-list): New procedures. (ssl-configuration)[capath, cafile], (prosody-configuration)[plugin-paths, groups-file]: Replace FILE-NAME with FILE-OBJECT. * guix/gexp.scm (file-like?): New exported procedure. --- doc/guix.texi | 13 +++-- gnu/services/configuration.scm | 17 +++---- gnu/services/messaging.scm | 106 ++++++++++++++++++++++------------------- guix/gexp.scm | 7 +++ 4 files changed, 83 insertions(+), 60 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 50438f7cb4..057272df46 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -14258,6 +14258,9 @@ There is also a way to specify the configuration as a string, if you have an old @code{prosody.cfg.lua} file that you want to port over from some other system; see the end for more details. +The @code{file-object} type designates either a file-like object +(@pxref{G-Expressions, file-like objects}) or a file name. + @c The following documentation was initially generated by @c (generate-documentation) in (gnu services messaging). Manually maintained @c documentation is better, so we shouldn't hesitate to edit below as @@ -14278,7 +14281,7 @@ Location of the Prosody data storage directory. See Defaults to @samp{"/var/lib/prosody"}. @end deftypevr -@deftypevr {@code{prosody-configuration} parameter} file-name-list plugin-paths +@deftypevr {@code{prosody-configuration} parameter} file-object-list plugin-paths Additional plugin directories. They are searched in all the specified paths in order. See @url{https://prosody.im/doc/plugins_directory}. Defaults to @samp{()}. @@ -14319,7 +14322,7 @@ should you want to disable them then add them to this list. Defaults to @samp{()}. @end deftypevr -@deftypevr {@code{prosody-configuration} parameter} file-name groups-file +@deftypevr {@code{prosody-configuration} parameter} file-object groups-file Path to a text file where the shared groups are defined. If this path is empty then @samp{mod_groups} does nothing. See @url{https://prosody.im/doc/modules/mod_groups}. @@ -14352,13 +14355,13 @@ Path to your private key file. Path to your certificate file. @end deftypevr -@deftypevr {@code{ssl-configuration} parameter} file-name capath +@deftypevr {@code{ssl-configuration} parameter} file-object capath Path to directory containing root certificates that you wish Prosody to trust when verifying the certificates of remote servers. Defaults to @samp{"/etc/ssl/certs"}. @end deftypevr -@deftypevr {@code{ssl-configuration} parameter} maybe-file-name cafile +@deftypevr {@code{ssl-configuration} parameter} maybe-file-object cafile Path to a file containing root certificates that you wish Prosody to trust. Similar to @code{capath} but with all certificates concatenated together. @end deftypevr @@ -14618,6 +14621,8 @@ string, you could instantiate a prosody service like this: (prosody.cfg.lua ""))) @end example +@c end of Prosody auto-generated documentation + @subsubheading BitlBee Service @cindex IRC (Internet Relay Chat) diff --git a/gnu/services/configuration.scm b/gnu/services/configuration.scm index c45340f02f..707944cbe0 100644 --- a/gnu/services/configuration.scm +++ b/gnu/services/configuration.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Andy Wingo ;;; Copyright © 2017 Mathieu Othacehe -;;; Copyright © 2017 Clément Lassieur +;;; Copyright © 2017, 2018 Clément Lassieur ;;; ;;; This file is part of GNU Guix. ;;; @@ -74,11 +74,12 @@ (documentation configuration-field-documentation)) (define (serialize-configuration config fields) - (for-each (lambda (field) - ((configuration-field-serializer field) - (configuration-field-name field) - ((configuration-field-getter field) config))) - fields)) + #~(string-append + #$@(map (lambda (field) + ((configuration-field-serializer field) + (configuration-field-name field) + ((configuration-field-getter field) config))) + fields))) (define (validate-configuration config fields) (for-each (lambda (field) @@ -105,7 +106,7 @@ (define (maybe-stem? val) (or (eq? val 'disabled) (stem? val))) (define (serialize-maybe-stem field-name val) - (when (stem? val) (serialize-stem field-name val))))))))) + (if (stem? val) (serialize-stem field-name val) "")))))))) (define-syntax define-configuration (lambda (stx) @@ -147,7 +148,7 @@ conf)))))))) (define (serialize-package field-name val) - #f) + "") ;; A little helper to make it easier to document all those fields. (define (generate-documentation documentation documentation-name) diff --git a/gnu/services/messaging.scm b/gnu/services/messaging.scm index 427e2121f6..80ffed0f2f 100644 --- a/gnu/services/messaging.scm +++ b/gnu/services/messaging.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Clément Lassieur +;;; Copyright © 2017, 2018 Clément Lassieur ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2015, 2017, 2018 Ludovic Courtès ;;; @@ -115,16 +115,9 @@ "_"))) (define (serialize-field field-name val) - (format #t "~a = ~a;\n" (uglify-field-name field-name) val)) + #~(format #f "~a = ~a;\n" #$(uglify-field-name field-name) #$val)) (define (serialize-field-list field-name val) - (serialize-field field-name - (with-output-to-string - (lambda () - (format #t "{\n") - (for-each (lambda (x) - (format #t "~a;\n" x)) - val) - (format #t "}"))))) + (serialize-field field-name #~(format #f "{\n~@{~a;\n~}}" #$@val))) (define (serialize-boolean field-name val) (serialize-field field-name (if val "true" "false"))) @@ -140,17 +133,17 @@ (define (non-negative-integer? val) (and (exact-integer? val) (not (negative? val)))) (define (serialize-non-negative-integer field-name val) - (serialize-field field-name val)) + (serialize-field field-name (number->string val))) (define-maybe non-negative-integer) (define (non-negative-integer-list? val) (and (list? val) (and-map non-negative-integer? val))) (define (serialize-non-negative-integer-list field-name val) - (serialize-field-list field-name val)) + (serialize-field-list field-name (map number->string val))) (define-maybe non-negative-integer-list) (define (enclose-quotes s) - (format #f "\"~a\"" s)) + #~(string-append "\"" #$s "\"")) (define (serialize-string field-name val) (serialize-field field-name (enclose-quotes val))) (define-maybe string) @@ -183,10 +176,22 @@ (serialize-string-list field-name val)) (define-maybe file-name) +(define (file-object? val) + (or (file-like? val) (file-name? val))) +(define (serialize-file-object field-name val) + (serialize-string field-name val)) +(define-maybe file-object) + +(define (file-object-list? val) + (and (list? val) (and-map file-object? val))) +(define (serialize-file-object-list field-name val) + (serialize-string-list field-name val)) +(define-maybe file-object) + (define (raw-content? val) (not (eq? val 'disabled))) (define (serialize-raw-content field-name val) - (format #t "~a" val)) + val) (define-maybe raw-content) (define-configuration mod-muc-configuration @@ -224,12 +229,12 @@ just joined the room.")) "Path to your certificate file.") (capath - (file-name "/etc/ssl/certs") + (file-object "/etc/ssl/certs") "Path to directory containing root certificates that you wish Prosody to trust when verifying the certificates of remote servers.") (cafile - (maybe-file-name 'disabled) + (maybe-file-object 'disabled) "Path to a file containing root certificates that you wish Prosody to trust. Similar to @code{capath} but with all certificates concatenated together.") @@ -273,9 +278,8 @@ can create such a file with: (maybe-string 'disabled) "Password for encrypted private keys.")) (define (serialize-ssl-configuration field-name val) - (format #t "ssl = {\n") - (serialize-configuration val ssl-configuration-fields) - (format #t "};\n")) + #~(format #f "ssl = {\n~a};\n" + #$(serialize-configuration val ssl-configuration-fields))) (define-maybe ssl-configuration) (define %default-modules-enabled @@ -303,20 +307,23 @@ can create such a file with: (define (virtualhost-configuration-list? val) (and (list? val) (and-map virtualhost-configuration? val))) (define (serialize-virtualhost-configuration-list l) - (for-each - (lambda (val) (serialize-virtualhost-configuration val)) l)) + #~(string-append + #$@(map (lambda (val) + (serialize-virtualhost-configuration val)) l))) (define (int-component-configuration-list? val) (and (list? val) (and-map int-component-configuration? val))) (define (serialize-int-component-configuration-list l) - (for-each - (lambda (val) (serialize-int-component-configuration val)) l)) + #~(string-append + #$@(map (lambda (val) + (serialize-int-component-configuration val)) l))) (define (ext-component-configuration-list? val) (and (list? val) (and-map ext-component-configuration? val))) (define (serialize-ext-component-configuration-list l) - (for-each - (lambda (val) (serialize-ext-component-configuration val)) l)) + #~(string-append + #$@(map (lambda (val) + (serialize-ext-component-configuration val)) l))) (define-all-configurations prosody-configuration (prosody @@ -331,7 +338,7 @@ can create such a file with: global) (plugin-paths - (file-name-list '()) + (file-object-list '()) "Additional plugin directories. They are searched in all the specified paths in order. See @url{https://prosody.im/doc/plugins_directory}." global) @@ -372,7 +379,7 @@ should you want to disable them then add them to this list." common) (groups-file - (file-name "/var/lib/prosody/sharedgroups.txt") + (file-object "/var/lib/prosody/sharedgroups.txt") "Path to a text file where the shared groups are defined. If this path is empty then @samp{mod_groups} does nothing. See @url{https://prosody.im/doc/modules/mod_groups}." @@ -566,8 +573,9 @@ See also @url{https://prosody.im/doc/modules/mod_muc}." '(domain)))) (let ((domain (virtualhost-configuration-domain config)) (rest (filter rest? virtualhost-configuration-fields))) - (format #t "VirtualHost \"~a\"\n" domain) - (serialize-configuration config rest))) + #~(string-append + #$(format #f "VirtualHost \"~a\"\n" domain) + #$(serialize-configuration config rest)))) ;; Serialize Component line first. (define (serialize-int-component-configuration config) @@ -577,8 +585,9 @@ See also @url{https://prosody.im/doc/modules/mod_muc}." (let ((hostname (int-component-configuration-hostname config)) (plugin (int-component-configuration-plugin config)) (rest (filter rest? int-component-configuration-fields))) - (format #t "Component \"~a\" \"~a\"\n" hostname plugin) - (serialize-configuration config rest))) + #~(string-append + #$(format #f "Component \"~a\" \"~a\"\n" hostname plugin) + #$(serialize-configuration config rest)))) ;; Serialize Component line first. (define (serialize-ext-component-configuration config) @@ -587,22 +596,24 @@ See also @url{https://prosody.im/doc/modules/mod_muc}." '(hostname)))) (let ((hostname (ext-component-configuration-hostname config)) (rest (filter rest? ext-component-configuration-fields))) - (format #t "Component \"~a\"\n" hostname) - (serialize-configuration config rest))) + #~(string-append + #$(format #f "Component \"~a\"\n" hostname) + #$(serialize-configuration config rest)))) ;; Serialize virtualhosts and components last. (define (serialize-prosody-configuration config) (define (rest? field) (not (memq (configuration-field-name field) '(virtualhosts int-components ext-components)))) - (let ((rest (filter rest? prosody-configuration-fields))) - (serialize-configuration config rest)) - (serialize-virtualhost-configuration-list - (prosody-configuration-virtualhosts config)) - (serialize-int-component-configuration-list - (prosody-configuration-int-components config)) - (serialize-ext-component-configuration-list - (prosody-configuration-ext-components config))) + #~(string-append + #$(let ((rest (filter rest? prosody-configuration-fields))) + (serialize-configuration config rest)) + #$(serialize-virtualhost-configuration-list + (prosody-configuration-virtualhosts config)) + #$(serialize-int-component-configuration-list + (prosody-configuration-int-components config)) + #$(serialize-ext-component-configuration-list + (prosody-configuration-ext-components config)))) (define-configuration opaque-prosody-configuration (prosody @@ -646,13 +657,12 @@ See also @url{https://prosody.im/doc/modules/mod_muc}." (default-certs-dir "/etc/prosody/certs") (data-path (prosody-configuration-data-path config)) (pidfile-dir (dirname (prosody-configuration-pidfile config))) - (config-str - (if (opaque-prosody-configuration? config) - (opaque-prosody-configuration-prosody.cfg.lua config) - (with-output-to-string - (lambda () - (serialize-prosody-configuration config))))) - (config-file (plain-file "prosody.cfg.lua" config-str))) + (config-str (if (opaque-prosody-configuration? config) + (opaque-prosody-configuration-prosody.cfg.lua config) + #~(begin + (use-modules (ice-9 format)) + #$(serialize-prosody-configuration config)))) + (config-file (mixed-text-file "prosody.cfg.lua" config-str))) #~(begin (use-modules (guix build utils)) (define %user (getpw "prosody")) diff --git a/guix/gexp.scm b/guix/gexp.scm index f005c4d296..8dea022e04 100644 --- a/guix/gexp.scm +++ b/guix/gexp.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès +;;; Copyright © 2018 Clément Lassieur ;;; ;;; This file is part of GNU Guix. ;;; @@ -86,6 +87,7 @@ define-gexp-compiler gexp-compiler? + file-like? lower-object lower-inputs @@ -182,6 +184,11 @@ procedure to lower it; otherwise return #f." (and=> (hashq-ref %gexp-compilers (struct-vtable object)) gexp-compiler-lower)) +(define (file-like? object) + "Return #t if OBJECT leads to a file in the store once unquoted in a +G-expression; otherwise return #f." + (and (struct? object) (->bool (lookup-compiler object)))) + (define (lookup-expander object) "Search for an expander for OBJECT. Upon success, return the three argument procedure to expand it; otherwise return #f." -- cgit v1.2.3 From f9e0fcb28f90a95048cad989ab405222c7eb4904 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 10 Dec 2017 22:26:47 +0100 Subject: gnu: Add texlive-fonts-iwona. * gnu/packages/tex.scm (texlive-fonts-iwona): New variable. --- gnu/packages/tex.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 4e8efc8faf..764f4fff15 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -3424,6 +3424,47 @@ TeX metrics (VF and TFM files) and macros for use with LaTeX.") ;; Any version of the GPL with font exception. (license license:gpl3+))) +(define-public texlive-fonts-iwona + (package + (name "texlive-fonts-iwona") + (version "0.995b") + (source (origin + (method url-fetch) + (uri (string-append "http://jmn.pl/pliki/Iwona-tex-" + (string-map (lambda (c) + (if (char=? c #\.) + #\_ c)) + version) + ".zip")) + (sha256 + (base32 + "13684iqx5granpc5rfvqnmyvdpgpbr1x9y7i7y7bcaq0qxv7ph1x")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip"))) + (system* unzip (assoc-ref %build-inputs "source")) + (mkdir-p target) + (copy-recursively "iwona" target))))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://jmn.pl/en/kurier-i-iwona/") + (synopsis "Sans-serif typeface for TeX") + (description "Iwona is a two-element sans-serif typeface. It was created +as an alternative version of the Kurier typeface, which was designed in 1975 +for a diploma in typeface design at the Warsaw Academy of Fine Arts under the +supervision of Roman Tomaszewski. Kurier was designed for linotype +typesetting of newspapers and similar periodicals. The Iwona fonts are an +alternative version of the Kurier fonts. The difference lies in the absence +of ink traps which typify the Kurier font.") + (license license:gfl1.0))) + (define-public texlive-latex-titlesec (package (name "texlive-latex-titlesec") -- cgit v1.2.3 From 30d554732a449c9d5dea630a07f687f1c9328393 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 22 Nov 2017 19:25:34 +0100 Subject: gnu: Add java-cisd-base. * gnu/packages/java.scm (java-cisd-base): New variable. --- gnu/packages/java.scm | 149 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 149 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 0f8c04e8ba..1e2b30d8d9 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2084,6 +2084,155 @@ Main-Class: org.eclipse.jdt.internal.compiler.batch.Main\n" (native-inputs `(("unzip" ,unzip))))) +(define-public java-cisd-base + (let ((revision 38938) + (base-version "14.12.0")) + (package + (name "java-cisd-base") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "base/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/base/")) + (revision revision))) + (file-name (string-append "java-cisd-base-" version "-checkout")) + (sha256 + (base32 + "1i5adyf7nzclb0wydgwa1az04qliid8035vpahaandmkmigbnxiy")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete included gradle jar + (delete-file-recursively "gradle/wrapper") + ;; Delete pre-built native libraries + (delete-file-recursively "libs") + #t)))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:test-target "jar-test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "build-resources") + "../build_resources") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar")) + (("\\$\\{lib\\}/commons-lang/commons-lang.jar") + (string-append (assoc-ref inputs "java-commons-lang") + "/share/java/commons-lang-" + ,(package-version java-commons-lang) ".jar")) + (("\\$\\{lib\\}/commons-io/commons-io.jar") + (string-append (assoc-ref inputs "java-commons-io") + "/share/java/commons-io-" + ,(package-version java-commons-io) + "-SNAPSHOT.jar")) + ;; Remove dependency on svn + (("string revision)) + (("\\$\\{version.number\\}") ,base-version)) + ;; Remove dependency on classycle + (substitute* "../build_resources/ant/build-common.xml" + ((" Date: Fri, 23 Feb 2018 10:09:50 +0100 Subject: gnu: Add java-cisd-args4j. * gnu/packages/java.scm (java-cisd-args4j): New variable. --- gnu/packages/java.scm | 114 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 114 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 1e2b30d8d9..7ad0c41268 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -2233,6 +2233,120 @@ libraries from the SIS division at ETH Zurich like jHDF5.") (license (list license:asl2.0 (license:non-copyleft "file://source/c/COPYING")))))) +(define-public java-cisd-args4j + (let ((revision 39162) + (base-version "9.11.2")) + (package + (name "java-cisd-args4j") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "args4j/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/args4j/")) + (revision revision))) + (file-name (string-append "java-cisd-args4j-" version "-checkout")) + (sha256 + (base32 + "0hhqznjaivq7ips7mkwas78z42s6djsm20rrs7g1zd59rcsakxn2")))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:tests? #f ; there are no tests + ;; There are weird build failures with JDK8, such as: "The type + ;; java.io.ObjectInputStream cannot be resolved. It is indirectly + ;; referenced from required .class files" + #:jdk ,icedtea-7 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "../build_resources") + (invoke "tar" "xf" (assoc-ref inputs "build-resources") + "-C" "../build_resources" + "--strip-components=1") + (mkdir-p "../build_resources/lib") + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + ;; FIXME: There should be a more convenient abstraction for + ;; editing XML files. + (with-directory-excursion "../build_resources/ant/" + (chmod "build-common.xml" #o664) + (call-with-output-file "build-common.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build-common.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove dependency on classycle and custom ant tasks + (taskdef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (or (member "build-info" name) + (member "dependency-checker" name) + (member "build-java-subprojects" name) + (member "project-classpath" name)) + '() ; skip + `(,tag ,@kids))))) + (typedef . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) kids))) + (if (member "recursive-jar" name) + '() ; skip + `(,tag ,@kids))))) + (build-java-subprojects . ,(lambda _ '())) + ;; Ignore everything else + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build-common.xml.new" "build-common.xml")) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/cisd-base/cisd-base.jar") + (string-append (assoc-ref inputs "java-cisd-base") + "/share/java/sis-base.jar")) + ;; Remove dependency on svn + (("string revision)) + (("\\$\\{version.number\\}") ,base-version) + ;; Don't use custom ant tasks. + (("recursive-jar") "jar") + ((" Date: Fri, 23 Feb 2018 10:10:12 +0100 Subject: gnu: Add java-cisd-jhdf5. * gnu/packages/java.scm (java-cisd-jhdf5): New variable. --- gnu/packages/java.scm | 176 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 176 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 7ad0c41268..298874f757 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -59,6 +59,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) ;alsa + #:use-module (gnu packages maths) #:use-module (gnu packages web) #:use-module (gnu packages wget) #:use-module (gnu packages pkg-config) @@ -2347,6 +2348,181 @@ libraries from the SIS division at ETH Zurich like jHDF5.") (description "This package provides a parser for command line arguments.") (license license:asl2.0)))) +(define-public java-cisd-jhdf5 + (let ((revision 39162) + (base-version "14.12.6")) + (package + (name "java-cisd-jhdf5") + (version (string-append base-version "-" (number->string revision))) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "jhdf5/tags/release/" + (version-major+minor base-version) + ".x/" base-version "/jhdf5/")) + (revision revision))) + (file-name (string-append "java-cisd-jhdf5-" version "-checkout")) + (sha256 + (base32 + "13i17s2hn0q9drdqvp8csy7770p3hdbh9rp30ihln2ldkfawdmz0")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete included gradle jar + (delete-file-recursively "gradle/wrapper") + ;; Delete pre-built native libraries + (delete-file-recursively "libs") + #t)))) + (build-system ant-build-system) + (arguments + `(#:make-flags '("-file" "build/build.xml") + #:build-target "jar-all" + #:test-target "jar-test" + #:jdk ,icedtea-8 + #:phases + (modify-phases %standard-phases + ;; Don't erase results from the build phase when building tests. + (add-after 'unpack 'separate-test-target-from-clean + (lambda _ + (substitute* "build/build.xml" + (("\"jar-test\" depends=\"clean, ") + "\"jar-test\" depends=\"")) + #t)) + (add-after 'unpack 'unpack-build-resources + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "build-resources") + "../build_resources") + (delete-file-recursively "../build_resources/lib/") + (mkdir-p "../build_resources/lib") + ;; Remove dependency on classycle + (substitute* "../build_resources/ant/build-common.xml" + (("string revision)) + (("\\$\\{version.number\\}") ,base-version)) + #t)) + (add-after 'unpack-build-resources 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "../build_resources/ant/build-common.xml" + (("../libraries/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar"))) + (substitute* "build/build.xml" + (("\\$\\{lib\\}/sis-base/sis-base.jar") + (string-append (assoc-ref inputs "java-cisd-base") + "/share/java/sis-base.jar")) + (("\\$\\{lib\\}/cisd-args4j/cisd-args4j.jar") + (string-append (assoc-ref inputs "java-cisd-args4j") + "/share/java/cisd-args4j.jar")) + (("\\$\\{lib\\}/commons-lang/commons-lang.jar") + (string-append (assoc-ref inputs "java-commons-lang") + "/share/java/commons-lang-" + ,(package-version java-commons-lang) ".jar")) + (("\\$\\{lib\\}/commons-io/commons-io.jar") + (string-append (assoc-ref inputs "java-commons-io") + "/share/java/commons-io-" + ,(package-version java-commons-io) + "-SNAPSHOT.jar")) + (("\\$\\{lib\\}/testng/testng-jdk15.jar") + (string-append (assoc-ref inputs "java-testng") + "/share/java/java-testng.jar")) + (("\\$\\{lib\\}/junit4/junit.jar") + (string-append (assoc-ref inputs "java-junit") + "/share/java/junit.jar")) + (("\\$\\{lib\\}/jmock/hamcrest/hamcrest-core.jar") + (string-append (assoc-ref inputs "java-hamcrest-core") + "/share/java/hamcrest-core.jar"))) + ;; Remove dependency on ch.rinn.restrictions + (with-directory-excursion "source/java/ch/systemsx/cisd/hdf5/" + (substitute* '("BitSetConversionUtils.java" + "HDF5Utils.java") + (("import ch.rinn.restrictions.Private;") "") + (("@Private") ""))) + (with-directory-excursion "sourceTest/java/ch/systemsx/cisd/hdf5/" + (substitute* '("BitSetConversionTest.java" + "h5ar/HDF5ArchiverTest.java") + (("import ch.rinn.restrictions.Friend;") "") + (("@Friend.