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 @@ (define-public ghc-8.0 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 @@ (define-public ghc-8 (file-pattern ".*\\.conf\\.d$") (file-type 'directory)))))) +(define-public ghc-8 ghc-8.4) + (define-public ghc ghc-8) (define-public ghc-hostname From cce84c34cd40610f49d7acc58eeea541edf45578 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Tue, 16 Jul 2019 08:45:40 +0200 Subject: [PATCH 02/52] gnu: Add ghc-8.6. * gnu/packages/haskell.scm (ghc-8.6): New variable. Co-authored-by: Timothy Sample --- gnu/packages/haskell.scm | 46 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm index 019f751307..4f283f7069 100644 --- a/gnu/packages/haskell.scm +++ b/gnu/packages/haskell.scm @@ -73,6 +73,7 @@ (define-module (gnu packages haskell) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) + #:use-module (ice-9 match) #:use-module (ice-9 regex) #:use-module ((srfi srfi-1) #:select (alist-delete))) @@ -572,6 +573,51 @@ (define-public ghc-8.4 (file-pattern ".*\\.conf\\.d$") (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-module (guix import hackage) (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 @@ (define ghc-standard-libraries "deepseq" "directory" "filepath" + "ghc" "ghc-boot" + "ghc-boot-th" "ghc-compact" "ghc-prim" "ghci" @@ -74,8 +77,11 @@ (define ghc-standard-libraries "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 @@ (define-public agda ("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 @@ (define-public ngless ("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 @@ (define-public darcs ("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 @@ (define-public git-annex ("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 @@ (define-public ghc-sdl2 `(("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 @@ (define-public ghc-sdl2-image (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 @@ (define-public ghc-tasty-ant-xml (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 @@ (define-public ghc-tasty "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 @@ (define-public ghc-tasty-rerun `(("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 @@ (define-public ghc-quickcheck-instances ("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 @@ (define-public ghc-hedgehog ("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 @@ (define-public ghc-asn1-encoding (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 @@ (define-public ghc-tagsoup (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 @@ (define-public ghc-cookie (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 @@ (define-public ghc-http-types ("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 @@ (define-public ghc-http ("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 @@ (define-public ghc-http-client ("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 @@ (define-public ghc-http2 ("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 @@ (define-public ghc-http-conduit ("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 @@ (define-public ghc-wai ("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 @@ (define-public ghc-wai-extra ("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 @@ (define-public ghc-warp ("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 @@ (define-public ghc-xss-sanitize ("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 @@ (define-public ghc-css-text "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 @@ (define-public ghc-mime-types (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 @@ (define-public ghc-html 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 @@ (define-public ghc-blaze-html (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 @@ (define-public ghc-aeson ("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 @@ (define-public ghc-aeson-pretty ("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 @@ (define-public ghc-aeson-qq (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 @@ (define-public ghc-multipart "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 @@ (define-public ghc-uri-encode "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 @@ (define-public ghc-path-pieces (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 @@ (define-public ghc-yesod-core (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 @@ (define-public ghc-yesod-core ("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 @@ (define-public ghc-yesod-persistent (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 @@ (define-public ghc-yesod-form ("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 @@ (define-public ghc-yesod ("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 @@ (define-public ghc-hxt-regex-xmlschema (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 @@ (define-public ghc-hxt "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 @@ (define-public ghc-convertible (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 @@ (define-public ghc-double-conversion (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 @@ (define-public ghc-tree-diff ("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 @@ (define-public ghc-tree-diff ("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 @@ (define-public ghc-cgi (("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 @@ (define-public hlint ("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 @@ (define-public ghc-openglraw (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 @@ (define-public ghc-opengl "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 @@ (define-public ghc-streaming-commons ("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 @@ (define-public ghc-hackage-security ("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 @@ (define-public cabal-install ("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 @@ (define-public ghc-parsec-numbers (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 @@ (define-public ghc-zlib 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 @@ (define-public ghc-safesemaphore (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 @@ (define-public ghc-safesemaphore 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 @@ (define-public ghc-text-binary (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 @@ (define-public ghc-hashable "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 @@ (define-public ghc-transformers-base "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 @@ (define-public ghc-indents ;; 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 @@ (define-public ghc-regex-tdfa-rc "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 @@ (define-public ghc-regex-tdfa-text "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 @@ (define-public ghc-regex ("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 @@ (define-public ghc-parsers (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 @@ (define-public ghc-attoparsec ((", 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 @@ (define-public ghc-attoparsec-bootstrap (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 @@ (define-public ghc-zip-archive (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 @@ (define-public ghc-polyparse (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 @@ (define-public ghc-reducers (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 @@ (define-public ghc-xml (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 @@ (define-public ghc-feed ("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 @@ (define-public ghc-exceptions ("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 @@ (define-public ghc-case-insensitive (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 @@ (define-public ghc-split 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 @@ (define-public ghc-megaparsec (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 @@ (define-public ghc-network-uri (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 @@ (define-public ghc-monad-control "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 @@ (define-public ghc-blaze-builder (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 @@ (define-public ghc-blaze-markup (("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 @@ (define-public ghc-async "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 @@ (define-public ghc-invariant ("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 @@ (define-public ghc-statevar (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 @@ (define-public ghc-lens ("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 @@ (define-public ghc-cheapskate "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 @@ (define-public ghc-semigroups `(("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 @@ (define-public ghc-semigroups-bootstrap `(("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 @@ (define-public ghc-fast-logger (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 @@ (define-public ghc-scientific (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 @@ (define-public ghc-scientific-bootstrap (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 @@ (define-public ghc-texmath ("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 @@ (define-public ghc-highlighting-kate `(("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 @@ (define-public ghc-cmark (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 @@ (define-public ghc-cmark-gfm (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 @@ (define-public ghc-th-lift-instances (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 @@ (define-public ghc-yaml ("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 @@ (define-public ghc-hslua (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 @@ (define-public ghc-hslua-module-text `(#: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 @@ (define-public ghc-skylighting-core ("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 @@ (define-public ghc-doctemplates `(("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 @@ (define-public ghc-pandoc ("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 @@ (define-public ghc-pandoc ("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 @@ (define-public ghc-typed-process "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 @@ (define-public ghc-conduit-extra `(("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 @@ (define-public ghc-conduit-extra ("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 @@ (define-public ghc-xml-types (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 @@ (define-public ghc-xml-conduit ("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 @@ (define-public ghc-pandoc-citeproc ("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 @@ (define-public ghc-pandoc-citeproc ("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 @@ (define-public ghc-regex-tdfa "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 @@ (define-public ghc-wl-pprint-text "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 @@ (define-public ghc-graphviz ("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 @@ (define ghc-system-filepath-bootstrap (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 @@ (define ghc-system-fileio-bootstrap `(#: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 @@ (define-public ghc-shelly ("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 @@ (define-public ghc-chell `(("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 @@ (define-public ghc-system-filepath ;; FilePath "/r2\ENQ52\t ;$/o\US=/okG\146\&6\n @@ -11544,7 +11329,6 @@ (define-public ghc-libmpd (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 @@ (define-public ghc-concurrent-output (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 @@ (define-public idris ("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 @@ (define-public xmobar `(("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 @@ (define-public ghc-validation (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 @@ (define-public ghc-validation (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 @@ (define-public ghc-concurrent-output ".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 @@ (define-public ghc-stylish-haskell (define-public ghc-validation (package (name "ghc-validation") - (version "1.1") + (version "1") (source (origin (method url-fetch) @@ -11879,8 +11879,11 @@ (define-public ghc-validation ".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 @@ (define-public ghc-hedgehog "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 @@ (define-public ghc-ansi-wl-pprint "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 @@ (define-public ghc-network-uri (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 @@ (define-public ghc-ansi-terminal ".tar.gz")) (sha256 (base32 - "1yr0ld0kqns3w3j9gl62bdwshvyazidx4dv1qkvq19ivnf08w23l")))) + "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b")))) (build-system haskell-build-system) (inputs `(("ghc-colour" ,ghc-colour))) @@ -4304,21 +4304,6 @@ (define-public ghc-ansi-terminal 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 @@ (define-public ghc-concurrent-output (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 @@ (define-module (gnu packages haskell-xyz) #: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 @@ (define-public ghc-prettyclass 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 @@ (define-public ghc-readable 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 @@ (define-public ghc-threads @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 @@ (define-public ghc-concurrent-extra 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 @@ (define-public ghc-io-streams 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 @@ (define-module (gnu packages haskell-crypto) #: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 @@ (define-public ghc-tls 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 @@ (define-module (gnu packages haskell-crypto) #: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 @@ (define-public ghc-hsopenssl @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 @@ (define-public ghc-hxt "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 @@ (define-module (gnu packages haskell-web) #: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 @@ (define-public ghc-http-common @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 @@ (define-public ghc-http-streams 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 @@ (define-public ghc-snap-core 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 @@ (define-public ghc-regex-compat @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 @@ (define-public ghc-haddock-api 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 @@ (define-public ghc-enclosed-exceptions 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 @@ (define-public ghc-libmpd (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 @@ (define-public ghc-yaml (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 @@ (define-public ghc-trifecta (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 @@ (define-public network-manager-vpnc (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 @@ (define-public tbsp 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 @@ (define-public tabixpp (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 @@ (define-public smithwaterman (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 @@ (define-public multichoose 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 @@ (define-public fsom (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 @@ (define-public tabixpp 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 @@ (define-public fastahack 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 @@ (define-public vcflib 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 @@ (define-public vcflib 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 @@ (define-public tabixpp 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 @@ (define-public fastahack 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 @@ (define-public tome4 ("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 @@ (define-public r-biomart (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 @@ (define-public r-hitc (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 @@ (define-public r-ggsci (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 @@ (define-public r-mime (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 @@ (define-public r-markdown ;; 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 @@ (define-public r-yaml (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 @@ (define-public r-matrixmodels (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 @@ (define-public r-readxl (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-module (gnu packages photo) (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 @@ (define-public weston (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 @@ (define-public exempi 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 @@ (define-public postgresql-11 (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 @@ (define-public postgresql-9.6 (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 @@ (define-public exempi (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 @@ (define-public ruby-redcloth (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 @@ (define-public ruby-pg ("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.")