From 94a420b92159ad979b97859a3db4779f91826a9f Mon Sep 17 00:00:00 2001 From: Eric Wolf Date: Mon, 23 Apr 2018 21:27:42 +0200 Subject: [PATCH 01/25] fetchFromGitLab: Use API archive download endpoint. According to https://gitlab.com/gitlab-org/gitlab-ce/issues/45586#note_69828451 this URL is something with guaranteed stability. --- pkgs/top-level/all-packages.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 67a5390aa6aa..7928f08f4581 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -288,7 +288,7 @@ with pkgs; ... # For hash agility }@args: fetchzip ({ inherit name; - url = "https://gitlab.com/${owner}/${repo}/-/archive/${rev}/${repo}-${rev}.tar.gz"; + url = "https://gitlab.com/api/v4/projects/${owner}%2F${repo}/repository/archive.tar.gz?sha=${rev}"; meta.homepage = "https://gitlab.com/${owner}/${repo}/"; } // removeAttrs args [ "owner" "repo" "rev" ]) // { inherit rev; }; From e05099fdde718fef86bb7991fa89c69815b7362f Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Tue, 24 Apr 2018 12:14:08 -0700 Subject: [PATCH 02/25] libfm-extra: 1.2.5 -> 1.3.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/libfm-extra/versions. These checks were done: - built on NixOS - Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.) - found 1.3.0 with grep in /nix/store/jfppsgl453gipb6vx66y4pcssxd7fq54-libfm-extra-1.3.0 - directory tree listing: https://gist.github.com/74991e480da532d6ef49f6fb5727d564 --- pkgs/development/libraries/libfm/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libfm/default.nix b/pkgs/development/libraries/libfm/default.nix index 851ee7f326b6..01bfe1653fe6 100644 --- a/pkgs/development/libraries/libfm/default.nix +++ b/pkgs/development/libraries/libfm/default.nix @@ -9,11 +9,11 @@ stdenv.mkDerivation rec { name = if extraOnly then "libfm-extra-${version}" else "libfm-${version}"; - version = "1.2.5"; + version = "1.3.0"; src = fetchurl { url = "mirror://sourceforge/pcmanfm/libfm-${version}.tar.xz"; - sha256 = "0nlvfwh09gbq8bkbvwnw6iqr918rrs9gc9ljb9pjspyg408bn1n7"; + sha256 = "151jyy8ipmp2h829gd9s4s429qafv1zxl7j6zaj1k1gzm9s5rmnb"; }; nativeBuildInputs = [ pkgconfig ]; From f827bd40072c7f275a09ccc57d36a468941c618e Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Tue, 24 Apr 2018 13:23:53 -0700 Subject: [PATCH 03/25] grib-api: 1.26.0 -> 1.26.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/grib-api/versions. These checks were done: - built on NixOS - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_histogram -h’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_histogram --help’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_info -v’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_filter -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_ls -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_dump -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib2ppm -h’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib2ppm --help’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_set -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_get -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_get_data -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_copy -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_packing help’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_compare -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_index_build help’ got 0 exit code - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_index_build -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_to_netcdf -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys -V’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys -v’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys --version’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys version’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys -h’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys --help’ and found version 1.26.1 - ran ‘/nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1/bin/grib_list_keys help’ and found version 1.26.1 - found 1.26.1 with grep in /nix/store/60krazh9fxzn8n99nx9rxx8mi78hf9sx-grib-api-1.26.1 - directory tree listing: https://gist.github.com/e201ebaf6d3662af211ceca919f68df1 --- pkgs/development/libraries/grib-api/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/grib-api/default.nix b/pkgs/development/libraries/grib-api/default.nix index 61409279ded7..9113b6716649 100644 --- a/pkgs/development/libraries/grib-api/default.nix +++ b/pkgs/development/libraries/grib-api/default.