*") "")) + ;; Remove leftovers from removing @Friend + (substitute* "h5ar/HDF5ArchiverTest.java" + (("\\{ HDF5Archiver.class, IdCache.class, LinkRecord.class \\}\\)") + ""))) + #t)) + (add-before 'configure 'build-native-library + (lambda* (#:key inputs #:allow-other-keys) + (let ((jdk (assoc-ref inputs "jdk")) + (hdf5 (assoc-ref inputs "hdf5")) + (dir ,(match (%current-system) + ("i686-linux" + "i386-Linux") + ((or "armhf-linux" "aarch64-linux") + "arm-Linux") + ((or "x86_64-linux") + "amd64-Linux") + (_ "unknown-Linux")))) + (with-directory-excursion "source/c" + (apply invoke `("gcc" "-shared" "-O3" + "-fPIC" + "-Wl,--exclude-libs,ALL" + ,@(find-files "jhdf5" "\\.c$") + ,@(find-files "hdf-java" "\\.c$") + ,(string-append "-I" hdf5 "/include") + ,(string-append "-I" jdk "/include") + ,(string-append "-I" jdk "/include/linux") + ,(string-append hdf5 "/lib/libhdf5.a") + "-o" "libjhdf5.so" "-lz"))) + (install-file "source/c/libjhdf5.so" + (string-append "libs/native/jhdf5/" dir)) + #t))) + ;; In the "check" phase we only build the test executable. + (add-after 'check 'run-tests + (lambda _ + (invoke "java" "-jar" "targets/dist/sis-jhdf5-test.jar") + (delete-file "targets/dist/sis-jhdf5-test.jar") + #t)) + (replace 'install + (install-jars "targets/dist"))))) + (inputs + `(("java-cisd-base" ,java-cisd-base) + ("java-cisd-args4j" ,java-cisd-args4j) + ("java-commons-lang" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("hdf5" ,hdf5) + ("zlib" ,zlib))) + (native-inputs + `(("jdk" ,icedtea-8) + ("java-testng" ,java-testng) + ("java-junit" ,java-junit) + ("java-jmock" ,java-jmock) + ("java-hamcrest-core" ,java-hamcrest-core) + ("build-resources" + ,(origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "http://svnsis.ethz.ch/repos/cisd/" + "jhdf5/tags/release/" + (version-major+minor base-version) + ".x/" base-version + "/build_resources/")) + (revision revision))) + (sha256 + (base32 + "0b6335gkm4x895rac6kfg9d3rpq0sy19ph4zpg2gyw6asfsisjhk")))))) + (home-page "https://wiki-bsse.ethz.ch/display/JHDF5/") + (synopsis "Java binding for HDF5") + (description "JHDF5 is a high-level API in Java for reading and writing +HDF5 files, building on the libraries provided by the HDF Group.") + ;; The C sources are under a non-copyleft license, which looks like a + ;; variant of the BSD licenses. The whole package is under the ASL2.0. + (license (list license:asl2.0 + (license:non-copyleft "file://source/c/COPYING")))))) + (define-public java-classpathx-servletapi (package (name "java-classpathx-servletapi") -- cgit v1.2.3 From bd975831c67af75c4603555195ac618765c06ccc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 23 Feb 2018 10:56:49 +0100 Subject: gnu: Add fastqc. * gnu/packages/bioinformatics.scm (fastqc): New variable. --- gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e13f1b369f..065dc477d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3195,6 +3195,85 @@ VCF.") ("jdk" ,icedtea-8 "jdk") ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) +(define-public fastqc + (package + (name "fastqc") + (version "0.11.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" + "projects/fastqc/fastqc_v" + version "_source.zip")) + (sha256 + (base32 + "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:build-target "build" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("jbzip2-0.9.jar") + (string-append (assoc-ref inputs "java-jbzip2") + "/share/java/jbzip2.jar")) + (("sam-1.103.jar") + (string-append (assoc-ref inputs "java-picard-1.113") + "/share/java/sam-1.112.jar")) + (("cisd-jhdf5.jar") + (string-append (assoc-ref inputs "java-cisd-jhdf5") + "/share/java/sis-jhdf5.jar"))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fastqc/")) + (exe (string-append share "/fastqc"))) + (for-each mkdir-p (list bin share)) + (copy-recursively "bin" share) + (substitute* exe + (("my \\$java_bin = 'java';") + (string-append "my $java_bin = '" + (assoc-ref inputs "java") + "/bin/java';"))) + (chmod exe #o555) + (symlink exe (string-append bin "/fastqc")) + #t)))))) + (inputs + `(("java" ,icedtea) + ("perl" ,perl) ; needed for the wrapper script + ("java-cisd-jhdf5" ,java-cisd-jhdf5) + ("java-picard-1.113" ,java-picard-1.113) + ("java-jbzip2" ,java-jbzip2))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (synopsis "Quality control tool for high throughput sequence data") + (description + "FastQC aims to provide a simple way to do some quality control +checks on raw sequence data coming from high throughput sequencing +pipelines. It provides a modular set of analyses which you can use to +give a quick impression of whether your data has any problems of which +you should be aware before doing any further analysis. + +The main functions of FastQC are: + +@itemize +@item Import of data from BAM, SAM or FastQ files (any variant); +@item Providing a quick overview to tell you in which areas there may + be problems; +@item Summary graphs and tables to quickly assess your data; +@item Export of results to an HTML based permanent report; +@item Offline operation to allow automated generation of reports + without running the interactive application. +@end itemize\n") + (license license:gpl3+))) + (define-public htslib (package (name "htslib") -- cgit v1.2.3 From c8d996080ee7aefddad89ec155fae370d5ae2726 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:33 +0100 Subject: gnu: Add java-la4j. * gnu/packages/algebra.scm (java-la4j): New variable. --- gnu/packages/algebra.scm | 48 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 47 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 2bc8431033..a59346bd56 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016, 2017, 2018 Nicolas Goaziou ;;; Copyright © 2014 Mark H Weaver -;;; Copyright © 2016 Ricardo Wurmus +;;; Copyright © 2016, 2018 Ricardo Wurmus ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; Copyright © 2017 Marius Bakke @@ -35,6 +35,7 @@ #:use-module (gnu packages gl) #:use-module (gnu packages graphviz) #:use-module (gnu packages image) + #:use-module (gnu packages java) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) @@ -46,9 +47,11 @@ #:use-module (gnu packages texinfo) #:use-module (gnu packages xiph) #:use-module (gnu packages xorg) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix download) + #:use-module (guix git-download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils)) @@ -612,6 +615,49 @@ cosine/ sine transforms or DCT/DST).") (synopsis "Computing the discrete Fourier transform (AVX2-optimized)") (supported-systems '("x86_64-linux")))) +(define-public java-la4j + (package + (name "java-la4j") + (version "0.6.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vkostyukov/la4j.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "la4j.jar" + #:jdk ,icedtea-8 + #:test-exclude (list "**/Abstract*.java" + "**/MatrixTest.java" + "**/DenseMatrixTest.java" + "**/SparseMatrixTest.java" + "**/VectorTest.java" + "**/SparseVectorTest.java" + "**/DenseVectorTest.java"))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://la4j.org/") + (synopsis "Java library that provides Linear Algebra primitives and algorithms") + (description "The la4j library is a Java library that provides Linear +Algebra primitives (matrices and vectors) and algorithms. The key features of +the la4j library are: + +@itemize +@item No dependencies and tiny size +@item Fluent object-oriented/functional API +@item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices +@item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other) +@item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other) +@item MatrixMarket/CSV IO formats support for matrices and vectors +@end itemize\n") + (license license:asl2.0))) + (define-public eigen (package (name "eigen") -- cgit v1.2.3 From 24074b0bddb6af9386239b4bbf0132b30b4358f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:34 +0100 Subject: gnu: Add java-jlargearrays. * gnu/packages/algebra.scm (java-jlargearrays): New variable. --- gnu/packages/algebra.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index a59346bd56..ebd75a7d36 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -658,6 +658,33 @@ the la4j library are: @end itemize\n") (license license:asl2.0))) +(define-public java-jlargearrays + (package + (name "java-jlargearrays") + (version "1.6") + (source (origin + (method url-fetch) + (uri (string-append "http://search.maven.org/remotecontent?" + "filepath=pl/edu/icm/JLargeArrays/" + version "/JLargeArrays-" version + "-sources.jar")) + (file-name (string-append name "-" version ".jar")) + (sha256 + (base32 + "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "jlargearrays.jar" + #:tests? #f ; tests are not included in the release archive + #:jdk ,icedtea-8)) + (propagated-inputs + `(("java-commons-math3" ,java-commons-math3))) + (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays") + (synopsis "Library of one-dimensional arrays that can store up to 263 elements") + (description "JLargeArrays is a Java library of one-dimensional arrays +that can store up to 263 elements.") + (license license:bsd-2))) + (define-public eigen (package (name "eigen") -- cgit v1.2.3 From 4e92911c828fda34636f90b653ec7046fd97602e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:35 +0100 Subject: gnu: Add java-jtransforms. * gnu/packages/algebra.scm (java-jtransforms): New variable. --- gnu/packages/algebra.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index ebd75a7d36..2aa1777db3 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -685,6 +685,34 @@ the la4j library are: that can store up to 263 elements.") (license license:bsd-2))) +(define-public java-jtransforms + (package + (name "java-jtransforms") + (version "3.1") + (source (origin + (method url-fetch) + (uri (string-append "http://search.maven.org/remotecontent?" + "filepath=com/github/wendykierp/JTransforms/" + version "/JTransforms-" version "-sources.jar")) + (sha256 + (base32 + "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "jtransforms.jar" + #:tests? #f ; tests are not included in the release archive + #:jdk ,icedtea-8)) + (propagated-inputs + `(("java-commons-math3" ,java-commons-math3) + ("java-jlargearrays" ,java-jlargearrays))) + (home-page "https://github.com/wendykierp/JTransforms") + (synopsis "Multithreaded FFT library written in pure Java") + (description "JTransforms is a multithreaded FFT library written in pure +Java. Currently, four types of transforms are available: @dfn{Discrete +Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete +Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).") + (license license:bsd-2))) + (define-public eigen (package (name "eigen") -- cgit v1.2.3 From dbb35813838bd4bcfbc1ea94207494bcfa2b5627 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:36 +0100 Subject: gnu: Add java-jdistlib. * gnu/packages/statistics.scm (java-jdistlib): New variable. --- gnu/packages/statistics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 620edfa9fb..baec1c47d2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -32,11 +32,13 @@ #:use-module (guix hg-download) #:use-module (guix git-download) #:use-module (guix utils) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages cran) @@ -5540,3 +5542,40 @@ inferring an appropriate positioning method.") (description "Did you ever wish you could make scatter plots with cat shaped points? Now you can!") (license license:asl2.0)))) + +(define-public java-jdistlib + (package + (name "java-jdistlib") + (version "0.4.5") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/jdistlib/jdistlib-" + version "-src.jar")) + (sha256 + (base32 + "1pkj8aahw9ydr1isbaqrkd05nvq98ik5jwwhf3yf3rky3z869v11")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "jdistlib.jar" + #:jdk ,icedtea-8 + #:tests? #f ; no dedicated test directory + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-broken-encoding + (lambda _ + (with-fluids ((%default-port-encoding "ISO-8859-1")) + (substitute* "src/jdistlib/Beta.java" + (("Scheff.+-Tukey") "Scheffe-Tukey"))) + #t))))) + (propagated-inputs + `(("java-jtransforms" ,java-jtransforms))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "http://jdistlib.sourceforge.net/") + (synopsis "Java library of statistical distributions") + (description "JDistlib is the Java Statistical Distribution Library, a +Java package that provides routines for various statistical distributions.") + ;; The files that were translated from R code are under GPLv2+; some files + ;; are under the GPLv3, which is a mistake. The author confirmed in an + ;; email that this whole project should be under GPLv2+. + (license license:gpl2+))) -- cgit v1.2.3 From 5fef15e50679a4e18df4fafede913c26d0029126 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:37 +0100 Subject: gnu: Add java-biojava-core. * gnu/packages/bioinformatics.scm (java-biojava-core): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 065dc477d8..4a90f30128 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11949,3 +11949,59 @@ variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) + +(define-public java-biojava-core + (package + (name "java-biojava-core") + (version "4.2.11") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biojava/biojava") + (commit (string-append "biojava-" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1bvryh2bpsvash8ln79cmc9sqm8qw72hz4xzwqxcrjm8ssxszhqk")))) + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-core.jar" + #:source-dir "biojava-core/src/main/java/" + #:test-dir "biojava-core/src/test" + ;; These tests seem to require internet access. + #:test-exclude (list "**/SearchIOTest.java" + "**/BlastXMLParserTest.java" + "**/GenbankCookbookTest.java" + "**/GenbankProxySequenceReaderTest.java") + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-core/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-core/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Core libraries of Java framework for processing biological data") + (description "BioJava is a project dedicated to providing a Java framework +for processing biological data. It provides analytical and statistical +routines, parsers for common file formats, reference implementations of +popular algorithms, and allows the manipulation of sequences and 3D +structures. The goal of the biojava project is to facilitate rapid +application development for bioinformatics. + +This package provides the core libraries.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 93abc975feca4d877b0a14a0dd8f3613dcbd7c9b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:38 +0100 Subject: gnu: Add java-openchart2. * gnu/packages/java.scm (java-openchart2): New variable. --- gnu/packages/java.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 298874f757..1e671b90bb 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -9292,3 +9292,44 @@ against expected outcomes.") ("java-junit" ,java-junit))) (native-inputs `(("java-mockito-1" ,java-mockito-1))))) + +(define-public java-openchart2 + (package + (name "java-openchart2") + (version "1.4.3") + (source (origin + (method url-fetch) + (uri (string-append "http://download.approximatrix.com/openchart2/" + "openchart2-" version ".source.zip")) + (sha256 + (base32 + "1xq96zm5r02n1blja0072jmmsifmxc40lbyfbnmcnr6mw42frh4g")))) + (build-system ant-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-junit-errors + (lambda _ + (with-directory-excursion "unittest/src/com/approximatrix/charting/" + (substitute* '("coordsystem/ticklocator/NumericXTickLocatorTest.java" + "coordsystem/ticklocator/NumericYTickLocatorTest.java" + "coordsystem/ticklocator/ObjectXTickLocatorTest.java" + "model/DefaultChartDataModelConstraintsTest.java" + "model/MultiScatterDataModelConstraintsTest.java" + "model/threedimensional/DotPlotDataModelConstraintsTest.java") + (("(assertEquals[^;]+);" before _) + (string-append (string-drop-right before 2) ", 1E-6);")))) + #t)) + (replace 'install (install-jars "."))))) + (native-inputs + `(("unzip" ,unzip) + ("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://approximatrix.com/products/openchart2/") + (synopsis "Simple plotting for Java") + (description "Openchart2 provides a simple, yet powerful, interface for +Java programmers to create two-dimensional charts and plots. The library +features an assortment of graph styles, including advanced scatter plots, bar +graphs, and pie charts.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From f09d16e5949b5d84529be9022034e217fbaad54d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:39 +0100 Subject: gnu: Add java-forester. * gnu/packages/bioinformatics.scm (java-forester): New variable. --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 76 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a90f30128..ef1e8606a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11950,6 +11950,82 @@ graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) +;; We cannot use the latest commit because it requires Java 9. +(define-public java-forester + (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") + (revision "1")) + (package + (name "java-forester") + (version (string-append "0-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cmzmasek/forester.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0vxavc1yrf84yrnf20dq26hi0lglidk8d382xrxsy4qmlbjd276z")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled jars and pre-built classes + (delete-file-recursively "forester/java/resources") + (delete-file-recursively "forester/java/classes") + (for-each delete-file (find-files "forester/java/" "\\.jar$")) + ;; Delete bundled applications + (delete-file-recursively "forester_applications") + #t)))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are none + #:jdk ,icedtea-8 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "forester/java") #t)) + (add-after 'chdir 'fix-dependencies + (lambda _ + (chmod "build.xml" #o664) + (call-with-output-file "build.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove all unjar tags to avoid repacking classes. + (unjar . ,(lambda _ '())) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build.xml.new" "build.xml") + #t)) + ;; FIXME: itext is difficult to package as it depends on a few + ;; unpackaged libraries. + (add-after 'chdir 'remove-dependency-on-unpackaged-itext + (lambda _ + (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") + (substitute* "src/org/forester/archaeopteryx/MainFrame.java" + (("pdf_written_to = PdfExporter.*") + "throw new IOException(\"PDF export is not available.\");")) + #t)) + ;; There is no install target + (replace 'install (install-jars "."))))) + (propagated-inputs + `(("java-commons-codec" ,java-commons-codec) + ("java-openchart2" ,java-openchart2))) + (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") + (synopsis "Phylogenomics libraries for Java") + (description "Forester is a collection of Java libraries for +phylogenomics and evolutionary biology research. It includes support for +reading, writing, and exporting phylogenetic trees.") + (license license:lgpl2.1+)))) + (define-public java-biojava-core (package (name "java-biojava-core") -- cgit v1.2.3 From 10645b9212d5eff74132edf60c90c3eb099a139f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:40 +0100 Subject: gnu: Add java-forester-1.005. * gnu/packages/bioinformatics.scm (java-forester-1.005): New variable. --- gnu/packages/bioinformatics.scm | 95 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 95 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef1e8606a9..d64cda2340 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12026,6 +12026,101 @@ phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.") (license license:lgpl2.1+)))) +(define-public java-forester-1.005 + (package + (name "java-forester") + (version "1.005") + (source (origin + (method url-fetch) + (uri (string-append "http://search.maven.org/remotecontent?" + "filepath=org/biojava/thirdparty/forester/" + version "/forester-" version "-sources.jar")) + (file-name (string-append name "-" version ".jar")) + (sha256 + (base32 + "04r8qv4rk3p71z4ajrvp11py1z46qrx0047j3zzs79s6lnsm3lcv")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are none + #:jdk ,icedtea-8 + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "build.xml" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "src/build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `(;; Remove all unjar tags to avoid repacking classes. + (unjar . ,(lambda _ '())) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (copy-file (assoc-ref inputs "synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (copy-file (assoc-ref inputs "phyloxml.xsd") + "phyloxml.xsd") + (substitute* "build.xml" + (("../resources/synth_laf/synth_look_and_feel_1.xml") + "synth_look_and_feel_1.xml") + (("../resources/phyloxml_schema/1.10/phyloxml.xsd") + "phyloxml.xsd")) + #t)) + ;; FIXME: itext is difficult to package as it depends on a few + ;; unpackaged libraries. + (add-after 'unpack 'remove-dependency-on-unpackaged-itext + (lambda _ + (delete-file "src/org/forester/archaeopteryx/PdfExporter.java") + (substitute* '("src/org/forester/archaeopteryx/MainFrame.java" + "src/org/forester/archaeopteryx/MainFrameApplication.java") + (("pdf_written_to = PdfExporter.*") + "throw new IOException(\"PDF export is not available.