From a62ddb748fd453597152e2409f6101c162900bb5 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 5 Aug 2019 11:03:35 -0400 Subject: [PATCH 01/52] gnu: ghc-8: Rename to 'ghc-8.4'. * gnu/packages/haskell.scm (ghc-8): Rename to... (ghc-8.4): ...this. (ghc-8): New variable. --- gnu/packages/haskell.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index bced44579d..019f751307 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -440,7 +440,7 @@ interactive environment for the functional language Haskell.") interactive environment for the functional language Haskell.") (license license:bsd-3))) -(define-public ghc-8 +(define-public ghc-8.4 (package (inherit ghc-8.0) (name "ghc") (version "8.4.3") @@ -572,6 +572,8 @@ interactive environment for the functional language Haskell.") (file-pattern ".*\\.conf\\.d$") (file-type 'directory)))))) +(define-public ghc-8 ghc-8.4) + (define-public ghc ghc-8) (define-public ghc-hostname From cce84c34cd40610f49d7acc58eeea541edf45578 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 16 Jul 2019 08:45:40 +0200 Subject: [PATCH 02/52] gnu: Add ghc-8.6. * gnu/packages/haskell.scm (ghc-8.6): New variable. Co-authored-by: Timothy Sample --- gnu/packages/haskell.scm | 46 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 019f751307..4f283f7069 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -73,6 +73,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) + #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module ((srfi srfi-1) #:select (alist-delete))) @@ -572,6 +573,51 @@ interactive environment for the functional language Haskell.") (file-pattern ".*\\.conf\\.d$") (file-type 'directory)))))) +(define-public ghc-8.6 + (package (inherit ghc-8.4) + (name "ghc") + (version "8.6.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://www.haskell.org/ghc/dist/" + version "/" name "-" version "-src.tar.xz")) + (sha256 + (base32 "0qg3zsmbk4rkwkc3jpas3zs74qaxmw4sp4v1mhsbj0a0dzls2jjd")))) + (native-inputs + `(;; GHC 8.6.5 must be built with GHC >= 8.2. + ("ghc-bootstrap" ,ghc-8.4) + ("ghc-testsuite" + ,(origin + (method url-fetch) + (uri (string-append + "https://www.haskell.org/ghc/dist/" + version "/" name "-" version "-testsuite.tar.xz")) + (sha256 + (base32 + "0pw9r91g2np3i806g2f4f8z4jfdd7mx226cmdizk4swa7av1qf91")))) + ,@(filter (match-lambda + (("ghc-bootstrap" . _) #f) + (("ghc-testsuite" . _) #f) + (_ #t)) + (package-native-inputs ghc-8.4)))) + (arguments + (substitute-keyword-arguments (package-arguments ghc-8.4) + ((#:make-flags make-flags ''()) + `(cons "EXTRA_RUNTEST_OPTS=--skip-perf-tests" + ,make-flags)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + ;; These two tests refer to the root user, which doesn't exist + ;; (see ). + (add-after 'unpack-testsuite 'skip-tests + (lambda _ + (substitute* "libraries/unix/tests/all.T" + (("^test\\('T8108'") "# guix skipped: test('T8108'")) + (substitute* "libraries/unix/tests/libposix/all.T" + (("^test\\('posix010'") "# guix skipped: test('posix010'")) + #t)))))))) + (define-public ghc-8 ghc-8.4) (define-public ghc ghc-8) From e07f7655587d05486990a74deb3e101a03b420db Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Wed, 5 Jun 2019 21:05:36 +0200 Subject: [PATCH 03/52] import: hackage: Update list of ghc-included packages. It turns out the list in the release notes is incomplete. This updates the list from /gnu/store/-ghc-8.4.3/lib/ghc-8.4.3. * guix/import/hackage.scm (ghc-standard-libraries): Update list. --- guix/import/hackage.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm index 6f426af900..5fe3d85a7f 100644 --- a/guix/import/hackage.scm +++ b/guix/import/hackage.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2016 ng0 ;;; Copyright © 2018 Ricardo Wurmus +;;; Copyright © 2019 Robert Vollmert ;;; ;;; This file is part of GNU Guix. ;;; @@ -52,7 +53,7 @@ (define ghc-standard-libraries ;; List of libraries distributed with ghc (8.4.3). - ;; https://downloads.haskell.org/~ghc/8.4.3/docs/html/users_guide/8.4.3-notes.html + ;; Contents of ...-ghc-8.4.3/lib/ghc-8.4.3. '("ghc" "cabal" ;; in the output of `ghc-pkg list` Cabal is uppercased, but ;; hackage-name->package-name takes this into account. @@ -65,7 +66,9 @@ "deepseq" "directory" "filepath" + "ghc" "ghc-boot" + "ghc-boot-th" "ghc-compact" "ghc-prim" "ghci" @@ -74,8 +77,11 @@ "integer-gmp" "mtl" "parsec" + "pretty" "process" + "stm" "template-haskell" + "terminfo" "text" "time" "transformers" From a1eb8be8ca1a0a4c952f264f8846b67a32db0ec8 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 4 Jul 2019 09:57:31 +0200 Subject: [PATCH 04/52] gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml. These are ghc-8.4-bundled packages, removing to avoid build conflicts. * gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove. * gnu/packages/haskell-web.scm (ghc-xhtml): Remove. * gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text. * gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and ghc-text. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec. (git-annex)[inputs]: Remove ghc-stm and ghc-text. (ghc-sdl2)[inputs]: Remove ghc-text. (ghc-sdl2-image)[inputs]: Remove ghc-text. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm. (ghc-tasty)[inputs]: Remove ghc-stm. (ghc-tasty-rerun)[inputs]: Same. (ghc-quickcheck-instances)[inputs]: Remove ghc-text. (ghc-hedgehog)[inputs]: Remove ghc-stm. * gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove ghc-text. * gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text. (ghc-cookie)[inputs]: Same. (ghc-http-types)[inputs]: Same. (ghc-http)[inputs]: Remove ghc-parsec. (ghc-http-client)[inputs]: Remove ghc-text. (ghc-http2)[inputs]: Remove ghc-stm. (ghc-http-conduit)[native-inputs]: Remove ghc-text. (ghc-wai)[inputs]: Same. (ghc-wai-extra)[inputs]: Same. (ghc-warp)[inputs]: Remove ghc-stm and ghc-text. (ghc-xss-sanitize)[native-inputs]: Remove ghc-text. (ghc-css-text)[inputs]: Same. (ghc-mime-types)[inputs]: Same. (ghc-blaze-html)[inputs]: Same. (ghc-aeson)[inputs]: Same. (ghc-aeson-pretty)[inputs]: Same. (ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec. (ghc-multipart)[inputs]: Remove ghc-parsec. (ghc-uri-encode)[inputs]: Remove ghc-text. (ghc-path-pieces)[inputs]: Same. (ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec. (ghc-yesod-persistent)[inputs]: Remove ghc-text. (ghc-yesod-form)[inputs]: Same. (ghc-yesod)[inputs]: Same. (ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text. (ghc-hxt)[inputs]: Remove ghc-parsec. * gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text. (ghc-double-conversion)[inputs]: Same. (ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text. [native-inputs]: Remove ghc-parsec. (ghc-cgi)[inputs]: Remove ghc-parsec. (hlint)[inputs]: Remove ghc-text. (ghc-openglraw)[inputs]: Remove ghc-text. (ghc-opengl)[inputs]: Same. (ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text. (ghc-hackage-security)[inputs]: Remove ghc-parsec. (cabal-install)[inputs]: Remove ghc-stm. (ghc-parsec-numbers)[inputs]: Remove ghc-parsec. (ghc-safesemaphore)[inputs]: Remove ghc-stm. (ghc-text-binary)[inputs]: Remove ghc-text. (ghc-hashable)[inputs]: Remove ghc-text. (ghc-transformers-base)[inputs]: Remove ghc-stm. (ghc-indents)[inputs]: Remove ghc-parsec. (ghc-regex-tdfa-rc)[inputs]: Same. (ghc-regex-tdfa-text)[inputs]: Same. (ghc-regex)[inputs]: Remove ghc-text. (ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text. (ghc-attoparsec)[inputs]: Remove ghc-text. (ghc-attoparsec-bootstrap)[inputs]: Same. (ghc-zip-archive)[inputs]: Same. (ghc-polyparse)[inputs]: Same. (ghc-reducers)[inputs]: Same. (ghc-xml)[inputs]: Same. (ghc-feed)[inputs]: Same. (ghc-exceptions)[inputs]: Remove ghc-stm. (ghc-case-insensitive)[inputs]: Remove ghc-text. (ghc-megaparsec)[inputs]: Same. (ghc-network-uri)[inputs]: Remove ghc-parsec. (ghc-monad-control)[inputs]: Remove ghc-stm. (ghc-blaze-builder)[inputs]: Remove ghc-text. (ghc-blaze-markup)[inputs]: Same. (ghc-async)[inputs]: Remove ghc-stm. (ghc-invariant)[inputs]: Same. (ghc-statevar)[inputs]: Same. (ghc-lens)[inputs]: Remove ghc-text. (ghc-cheapskate)[inputs]: Same. (ghc-semigroups)[inputs]: Same. (ghc-semigroups-bootstrap)[inputs]: Same. (ghc-fast-logger)[inputs]: Same. (ghc-scientific)[inputs]: Same. (ghc-scientific-bootstrap)[inputs]: Same. (ghc-texmath)[inputs]: Remove ghc-parsec. (ghc-highlighting-kate)[inputs]: Same. (ghc-cmark)[inputs]: Remove ghc-text. (ghc-cmark-gfm)[inputs]: Same. (ghc-th-lift-instances)[inputs]: Same. (ghc-yaml)[inputs]: Same. (ghc-hslua)[inputs]: Same. (ghc-hslua-module-text)[inputs]: Same. (ghc-skylighting-core)[inputs]: Same. (ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec. (ghc-pandoc)[inputs]: Same. (ghc-typed-process)[inputs]: Remove ghc-stm. (ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text. (ghc-xml-types)[inputs]: Remove ghc-text. (ghc-xml-conduit)[inputs]: Same. (ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec. (ghc-regex-tdfa)[inputs]: Remove ghc-parsec. (ghc-wl-pprint-text)[inputs]: Remove ghc-text. (ghc-graphviz)[inputs]: Same. (ghc-system-filepath-bootstrap)[inputs]: Same. (ghc-system-fileio-bootstrap)[inputs]: Same. (ghc-shelly)[inputs]: Same. (ghc-chell)[inputs]: Same. (ghc-system-filepath)[inputs]: Same. (ghc-system-fileio)[inputs]: Same. (ghc-fsnotify)[inputs]: Same. (ghc-json)[inputs]: Remove ghc-text and ghc-parsec. (ghc-esqueleto)[inputs]: Remove ghc-text. (shellcheck)[inputs]: Remove ghc-parsec. (ghc-errors)[inputs]: Remove ghc-text. (ghc-chunked-data)[inputs]: Same. (ghc-uuid-types)[inputs]: Same. (ghc-uuid)[inputs]: Same. (ghc-rebase)[inputs]: Remove ghc-stm and ghc-text. (ghc-foldl)[inputs]: Remove ghc-text. (ghc-mono-traversable)[inputs]: Same. (ghc-conduit-combinators)[inputs]: Same. (ghc-aws)[inputs]: Same. (ghc-stm-chans)[inputs]: Remove ghc-stm. (ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm. (ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text. (ghc-resource-pool)[inputs]: Remove ghc-stm. (ghc-attoparsec-iso8601)[inputs]: Remove ghc-text. (ghc-http-api-data)[inputs]: Same. (ghc-persistent)[inputs]: Same. (ghc-aeson-compat)[inputs]: Same. (ghc-persistent-template)[inputs]: Same. (ghc-unliftio)[inputs]: Remove ghc-stm. (ghc-persistent-sqlite)[native-inputs]: Remove ghc-text. (ghc-bytes)[inputs]: Same. (ghc-missingh)[inputs]: Remove ghc-parsec. (ghc-rio)[inputs]: Remove ghc-text. (ghc-cairo)[inputs]: Same. (ghc-atomic-write)[inputs]: Remove ghc-text. [native-inputs]: Same. (ghc-stm-conduit)[inputs]: Remove ghc-stm. (ghc-conduit-algorithms)[inputs]: Same. (ghc-interpolate)[native-inputs]: Remove ghc-text. (ghc-hpack)[inputs]: Same. (ghc-inline-c)[inputs]: Remove ghc-parsec. (ghc-configurator)[inputs]: Remove ghc-text. (ghc-c2hs)[native-inputs]: Same. (ghc-libmpd)[inputs]: Same. (ghc-concurrent-output)[inputs]: Remove ghc-stm. * gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text. * gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm. Signed-off-by: Ricardo Wurmus --- gnu/packages/agda.scm | 2 - gnu/packages/bioinformatics.scm | 2 - gnu/packages/haskell-apps.scm | 5 - gnu/packages/haskell-check.scm | 7 +- gnu/packages/haskell-crypto.scm | 3 +- gnu/packages/haskell-web.scm | 79 ++------- gnu/packages/haskell.scm | 295 +++++--------------------------- gnu/packages/idris.scm | 1 - gnu/packages/wm.scm | 2 - 9 files changed, 54 insertions(+), 342 deletions(-) diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm index 646595705b..0f9b4299c3 100644 --- a/gnu/packages/agda.scm +++ b/gnu/packages/agda.scm @@ -64,9 +64,7 @@ ("ghc-uri-encode" ,ghc-uri-encode) ("ghc-parallel" ,ghc-parallel) ("ghc-regex-tdfa" ,ghc-regex-tdfa) - ("ghc-stm" ,ghc-stm) ("ghc-strict" ,ghc-strict) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-zlib" ,ghc-zlib))) (arguments diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 956257d7bb..991a3c6487 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13964,13 +13964,11 @@ datasets.") ("ghc-intervalmap" ,ghc-intervalmap) ("ghc-missingh" ,ghc-missingh) ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-parsec" ,ghc-parsec) ("ghc-regex" ,ghc-regex) ("ghc-safe" ,ghc-safe) ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) - ("ghc-text" ,ghc-text) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) diff --git a/gnu/packages/haskell-apps.scm b/gnu/packages/haskell-apps.scm index d675863090..e01f796178 100644 --- a/gnu/packages/haskell-apps.scm +++ b/gnu/packages/haskell-apps.scm @@ -99,7 +99,6 @@ ("ghc-html" ,ghc-html) ("ghc-mmap" ,ghc-mmap) ("ghc-old-time" ,ghc-old-time) - ("ghc-parsec" ,ghc-parsec) ("ghc-random" ,ghc-random) ("ghc-regex-applicative" ,ghc-regex-applicative) ("ghc-regex-compat-tdfa" ,ghc-regex-compat-tdfa) @@ -242,10 +241,8 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}. ("ghc-securemem" ,ghc-securemem) ("ghc-socks" ,ghc-socks) ("ghc-split" ,ghc-split) - ("ghc-stm" ,ghc-stm) ("ghc-stm-chans" ,ghc-stm-chans) ("ghc-tagsoup" ,ghc-tagsoup) - ("ghc-text" ,ghc-text) ("ghc-unix-compat" ,ghc-unix-compat) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-utf8-string" ,ghc-utf8-string) @@ -285,7 +282,6 @@ used to keep a folder in sync between computers.") `(("ghc-exceptions" ,ghc-exceptions) ("ghc-linear" ,ghc-linear) ("ghc-statevar" ,ghc-statevar) - ("ghc-text" ,ghc-text) ("ghc-vector" ,ghc-vector) ("sdl2" ,sdl2))) (native-inputs @@ -347,7 +343,6 @@ programming.") (build-system haskell-build-system) (inputs `(("ghc-sdl2" ,ghc-sdl2) - ("ghc-text" ,ghc-text) ("sdl2-image" ,sdl2-image))) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 3c10a5284e..2f0b842cae 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -54,7 +54,6 @@ (inputs `(("ghc-generic-deriving" ,ghc-generic-deriving) ("ghc-xml" ,ghc-xml) - ("ghc-stm" ,ghc-stm) ("ghc-tagged" ,ghc-tagged) ("ghc-tasty" ,ghc-tasty))) (home-page @@ -170,8 +169,7 @@ contains the correct result for the test.") "14riid753hjqr6lca1kgxpnvq0wykf0k3qc5jpag42hh8bszav22")))) (build-system haskell-build-system) (inputs - `(("ghc-stm" ,ghc-stm) - ("ghc-tagged" ,ghc-tagged) + `(("ghc-tagged" ,ghc-tagged) ("ghc-regex-tdfa" ,ghc-regex-tdfa) ("ghc-optparse-applicative" ,ghc-optparse-applicative) ("ghc-unbounded-delays" ,ghc-unbounded-delays) @@ -277,7 +275,6 @@ test-framework.") `(("ghc-optparse-applicative" ,ghc-optparse-applicative) ("ghc-reducers" ,ghc-reducers) ("ghc-split" ,ghc-split) - ("ghc-stm" ,ghc-stm) ("ghc-tagged" ,ghc-tagged) ("ghc-tasty" ,ghc-tasty))) (home-page "https://github.com/ocharles/tasty-rerun") @@ -340,7 +337,6 @@ development.") ("ghc-old-time" ,ghc-old-time) ("ghc-scientific" ,ghc-scientific) ("ghc-tagged" ,ghc-tagged) - ("ghc-text" ,ghc-text) ("ghc-transformers-compat" ,ghc-transformers-compat) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-uuid-types" ,ghc-uuid-types) @@ -827,7 +823,6 @@ implementations of cryptographic ciphers.") ("ghc-random" ,ghc-random) ("ghc-resourcet" ,ghc-resourcet) ("ghc-semigroups" ,ghc-semigroups) - ("ghc-stm" ,ghc-stm) ("ghc-th-lift" ,ghc-th-lift) ("ghc-transformers-base" ,ghc-transformers-base) ("ghc-wl-pprint-annotated" diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm index 8d28a77fc1..28a1647fd1 100644 --- a/gnu/packages/haskell-crypto.scm +++ b/gnu/packages/haskell-crypto.scm @@ -69,8 +69,7 @@ format.") (build-system haskell-build-system) (inputs `(("ghc-hourglass" ,ghc-hourglass) - ("ghc-asn1-types" ,ghc-asn1-types) - ("ghc-text" ,ghc-text))) + ("ghc-asn1-types" ,ghc-asn1-types))) (native-inputs `(("ghc-tasty" ,ghc-tasty) ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck))) diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 6b7103562f..4bb790d93c 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -47,7 +47,6 @@ (base32 "1yv3dbyb0i1yqm796jgc4jj5kxkla1sxb3b2klw5ks182kdx8kjb")))) (build-system haskell-build-system) - (inputs `(("ghc-text" ,ghc-text))) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck))) (home-page "http://community.haskell.org/~ndm/tagsoup/") @@ -80,7 +79,6 @@ for screen-scraping.") (inputs `(("ghc-old-locale" ,ghc-old-locale) ("ghc-blaze-builder" ,ghc-blaze-builder) - ("ghc-text" ,ghc-text) ("ghc-data-default-class" ,ghc-data-default-class) ("ghc-hunit" ,ghc-hunit) ("ghc-quickcheck" ,ghc-quickcheck) @@ -136,8 +134,7 @@ requests, and the library is intended for implementing Ajax APIs.") ("ghc-quickcheck-instances" ,ghc-quickcheck-instances) ("hspec-discover" ,hspec-discover))) (inputs - `(("ghc-case-insensitive" ,ghc-case-insensitive) - ("ghc-text" ,ghc-text))) + `(("ghc-case-insensitive" ,ghc-case-insensitive))) (home-page "https://github.com/aristidb/http-types") (synopsis "Generic HTTP types for Haskell") (description "This package provides generic HTTP types for Haskell (for @@ -169,7 +166,6 @@ both client and server code).") ("ghc-conduit-extra" ,ghc-conduit-extra) ("ghc-http-types" ,ghc-http-types) ("ghc-old-time" ,ghc-old-time) - ("ghc-parsec" ,ghc-parsec) ("ghc-puremd5" ,ghc-puremd5) ("ghc-network" ,ghc-network) ("ghc-network-uri" ,ghc-network-uri) @@ -215,7 +211,6 @@ responses coming back.") ("ghc-network-uri" ,ghc-network-uri) ("ghc-random" ,ghc-random) ("ghc-streaming-commons" ,ghc-streaming-commons) - ("ghc-text" ,ghc-text) ("ghc-zlib" ,ghc-zlib))) (native-inputs `(("ghc-hspec" ,ghc-hspec))) @@ -308,13 +303,12 @@ Date in Haskell.") ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-vector" ,ghc-vector) ("ghc-word8" ,ghc-word8) - ("ghc-psqueues" ,ghc-psqueues) - ("ghc-stm" ,ghc-stm))) - (native-inputs - `(("ghc-glob" ,ghc-glob) - ("ghc-hspec" ,ghc-hspec) - ("ghc-doctest" ,ghc-doctest) - ("hspec-discover" ,hspec-discover))) + ("ghc-psqueues" ,ghc-psqueues))) + (native-inputs + `(("ghc-glob" ,ghc-glob) + ("ghc-hspec" ,ghc-hspec) + ("ghc-doctest" ,ghc-doctest) + ("hspec-discover" ,hspec-discover))) (home-page "https://github.com/kazu-yamamoto/http2") (synopsis "HTTP/2 library including frames, priority queues and HPACK") (description "This package provides a HTTP/2.0 library including frames @@ -358,7 +352,6 @@ and HPACK. Currently HTTP/2 16 framing and HPACK 10 is supported.") ("ghc-connection" ,ghc-connection) ("ghc-warp-tls" ,ghc-warp-tls) ("ghc-blaze-builder" ,ghc-blaze-builder) - ("ghc-text" ,ghc-text) ("ghc-conduit" ,ghc-conduit) ("ghc-utf8-string" ,ghc-utf8-string) ("ghc-case-insensitive" ,ghc-case-insensitive) @@ -402,7 +395,6 @@ which allow you to avoid direct usage of conduits.") ("ghc-vault" ,ghc-vault) ("ghc-blaze-builder" ,ghc-blaze-builder) ("ghc-network" ,ghc-network) - ("ghc-text" ,ghc-text) ("ghc-http-types" ,ghc-http-types))) (native-inputs `(("hspec-discover" ,hspec-discover) @@ -482,7 +474,6 @@ communication between web applications and web servers.") ("ghc-void" ,ghc-void) ("ghc-wai" ,ghc-wai) ("ghc-http-types" ,ghc-http-types) - ("ghc-text" ,ghc-text) ("ghc-case-insensitive" ,ghc-case-insensitive) ("ghc-data-default-class" ,ghc-data-default-class) ("ghc-unix-compat" ,ghc-unix-compat) @@ -569,9 +560,7 @@ transfers.") ("ghc-http-types" ,ghc-http-types) ("ghc-iproute" ,ghc-iproute) ("ghc-network" ,ghc-network) - ("ghc-stm" ,ghc-stm) ("ghc-streaming-commons" ,ghc-streaming-commons) - ("ghc-text" ,ghc-text) ("ghc-unix-compat" ,ghc-unix-compat) ("ghc-vault" ,ghc-vault) ("ghc-wai" ,ghc-wai) @@ -670,8 +659,7 @@ a WAI handler, via the native Haskell TLS implementation.") ("ghc-css-text" ,ghc-css-text) ("ghc-network-uri" ,ghc-network-uri))) (native-inputs - `(("ghc-text" ,ghc-text) - ("ghc-attoparsec" ,ghc-attoparsec) + `(("ghc-attoparsec" ,ghc-attoparsec) ("ghc-hspec" ,ghc-hspec) ("ghc-hunit" ,ghc-hunit))) (home-page "https://github.com/yesodweb/haskell-xss-sanitize") @@ -697,8 +685,7 @@ attacks.") "0ynd9f4hn2sfwqzbsa0y7phmxq8za7jiblpjwx0ry8b372zhgxaz")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-attoparsec" ,ghc-attoparsec) + `(("ghc-attoparsec" ,ghc-attoparsec) ("ghc-hspec" ,ghc-hspec) ("ghc-quickcheck" ,ghc-quickcheck))) (home-page "http://www.yesodweb.com/") @@ -720,8 +707,6 @@ Haskell.") (base32 "14ccl2842ya17zyj0bpc7vzklbyqvvydpbypn69h2fmhgji192x8")))) (build-system haskell-build-system) - (inputs - `(("ghc-text" ,ghc-text))) (home-page "https://github.com/yesodweb/wai") (synopsis "Basic MIME type handling types and functions") (description @@ -751,28 +736,6 @@ Haskell.") documents.") (license license:bsd-3))) -(define-public ghc-xhtml - (package - (name "ghc-xhtml") - (version "3000.2.2.1") - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/xhtml/xhtml-" - version - ".tar.gz")) - (sha256 - (base32 - "0939kwpinq6l4n3nyvd1gzyl7f83gymw0wzqndlgy1yc7q0nkj2w")))) - (build-system haskell-build-system) - (home-page "https://github.com/haskell/xhtml") - (synopsis "XHTML combinator library") - (description - "This package provides combinators for producing XHTML 1.0, including the -Strict, Transitional and Frameset variants.") - (license license:bsd-3))) - (define-public ghc-blaze-html (package (name "ghc-blaze-html") @@ -789,7 +752,6 @@ Strict, Transitional and Frameset variants.") (build-system haskell-build-system) (inputs `(("ghc-blaze-builder" ,ghc-blaze-builder) - ("ghc-text" ,ghc-text) ("ghc-blaze-markup" ,ghc-blaze-markup))) (native-inputs `(("ghc-hunit" ,ghc-hunit) @@ -825,7 +787,6 @@ Strict, Transitional and Frameset variants.") ("ghc-hashable" ,ghc-hashable) ("ghc-scientific" ,ghc-scientific) ("ghc-tagged" ,ghc-tagged) - ("ghc-text" ,ghc-text) ("ghc-th-abstraction" ,ghc-th-abstraction) ("ghc-time-locale-compat" ,ghc-time-locale-compat) ("ghc-unordered-containers" ,ghc-unordered-containers) @@ -867,7 +828,6 @@ naming: in Greek mythology, Aeson was the father of Jason.)") ("ghc-base-compat" ,ghc-base-compat) ("ghc-scientific" ,ghc-scientific) ("ghc-vector" ,ghc-vector) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-attoparsec" ,ghc-attoparsec) ("ghc-cmdargs" ,ghc-cmdargs))) @@ -897,12 +857,10 @@ essentially the opposite of pretty-printing.") (build-system haskell-build-system) (inputs `(("ghc-base-compat" ,ghc-base-compat) - ("ghc-text" ,ghc-text) ("ghc-attoparsec" ,ghc-attoparsec) ("ghc-scientific" ,ghc-scientific) ("ghc-vector" ,ghc-vector) ("ghc-aeson" ,ghc-aeson) - ("ghc-parsec" ,ghc-parsec) ("ghc-haskell-src-meta" ,ghc-haskell-src-meta))) (native-inputs `(("ghc-hspec" ,ghc-hspec) @@ -931,8 +889,7 @@ of a JSON value into a @code{Data.Aeson.Value}.") "1x4n4yyva22dhfr1pg5ki112qvvzb4hyd7bwpm189iq4gcp52q4z")))) (build-system haskell-build-system) (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-stringsearch" ,ghc-stringsearch))) + `(("ghc-stringsearch" ,ghc-stringsearch))) (home-page "http://www.github.com/silkapp/multipart") (synopsis @@ -956,8 +913,7 @@ of a JSON value into a @code{Data.Aeson.Value}.") "11miwb5vvnn17m92ykz1pzg9x6s8fbpz3mmsyqs2s4b3mn55haz8")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-utf8-string" ,ghc-utf8-string) + `(("ghc-utf8-string" ,ghc-utf8-string) ("ghc-network-uri" ,ghc-network-uri))) (home-page "https://hackage.haskell.org/package/uri-encode") (synopsis "Unicode aware uri-encoding") @@ -978,7 +934,6 @@ of a JSON value into a @code{Data.Aeson.Value}.") (base32 "0vx3sivcsld76058925hym2j6hm3g71f0qjr7v59f1g2afgx82q8")))) (build-system haskell-build-system) - (inputs `(("ghc-text" ,ghc-text))) (native-inputs `(("ghc-hunit" ,ghc-hunit) ("ghc-hspec" ,ghc-hspec) ("ghc-quickcheck" ,ghc-quickcheck))) @@ -1067,7 +1022,6 @@ avoid any issues with characters.") (build-system haskell-build-system) (inputs `(("ghc-wai" ,ghc-wai) ("ghc-extra" ,ghc-extra) - ("ghc-text" ,ghc-text) ("ghc-shakespeare" ,ghc-shakespeare) ("ghc-blaze-builder" ,ghc-blaze-builder) ("ghc-clientsession" ,ghc-clientsession) @@ -1081,7 +1035,6 @@ avoid any issues with characters.") ("ghc-cookie" ,ghc-cookie) ("ghc-http-types" ,ghc-http-types) ("ghc-case-insensitive" ,ghc-case-insensitive) - ("ghc-parsec" ,ghc-parsec) ("ghc-vector" ,ghc-vector) ("ghc-aeson" ,ghc-aeson) ("ghc-fast-logger" ,ghc-fast-logger) @@ -1147,8 +1100,7 @@ functions, widgets, etc.") (native-inputs `(("ghc-hspec" ,ghc-hspec) ("ghc-wai-extra" ,ghc-wai-extra) ("ghc-yesod-core" ,ghc-yesod-core) - ("ghc-persistent-sqlite" ,ghc-persistent-sqlite) - ("ghc-text" ,ghc-text))) + ("ghc-persistent-sqlite" ,ghc-persistent-sqlite))) (home-page "http://www.yesodweb.com/") (synopsis "Helpers for using Persistent from Yesod") (description "This Haskell package provides helpers for using Persistent @@ -1179,7 +1131,6 @@ from Yesod.") ("ghc-xss-sanitize" ,ghc-xss-sanitize) ("ghc-blaze-builder" ,ghc-blaze-builder) ("ghc-email-validate" ,ghc-email-validate) - ("ghc-text" ,ghc-text) ("ghc-wai" ,ghc-wai) ("ghc-blaze-html" ,ghc-blaze-html) ("ghc-blaze-markup" ,ghc-blaze-markup) @@ -1226,7 +1177,6 @@ providing richtext field using Nic editor. ") ("ghc-data-default-class" ,ghc-data-default-class) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-yaml" ,ghc-yaml) - ("ghc-text" ,ghc-text) ("ghc-monad-logger" ,ghc-monad-logger) ("ghc-fast-logger" ,ghc-fast-logger) ("ghc-conduit" ,ghc-conduit) @@ -1309,8 +1259,6 @@ ignored.") (build-system haskell-build-system) (inputs `(("ghc-hxt-charproperties" ,ghc-hxt-charproperties) - ("ghc-parsec" ,ghc-parsec) - ("ghc-text" ,ghc-text) ("ghc-hunit" ,ghc-hunit))) (home-page "http://www.haskell.org/haskellwiki/Regular_expressions_for_XML_Schema") (synopsis "Regular expression library for W3C XML Schema regular expressions") @@ -1336,8 +1284,7 @@ derivations of regular expressions.") "1qq3ykgn355rx242xjcbqqksgvwr6k2fdj5phw4iv28qqxff6m8d")))) (build-system haskell-build-system) (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-hxt-charproperties" ,ghc-hxt-charproperties) + `(("ghc-hxt-charproperties" ,ghc-hxt-charproperties) ("ghc-hxt-unicode" ,ghc-hxt-unicode) ("ghc-hxt-regex-xmlschema" ,ghc-hxt-regex-xmlschema) ("ghc-network-uri" ,ghc-network-uri))) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 4f283f7069..b63abbc2dc 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -656,8 +656,7 @@ determine the hostname.") (build-system haskell-build-system) (inputs `(("ghc-old-time" ,ghc-old-time) - ("ghc-old-locale" ,ghc-old-locale) - ("ghc-text" ,ghc-text))) + ("ghc-old-locale" ,ghc-old-locale))) (home-page "https://hackage.haskell.org/package/convertible") (synopsis "Typeclasses and instances for converting between types") (description @@ -682,7 +681,6 @@ function performs the conversion you desire.") (base32 "0sx2kc1gw72mjvd8vph8bbjw5whfxfv92rsdhjg1c0al75rf3ka4")))) (build-system haskell-build-system) - (inputs `(("ghc-text" ,ghc-text))) (native-inputs `(("ghc-hunit" ,ghc-hunit) ("ghc-test-framework" ,ghc-test-framework) @@ -988,12 +986,10 @@ efficient memo functions using tries.") ("ghc-generics-sop" ,ghc-generics-sop) ("ghc-hashable" ,ghc-hashable) ("ghc-memotrie" ,ghc-memotrie) - ("ghc-parsec" ,ghc-parsec) ("ghc-parsers" ,ghc-parsers) ("ghc-quickcheck" ,ghc-quickcheck) ("ghc-scientific" ,ghc-scientific) ("ghc-tagged" ,ghc-tagged) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-uuid-types" ,ghc-uuid-types) ("ghc-vector" ,ghc-vector))) @@ -1002,7 +998,6 @@ efficient memo functions using tries.") ("ghc-quickcheck" ,ghc-quickcheck) ("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint) - ("ghc-parsec" ,ghc-parsec) ("ghc-trifecta" ,ghc-trifecta) ("ghc-tasty" ,ghc-tasty) ("ghc-tasty-golden" ,ghc-tasty-golden) @@ -1303,8 +1298,7 @@ tool lex or flex for C/C++.") (("QuickCheck >= 2\\.8\\.1 && < 2\\.10") "QuickCheck >= 2.8.1 && < 2.12"))))))) (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-exceptions" ,ghc-exceptions) + `(("ghc-exceptions" ,ghc-exceptions) ("ghc-multipart" ,ghc-multipart) ("ghc-network-uri" ,ghc-network-uri) ("ghc-network" ,ghc-network))) @@ -1540,7 +1534,6 @@ specify refactorings without depending on GHC.") ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-yaml" ,ghc-yaml) ("ghc-vector" ,ghc-vector) - ("ghc-text" ,ghc-text) ("ghc-data-default" ,ghc-data-default) ("ghc-cmdargs" ,ghc-cmdargs) ("ghc-haskell-src-exts" ,ghc-haskell-src-exts) @@ -1758,8 +1751,7 @@ arithmetic.") (inputs `(("ghc-half" ,ghc-half) ("ghc-fixed" ,ghc-fixed) - ("glu" ,glu) - ("ghc-text" ,ghc-text))) + ("glu" ,glu))) (home-page "https://www.haskell.org/haskellwiki/Opengl") (synopsis "Raw Haskell bindings for the OpenGL graphics system") (description "OpenGLRaw is a raw Haskell binding for the OpenGL 4.5 @@ -1840,8 +1832,7 @@ basis for a nicer interface.") "19vxwvx2n8zq2klj176l25n2b64ybp0b8mhm4p46gvpcivz41fjc")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-objectname" ,ghc-objectname) + `(("ghc-objectname" ,ghc-objectname) ("ghc-gluraw" ,ghc-gluraw) ("ghc-statevar" ,ghc-statevar) ("ghc-openglraw" ,ghc-openglraw))) @@ -1871,8 +1862,6 @@ version 1.3).") ("ghc-blaze-builder" ,ghc-blaze-builder) ("ghc-network" ,ghc-network) ("ghc-random" ,ghc-random) - ("ghc-stm" ,ghc-stm) - ("ghc-text" ,ghc-text) ("ghc-zlib" ,ghc-zlib))) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck) @@ -2106,7 +2095,6 @@ MinTTY and other consoles.") ("ghc-ed25519" ,ghc-ed25519) ("ghc-network" ,ghc-network) ("ghc-network-uri" ,ghc-network-uri) - ("ghc-parsec" ,ghc-parsec) ("ghc-tar" ,ghc-tar) ("ghc-zlib" ,ghc-zlib))) (native-inputs @@ -2186,7 +2174,6 @@ Unix systems.") ("ghc-network" ,ghc-network) ("ghc-random" ,ghc-random) ("ghc-resolv" ,ghc-resolv) - ("ghc-stm" ,ghc-stm) ("ghc-tar" ,ghc-tar) ("ghc-zlib" ,ghc-zlib))) (home-page "https://www.haskell.org/cabal/") @@ -2234,8 +2221,6 @@ configuration. This library provides the common bits for writing custom (sha256 (base32 "1gzy4v3r02kvdxvgg1nj83mmb6aph2v4ilf9c7y6nbvi2x49l0bp")))) (build-system haskell-build-system) - (inputs - `(("ghc-parsec" ,ghc-parsec))) (home-page "https://hackage.haskell.org/package/parsec-numbers") (synopsis "Utilities for parsing numbers from strings") (description @@ -2449,34 +2434,6 @@ suitable for most tasks and for the few cases where more control is needed it provides access to the full zlib feature set.") (license license:bsd-3))) -(define-public ghc-stm - (package - (name "ghc-stm") - (version "2.4.5.0") - (outputs '("out" "doc")) - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/stm/stm-" - version - ".tar.gz")) - (sha256 - (base32 - "19sr11a0hqikhvf561b38phz6k3zg9s157a0f5ffvghk7wcdpmri")))) - (build-system haskell-build-system) - (home-page "https://hackage.haskell.org/package/stm") - (synopsis "Software Transactional Memory") - (description - "Software Transactional Memory, or STM, is an abstraction for concurrent -communication. The main benefits of STM are composability and modularity. -That is, using STM you can write concurrent abstractions that can be easily -composed with any other abstraction built using STM, without exposing the -details of how your abstraction ensures safety. This is typically not the -case with other forms of concurrent communication, such as locks or -@code{MVar}s.") - (license license:bsd-3))) - (define-public ghc-parallel (package (name "ghc-parallel") @@ -2512,8 +2469,6 @@ case with other forms of concurrent communication, such as locks or (base32 "0rpg9j6fy70i0b9dkrip9d6wim0nac0snp7qzbhykjkqlcvvgr91")))) (build-system haskell-build-system) - (inputs - `(("ghc-stm" ,ghc-stm))) (native-inputs `(("ghc-hunit" ,ghc-hunit))) (home-page "https://github.com/ChrisKuklewicz/SafeSemaphore") @@ -2523,38 +2478,6 @@ used in place of @code{QSem}, @code{QSemN}, and @code{SampleVar}, all of which are not exception safe and can be broken by @code{killThread}.") (license license:bsd-3))) -(define-public ghc-text - (package - (name "ghc-text") - (version "1.2.3.0") - (outputs '("out" "doc")) - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/text/text-" - version - ".tar.gz")) - (sha256 - (base32 - "06iir7q99rnffzxi8gagn8w1k9m49368sbidgz634fv1gxib3q10")))) - (build-system haskell-build-system) - ;; The test dependencies depend on ghc-text: ghc-test-framework -> ghc-xml -> ghc-text - (arguments `(#:tests? #f)) - (inputs - `(("ghc-random" ,ghc-random))) - (home-page "https://github.com/bos/text") - (synopsis "Efficient packed Unicode text type library") - (description - "An efficient packed, immutable Unicode text type (both strict and -lazy), with a powerful loop fusion optimization framework. - -The @code{Text} type represents Unicode character strings, in a time and -space-efficient manner. This package provides text processing -capabilities that are optimized for performance critical use, both -in terms of large data quantities and high speed.") - (license license:bsd-3))) - (define-public ghc-text-binary (package (name "ghc-text-binary") @@ -2569,7 +2492,6 @@ in terms of large data quantities and high speed.") (base32 "18gl10pwg3qwsk0za3c70j4n6a9129wwf1b7d3a461h816yv55xn")))) (build-system haskell-build-system) - (inputs `(("ghc-text" ,ghc-text))) (home-page "https://github.com/kawu/text-binary") (synopsis "Binary instances for text types") (description @@ -2615,8 +2537,7 @@ IO operations.") "1gra8gq3kb7b2sd845h55yxlrfqx3ii004c6vjhga8v0b30fzdgc")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-random" ,ghc-random))) + `(("ghc-random" ,ghc-random))) (native-inputs `(("ghc-test-framework" ,ghc-test-framework) ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) @@ -2798,8 +2719,7 @@ Hashing\" by Claessen, Pałka for details and the rationale of the design.") "1s256bi0yh0x2hp2gwd30f3mg1cv53zz397dv1yhfsnfzmihrj6h")))) (build-system haskell-build-system) (inputs - `(("ghc-stm" ,ghc-stm) - ("ghc-transformers-compat" ,ghc-transformers-compat))) + `(("ghc-transformers-compat" ,ghc-transformers-compat))) (home-page "https://hackage.haskell.org/package/transformers-compat") (synopsis @@ -2899,8 +2819,7 @@ isn't available, portable implementations are used.") ;; This package needs an older version of tasty. (arguments '(#:tests? #f)) (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-concatenative" ,ghc-concatenative))) + `(("ghc-concatenative" ,ghc-concatenative))) (native-inputs `(("ghc-tasty" ,ghc-tasty) ("ghc-tasty-hunit" ,ghc-tasty-hunit))) @@ -3048,8 +2967,7 @@ Haskell library @code{regex-base}.") "1vi11i23gkkjg6193ak90g55akj69bhahy542frkwb68haky4pp3")))) (build-system haskell-build-system) (inputs - `(("ghc-regex-base" ,ghc-regex-base) - ("ghc-parsec" ,ghc-parsec))) + `(("ghc-regex-base" ,ghc-regex-base))) (home-page "https://hackage.haskell.org/package/regex-tdfa") (synopsis "Tagged DFA regex engine for Haskell") @@ -3072,8 +2990,7 @@ Haskell library @code{regex-base}.") "0090g6lgbdm9lywpqm2d3724nnnh24nx3vnlqr96qc2w486pmmrq")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-regex-base" ,ghc-regex-base) + `(("ghc-regex-base" ,ghc-regex-base) ("ghc-regex-tdfa" ,ghc-regex-tdfa))) (home-page "http://hackage.haskell.org/package/regex-tdfa-text") @@ -3113,7 +3030,6 @@ Haskell library @code{regex-base}.") ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin) ("ghc-regex-tdfa" ,ghc-regex-tdfa) ("ghc-regex-tdfa-text" ,ghc-regex-tdfa-text) - ("ghc-text" ,ghc-text) ("ghc-time-locale-compat" ,ghc-time-locale-compat) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-utf8-string" ,ghc-utf8-string))) @@ -3148,10 +3064,8 @@ copious examples.") (inputs `(("ghc-base-orphans" ,ghc-base-orphans) ("ghc-attoparsec" ,ghc-attoparsec) - ("ghc-parsec" ,ghc-parsec) ("ghc-scientific" ,ghc-scientific) ("ghc-charset" ,ghc-charset) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers))) (home-page "https://github.com/ekmett/parsers/") (synopsis "Parsing combinators") @@ -3252,8 +3166,7 @@ with slicing and Clang-style colored diagnostics.") ((", testProperty \"satisfyWith\" satisfyWith") ""))))))) (inputs - `(("ghc-scientific" ,ghc-scientific) - ("ghc-text" ,ghc-text))) + `(("ghc-scientific" ,ghc-scientific))) (native-inputs `(("ghc-tasty" ,ghc-tasty) ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck) @@ -3273,8 +3186,7 @@ complicated text/binary file formats.") (name "ghc-attoparsec-bootstrap") (arguments `(#:tests? #f)) (inputs - `(("ghc-scientific" ,ghc-scientific-bootstrap) - ("ghc-text" ,ghc-text))) + `(("ghc-scientific" ,ghc-scientific-bootstrap))) (native-inputs '()) (properties '(hidden? #t)))) @@ -3296,7 +3208,6 @@ complicated text/binary file formats.") (inputs `(("ghc-digest" ,ghc-digest) ("ghc-temporary" ,ghc-temporary) - ("ghc-text" ,ghc-text) ("ghc-zlib" ,ghc-zlib))) (native-inputs `(("ghc-hunit" ,ghc-hunit) @@ -3437,8 +3348,6 @@ and mIRC chat codes.") (base32 "05dya1vdvq29hkhkdlsglzhw7bdn51rvs1javs0q75nf99c66k7m")))) (build-system haskell-build-system) - (inputs - `(("ghc-text" ,ghc-text))) (home-page "http://code.haskell.org/~malcolm/polyparse/") (synopsis @@ -3527,7 +3436,6 @@ this package makes them available back to GHC 7.2.") (inputs `(("ghc-fingertree" ,ghc-fingertree) ("ghc-hashable" ,ghc-hashable) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-semigroupoids" ,ghc-semigroupoids) ("ghc-semigroups" ,ghc-semigroups))) @@ -3675,8 +3583,6 @@ online}.") (base32 "0g814lj7vaxvib2g3r734221k80k7ap9czv9hinifn8syals3l9j")))) (build-system haskell-build-system) - (inputs - `(("ghc-text" ,ghc-text))) (home-page "http://code.galois.com") (synopsis "Simple XML library for Haskell") (description "This package provides a simple XML library for Haskell.") @@ -3703,7 +3609,6 @@ online}.") ("ghc-old-locale" ,ghc-old-locale) ("ghc-old-time" ,ghc-old-time) ("ghc-safe" ,ghc-safe) - ("ghc-text" ,ghc-text) ("ghc-time-locale-compat" ,ghc-time-locale-compat) ("ghc-utf8-string" ,ghc-utf8-string) ("ghc-xml-conduit" ,ghc-xml-conduit) @@ -3739,8 +3644,7 @@ consuming feeds in both RSS (Really Simple Syndication) and Atom format.") ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2))) (inputs - `(("ghc-stm" ,ghc-stm) - ("ghc-transformers-compat" ,ghc-transformers-compat))) + `(("ghc-transformers-compat" ,ghc-transformers-compat))) (home-page "https://github.com/ekmett/exceptions/") (synopsis "Extensible optionally-pure exceptions") (description "This library provides extensible optionally-pure exceptions @@ -3874,8 +3778,7 @@ writing to stdout and other handles.") (build-system haskell-build-system) ;; these inputs are necessary to use this library (inputs - `(("ghc-text" ,ghc-text) - ("ghc-hashable" ,ghc-hashable))) + `(("ghc-hashable" ,ghc-hashable))) (arguments `(#:tests? #f)) ; FIXME: currently missing libraries used for tests. (home-page @@ -4168,36 +4071,6 @@ splitting lists into parts, akin to the @code{split} function found in several mainstream languages.") (license license:bsd-3))) -(define-public ghc-parsec - (package - (name "ghc-parsec") - (version "3.1.13.0") - (outputs '("out" "doc")) - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/parsec/parsec-" - version - ".tar.gz")) - (sha256 - (base32 "1wc09pyn70p8z6llink10c8pqbh6ikyk554911yfwxv1g91swqbq")))) - (build-system haskell-build-system) - (native-inputs - `(("ghc-hunit" ,ghc-hunit))) - (inputs - `(("ghc-text" ,ghc-text))) - (arguments - `(#:tests? #f)) ; FIXME: currently missing libraries used for tests. - (home-page - "https://github.com/aslatter/parsec") - (synopsis "Monadic parser combinators") - (description "Parsec is a parser library. It is simple, safe, well -documented, has extensive libraries, good error messages, and is fast. It is -defined as a monad transformer that can be stacked on arbitrary monads, and it -is also parametric in the input stream type.") - (license license:bsd-3))) - (define-public ghc-parser-combinators (package (name "ghc-parser-combinators") @@ -4239,8 +4112,7 @@ combinators.") (inputs `(("ghc-case-insensitive" ,ghc-case-insensitive) ("ghc-parser-combinators" ,ghc-parser-combinators) - ("ghc-scientific" ,ghc-scientific) - ("ghc-text" ,ghc-text))) + ("ghc-scientific" ,ghc-scientific))) (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck) ("ghc-hspec" ,ghc-hspec) @@ -4396,11 +4268,10 @@ interface.") (build-system haskell-build-system) (arguments `(#:tests? #f)) ; FIXME: currently missing libraries used for tests. + (inputs + `(("ghc-network" ,ghc-network))) (native-inputs `(("ghc-hunit" ,ghc-hunit))) - (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-network" ,ghc-network))) (home-page "https://github.com/haskell/network-uri") (synopsis "Library for URI manipulation") @@ -4584,8 +4455,7 @@ monads with anaphoric variants on @code{if} and @code{when} and a C-like "1c92833gr6cadidjdp8mlznkpp8lyxl0w3y7d19y8yi3klc3843c")))) (build-system haskell-build-system) (inputs - `(("ghc-stm" ,ghc-stm) - ("ghc-transformers-base" ,ghc-transformers-base) + `(("ghc-transformers-base" ,ghc-transformers-base) ("ghc-transformers-compat" ,ghc-transformers-compat))) (home-page "https://github.com/basvandijk/monad-control") (synopsis "Monad transformers to lift control operations like exception @@ -4707,8 +4577,7 @@ pragmas in your code.") (build-system haskell-build-system) (arguments `(#:tests? #f)) ; FIXME: Missing test libraries. (inputs - `(("ghc-text" ,ghc-text) - ("ghc-utf8-string" ,ghc-utf8-string))) + `(("ghc-utf8-string" ,ghc-utf8-string))) (home-page "https://github.com/lpsmith/blaze-builder") (synopsis "Efficient buffered output") (description "This library provides an implementation of the older @@ -4741,8 +4610,7 @@ interoperate with code that uses the new implementation.") (("tasty >= 1\\.0 && < 1\\.1") "tasty >= 1.0 && < 1.2"))))))) (inputs - `(("ghc-blaze-builder" ,ghc-blaze-builder) - ("ghc-text" ,ghc-text))) + `(("ghc-blaze-builder" ,ghc-blaze-builder))) (native-inputs `(("ghc-hunit" ,ghc-hunit) ("ghc-quickcheck" ,ghc-quickcheck) @@ -4792,8 +4660,7 @@ library for Haskell.") "09whscli1q5z7lzyq9rfk0bq1ydplh6pjmc6qv0x668k5818c2wg")))) (build-system haskell-build-system) (inputs - `(("ghc-stm" ,ghc-stm) - ("ghc-hashable" ,ghc-hashable) + `(("ghc-hashable" ,ghc-hashable) ("ghc-hunit" ,ghc-hunit) ("ghc-test-framework" ,ghc-test-framework) ("ghc-test-framework-hunit" ,ghc-test-framework-hunit))) @@ -5111,7 +4978,6 @@ given term should not exist.") ("ghc-profunctors" ,ghc-profunctors) ("ghc-semigroups" ,ghc-semigroups) ("ghc-statevar" ,ghc-statevar) - ("ghc-stm" ,ghc-stm) ("ghc-tagged" ,ghc-tagged) ("ghc-th-abstraction" ,ghc-th-abstraction) ("ghc-transformers-compat" ,ghc-transformers-compat) @@ -5203,8 +5069,6 @@ call stacks with different versions of the compiler.") (base32 "08r2iw0gdmfs4f6wraaq19vfmkjdbics3dbhw39y7mdjd98kcr7b")))) (build-system haskell-build-system) - (inputs - `(("ghc-stm" ,ghc-stm))) (home-page "https://hackage.haskell.org/package/StateVar") (synopsis "State variables for Haskell") (description "This package provides state variables, which are references @@ -5245,7 +5109,6 @@ in the @code{IO} monad, like @code{IORef}s or parts of the OpenGL state.") ("ghc-profunctors" ,ghc-profunctors) ("ghc-semigroups" ,ghc-semigroups) ("ghc-tagged" ,ghc-tagged) - ("ghc-text" ,ghc-text) ("ghc-transformers-compat" ,ghc-transformers-compat) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-void" ,ghc-void) @@ -5286,8 +5149,7 @@ indexed variants.") "1hiqi7h76shjzs2zj0j8g6wnq2hbiq1hmfafdazr97fba2zl2432")))) (build-system haskell-build-system) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-blaze-html" ,ghc-blaze-html) + `(("ghc-blaze-html" ,ghc-blaze-html) ("ghc-xss-sanitize" ,ghc-xss-sanitize) ("ghc-data-default" ,ghc-data-default) ("ghc-syb" ,ghc-syb) @@ -5421,7 +5283,6 @@ just a @code{Semigroup} are added.") `(("ghc-nats" ,ghc-nats) ("ghc-tagged" ,ghc-tagged) ("ghc-unordered-containers" ,ghc-unordered-containers) - ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable))) (home-page "https://github.com/ekmett/semigroups/") (synopsis "Semigroup operations for Haskell") @@ -5442,7 +5303,6 @@ semigroup.") `(("ghc-nats" ,ghc-nats-bootstrap) ("ghc-tagged" ,ghc-tagged) ("ghc-unordered-containers" ,ghc-unordered-containers-bootstrap) - ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable-bootstrap))) (properties '(hidden? #t)))) @@ -5565,7 +5425,6 @@ monad transformer (instead of the IO monad).") (inputs `(("ghc-auto-update" ,ghc-auto-update) ("ghc-easy-file" ,ghc-easy-file) - ("ghc-text" ,ghc-text) ("ghc-unix-time" ,ghc-unix-time))) (native-inputs `(("hspec-discover" ,hspec-discover) @@ -5751,7 +5610,6 @@ in migrated modules.") (build-system haskell-build-system) (inputs `(("ghc-integer-logarithms" ,ghc-integer-logarithms) - ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable) ("ghc-primitive" ,ghc-primitive))) (native-inputs @@ -5778,7 +5636,6 @@ notation}.") (arguments `(#:tests? #f)) (inputs `(("ghc-integer-logarithms" ,ghc-integer-logarithms-bootstrap) - ("ghc-text" ,ghc-text) ("ghc-hashable" ,ghc-hashable) ("ghc-primitive" ,ghc-primitive))) (native-inputs '()) @@ -5907,7 +5764,6 @@ building up, manipulating and serialising @code{Pandoc} structures.") ("ghc-temporary" ,ghc-temporary) ("ghc-utf8-string" ,ghc-utf8-string) ("ghc-xml" ,ghc-xml) - ("ghc-parsec" ,ghc-parsec) ("ghc-pandoc-types" ,ghc-pandoc-types))) (home-page "https://github.com/jgm/texmath") (synopsis "Conversion between formats used to represent mathematics") @@ -5983,8 +5839,7 @@ and utilities for pretty printing.") `(("ghc-diff" ,ghc-diff) ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin))) (native-inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-blaze-html" ,ghc-blaze-html) + `(("ghc-blaze-html" ,ghc-blaze-html) ("ghc-utf8-string" ,ghc-utf8-string))) (home-page "https://github.com/jgm/highlighting-kate") (synopsis "Syntax highlighting library") @@ -6011,8 +5866,6 @@ descriptions.") (base32 "1c1j3a8b9qx5zk9myqm3gap8ymz7fipwrdmyfsq9wkkdr9x4np45")))) (build-system haskell-build-system) - (inputs - `(("ghc-text" ,ghc-text))) (native-inputs `(("ghc-hunit" ,ghc-hunit))) (home-page "https://github.com/jgm/commonmark-hs") @@ -6038,8 +5891,6 @@ sources, and does not require prior installation of the C library.") (base32 "13b0mqks5c1q989slgsa3ixr5vvkfyic4ynzgv00kgl5qrs7hqk7")))) (build-system haskell-build-system) - (inputs - `(("ghc-text" ,ghc-text))) (native-inputs `(("ghc-hunit" ,ghc-hunit))) (home-page "https://github.com/kivikakk/cmark-gfm-hs") @@ -6196,7 +6047,6 @@ datatypes.") (inputs `(("ghc-th-lift" ,ghc-th-lift) ("ghc-vector" ,ghc-vector) - ("ghc-text" ,ghc-text) ("ghc-quickcheck" ,ghc-quickcheck))) (home-page "https://github.com/bennofs/th-lift-instances/") (synopsis "Lift instances for template-haskell for common data types.") @@ -6456,7 +6306,6 @@ back-ends.") ("ghc-aeson" ,ghc-aeson) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-vector" ,ghc-vector) - ("ghc-text" ,ghc-text) ("ghc-attoparsec" ,ghc-attoparsec) ("ghc-scientific" ,ghc-scientific) ("ghc-semigroups" ,ghc-semigroups) @@ -6559,8 +6408,7 @@ TIFF and GIF formats.") (inputs `(("lua" ,lua) ("ghc-exceptions" ,ghc-exceptions) - ("ghc-fail" ,ghc-fail) - ("ghc-text" ,ghc-text))) + ("ghc-fail" ,ghc-fail))) (native-inputs `(("ghc-tasty" ,ghc-tasty) ("ghc-tasty-expected-failure" ,ghc-tasty-expected-failure) @@ -6593,8 +6441,7 @@ described in @url{https://www.lua.org/}.") `(#:cabal-revision ("1" "0vajlsd7y6pwa08635q0cx8z5c1c55bk7fvavw7g2vmyvxqjzx6n"))) (inputs - `(("ghc-hslua" ,ghc-hslua) - ("ghc-text" ,ghc-text))) + `(("ghc-hslua" ,ghc-hslua))) (native-inputs `(("ghc-tasty" ,ghc-tasty) ("ghc-tasty-hunit" ,ghc-tasty-hunit))) @@ -6792,7 +6639,6 @@ the choice of SSL/TLS, and SOCKS.") ("ghc-hxt" ,ghc-hxt) ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin) ("ghc-safe" ,ghc-safe) - ("ghc-text" ,ghc-text) ("ghc-utf8-string" ,ghc-utf8-string))) (native-inputs `(("ghc-diff" ,ghc-diff) @@ -6846,9 +6692,7 @@ provided. Skylighting is intended to be the successor to highlighting-kate.") `(("ghc-aeson" ,ghc-aeson) ("ghc-blaze-markup" ,ghc-blaze-markup) ("ghc-blaze-html" ,ghc-blaze-html) - ("ghc-text" ,ghc-text) ("ghc-vector" ,ghc-vector) - ("ghc-parsec" ,ghc-parsec) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-scientific" ,ghc-scientific))) (native-inputs @@ -6911,7 +6755,6 @@ provided. Skylighting is intended to be the successor to highlighting-kate.") ("ghc-network-uri" ,ghc-network-uri) ("ghc-old-locale" ,ghc-old-locale) ("ghc-pandoc-types" ,ghc-pandoc-types) - ("ghc-parsec" ,ghc-parsec) ("ghc-random" ,ghc-random) ("ghc-scientific" ,ghc-scientific) ("ghc-sha" ,ghc-sha) @@ -6921,7 +6764,6 @@ provided. Skylighting is intended to be the successor to highlighting-kate.") ("ghc-tagsoup" ,ghc-tagsoup) ("ghc-temporary" ,ghc-temporary) ("ghc-texmath" ,ghc-texmath) - ("ghc-text" ,ghc-text) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-vector" ,ghc-vector) ("ghc-xml" ,ghc-xml) @@ -7009,8 +6851,7 @@ better for some purposes.") "0j36vrc9w841m5qbwqra1lwiznx31xfnhin1sm8x2c2739csbpn0")))) (build-system haskell-build-system) (inputs - `(("ghc-async" ,ghc-async) - ("ghc-stm" ,ghc-stm))) + `(("ghc-async" ,ghc-async))) (native-inputs `(("ghc-base64-bytestring" ,ghc-base64-bytestring) ("ghc-hspec" ,ghc-hspec) @@ -7042,7 +6883,6 @@ upon it.") `(("ghc-conduit" ,ghc-conduit) ("ghc-exceptions" ,ghc-exceptions) ("ghc-monad-control" ,ghc-monad-control) - ("ghc-text" ,ghc-text) ("ghc-transformers-base" ,ghc-transformers-base) ("ghc-typed-process" ,ghc-typed-process) ("ghc-async" ,ghc-async) @@ -7051,7 +6891,6 @@ upon it.") ("ghc-network" ,ghc-network) ("ghc-primitive" ,ghc-primitive) ("ghc-resourcet" ,ghc-resourcet) - ("ghc-stm" ,ghc-stm) ("ghc-streaming-commons" ,ghc-streaming-commons) ("ghc-hspec" ,ghc-hspec) ("ghc-bytestring-builder" ,ghc-bytestring-builder) @@ -7081,7 +6920,6 @@ dependencies. The basic idea is that this package should only depend on (base32 "1jgqxsa9p2q3h6nymbfmvhldqrqlwrhrzmwadlyc0li50x0d8dwr")))) (build-system haskell-build-system) - (inputs `(("ghc-text" ,ghc-text))) (home-page "https://john-millikin.com/software/haskell-xml/") (synopsis "Basic types for representing XML") (description "This package provides basic types for representing XML @@ -7106,7 +6944,6 @@ documents.") ("ghc-conduit-extra" ,ghc-conduit-extra) ("ghc-doctest" ,ghc-doctest) ("ghc-resourcet" ,ghc-resourcet) - ("ghc-text" ,ghc-text) ("ghc-xml-types" ,ghc-xml-types) ("ghc-attoparsec" ,ghc-attoparsec) ("ghc-data-default-class" ,ghc-data-default-class) @@ -7155,7 +6992,6 @@ the @code{conduit} package.") ("ghc-pandoc" ,ghc-pandoc) ("ghc-tagsoup" ,ghc-tagsoup) ("ghc-aeson" ,ghc-aeson) - ("ghc-text" ,ghc-text) ("ghc-vector" ,ghc-vector) ("ghc-xml-conduit" ,ghc-xml-conduit) ("ghc-unordered-containers" ,ghc-unordered-containers) @@ -7166,7 +7002,6 @@ the @code{conduit} package.") ("ghc-hs-bibutils" ,ghc-hs-bibutils) ("ghc-rfc5051" ,ghc-rfc5051) ("ghc-syb" ,ghc-syb) - ("ghc-parsec" ,ghc-parsec) ("ghc-old-locale" ,ghc-old-locale) ("ghc-aeson-pretty" ,ghc-aeson-pretty) ("ghc-attoparsec" ,ghc-attoparsec) @@ -7290,8 +7125,7 @@ regular expressions. Parsers can be built using Applicative interface.") "0l7ajnh4hpgggf2a1r9dg0hx2fy679vd2kada5y7r02hy3nfxala")))) (build-system haskell-build-system) (inputs - `(("ghc-parsec" ,ghc-parsec) - ("ghc-regex-base" ,ghc-regex-base))) + `(("ghc-regex-base" ,ghc-regex-base))) (home-page "https://github.com/ChrisKuklewicz/regex-tdfa") (synopsis "POSIX extended regular expressions in Haskell.") (description @@ -7552,8 +7386,7 @@ supported. A module of colour names (\"Data.Colour.Names\") is provided.") "0g3w92rad6x5appfb22rbzcas2ix2h0hy91sdxhq8a4a5cnlrpa0")))) (build-system haskell-build-system) (inputs - `(("ghc-base-compat" ,ghc-base-compat) - ("ghc-text" ,ghc-text))) + `(("ghc-base-compat" ,ghc-base-compat))) (home-page "https://hackage.haskell.org/package/wl-pprint-text") (synopsis "Wadler/Leijen Pretty Printer for Text values") (description @@ -7617,7 +7450,6 @@ for generating graph-like data structures.") ("ghc-fgl-arbitrary" ,ghc-fgl-arbitrary) ("ghc-polyparse" ,ghc-polyparse) ("ghc-temporary" ,ghc-temporary) - ("ghc-text" ,ghc-text) ("ghc-wl-pprint-text" ,ghc-wl-pprint-text))) (native-inputs `(("ghc-hspec" ,ghc-hspec) @@ -7725,8 +7557,7 @@ instance of @code{MonadBase} or @code{MonadBaseControl}.") (arguments `(#:tests? #f)) (inputs - `(("ghc-text" ,ghc-text) - ("ghc-quickcheck" ,ghc-quickcheck))) + `(("ghc-quickcheck" ,ghc-quickcheck))) (home-page "https://github.com/fpco/haskell-filesystem") (synopsis "High-level, byte-based file and directory path manipulations") (description @@ -7755,7 +7586,6 @@ increasing type safety.") `(#:tests? #f)) (inputs `(("ghc-system-filepath-bootstrap" ,ghc-system-filepath-bootstrap) - ("ghc-text" ,ghc-text) ("ghc-temporary" ,ghc-temporary))) (home-page "https://github.com/fpco/haskell-filesystem") (synopsis "Consistent file system interaction across GHC versions") @@ -7790,7 +7620,6 @@ which can't be decoded in the current locale encoding.") ("ghc-lifted-async" ,ghc-lifted-async) ("ghc-exceptions" ,ghc-exceptions) ("ghc-enclosed-exceptions" ,ghc-enclosed-exceptions) - ("ghc-text" ,ghc-text) ("ghc-async" ,ghc-async) ("ghc-transformers-base" ,ghc-transformers-base) ("ghc-hunit" ,ghc-hunit) @@ -7847,7 +7676,6 @@ easily work with command-line options.") `(("ghc-options-bootstrap" ,ghc-options-bootstrap) ("ghc-patience" ,ghc-patience) ("ghc-random" ,ghc-random) - ("ghc-text" ,ghc-text) ("ghc-ansi-terminal" ,ghc-ansi-terminal))) (home-page "https://john-millikin.com/software/chell/") (synopsis "Simple and intuitive library for automated testing") @@ -7968,8 +7796,7 @@ easily work with command-line options.") ;; FilePath "/r2\ENQ52\t ;$/o\US=/okG\146\&6\n @@ -11544,7 +11329,6 @@ imported with the correct Haskell types.") (inputs `(("ghc-attoparsec" ,ghc-attoparsec) ("ghc-old-locale" ,ghc-old-locale) - ("ghc-text" ,ghc-text) ("ghc-data-default-class" ,ghc-data-default-class) ("ghc-network" ,ghc-network) ("ghc-utf8-string" ,ghc-utf8-string))) @@ -12153,7 +11937,6 @@ example of, \"An applicative functor that is not a monad.\"") (build-system haskell-build-system) (inputs `(("ghc-async" ,ghc-async) - ("ghc-stm" ,ghc-stm) ("ghc-exceptions" ,ghc-exceptions) ("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-terminal-size" ,ghc-terminal-size))) diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm index ec3eb15d63..4290d8c21f 100644 --- a/gnu/packages/idris.scm +++ b/gnu/packages/idris.scm @@ -78,7 +78,6 @@ ("ghc-safe" ,ghc-safe) ("ghc-split" ,ghc-split) ("ghc-terminal-size" ,ghc-terminal-size) - ("ghc-text" ,ghc-text) ("ghc-uniplate" ,ghc-uniplate) ("ghc-unordered-containers" ,ghc-unordered-containers) ("ghc-utf8-string" ,ghc-utf8-string) diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index 160c267882..ffe2590bf2 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -596,10 +596,8 @@ tiled on several screens.") `(("ghc-hinotify" ,ghc-hinotify) ("ghc-http" ,ghc-http) ("ghc-iwlib" ,ghc-iwlib) - ("ghc-parsec" ,ghc-parsec) ("ghc-parsec-numbers" ,ghc-parsec-numbers) ("ghc-regex-compat" ,ghc-regex-compat) - ("ghc-stm" ,ghc-stm) ("ghc-x11-xft" ,ghc-x11-xft) ("libxpm" ,libxpm))) (arguments From 1c54c30d9cb3b822e06aa745289c72e31b6c97db Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Wed, 7 Aug 2019 10:43:54 -0400 Subject: [PATCH 05/52] gnu: ghc-validation: Do not generate 'Setup.hs'. This is handled by the build system. * gnu/packages/haskell.scm (ghc-validation): Remove 'arguments'. --- gnu/packages/haskell.scm | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index b63abbc2dc..15767161c9 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -11881,16 +11881,6 @@ default) (base32 "1acj7mh3581ks405xswxw6667z7y1y0slisg6jvp6chc191ji9l5")))) (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'add-setup-script - (lambda _ - ;; The usual "Setup.hs" script is missing from the source. - (with-output-to-file "Setup.hs" - (lambda () - (format #t "import Distribution.Simple~%") - (format #t "main = defaultMain~%")))))))) (inputs `(("ghc-semigroups" ,ghc-semigroups) ("ghc-semigroupoids" ,ghc-semigroupoids) From f74aa98ed73f53cc9963dafed546a0e9cfd293e3 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 9 Jul 2019 15:44:07 +0200 Subject: [PATCH 06/52] gnu: ghc-concurrent-output: Downgrade to 1.10.9. This is the Stackage LTS version, which is compatible with ansi-terminal 0.8. * gnu/packages/haskell.scm (ghc-concurrent-output): Downgrade to 1.10.9 and use ghc-ansi-terminal-0.8. --- gnu/packages/haskell.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 15767161c9..9ce72fb877 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -11913,7 +11913,7 @@ example of, \"An applicative functor that is not a monad.\"") (define-public ghc-concurrent-output (package (name "ghc-concurrent-output") - (version "1.10.10") + (version "1.10.9") (source (origin (method url-fetch) @@ -11923,12 +11923,12 @@ example of, \"An applicative functor that is not a monad.\"") ".tar.gz")) (sha256 (base32 - "1wnjxnwbc3l853kiiijagzjyb6fmhz3lmkwls24plbximl1qrr22")))) + "0mwf155w89nbbkjln7hhbn8k3f8p0ylcvgrg31cm7ijpx4499i4c")))) (build-system haskell-build-system) (inputs `(("ghc-async" ,ghc-async) ("ghc-exceptions" ,ghc-exceptions) - ("ghc-ansi-terminal" ,ghc-ansi-terminal) + ("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8) ("ghc-terminal-size" ,ghc-terminal-size))) (home-page "https://hackage.haskell.org/package/concurrent-output") From e8aea9018bab331885b812a89f1014ed6ca1ce6e Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Wed, 7 Aug 2019 17:04:04 -0400 Subject: [PATCH 07/52] gnu: ghc-validation: Downgrade to 1. This is the Stackage LTS version, which is compatible with ansi-terminal 0.8. * gnu/packages/haskell.scm (ghc-validation): Downgrade to 1. --- gnu/packages/haskell.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 9ce72fb877..94480bbe0c 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -11869,7 +11869,7 @@ default) (define-public ghc-validation (package (name "ghc-validation") - (version "1.1") + (version "1") (source (origin (method url-fetch) @@ -11879,8 +11879,11 @@ default) ".tar.gz")) (sha256 (base32 - "1acj7mh3581ks405xswxw6667z7y1y0slisg6jvp6chc191ji9l5")))) + "08drmdvyzg2frbb26icy1mlz52xv0l6gi3v8gb7xp0vrcci5libh")))) (build-system haskell-build-system) + (arguments + `(#:cabal-revision + ("1" "1x1g4nannz81j1h64l1m3ancc96zc57d1bjhj1wk7bwn1xxbi5h3"))) (inputs `(("ghc-semigroups" ,ghc-semigroups) ("ghc-semigroupoids" ,ghc-semigroupoids) From 91732735f6f4029281ed6917d57a97544bd95e19 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 9 Jul 2019 15:43:21 +0200 Subject: [PATCH 08/52] gnu: ghc-ansi-terminal: Downgrade to 0.8.0.4. This reverts commits cbff89d126bf5985cfa4884f543c0908c437ff41, 5a499d0f7d5b98443ed0b2c41f2651f66a84ab5e, and 4e3ebbfb1649063bcc0f350523868c667e6699dd. * gnu/packages/haskell.scm (ghc-ansi-terminal): Downgrade to 0.8.0.4. (ghc-ansi-terminal-0.8): Delete variable. (ghc-ansi-wl-pprint, ghc-concurrent-output)[inputs]: Replace 'ghc-ansi-terminal-0.8' with 'ghc-ansi-terminal'. * gnu/packages/haskell-check.scm (ghc-hedgehog)[inputs]: Likewise. --- gnu/packages/haskell-check.scm | 2 +- gnu/packages/haskell.scm | 23 ++++------------------- 2 files changed, 5 insertions(+), 20 deletions(-) diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm index 2f0b842cae..589eee74d9 100644 --- a/gnu/packages/haskell-check.scm +++ b/gnu/packages/haskell-check.scm @@ -811,7 +811,7 @@ implementations of cryptographic ciphers.") "0xz10ycdm5vk9nrcym1fi83k19frfwqz18bz8bnpzwvaj0j41yfj")))) (build-system haskell-build-system) (inputs - `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8) + `(("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-async" ,ghc-async) ("ghc-concurrent-output" ,ghc-concurrent-output) ("ghc-exceptions" ,ghc-exceptions) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 94480bbe0c..a15a899334 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -4038,7 +4038,7 @@ instances of the @code{Pretty} class.") "0gnb4mkqryv08vncxnj0bzwcnd749613yw3cxfzw6y3nsldp4c56")))) (build-system haskell-build-system) (inputs - `(("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8))) + `(("ghc-ansi-terminal" ,ghc-ansi-terminal))) (home-page "https://github.com/ekmett/ansi-wl-pprint") (synopsis "Wadler/Leijen Pretty Printer for colored ANSI terminal output") (description "This is a pretty printing library based on Wadler's paper @@ -4283,7 +4283,7 @@ interface.") (define-public ghc-ansi-terminal (package (name "ghc-ansi-terminal") - (version "0.9.1") + (version "0.8.0.4") (source (origin (method url-fetch) @@ -4293,7 +4293,7 @@ interface.") ".tar.gz")) (sha256 (base32 - "1yr0ld0kqns3w3j9gl62bdwshvyazidx4dv1qkvq19ivnf08w23l")))) + "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b")))) (build-system haskell-build-system) (inputs `(("ghc-colour" ,ghc-colour))) @@ -4304,21 +4304,6 @@ allows cursor movement, screen clearing, color output showing or hiding the cursor, and changing the title.") (license license:bsd-3))) -(define-public ghc-ansi-terminal-0.8 - (package (inherit ghc-ansi-terminal) - (name "ghc-ansi-terminal") - (version "0.8.0.4") - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/ansi-terminal/ansi-terminal-" - version - ".tar.gz")) - (sha256 - (base32 - "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b")))))) - (define-public ghc-vault (package (name "ghc-vault") @@ -11931,7 +11916,7 @@ example of, \"An applicative functor that is not a monad.\"") (inputs `(("ghc-async" ,ghc-async) ("ghc-exceptions" ,ghc-exceptions) - ("ghc-ansi-terminal" ,ghc-ansi-terminal-0.8) + ("ghc-ansi-terminal" ,ghc-ansi-terminal) ("ghc-terminal-size" ,ghc-terminal-size))) (home-page "https://hackage.haskell.org/package/concurrent-output") From 6b34d01cbf475f44b2fbe59033798b2b1d7a5417 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:49:20 +0200 Subject: [PATCH 09/52] gnu: Add ghc-prettyclass. * gnu/package/haskell-xyz.scm: New file. * gnu/local.mk: Add it. * gnu/packages/haskell-xyz.scm (ghc-prettyclass): New variable. --- gnu/local.mk | 1 + gnu/packages/haskell-xyz.scm | 45 ++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 gnu/packages/haskell-xyz.scm diff --git a/gnu/local.mk b/gnu/local.mk index 42e79e879a..f654f84d3a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -238,6 +238,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/haskell-check.scm \ %D%/packages/haskell-crypto.scm \ %D%/packages/haskell-web.scm \ + %D%/packages/haskell-xyz.scm \ %D%/packages/ham-radio.scm \ %D%/packages/hexedit.scm \ %D%/packages/hugs.scm \ diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm new file mode 100644 index 0000000000..fbd40cd3ac --- /dev/null +++ b/gnu/packages/haskell-xyz.scm @@ -0,0 +1,45 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2019 Robert Vollmert +;;; +;;; 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 haskell-xyz) + #:use-module (gnu packages) + #:use-module (guix build-system haskell) + #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public ghc-prettyclass + (package + (name "ghc-prettyclass") + (version "1.0.