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec{ name = "grib-api-${version}"; - version = "1.26.0"; + version = "1.26.1"; src = fetchurl { url = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-${version}-Source.tar.gz"; - sha256 = "00cmmj44bhdlzhqbvwb3bb4xks3bpva669m6g3g6ffjaqm25b90c"; + sha256 = "1v1apx9421m8zkjmych5yr66mvqjrrygc98bvyl4miasmsb4ndfs"; }; preConfigure = '' From 40bb3374e91cbdbace29594a0f620d4402bc703c Mon Sep 17 00:00:00 2001 From: Bas van Dijk Date: Tue, 24 Apr 2018 23:12:40 +0200 Subject: [PATCH 04/25] source-and-tags: fix default.nix Tested by observing that the following command produces a correctly looking TAGS file: $ nix-shell -E 'let pkgs = import ./. {}; in pkgs.myEnvFun {name = "myEnvFun-htags-test"; buildInputs = [(pkgs.sourceAndTags.sourceWithTagsDerivation (pkgs.sourceAndTags.addHasktagsTaggingInfo pkgs.haskellPackages.scientific).passthru.sourceWithTags)];}' --run 'cat $TAG_FILES' --- pkgs/misc/source-and-tags/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/misc/source-and-tags/default.nix b/pkgs/misc/source-and-tags/default.nix index 981c01e2b4a7..7c082cbbbb0f 100644 --- a/pkgs/misc/source-and-tags/default.nix +++ b/pkgs/misc/source-and-tags/default.nix @@ -1,4 +1,4 @@ -args: with args; { +{ stdenv, lib, glibcLocales, unzip, hasktags, ctags } : { # optional srcDir annotatedWithSourceAndTagInfo = x : (x ? passthru && x.passthru ? sourceWithTags || x ? meta && x.meta ? sourceWithTags ); @@ -59,8 +59,8 @@ args: with args; { # without this creating tag files for lifted-base fails export LC_ALL=en_US.UTF-8 export LANG=en_US.UTF-8 - ${if args.stdenv.isLinux then "export LOCALE_ARCHIVE=${args.pkgs.glibcLocales}/lib/locale/locale-archive;" else ""} - + ${if stdenv.isLinux then "export LOCALE_ARCHIVE=${glibcLocales}/lib/locale/locale-archive;" else ""} + ${toString hasktags}/bin/hasktags --ignore-close-implementation --ctags . mv tags \$TAG_FILE }"; From 72ec248eda744ccdf1233cebbeeb176355f4b0d8 Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Wed, 25 Apr 2018 06:27:21 +0000 Subject: [PATCH 05/25] coqPackages.contribs.containers: make available for Coq 8.8 --- pkgs/development/coq-modules/contribs/default.nix | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/pkgs/development/coq-modules/contribs/default.nix b/pkgs/development/coq-modules/contribs/default.nix index 82d1f7a4746b..7b274812737e 100644 --- a/pkgs/development/coq-modules/contribs/default.nix +++ b/pkgs/development/coq-modules/contribs/default.nix @@ -189,7 +189,7 @@ let mkContrib = repo: revs: param: sha256 = "1ddwzg12pbzpnz3njin4zhpph92kscrbsn3bzds26yj8fp76zc33"; }; - containers = mkContrib "containers" [ "8.6" "8.7" ] { + containers = mkContrib "containers" [ "8.6" "8.7" "8.8" ] { "8.6" = { version = "8.6.0"; rev = "fa1fec7"; @@ -200,6 +200,11 @@ let mkContrib = repo: revs: param: rev = "77ac16366529c9e558f70ba86f0168a76ca76b8f"; sha256 = "01gp8injb0knaxgqsdc4x9h8714k7qxg7j5w7y6i45dnpd81ndr4"; }; + "8.8" = { + version = "20180330"; + rev = "52b86bed1671321b25fe4d7495558f9f221b12aa"; + sha256 = "0hbnrwdgryr52170cfrlbiymr88jsyxilnpr343vnprqq3zk1xz0"; + }; }."${coq.coq-version}"; continuations = mkContrib "continuations" [ ] { From 3a8b8bcb693bcae570d2541bc9eb4849ad73d2e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Katona=20L=C3=A1szl=C3=B3?