\"); /*") + ((".getPrintSizeX\\(\\), getOptions\\(\\).getPrintSizeY\\(\\) \\);") "*/") + (("getCurrentTreePanel\\(\\).getHeight\\(\\) \\);") "*/")) + #t)) + (add-after 'unpack 'delete-pre-built-classes + (lambda _ (delete-file-recursively "src/classes") #t)) + ;; There is no install target + (replace 'install (install-jars "."))))) + (propagated-inputs + `(("java-commons-codec" ,java-commons-codec) + ("java-openchart2" ,java-openchart2))) + ;; The source archive does not contain the resources. + (native-inputs + `(("phyloxml.xsd" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "b61cc2dcede0bede317db362472333115756b8c6/" + "forester/resources/phyloxml_schema/1.10/phyloxml.xsd")) + (file-name (string-append name "-phyloxml-" version ".xsd")) + (sha256 + (base32 + "1zxc4m8sn4n389nqdnpxa8d0k17qnr3pm2y5y6g6vh4k0zm52npv")))) + ("synth_look_and_feel_1.xml" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" + "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" + "forester/java/classes/resources/synth_look_and_feel_1.xml")) + (file-name (string-append name "-synth-look-and-feel-" version ".xml")) + (sha256 + (base32 + "1gv5602gv4k7y7713y75a4jvj7i9s7nildsbdl7n9q10sc2ikg8h")))))) + (home-page "https://sites.google.com/site/cmzmasek/home/software/forester") + (synopsis "Phylogenomics libraries for Java") + (description "Forester is a collection of Java libraries for +phylogenomics and evolutionary biology research. It includes support for +reading, writing, and exporting phylogenetic trees.") + (license license:lgpl2.1+))) + (define-public java-biojava-core (package (name "java-biojava-core") -- cgit v1.2.3 From b28c803708d41c4a5323e31e01f7b6044fcc6dda Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:41 +0100 Subject: gnu: Add java-biojava-phylo. * gnu/packages/bioinformatics.scm (java-biojava-phylo): 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 d64cda2340..fbb3264ef5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12176,3 +12176,39 @@ application development for bioinformatics. This package provides the core libraries.") (license license:lgpl2.1+))) + +(define-public java-biojava-phylo + (package (inherit java-biojava-core) + (name "java-biojava-phylo") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-phylo.jar" + #:source-dir "biojava-phylo/src/main/java/" + #:test-dir "biojava-phylo/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-phylo/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-phylo/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core) + ("java-forester" ,java-forester))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava interface to the forester phylogenomics library") + (description "The phylo module provides a biojava interface layer to the +forester phylogenomics library for constructing phylogenetic trees."))) -- cgit v1.2.3 From 22c09c335beff3caa2b434165f09d88267269794 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:42 +0100 Subject: gnu: Add java-biojava-alignment. * gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fbb3264ef5..08d9be4bd7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12212,3 +12212,47 @@ This package provides the core libraries.") (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) + +(define-public java-biojava-alignment + (package (inherit java-biojava-core) + (name "java-biojava-alignment") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-alignment.jar" + #:source-dir "biojava-alignment/src/main/java/" + #:test-dir "biojava-alignment/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-alignment/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-alignment/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core) + ("java-biojava-phylo" ,java-biojava-phylo) + ("java-forester" ,java-forester))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava API for genetic sequence alignment") + (description "The alignment module of BioJava provides an API that +contains + +@itemize +@item implementations of dynamic programming algorithms for sequence + alignment; +@item reading and writing of popular alignment file formats; +@item a single-, or multi- threaded multiple sequence alignment algorithm. +@end itemize\n"))) -- cgit v1.2.3 From e44da58c16f8c0dd8d9fb80f38f3e86a08fa22f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:43 +0100 Subject: gnu: Add java-biojava-core-4.0. * gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable. --- gnu/packages/bioinformatics.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 08d9be4bd7..2f5413b35e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12256,3 +12256,17 @@ contains @item reading and writing of popular alignment file formats; @item a single-, or multi- threaded multiple sequence alignment algorithm. @end itemize\n"))) + +(define-public java-biojava-core-4.0 + (package (inherit java-biojava-core) + (name "java-biojava-core") + (version "4.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biojava/biojava") + (commit (string-append "biojava-" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8")))))) -- cgit v1.2.3 From 5528f9e8f09f4a63b40647d61ec100c4c5326b3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:44 +0100 Subject: gnu: Add java-biojava-phylo-4.0. * gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): 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 2f5413b35e..37647a9b9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12270,3 +12270,39 @@ contains (sha256 (base32 "13675f6y9aqi7bi2lk3s1z7a22ynccjiqwa8izh7p97xi9wsfmd8")))))) + +(define-public java-biojava-phylo-4.0 + (package (inherit java-biojava-core-4.0) + (name "java-biojava-phylo") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-phylo.jar" + #:source-dir "biojava-phylo/src/main/java/" + #:test-dir "biojava-phylo/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-phylo/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-phylo/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-forester" ,java-forester-1.005))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava interface to the forester phylogenomics library") + (description "The phylo module provides a biojava interface layer to the +forester phylogenomics library for constructing phylogenetic trees."))) -- cgit v1.2.3 From 9ac7db1830a1b324524aa7d383c5f1b5e348237f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:45 +0100 Subject: gnu: Add java-biojava-alignment-4.0. * gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable. --- gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37647a9b9b..f44dc32aa7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12306,3 +12306,47 @@ contains (synopsis "Biojava interface to the forester phylogenomics library") (description "The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees."))) + +(define-public java-biojava-alignment-4.0 + (package (inherit java-biojava-core-4.0) + (name "java-biojava-alignment") + (build-system ant-build-system) + (arguments + `(#:jdk ,icedtea-8 + #:jar-name "biojava-alignment.jar" + #:source-dir "biojava-alignment/src/main/java/" + #:test-dir "biojava-alignment/src/test" + #:phases + (modify-phases %standard-phases + (add-before 'build 'copy-resources + (lambda _ + (copy-recursively "biojava-alignment/src/main/resources" + "build/classes") + #t)) + (add-before 'check 'copy-test-resources + (lambda _ + (copy-recursively "biojava-alignment/src/test/resources" + "build/test-classes") + #t))))) + (propagated-inputs + `(("java-log4j-api" ,java-log4j-api) + ("java-log4j-core" ,java-log4j-core) + ("java-slf4j-api" ,java-slf4j-api) + ("java-slf4j-simple" ,java-slf4j-simple) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-biojava-phylo" ,java-biojava-phylo-4.0) + ("java-forester" ,java-forester-1.005))) + (native-inputs + `(("java-junit" ,java-junit) + ("java-hamcrest-core" ,java-hamcrest-core))) + (home-page "http://biojava.org") + (synopsis "Biojava API for genetic sequence alignment") + (description "The alignment module of BioJava provides an API that +contains + +@itemize +@item implementations of dynamic programming algorithms for sequence + alignment; +@item reading and writing of popular alignment file formats; +@item a single-, or multi- threaded multiple sequence alignment algorithm. +@end itemize\n"))) -- cgit v1.2.3 From 9a599c17b7dfca56ff8290902057ee6da933aed2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:46 +0100 Subject: gnu: Add java-htsjdk-latest. * gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f44dc32aa7..505672624d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3003,6 +3003,49 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +(define-public java-htsjdk-latest + (package + (name "java-htsjdk") + (version "2.14.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1lmya1fdjy03mz6zmdmd86j9v9vfhqb3952mqq075navx1i6g4bc")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test require Scala + #:jdk ,icedtea-8 + #:jar-name "htsjdk.jar" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; The tests require the scalatest package. + (add-after 'unpack 'remove-tests + (lambda _ (delete-file-recursively "src/test") #t))))) + (inputs + `(("java-ngs" ,java-ngs) + ("java-snappy-1" ,java-snappy-1) + ("java-commons-compress" ,java-commons-compress) + ("java-commons-logging-minimal" ,java-commons-logging-minimal) + ("java-commons-jexl-2" ,java-commons-jexl-2) + ("java-xz" ,java-xz))) + (native-inputs + `(("java-junit" ,java-junit))) + (home-page "http://samtools.github.io/htsjdk/") + (synopsis "Java API for high-throughput sequencing data (HTS) formats") + (description + "HTSJDK is an implementation of a unified Java library for accessing +common file formats, such as SAM and VCF, used for high-throughput +sequencing (HTS) data. There are also an number of useful utilities for +manipulating HTS data.") + (license license:expat))) + ;; This version matches java-htsjdk 2.3.0. Later versions also require a more ;; recent version of java-htsjdk, which depends on gradle. (define-public java-picard -- cgit v1.2.3 From 719fa958f395a44c87377eb61a6f81a7a57603fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:47 +0100 Subject: gnu: Add java-htsjdk-2.10.1. * gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 505672624d..09a64a8d4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3046,6 +3046,33 @@ sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.") (license license:expat))) +;; This is needed for picard 2.10.3 +(define-public java-htsjdk-2.10.1 + (package (inherit java-htsjdk-latest) + (name "java-htsjdk") + (version "2.10.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/samtools/htsjdk.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1kxh7slm2pm3x9p6jxa1wqsq9a31dhiiflhxnxqcisan4k3rwia2")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; tests require Scala + #:jdk ,icedtea-8 + #:jar-name "htsjdk.jar" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; The tests require the scalatest package. + (add-after 'unpack 'remove-tests + (lambda _ (delete-file-recursively "src/test") #t))))))) + ;; This version matches java-htsjdk 2.3.0. Later versions also require a more ;; recent version of java-htsjdk, which depends on gradle. (define-public java-picard -- cgit v1.2.3 From 72299db9feb6d9e1e0b5cc3262ec7c9cbf7fe729 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:48 +0100 Subject: gnu: Add java-picard-2.10.3. * gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable. --- gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09a64a8d4d..719f3e5f23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3151,6 +3151,90 @@ commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.") (license license:expat))) +;; This is needed for dropseq-tools +(define-public java-picard-2.10.3 + (package + (name "java-picard") + (version "2.10.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/broadinstitute/picard.git") + (commit version))) + (file-name (string-append "java-picard-" version "-checkout")) + (sha256 + (base32 + "1ajlx31l6i1k3y2rhnmgq07sz99g2czqfqgkr9mihmdjp3gwjhvi")))) + (build-system ant-build-system) + (arguments + `(#:jar-name "picard.jar" + ;; Tests require jacoco:coverage. + #:tests? #f + #:jdk ,icedtea-8 + #:main-class "picard.cmdline.PicardCommandLine" + #:modules ((guix build ant-build-system) + (guix build utils) + (guix build java-utils) + (sxml simple) + (sxml transform) + (sxml xpath)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-useless-build.xml + (lambda _ (delete-file "build.xml") #t)) + ;; This is necessary to ensure that htsjdk is found when using + ;; picard.jar as an executable. + (add-before 'build 'edit-classpath-in-manifest + (lambda* (#:key inputs #:allow-other-keys) + (chmod "build.xml" #o664) + (call-with-output-file "build.xml.new" + (lambda (port) + (sxml->xml + (pre-post-order + (with-input-from-file "build.xml" + (lambda _ (xml->sxml #:trim-whitespace? #t))) + `((target . ,(lambda (tag . kids) + (let ((name ((sxpath '(name *text*)) + (car kids))) + ;; FIXME: We're breaking the line + ;; early with a dummy path to + ;; ensure that the store reference + ;; isn't broken apart and can still + ;; be found by the reference + ;; scanner. + (msg (format #f + "\ +Class-Path: /~a \ + ~a/share/java/htsjdk.jar${line.separator}" + ;; maximum line length is 70 + (string-tabulate (const #\b) 57) + (assoc-ref inputs "java-htsjdk")))) + (if (member "manifest" name) + `(,tag ,@kids + (echo + (@ (message ,msg) + (file "${manifest.file}") + (append "true")))) + `(,tag ,@kids))))) + (*default* . ,(lambda (tag . kids) `(,tag ,@kids))) + (*text* . ,(lambda (_ txt) txt)))) + port))) + (rename-file "build.xml.new" "build.xml") + #t))))) + (propagated-inputs + `(("java-htsjdk" ,java-htsjdk-2.10.1))) + (native-inputs + `(("java-testng" ,java-testng) + ("java-guava" ,java-guava))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "Tools for manipulating high-throughput sequencing data and formats") + (description "Picard is a set of Java command line tools for manipulating +high-throughput sequencing (HTS) data and formats. Picard is implemented +using the HTSJDK Java library to support accessing file formats that are +commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and +VCF.") + (license license:expat))) + ;; This is the last version of Picard to provide net.sf.samtools (define-public java-picard-1.113 (package (inherit java-picard) -- cgit v1.2.3 From 1adeef3194dd7c8da6e78b17fb33e71bb0c9e24f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 1 Mar 2018 19:41:49 +0100 Subject: gnu: Add dropseq-tools. * gnu/packages/bioinformatics.scm (dropseq-tools): New variable. --- gnu/packages/bioinformatics.scm | 137 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 137 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 719f3e5f23..75468aa967 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12504,3 +12504,140 @@ contains @item reading and writing of popular alignment file formats; @item a single-, or multi- threaded multiple sequence alignment algorithm. @end itemize\n"))) + +(define-public dropseq-tools + (package + (name "dropseq-tools") + (version "1.13") + (source + (origin + (method url-fetch) + (uri "http://mccarrolllab.com/download/1276/") + (file-name (string-append "dropseq-tools-" version ".zip")) + (sha256 + (base32 + "0yrffckxqk5l8b5xb6z4laq157zd9mdypr2p4b4vq2bhjzi1sj0s")) + ;; Delete bundled libraries + (modules '((guix build utils))) + (snippet + '(begin + (for-each delete-file (find-files "jar/lib" "\\.jar$")) + (delete-file-recursively "3rdParty"))))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; test data are not included + #:test-target "test" + #:build-target "all" + #:source-dir "public/src/" + #:jdk ,icedtea-8 + #:make-flags + (list (string-append "-Dpicard.executable.dir=" + (assoc-ref %build-inputs "java-picard") + "/share/java/")) + #:modules ((ice-9 match) + (srfi srfi-1) + (guix build utils) + (guix build java-utils) + (guix build ant-build-system)) + #:phases + (modify-phases %standard-phases + ;; All dependencies must be linked to "lib", because that's where + ;; they will be searched for when the Class-Path property of the + ;; manifest is computed. + (add-after 'unpack 'record-references + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "jar/lib") + (let ((dirs (filter-map (match-lambda + ((name . dir) + (if (and (string-prefix? "java-" name) + (not (string=? name "java-testng"))) + dir #f))) + inputs))) + (for-each (lambda (jar) + (symlink jar (string-append "jar/lib/" (basename jar)))) + (append-map (lambda (dir) (find-files dir "\\.jar$")) + dirs))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/")) + (scripts (list "BAMTagHistogram" + "BAMTagofTagCounts" + "BaseDistributionAtReadPosition" + "CollapseBarcodesInPlace" + "CollapseTagWithContext" + "ConvertToRefFlat" + "CreateIntervalsFiles" + "DetectBeadSynthesisErrors" + "DigitalExpression" + "Drop-seq_alignment.sh" + "FilterBAM" + "FilterBAMByTag" + "GatherGeneGCLength" + "GatherMolecularBarcodeDistributionByGene" + "GatherReadQualityMetrics" + "PolyATrimmer" + "ReduceGTF" + "SelectCellsByNumTranscripts" + "SingleCellRnaSeqMetricsCollector" + "TagBamWithReadSequenceExtended" + "TagReadWithGeneExon" + "TagReadWithInterval" + "TrimStartingSequence" + "ValidateReference"))) + (for-each mkdir-p (list bin share lib)) + (install-file "dist/dropseq.jar" share) + (for-each (lambda (script) + (chmod script #o555) + (install-file script bin)) + scripts) + (substitute* (map (lambda (script) + (string-append bin "/" script)) + scripts) + (("^java") (which "java")) + (("jar_deploy_dir=.*") + (string-append "jar_deploy_dir=" share "\n")))) + #t)) + ;; FIXME: We do this after stripping jars because we don't want it to + ;; copy all these jars and strip them. We only want to install + ;; links. Arguably, this is a problem with the ant-build-system. + (add-after 'strip-jar-timestamps 'install-links + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/java/")) + (lib (string-append share "/lib/"))) + (for-each (lambda (jar) + (symlink (readlink jar) + (string-append lib (basename jar)))) + (find-files "jar/lib" "\\.jar$"))) + #t))))) + (inputs + `(("jdk" ,icedtea-8) + ("java-picard" ,java-picard-2.10.3) + ("java-log4j-1.2-api" ,java-log4j-1.2-api) + ("java-commons-math3" ,java-commons-math3) + ("java-commons-jexl2" ,java-commons-jexl-2) + ("java-commons-collections4" ,java-commons-collections4) + ("java-commons-lang2" ,java-commons-lang) + ("java-commons-io" ,java-commons-io) + ("java-snappy-1.0.3-rc3" ,java-snappy-1) + ("java-guava" ,java-guava) + ("java-la4j" ,java-la4j) + ("java-biojava-core" ,java-biojava-core-4.0) + ("java-biojava-alignment" ,java-biojava-alignment-4.0) + ("java-jdistlib" ,java-jdistlib) + ("java-simple-xml" ,java-simple-xml) + ("java-snakeyaml" ,java-snakeyaml))) + (native-inputs + `(("unzip" ,unzip) + ("java-testng" ,java-testng))) + (home-page "http://mccarrolllab.com/dropseq/") + (synopsis "Tools for Drop-seq analyses") + (description "Drop-seq is a technology to enable biologists to +analyze RNA expression genome-wide in thousands of individual cells at +once. This package provides tools to perform Drop-seq analyses.") + (license license:expat))) -- cgit v1.2.3 From c94752ad22da4f90e16bc2402751bcc6bb6fd79a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 3 Mar 2018 21:01:20 +0100 Subject: gnu: tor: Update to 0.3.2.10 [security fixes]. This release fixes TROVE-2018-001 (also tracked as CVE-2018-0490), TROVE-2018-002 (CVE-2018-049), and TROVEs-2018-00{3,4} as well. * gnu/packages/tor.scm (tor): Update to 0.3.2.10. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 50295da5dc..2d685fc7d5 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -47,14 +47,14 @@ (define-public tor (package (name "tor") - (version "0.3.2.9") + (version "0.3.2.10") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "03qn55c969zynnx71r82iaqnadpzq0qclq0zmjhb3n4qma8pnnj3")))) + "1vnb2wkcmm8rnz0fqi3k7arl60mpycs8rjn8hvbgv56g3p1pgpv0")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-gcc-hardening" -- cgit v1.2.3 From 8b2219d84704a362e9a6c34d94458af275aac88f Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 3 Mar 2018 14:55:27 +0100 Subject: linux-modules: Add module-aliases. * gnu/build/linux-modules.scm (module-aliases): New variable. --- gnu/build/linux-modules.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'gnu') diff --git a/gnu/build/linux-modules.scm b/gnu/build/linux-modules.scm index 4a6d4ff089..4fe673cca2 100644 --- a/gnu/build/linux-modules.scm +++ b/gnu/build/linux-modules.scm @@ -30,6 +30,7 @@ #:use-module (ice-9 rdelim) #:export (dot-ko ensure-dot-ko + module-aliases module-dependencies recursive-module-dependencies modules-loaded @@ -95,6 +96,15 @@ contains module names, not actual file names." (('depends . what) (string-tokenize what %not-comma))))) +(define (module-aliases file) + "Return the list of aliases of module FILE." + (let ((info (modinfo-section-contents file))) + (filter-map (match-lambda + (('alias . value) + value) + (_ #f)) + (modinfo-section-contents file)))) + (define dot-ko (cut string-append <> ".ko")) -- cgit v1.2.3 From 1e6b9c6e164df01ecf1b255fa95a246f698a8c34 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 18 Jan 2018 22:45:26 +0000 Subject: services: postgresql: Add a default-value to the postgresql-service-type. * gnu/packages/databases.scm () [config-file,data-directory]: Add default. (postgresql-service-type)[default-value]: Set to (postgresql-configuration). --- gnu/services/databases.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/services/databases.scm b/gnu/services/databases.scm index b34a67aa95..3db9472ee3 100644 --- a/gnu/services/databases.scm +++ b/gnu/services/databases.scm @@ -77,8 +77,10 @@ (default 5432)) (locale postgresql-configuration-locale (default "en_US.utf8")) - (config-file postgresql-configuration-file) - (data-directory postgresql-configuration-data-directory)) + (config-file postgresql-configuration-file + (default %default-postgres-config)) + (data-directory postgresql-configuration-data-directory + (default "/var/lib/postgresql/data"))) (define %default-postgres-hba (plain-file "pg_hba.conf" @@ -184,7 +186,8 @@ host all all ::1/128 trust")) (service-extension activation-service-type postgresql-activation) (service-extension account-service-type - (const %postgresql-accounts)))))) + (const %postgresql-accounts)))) + (default-value (postgresql-configuration)))) (define* (postgresql-service #:key (postgresql postgresql) (port 5432) -- cgit v1.2.3 From e903738f86a0be92c5c8c56adc71f8177c14f49a Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 18 Jan 2018 22:45:35 +0000 Subject: services: mysql: Add a default-value to the mysql-service-type. * gnu/services/databases.scm (mysql-service-type)[default-value]: Set to (mysql-configuration). --- gnu/services/databases.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/databases.scm b/gnu/services/databases.scm index 3db9472ee3..1d56015b75 100644 --- a/gnu/services/databases.scm +++ b/gnu/services/databases.scm @@ -469,7 +469,8 @@ FLUSH PRIVILEGES; (service-extension activation-service-type %mysql-activation) (service-extension shepherd-root-service-type - mysql-shepherd-service))))) + mysql-shepherd-service))) + (default-value (mysql-configuration)))) (define* (mysql-service #:key (config (mysql-configuration))) "Return a service that runs @command{mysqld}, the MySQL or MariaDB -- cgit v1.2.3 From bc037c1bd1a10ea00e260cf2ce184120c2c6fb3c Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 18 Jan 2018 22:45:40 +0000 Subject: services: redis: Add a default-value to the redis-service-type. * gnu/packages/databases.scm (redis-service-type)[default-value]: Set to (redis-configuration). --- gnu/services/databases.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/services/databases.scm b/gnu/services/databases.scm index 1d56015b75..3ca8f471fc 100644 --- a/gnu/services/databases.scm +++ b/gnu/services/databases.scm @@ -552,4 +552,5 @@ The optional @var{config} argument specifies the configuration for (service-extension activation-service-type redis-activation) (service-extension account-service-type - (const %redis-accounts)))))) + (const %redis-accounts)))) + (default-value (redis-configuration)))) -- cgit v1.2.3 From 7fc944273d17ad0aa7dccd6eb1d730e5ea87bcfc Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:48:46 +0200 Subject: gnu: masscan: Declare a source file-name. * gnu/packages/admin.scm (masscan)[source]: Declare a source file-name. --- 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 80cf8c391c..554c1679e6 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2433,6 +2433,7 @@ on systems running the Linux kernel.") (method url-fetch) (uri (string-append "https://github.com/robertdavidgraham/masscan" "/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1y9af345g00z83rliv6bmlqg37xwc7xpnx5xqdgmjikzcxgk9pji")))) -- cgit v1.2.3 From a18ee793d7ada1bb46ecc2de91d8177ea6e15531 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:52:08 +0200 Subject: gnu: papagayo: Declare a source file-name. * gnu/packages/animation.scm (papagayo)[source]: Declare a source file-name. --- gnu/packages/animation.