JakeHillion/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'upstream/master' into staging

Browse Source
This commit is contained in:
Tuomas Tynkkynen 2018-01-27 21:53:16 +02:00
commit c3a658deb1
13 changed files with 80 additions and 26 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
pkgs/applications/misc/mdp/default.nix
View File

@ -1,14 +1,14 @@
{ stdenv, fetchFromGitHub, ncurses }:
stdenv.mkDerivation rec {
version = "1.0.10";
version = "1.0.12";
name = "mdp-${version}";
src = fetchFromGitHub {
owner = "visit1985";
repo = "mdp";
rev = version;
sha256 = "1swp1hqryai84c8dpzsvjpgg5rz2vnn2vrp0dhwy8r0qgpmby2nn";
sha256 = "04izj9i9rxmgswjh2iawqs6qglfv44zfv042smmcvfh1pm43361i";
};
makeFlags = [ "PREFIX=$(out)" ];

34
pkgs/applications/science/biology/star/default.nix Normal file
View File

@ -0,0 +1,34 @@
{ stdenv, fetchFromGitHub, zlib }:
stdenv.mkDerivation rec {
name = "star-${version}";
version = "2.5.3a";
src = fetchFromGitHub {
repo = "STAR";
owner = "alexdobin";
rev = version;
sha256 = "1fd9xl7i1zxgsxn2qf6gz8s42g2djm29qmp6qb35d8nnxh8ns54x";
};
sourceRoot = "source/source";
postPatch = "sed 's:/bin/rm:rm:g' -i Makefile";
buildInputs = [ zlib ];
buildPhase = "make STAR STARlong";
installPhase = ''
mkdir -p $out/bin
cp STAR STARlong $out/bin
'';
meta = with stdenv.lib; {
description = "Spliced Transcripts Alignment to a Reference";
homepage = https://github.com/alexdobin/STAR;
license = licenses.gpl3Plus;
platforms = platforms.linux;
maintainers = [ maintainers.arcadio ];
};
}

6
pkgs/applications/video/streamlink/default.nix
View File

@ -1,17 +1,17 @@
{ stdenv, pythonPackages, fetchFromGitHub, rtmpdump, ffmpeg }:
pythonPackages.buildPythonApplication rec {
version = "0.9.0";
version = "0.10.0";
name = "streamlink-${version}";
src = fetchFromGitHub {
owner = "streamlink";
repo = "streamlink";
rev = "${version}";
sha256 = "11jczkar3aqsbl5amkm7lsv4fz6xdaydd5izn222wjzsbvnzrcgd";
sha256 = "1p9gkwcvqlnv09ihqh71nh82nnmq9ybp1v8d8kd2vhkg1vm5ximn";
};
buildInputs = with pythonPackages; [ pytest mock ];
checkInputs = with pythonPackages; [ pytest mock requests-mock ];
propagatedBuildInputs = (with pythonPackages; [ pycryptodome requests iso-639 iso3166 websocket_client ]) ++ [ rtmpdump ffmpeg ];

9
pkgs/development/compilers/rust/rustc.nix
View File

@ -37,6 +37,12 @@ stdenv.mkDerivation {
# The build will fail at the very end on AArch64 without this.
dontUpdateAutotoolsGnuConfigScripts = if stdenv.isAarch64 then true else null;
# Running the default `strip -S` command on Darwin corrupts the
# .rlib files in "lib/".
#
# See https://github.com/NixOS/nixpkgs/pull/34227
stripDebugList = if stdenv.isDarwin then [ "bin" ] else null;
NIX_LDFLAGS = optionalString stdenv.isDarwin "-rpath ${llvmShared}/lib";
# Enable nightly features in stable compiles (used for
@ -78,8 +84,9 @@ stdenv.mkDerivation {
#[ -f src/liballoc_jemalloc/lib.rs ] && sed -i 's,je_,,g' src/liballoc_jemalloc/lib.rs
#[ -f src/liballoc/heap.rs ] && sed -i 's,je_,,g' src/liballoc/heap.rs # Remove for 1.4.0+
# Disable fragile linker-output-non-utf8 test
# Disable fragile tests.
rm -vr src/test/run-make/linker-output-non-utf8 || true
rm -vr src/test/run-make/issue-26092.rs || true
# Remove test targeted at LLVM 3.9 - https://github.com/rust-lang/rust/issues/36835
rm -vr src/test/run-pass/issue-36023.rs || true