= Date: Mon, 4 Dec 2017 19:37:09 +0100 Subject: [PATCH 06/25] all-packages.nix: made new block CHEMISTRY --- pkgs/top-level/all-packages.nix | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index eaa458529e3c..5ede261d5c55 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -2770,8 +2770,6 @@ with pkgs; gvolicon = callPackage ../tools/audio/gvolicon {}; - gwyddion = callPackage ../applications/science/chemistry/gwyddion {}; - gzip = callPackage ../tools/compression/gzip { }; gzrt = callPackage ../tools/compression/gzrt { }; @@ -3114,8 +3112,6 @@ with pkgs; jmespath = callPackage ../development/tools/jmespath { }; - jmol = callPackage ../applications/science/chemistry/jmol { }; - jmtpfs = callPackage ../tools/filesystems/jmtpfs { }; jnettop = callPackage ../tools/networking/jnettop { }; @@ -3744,8 +3740,6 @@ with pkgs; modsecurity_standalone = callPackage ../tools/security/modsecurity { }; - molden = callPackage ../applications/science/chemistry/molden { }; - molly-guard = callPackage ../os-specific/linux/molly-guard { }; moneyplex = callPackage ../applications/office/moneyplex { }; @@ -7151,8 +7145,6 @@ with pkgs; ocropus = callPackage ../applications/misc/ocropus { }; - octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; }; - inherit (callPackages ../development/interpreters/perl {}) perl perl522 perl524 perl526; pachyderm = callPackage ../applications/networking/cluster/pachyderm { }; @@ -14842,10 +14834,6 @@ with pkgs; avidemux = libsForQt5.callPackage ../applications/video/avidemux { }; - avogadro = callPackage ../applications/science/chemistry/avogadro { - eigen = eigen2; - }; - avrdudess = callPackage ../applications/misc/avrdudess { }; avxsynth = callPackage ../applications/video/avxsynth { @@ -17404,8 +17392,6 @@ with pkgs; puremapping = callPackage ../applications/audio/pd-plugins/puremapping { }; - pymol = callPackage ../applications/science/chemistry/pymol { }; - pybitmessage = callPackage ../applications/networking/instant-messengers/pybitmessage { }; pythonmagick = callPackage ../applications/graphics/PythonMagick { }; @@ -19730,6 +19716,22 @@ with pkgs; ### SCIENCE + ### SCIENCE/CHEMISTY + + avogadro = callPackage ../applications/science/chemistry/avogadro { + eigen = eigen2; + }; + + gwyddion = callPackage ../applications/science/chemistry/gwyddion {}; + + jmol = callPackage ../applications/science/chemistry/jmol { }; + + molden = callPackage ../applications/science/chemistry/molden { }; + + octopus = callPackage ../applications/science/chemistry/octopus { openblas=openblasCompat; }; + + pymol = callPackage ../applications/science/chemistry/pymol { }; + ### SCIENCE/GEOMETRY drgeo = callPackage ../applications/science/geometry/drgeo { From 75d8c81868fdbffbc27fe0ae94c6870da5f42143 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Katona=20L=C3=A1szl=C3=B3?= Date: Mon, 26 Mar 2018 13:01:25 +0200 Subject: [PATCH 07/25] pymol: 1.8.4 -> 2.1.0 --- .../applications/science/chemistry/pymol/default.nix | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 39c027706ee3..e7dd04377be7 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, makeDesktopItem , python3, python3Packages -, glew, freeglut, libpng, libxml2, tk, freetype }: +, glew, freeglut, libpng, libxml2, tk, freetype, libmsgpack }: with stdenv.lib; let pname = "pymol"; - ver_maj = "1.8"; - ver_min = "4"; + ver_maj = "2"; + ver_min = "1"; version = "${ver_maj}.${ver_min}.0"; description = "A Python-enhanced molecular graphics tool"; @@ -16,7 +16,7 @@ let name = "${pname}"; exec = "${pname}"; desktopName = "PyMol Molecular Graphics System"; - genericName = "Molecular Modeller"; + genericName = "Molecular Modeler"; comment = description; mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"; categories = "Graphics;Education;Science;Chemistry;"; @@ -26,10 +26,10 @@ python3Packages.buildPythonApplication { name = "pymol-${version}"; src = fetchurl { url = "mirror://sourceforge/project/pymol/pymol/${ver_maj}/pymol-v${version}.tar.bz2"; - sha256 = "0yfj8g5yic9zz6f0bw2n8h6ifvgsn8qvhq84alixsi28wzppn55n"; + sha256 = "1qpacd5w4r9a0nm5iqmkd92ym3ai00dp7v61cwd6jgakk6wfps3s"; }; - buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype ]; + buildInputs = [ python3Packages.numpy glew freeglut libpng libxml2 tk freetype libmsgpack ]; NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2"; installPhase = '' From 329d1ba69a3b8b16af228bff28066274bc4cf085 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Katona=20L=C3=A1szl=C3=B3?