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/animation.scm b/gnu/packages/animation.scm index 952d3bab0d..b56a081984 100644 --- a/gnu/packages/animation.scm +++ b/gnu/packages/animation.scm @@ -200,6 +200,7 @@ contains the graphical user interface for synfig.") (uri (git-reference (url "https://github.com/LostMoho/Papagayo.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1p9gffjhbph34jhrvgpg93yha75bf88vkvlnk06x1r9601ph5321")) -- cgit v1.2.3 From 35a01e67c8fd5a9d06085e56a69465881999c11c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:53:55 +0200 Subject: gnu: lv2-mda-piano: Declare a source file-name. * gnu/packages/audio.scm (lv2-mda-piano)[source]: Declare a source file-name. --- gnu/packages/audio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index a9d29345a6..e3d3819427 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1796,6 +1796,7 @@ software.") (uri (git-reference (url "http://git.elephly.net/software/lv2-mdametapiano.git") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "07lywf6lpfpndg3i9w752mmlg2hgn1bwp23h8b0mdj6awh67abqd")))) -- cgit v1.2.3 From 6677c99a8b9d334e55e23efe9e864b90b9b9f015 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:54:51 +0200 Subject: gnu: lv2-devel: Declare a source file-name. * gnu/packages/audio.scm (lv2-devel)[source]: Declare a source file-name. --- gnu/packages/audio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index e3d3819427..f00ac246c1 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1783,6 +1783,7 @@ software.") (uri (git-reference (url "http://lv2plug.in/git/lv2.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1gp2rd99dfmpibvpixrqn115mrhybzf3if3h8bssf6siyi13f29r"))))))) -- cgit v1.2.3 From 70aa07d296f28063313d48ebcfbc6c69fec2ac82 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:55:46 +0200 Subject: gnu: qjackrcd: Declare a source file-name. * gnu/packages/audio.scm (qjackrcd)[source]: Declare a source file-name. --- gnu/packages/audio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index f00ac246c1..8c48e2a0ff 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2026,6 +2026,7 @@ into various outputs and to start, stop and configure jackd") (uri (git-reference (url "https://github.com/orouits/qjackrcd.git") (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "1l5iq2mkqd4gn9yr8xbh9qlpp1clcflazychl4vhdbz0bzq4c6al")))) -- cgit v1.2.3 From fdf359f82bb414754f299bc55fd314a5f107a332 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:57:24 +0200 Subject: gnu: rubberband: Declare a source file-name. * gnu/packages/audio.scm (rubberband)[source]: Declare a source file-name. --- gnu/packages/audio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 8c48e2a0ff..54bf6c1982 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2106,6 +2106,7 @@ aimed at audio/musical applications.") (string-append "https://bitbucket.org/breakfastquay/rubberband/get/v" version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.bz2")) (sha256 (base32 "05amrbrxx0da3w7m237q51799r8xgs4ffqabi2qv06hq8dpcj386")))) -- cgit v1.2.3 From a1eb506cf3ba5fd0ea832ae564f9c8dae5f386e7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 09:58:23 +0200 Subject: gnu: faust@2: Declare a source file-name. * gnu/packages/audio.scm (faust@2)[source]: Declare a source file-name. --- gnu/packages/audio.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 54bf6c1982..3ae2b1ba47 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1155,6 +1155,7 @@ PS, and DAB+.") (string-map (lambda (c) (if (char=? c #\.) #\- c)) version))))) + (file-name (string-append "faust-" version "-checkout")) (sha256 (base32 "06km0ygwxxwgw1lqldccqidxhmjfz8ck0wnbd95qk5sg8sbpc068")))) -- cgit v1.2.3 From b1d4026dfb0a5f1fd12c6c0c03fe963c8fd49333 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:45:40 +0200 Subject: gnu: r-dropbead: Declare a source file-name. * gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75468aa967..6a9f13bdc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10888,6 +10888,7 @@ memory usage and processing time is minimized.") (uri (git-reference (url "https://github.com/rajewsky-lab/dropbead.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) -- cgit v1.2.3 From 51106724749a904b45738f9b4d1201ea4e11e760 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:46:43 +0200 Subject: gnu: seek: Declare a source file-name. * gnu/packages/bioinformatics.scm (seek)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a9f13bdc6..139828111a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4846,6 +4846,7 @@ distribution, coverage uniformity, strand specificity, etc.") (uri (hg-reference (url "https://bitbucket.org/libsleipnir/sleipnir") (changeset changeset))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx")))) -- cgit v1.2.3 From d9a069c2d975e37ac2f01261d1c5b4b98f856228 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:47:42 +0200 Subject: gnu: libdivsufsort: Declare a source file-name. * gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 139828111a..fd00984dd5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11650,6 +11650,7 @@ dependency like SeqAn.") (uri (git-reference (url "https://github.com/y-256/libdivsufsort.git") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) -- cgit v1.2.3 From da49d137104229f35816bd09bf24c1756ac1613e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:48:40 +0200 Subject: gnu: piranha: Declare a source file-name. * gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source file-name. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd00984dd5..4756444d95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8924,6 +8924,7 @@ intervals (e.g. genes, sequence alignments).") (uri (git-reference (url "https://github.com/smithlabcode/piranha.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) -- cgit v1.2.3 From eafe96ea9e0e30e4083c001b3908fafd97394554 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:50:16 +0200 Subject: gnu: sfarkxtc: Declare a source file-name. * gnu/packages/compression.scm (sfarkxtc)[source]: Declare a source file-name. --- gnu/packages/compression.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index f25c4bba3a..88b7af82d8 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -600,6 +600,7 @@ with the sfArk algorithm.") (uri (git-reference (url "https://github.com/raboof/sfarkxtc.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "0f5x6i46qfl6ry21s7g2p4sd4b2r1g4fb03yqi2vv4kq3saryhvj")))) -- cgit v1.2.3 From 277be74fa713654c51a4cc39b7318a2a3e15f529 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:51:08 +0200 Subject: gnu: unshield: Declare a source file-name. * gnu/packages/compression.scm (unshield)[source]: Declare a source file-name. --- gnu/packages/compression.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 88b7af82d8..54c5928cb7 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1534,6 +1534,7 @@ or junctions, and always follows hard links.") (origin (method url-fetch) (uri (string-append "http://github.com/twogood/unshield/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0x7ps644yp5dka2zhb8w0ifqmw3d255jafpzfwv8xbcpgq6fmm2x")))) -- cgit v1.2.3 From c2c04cde9b8016808c45db7c4d5986d717f09604 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:55:08 +0200 Subject: gnu: kurly: Declare a source file-name. * gnu/packages/curl.scm (kurly)[source]: Declare a source file-name. --- gnu/packages/curl.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm index e51e014e99..32509fc3fc 100644 --- a/gnu/packages/curl.scm +++ b/gnu/packages/curl.scm @@ -158,6 +158,7 @@ tunneling, and so on.") (uri (git-reference (url "https://github.com/davidjpeacock/kurly.git") (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "1q192f457sjypgvwq7grrf8gq8w272p3zf1d5ppc20mriqm0mbc3")))) -- cgit v1.2.3 From f5c847ebd067e4b56fdeb40e64a2a44e3ae2c19d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 11:55:37 +0200 Subject: gnu: python-apsw: Declare a source file-name. * gnu/packages/databases.scm (python-apsw)[source]: Declare a source file-name. --- gnu/packages/databases.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index ba4ad9f9b9..7057c466d0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2285,6 +2285,7 @@ PickleShare.") (method url-fetch) (uri (string-append "https://github.com/rogerbinns/apsw/archive/" version ".tar.gz")) + (file-name (string-append "apsw-" version ".tar.gz")) (sha256 (base32 "00ai7m2pqi26qaflhz314d8k5i3syw7xzr145fhfl0crhyh6adz2")))) -- cgit v1.2.3 From c553b08b4949c9bb53ffd9b83b5a6de8e459ac25 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:03:27 +0200 Subject: gnu: python-apsw: Use invoke. * gnu/packages/databases.scm (python-apsw)[arguments]: Use invoke. --- gnu/packages/databases.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7057c466d0..269a1ffcea 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2291,25 +2291,25 @@ PickleShare.") "00ai7m2pqi26qaflhz314d8k5i3syw7xzr145fhfl0crhyh6adz2")))) (build-system python-build-system) (inputs - `(("sqlite" ,sqlite))) + `(("sqlite" ,sqlite))) (arguments `(#:phases (modify-phases %standard-phases (replace 'build (lambda _ - (zero? - (system* "python" "setup.py" "build" "--enable-all-extensions")))) + (invoke "python" "setup.py" "build" "--enable-all-extensions") + #t)) (add-after 'build 'build-test-helper (lambda _ - (zero? - (system - (string-append "gcc -fPIC -shared -o ./testextension.sqlext " - "-I. -Isqlite3 src/testextension.c") )))) + (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext" + "-I." "-Isqlite3" "src/testextension.c") + #t)) (delete 'check) (add-after 'install 'check (lambda* (#:key inputs outputs #:allow-other-keys) (add-installed-pythonpath inputs outputs) - (zero? (system* "python" "setup.py" "test"))))))) + (invoke "python" "setup.py" "test") + #t))))) (home-page "https://github.com/rogerbinns/apsw/") (synopsis "Another Python SQLite Wrapper") (description "APSW is a Python wrapper for the SQLite -- cgit v1.2.3 From 5a6f7a68054aed1d0f75eb250d665de9706c8615 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:30:08 +0200 Subject: gnu: emacs-epl: Declare a source file-name. * gnu/packages/emacs.scm (emacs-epl)[source]: Declare a source file-name. --- gnu/packages/emacs.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 67bbb153fb..73c0429095 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -3546,6 +3546,7 @@ It is recommended to use @code{clojure-mode} with paredit or smartparens.") (uri (string-append "https://github.com/cask/epl/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1511n3a3f5gvaf2b4nh018by61ciyzi3y3603fzqma7p9hrckarc")))) -- cgit v1.2.3 From aeb95f1f978cc47a04b644308a5b171ff96c6cee Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:30:53 +0200 Subject: gnu: emacs-sly: Declare a source file-name. * gnu/packages/emacs.scm (emacs-sly)[source]: Declare a source file-name. --- gnu/packages/emacs.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 73c0429095..69950cc6d7 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4301,6 +4301,7 @@ CIDER).") (uri (git-reference (url "https://github.com/joaotavora/sly.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "0ib4q4k3h3qn88pymyjjmlmnpizdn1mfg5gpk5a715nqsgxlg09l")))) -- cgit v1.2.3 From a1dc853ef4f0da0acc1a2c50fb3e5365bff305c9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:32:39 +0200 Subject: gnu: disorderfs: Declare a source file-name. * gnu/packages/file-systems.scm (disorderfs)[source]: Declare a source file-name. --- gnu/packages/file-systems.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm index 1d73f4aef4..0e65213c72 100644 --- a/gnu/packages/file-systems.scm +++ b/gnu/packages/file-systems.scm @@ -114,6 +114,7 @@ single file can be mounted.") (uri (git-reference (url "https://github.com/ReproducibleBuilds/disorderfs.git") (commit "0.5.2"))) + (file-name (git-file-name name version)) (sha256 (base32 "1j028dq3d4m64mn9xmfamcnnc7i2drmra4pdmxdmqdsi8p7yj4sv")))) -- cgit v1.2.3 From 661ad6f0c205c64c5681d1805f42d743f316ab57 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:33:55 +0200 Subject: gnu: freegish: Declare a source file-name. * gnu/packages/games.scm (freegish)[source]: Declare a source file-name. --- gnu/packages/games.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 5917bbd69c..a33da03ad5 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -3491,6 +3491,7 @@ Magic, Egypt, Indians, Norsemen, Persian or Romans.") (uri (git-reference (url "https://github.com/freegish/freegish.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "1p1zf5qqagmcpi1db2bs02cnalpy3qiymp6yzan7k1bhmv859gsx")) -- cgit v1.2.3 From fdbece74aa9582724801225e52b25e71a7a73797 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:35:31 +0200 Subject: gnu: go-github-com-alsm-ioprogress: Declare a source file-name. * gnu/packages/golang.scm (go-github-com-alsm-ioprogress)[source]: Declare a source file-name. --- gnu/packages/golang.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index e201ac8e4c..3a8c889a42 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -502,6 +502,7 @@ in the style of communicating sequential processes (@dfn{CSP}).") (uri (git-reference (url "https://github.com/alsm/ioprogress.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "10ym5qlq77nynmkxbk767f2hfwyxg2k7hrzph05hvgzv833dhivh")))) -- cgit v1.2.3 From 6de107b0c907664338270a493487e7ac0f75a519 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:36:34 +0200 Subject: gnu: go-github-com-davidjpeacock-cli: Declare a source file-name. * gnu/packages/golang.scm (go-github-com-davidjpeacock-cli)[source]: Declare a source file-name. --- gnu/packages/golang.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 3a8c889a42..f3847c1b57 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -552,6 +552,7 @@ jar struct to manage the cookies added to the cookie jar.") (uri (git-reference (url "https://github.com/davidjpeacock/cli.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "01s53ny3p0fdx64rnwcnmjj4xpc5adihnh6islsfq5z1ph2phhnj")))) -- cgit v1.2.3 From 82f09c0e8ee64f39ac453fc8be94c096f7e0b266 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 4 Mar 2018 12:37:33 +0200 Subject: gnu: go-github-com-aki237-nscjar: Declare a source file-name. * gnu/packages/golang.scm (go-github-com-aki237-nscjar)[source]: Declare a source file-name. --- gnu/packages/golang.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index f3847c1b57..20a8c538be 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -528,6 +528,7 @@ writers can be supplied for alternate environments.") (uri (git-reference (url "https://github.com/aki237/nscjar.git") (commit commit))) + (file-name (git-file-name name version)) (sha256 (base32 "03y7zzq12qvhsq86lb06sgns8xrkblbn7i7wd886wk3zr5574b96")))) -- cgit v1.2.3 From 4c763b4d6792adb0a8d3f61a241e490385cc0683 Mon Sep 17 00:00:00 2001 From: Gábor Boskovits Date: Sun, 4 Mar 2018 14:13:47 +0100 Subject: gnu: antlr3-3.1: Fix java8 issue. * gnu/packages/java.scm (antlr3-3.1)[source]: Add patch. * gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Danny Milosavljevic --- gnu/local.mk | 1 + gnu/packages/java.scm | 4 ++- .../patches/antlr3-3_1-fix-java8-compilation.patch | 35 ++++++++++++++++++++++ 3 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 9684d949f6..dffecfc7e9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -553,6 +553,7 @@ dist_patch_DATA = \ %D%/packages/patches/agg-am_c_prototype.patch \ %D%/packages/patches/ansible-wrap-program-hack.patch \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ + %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ %D%/packages/patches/ao-cad-aarch64-support.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ %D%/packages/patches/aspell-default-dict-dir.patch \ diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 1e671b90bb..cda7f0e01f 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -6113,7 +6113,9 @@ import org.antlr.grammar.v2.ANTLRTreePrinter;")) version ".tar.gz")) (sha256 (base32 - "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z")))) + "0sfimc9cpbgrihz4giyygc8afgpma2c93yqpwb951giriri6x66z")) + (patches + (search-patches "antlr3-3_1-fix-java8-compilation.patch")))) (arguments `(#:jar-name (string-append "antlr3-" ,version ".jar") #:source-dir "src:runtime/Java/src" diff --git a/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch b/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch new file mode 100644 index 0000000000..0c4deb024b --- /dev/null +++ b/gnu/packages/patches/antlr3-3_1-fix-java8-compilation.patch @@ -0,0 +1,35 @@ +Based on the upstream fix for the java8 compilation issue. +Simplified patch. +Upstream version of patch does not work with this source tree. + +The issue is that in java8 it is an error to pass null to +removeAll. Results in null pointer exception. java7 +behaviour was to return the list unmodified. + +From db2a350c6d90efaa8dde949fa76005c2c5af45c4 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= +Date: Fri, 5 Jan 2018 17:05:31 +0100 +Subject: [PATCH] Fix java8 compilation. + +--- + src/org/antlr/tool/CompositeGrammar.java | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/src/org/antlr/tool/CompositeGrammar.java b/src/org/antlr/tool/CompositeGrammar.java +index f1408e7..7e02431 100644 +--- a/src/org/antlr/tool/CompositeGrammar.java ++++ b/src/org/antlr/tool/CompositeGrammar.java +@@ -218,7 +218,9 @@ public class CompositeGrammar { + public List getIndirectDelegates(Grammar g) { + List direct = getDirectDelegates(g); + List delegates = getDelegates(g); +- delegates.removeAll(direct); ++ if (direct != null) { ++ delegates.removeAll(direct); ++ } + return delegates; + } + +-- +2.15.1 + -- cgit v1.2.3 From 48c8622010bd0cfc7bc82578772993178308a0b7 Mon Sep 17 00:00:00 2001 From: Gábor Boskovits Date: Sun, 4 Mar 2018 14:16:37 +0100 Subject: gnu: antlr3-3.3: Fix java8 issue. * gnu/packages/java.scm (antlr3-3.3)[source]: Add patch. * gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Danny Milosavljevic --- gnu/local.mk | 1 + gnu/packages/java.scm | 4 ++- .../patches/antlr3-3_3-fix-java8-compilation.patch | 35 ++++++++++++++++++++++ 3 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index dffecfc7e9..2ef9b68590 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -554,6 +554,7 @@ dist_patch_DATA = \ %D%/packages/patches/ansible-wrap-program-hack.patch \ %D%/packages/patches/antiword-CVE-2014-8123.patch \ %D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \ + %D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch \ %D%/packages/patches/ao-cad-aarch64-support.patch \ %D%/packages/patches/apr-skip-getservbyname-test.patch \ %D%/packages/patches/aspell-default-dict-dir.patch \ diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index cda7f0e01f..21e241d0fe 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -6023,7 +6023,9 @@ tree walking, and translation.") version ".tar.gz")) (sha256 (base32 - "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m")))) + "0qgg5vgsm4l1d6dj9pfbaa25dpv2ry2gny8ajy4vvgvfklw97b3m")) + (patches + (search-patches "antlr3-3_3-fix-java8-compilation.patch")))) (arguments `(#:jar-name (string-append ,name "-" ,version ".jar") #:source-dir (string-join '("tool/src/main/java" diff --git a/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch b/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch new file mode 100644 index 0000000000..a7d6be9b6b --- /dev/null +++ b/gnu/packages/patches/antlr3-3_3-fix-java8-compilation.patch @@ -0,0 +1,35 @@ +Based on the upstream fix for the java8 compilation issue. +Simplified patch. +Upstream version of patch does not work with this source tree. + +The issue is that in java8 it is an error to pass null to +removeAll. Results in null pointer exception. java7 +behaviour was to return the list unmodified. + +From 43867d50c05d1c06ab7220eb974a8874ae10c308 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?G=C3=A1bor=20Boskovits?= +Date: Fri, 5 Jan 2018 19:08:24 +0100 +Subject: [PATCH] Fix java8 complilation error. + +--- + tool/src/main/java/org/antlr/tool/CompositeGrammar.java | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/tool/src/main/java/org/antlr/tool/CompositeGrammar.java b/tool/src/main/java/org/antlr/tool/CompositeGrammar.java +index f34ea73..63740a6 100644 +--- a/tool/src/main/java/org/antlr/tool/CompositeGrammar.java ++++ b/tool/src/main/java/org/antlr/tool/CompositeGrammar.java +@@ -226,7 +226,9 @@ public class CompositeGrammar { + public List getIndirectDelegates(Grammar g) { + List direct = getDirectDelegates(g); + List delegates = getDelegates(g); +- delegates.removeAll(direct); ++ if(direct != null) { ++ delegates.removeAll(direct); ++ } + return delegates; + } + +-- +2.15.1 + -- cgit v1.2.3 From 64cdd73c221fa43bdbde52946ed7edfe9c7b2009 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sun, 4 Mar 2018 15:42:41 +0100 Subject: gnu: python-funcy: Fix tests. * gnu/packages/python.scm (python-funcy)[native-inputs]: Delete python-pytest-warnings. --- gnu/packages/python.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5f701701a4..970c835de6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12733,7 +12733,6 @@ functions by partial application of operators.") (invoke "py.test")))))) (native-inputs `(("python-pytest" ,python-pytest) - ("python-pytest-warnings" ,python-pytest-warnings) ("python-whatever" ,python-whatever))) (home-page "http://github.com/Suor/funcy") (synopsis "Functional tools") -- cgit v1.2.3 From 692f6e457ee2eb9cdc9d95c3f8487155ecca81d4 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sun, 4 Mar 2018 15:43:46 +0100 Subject: gnu: abiword: Disable duplicate icon cache generation. * gnu/packages/abiword.scm (abiword): Disable duplicate icon cache generation. --- gnu/packages/abiword.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/abiword.scm b/gnu/packages/abiword.scm index b00dac9a63..cf906c6ea4 100644 --- a/gnu/packages/abiword.scm +++ b/gnu/packages/abiword.scm @@ -82,7 +82,7 @@ ;; the tests to pass. #:tests? #f #:make-flags - (list "CXXFLAGS=-std=c++11"))) + (list "CXXFLAGS=-std=c++11" "gtk_update_icon_cache=true"))) (inputs `(("boost" ,boost) ("enchant" ,enchant) -- cgit v1.2.3 From 81ed306dee3b1049041edaa4b7beab8ef2743aea Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sun, 4 Mar 2018 15:44:34 +0100 Subject: gnu: inkscape: Disable duplicate icon cache generation. * gnu/packages/inkscape.scm (inkscape): Disable duplicate icon cache generation. --- gnu/packages/inkscape.