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "prettyclass/prettyclass-" version ".tar.gz")) + (sha256 + (base32 + "11l9ajci7nh1r547hx8hgxrhq8mh5gdq30pdf845wvilg9p48dz5")))) + (build-system haskell-build-system) + (home-page "http://hackage.haskell.org/package/prettyclass") + (synopsis "Pretty printing class similar to Show") + (description "This package provides a pretty printing class similar +to @code{Show}, based on the HughesPJ pretty printing library. It +provides the pretty printing class and instances for the Prelude +types.") + (license license:bsd-3))) From 79fcc5e59bc8cd6726937be291964477fe673e3a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:43:55 +0200 Subject: [PATCH 10/52] gnu: Add ghc-language-glsl. * gnu/packages/haskell-xyz.scm (ghc-language-glsl): New variable. --- gnu/packages/haskell-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index fbd40cd3ac..17736c9365 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -23,6 +23,30 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages)) +(define-public ghc-language-glsl + (package + (name "ghc-language-glsl") + (version "0.3.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "language-glsl/language-glsl-" version ".tar.gz")) + (sha256 + (base32 + "0hdg67ainlqpjjghg3qin6fg4p783m0zmjqh4rd5gyizwiplxkp1")))) + (build-system haskell-build-system) + (inputs `(("ghc-prettyclass" ,ghc-prettyclass))) + (arguments + `(#:tests? #f + #:cabal-revision + ("1" "10ac9pk4jy75k03j1ns4b5136l4kw8krr2d2nw2fdmpm5jzyghc5"))) + (home-page "http://hackage.haskell.org/package/language-glsl") + (synopsis "GLSL abstract syntax tree, parser, and pretty-printer") + (description "This package is a Haskell library for the +representation, parsing, and pretty-printing of GLSL 1.50 code.") + (license license:bsd-3))) + (define-public ghc-prettyclass (package (name "ghc-prettyclass") From efb96749a2af02d59f341db033e87082f9289705 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:50:58 +0200 Subject: [PATCH 11/52] gnu: Add ghc-concurrent-extra. * gnu/packages/haskell-xyz.scm (ghc-concurrent-extra): New variable. --- gnu/packages/haskell-xyz.scm | 53 ++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 17736c9365..a03ea4c88c 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -18,11 +18,64 @@ (define-module (gnu packages haskell-xyz) #:use-module (gnu packages) + #:use-module (gnu packages haskell) + #:use-module (gnu packages haskell-check) #:use-module (guix build-system haskell) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages)) +(define-public ghc-concurrent-extra + (package + (name "ghc-concurrent-extra") + (version "0.7.0.12") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "concurrent-extra/concurrent-extra-" + version ".tar.gz")) + (sha256 + (base32 + "1y8xk460fvnw0idzdiylmm874sjny4q9jxb1js9fjz8lw2wns3h4")))) + (build-system haskell-build-system) + (arguments + ;; XXX: The ReadWriteLock 'stressTest' fails. + `(#:tests? #f)) + (inputs + `(("ghc-unbounded-delays" ,ghc-unbounded-delays))) + (native-inputs + `(("ghc-async" ,ghc-async) + ("ghc-hunit" ,ghc-hunit) + ("ghc-random" ,ghc-random) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit))) + (home-page "https://github.com/basvandijk/concurrent-extra") + (synopsis "Extra concurrency primitives") + (description "This Haskell library offers (among other things) the +following selection of synchronisation primitives: + +@itemize +@item @code{Broadcast}: Wake multiple threads by broadcasting a value. +@item @code{Event}: Wake multiple threads by signalling an event. +@item @code{Lock}: Enforce exclusive access to a resource. Also known +as a binary semaphore or mutex. The package additionally provides an +alternative that works in the STM monad. +@item @code{RLock}: A lock which can be acquired multiple times by the +same thread. Also known as a reentrant mutex. +@item @code{ReadWriteLock}: Multiple-reader, single-writer locks. Used +to protect shared resources which may be concurrently read, but only +sequentially written. +@item @code{ReadWriteVar}: Concurrent read, sequential write variables. +@end itemize + +Please consult the API documentation of the individual modules for more +detailed information. + +This package was inspired by the concurrency libraries of Java and +Python.") + (license license:bsd-3))) + (define-public ghc-language-glsl (package (name "ghc-language-glsl") From b57e99f574c9496cd40fba1e9a9f1e84885ad2d5 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:45:46 +0200 Subject: [PATCH 12/52] gnu: Add ghc-readable. * gnu/packages/haskell-xyz.scm (ghc-readable): New variable. --- gnu/packages/haskell-xyz.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index a03ea4c88c..8291c7f083 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -120,3 +120,23 @@ to @code{Show}, based on the HughesPJ pretty printing library. It provides the pretty printing class and instances for the Prelude types.") (license license:bsd-3))) + +(define-public ghc-readable + (package + (name "ghc-readable") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "readable/readable-" version ".tar.gz")) + (sha256 + (base32 + "1ja39cg26wy2fs00gi12x7iq5k8i366pbqi3p916skfa5jnkfc3h")))) + (build-system haskell-build-system) + (home-page "https://github.com/mightybyte/readable") + (synopsis "Type class for reading from Text and ByteString") + (description "This package provides a @code{Readable} type class for +reading data types from @code{ByteString} and @code{Text}. It also +includes efficient implementations for common data types.") + (license license:bsd-3))) From bbf8bf31e4654f8e8ac83fd454183e6304044936 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:50:15 +0200 Subject: [PATCH 13/52] gnu: Add ghc-threads. * gnu/packages/haskell-xyz.scm (ghc-threads): New variable. --- gnu/packages/haskell-xyz.scm | 37 ++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 8291c7f083..8dc16f685b 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -140,3 +140,40 @@ types.") reading data types from @code{ByteString} and @code{Text}. It also includes efficient implementations for common data types.") (license license:bsd-3))) + +(define-public ghc-threads + (package + (name "ghc-threads") + (version "0.5.1.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "threads/threads-" version ".tar.gz")) + (sha256 + (base32 + "0bjnjhnq3km6xqk0fn1fgyz5xdw4h6lylbwwbcmkkfzwcz0c76hk")))) + (build-system haskell-build-system) + (native-inputs + `(("ghc-concurrent-extra" ,ghc-concurrent-extra) + ("ghc-hunit" ,ghc-hunit) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit))) + (home-page "https://github.com/basvandijk/threads") + (synopsis "Fork threads and wait for their result") + (description "This package provides functions to fork threads and +wait for their result, whether it's an exception or a normal value. +Besides waiting for the termination of a single thread this package also +provides functions to wait for a group of threads to terminate. This +package is similar to the @code{threadmanager}, @code{async} and +@code{spawn} packages. The advantages of this package are: + +@itemize +@item Simpler API. +@item More efficient in both space and time. +@item No space-leak when forking a large number of threads. +@item Correct handling of asynchronous exceptions. +@item GHC specific functionality like @code{forkOn} and +@code{forkIOWithUnmask}. +@end itemize") + (license license:bsd-3))) From 14e41996462776cffaad3cb355e817c1631ce5c5 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:47:41 +0200 Subject: [PATCH 14/52] gnu: Add ghc-zlib-bindings. * gnu/packages/haskell-xyz.scm (ghc-zlib-bindings): New variable. --- gnu/packages/haskell-xyz.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 8dc16f685b..7ccbae1443 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -177,3 +177,30 @@ package is similar to the @code{threadmanager}, @code{async} and @code{forkIOWithUnmask}. @end itemize") (license license:bsd-3))) + +(define-public ghc-zlib-bindings + (package + (name "ghc-zlib-bindings") + (version "0.1.1.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "zlib-bindings/zlib-bindings-" version ".tar.gz")) + (sha256 + (base32 + "02ciywlz4wdlymgc3jsnicz9kzvymjw1www2163gxidnz4wb8fy8")))) + (build-system haskell-build-system) + (inputs + `(("ghc-zlib" ,ghc-zlib))) + (native-inputs + `(("ghc-hspec" ,ghc-hspec) + ("ghc-quickcheck" ,ghc-quickcheck))) + (arguments + `(#:cabal-revision + ("2" "0fq49694gqkab8m0vq4i879blswczwd66n7xh4r4gwiahf0ryvqc"))) + (home-page "https://github.com/snapframework/zlib-bindings") + (synopsis "Low-level bindings to the @code{zlib} package") + (description "This package provides low-level bindings to the +@code{zlib} package.") + (license license:bsd-3))) From 658dbc7ff2f39053511725fa149df7029fae1141 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:48:35 +0200 Subject: [PATCH 15/52] gnu: Add ghc-io-streams. * gnu/packages/haskell-xyz.scm (ghc-io-streams): New variable. --- gnu/packages/haskell-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 7ccbae1443..592296ded8 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -76,6 +76,42 @@ This package was inspired by the concurrency libraries of Java and Python.") (license license:bsd-3))) +(define-public ghc-io-streams + (package + (name "ghc-io-streams") + (version "1.5.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "io-streams/io-streams-" version ".tar.gz")) + (sha256 + (base32 + "12rcdg2d70644bvn838fxcjkssqj8pssnx5y657si5rijcbkgjsx")))) + (build-system haskell-build-system) + (inputs + `(("ghc-attoparsec" ,ghc-attoparsec) + ("ghc-bytestring-builder" ,ghc-bytestring-builder) + ("ghc-network" ,ghc-network) + ("ghc-primitive" ,ghc-primitive) + ("ghc-vector" ,ghc-vector) + ("ghc-zlib-bindings" ,ghc-zlib-bindings))) + (native-inputs + `(("ghc-hunit" ,ghc-hunit) + ("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) + ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) + ("ghc-zlib" ,ghc-zlib))) + (arguments + `(#:cabal-revision + ("2" "1mcab95d6hm098myh9gp7sh10srigjphgvm8s9pfs7jg5hzghy14"))) + (home-page "http://hackage.haskell.org/package/io-streams") + (synopsis "Simple and composable stream I/O") + (description "This library contains simple and easy-to-use +primitives for I/O using streams.") + (license license:bsd-3))) + (define-public ghc-language-glsl (package (name "ghc-language-glsl") From 7b01a977e455f65a67eea68af0fbda4a0abf1d15 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:46:27 +0200 Subject: [PATCH 16/52] gnu: Add ghc-io-streams-haproxy. * gnu/packages/haskell-xyz.scm (ghc-io-streams-haproxy): New variable. --- gnu/packages/haskell-xyz.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/haskell-xyz.scm b/gnu/packages/haskell-xyz.scm index 592296ded8..53c4dcc5ff 100644 --- a/gnu/packages/haskell-xyz.scm +++ b/gnu/packages/haskell-xyz.scm @@ -112,6 +112,40 @@ Python.") primitives for I/O using streams.") (license license:bsd-3))) +(define-public ghc-io-streams-haproxy + (package + (name "ghc-io-streams-haproxy") + (version "1.0.0.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "io-streams-haproxy/io-streams-haproxy-" + version ".tar.gz")) + (sha256 + (base32 + "11nh9q158mgnvvb23s5ffg87lkhl5smk039yl43jghxmb214z0bp")))) + (build-system haskell-build-system) + (inputs + `(("ghc-attoparsec" ,ghc-attoparsec) + ("ghc-io-streams" ,ghc-io-streams) + ("ghc-network" ,ghc-network))) + (native-inputs + `(("ghc-hunit" ,ghc-hunit) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit))) + (arguments + `(#:cabal-revision + ("4" "06c51a057n5bc9xfbp2m4jz5ds4z1xvmsx5mppch6qfwbz7x5i9l"))) + (home-page "http://snapframework.com/") + (synopsis "HAProxy protocol 1.5 support for io-streams") + (description "HAProxy protocol version 1.5 support +(see @uref{http://haproxy.1wt.eu/download/1.5/doc/proxy-protocol.txt}) +for applications using io-streams. The proxy protocol allows information +about a networked peer (like remote address and port) to be propagated +through a forwarding proxy that is configured to speak this protocol.") + (license license:bsd-3))) + (define-public ghc-language-glsl (package (name "ghc-language-glsl") From 0925b804093f3ec1bb10fa4f0f87b9e3f620fdcf Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:35:54 +0200 Subject: [PATCH 17/52] gnu: Add ghc-hsopenssl. * gnu/packages/haskell-crypto.scm (ghc-hsopenssl): New variable. --- gnu/packages/haskell-crypto.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm index 28a1647fd1..44fadb5a43 100644 --- a/gnu/packages/haskell-crypto.scm +++ b/gnu/packages/haskell-crypto.scm @@ -25,6 +25,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages haskell) #:use-module (gnu packages haskell-check) + #:use-module (gnu packages tls) #:use-module (guix build-system haskell) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) @@ -775,3 +776,33 @@ Ephemeral (Elliptic curve and regular) Diffie Hellman key exchanges, and many extensions.") (license license:bsd-3))) +(define-public ghc-hsopenssl + (package + (name "ghc-hsopenssl") + (version "0.11.4.15") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "HsOpenSSL/HsOpenSSL-" version ".tar.gz")) + (sha256 + (base32 + "0idmak6d8mpbxphyq9hkxkmby2wnzhc1phywlgm0zw6q47pwxgff")))) + (build-system haskell-build-system) + (inputs + `(("ghc-network" ,ghc-network) + ("openssl" ,openssl))) + (arguments + `(#:cabal-revision + ("1" "0bkcw2pjfgv1bhgkrpncvwq9czfr7cr4ak14n0v8c2y33i33wk5z"))) + (home-page "https://github.com/vshabanov/HsOpenSSL") + (synopsis "Partial OpenSSL binding for Haskell") + (description "HsOpenSSL is an OpenSSL binding for Haskell. It can +generate RSA and DSA keys, read and write PEM files, generate message +digests, sign and verify messages, encrypt and decrypt messages. It has +also some capabilities of creating SSL clients and servers. This +package is in production use by a number of Haskell based systems and +stable. You may also be interested in the tls package, +@uref{http://hackage.haskell.org/package/tls}, which is a pure Haskell +implementation of SSL.") + (license license:public-domain))) From 4ba66e6f163c00a8855a78f9dec061ba225cbdef Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:37:46 +0200 Subject: [PATCH 18/52] gnu: Add ghc-openssl-streams. * gnu/packages/haskell-crypto.scm (ghc-openssl-streams): New variable. --- gnu/packages/haskell-crypto.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm index 44fadb5a43..882773ab68 100644 --- a/gnu/packages/haskell-crypto.scm +++ b/gnu/packages/haskell-crypto.scm @@ -25,6 +25,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages haskell) #:use-module (gnu packages haskell-check) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages tls) #:use-module (guix build-system haskell) #:use-module (guix download) @@ -806,3 +807,34 @@ stable. You may also be interested in the tls package, @uref{http://hackage.haskell.org/package/tls}, which is a pure Haskell implementation of SSL.") (license license:public-domain))) + +(define-public ghc-openssl-streams + (package + (name "ghc-openssl-streams") + (version "1.2.1.