= Date: Mon, 4 Dec 2017 19:53:36 +0100 Subject: [PATCH 08/25] jmol: made it runnable --- .../science/chemistry/jmol/default.nix | 27 ++++++++++++------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index c85e1143d103..4c4278c30faa 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -1,9 +1,20 @@ { stdenv , fetchurl , unzip +, makeDesktopItem , jre }: +let + desktopItem = makeDesktopItem { + name = "jmol"; + exec = "jmol"; + desktopName = "JMol"; + genericName = "Molecular Modeler"; + mimeType = "chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"; + categories = "Graphics;Education;Science;Chemistry;"; + }; +in stdenv.mkDerivation rec { version = "${baseVersion}.${patchVersion}"; baseVersion = "14.29"; @@ -16,19 +27,18 @@ stdenv.mkDerivation rec { sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv"; }; - buildInputs = [ - jre - ]; + patchPhase = '' + sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol + ''; installPhase = '' - mkdir -p "$out/share/jmol" - mkdir -p "$out/bin" + mkdir -p "$out/share/jmol" "$out/bin" ${unzip}/bin/unzip jsmol.zip -d "$out/share/" - sed -i -e 's|command=java|command=${jre}/bin/java|' jmol.sh cp *.jar jmol.sh "$out/share/jmol" - ln -s $out/share/jmol/jmol.sh "$out/bin/jmol" + cp -r ${desktopItem}/share/applications $out/share + cp jmol $out/bin ''; enableParallelBuilding = true; @@ -38,7 +48,6 @@ stdenv.mkDerivation rec { homepage = https://sourceforge.net/projects/jmol; license = licenses.lgpl2; platforms = platforms.all; - maintainers = with maintainers; [ timokau ]; + maintainers = with maintainers; [ timokau mounium ]; }; } - From 274579cc95ae33457b5cd643ea030d1f530eb31e Mon Sep 17 00:00:00 2001 From: Gregor Kleen Date: Thu, 24 Nov 2016 15:40:04 +0100 Subject: [PATCH 09/25] nixos/infinoted: Abstract over libinfinity version --- nixos/modules/services/editors/infinoted.nix | 2 +- pkgs/development/libraries/libinfinity/default.nix | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/nixos/modules/services/editors/infinoted.nix b/nixos/modules/services/editors/infinoted.nix index 963147b18a04..9074a4345eae 100644 --- a/nixos/modules/services/editors/infinoted.nix +++ b/nixos/modules/services/editors/infinoted.nix @@ -129,7 +129,7 @@ in { serviceConfig = { Type = "simple"; Restart = "always"; - ExecStart = "${cfg.package}/bin/infinoted-0.6 --config-file=/var/lib/infinoted/infinoted.conf"; + ExecStart = "${cfg.package}/bin/infinoted-${versions.majorMinor cfg.package.version} --config-file=/var/lib/infinoted/infinoted.conf"; User = cfg.user; Group = cfg.group; PermissionsStartOnly = true; diff --git a/pkgs/development/libraries/libinfinity/default.nix b/pkgs/development/libraries/libinfinity/default.nix index 944cf7a6f5e2..208e01110625 100644 --- a/pkgs/development/libraries/libinfinity/default.nix +++ b/pkgs/development/libraries/libinfinity/default.nix @@ -12,7 +12,8 @@ let in stdenv.mkDerivation rec { - name = "libinfinity-0.7.1"; + name = "libinfinity-${version}"; + version = "0.7.1"; src = fetchurl { url = "http://releases.0x539.de/libinfinity/${name}.tar.gz"; sha256 = "1jw2fhrcbpyz99bij07iyhy9ffyqdn87vl8cb1qz897y3f2f0vk2"; @@ -36,6 +37,10 @@ in stdenv.mkDerivation rec { ${edf avahiSupport "avahi"} ''; + passthru = { + inherit version; + }; + meta = { homepage = http://gobby.0x539.de/; description = "An implementation of the Infinote protocol written in GObject-based C"; From cd3047f313773bbe60df63f512dcf9271c60b34a Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Thu, 26 Apr 2018 03:33:31 -0700 Subject: [PATCH 10/25] libraw: 0.18.8 -> 0.18.9 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/libraw/versions. These checks were done: - built on NixOS - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/raw-identify -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/raw-identify --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/raw-identify help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/unprocessed_raw -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/unprocessed_raw --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/unprocessed_raw help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/4channels -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/4channels --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/4channels help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/simple_dcraw -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/simple_dcraw --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/simple_dcraw help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/mem_image -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/mem_image --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/mem_image help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/dcraw_half -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/dcraw_half --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/dcraw_half help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/half_mt -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/half_mt --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/half_mt help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/multirender_test -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/multirender_test --help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/multirender_test help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/postprocessing_benchmark -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/postprocessing_benchmark help’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/dcraw_emu -h’ got 0 exit code - ran ‘/nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9/bin/dcraw_emu help’ got 0 exit code - found 0.18.9 with grep in /nix/store/87k97dwlfma7hj6yrsyw7av631pzk3bh-libraw-0.18.9 - directory tree listing: https://gist.github.com/5d0a0f5fe58f15c25701c4dc878c5080 --- pkgs/development/libraries/libraw/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libraw/default.nix b/pkgs/development/libraries/libraw/default.nix index d4ad1c038601..4ad2f7ba34dc 100644 --- a/pkgs/development/libraries/libraw/default.nix +++ b/pkgs/development/libraries/libraw/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "libraw-${version}"; - version = "0.18.8"; + version = "0.18.9"; src = fetchurl { url = "http://www.libraw.org/data/LibRaw-${version}.tar.gz"; - sha256 = "1qi0fkw2zmd0yplrf79z7lgpz0hxl45dj5rdgpaj7283jzys9b2n"; + sha256 = "0kmjfdr409k9q9n17k9ywims5z4kqc16s81ba7y09n7669q1gvyj"; }; outputs = [ "out" "lib" "dev" "doc" ]; From 8a3cdb993d1c7e62dc62dd7239852930f2e71997 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Thu, 26 Apr 2018 06:18:41 -0700 Subject: [PATCH 11/25] containerd: 1.0.3 -> 1.1.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/containerd/versions. These checks were done: - built on NixOS - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd -h’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd --help’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd help’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd-release -h’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd-release --help’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/containerd-release help’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/ctr -h’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/ctr --help’ got 0 exit code - ran ‘/nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0/bin/ctr help’ got 0 exit code - found 1.1.0 with grep in /nix/store/lmnlz9w8fhf71pxl7wlhv9vsv4k3bnxd-containerd-1.1.0 - directory tree listing: https://gist.github.com/7b4a990853acfbf946f8abe02582f41d --- pkgs/applications/virtualization/containerd/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/virtualization/containerd/default.nix b/pkgs/applications/virtualization/containerd/default.nix index 533721034575..3854c577188f 100644 --- a/pkgs/applications/virtualization/containerd/default.nix +++ b/pkgs/applications/virtualization/containerd/default.nix @@ -5,13 +5,13 @@ with lib; stdenv.mkDerivation rec { name = "containerd-${version}"; - version = "1.0.3"; + version = "1.1.0"; src = fetchFromGitHub { owner = "containerd"; repo = "containerd"; rev = "v${version}"; - sha256 = "0k1zjn0mpd7q3p5srxld2fr4k6ijzbk0r34r6w69sh0d0rd2fvbs"; + sha256 = "0nknqprmi04jfiivrk158jyddc95q4jggfsm7cg7rpvjamkzn6c8"; }; hardeningDisable = [ "fortify" ]; From ff3b88713c4e5bfeb839e59b3ad4753043d3b47c Mon Sep 17 00:00:00 2001 From: Roger Qiu Date: Fri, 27 Apr 2018 12:01:24 +1000 Subject: [PATCH 12/25] labelImg: init at 1.6.0 --- .../machine-learning/labelimg/default.nix | 23 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 25 insertions(+) create mode 100644 pkgs/applications/science/machine-learning/labelimg/default.nix diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix new file mode 100644 index 000000000000..802a03bd4c7a --- /dev/null +++ b/pkgs/applications/science/machine-learning/labelimg/default.nix @@ -0,0 +1,23 @@ +{ stdenv, python2Packages, fetchurl }: + python2Packages.buildPythonApplication rec { + name = "labelImg-${version}"; + version = "1.6.0"; + src = fetchurl { + url = "https://github.com/tzutalin/labelImg/archive/v${version}.tar.gz"; + sha256 = "126kc4r7xm9170kh7snqsfkkc868m5bcnswrv7b4cq9ivlrdwbm4"; + }; + propagatedBuildInputs = with python2Packages; [ + pyqt4 + lxml + ]; + preBuild = '' + make qt4py2 + ''; + meta = with stdenv.lib; { + description = "LabelImg is a graphical image annotation tool and label object bounding boxes in images"; + homepage = https://github.com/tzutalin/labelImg; + license = licenses.mit; + platforms = platforms.linux; + maintainers = [ maintainers.cmcdragonkai ]; + }; + } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 0e07f2374482..fbb5d864e88b 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -12428,6 +12428,8 @@ with pkgs; lwan = callPackage ../servers/http/lwan { }; + labelImg = callPackage ../applications/science/machine-learning/labelimg { }; + mailman = callPackage ../servers/mail/mailman { }; mattermost = callPackage ../servers/mattermost { }; From fa850e8fda68c92984760f9ff9086e8cde6ef835 Mon Sep 17 00:00:00 2001 From: Ben Darwin Date: Fri, 27 Apr 2018 18:52:46 -0400 Subject: [PATCH 13/25] conglomerate: init at 2017-09-10 --- .../science/biology/conglomerate/default.nix | 34 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 +++ 2 files changed, 38 insertions(+) create mode 100644 pkgs/applications/science/biology/conglomerate/default.nix diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix new file mode 100644 index 000000000000..c04bc84c156d --- /dev/null +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, cmake, coreutils, perl, bicpl, libminc, zlib, minc_tools, + makeWrapper, GetoptTabular, MNI-Perllib }: + +stdenv.mkDerivation rec { + pname = "conglomerate"; + name = "${pname}-2017-09-10"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "7343238bc6215942c7ecc885a224f24433a291b0"; + sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc zlib bicpl ]; + propagatedBuildInputs = [ coreutils minc_tools perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}"; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/conglomerate; + description = "More command-line utilities for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 10053f926da1..d98e2aec1d2c 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -19740,6 +19740,10 @@ with pkgs; bcftools = callPackage ../applications/science/biology/bcftools { }; + conglomerate = callPackage ../applications/science/biology/conglomerate { + inherit (perlPackages) GetoptTabular MNI-Perllib; + }; + dcm2niix = callPackage ../applications/science/biology/dcm2niix { }; diamond = callPackage ../applications/science/biology/diamond { }; From 9c01a7745093c8698c60df066bb50e6060ea1168 Mon Sep 17 00:00:00 2001 From: Francesco Gazzetta Date: Tue, 1 May 2018 09:13:59 +0000 Subject: [PATCH 14/25] gron: 0.5.1 -> 0.5.2 --- pkgs/development/tools/gron/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/gron/default.nix b/pkgs/development/tools/gron/default.nix index 59f7360df2ae..14c8f53a3944 100644 --- a/pkgs/development/tools/gron/default.nix +++ b/pkgs/development/tools/gron/default.nix @@ -2,7 +2,7 @@ buildGoPackage rec { name = "gron-${version}"; - version = "0.5.1"; + version = "0.5.2"; owner = "tomnomnom"; repo = "gron"; @@ -11,7 +11,7 @@ buildGoPackage rec { src = fetchFromGitHub { inherit owner repo; rev = "v${version}"; - sha256 = "1s688ynjddchviwbiggnfbw28s4wsff2941f4b1q1j7mfak7iym2"; + sha256 = "0nxcvih8n5a4f0a53dxaipab5ckqxgnsznzymhfw5kv4inr9v6j6"; }; goDeps = ./deps.nix; From 3434cf40e12d8c99d35bd7ef4272ff7cf0f9a64c Mon Sep 17 00:00:00 2001 From: Mitsuhiro Nakamura Date: Tue, 24 Apr 2018 01:27:51 +0900 Subject: [PATCH 15/25] gnucash: 2.4.15 -> 3.1-1 --- pkgs/applications/office/gnucash/default.nix | 102 +++++++++++-------- pkgs/top-level/all-packages.nix | 6 +- 2 files changed, 61 insertions(+), 47 deletions(-) diff --git a/pkgs/applications/office/gnucash/default.nix b/pkgs/applications/office/gnucash/default.nix index 252c6d878d0c..d12b1327e8f7 100644 --- a/pkgs/applications/office/gnucash/default.nix +++ b/pkgs/applications/office/gnucash/default.nix @@ -1,63 +1,81 @@ -{ fetchurl, stdenv, pkgconfig, libxml2, gconf, glib, gtk2, libgnomeui, libofx -, libgtkhtml, gtkhtml, libgnomeprint, goffice, enchant, gettext, libbonoboui -, intltool, perl, guile, slibGuile, swig, isocodes, bzip2, makeWrapper, libglade -, libgsf, libart_lgpl, perlPackages, aqbanking, gwenhywfar +{ fetchurl, stdenv, pkgconfig, makeWrapper, cmake, gtest +, boost, icu, libxml2, libxslt, gettext, swig, isocodes, gtk3, glibcLocales +, webkit, dconf, hicolor-icon-theme, libofx, aqbanking, gwenhywfar, libdbi +, libdbiDrivers, guile, perl, perlPackages }: -/* If you experience GConf errors when running GnuCash on NixOS, see - * http://wiki.nixos.org/wiki/Solve_GConf_errors_when_running_GNOME_applications - * for a possible solution. - */ +let + + # Enable gnc-fq-* to run in command line. + perlWrapper = stdenv.mkDerivation { + name = perl.name + "-wrapper-for-gnucash"; + nativeBuildInputs = [ makeWrapper ]; + buildInputs = [ perl ] ++ (with perlPackages; [ FinanceQuote DateManip ]); + phases = [ "installPhase" ]; + installPhase = '' + mkdir -p $out/bin + for script in ${perl}/bin/*; do + makeWrapper $script $out''${script#${perl}} \ + --prefix "PERL5LIB" ":" "$PERL5LIB" + done + ''; + }; + +in stdenv.mkDerivation rec { - name = "gnucash-2.4.15"; + name = "gnucash-${version}"; + version = "3.1-1"; src = fetchurl { url = "mirror://sourceforge/gnucash/${name}.tar.bz2"; - sha256 = "058mgfwic6a2g7jq6iip5hv45md1qaxy25dj4lvlzjjr141wm4gx"; + sha256 = "0qfjpmr6hnr0v7l2fi00rilnlyan4kqiyygyidxlpdxqqg76dvx1"; }; - nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ - libxml2 gconf glib gtk2 libgnomeui libgtkhtml gtkhtml - libgnomeprint goffice enchant gettext intltool perl guile slibGuile - swig isocodes bzip2 makeWrapper libofx libglade libgsf libart_lgpl - perlPackages.DateManip perlPackages.FinanceQuote aqbanking gwenhywfar - ]; - propagatedUserEnvPkgs = [ gconf ]; + nativeBuildInputs = [ pkgconfig makeWrapper cmake gtest ]; - configureFlags = "CFLAGS=-O3 CXXFLAGS=-O3 --disable-dbi --enable-ofx --enable-aqbanking"; + buildInputs = [ + boost icu libxml2 libxslt gettext swig isocodes gtk3 glibcLocales + webkit dconf hicolor-icon-theme libofx aqbanking gwenhywfar libdbi + libdbiDrivers guile perlWrapper + ]; + + propagatedUserEnvPkgs = [ dconf ]; + + postPatch = '' + patchShebangs . + ''; + + makeFlags = [ "GUILE_AUTO_COMPILE=0" ]; postInstall = '' # Auto-updaters don't make sense in Nix. rm $out/bin/gnc-fq-update - sed -i $out/bin/update-gnucash-gconf \ - -e 's|--config-source=[^ ]* --install-schema-file|--makefile-install-rule|' + # Unnecessary in the release build. + rm $out/bin/gnucash-valgrind - for prog in $(echo "$out/bin/"*) - do - # Don't wrap the gnc-fq-* scripts, since gnucash calls them as - # "perl