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/inkscape.scm b/gnu/packages/inkscape.scm index f1a3cb23f4..dc5a30b868 100644 --- a/gnu/packages/inkscape.scm +++ b/gnu/packages/inkscape.scm @@ -87,7 +87,10 @@ ("perl" ,perl) ("pkg-config" ,pkg-config))) ;; FIXME: tests require gmock - (arguments `(#:tests? #f)) + (arguments + `(#:tests? #f + #:make-flags + '("gtk_update_icon_cache=true"))) (home-page "https://inkscape.org/") (synopsis "Vector graphics editor") (description "Inkscape is a vector graphics editor. What sets Inkscape -- cgit v1.2.3 From 7fa9cca84afce09d3816b70ae6d42bfc08635e9d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 21 Feb 2018 03:06:39 +0100 Subject: gnu: rocksdb: Update to 5.10.4. * gnu/packages/databases.scm (rocksdb): Update to 5.10.4. [source]: Substitute the unbundled copy of GNU Parallel. [arguments]: Add "V=1" "USE_RTTI=1" and "ROCKSDBTESTS_END=db_tailing_iter_test" to #:make-flags. Set #:test-target to "check_some". Respect parallel jobs in 'build-release-libraries' phase and rename to 'build'. [license]: Update for changes in 5.5.4. --- gnu/packages/databases.scm | 44 +++++++++++++++++++++++++++----------------- 1 file changed, 27 insertions(+), 17 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 269a1ffcea..87f65404f8 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -17,7 +17,7 @@ ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; Copyright © 2016 Andy Patterson ;;; Copyright © 2016 Danny Milosavljevic -;;; Copyright © 2016, 2017 Marius Bakke +;;; Copyright © 2016, 2017, 2018 Marius Bakke ;;; Copyright © 2017 Julien Lepiller ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2017 Jelle Licht @@ -841,7 +841,7 @@ types are supported, as is encryption.") (define-public rocksdb (package (name "rocksdb") - (version "5.2.1") + (version "5.10.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/facebook/rocksdb" @@ -849,18 +849,28 @@ types are supported, as is encryption.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1v2q05bl56sfp51m09z7g6489hkfq4vf6b4qgfg3d96ylgmay9yb")) + "0hp7jxr99vyc57n708hiqk4lks9a9zmjgfjc21mx6v1rmabj2944")) (modules '((guix build utils))) (snippet '(begin ;; TODO: unbundle gtest. (delete-file "build_tools/gnu_parallel") + (substitute* "Makefile" + (("build_tools/gnu_parallel") "parallel")) #t)))) (build-system gnu-build-system) (arguments - `(#:make-flags (list "CC=gcc" + `(#:make-flags (list "CC=gcc" "V=1" + ;; Ceph requires that RTTI is enabled. + "USE_RTTI=1" (string-append "INSTALL_PATH=" - (assoc-ref %outputs "out"))) + (assoc-ref %outputs "out")) + + ;; Running the full test suite takes hours and require + ;; a lot of disk space. Instead we only run a subset + ;; (see .travis.yml and Makefile). + "ROCKSDBTESTS_END=db_tailing_iter_test") + #:test-target "check_some" ;; Many tests fail on 32-bit platforms. There are multiple reports about ;; this upstream, but it's not going to be supported any time soon. #:tests? (let ((system ,(or (%current-target-system) @@ -872,7 +882,6 @@ types are supported, as is encryption.") (add-after 'unpack 'patch-Makefile (lambda _ (substitute* "Makefile" - (("build_tools/gnu_parallel") "parallel") ;; Don't depend on the static library when installing. (("install: install-static") "install: install-shared") @@ -889,20 +898,20 @@ types are supported, as is encryption.") (add-before 'check 'disable-failing-tests (lambda _ (substitute* "Makefile" - ;; This test fails with GCC-5 and is unmaintained. - ;; https://github.com/facebook/rocksdb/issues/2148 - (("^[[:blank:]]+spatial_db_test[[:blank:]]+\\\\") "\\") ;; These tests reliably fail due to "Too many open files". (("^[[:blank:]]+env_test[[:blank:]]+\\\\") "\\") (("^[[:blank:]]+persistent_cache_test[[:blank:]]+\\\\") "\\")) #t)) - (add-after 'check 'build-release-libraries + (add-after 'check 'build ;; The default build target is a debug build for tests. The - ;; install target depends on "shared_lib" and "static_lib" - ;; targets for release builds so we build them here for clarity. - ;; TODO: Add debug output. - (lambda* (#:key (make-flags '()) #:allow-other-keys) - (zero? (apply system* "make" "shared_lib" make-flags))))))) + ;; install target depends on the "shared_lib" release target + ;; so we build it here for clarity. + (lambda* (#:key (make-flags '()) parallel-build? #:allow-other-keys) + (apply invoke "make" "shared_lib" + `(,@(if parallel-build? + `("-j" ,(number->string (parallel-job-count))) + '()) + ,@make-flags))))))) (native-inputs `(("parallel" ,parallel) ("perl" ,perl) @@ -926,8 +935,9 @@ between @dfn{Write-Amplification-Factor} (WAF), @dfn{Read-Amplification-Factor} (RAF) and @dfn{Space-Amplification-Factor} (SAF). It has multi-threaded compactions, making it specially suitable for storing multiple terabytes of data in a single database. RocksDB is partially based on @code{LevelDB}.") - ;; RocksDB is BSD-3 and the JNI adapter is Apache 2.0. - (license (list license:bsd-3 license:asl2.0)))) + ;; RocksDB is dual licensed under GPL2 and ASL 2.0. Some header + ;; files carry the 3-clause BSD license. + (license (list license:gpl2 license:asl2.0 license:bsd-3)))) (define-public sparql-query (package -- cgit v1.2.3 From 5a4373572232a017a3579c164d37b981a370fc6f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 21 Feb 2018 03:14:52 +0100 Subject: gnu: snappy: Update to 1.1.7. * gnu/packages/compression.scm (snappy): Update to 1.1.7. [source]: Change to git archive. Set file-name. [build-system]: Change to CMAKE-BUILD-SYSTEM. [arguments]: Add #:configure-flags. [description]: Fix infractions. --- gnu/packages/compression.scm | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 54c5928cb7..f55f0c2067 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1071,21 +1071,23 @@ algorithm within the Numpy framework.") (define-public snappy (package (name "snappy") - (version "1.1.3") + (version "1.1.7") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/google/snappy/releases/download/" - version "/" name "-" version ".tar.gz")) + (uri (string-append "https://github.com/google/snappy/archive/" + version ".tar.gz")) + (file-name (string-append "snappy-" version ".tar.gz")) (sha256 (base32 - "1wzf8yif5ym2gj52db6v5m1pxnmn258i38x7llk9x346y2nq47ig")))) - (build-system gnu-build-system) + "1m7rcdqzkys5lspj8jcsaah8w33zh28s771bw0ga2lgzfgl05yix")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) (home-page "https://github.com/google/snappy") (synopsis "Fast compressor/decompressor") - (description "Snappy is a compression/decompression library. It does not + (description "Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; -instead, it aims for very high speeds and reasonable compression. For instance, +instead, it aims for very high speeds and reasonable compression. For instance, compared to the fastest mode of zlib, Snappy is an order of magnitude faster for most inputs, but the resulting compressed files are anywhere from 20% to 100% bigger.") -- cgit v1.2.3 From 8293d21c660a8c210a0fb3fd431e3dc7053f2326 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 21 Feb 2018 04:26:29 +0100 Subject: gnu: java-snappy: Update to 1.1.7. * gnu/packages/compression.scm (java-snappy): Update to 1.1.7. [arguments]: Use INVOKE instead of SYSTEM*. Avoid CMAKE dependency. Delete Hadoop test. Enable fixed test. [native-inputs]: Add JAVA-COMMONS-LANG and JAVA-COMMONS-IO. --- gnu/packages/compression.scm | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index f55f0c2067..423d3989aa 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1133,7 +1133,7 @@ install: libbitshuffle.so (define-public java-snappy (package (name "java-snappy") - (version "1.1.4") + (version "1.1.7") (source (origin (method url-fetch) (uri (string-append "https://github.com/xerial/snappy-java/archive/" @@ -1141,7 +1141,7 @@ install: libbitshuffle.so (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1w58diryma7qz7aa24yv8shf3flxcbbw8jgcn2lih14wgmww58ww")))) + "0q4kxz2n97czf6g5gzq0d8yz22cgiaj7wp51rzsswh3bi99bpgg5")))) (build-system ant-build-system) (arguments `(#:jar-name "snappy.jar" @@ -1181,7 +1181,9 @@ install: libbitshuffle.so (("NAME\\): \\$\\(SNAPPY_OBJ\\)") "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)")) ;; Finally we can run the Makefile to build the dynamic library. - (zero? (system* "make" "native")))) + ;; Use the -nocmake target to avoid a dependency on cmake, + ;; which in turn requires the "git_unpacked" directory. + (invoke "make" "native-nocmake"))) ;; Once we have built the shared library, we need to place it in the ;; "build" directory so it can be added to the jar file. (add-after 'build-jni 'copy-jni @@ -1190,13 +1192,14 @@ install: libbitshuffle.so "build/classes/org/xerial/snappy/native"))) (add-before 'check 'fix-failing (lambda _ - ;; This package assumes maven build, which puts results in "target". - ;; We put them in "build" instead, so fix that. - (substitute* "src/test/java/org/xerial/snappy/SnappyLoaderTest.java" - (("target/classes") "build/classes")) - ;; FIXME: probably an error - (substitute* "src/test/java/org/xerial/snappy/SnappyOutputStreamTest.java" - (("91080") "91013"))))))) + (with-directory-excursion "src/test/java/org/xerial/snappy" + ;; This package assumes maven build, which puts results in "target". + ;; We put them in "build" instead, so fix that. + (substitute* "SnappyLoaderTest.java" + (("target/classes") "build/classes")) + ;; This requires Hadoop, which is not in Guix yet. + (delete-file "SnappyHadoopCompatibleOutputStreamTest.java")) + #t))))) (inputs `(("osgi-framework" ,java-osgi-framework))) (propagated-inputs @@ -1207,6 +1210,8 @@ install: libbitshuffle.so ("hamcrest" ,java-hamcrest-core) ("xerial-core" ,java-xerial-core) ("classworlds" ,java-plexus-classworlds) + ("commons-lang" ,java-commons-lang) + ("commons-io" ,java-commons-io) ("perl" ,perl))) (home-page "https://github.com/xerial/snappy-java") (synopsis "Compression/decompression algorithm in Java") -- cgit v1.2.3 From bbce53c4b3a6576c5a13db39d558331dc0eabd29 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 24 Feb 2018 19:42:36 +0100 Subject: gnu: Add boost@1.66.0. * gnu/packages/boost.scm (boost-1.66): New public variable. --- gnu/packages/boost.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index 91dd2f9156..f4ba82810a 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -110,6 +110,20 @@ across a broad spectrum of applications.") (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt" "Some components have other similar licences.")))) +(define-public boost-1.66 + (package + (inherit boost) + (version "1.66.0") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/boost/boost/" version "/boost_" + (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) + ".tar.bz2")) + (sha256 + (base32 + "1aaw48cmimsskzgiclwn0iifp62a5iw9cbqrhfari876af1828ap")))))) + (define-public mdds (package (name "mdds") -- cgit v1.2.3 From 1568cc14fa7b8f93eb73d21be109b0e5e00cb718 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 24 Feb 2018 19:44:47 +0100 Subject: gnu: Add cmake@3.11. * gnu/packages/cmake.scm (cmake-3.11): New public variable. --- gnu/packages/cmake.scm | 59 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 58 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/cmake.scm b/gnu/packages/cmake.scm index a4e2d38e36..e6c5c4e793 100644 --- a/gnu/packages/cmake.scm +++ b/gnu/packages/cmake.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014 Ian Denhardt ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2017 Marius Bakke +;;; Copyright © 2017, 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -31,6 +31,7 @@ #:use-module (gnu packages) #:use-module (gnu packages backup) #:use-module (gnu packages compression) + #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages file) #:use-module (gnu packages libevent) @@ -149,3 +150,59 @@ and workspaces that can be used in the compiler environment of your choice.") license:bsd-2 ; cmlibarchive license:expat ; cmjsoncpp is dual MIT/public domain license:public-domain)))) ; cmlibarchive/archive_getdate.c + +;; Recent Ceph requires Boost 1.66, which in turn requires CMake 3.11 for +;; its updated "FindBoost.cmake" facility. +(define-public cmake-3.11 + (package + (inherit cmake) + (version "3.11.0-rc2") + (source (origin + (inherit (package-source cmake)) + (uri (string-append "https://www.cmake.org/files/v" + (version-major+minor version) + "/cmake-" version ".tar.gz")) + (sha256 + (base32 + "14p6ais19nfcwl914n4n5rbzaqwafv3qkg6nd8jw54ykn6lz6mf3")) + (snippet + '(begin + ;; Drop bundled software. + (with-directory-excursion "Utilities" + (for-each delete-file-recursively + '("cmbzip2" + "cmcurl" + "cmexpat" + "cmliblzma" + "cmzlib")) + #t))))) + (build-system gnu-build-system) + (arguments + (substitute-keyword-arguments (package-arguments cmake) + ((#:make-flags flags ''()) `(cons (string-append + "ARGS=-j " + (number->string (parallel-job-count)) + " --output-on-failure") + ,flags)) + ((#:phases phases) + `(modify-phases ,phases + (replace 'patch-bin-sh + (lambda _ + (substitute* + '("Modules/CompilerId/Xcode-3.pbxproj.in" + "Modules/CPack.RuntimeScript.in" + "Source/cmakexbuild.cxx" + "Source/cmGlobalXCodeGenerator.cxx" + "Source/cmLocalUnixMakefileGenerator3.cxx" + "Source/cmExecProgramCommand.cxx" + "Utilities/Release/release_cmake.cmake" + "Utilities/cmlibarchive/libarchive/archive_write_set_format_shar.c" + "Tests/CMakeLists.txt" + "Tests/RunCMake/File_Generate/RunCMakeTest.cmake") + (("/bin/sh") (which "sh"))) + #t)) + ;; This is now passed through #:make-flags. + (delete 'set-test-environment))))) + (inputs + `(("rhash" ,rhash) + ,@(package-inputs cmake))))) -- cgit v1.2.3 From 5b0b520e22cc4d8e08078e50e036b093efdde49c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 21 Feb 2018 15:24:00 +0100 Subject: gnu: ceph: Update to 12.2.4. * gnu/packages/patches/ceph-disable-cpu-optimizations.patch: Adjust to upstream changes. * gnu/packages/patches/ceph-disable-unittest-throttle.patch: Delete file. * gnu/packages/patches/ceph-rocksdb-compat.patch: New file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/storage.scm (ceph): Update to 12.2.4. [source](patches): Adjust. [arguments]: Add "-DWITH_BABELTRACE=OFF" in #:configure-flags. Build with CMAKE-3.11. Adjust file substitutions. Wrap 'ceph' executable. [native-inputs]: Add GPERF. [inputs]: Replace BOOST with BOOST-1.66. Add PYTHON2-PRETTYTABLE. --- gnu/local.mk | 2 +- .../patches/ceph-disable-cpu-optimizations.patch | 64 +++++++++------------- .../patches/ceph-disable-unittest-throttle.patch | 52 ------------------ gnu/packages/patches/ceph-rocksdb-compat.patch | 63 +++++++++++++++++++++ gnu/packages/storage.scm | 42 ++++++++------ 5 files changed, 116 insertions(+), 107 deletions(-) delete mode 100644 gnu/packages/patches/ceph-disable-unittest-throttle.patch create mode 100644 gnu/packages/patches/ceph-rocksdb-compat.patch (limited to 'gnu') diff --git a/gnu/local.mk b/gnu/local.mk index 2ef9b68590..d091a89b82 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -581,7 +581,7 @@ dist_patch_DATA = \ %D%/packages/patches/cdparanoia-fpic.patch \ %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch \ %D%/packages/patches/ceph-disable-cpu-optimizations.patch \ - %D%/packages/patches/ceph-disable-unittest-throttle.patch \ + %D%/packages/patches/ceph-rocksdb-compat.patch \ %D%/packages/patches/ceph-skip-collect-sys-info-test.patch \ %D%/packages/patches/ceph-skip-unittest_blockdev.patch \ %D%/packages/patches/chmlib-inttypes.patch \ diff --git a/gnu/packages/patches/ceph-disable-cpu-optimizations.patch b/gnu/packages/patches/ceph-disable-cpu-optimizations.patch index f33eb629d6..421b1d4fe1 100644 --- a/gnu/packages/patches/ceph-disable-cpu-optimizations.patch +++ b/gnu/packages/patches/ceph-disable-cpu-optimizations.patch @@ -1,5 +1,4 @@ -Disable CPU optimizations not supported by all x86_64 systems. Also -don't add anything for i686. +Disable CPU optimizations not supported by all x86_64 systems. --- a/cmake/modules/SIMDExt.cmake 2017-03-23 22:22:58.254071694 +0100 +++ b/cmake/modules/SIMDExt.cmake 2017-03-23 22:23:22.446848845 +0100 @@ -15,39 +14,30 @@ don't add anything for i686. # # SIMD_COMPILE_FLAGS # -@@ -73,7 +68,7 @@ - set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mfpu=neon") - endif() - --elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "i386|i686|amd64|x86_64|AMD64") -+elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64|x86_64|AMD64") - set(HAVE_INTEL 1) - CHECK_C_COMPILER_FLAG(-msse HAVE_INTEL_SSE) - if(HAVE_INTEL_SSE) -@@ -83,26 +78,6 @@ - if(HAVE_INTEL_SSE2) - set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse2") - endif() -- CHECK_C_COMPILER_FLAG(-msse3 HAVE_INTEL_SSE3) -- if(HAVE_INTEL_SSE3) -- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse3") -- endif() -- CHECK_C_COMPILER_FLAG(-mssse3 HAVE_INTEL_SSSE3) -- if(HAVE_INTEL_SSSE3) -- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mssse3") -- endif() -- CHECK_C_COMPILER_FLAG(-mpclmul HAVE_INTEL_PCLMUL) -- if(HAVE_INTEL_PCLMUL) -- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mpclmul") -- endif() -- CHECK_C_COMPILER_FLAG(-msse4.1 HAVE_INTEL_SSE4_1) -- if(HAVE_INTEL_SSE4_1) -- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.1") -- endif() -- CHECK_C_COMPILER_FLAG(-msse4.2 HAVE_INTEL_SSE4_2) -- if(HAVE_INTEL_SSE4_2) -- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.2") -- endif() +@@ -85,26 +80,6 @@ + if(HAVE_INTEL_SSE2) + set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse2") + endif() +- CHECK_C_COMPILER_FLAG(-msse3 HAVE_INTEL_SSE3) +- if(HAVE_INTEL_SSE3) +- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse3") +- endif() +- CHECK_C_COMPILER_FLAG(-mssse3 HAVE_INTEL_SSSE3) +- if(HAVE_INTEL_SSSE3) +- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mssse3") +- endif() +- CHECK_C_COMPILER_FLAG(-mpclmul HAVE_INTEL_PCLMUL) +- if(HAVE_INTEL_PCLMUL) +- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -mpclmul") +- endif() +- CHECK_C_COMPILER_FLAG(-msse4.1 HAVE_INTEL_SSE4_1) +- if(HAVE_INTEL_SSE4_1) +- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.1") +- endif() +- CHECK_C_COMPILER_FLAG(-msse4.2 HAVE_INTEL_SSE4_2) +- if(HAVE_INTEL_SSE4_2) +- set(SIMD_COMPILE_FLAGS "${SIMD_COMPILE_FLAGS} -msse4.2") +- endif() + endif(CMAKE_SYSTEM_PROCESSOR MATCHES "amd64|x86_64|AMD64") + endif(CMAKE_SYSTEM_PROCESSOR MATCHES "i686|amd64|x86_64|AMD64") elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "(powerpc|ppc)64le") - set(HAVE_PPC64LE 1) - message(STATUS " we are ppc64le") diff --git a/gnu/packages/patches/ceph-disable-unittest-throttle.patch b/gnu/packages/patches/ceph-disable-unittest-throttle.patch deleted file mode 100644 index 08ae5f9e24..0000000000 --- a/gnu/packages/patches/ceph-disable-unittest-throttle.patch +++ /dev/null @@ -1,52 +0,0 @@ -FIXME: This test broke after the gcc-5/glibc-2.25 core-updates merge. -Not sure what's going on here, it hangs after spawning the first thread. - -diff --git a/src/test/common/Throttle.cc b/src/test/common/Throttle.cc -index 5b6d73217d..40a477b2a3 100644 ---- a/src/test/common/Throttle.cc -+++ b/src/test/common/Throttle.cc -@@ -216,44 +216,6 @@ TEST_F(ThrottleTest, wait) { - } while(!waited); - } - --TEST_F(ThrottleTest, destructor) { -- Thread_get *t; -- { -- int64_t throttle_max = 10; -- Throttle *throttle = new Throttle(g_ceph_context, "throttle", throttle_max); -- -- ASSERT_FALSE(throttle->get(5)); -- -- t = new Thread_get(*throttle, 7); -- t->create("t_throttle"); -- bool blocked; -- useconds_t delay = 1; -- do { -- usleep(delay); -- if (throttle->get_or_fail(1)) { -- throttle->put(1); -- blocked = false; -- } else { -- blocked = true; -- } -- delay *= 2; -- } while(!blocked); -- delete throttle; -- } -- -- { // -- // The thread is left hanging, otherwise it will abort(). -- // Deleting the Throttle on which it is waiting creates a -- // inconsistency that will be detected: the Throttle object that -- // it references no longer exists. -- // -- pthread_t id = t->get_thread_id(); -- ASSERT_EQ(pthread_kill(id, 0), 0); -- delete t; -- ASSERT_EQ(pthread_kill(id, 0), 0); -- } --} -- - std::pair > test_backoff( - double low_threshhold, - double high_threshhold, diff --git a/gnu/packages/patches/ceph-rocksdb-compat.patch b/gnu/packages/patches/ceph-rocksdb-compat.patch new file mode 100644 index 0000000000..1a3c6b0b23 --- /dev/null +++ b/gnu/packages/patches/ceph-rocksdb-compat.patch @@ -0,0 +1,63 @@ +Fix compatibility with newer versions of RocksDB. + +Adapted from this upstream patch, with some additional changes for 12.2: +https://github.com/ceph/ceph/commit/9d73a7121fdb1ae87cb1aa6f7d9d7a13f329ae68 + +diff --git a/src/kv/RocksDBStore.cc b/src/kv/RocksDBStore.cc +index 8660afe1886d..bc0de79e23cb 100644 +--- a/src/kv/RocksDBStore.cc ++++ b/src/kv/RocksDBStore.cc +@@ -505,7 +505,7 @@ + // considering performance overhead, default is disabled + if (g_conf->rocksdb_perf) { + rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex); +- rocksdb::perf_context.Reset(); ++ rocksdb::get_perf_context()->Reset(); + } + + RocksDBTransactionImpl * _t = +@@ -532,13 +532,13 @@ + utime_t write_wal_time; + utime_t write_pre_and_post_process_time; + write_wal_time.set_from_double( +- static_cast(rocksdb::perf_context.write_wal_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_wal_time)/1000000000); + write_memtable_time.set_from_double( +- static_cast(rocksdb::perf_context.write_memtable_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_memtable_time)/1000000000); + write_delay_time.set_from_double( +- static_cast(rocksdb::perf_context.write_delay_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_delay_time)/1000000000); + write_pre_and_post_process_time.set_from_double( +- static_cast(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000); + logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time); + logger->tinc(l_rocksdb_write_delay_time, write_delay_time); + logger->tinc(l_rocksdb_write_wal_time, write_wal_time); +@@ -558,7 +558,7 @@ + // considering performance overhead, default is disabled + if (g_conf->rocksdb_perf) { + rocksdb::SetPerfLevel(rocksdb::PerfLevel::kEnableTimeExceptForMutex); +- rocksdb::perf_context.Reset(); ++ rocksdb::get_perf_context()->Reset(); + } + + RocksDBTransactionImpl * _t = +@@ -586,13 +586,13 @@ + utime_t write_wal_time; + utime_t write_pre_and_post_process_time; + write_wal_time.set_from_double( +- static_cast(rocksdb::perf_context.write_wal_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_wal_time)/1000000000); + write_memtable_time.set_from_double( +- static_cast(rocksdb::perf_context.write_memtable_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_memtable_time)/1000000000); + write_delay_time.set_from_double( +- static_cast(rocksdb::perf_context.write_delay_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_delay_time)/1000000000); + write_pre_and_post_process_time.set_from_double( +- static_cast(rocksdb::perf_context.write_pre_and_post_process_time)/1000000000); ++ static_cast(rocksdb::get_perf_context()->write_pre_and_post_process_time)/1000000000); + logger->tinc(l_rocksdb_write_memtable_time, write_memtable_time); + logger->tinc(l_rocksdb_write_delay_time, write_delay_time); + logger->tinc(l_rocksdb_write_wal_time, write_wal_time); diff --git a/gnu/packages/storage.scm b/gnu/packages/storage.scm index bee349f6f6..54d91c1f3c 100644 --- a/gnu/packages/storage.scm +++ b/gnu/packages/storage.