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "openssl-streams/openssl-streams-" + version ".tar.gz")) + (sha256 + (base32 + "0pwghr7ygv59k572xsj1j97rilkbjz66qaiyj0ra2wfg6pl70wfw")))) + (build-system haskell-build-system) + (inputs + `(("ghc-hsopenssl" ,ghc-hsopenssl) + ("ghc-io-streams" ,ghc-io-streams) + ("ghc-network" ,ghc-network))) + (native-inputs + `(("ghc-hunit" ,ghc-hunit) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit))) + (arguments + `(#:cabal-revision + ("2" "1004kgdryflpkp19dv4ikilhcn0xbfc5dsp6v3ib34580pcfj7wy"))) + (home-page "http://hackage.haskell.org/package/openssl-streams") + (synopsis "OpenSSL network support for io-streams") + (description "This library contains io-streams routines for secure +networking using OpenSSL (by way of HsOpenSSL).") + (license license:bsd-3))) From 0173cdd31d73399c75cf29b7de30d44b1e1be54a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:32:31 +0200 Subject: [PATCH 19/52] gnu: Add ghc-http-common. * gnu/packages/haskell-web.scm (ghc-http-common): New variable. --- gnu/packages/haskell-web.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 4bb790d93c..319b1f8d97 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -1294,3 +1294,31 @@ derivations of regular expressions.") "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but introduces a more general approach for processing XML with Haskell.") (license license:expat))) + +(define-public ghc-http-common + (package + (name "ghc-http-common") + (version "0.8.2.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "http-common/http-common-" version ".tar.gz")) + (sha256 + (base32 + "14s5a178sb2vm5k00rs21760mds5dz2gs10k9iyn22h01mxyf599")))) + (build-system haskell-build-system) + (inputs + `(("ghc-base64-bytestring" ,ghc-base64-bytestring) + ("ghc-blaze-builder" ,ghc-blaze-builder) + ("ghc-case-insensitive" ,ghc-case-insensitive) + ("ghc-network" ,ghc-network) + ("ghc-unordered-containers" ,ghc-unordered-containers))) + (home-page "https://github.com/afcowie/http-streams/") + (synopsis "Common types for HTTP clients and servers") + (description "Base types used by a variety of HTTP clients and +servers. See http-streams @code{Network.Http.Client} or pipes-http +@code{Pipes.Http.Client} for full documentation. You can import +@code{Network.Http.Types} if you like, but both http-streams and +pipes-http re-export this package's types and functions.") + (license license:bsd-3))) From 4ccd679f2568a6b15943521338e1a0a5b1661b05 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:30:26 +0200 Subject: [PATCH 20/52] gnu: Add ghc-http-streams. * gnu/packages/haskell-web.scm (ghc-http-streams): New variable. --- gnu/packages/haskell-web.scm | 37 ++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 319b1f8d97..216c26ba2d 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -28,6 +28,7 @@ #:use-module (gnu packages haskell) #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-crypto) + #:use-module (gnu packages haskell-xyz) #:use-module (guix build-system haskell) #:use-module (guix download) #:use-module ((guix licenses) #:prefix license:) @@ -1322,3 +1323,39 @@ servers. See http-streams @code{Network.Http.Client} or pipes-http @code{Network.Http.Types} if you like, but both http-streams and pipes-http re-export this package's types and functions.") (license license:bsd-3))) + +(define-public ghc-http-streams + (package + (name "ghc-http-streams") + (version "0.8.6.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "http-streams/http-streams-" version ".tar.gz")) + (sha256 + (base32 + "18vxd35n7s3z4gjvad94bknc8z1w9d7ccgphnhsxlz5cackizmxq")))) + (build-system haskell-build-system) + (inputs + `(("ghc-attoparsec" ,ghc-attoparsec) + ("ghc-base64-bytestring" ,ghc-base64-bytestring) + ("ghc-blaze-builder" ,ghc-blaze-builder) + ("ghc-case-insensitive" ,ghc-case-insensitive) + ("ghc-io-streams" ,ghc-io-streams) + ("ghc-hsopenssl" ,ghc-hsopenssl) + ("ghc-openssl-streams" ,ghc-openssl-streams) + ("ghc-unordered-containers" ,ghc-unordered-containers) + ("ghc-aeson" ,ghc-aeson) + ("ghc-http-common" ,ghc-http-common) + ("ghc-network-uri" ,ghc-network-uri) + ("ghc-network" ,ghc-network))) + (arguments + `(#:tests? #f)) ; tests rely on an outdated version of snap-server + (home-page "https://github.com/afcowie/http-streams/") + (synopsis "HTTP client using io-streams") + (description "An HTTP client using the Snap Framework's io-streams +library to handle the streaming IO. The API is optimized for ease of +use for the rather common case of code needing to query web services and +deal with the result.") + (license license:bsd-3))) From 4f1793a2be5ea2b3701d5e15321505225c56084d Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:19:49 +0200 Subject: [PATCH 21/52] gnu: Add ghc-snap-core. * gnu/packages/haskell-web.scm (ghc-snap-core): New variable. --- gnu/packages/haskell-web.scm | 50 ++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index 216c26ba2d..ee37b7eeda 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -1359,3 +1359,53 @@ library to handle the streaming IO. The API is optimized for ease of use for the rather common case of code needing to query web services and deal with the result.") (license license:bsd-3))) + +(define-public ghc-snap-core + (package + (name "ghc-snap-core") + (version "1.0.3.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "snap-core/snap-core-" version ".tar.gz")) + (sha256 + (base32 + "136q7l4hd5yn5hb507q1ziqx124ma1lkzh5dx0n150p8dx3rhhsc")))) + (build-system haskell-build-system) + (inputs + `(("ghc-old-locale" ,ghc-old-locale) + ("ghc-hunit" ,ghc-hunit) + ("ghc-attoparsec" ,ghc-attoparsec) + ("ghc-bytestring-builder" ,ghc-bytestring-builder) + ("ghc-case-insensitive" ,ghc-case-insensitive) + ("ghc-lifted-base" ,ghc-lifted-base) + ("ghc-io-streams" ,ghc-io-streams) + ("ghc-hashable" ,ghc-hashable) + ("ghc-monad-control" ,ghc-monad-control) + ("ghc-random" ,ghc-random) + ("ghc-readable" ,ghc-readable) + ("ghc-regex-posix" ,ghc-regex-posix) + ("ghc-transformers-base" ,ghc-transformers-base) + ("ghc-unix-compat" ,ghc-unix-compat) + ("ghc-unordered-containers" ,ghc-unordered-containers) + ("ghc-vector" ,ghc-vector) + ("ghc-network-uri" ,ghc-network-uri) + ("ghc-network" ,ghc-network))) + (native-inputs + `(("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-parallel" ,ghc-parallel) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) + ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2) + ("ghc-zlib" ,ghc-zlib))) + (arguments + `(#:cabal-revision + ("3" "0wlhn33r7c9g7j23y006ddq9d87lkmianvvfrbl8jd8mvjvj2gfa"))) + (home-page "http://snapframework.com/") + (synopsis "Haskell Web Framework (core interfaces and types)") + (description "Snap is a simple and fast web development framework +and server written in Haskell. For more information, you can visit the +Snap project website at @uref{http://snapframework.com/}. This library +contains the core definitions and types for the Snap framework.") + (license license:bsd-3))) From 8ede1021c80eca0b4481454cbdd05cb1d5eb379a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Mon, 15 Jul 2019 10:25:43 +0200 Subject: [PATCH 22/52] gnu: Add ghc-snap-server. * gnu/packages/haskell-web.scm (ghc-snap-server): New variable. --- gnu/packages/haskell-web.scm | 54 ++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm index ee37b7eeda..7cbf8932e6 100644 --- a/gnu/packages/haskell-web.scm +++ b/gnu/packages/haskell-web.scm @@ -1409,3 +1409,57 @@ and server written in Haskell. For more information, you can visit the Snap project website at @uref{http://snapframework.com/}. This library contains the core definitions and types for the Snap framework.") (license license:bsd-3))) + +(define-public ghc-snap-server + (package + (name "ghc-snap-server") + (version "1.1.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://hackage.haskell.org/package/" + "snap-server/snap-server-" version ".tar.gz")) + (sha256 + (base32 + "0vvw9n8xs272qdlrf3dxhnva41zh3awi7pf022rrjj75lj8a77i4")))) + (build-system haskell-build-system) + (inputs + `(("ghc-attoparsec" ,ghc-attoparsec) + ("ghc-blaze-builder" ,ghc-blaze-builder) + ("ghc-bytestring-builder" ,ghc-bytestring-builder) + ("ghc-case-insensitive" ,ghc-case-insensitive) + ("ghc-clock" ,ghc-clock) + ("ghc-io-streams" ,ghc-io-streams) + ("ghc-io-streams-haproxy" ,ghc-io-streams-haproxy) + ("ghc-lifted-base" ,ghc-lifted-base) + ("ghc-network" ,ghc-network) + ("ghc-old-locale" ,ghc-old-locale) + ("ghc-snap-core" ,ghc-snap-core) + ("ghc-unix-compat" ,ghc-unix-compat) + ("ghc-vector" ,ghc-vector))) + (native-inputs + `(("ghc-base16-bytestring" ,ghc-base16-bytestring) + ("ghc-monad-control" ,ghc-monad-control) + ("ghc-random" ,ghc-random) + ("ghc-threads" ,ghc-threads) + ("ghc-hunit" ,ghc-hunit) + ("ghc-quickcheck" ,ghc-quickcheck) + ("ghc-http-streams" ,ghc-http-streams) + ("ghc-http-common" ,ghc-http-common) + ("ghc-parallel" ,ghc-parallel) + ("ghc-test-framework" ,ghc-test-framework) + ("ghc-test-framework-hunit" ,ghc-test-framework-hunit) + ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2))) + (arguments + `(#:cabal-revision + ("3" "0a9d3nqb5rvgm25nak68lp6yj9m6cwhbgdbg5l7ib5i2czcg7yjh"))) + (home-page "http://snapframework.com/") + (synopsis "Web server for the Snap Framework") + (description "Snap is a simple and fast web development framework +and server written in Haskell. For more information, you can visit the +Snap project website at @uref{http://snapframework.com/}. The Snap HTTP +server is a high performance web server library written in Haskell. +Together with the snap-core library upon which it depends, it provides a +clean and efficient Haskell programming interface to the HTTP +protocol.") + (license license:bsd-3))) From 0d59302ebace0ac294a3fcf7d32b2db3c75cd16a Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 25 Jul 2019 13:06:04 +0200 Subject: [PATCH 23/52] gnu: Remove ghc-regex-tdfa-rc. The package doesn't build, has no reverse dependencies, and is deprecated upstream. * gnu/packages/haskell.scm (ghc-regex-tdfa-rc): Remove variable. --- gnu/packages/haskell.scm | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index a15a899334..1177e6f80d 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -2951,30 +2951,6 @@ Haskell library @code{regex-base}.") @code{regex-posix} to replace @code{Text.Regex}.") (license license:bsd-3))) -(define-public ghc-regex-tdfa-rc - (package - (name "ghc-regex-tdfa-rc") - (version "1.1.8.3") - (source - (origin - (method url-fetch) - (uri (string-append - "https://hackage.haskell.org/package/regex-tdfa-rc/regex-tdfa-rc-" - version - ".tar.gz")) - (sha256 - (base32 - "1vi11i23gkkjg6193ak90g55akj69bhahy542frkwb68haky4pp3")))) - (build-system haskell-build-system) - (inputs - `(("ghc-regex-base" ,ghc-regex-base))) - (home-page - "https://hackage.haskell.org/package/regex-tdfa") - (synopsis "Tagged DFA regex engine for Haskell") - (description "A new all-Haskell \"tagged\" DFA regex engine, inspired by -@code{libtre} (fork by Roman Cheplyaka).") - (license license:bsd-3))) - (define-public ghc-regex-tdfa-text (package (name "ghc-regex-tdfa-text") From 63edeca7730e877441af1946ff9b6e255d17afc7 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 25 Jul 2019 13:08:47 +0200 Subject: [PATCH 24/52] gnu: Remove ghc-haddock-test. The package doesn't build, has no reverse dependencies, and is deprecated upstream. * gnu/packages/haskell.scm (ghc-haddock-test): Remove variable. --- gnu/packages/haskell.scm | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 1177e6f80d..403827f0d9 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -1102,28 +1102,6 @@ the ‘haddock’ package.") documentation-generation tool for Haskell libraries.") (license license:bsd-3))) -(define-public ghc-haddock-test - (package - (name "ghc-haddock-test") - (version "0.0.1") - (source - (origin - (method url-fetch) - (uri (string-append "https://hackage.haskell.org/package/" - "haddock-test/haddock-test-" - version ".tar.gz")) - (sha256 - (base32 - "1ax8fnfrwx66csj952f3virxzapipan9da7z5l1zc12nqkifbs7w")))) - (build-system haskell-build-system) - (inputs - `(("ghc-xml" ,ghc-xml) - ("ghc-syb" ,ghc-syb))) - (home-page "http://www.haskell.org/haddock/") - (synopsis "Test utilities for Haddock") - (description "This package provides test utilities for Haddock.") - (license license:bsd-3))) - (define-public ghc-haddock (package (name "ghc-haddock") From 3755088b54ba83bf539d5afd8ec4f6dbc44be560 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 1 Aug 2019 18:11:35 +0200 Subject: [PATCH 25/52] gnu: Remove ghc-packedstring. The package has no reverse dependencies and is deprecated upstream. * gnu/packages/haskell.scm (ghc-packedstring): Remove variable. --- gnu/packages/haskell.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 403827f0d9..d7cbd37394 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -5896,35 +5896,6 @@ within an enclosed computation, while remaining responsive to (external) asynchronous exceptions.") (license license:expat))) -(define-public ghc-packedstring - (package - (name "ghc-packedstring") - (version "0.1.0.1") - (source (origin - (method url-fetch) - (uri (string-append "https://hackage.haskell.org/package/" - "packedstring/packedstring-" - version ".tar.gz")) - (sha256 - (base32 - "1x78pzzdlnpcmh9p37rlf8m5cxf3yqm2alf3whl4zpr9w25r0qj8")))) - (build-system haskell-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'enable-extension - (lambda _ - ;; This package won't compile without the StandaloneDeriving - ;; extension. - (substitute* "packedstring.cabal" - (("CPP") "CPP, StandaloneDeriving")) - #t))))) - (home-page "https://hackage.haskell.org/package/packedstring") - (synopsis "Library for packed strings") - (description - "This deprecated library provides an implementation of packed strings.") - (license license:bsd-3))) - (define-public ghc-th-abstraction (package (name "ghc-th-abstraction") From 9ec2d6f84c67125865b92aecb5f64486dfbc570e Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 25 Jul 2019 23:56:47 +0200 Subject: [PATCH 26/52] gnu: ghc-libmpd-haskell: Disable tests. * gnu/packages/haskell.scm (ghc-libmpd-haskell)[arguments]: Disable tests. --- gnu/packages/haskell.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index d7cbd37394..f6ced263ac 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -11236,6 +11236,9 @@ imported with the correct Haskell types.") (base32 "1931m23iqb4wddpdidm4ph746zpaw41kkjzmb074j7yyfpk7x1jv")))) (build-system haskell-build-system) + ;; Tests fail on i686. + ;; See https://github.com/vimus/libmpd-haskell/issues/112 + (arguments `(#:tests? #f)) (inputs `(("ghc-attoparsec" ,ghc-attoparsec) ("ghc-old-locale" ,ghc-old-locale) From dbfaac113a7530e04cb5058bee1e308e1d178daf Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Fri, 26 Jul 2019 00:07:58 +0200 Subject: [PATCH 27/52] gnu: ghc-yaml: Disable tests. * gnu/packages/haskell.scm (ghc-yaml)[arguments]: Disable tests. --- gnu/packages/haskell.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index f6ced263ac..dac8e46652 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -6210,6 +6210,9 @@ back-ends.") (base32 "0cbsyh4ilvjzq1q7pxls43k6pdqxg1l85xzibcwpbvmlvrizh86w")))) (build-system haskell-build-system) + ;; The tests are broken on i686. They are fixed in 0.10.3.0. + ;; See https://github.com/snoyberg/yaml/issues/158 + (arguments `(#:tests? #f)) (inputs `(("ghc-conduit" ,ghc-conduit) ("ghc-resourcet" ,ghc-resourcet) From caa366ec230ccc42f5c8d90d36e8cac933053a81 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 30 Jul 2019 19:49:14 +0200 Subject: [PATCH 28/52] gnu: ghc-trifecta: Disable tests. * gnu/packages/haskell.scm (ghc-trifecta)[arguments]: Disable tests. --- gnu/packages/haskell.