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2017 Marius Bakke +;;; Copyright © 2017, 2018 Marius Bakke ;;; Copyright © 2017 Rutger Helling ;;; ;;; This file is part of GNU Guix. @@ -29,6 +29,7 @@ #:use-module (gnu packages bdw-gc) #: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 cryptsetup) @@ -36,6 +37,7 @@ #:use-module (gnu packages databases) #:use-module (gnu packages disk) #:use-module (gnu packages gnuzilla) + #:use-module (gnu packages gperf) #:use-module (gnu packages jemalloc) #:use-module (gnu packages linux) #:use-module (gnu packages lua) @@ -50,18 +52,18 @@ (define-public ceph (package (name "ceph") - (version "12.0.2") + (version "12.2.4") (source (origin (method url-fetch) (uri (string-append "https://download.ceph.com/tarballs/ceph-" version ".tar.gz")) (sha256 (base32 - "0l9v072ba28i984y5rwny9i11nmpyx5bl7awxg48plyadm2l3g14")) + "13hv8scaxc1gdvrhzbfnsk4yy3pla6n1i4j4j4zf7schmbf0j8mp")) (patches (search-patches "ceph-skip-unittest_blockdev.patch" "ceph-skip-collect-sys-info-test.patch" - "ceph-disable-unittest-throttle.patch" + "ceph-rocksdb-compat.patch" "ceph-disable-cpu-optimizations.patch")) (modules '((guix build utils))) (snippet @@ -74,7 +76,6 @@ ;"src/xxHash" ;"src/zstd" ;"src/civetweb" - ;"src/Beast" "src/test/downloads" "src/dpdk" "src/spdk" @@ -105,6 +106,7 @@ "-DWITH_SYSTEM_BOOST=ON" "-DWITH_PYTHON3=ON" ;; TODO: Enable these when available in Guix. + "-DWITH_BABELTRACE=OFF" "-DWITH_LTTNG=OFF" "-DWITH_XFS=OFF" "-DWITH_XIO=OFF" @@ -114,6 +116,7 @@ ;; for details. Disable tests until ;; resolved. #:tests? #f + #:cmake ,cmake-3.11 #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-source @@ -152,21 +155,17 @@ (substitute* "src/test/test_subprocess.cc" (("/bin/sh") (which "sh"))) - (substitute* "src/test/ceph_objectstore_tool.py" + (substitute* "qa/standalone/special/ceph_objectstore_tool.py" (("/bin/rm") (which "rm"))) (substitute* "src/ceph-disk/ceph_disk/main.py" (("/bin/mount") "mount") (("/bin/umount") "umount") (("/sbin/blkid") (which "blkid")) + (("'cryptsetup'") (string-append "'" (which "cryptsetup") "'")) (("'sgdisk'") (string-append "'" (which "sgdisk") "'")) (("'parted'") (string-append "'" (which "parted") "'")) (("'udevadm'") (string-append "'" (which "udevadm") "'"))) - (substitute* "src/ceph-disk-udev" - (("/sbin/cryptsetup") (which "cryptsetup")) - (("/usr/sbin/sgdisk") (which "sgdisk")) - (("/usr/sbin/ceph-disk") - (string-append out "/bin/ceph-disk"))) (substitute* "udev/50-rbd.rules" (("/usr/bin/ceph-rbdnamer") (string-append out "/bin/ceph-rbdnamer"))) @@ -263,23 +262,31 @@ (getenv "PYTHONPATH"))) #t))) (add-after 'install 'wrap-python-scripts - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) + (ceph (string-append out "/bin/ceph")) (ceph-disk (string-append out "/bin/ceph-disk")) (ceph-detect-init (string-append out "/bin/ceph-detect-init")) - (PYTHONPATH (string-append - out "/lib/python2.7/site-packages"))) + (prettytable (assoc-ref inputs "python2-prettytable")) + + (sitedir (lambda (package) + (string-append package + "/lib/python2.7/site-packages"))) + (PYTHONPATH (string-append + (sitedir out) ":" + (sitedir prettytable)))) (for-each (lambda (executable) (wrap-program executable `("PYTHONPATH" ":" prefix (,PYTHONPATH)))) - (list ceph-disk ceph-detect-init)) + (list ceph ceph-disk ceph-detect-init)) #t)))))) (outputs '("out" "lib")) (native-inputs - `(("pkg-config" ,pkg-config) + `(("gperf" ,gperf) + ("pkg-config" ,pkg-config) ("python-cython" ,python-cython) ("python-sphinx" ,python-sphinx) ("yasm" ,yasm) @@ -310,7 +317,7 @@ ("python2-testtools" ,python2-testtools) ("python2-tox" ,python2-tox))) (inputs - `(("boost" ,boost) + `(("boost" ,boost-1.66) ("curl" ,curl) ("cryptsetup" ,cryptsetup) ("expat" ,expat) @@ -329,6 +336,7 @@ ("nss" ,nss) ("parted" ,parted) ("python@2" ,python-2) + ("python2-prettytable" ,python2-prettytable) ;used by ceph_daemon.py ("python@3" ,python-3) ("rocksdb" ,rocksdb) ("snappy" ,snappy) -- cgit v1.2.3 From 5275f69e6ea445f7ac7b7c3769bd652f96753817 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 4 Mar 2018 04:40:38 +0100 Subject: gnu: freexl: Update to 1.0.5 [security fixes]. Fixes CVE-2018-7435, CVE-2018-7436, CVE-2018-7437, CVE-2018-7438 and CVE-2018-7439. * gnu/packages/xml.scm (freexl): Update to 1.0.5. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index add374c899..eabd28233a 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -1249,14 +1249,14 @@ libxls cannot write Excel files.") (define-public freexl (package (name "freexl") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (string-append "http://www.gaia-gis.it/gaia-sins/" name "-" version ".tar.gz")) (sha256 (base32 - "09bwzqjc41cc8qw8qkw9wq58rg9nax8r3fg19iny5vmw1c0z23sh")))) + "03bmwq6hngmzwpqpb7c2amqlspz4q69iv96nlf0f5c0qs98b3j9x")))) (build-system gnu-build-system) (home-page "https://www.gaia-gis.it/fossil/freexl/index") (synopsis "Read Excel files") -- cgit v1.2.3 From 3e57b7d99b49472470ca1134c4e6e1f7d334361e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 4 Mar 2018 05:54:48 +0100 Subject: gnu: multipath-tools: Update to 0.7.4. * gnu/packages/linux.scm (multipath-tools): Update to 0.7.4. [source]: Download using HTTPS. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 1f9e084e85..2c3a1a84c2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2864,15 +2864,15 @@ arrays when needed.") (define-public multipath-tools (package (name "multipath-tools") - (version "0.7.1") + (version "0.7.4") (source (origin (method url-fetch) - (uri (string-append "http://git.opensvc.com/?p=multipath-tools/" + (uri (string-append "https://git.opensvc.com/?p=multipath-tools/" ".git;a=snapshot;h=" version ";sf=tgz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0w0rgi3lqksaki30yvd4l5rgjqb0d7js1sh7masl8aw6xbrsm26p")) + "02lk453wa2gfxkl8zmdws15nkcibln2yw76zm779pkngkhggl6w8")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 03b71957947c219a74b77b0831d9abc8d4bbfd24 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sat, 3 Mar 2018 23:17:04 +0100 Subject: gnu: liblo: Mark up description. * gnu/packages/audio.scm (liblo)[description]: Use @dfn. --- gnu/packages/audio.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3ae2b1ba47..d8569096ab 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1646,7 +1646,7 @@ essential distortions.") (synopsis "Implementation of the Open Sound Control protocol") (description "liblo is a lightweight library that provides an easy to use -implementation of the Open Sound Control (OSC) protocol.") +implementation of the Open Sound Control (@dfn{OSC}) protocol.") (license license:lgpl2.1+))) (define-public python-pyaudio -- cgit v1.2.3 From 95943ed7dca205e81c22cd0723a3ab1ba67d4040 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 01:09:57 +0100 Subject: gnu: cloc: Update to 1.76. * gnu/packages/code.scm (cloc): Update to 1.76. [source]: Update origin URI scheme. [inputs]: Add perl-parallel-forkmanager. --- gnu/packages/code.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 2067067f20..4a63cba7a0 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -204,23 +204,24 @@ COCOMO model or user-provided parameters.") (define-public cloc (package (name "cloc") - (version "1.74") + (version "1.76") (source (origin (method url-fetch) (uri (string-append - "https://github.com/AlDanial/cloc/releases/download/" version + "https://github.com/AlDanial/cloc/releases/download/v" version "/cloc-" version ".tar.gz")) (sha256 (base32 - "0rq5xfiln1wlv3yr9mg18ax4gskbss786iqaf0v45iv6awyl5b2m")))) + "05srlvzwisr7y7ymvzb5yfdsrspja27ysqdmkwhiiivy84mq2gnl")))) (build-system gnu-build-system) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) ("perl-algorithm-diff" ,perl-algorithm-diff) - ("perl-regexp-common" ,perl-regexp-common) - ("perl-digest-md5" ,perl-digest-md5))) + ("perl-digest-md5" ,perl-digest-md5) + ("perl-parallel-forkmanager" ,perl-parallel-forkmanager) + ("perl-regexp-common" ,perl-regexp-common))) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) -- cgit v1.2.3 From 53244d1ffa544305d4b6c19907dfcaf2bff2fd21 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 01:11:47 +0100 Subject: gnu: cloc: Update phase style. * gnu/packages/code.scm (cloc)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/code.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index 4a63cba7a0..8d9c661302 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -229,13 +229,13 @@ COCOMO model or user-provided parameters.") (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out"))) - (zero? - (system* "make" "-C" "Unix" - (string-append "prefix=" out) - (string-append "INSTALL=" - (assoc-ref inputs "coreutils") - "/bin/install") - "install"))))) + (invoke "make" "-C" "Unix" + (string-append "prefix=" out) + (string-append "INSTALL=" + (assoc-ref inputs "coreutils") + "/bin/install") + "install") + #t))) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) -- cgit v1.2.3 From e0dbead5a73ffc666af38e044bb48ca94f261794 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 01:26:07 +0100 Subject: gnu: ii: Update to 1.8. * gnu/packages/irc.scm (ii): Update to 1.8. --- gnu/packages/irc.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index b00fd6cc19..3521b18dcd 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 ng0 ;;; Copyright © 2017 Marius Bakke -;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -272,22 +272,22 @@ using a mouse. It is customizable and extensible with plugins and scripts.") (define-public ii (package (name "ii") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (string-append "http://dl.suckless.org/tools/" name "-" version ".tar.gz")) (sha256 (base32 - "176cqwnn6h7w4kbfd66hzqa243l26pqp2b06bii0nmnm0rkaqwis")))) + "1lk8vjl7i8dcjh4jkg8h8bkapcbs465sy8g9c0chfqsywbmf3ndr")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; no tests + `(#:tests? #f ; no tests #:make-flags (list (string-append "PREFIX=" %output) "CC=gcc") #:phases (modify-phases %standard-phases - (delete 'configure)))) ; no configure + (delete 'configure)))) ; no configure (home-page "http://tools.suckless.org/ii/") (synopsis "FIFO and file system based IRC client") (description -- cgit v1.2.3 From d035eaa3049d58314680a3b10acbe832ca1ed22f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 01:27:15 +0100 Subject: gnu: ii, sic: Use HTTPS home pages. * gnu/packages/irc.scm (ii, sic)[home-page]: Use HTTPS. --- gnu/packages/irc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 3521b18dcd..e59b34417b 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -288,7 +288,7 @@ using a mouse. It is customizable and extensible with plugins and scripts.") #:phases (modify-phases %standard-phases (delete 'configure)))) ; no configure - (home-page "http://tools.suckless.org/ii/") + (home-page "https://tools.suckless.org/ii/") (synopsis "FIFO and file system based IRC client") (description "ii (Irc it) is a minimalist FIFO and file system based IRC client.") @@ -313,7 +313,7 @@ using a mouse. It is customizable and extensible with plugins and scripts.") #:phases (modify-phases %standard-phases (delete 'configure)))) ; no configure - (home-page "http://tools.suckless.org/sic/") + (home-page "https://tools.suckless.org/sic/") (synopsis "Simple IRC client") (description "sic is a simple IRC client, even more minimalistic than ii.") -- cgit v1.2.3 From 7730b7179c615319cf038f4d83939dc9bbe7b750 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 16:56:27 +0100 Subject: gnu: gitolite: Update to 3.6.7. * gnu/packages/version-control.scm (gitolite): Update to 3.6.7. --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 05f50869a3..f6b346fff8 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -928,7 +928,7 @@ also walk each side of a merge and test those changes individually.") (define-public gitolite (package (name "gitolite") - (version "3.6.6") + (version "3.6.7") (source (origin (method url-fetch) (uri (string-append @@ -937,7 +937,7 @@ also walk each side of a merge and test those changes individually.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "07q33f86694s0x3k9lcmy1vzfw9appdrlmmb9j3bz4qkrxqdnwb9")))) + "1idxipg0df80bhjcxgwxs3lllqnkvhwpinmfv1xvg1l98fxiapgp")))) (build-system gnu-build-system) (arguments '(#:tests? #f ; no tests -- cgit v1.2.3 From 92793c7b0287558becefeaa4832ebcb16e34a243 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 16:57:01 +0100 Subject: gnu: gitolite: Update phase style. * gnu/packages/version-control.scm (gitolite): Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/version-control.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index f6b346fff8..209df2bb12 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -958,7 +958,8 @@ also walk each side of a merge and test those changes individually.") ;; This works because gitolite-shell is in the PATH. (substitute* "src/triggers/post-compile/ssh-authkeys" (("\\$glshell \\$user") - "gitolite-shell $user"))))) + "gitolite-shell $user")) + #t))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((output (assoc-ref outputs "out")) @@ -966,7 +967,7 @@ also walk each side of a merge and test those changes individually.") (bindir (string-append output "/bin"))) (mkdir-p sharedir) (mkdir-p bindir) - (system* "./install" "-to" sharedir) + (invoke "./install" "-to" sharedir) ;; Create symlinks for executable scripts in /bin. (for-each (lambda (script) (symlink (string-append sharedir "/" script) -- cgit v1.2.3 From bd128d5e880ba73ce217e864f1cce6fe1b655ff1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:06:10 +0100 Subject: gnu: footswitch: Remove redundant MKDIR-P. * gnu/packages/accessibility.scm (footswitch)[arguments]: Remove MKDIR-P before INSTALL-FILE. --- gnu/packages/accessibility.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm index 2ca4e27f81..53ea99739b 100644 --- a/gnu/packages/accessibility.scm +++ b/gnu/packages/accessibility.scm @@ -109,7 +109,6 @@ available to help to click.") (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) (install-file "footswitch" bin) #t)))))) (home-page "https://github.com/rgerganov/footswitch") -- cgit v1.2.3 From ed36949a9d0e5fd5582cc85e533c1ef8a8b2543e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:09:27 +0100 Subject: gnu: footswitch: Update to 0.1-2.deedd87. * gnu/packages/accessibility.scm (footswitch): Update to 0.1-2.deedd87. --- gnu/packages/accessibility.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/accessibility.scm b/gnu/packages/accessibility.scm index 53ea99739b..f2cbfc480b 100644 --- a/gnu/packages/accessibility.scm +++ b/gnu/packages/accessibility.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Stefan Reichör +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -82,10 +83,11 @@ available to help to click.") (license license:gpl2+))) (define-public footswitch - (let ((commit "7cb0a9333a150c27c7e4746ee827765d244e567a")) + (let ((commit "deedd87fd90fad90ce342aeabafd4a3198d7d3d4") + (revision "2")) (package (name "footswitch") - (version (git-version "0.1" "1" commit)) + (version (git-version "0.1" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -93,7 +95,7 @@ available to help to click.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "0mg1vr4a9vls5y435w7wdnr1vb5059gy60lvrdfjgzhd2wwf47iw")))) + (base32 "1ys90wqyz62kffa8m3hgaq1dl7f29x3mrc3zqfjrkbn2ps0k6ps0")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 9539016e3addb4bd5b4adfab27334131a532a11c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 00:33:28 +0100 Subject: gnu: tomb: Use HTTPS home page. * gnu/packages/crypto.scm (tomb)[home-page]: Use HTTPS. --- gnu/packages/crypto.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 695f6ca088..7cac132b64 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -412,7 +412,7 @@ no man page, refer to the home page for usage details.") (let ((tomb (string-append (assoc-ref outputs "out") "/bin/tomb"))) (zero? (system* tomb "dig" "-s" "10" "secrets.tomb")))))))) - (home-page "http://www.dyne.org/software/tomb") + (home-page "https://www.dyne.org/software/tomb") (synopsis "File encryption for secret data") (description "Tomb is an application to manage the creation and access of encrypted -- cgit v1.2.3 From 635dd0cc96a5d06933a52a48bb9520efbd567550 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 00:37:59 +0100 Subject: gnu: tomb: Update phase style. * gnu/packages/crypto.scm (tomb)[arguments]: Substitute INVOKE for SYSTEM* and end phases with #t. --- gnu/packages/crypto.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 7cac132b64..b498aabf4d 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -384,9 +384,9 @@ no man page, refer to the home page for usage details.") (delete 'configure) ;no configuration to be done (add-after 'install 'i18n (lambda* (#:key make-flags #:allow-other-keys) - (zero? (apply system* - "make" "-C" "extras/translations" - "install" make-flags)))) + (apply invoke "make" "-C" "extras/translations" + "install" make-flags) + #t)) (add-after 'install 'wrap (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -411,7 +411,8 @@ no man page, refer to the home page for usage details.") ;; querying `tomb -h`. (let ((tomb (string-append (assoc-ref outputs "out") "/bin/tomb"))) - (zero? (system* tomb "dig" "-s" "10" "secrets.tomb")))))))) + (invoke tomb "dig" "-s" "10" "secrets.tomb") + #t)))))) (home-page "https://www.dyne.org/software/tomb") (synopsis "File encryption for secret data") (description -- cgit v1.2.3 From ac1a9ce8b07f3b80900ee08436ff6e683e8dc195 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:20:03 +0100 Subject: gnu: papi: Update phase style. * gnu/packages/profiling.scm (papi)[arguments]: Substitute INVOKE for SYSTEM*, end phases with #t, and don't explicitly install LICENSE.txt. --- gnu/packages/profiling.scm | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm index 4fdf260c67..35f9d3884f 100644 --- a/gnu/packages/profiling.scm +++ b/gnu/packages/profiling.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Dave Love +;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -84,7 +85,8 @@ stealtime lmsensors infiniband powercap" (add-before 'configure 'autoconf (lambda _ (chdir "src") - (zero? (system* "autoconf")))) + (invoke "autoconf") + #t)) ;; Amalgamating with the following clause gives double substitution. (add-before 'patch-source-shebangs 'patch-components (lambda _ @@ -95,26 +97,24 @@ stealtime lmsensors infiniband powercap" (add-after 'configure 'components (lambda* (#:key inputs #:allow-other-keys) (with-directory-excursion "components" - (and - (with-directory-excursion "infiniband_umad" - (zero? (system* "./configure"))) - (with-directory-excursion "lmsensors" - (let ((base (assoc-ref inputs "lm-sensors"))) - (zero? - (system* - "./configure" - (string-append "--with-sensors_incdir=" base - "/include/sensors") - (string-append "--with-sensors_libdir=" base "/lib"))))))))) + (with-directory-excursion "infiniband_umad" + (invoke "./configure")) + (with-directory-excursion "lmsensors" + (let ((base (assoc-ref inputs "lm-sensors"))) + (invoke "./configure" + (string-append "--with-sensors_incdir=" + base "/include/sensors") + (string-append "--with-sensors_libdir=" + base "/lib"))))) + #t)) (add-after 'install 'extra-doc (lambda* (#:key outputs #:allow-other-keys) (let ((doc (string-append (assoc-ref outputs "out") "/share/doc"))) - (mkdir-p doc) (chdir "..") ; we went into src above (for-each (lambda (file) (install-file file doc)) - '("README" "RELEASENOTES.txt" "LICENSE.txt")) + '("README" "RELEASENOTES.txt")) #t)))))) (home-page "http://icl.cs.utk.edu/papi/") (synopsis "Performance Application Programming Interface") -- cgit v1.2.3 From 16718b6776b6cb918cddb3abb3bfcf2405b0b297 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 28 Nov 2017 10:19:11 +0200 Subject: services: Add openntpd service. * gnu/packages/ntp.scm (openntpd)[arguments]: Add 'configure-flags to set openntpd daemon's user and localstatedir. Add a custom phase to not try to create said directory at install time. * gnu/services/networking.scm (): New record type. (openntpd-shepherd-service, openntpd-service-activation): New procedures. (openntpd-service-type): New variable. * doc/guix.texi (Networking Services): Add openntpd documentation. --- doc/guix.texi | 55 +++++++++++++++++++++++- gnu/packages/ntp.scm | 13 +++++- gnu/services/networking.scm | 102 +++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 167 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index 057272df46..60703875f6 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -24,7 +24,7 @@ Copyright @copyright{} 2015, 2016, 2017 Leo Famulari@* Copyright @copyright{} 2015, 2016, 2017, 2018 Ricardo Wurmus@* Copyright @copyright{} 2016 Ben Woodcroft@* Copyright @copyright{} 2016, 2017 Chris Marusich@* -Copyright @copyright{} 2016, 2017 Efraim Flashner@* +Copyright @copyright{} 2016, 2017, 2018 Efraim Flashner@* Copyright @copyright{} 2016 John Darrington@* Copyright @copyright{} 2016, 2017 ng0@* Copyright @copyright{} 2016, 2017 Jan Nieuwenhuizen@* @@ -10767,6 +10767,59 @@ make an initial adjustment of more than 1,000 seconds. List of host names used as the default NTP servers. @end defvr +@cindex OpenNTPD +@deffn {Scheme Procedure} openntpd-service-type +Run the @command{ntpd}, the Network Time Protocol (NTP) daemon, as implemented +by @uref{http://www.openntpd.org, OpenNTPD}. The daemon will keep the system +clock synchronized with that of the given servers. + +@example +(service + openntpd-service-type + (openntpd-configuration + (listen-on '("127.0.0.1" "::1")) + (sensor '("udcf0 correction 70000")) + (constraint-from '("www.gnu.org")) + (constraints-from '("https://www.google.com/")) + (allow-large-adjustment? #t))) + +@end example +@end deffn + +@deftp {Data Type} openntpd-configuration +@table @asis +@item @code{openntpd} (default: @code{(file-append openntpd "/sbin/ntpd")}) +The openntpd executable to use. +@item @code{listen-on} (default: @code{'("127.0.0.1" "::1")}) +A list of local IP addresses or hostnames the ntpd daemon should listen on. +@item @code{query-from} (default: @code{'()}) +A list of local IP address the ntpd daemon should use for outgoing queries. +@item @code{sensor} (default: @code{'()}) +Specify a list of timedelta sensor devices ntpd should use. @code{ntpd} +will listen to each sensor that acutally exists and ignore non-existant ones. +See @uref{https://man.openbsd.org/ntpd.conf, upstream documentation} for more +information. +@item @code{server} (default: @var{%ntp-servers}) +Specify a list of IP addresses or hostnames of NTP servers to synchronize to. +@item @code{servers} (default: @code{'()}) +Specify a list of IP addresses or hostnames of NTP pools to synchronize to. +@item @code{constraint-from} (default: @code{'()}) +@code{ntpd} can be configured to query the ‘Date’ from trusted HTTPS servers via TLS. +This time information is not used for precision but acts as an authenticated +constraint, thereby reducing the impact of unauthenticated NTP +man-in-the-middle attacks. +Specify a list of URLs, IP addresses or hostnames of HTTPS servers to provide +a constraint. +@item @code{constraints-from} (default: @code{'()}) +As with constraint from, specify a list of URLs, IP addresses or hostnames of +HTTPS servers to provide a constraint. Should the hostname resolve to multiple +IP addresses, @code{ntpd} will calculate a median constraint from all of them. +@item @code{allow-large-adjustment?} (default: @code{#f}) +Determines if @code{ntpd} is allowed to make an initial adjustment of more +than 180 seconds. +@end table +@end deftp + @cindex inetd @deffn {Scheme variable} inetd-service-type This service runs the @command{inetd} (@pxref{inetd invocation,,, diff --git a/gnu/packages/ntp.scm b/gnu/packages/ntp.scm index d270f513dc..1c3b8cd313 100644 --- a/gnu/packages/ntp.scm +++ b/gnu/packages/ntp.