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index dac8e46652..8787f10789 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -3043,6 +3043,7 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s (base32 "0hznd8i65s81xy13i2qc7cvipw3lfb2yhkv53apbdsh6sbljz5sk")))) (build-system haskell-build-system) + (arguments `(#:tests? #f)) ; doctest suite fails to build on i686 (inputs `(("ghc-reducers" ,ghc-reducers) ("ghc-semigroups" ,ghc-semigroups) From 8378c87a590788921b5cb78eae4b4a53280a4d96 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 7 Aug 2019 18:48:17 +0200 Subject: [PATCH 29/52] gnu: Add network-manager-openconnect. * gnu/packages/gnome.scm (network-manager-openconnect): New variable. --- gnu/packages/gnome.scm | 51 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 601248b7f5..da6cbf2a05 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5535,6 +5535,57 @@ Compatible with Cisco VPN concentrators configured to use IPsec.") (license license:gpl2+) (properties `((upstream-name . "NetworkManager-vpnc"))))) +(define-public network-manager-openconnect + (package + (name "network-manager-openconnect") + (version "1.2.6") + (source (origin + (method url-fetch) + (uri (string-append + "mirror://gnome/sources/NetworkManager-openconnect/" + (version-major+minor version) + "/NetworkManager-openconnect-" version ".tar.xz")) + (sha256 + (base32 + "0nlp290nkawc4wqm978n4vhzg3xdqi8kpjjx19l855vab41rh44m")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--enable-absolute-paths" "--localstatedir=/var") + #:phases + (modify-phases %standard-phases + (add-after 'configure 'patch-path + (lambda* (#:key inputs outputs #:allow-other-keys #:rest args) + (let* ((openconnect (string-append (assoc-ref inputs "openconnect") + "/sbin/openconnect")) + (modprobe (string-append (assoc-ref inputs "kmod") + "/bin/modprobe")) + (pretty-ovpn (string-append "\"" openconnect "\""))) + (substitute* "src/nm-openconnect-service.c" + (("\"/usr/local/sbin/openconnect\"") pretty-ovpn) + (("\"/usr/sbin/openconnect\"") pretty-ovpn) + (("/sbin/modprobe") modprobe))) + #t))))) + (native-inputs + `(("intltool" ,intltool) + ("network-manager-applet" ,network-manager-applet) ;for libnma + ("pkg-config" ,pkg-config))) + (inputs + `(("gcr" ,gcr) + ("gtk+" ,gtk+) + ("kmod" ,kmod) + ("libsecret" ,libsecret) + ("libxml2" ,libxml2) + ("network-manager" ,network-manager) + ("openconnect" ,openconnect))) + (home-page "https://wiki.gnome.org/Projects/NetworkManager/VPN") + (synopsis "OpenConnect plug-in for NetworkManager") + (description + "This extension of NetworkManager allows it to take care of connections +to @acronym{VPNs, virtual private networks} via OpenConnect, an open client for +Cisco's AnyConnect SSL VPN.") + (license license:gpl2+) + (properties `((upstream-name . "NetworkManager-openconnect"))))) + (define-public mobile-broadband-provider-info (package (name "mobile-broadband-provider-info") From 62a031afc438dcf2c2b38259334cb6e3b369a908 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:34 +0200 Subject: [PATCH 30/52] gnu: Add tabixpp. * gnu/packages/bioinformatics.scm (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 40 +++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 991a3c6487..5a63399967 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14827,3 +14827,43 @@ trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.") (license license:expat)))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8")))) + (build-system gnu-build-system) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix++" bin)) + #t))))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in tabix-indexed files.") + (license license:expat))) From 7faa70cf2b6a81f2670b52e5caa502e409626faa Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:35 +0200 Subject: [PATCH 31/52] gnu: Add smithwaterman. * gnu/packages/bioinformatics.scm (smithwaterman): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a63399967..2105393473 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14867,3 +14867,34 @@ mutations from scRNA-Seq data.") (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "smithwaterman" bin)) + #t))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat))))) From 8cd51276e53fc4988029bcd2de2b69db68ea6e05 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:36 +0200 Subject: [PATCH 32/52] gnu: Add multichoose. * gnu/packages/bioinformatics.scm (multichoose): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2105393473..086e9324cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14898,3 +14898,37 @@ some of the details of opening and jumping in tabix-indexed files.") (description "Implementation of the Smith-Waterman algorithm.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) + +(define-public multichoose + (package + (name "multichoose") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/multichoose/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; Tests require node. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + ;; TODO: There are Python modules for these programs too. + (install-file "multichoose" bin) + (install-file "multipermute" bin)) + #t))))) + (home-page "https://github.com/ekg/multichoose") + (synopsis "Efficient loopless multiset combination generation algorithm") + (description "This library implements an efficient loopless multiset +combination generation algorithm which is (approximately) described in +\"Loopless algorithms for generating permutations, combinations, and other +combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), +1973. (Algorithm 7.)") + (license license:expat))) From 70782dddffc2da05fed6aba35c3121a2265fd649 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:37 +0200 Subject: [PATCH 33/52] gnu: Add fsom. * gnu/packages/bioinformatics.scm (fsom): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 086e9324cb..a3c83f73bb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14932,3 +14932,33 @@ combination generation algorithm which is (approximately) described in combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)") (license license:expat))) + +(define-public fsom + (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3")) + (package + (name "fsom") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fsom/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fsom" bin)) + #t))))) + (home-page "https://github.com/ekg/fsom") + (synopsis "Manage SOM (Self-Organizing Maps) neural networks") + (description "A tiny C library for managing SOM (Self-Organizing Maps) +neural networks.") + (license license:gpl3)))) From 7d71557d4d3ca5bdd33eb8c9bdf0cd2aba624554 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:38 +0200 Subject: [PATCH 34/52] gnu: Add fastahack. * gnu/packages/bioinformatics.scm (fastahack): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a3c83f73bb..4dae22082d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14962,3 +14962,36 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (description "A tiny C library for managing SOM (Self-Organizing Maps) neural networks.") (license license:gpl3)))) + +(define-public fastahack + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) + (package + (name "fastahack") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fastahack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "fastahack" bin)) + #t))))) + (home-page "https://github.com/ekg/fastahack") + (synopsis "Indexing and sequence extraction from FASTA files") + (description "Fastahack is a small application for indexing and +extracting sequences and subsequences from FASTA files. The included library +provides a FASTA reader and indexer that can be embedded into applications +which would benefit from directly reading subsequences from FASTA files. The +library automatically handles index file generation and use.") + (license (list license:expat license:gpl2))))) From 194e45f90addf5f9bd3e7e2de1dd50b3071f053b Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:39 +0200 Subject: [PATCH 35/52] gnu: Add vcflib. * gnu/packages/bioinformatics.scm (vcflib): New variable. --- gnu/packages/bioinformatics.scm | 105 ++++++++++++++++++++++++++++++++ 1 file changed, 105 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dae22082d..7808976a1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14868,6 +14868,24 @@ mutations from scRNA-Seq data.") some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define tabixpp-freebayes + ;; This version works with FreeBayes while the released + ;; version doesn't. The released creates a variable with the name \"vcf\" + ;; somewhere, which is also the name of a namespace in vcflib. + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) + (package + (inherit tabixpp) + (name "tabixpp-freebayes") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) + (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -14995,3 +15013,90 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) + +(define-public vcflib + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92") + (revision "1")) + (name "vcflib") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("perl" ,perl) + ("python" ,python-2) + ;; Submodules. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (invoke "make")) + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " "\"") + "all"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + ;; The header files in src/ do not interface libvcflib, + ;; therefore they are left out. + (install-file "libvcflib.a" lib)) + #t))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) From 173e046950e153477a6aaa0f4860d8f080df6843 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:40 +0200 Subject: [PATCH 36/52] gnu: Add freebayes. * gnu/packages/bioinformatics.scm (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 123 ++++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7808976a1f..311a83e53b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15100,3 +15100,126 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) + +(define-public freebayes + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") + (revision "1") + (version "1.0.2")) + (package + (name "freebayes") + (version (git-version version revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/freebayes.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (native-inputs + `(("bc" ,bc) ; Needed for running tests. + ("samtools" ,samtools) ; Needed for running tests. + ("parallel" ,parallel) ; Needed for running tests. + ("perl" ,perl) ; Needed for running tests. + ("procps" ,procps) ; Needed for running tests. + ("python" ,python-2) ; Needed for running tests. + ("bamtools" ,bamtools) + ("vcflib-src" ,(package-source vcflib)) + ;; These are submodules for the vcflib version used in freebayes. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("smithwaterman-src" ,(package-source smithwaterman)) + ("multichoose-src" ,(package-source multichoose)) + ("fsom-src" ,(package-source fsom)) + ("filevercmp-src" ,(package-source filevercmp)) + ("fastahack-src" ,(package-source fastahack)) + ("intervaltree-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) + ;; These submodules are needed to run the tests. + ("bash-tap-src" ,(package-source bash-tap)) + ("test-simple-bash-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ingydotnet/test-simple-bash/") + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) + (file-name "test-simple-bash-src-checkout") + (sha256 + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) + (arguments + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (with-directory-excursion target + (if (file-is-directory? (assoc-ref inputs source)) + (copy-recursively (assoc-ref inputs source) ".") + (invoke "tar" "xvf" + (assoc-ref inputs source) + "--strip-components=1")))))) + (and + (unpack "vcflib-src" "vcflib") + (unpack "fastahack-src" "vcflib/fastahack") + (unpack "filevercmp-src" "vcflib/filevercmp") + (unpack "fsom-src" "vcflib/fsom") + (unpack "intervaltree-src" "vcflib/intervaltree") + (unpack "multichoose-src" "vcflib/multichoose") + (unpack "smithwaterman-src" "vcflib/smithwaterman") + (unpack "tabixpp-src" "vcflib/tabixpp") + (unpack "test-simple-bash-src" "test/test-simple-bash") + (unpack "bash-tap-src" "test/bash-tap"))))) + (add-after 'unpack-submodule-sources 'fix-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "bin/freebayes" bin) + (install-file "bin/bamleftalign" bin)) + #t))))) + (home-page "https://github.com/ekg/freebayes") + (synopsis "Haplotype-based variant detector") + (description "FreeBayes is a Bayesian genetic variant detector designed to +find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), +indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and +complex events (composite insertion and substitution events) smaller than the +length of a short-read sequencing alignment.") + (license license:expat)))) From 6bc63fd8a7a44a3b2bd1686be619237e7dd94ef1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Aug 2019 15:32:39 +0300 Subject: [PATCH 37/52] Revert "gnu: Add freebayes." This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843. --- gnu/packages/bioinformatics.scm | 123 -------------------------------- 1 file changed, 123 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 311a83e53b..7808976a1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15100,126 +15100,3 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) - -(define-public freebayes - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") - (revision "1") - (version "1.0.2")) - (package - (name "freebayes") - (version (git-version version revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/freebayes.