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer ;;; Copyright © 2015 Ludovic Courtès -;;; Copyright © 2016, 2017 Efraim Flashner +;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -107,6 +107,17 @@ computers over a network.") (base32 "0fn12i4kzsi0zkr4qp3dp9bycmirnfapajqvdfx02zhr4hanj0kv")))) (build-system gnu-build-system) + (arguments + '(#:configure-flags '("--with-privsep-user=ntpd" + "--localstatedir=/var") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'modify-install-locations + (lambda _ + ;; Don't try to create /var/run or /var/db + (substitute* "src/Makefile.in" + (("DESTDIR\\)\\$\\(localstatedir") "TMPDIR")) + #t))))) (inputs `(("libressl" ,libressl))) ; enable TLS time constraints. See ntpd.conf(5). (home-page "http://www.openntpd.org/") diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 5ba3c5eed6..6ac440fd26 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2016 John Darrington ;;; Copyright © 2017 Clément Lassieur ;;; Copyright © 2017 Thomas Danckaert @@ -64,6 +64,10 @@ ntp-service ntp-service-type + openntpd-configuration + openntpd-configuration? + openntpd-service-type + inetd-configuration inetd-entry inetd-service-type @@ -446,6 +450,102 @@ make an initial adjustment of more than 1,000 seconds." (allow-large-adjustment? allow-large-adjustment?)))) + +;;; +;;; OpenNTPD. +;;; + +(define-record-type* + openntpd-configuration make-openntpd-configuration + openntpd-configuration? + (openntpd openntpd-configuration-openntpd + (default openntpd)) + (listen-on openntpd-listen-on + (default '("127.0.0.1" + "::1"))) + (query-from openntpd-query-from + (default '())) + (sensor openntpd-sensor + (default '())) + (server openntpd-server + (default %ntp-servers)) + (servers openntpd-servers + (default '())) + (constraint-from openntpd-constraint-from + (default '())) + (constraints-from openntpd-constraints-from + (default '())) + (allow-large-adjustment? openntpd-allow-large-adjustment? + (default #f))) ; upstream default + +(define (openntpd-shepherd-service config) + (match-record config + (openntpd listen-on query-from sensor server servers constraint-from + constraints-from allow-large-adjustment?) + (let () + (define config + (string-join + (filter-map + (lambda (field value) + (string-join + (map (cut string-append field <> "\n") + value))) + '("listen on " "query from " "sensor " "server " "servers " + "constraint from ") + (list listen-on query-from sensor server servers constraint-from)) + ;; The 'constraints from' field needs to be enclosed in double quotes. + (string-join + (map (cut string-append "constraints from \"" <> "\"\n") + constraints-from)))) + + (define ntpd.conf + (plain-file "ntpd.conf" config)) + + (list (shepherd-service + (provision '(ntpd)) + (documentation "Run the Network Time Protocol (NTP) daemon.") + (requirement '(user-processes networking)) + (start #~(make-forkexec-constructor + (list (string-append #$openntpd "/sbin/ntpd") + "-f" #$ntpd.conf + "-d" ;; don't daemonize + #$@(if allow-large-adjustment? + '("-s") + '())) + ;; When ntpd is daemonized it repeatedly tries to respawn + ;; while running, leading shepherd to disable it. To + ;; prevent spamming stderr, redirect output to logfile. + #:log-file "/var/log/ntpd")) + (stop #~(make-kill-destructor))))))) + +(define (openntpd-service-activation config) + "Return the activation gexp for CONFIG." + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + + (mkdir-p "/var/db") + (mkdir-p "/var/run") + (unless (file-exists? "/var/db/ntpd.drift") + (with-output-to-file "/var/db/ntpd.drift" + (lambda _ + (format #t "0.0"))))))) + +(define openntpd-service-type + (service-type (name 'openntpd) + (extensions + (list (service-extension shepherd-root-service-type + openntpd-shepherd-service) + (service-extension account-service-type + (const %ntp-accounts)) + (service-extension activation-service-type + openntpd-service-activation))) + (default-value (openntpd-configuration)) + (description + "Run the @command{ntpd}, the Network Time Protocol (NTP) +daemon, as implemented by @uref{http://www.openntpd.org, OpenNTPD}. The +daemon will keep the system clock synchronized with that of the given servers."))) + ;;; ;;; Inetd. -- cgit v1.2.3 From dc97f7e20e880f594cf2c9a16b4a1859469b9df5 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 18 Jan 2018 22:37:59 +0000 Subject: gnu: Add emacs-hcl-mode. * gnu/packages/emacs.scm (emacs-hcl-mode): New variable. --- gnu/packages/emacs.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 69950cc6d7..646aee7ba4 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7313,3 +7313,26 @@ Features: (description "@code{epipe} provides an utility to use your editor in the pipeline, featuring the support for running @code{emacsclient}.") (license license:gpl3+))) + +(define-public emacs-hcl-mode + (package + (name "emacs-hcl-mode") + (version "0.03") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/syohex/emacs-hcl-mode/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0pvw74qpwh0znqzp6syp4wxjqs7dp1hbn5h7xfk97mff9l5d8k6x")))) + (build-system emacs-build-system) + (home-page "https://github.com/syohex/emacs-hcl-mode") + (synopsis "Major mode for the Hashicorp Configuration Language") + (description + "@code{emacs-hcl-mode} provides an Emacs major mode for working with +@acronym{HCL, Hashicorp Configuration Language}. It provides syntax +highlighting and indentation support.") + (license license:gpl3+))) -- cgit v1.2.3 From 68d70f6ae31865bba73a655e212f1cdf999d6225 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 18 Jan 2018 22:38:12 +0000 Subject: gnu: Add emacs-terraform-mode. * gnu/packages/emacs.scm (emacs-terraform-mode): New variable. --- 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 646aee7ba4..54eb816c15 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7336,3 +7336,28 @@ the pipeline, featuring the support for running @code{emacsclient}.") @acronym{HCL, Hashicorp Configuration Language}. It provides syntax highlighting and indentation support.") (license license:gpl3+))) + +(define-public emacs-terraform-mode + (package + (name "emacs-terraform-mode") + (version "0.06") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/syohex/emacs-terraform-mode/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0h9267ifdjmcin4sj8slxydbacx4bqicbvg8pa1qq2l72h9m5381")))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-hcl-mode" ,emacs-hcl-mode))) + (home-page "https://github.com/syohex/emacs-terraform-mode") + (synopsis "Major mode for Terraform") + (description + "@code{emacs-terraform-mode} provides a major mode for working with +@uref{https://www.terraform.io/, Terraform} configuration files. Most of the +functionality is inherited from @code{hcl-mode}.") + (license license:gpl3+))) -- cgit v1.2.3 From 88b1a38e26644308cd0a53ce988cf6b344ae445d Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 5 Mar 2018 03:42:07 -0500 Subject: gnu: linux-libre@4.4: Update to 4.4.120. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.120. --- 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 2c3a1a84c2..02fa9b3249 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -408,8 +408,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.119" - "1cicg1yxf6rvaz8jcz8mdvnkrba9hd16pkp9mm602bzgks6s1fy9" + (make-linux-libre "4.4.120" + "17zk5dbpa3kilf8m8i6r2jifjgi4yjim42gyk9j6n4218jjcszv6" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From ee483a5626ef695320ef2d5d57db4dd99da98a88 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 5 Mar 2018 03:43:02 -0500 Subject: gnu: linux-libre@4.9: Update to 4.9.86. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.86. --- 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 02fa9b3249..e1ec8c0060 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -402,8 +402,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.85" - "17anlawvbzw6m2lrbriy7kfncdllkl7n8vjzwl2dnrgxddavd3rf" + (make-linux-libre "4.9.86" + "0fqixx3yyvznianygk8bfxzfqj8zpnjcalifhpfyb7rm3dyvi3wd" %intel-compatible-systems #:configuration-file kernel-config)) -- cgit v1.2.3 From 6a4eaafee06c167f5628ce06b7834d4a249a3600 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 5 Mar 2018 03:43:45 -0500 Subject: gnu: linux-libre@4.14: Update to 4.14.24. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.24. (%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 e1ec8c0060..d4b9d0d0b9 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 "4.14.23") -(define %linux-libre-4.14-hash "0mz8v67zj3wn3kdjb2a781vx7nc1imi7kmlvf1h1m0f37hw0s47y") +(define %linux-libre-4.14-version "4.14.24") +(define %linux-libre-4.14-hash "1i14djw3rmxb6syl6vfd5w76rjksbbaviynwj2dwwp9ki1h6p1hr") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version -- cgit v1.2.3 From 0ebc1b934d39b6c924cbe17fd37ceb2b201e9ac2 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Mon, 5 Mar 2018 12:28:34 +0100 Subject: gnu: xpra: Update to 2.2.5. * gnu/packages/xorg.scm (xpra): Update to 2.2.5. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index a7099b4516..b73d7d6cd2 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5944,7 +5944,7 @@ basic eye-candy effects.") (define-public xpra (package (name "xpra") - (version "2.2.4") + (version "2.2.5") (source (origin (method url-fetch) @@ -5952,7 +5952,7 @@ basic eye-candy effects.") version ".tar.xz")) (sha256 (base32 - "0v8yflvisk94bfj0zg4ggdfwrig0f3ss9kjnws3zflsr33cb2hxy")))) + "1q2l00nc3bgwlhjzkbk4a8x2l8z9w1799yn31icsx5hrgh98a1js")))) (build-system python-build-system) (inputs `(("ffmpeg" ,ffmpeg) ("flac" ,flac) -- cgit v1.2.3 From f7c870f78afa5cdb27726ad9b0db931bbd87ca65 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:28:37 +0100 Subject: gnu: papi: Fix documentation location. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/profiling.scm (papi)[arguments]: Install ‘documentation’ to a customary subdirectory of /share/doc. --- gnu/packages/profiling.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm index 35f9d3884f..e70269e9a1 100644 --- a/gnu/packages/profiling.scm +++ b/gnu/packages/profiling.scm @@ -66,7 +66,7 @@ `(("autoconf" ,autoconf) ("gfortran" ,gfortran))) (arguments - '(#:tests? #f ; no check target + `(#:tests? #f ; no check target #:configure-flags ;; These are roughly per Fedora, but elide mx (assumed to be dead, even ;; Open-MX) and add and powercap -- I don't know the pros/cons of @@ -110,7 +110,7 @@ stealtime lmsensors infiniband powercap" (add-after 'install 'extra-doc (lambda* (#:key outputs #:allow-other-keys) (let ((doc (string-append (assoc-ref outputs "out") - "/share/doc"))) + "/share/doc/" ,name "-" ,version))) (chdir "..") ; we went into src above (for-each (lambda (file) (install-file file doc)) -- cgit v1.2.3 From 211748d4754f26a56655bea5dfcecc79ac9667c2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:16:46 +0100 Subject: gnu: papi: Use HTTPS home page. * gnu/packages/profiling.scm (papi)[home-page]: Use HTTPS. --- gnu/packages/profiling.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/profiling.scm b/gnu/packages/profiling.scm index e70269e9a1..d6f3aede28 100644 --- a/gnu/packages/profiling.scm +++ b/gnu/packages/profiling.scm @@ -116,7 +116,7 @@ stealtime lmsensors infiniband powercap" (install-file file doc)) '("README" "RELEASENOTES.txt")) #t)))))) - (home-page "http://icl.cs.utk.edu/papi/") + (home-page "https://icl.utk.edu/papi/") (synopsis "Performance Application Programming Interface") (description "PAPI provides the tool designer and application engineer with a consistent -- cgit v1.2.3 From 0d34993a6579d294cad4fad667b0c2a0b8173d06 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:32:56 +0100 Subject: gnu: openvpn: Update to 2.4.5. * gnu/packages/vpn.scm (openvpn): Update to 2.4.5. --- gnu/packages/vpn.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 952f12ce55..8dd3333eea 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -241,7 +241,7 @@ and probably others.") (define-public openvpn (package (name "openvpn") - (version "2.4.4") + (version "2.4.5") (source (origin (method url-fetch) (uri (string-append @@ -249,7 +249,7 @@ and probably others.") version ".tar.xz")) (sha256 (base32 - "102an395nv8l7qfx3syydzhmd9xfbycd6gvwy0h2kjz8w67ipkcn")))) + "17njq59hsraqyxrbhkrxr7dvx0p066s3pn8w1mi0yd9jldis7h23")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-iproute2=yes"))) -- cgit v1.2.3 From 9599339c5982d0c446d04c1c1c7baef319ee6421 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 4 Mar 2018 17:33:56 +0100 Subject: gnu: openvpn: Mark up description. * gnu/packages/vpn.scm (openvpn)[description]: Use @dfn. --- gnu/packages/vpn.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 8dd3333eea..642ca1c044 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -262,11 +262,12 @@ and probably others.") ("linux-pam" ,linux-pam))) (home-page "https://openvpn.net/") (synopsis "Virtual private network daemon") - (description "OpenVPN implements virtual private network (VPN) techniques + (description + "OpenVPN implements virtual private network (@dfn{VPN}) techniques for creating secure point-to-point or site-to-site connections in routed or bridged configurations and remote access facilities. It uses a custom security protocol that utilizes SSL/TLS for key exchange. It is capable of -traversing network address translators (NATs) and firewalls.") +traversing network address translators (@dfn{NAT}s) and firewalls.") (license license:gpl2))) (define-public tinc -- cgit v1.2.3 From 530df311ac0f04d5bddf2d538d060440b9850cd1 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 00:03:17 +0100 Subject: gnu: perl-www-mechanize: Update to 1.87. * gnu/packages/web.scm (perl-www-mechanize): Update to 1.87. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 23bcc5fb1c..07e4a1ad93 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3657,7 +3657,7 @@ library.") (define-public perl-www-mechanize (package (name "perl-www-mechanize") - (version "1.86") + (version "1.87") (source (origin (method url-fetch) @@ -3665,7 +3665,7 @@ library.") "WWW-Mechanize-" version ".tar.gz")) (sha256 (base32 - "0sfl6b7mx8nannnh3ys5jk44d1s1b2d1mffrnrphkzzykaw6hm0f")))) + "1kxrydhl7nxlyjv0xvyiyj4igdv4fwnggv0ihlp79bysbjjl54w1")))) (build-system perl-build-system) (native-inputs ;only for tests `(("perl-cgi" ,perl-cgi) -- cgit v1.2.3 From 55b7cd10c28934aaea144c06e5d4a8bb8b88bfbb Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 00:04:17 +0100 Subject: gnu: perl-io-socket-ip: Update to 0.39. * gnu/packages/web.scm (perl-io-socket-ip): Update to 0.39. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 07e4a1ad93..cfae9f9253 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -2933,7 +2933,7 @@ algorithm specified in section 8.2.2.1 of the draft standard.") (define-public perl-io-socket-ip (package (name "perl-io-socket-ip") - (version "0.38") + (version "0.39") (source (origin (method url-fetch) @@ -2941,7 +2941,7 @@ algorithm specified in section 8.2.2.1 of the draft standard.") "IO-Socket-IP-" version ".tar.gz")) (sha256 (base32 - "0scsnahxwnymg80a3k0p0cnr574nk7x9inn9wjniz0iycicclyhb")))) + "15kv5g1yb4a345sk3r5wfr99f868lhfqkddzsgpqddvccfkhv58i")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build))) (home-page "http://search.cpan.org/dist/IO-Socket-IP") -- cgit v1.2.3 From cc7a4bbd27a9d55e3c942d95ae9cfcf8157e401c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 00:30:42 +0100 Subject: gnu: tocc, libtocc: Use HTTPS home page. * gnu/packages/search.scm (libtocc, tocc)[home-page]: Use HTTPS. --- gnu/packages/search.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm index 1479d1bbbb..a719819927 100644 --- a/gnu/packages/search.scm +++ b/gnu/packages/search.scm @@ -137,7 +137,7 @@ rich set of boolean query operators.") "-Wl,-rpath=../src/.libs"))) (zero? (system* "make")) (zero? (system* "./libtocctests"))))))))) - (home-page "http://t-o-c-c.com/") + (home-page "https://t-o-c-c.com/") (synopsis "Tool for Obsessive Compulsive Classifiers") (description "libtocc is the engine of the Tocc project, a tag-based file management @@ -161,7 +161,7 @@ files and directories.") (add-after 'unpack 'chdir-source (lambda _ (chdir "cli/src")))))) - (home-page "http://t-o-c-c.com/") + (home-page "https://t-o-c-c.com/") (synopsis "Command-line interface to libtocc") (description "Tocc is a tag-based file management system. This package contains the -- cgit v1.2.3 From 437e5fae131d147e1b0675e5f9df9fc17439816d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 15:23:28 +0100 Subject: gnu: editres: Update to 1.0.7. * gnu/packages/xorg.scm (editres): Update to 1.0.7. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index b73d7d6cd2..c63b87218a 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -357,7 +357,7 @@ provided.") (define-public editres (package (name "editres") - (version "1.0.6") + (version "1.0.7") (source (origin (method url-fetch) @@ -367,7 +367,7 @@ provided.") ".tar.bz2")) (sha256 (base32 - "1w2d5hb5pw9ii2jlf4yjlp899402zfwc8hdkpdr3i1fy1cjd2riv")))) + "04awfwmy3f9f0bchidc4ssbgrbicn5gzasg3jydpfnp5513d76h8")))) (build-system gnu-build-system) (arguments `(#:configure-flags -- cgit v1.2.3 From b5de208e84419ba93fdb8d265b93526ed3b27d3a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 15:25:54 +0100 Subject: gnu: perl-xml-rss: Update to 1.60. * gnu/packages/xml.scm (perl-xml-rss): Update to 1.60. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index eabd28233a..5db398bce6 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -469,14 +469,14 @@ checks.") (define-public perl-xml-rss (package (name "perl-xml-rss") - (version "1.59") + (version "1.60") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/S/SH/SHLOMIF/" "XML-RSS-" version ".tar.gz")) (sha256 (base32 - "0v6vfizn2psy6av057kp7fv3z3y73s6b3w56jm3zr6hlq48llsx2")))) + "0xw6aaqka3vqwbv152sbh6fbi8j306q1gvg7v83br8miif3mjcsb")))) (build-system perl-build-system) (native-inputs `(("perl-module-build" ,perl-module-build) -- cgit v1.2.3 From 503a00597b1581db03219483fe19052ba6ee58ec Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 15:27:51 +0100 Subject: gnu: perl-xml-compile-cache: Update to 1.06. * gnu/packages/xml.scm (perl-xml-compile-cache): Update to 1.06. --- gnu/packages/xml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 5db398bce6..5f7a95463a 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -684,14 +684,14 @@ a schema.") (define-public perl-xml-compile-cache (package (name "perl-xml-compile-cache") - (version "1.05") + (version "1.06") (source (origin (method url-fetch) (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/" "XML-Compile-Cache-" version ".tar.gz")) (sha256 (base32 - "0xbwlszhi9hg8sxm5ylglm2qvnb689i595p913awrj2g4mp9yfsw")))) + "181qf1s7ymgi7saph3cf9p6dbxkxyh1ja23na4dchhi8v5mi66sr")))) (build-system perl-build-system) (propagated-inputs `(("perl-log-report" ,perl-log-report) -- cgit v1.2.3 From 1c3de94cff14c07b173fe391e65b1992279ba8bc Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 15:30:12 +0100 Subject: gnu: perl-sub-quote: Update to 2.005000. * gnu/packages/xml.scm (perl-sub-quote): Update to 2.005000. --- gnu/packages/perl.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index e44d5c3f0f..badff6e4d1 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -7340,7 +7340,7 @@ return value is the sub.") (define-public perl-sub-quote (package (name "perl-sub-quote") - (version "2.004000") + (version "2.005000") (source (origin (method url-fetch) @@ -7349,7 +7349,7 @@ return value is the sub.") version ".tar.gz")) (sha256 (base32 - "1zrh3apxsw1ks25zkh9dcn00656rsvq4mimqz3w8p37s2c1m4qaq")))) + "1zv45cvj4ifkbr61ydcpphnj6lvib37gfxwfh40h0yzf3c8lbca4")))) (build-system perl-build-system) (native-inputs `(("perl-test-fatal" ,perl-test-fatal))) -- cgit v1.2.3 From c8213ffc520ea34d1ca4bb5db22ec79fe23b5aa3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 5 Mar 2018 16:42:08 +0100 Subject: gnu: perl-email-address: Update to 1.909. * gnu/packages/perl.scm (perl-email-address): Update to 1.909. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 8d3544f908..7d85d5208a 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1375,7 +1375,7 @@ write simple, representation-independent mail handling code.") (define-public perl-email-address (package (name "perl-email-address") - (version "1.908") + (version "1.909") (source (origin (method url-fetch) @@ -1383,7 +1383,7 @@ write simple, representation-independent mail handling code.") "Email-Address-" version ".tar.gz")) (sha256 (base32 - "0i6ljdvpy279hpbqf6lgv4figr376rb2sh4yphj86xkdzsyn1y75")))) + "0l7x6sl06j9ffgfz5f9vgms2b5axd4cgp5fj03ivb3kia4km6b3g")))) (build-system perl-build-system) (home-page "http://search.cpan.org/dist/Email-Address") (synopsis "Email address parsing and creation") -- cgit v1.2.3 From 0f2778029a536ceac93208f2e66af9d3e1ef44a7 Mon Sep 17 00:00:00 2001 From: Gábor Boskovits Date: Sat, 3 Mar 2018 22:59:05 +0100 Subject: gnu: java-ops4j-pax-tinybundles: Use distribution bndlib version. * gnu/packages/java.scm (java-ops4j-pax-tinybundles)[arguments]<#:phases>: Modify fix-version to use the distibution version of java-aqute-bndlib. --- gnu/packages/java.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 21e241d0fe..5cc4a56f81 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -6980,7 +6980,8 @@ it manages project dependencies, gives diffs jars, and much more.") ;; packaging. It uses the version referenced in pom.xml. We replace ;; it with our own version. (substitute* "src/test/java/org/ops4j/pax/tinybundles/bnd/BndTest.java" - (("2.4.0.201411031534") "3.4.0"))))))) + (("[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*\\.[0-9][0-9]*") + ,(package-version java-aqute-bndlib)))))))) (inputs `(("lang" ,java-ops4j-base-lang) ("io" ,java-ops4j-base-io) -- cgit v1.2.3 From cee03b267cbe6e7360b106095ee2861bf010f915 Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Tue, 6 Mar 2018 08:24:01 +0100 Subject: gnu: ovmf: Fix build and add FIXME. * gnu/packages/firmware.scm (ovmf): Replace 'invoke' with 'system*'. Add FIXME about failing script. --- gnu/packages/firmware.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm index da7430b063..714af3df72 100644 --- a/gnu/packages/firmware.scm +++ b/gnu/packages/firmware.scm @@ -258,7 +258,9 @@ coreboot.") (setenv "WORKSPACE" cwd) (setenv "EDK_TOOLS_PATH" tools) (setenv "PATH" (string-append (getenv "PATH") ":" bin)) - (invoke "bash" "edksetup.sh" "BaseTools") + ; FIXME: The below script errors out. When using 'invoke' instead + ; of 'system*' this causes the build to fail. + (system* "bash" "edksetup.sh" "BaseTools") (substitute* "Conf/target.txt" (("^TARGET[ ]*=.*$") "TARGET = RELEASE\n") (("^TOOL_CHAIN_TAG[ ]*=.*$") "TOOL_CHAIN_TAG = GCC49\n") -- cgit v1.2.3 From 69611d3eacfae2d22b6b3ebc2ff4f3bfbff925b5 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Sun, 4 Mar 2018 12:28:52 +0300 Subject: gnu: haskell-mode: Fix find emacs-stream elisp directory. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/emacs.scm (haskell-mode)[arguments]: Find only directories with "\\.el$" in ‘el-dir’. --- gnu/packages/emacs.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 54eb816c15..f27f8df8d3 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -614,7 +614,7 @@ process, passing on the arguments as command line arguments.") 'build 'pre-build (lambda* (#:key inputs #:allow-other-keys) (define (el-dir store-dir) - (match (find-files store-dir) + (match (find-files store-dir "\\.el$") ((f1 f2 ...) (dirname f1)) (_ ""))) -- cgit v1.2.3 From 5ad13e6cdf77311b3c1ea93d45378f7e92081145 Mon Sep 17 00:00:00 2001 From: Oleg Pykhalov Date: Tue, 6 Mar 2018 12:09:02 +0300 Subject: gnu: emacs-transmission: Update to 0.12.1. * gnu/packages/emacs.scm (emacs-transmission): Update to 0.12.1. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index f27f8df8d3..a6f398ac3b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -6891,7 +6891,7 @@ in a generalized CSV (character-separated values) format.") (define-public emacs-transmission (package (name "emacs-transmission") - (version "0.12") + (version "0.12.1") (source (origin (method url-fetch) (uri (string-append @@ -6900,7 +6900,7 @@ in a generalized CSV (character-separated values) format.