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) - (build-system gnu-build-system) - (inputs - `(("zlib" ,zlib) - ("htslib" ,htslib))) - (native-inputs - `(("bc" ,bc) ; Needed for running tests. - ("samtools" ,samtools) ; Needed for running tests. - ("parallel" ,parallel) ; Needed for running tests. - ("perl" ,perl) ; Needed for running tests. - ("procps" ,procps) ; Needed for running tests. - ("python" ,python-2) ; Needed for running tests. - ("bamtools" ,bamtools) - ("vcflib-src" ,(package-source vcflib)) - ;; These are submodules for the vcflib version used in freebayes. - ;; This package builds against the .o files so we need to extract the source. - ("tabixpp-src" ,(package-source tabixpp-freebayes)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("multichoose-src" ,(package-source multichoose)) - ("fsom-src" ,(package-source fsom)) - ("filevercmp-src" ,(package-source filevercmp)) - ("fastahack-src" ,(package-source fastahack)) - ("intervaltree-src" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/intervaltree/") - (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) - (file-name "intervaltree-src-checkout") - (sha256 - (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) - ;; These submodules are needed to run the tests. - ("bash-tap-src" ,(package-source bash-tap)) - ("test-simple-bash-src" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ingydotnet/test-simple-bash/") - (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) - (file-name "test-simple-bash-src-checkout") - (sha256 - (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) - (arguments - `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "vcflib-src" "vcflib") - (unpack "fastahack-src" "vcflib/fastahack") - (unpack "filevercmp-src" "vcflib/filevercmp") - (unpack "fsom-src" "vcflib/fsom") - (unpack "intervaltree-src" "vcflib/intervaltree") - (unpack "multichoose-src" "vcflib/multichoose") - (unpack "smithwaterman-src" "vcflib/smithwaterman") - (unpack "tabixpp-src" "vcflib/tabixpp") - (unpack "test-simple-bash-src" "test/test-simple-bash") - (unpack "bash-tap-src" "test/bash-tap"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) - ;; We don't have the .git folder to get the version tag from. - (substitute* '("vcflib/Makefile") - (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "vcflib" - (with-directory-excursion "tabixpp" - (pk "Compile tabixpp before compiling the main project.") - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" "HTS_HEADERS=" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) - (pk "Compile vcflib before compiling the main project.") - (invoke "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") - "all")) - (pk "Compile the main project.") - (with-directory-excursion "src" - (substitute* "Makefile" - (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) - (invoke "make" - (string-append "BAMTOOLS_ROOT=" - (assoc-ref inputs "bamtools")))))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "bin/freebayes" bin) - (install-file "bin/bamleftalign" bin)) - #t))))) - (home-page "https://github.com/ekg/freebayes") - (synopsis "Haplotype-based variant detector") - (description "FreeBayes is a Bayesian genetic variant detector designed to -find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), -indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and -complex events (composite insertion and substitution events) smaller than the -length of a short-read sequencing alignment.") - (license license:expat)))) From 1a069a170c636751695d54c2b282a196eda773c6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Aug 2019 15:33:37 +0300 Subject: [PATCH 38/52] Revert "gnu: Add vcflib." This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master --- gnu/packages/bioinformatics.scm | 105 -------------------------------- 1 file changed, 105 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7808976a1f..4dae22082d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14868,24 +14868,6 @@ mutations from scRNA-Seq data.") some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) -(define tabixpp-freebayes - ;; This version works with FreeBayes while the released - ;; version doesn't. The released creates a variable with the name \"vcf\" - ;; somewhere, which is also the name of a namespace in vcflib. - (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) - (package - (inherit tabixpp) - (name "tabixpp-freebayes") - (version (git-version "0.0.0" "1" commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) - (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -15013,90 +14995,3 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) - -(define-public vcflib - (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92") - (revision "1")) - (name "vcflib") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/vcflib/vcflib/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) - (build-system gnu-build-system) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("perl" ,perl) - ("python" ,python-2) - ;; Submodules. - ;; This package builds against the .o files so we need to extract the source. - ("tabixpp-src" ,(package-source tabixpp-freebayes)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("multichoose-src" ,(package-source multichoose)) - ("fsom-src" ,(package-source fsom)) - ("filevercmp-src" ,(package-source filevercmp)) - ("fastahack-src" ,(package-source fastahack)) - ("intervaltree-src" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/intervaltree/") - (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) - (file-name "intervaltree-src-checkout") - (sha256 - (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) - (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "fastahack") - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "tabixpp" - (invoke "make")) - (invoke "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " "\"") - "all"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - ;; The header files in src/ do not interface libvcflib, - ;; therefore they are left out. - (install-file "libvcflib.a" lib)) - #t))))) - (home-page "https://github.com/vcflib/vcflib/") - (synopsis "Library for parsing and manipulating VCF files") - (description "Vcflib provides methods to manipulate and interpret -sequence variation as it can be described by VCF. It is both an API for parsing -and operating on records of genomic variation as it can be described by the VCF -format, and a collection of command-line utilities for executing complex -manipulations on VCF files.") - (license license:expat)))) From ba73c434e0a3d31a0800fbb20f5779f9a8f77809 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 16:45:14 +0200 Subject: [PATCH 39/52] gnu: ToME4: Disable parallel build. * gnu/packages/games.scm (tome4)[arguments]: Add <#:parallel-build?>. --- gnu/packages/games.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 07ed02ba18..92df556970 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4977,6 +4977,10 @@ Crowther & Woods, its original authors, in 1995. It has been known as ("luajit" ,luajit))) (arguments `(#:make-flags '("CC=gcc" "config=release") + ;; XXX: Building in parallel occasionally causes this build failure: + ;; ../src/luajit2/src/host/buildvm.c:73:10: fatal error: buildvm_arch.h: + ;; No such file or directory + #:parallel-build? #f #:phases (modify-phases %standard-phases (delete 'bootstrap) (replace 'configure From a39f2e4cea3954497b541eba71e24627ce111b15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:00 +0200 Subject: [PATCH 40/52] gnu: r-biocparallel: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dae22082d..1bf9278c5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,13 +7691,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x")))) + "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) From 90060e2071cf3c21430d6470d15324c502bccc4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:07 +0200 Subject: [PATCH 41/52] gnu: r-hdf5array: Update to 1.12.2. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf9278c5d..e860b5b881 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10425,14 +10425,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp")))) + "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs From d099499e0bf7f86e182e68562a76dc1efa795267 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:12 +0200 Subject: [PATCH 42/52] gnu: r-ggsignif: Update to 0.6.0. * gnu/packages/cran.scm (r-ggsignif): Update to 0.6.0. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4b998eb1fb..87288c2548 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5544,14 +5544,14 @@ movies, and TV shows.") (define-public r-ggsignif (package (name "r-ggsignif") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggsignif" version)) (sha256 (base32 - "0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x")))) + "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2))) From 9649072cbde9d489b41ea06d6b37d0fdec1055bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:18 +0200 Subject: [PATCH 43/52] gnu: r-markdown: Update to 1.1. * gnu/packages/statistics.scm (r-markdown): Update to 1.1. [propagated-inputs]: Add r-xfun. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f27f2229f7..f5c822d532 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1404,13 +1404,13 @@ data derived from /etc/mime.types in UNIX-type systems.") (define-public r-markdown (package (name "r-markdown") - (version "1.0") + (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "markdown" version)) (sha256 (base32 - "19nrz0ba1yd5kicd65crkkz2r3kialm2hm6zdkp495l2s5r80b8p")))) + "06zwbrp14bri3470anadd7dvgmw06xf8df6v2pk64wx3f9sd934d")))) (build-system r-build-system) ;; Skip check phase because the tests require the r-knitr package to be ;; installed. This prevents installation failures. Knitr normally @@ -1418,7 +1418,8 @@ data derived from /etc/mime.types in UNIX-type systems.") ;; package. (arguments `(#:tests? #f)) (propagated-inputs - `(("r-mime" ,r-mime))) + `(("r-mime" ,r-mime) + ("r-xfun" ,r-xfun))) (home-page "https://github.com/rstudio/markdown") (synopsis "Markdown rendering for R") (description From eaca771e88581023b886327ea13352d4b3f22eb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:31 +0200 Subject: [PATCH 44/52] gnu: r-knitr: Update to 1.24. * gnu/packages/statistics.scm (r-knitr): Update to 1.24. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f5c822d532..7f4769ec01 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1449,13 +1449,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.23") + (version "1.24") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "16ba4258c915xydhniw4cw7fvv1vp4cnwd1w49ykx7zw00rznfq6")))) + "12bvs9fd61m7k7bq321qzrh2ccl9rq653s1anrvfb9s5ni1j0378")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) From eb8963d98910b728df2968a3fd15f361afc44b85 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:35 +0200 Subject: [PATCH 45/52] gnu: r-quantreg: Update to 5.51. * gnu/packages/statistics.scm (r-quantreg): Update to 5.51. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f4769ec01..248bf39eff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5141,14 +5141,14 @@ using modular prediction and response module classes.") (define-public r-quantreg (package (name "r-quantreg") - (version "5.42.1") + (version "5.51") (source (origin (method url-fetch) (uri (cran-uri "quantreg" version)) (sha256 (base32 - "1aycnghci329yqw63kybv7sfjjx5whq3xs7xzic4wsaj7j4b1hjc")))) + "1cdx51a9g6fjq2g9arr6wp6ghkyl2m6bs2dj4kcycvpn8p9304yz")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) From 7ef25083f0f9a4fc260a3b032a1b01a5927f1fb0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 17:20:46 +0200 Subject: [PATCH 46/52] gnu: r-modelr: Update to 0.1.5. * gnu/packages/cran.scm (r-modelr): Update to 0.1.5. [propagated-inputs]: Remove r-lazyeval; add r-rlang. --- gnu/packages/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 87288c2548..d928f971d0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -420,21 +420,21 @@ the embedded @code{RapidXML} C++ library.") (define-public r-modelr (package (name "r-modelr") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "modelr" version)) (sha256 (base32 - "1ngxphbjkv7yl1rg30sj36mfwhc76g452drjrq9abgab4k0pgnml")))) + "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5")))) (build-system r-build-system) (propagated-inputs `(("r-broom" ,r-broom) ("r-dplyr" ,r-dplyr) - ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) + ("r-rlang" ,r-rlang) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr))) (home-page "https://github.com/tidyverse/modelr") From bd12be346b728619528d22e9ee86aaa40076f86a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:20:59 +0200 Subject: [PATCH 47/52] gnu: LibRaw: Update to 0.19.4. * gnu/packages/photo.scm (libraw): Update to 0.19.4. --- gnu/packages/photo.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index cbfc2debd8..b445374718 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -70,14 +70,14 @@ (define-public libraw (package (name "libraw") - (version "0.19.3") + (version "0.19.4") (source (origin (method url-fetch) (uri (string-append "https://www.libraw.org/data/LibRaw-" version ".tar.gz")) (sha256 (base32 - "0xs1qb6pcvc4c43fy5xi3nkqxcif77gakkw99irf0fc5iccdd5px")))) + "07wnzw9k3mwdq9dmpmg94al3ksc065kskfbxkknnmhvrsv2iri8k")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From df3db975875962c47a0329e15ad1f477c9de73e3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:25:36 +0200 Subject: [PATCH 48/52] gnu: exempi: Update to 2.5.1. * gnu/packages/freedesktop.scm (exempi): Update to 2.5.1. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index d77d6c58c4..aa783c3b53 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -718,7 +718,7 @@ multiplexer to the KMS/DRM Linux kernel devices.") (define-public exempi (package (name "exempi") - (version "2.5.0") + (version "2.5.1") (source (origin (method url-fetch) (uri (string-append @@ -726,7 +726,7 @@ multiplexer to the KMS/DRM Linux kernel devices.") name "-" version ".tar.bz2")) (sha256 (base32 - "06vi7dc2gappwqm3xpfyy5ihxq14bmvj3bd47yk482jlq0jgr0nw")))) + "1j4vx054l1c2cggw4aka4iw48jkcf68qk5y064pbqw1k3ddks2qh")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "--with-boost=" From cbfddc2f33b9a4e161627fe55823bf17b21b5b0b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:34:21 +0200 Subject: [PATCH 49/52] gnu: postgresql@11: Update to 11.5 [fixes CVE-2019-10208, CVE-2019-10209]. * gnu/packages/databases.scm (postgresql-11): Update to 11.5. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 4e2db8ed44..57f7a79e03 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -853,14 +853,14 @@ pictures, sounds, or video.") (package (inherit postgresql) (name "postgresql") - (version "11.4") + (version "11.5") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "12ycjlqncijgmd5z078ybwda8ilas96lc7nxxmdq140mzpgjv002")))))) + "106ikalvrilihlvhq7xj7snq98hgbgq6qsgjrd252wgw1c327pvz")))))) (define-public postgresql-9.6 (package From 14b80bf6cac7ec172d96084965b322d758107c61 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:35:54 +0200 Subject: [PATCH 50/52] gnu: postgresql@9: Update to 9.6.15 [fixes CVE-2019-10208]. * gnu/packages/databases.scm (postgresql-9.6): Update to 9.6.15. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 57f7a79e03..f8b8dc3431 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -866,14 +866,14 @@ pictures, sounds, or video.") (package (inherit postgresql) (name "postgresql") - (version "9.6.14") + (version "9.6.15") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "08hsqczy1ixkjyf2vr3s9x69agfz9yr8lh31fir4z0dfr5jw421z")))))) + "02hp69h2p02asfblkaahblzdz2zmawd2r11h6237y5j7yadgxn9w")))))) (define-public python-pymysql (package From c96ec77198df8fb1d8c411c857204b75c486dbbe Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:41:21 +0200 Subject: [PATCH 51/52] gnu: exempi: Update home page. * gnu/packages/freedesktop.scm (exempi)[home-page]: Update to current. --- gnu/packages/freedesktop.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index aa783c3b53..9cfdbca3fb 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -736,7 +736,7 @@ multiplexer to the KMS/DRM Linux kernel devices.") (inputs `(("expat" ,expat) ("zlib" ,zlib))) - (home-page "https://wiki.freedesktop.org/libopenraw/Exempi") + (home-page "https://libopenraw.freedesktop.org/exempi/") (synopsis "XMP metadata handling library") (description "Exempi is an implementation of the Extensible Metadata Platform (@dfn{XMP}), which enables embedding metadata in PDF and image From ffc4869e45e852414b6ead19e7d93fca96d4e833 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 8 Aug 2019 17:47:54 +0200 Subject: [PATCH 52/52] gnu: ruby-pg: Update to 1.1.4. * gnu/packages/ruby.scm (ruby-pg): Update to 1.1.4. [inputs]: Change from POSTGRESQL-9.6 to POSTGRESQL. --- gnu/packages/ruby.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index d47c2ed07d..1b70f842ae 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -4849,14 +4849,14 @@ alternative to Marshal for Object serialization. ") (define-public ruby-pg (package (name "ruby-pg") - (version "1.1.3") + (version "1.1.4") (source (origin (method url-fetch) (uri (rubygems-uri "pg" version)) (sha256 (base32 - "1pnjw3rspdfjssxyf42jnbsdlgri8ylysimp0s28wxb93k6ff2qb")))) + "0fmnyxcyrvgdbgq7m09whgn9i8rwfybk0w8aii1nc4g5kqw0k2jy")))) (build-system ruby-build-system) (arguments '(#:test-target "spec")) @@ -4865,7 +4865,7 @@ alternative to Marshal for Object serialization. ") ("ruby-hoe" ,ruby-hoe) ("ruby-rspec" ,ruby-rspec))) (inputs - `(("postgresql" ,postgresql-9.6))) + `(("postgresql" ,postgresql))) (synopsis "Ruby interface to PostgreSQL") (description "Pg is the Ruby interface to the PostgreSQL RDBMS. It works with PostgreSQL 9.0 and later.")