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1y0bpsy16pycp6m9aqvfjh2x1yswfb305ib7m2slcjpb6njgxfi6")))) + "1rrlgn96gi1ljfwbwvlyyxbq75xzamlbdhq1bpyadxxmxcvlmk3n")))) (build-system emacs-build-system) (home-page "https://github.com/holomorph/transmission") (synopsis "Emacs interface to a Transmission session") -- cgit v1.2.3 From 08ddb98aefc9d3831cea7c6dc6b68039836d09dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 10:26:59 +0100 Subject: gnu: r-gtools: Make output deterministic. * gnu/packages/statistics.scm (r-gtools)[arguments]: Add build phase to avoid running tempdir at build time. --- gnu/packages/statistics.scm | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index baec1c47d2..338db28222 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4042,6 +4042,14 @@ Zurich, including many that are related to graphics.") (base32 "1xknwk9xlsj027pg0nwiizigcrsc84hdrig0jn0cgcyxj8dabdl6")))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-deterministic + (lambda _ + (substitute* "R/checkReverseDependencies.R" + (("tempdir\\(\\)") "\"/tmp\"")) + #t))))) (home-page "https://cran.r-project.org/web/packages/gtools") (synopsis "Various R programming tools") (description -- cgit v1.2.3 From fe58ab013be8b8232ed4de356b3d0cb8b1bbb847 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 11:51:33 +0100 Subject: gnu: r-lambda-r: Run unit tests. * gnu/packages/statistics.scm (r-lambda-r)[native-inputs]: Add r-runit. [arguments]: Add build phase to delete test logs. --- gnu/packages/statistics.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 338db28222..8ebdce1376 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2814,6 +2814,19 @@ plotted and compared with the asymptotic curve.") "0vql32np716dpd0kjn7s7wgawd02ysgp2a5il4kb19nlw661ii3x")))) (properties `((upstream-name . "lambda.r"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'check 'delete-test-log + ;; The test report contains time stamps and is not important for + ;; the installed package. + (lambda* (#:key outputs #:allow-other-keys) + (delete-file-recursively + (string-append (assoc-ref outputs "out") + "/site-library/lambda.r/unitTests")) + #t))))) + (native-inputs + `(("r-runit" ,r-runit))) (home-page "https://cran.r-project.org/web/packages/lambda.r") (synopsis "Functional programming extension for R") (description -- cgit v1.2.3 From e325c890763e89b9baeeeb78110b3a50c822b25a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 13:55:13 +0100 Subject: gnu: r-rhdf5: Make build reproducible. * gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and host system information from settings file. --- gnu/packages/bioinformatics.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4756444d95..947f99aa71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8760,6 +8760,16 @@ of gene-level counts.") "src/hdf5source/hdf5small.tgz" "-C" "src/" ) (substitute* "src/hdf5/configure" (("/bin/mv") "mv")) + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "src/hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) #t))))) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit v1.2.3 From 727d847980e61d8d0deaa4219ea730dc85e0a515 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 15:50:08 +0100 Subject: gnu: htslib: Update to 1.7. * gnu/packages/bioinformatics.scm (htslib): Update to 1.7. [arguments]: Remove field. --- gnu/packages/bioinformatics.scm | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 947f99aa71..c098562d2d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3431,7 +3431,7 @@ The main functions of FastQC are: (define-public htslib (package (name "htslib") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (string-append @@ -3439,17 +3439,8 @@ The main functions of FastQC are: version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m")))) + "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after - 'unpack 'patch-tests - (lambda _ - (substitute* "test/test.pl" - (("/bin/bash") (which "bash"))) - #t))))) (inputs `(("openssl" ,openssl) ("curl" ,curl) -- cgit v1.2.3 From c072cf57b927111d9a63b7349074052cb696280b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Mar 2018 15:50:32 +0100 Subject: gnu: samtools: Update to 1.7. * gnu/packages/bioinformatics.scm (samtools): Update to 1.7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c098562d2d..546b240f84 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4896,7 +4896,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.5") + (version "1.7") (source (origin (method url-fetch) @@ -4905,7 +4905,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5")))) + "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) -- cgit v1.2.3 From 6f1f8d131299ce1e8cd4243df29459d86ca9a911 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 6 Mar 2018 17:38:12 +0100 Subject: gnu: python-django: Update to 1.11.11 [fixes CVE-2018-7536 and CVE-2018-7537]. See for more information about the vulnerabilities. * gnu/packages/django.scm (python-django): Update to 1.11.11. --- gnu/packages/django.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 0b447b5176..c52c812f00 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -36,13 +36,13 @@ (define-public python-django (package (name "python-django") - (version "1.11.10") + (version "1.11.11") (source (origin (method url-fetch) (uri (pypi-uri "Django" version)) (sha256 (base32 - "1ndc7axr7cz8jwhr4mz16fvwd0jcd6i81q2wi9nl172s71kkaf12")))) + "1p0fk0dszci9gx76hyhay3n8n0k8r4sznbdcrpd9g2xl15rps1vl")))) (build-system python-build-system) (arguments '(#:modules ((srfi srfi-1) -- cgit v1.2.3 From 6836c228ae538a06827b47c4f7bc94b02c087be9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 6 Mar 2018 18:16:51 +0100 Subject: gnu: iceauth: Update to 1.0.8. * gnu/packages/xorg.scm (iceauth): Update to 1.0.8. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index c63b87218a..3ae936923c 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -918,7 +918,7 @@ rendering commands to the X server.") (define-public iceauth (package (name "iceauth") - (version "1.0.7") + (version "1.0.8") (source (origin (method url-fetch) @@ -928,7 +928,7 @@ rendering commands to the X server.") ".tar.bz2")) (sha256 (base32 - "02izdyzhwpgiyjd8brzilwvwnfr72ncjb6mzz3y1icwrxqnsy5hj")))) + "1ik0mdidmyvy48hn8p2hwvf3535rf3m96hhf0mvcqrbj44x23vp6")))) (build-system gnu-build-system) (inputs `(("libice" ,libice))) -- cgit v1.2.3 From 37204750b188edca17559dfc57d6f47bd9f63c62 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 6 Mar 2018 18:22:26 +0100 Subject: gnu: feh: Update to 2.25. * gnu/packages/image-viewers.scm (feh): Update to 2.25. --- gnu/packages/image-viewers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index a3887ee22d..7a33f6c871 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -59,7 +59,7 @@ (define-public feh (package (name "feh") - (version "2.24") + (version "2.25") (home-page "https://feh.finalrewind.org/") (source (origin (method url-fetch) @@ -67,7 +67,7 @@ name "-" version ".tar.bz2")) (sha256 (base32 - "148qbxkk5m7i3cxymnfwi7aikqjyfxr306dlqm9ndp6x932js5wq")))) + "102rwi30n09l8rih6kv6bb7lhv3djklgzill4p2zag0h700yqfq6")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases (delete 'configure)) -- cgit v1.2.3 From 77412c45b1cd1dee8443d4391080f196f8b5483f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 6 Mar 2018 18:23:42 +0100 Subject: gnu: re2: Update to 2018-03-01. * gnu/packages/regex.scm (re2): Update to 2018-03-01. --- gnu/packages/regex.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm index e6fcfe304c..1294149609 100644 --- a/gnu/packages/regex.scm +++ b/gnu/packages/regex.scm @@ -29,7 +29,7 @@ (define-public re2 (package (name "re2") - (version "2018-02-01") + (version "2018-03-01") (source (origin (method url-fetch) (uri @@ -39,7 +39,7 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1131hwgid76la15hh2g15gj20fzz8iq3krniwks6wxn9h4q87ay8")))) + "0y21g321a802xmxdbkfz0rkcark7ypglpb3jjqhf13m6s7lpxp2i")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build gnu-build-system) -- cgit v1.2.3 From 78f19a4754628b42f4363a624bf3500c54e861cc Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:01:00 -0500 Subject: gnu: Remove go-github-com-xtaci-smux. * gnu/packages/syncthing.scm (go-github-com-xtaci-smux): Remove variable. --- gnu/packages/syncthing.scm | 28 ---------------------------- 1 file changed, 28 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index f5e5bb85be..cf7dfd6910 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1640,34 +1640,6 @@ over UDP packets.") (home-page "https://github.com/templexxx/xor") (license expat))) -(define-public go-github-com-xtaci-smux - (let ((commit "c3e18246ff2252a6e9d6b529fcbf22ae5c74c007") - (revision "0")) - (package - (name "go-github-com-xtaci-smux") - (version (git-version "1.0.6" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/xtaci/smux.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1dfmxd9g31idldhq6n7r998gi4jw51ji3xvkjrzypsw2ypbjx1dz")))) - (build-system go-build-system) - (propagated-inputs - `(("go-github-com-pkg-errors" ,go-github-com-pkg-errors))) - (arguments - '(#:import-path "github.com/xtaci/smux")) - (synopsis "Network multiplexing in Go") - (description "Smux ( Simple MUltipleXing) is a multiplexing library for -Golang. It relies on an underlying connection to provide reliability and -ordering, such as TCP or KCP, and provides stream-oriented multiplexing.") - (home-page "https://github.com/xtaci/smux") - (license expat)))) - (define-public go-github-com-pkg-errors (let ((commit "e881fd58d78e04cf6d0de1217f8707c8cc2249bc") (revision "1")) -- cgit v1.2.3 From bb0a84f89dd33a14062487dfd2704ff4595c07f2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:01:38 -0500 Subject: gnu: Remove go-github-com-xtaci-kcp-go. * gnu/packages/syncthing.scm (go-github-com-xtaci-kcp-go): Remove variable. --- gnu/packages/syncthing.scm | 39 --------------------------------------- 1 file changed, 39 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index cf7dfd6910..3d97ce09f0 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1577,45 +1577,6 @@ rolling hash.") (home-page "https://github.com/chmduquesne/rollinghash") (license expat)))) -(define-public go-github-com-xtaci-kcp-go - (let ((commit "86eebd5cadb519b7c9306082c7eb3bcee2c49a7b") - (revision "0")) - (package - (name "go-github-com-xtaci-kcp-go") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/xtaci/kcp-go") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1mdfsya4y04nycfgsk9ghm67zpim5pw78si3f1566xgrv4ghl0ni")))) - (build-system go-build-system) - (propagated-inputs - `(("go-golang-org-x-net-ipv4" ,go-golang-org-x-net-ipv4) - ("go-github-com-klauspost-reedsolomon" - ,go-github-com-klauspost-reedsolomon) - ("go-github-com-tjfoc-gmsm-sm4" ,go-github-com-tjfoc-gmsm-sm4) - ("go-github-com-pkg-errors" ,go-github-com-pkg-errors) - ("go-golang-org-x-crypto" ,(go-golang-org-x-crypto-union)) - ("go-github-com-templexxx-xor" ,go-github-com-templexxx-xor))) - (arguments - '(#:import-path "github.com/xtaci/kcp-go" - ;; XXX update comment - ;; 'TestListenerClose' is known to fail. It seems that the test suite - ;; is not being used upstream: - ;; https://github.com/AudriusButkevicius/kcp-go/pull/1 - #:tests? #f)) - (synopsis "Reliable UDP connections in Go") - (description "This package provides @code{kcp-go}, a reliable UDP library -written in Go. It offers fast, ordered and error-checked delivery of streams -over UDP packets.") - (home-page "https://github.com/xtaci/kcp-go") - (license expat)))) - (define-public go-github-com-templexxx-xor (package (name "go-github-com-templexxx-xor") -- cgit v1.2.3 From eaca421063e23b42dbac26a2957c188bcf21323a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:02:10 -0500 Subject: gnu: Remove go-github-com-ccding-go-stun. * gnu/packages/syncthing.scm (go-github-com-ccding-go-stun): Remove variable. --- gnu/packages/syncthing.scm | 25 ------------------------- 1 file changed, 25 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 3d97ce09f0..90389d3098 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1526,31 +1526,6 @@ virtual connections from a single physical connection.") (home-page "https://github.com/AudriusButkevicius/pfilter") (license expat)))) -(define-public go-github-com-ccding-go-stun - (let ((commit "d9bbe8f8fa7bf7ed03e6cfc6a2796bb36139e1f4") - (revision "1")) - (package - (name "go-github-com-ccding-go-stun") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ccding/go-stun.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "04a4q69cmw6snlx54wikyj1y6gk94qzm9xv9als17inmj8z60xv7")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/ccding/go-stun")) - (synopsis "STUN client implementation") - (description "Go-stun is a go implementation of the STUN client (RFC 3489 -and RFC 5389).") - (home-page "https://github.com/ccding/go-stun") - (license asl2.0)))) - (define-public go-github-com-chmduquesne-rollinghash-adler32 (let ((commit "3dc7875a1f890f9bcf0619adb5571fc6f7d516bb") (revision "1")) -- cgit v1.2.3 From abb8973544b7e27a4c17bacfbb56538974244009 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:03:59 -0500 Subject: gnu: Remove go-github-com-klauspost-cpuid. * gnu/packages/syncthing.scm (go-github-com-klauspost-cpuid): Remove variable. --- gnu/packages/syncthing.scm | 23 ----------------------- 1 file changed, 23 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 90389d3098..e320512ed7 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1776,29 +1776,6 @@ notification library in Go.") (home-page "https://github.com/zillode/notify") (license expat)))) -(define-public go-github-com-klauspost-cpuid - (let ((commit "eae9b3e628d72774e13bdf024e78c0802f85a5b9") - (revision "0")) - (package - (name "go-github-com-klauspost-cpuid") - (version (git-version "1.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/klauspost/cpuid.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dgxlsxdfhfapmz1qlvc919m3kcbmfqcfpxk78zl9am5zc3zr689")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/klauspost/cpuid")) - (synopsis "CPU feature identification library") - (description "This package provides @code{cpuid}, a Go library that provides information about the CPU running the current program") - (home-page "https://github.com/klauspost/cpuid") - (license expat)))) - (define-public go-github-com-klauspost-reedsolomon (let ((commit "0b30fa71cc8e4e9010c9aba6d0320e2e5b163b29") (revision "0")) -- cgit v1.2.3 From 7915ef0bff3392f6f7773b054935c1f88704dfac Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:04:33 -0500 Subject: gnu: Remove go-github-com-klauspost-reedsolomon. * gnu/packages/syncthing.scm (go-github-com-klauspost-reedsolomon): Remove variable. --- gnu/packages/syncthing.scm | 27 --------------------------- 1 file changed, 27 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index e320512ed7..f67aa89e8f 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1776,33 +1776,6 @@ notification library in Go.") (home-page "https://github.com/zillode/notify") (license expat)))) -(define-public go-github-com-klauspost-reedsolomon - (let ((commit "0b30fa71cc8e4e9010c9aba6d0320e2e5b163b29") - (revision "0")) - (package - (name "go-github-com-klauspost-reedsolomon") - (version (git-version "1.6" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/klauspost/reedsolomon.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "04jvf65ybsa7w4d7s2n0s174p0q2fl0dqd5hhn2krw66z9i3rc6d")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/klauspost/reedsolomon")) - (propagated-inputs - `(("go-github-com-klauspost-cpuid" - ,go-github-com-klauspost-cpuid))) - (synopsis "Reed-Solomon Erasure Coding in Go") - (description "This package provides and implemenation of Reed-Solomon -Erasure Coding in Go.") - (home-page "https://github.com/klauspost/reedsolomon") - (license expat)))) - (define-public go-github-com-beorn7-perks-quantile (let ((commit "4c0e84591b9aa9e6dcfdf3e020114cd81f89d5f9") (revision "0")) -- cgit v1.2.3 From 7d02ae4b85d16f34d14dfb6375b7900ca1a81b4a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:05:10 -0500 Subject: gnu: Remove go-github-com-tjfoc-gmsm-sm4. * gnu/packages/syncthing.scm (go-github-com-tjfoc-gmsm-sm4): Remove variable. --- gnu/packages/syncthing.scm | 26 -------------------------- 1 file changed, 26 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index f67aa89e8f..9b7ea9b0c4 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1724,32 +1724,6 @@ processor feature detection used by the Go standard libary.") (home-page "https://github.com/templexxx/cpufeat") (license bsd-3)))) -(define-public go-github-com-tjfoc-gmsm-sm4 - (let ((commit "98aa888b79d8de04afe0fccf45ed10594efc858b") - (revision "1")) - (package - (name "go-github-com-tjfoc-gmsm-sm4") - (version (git-version "0.0.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/tjfoc/gmsm") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1ii4imnz3ims2s23pdv0l4ijzxjsvl82h4yzgfqm5y809ph6pjq9")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/tjfoc/gmsm/sm4" - #:unpack-path "github.com/tjfoc/gmsm")) - (synopsis "SM4 block cipher") - (description "This package provides a Go implementation of SM4, a block -cipher used in the Chinese National Standard for Wireless LAN WAPI (Wired -Authentication and Privacy Infrastructure).") - (home-page "https://github.com/tjfoc/gmsm") - (license asl2.0)))) - (define-public go-github-com-zillode-notify (let ((commit "a8abcfb1ce88ee8d79a300ed65d94b8fb616ddb3") (revision "2")) -- cgit v1.2.3 From 6482d3047247aeeac07a5a90bf6165586a039b27 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:05:47 -0500 Subject: gnu: Remove go-github-com-templexxx-cpufeat. * gnu/packages/syncthing.scm (go-github-com-templexxx-cpufeat): Remove variable. --- gnu/packages/syncthing.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 9b7ea9b0c4..17aa12782b 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1700,30 +1700,6 @@ using sh's word-splitting rules.") (home-page "https://github.com/kballard/go-shellquote") (license expat)))) -(define-public go-github-com-templexxx-cpufeat - (let ((commit "3794dfbfb04749f896b521032f69383f24c3687e") - (revision "0")) - (package - (name "go-github-com-templexxx-cpufeat") - (version (git-version "0.0.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/templexxx/cpufeat.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0b9f5p6nsiv907rz5d66qzgxnsz4k68r2f45vxi2hwdbnkjfxz8j")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/templexxx/cpufeat")) - (synopsis "CPU feature identification for Go") - (description "This package provides @code{cpu}, which implements -processor feature detection used by the Go standard libary.") - (home-page "https://github.com/templexxx/cpufeat") - (license bsd-3)))) - (define-public go-github-com-zillode-notify (let ((commit "a8abcfb1ce88ee8d79a300ed65d94b8fb616ddb3") (revision "2")) -- cgit v1.2.3 From 01794ffce0c34d3c0b5c2bded95f634bac4ffaca Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 09:06:14 -0500 Subject: gnu: Remove go-github-com-templexxx-xor. * gnu/packages/syncthing.scm (go-github-com-templexxx-xor): Remove variable. --- gnu/packages/syncthing.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 17aa12782b..60ad23440d 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -1552,30 +1552,6 @@ rolling hash.") (home-page "https://github.com/chmduquesne/rollinghash") (license expat)))) -(define-public go-github-com-templexxx-xor - (package - (name "go-github-com-templexxx-xor") - (version "0.1.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/templexxx/xor.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0v1maiii0sggmxk9bgpy6pypb40j3hy2328pc4kd5bldkpdb67d5")))) - (build-system go-build-system) - (arguments - '(#:import-path "github.com/templexxx/xor")) - (propagated-inputs - `(("go-github-com-templexxx-cpufeat" ,go-github-com-templexxx-cpufeat))) - (synopsis "XOR in Go") - (description "This packages provides a Go implementation of XOR.") - (home-page "https://github.com/templexxx/xor") - (license expat))) - (define-public go-github-com-pkg-errors (let ((commit "e881fd58d78e04cf6d0de1217f8707c8cc2249bc") (revision "1")) -- cgit v1.2.3 From 3b5262865c4d5ca1d73cdda86acf1e2a0b48d470 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 20 Feb 2018 08:59:31 -0500 Subject: gnu: syncthing: Update to 0.14.45. * gnu/packages/syncthing.scm (syncthing): Update to 0.14.45. [inputs]: Remove go-github-com-xtaci-kcp-go, go-github-com-ccding-go-stun, and go-github-com-xtaci-smux. Add go-github-com-pkg-errors. --- gnu/packages/syncthing.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm index 60ad23440d..6c3792b92f 100644 --- a/gnu/packages/syncthing.scm +++ b/gnu/packages/syncthing.scm @@ -28,7 +28,7 @@ (define-public syncthing (package (name "syncthing") - (version "0.14.44") + (version "0.14.45") (source (origin (method url-fetch) (uri (string-append "https://github.com/syncthing/syncthing" @@ -36,7 +36,7 @@ "/syncthing-source-v" version ".tar.gz")) (sha256 (base32 - "0fxq52w1b05928xp0a333rg23fabj0nykgg7v4gz01f3vrxyydi1")) + "0nv5g9ymykl4316l2g3mnac77y2rx9ps4j2kg3pymxlq6qms2dij")) (modules '((guix build utils))) ;; Delete bundled ("vendored") free software source code. (snippet @@ -110,8 +110,6 @@ (inputs `(("go-github-com-audriusbutkevicius-cli" ,go-github-com-audriusbutkevicius-cli) - ("go-github-com-xtaci-kcp-go" - ,go-github-com-xtaci-kcp-go) ("go-github-com-audriusbutkevicius-go-nat-pmp" ,go-github-com-audriusbutkevicius-go-nat-pmp) ("go-github-com-audriusbutkevicius-pfilter" @@ -119,8 +117,6 @@ ("go-github-com-bkaradzic-go-lz4" ,go-github-com-bkaradzic-go-lz4) ("go-github-com-calmh-du" ,go-github-com-calmh-du) ("go-github-com-calmh-xdr" ,go-github-com-calmh-xdr) - ("go-github-com-ccding-go-stun" - ,go-github-com-ccding-go-stun) ("go-github-com-prometheus-union" ,(go-github-com-prometheus-union)) ("go-github-com-chmduquesne-rollinghash-adler32" ,go-github-com-chmduquesne-rollinghash-adler32) @@ -137,12 +133,12 @@ ("go-github-com-minio-sha256-simd" ,go-github-com-minio-sha256-simd) ("go-github-com-oschwald-geoip2-golang" ,go-github-com-oschwald-geoip2-golang) + ("go-github-com-pkg-errors" ,go-github-com-pkg-errors) ("go-github-com-rcrowley-go-metrics" ,go-github-com-rcrowley-go-metrics) ("go-github-com-sasha-s-go-deadlock" ,go-github-com-sasha-s-go-deadlock) ("go-github-com-syndtr-goleveldb" ,go-github-com-syndtr-goleveldb) ("go-github-com-thejerf-suture" ,go-github-com-thejerf-suture) ("go-github-com-vitrun-qart" ,(go-github-com-vitrun-qart-union)) - ("go-github-com-xtaci-smux" ,go-github-com-xtaci-smux) ("go-golang-org-x-crypto" ,(go-golang-org-x-crypto-union)) ("go-golang-org-x-net-union" ,(go-golang-org-x-net-union)) ("go-golang-org-x-text" ,(go-golang-org-x-text-union)) -- cgit v1.2.3 From 8a325748fb8c3709beb2c26966a3e3c86831f95e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 6 Mar 2018 13:30:49 -0500 Subject: gnu: isc-dhcp: Update to 4.3.6-P1 [fixes CVE-2018-{5732,5733}]. * gnu/packages/admin.scm (isc-dhcp): Update to 4.3.6-P1. --- 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 554c1679e6..78b7b64dd1 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -610,14 +610,14 @@ connection alive.") bind-release-version))) (package (name "isc-dhcp") - (version "4.3.6") + (version "4.3.6-P1") (source (origin (method url-fetch) (uri (string-append "http://ftp.isc.org/isc/dhcp/" version "/dhcp-" version ".tar.gz")) (sha256 (base32 - "06vgxhm6agzkp6r1jy10467vrfw2rzcp2mnkcph7ydziciisy7m4")))) + "1hx3az6ckvgvybr1ag4k9kqr8zfcpzcww4vpw5gz0mi8y2z7gl9g")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f -- cgit v1.2.3