4
pkgs/development/libraries/ldb/default.nix
View File

@ -3,11 +3,11 @@
}:
stdenv.mkDerivation rec {
name = "ldb-1.3.1";
name = "ldb-1.1.27";
src = fetchurl {
url = "mirror://samba/ldb/${name}.tar.gz";
sha256 = "1b1mkggp8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
sha256 = "1b1mkl5p8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
};
outputs = [ "out" "dev" ];

4
pkgs/development/libraries/libbsd/default.nix
View File

@ -2,11 +2,11 @@
stdenv.mkDerivation rec {
name = "libbsd-${version}";
version = "0.8.6";
version = "0.8.7";
src = fetchurl {
url = "http://libbsd.freedesktop.org/releases/${name}.tar.xz";
sha256 = "11wnkzims5grprvhb1ssmq9pc2lcgh2r2rk8gwgz36ply6fvyzs6";
sha256 = "0c9bl49zs0xdddcwj5dh0lay9sxi2m1yi74848g8p87mb87g2j7m";
};
# darwin changes configure.ac which means we need to regenerate

16
pkgs/development/tools/fac/default.nix
View File

@ -1,8 +1,14 @@
{ stdenv, buildGoPackage, fetchFromGitHub, makeWrapper, git }:
{ stdenv, buildGoPackage, fetchFromGitHub, fetchurl, makeWrapper, git }:
buildGoPackage rec {
let
# TODO: Remove this on next update, should be included
fac_1 = fetchurl {
url = https://raw.githubusercontent.com/mkchoi212/fac/0a500c2a2dba9017fe7c2a45f15c328755f561a6/doc/fac.1;
sha256 = "1fsyx9i20ryhpihdpvs2z7vccl13b9bnh5hcdxn7bvqjz78mbqhw";
};
in buildGoPackage rec {
name = "fac-${version}";
version = "1.0.1";
version = "1.0.4";
goPackagePath = "github.com/mkchoi212/fac";
@ -10,7 +16,7 @@ buildGoPackage rec {
owner = "mkchoi212";
repo = "fac";
rev = "v${version}";
sha256 = "1j5kip3l3p9qlly03pih905sdz3ncvpj7135jpnfhckbk1s5x9dc";
sha256 = "0jhx80jbkxfxj95hmdpb9wwwya064xpfkaa218l1lwm3qwfbpk95";
};
nativeBuildInputs = [ makeWrapper ];
@ -18,6 +24,8 @@ buildGoPackage rec {
postInstall = ''
wrapProgram $bin/bin/fac \
--prefix PATH : ${git}/bin
install -D ${fac_1} $out/share/man/man1/fac.1
'';
meta = with stdenv.lib; {

4
pkgs/development/tools/packer/default.nix
View File

@ -1,7 +1,7 @@
{ stdenv, buildGoPackage, fetchFromGitHub }:
buildGoPackage rec {
name = "packer-${version}";
version = "1.1.0";
version = "1.1.3";
goPackagePath = "github.com/hashicorp/packer";
@ -11,7 +11,7 @@ buildGoPackage rec {
owner = "hashicorp";
repo = "packer";
rev = "v${version}";
sha256 = "09hwq6dxyzhpl97akwbb02bjrisz9rf296avg5zj2p5qdsf4y777";
sha256 = "0bfjv4sqci10jzy11qg6q1xyik36v98vd6ck91sarawvgbaprsp2";
};
meta = with stdenv.lib; {

5
pkgs/development/tools/yq/default.nix
View File

@ -2,9 +2,8 @@
buildPythonApplication rec {
name = "${pname}-${version}";
pname = "yq";
version = "2.3.3";
version = "2.3.4";
propagatedBuildInputs = [ pyyaml jq ];
@ -13,7 +12,7 @@ buildPythonApplication rec {
src = fetchPypi {
inherit pname version;
sha256 = "14ywdi464z68qclsqzb8r50rzmypknaz74zmpppkahjigfcfppm3";
sha256 = "04ckrlmin8m176iicyfhddp4r0yry5hx306vhfglf8mcp1jkga78";
};
meta = with lib; {

2
pkgs/tools/audio/beets/default.nix
View File

@ -195,7 +195,7 @@ in pythonPackages.buildPythonApplication rec {
BASH_COMPLETION_SCRIPT="${completion}" \
HOME="$(mktemp -d)" \
# Exclude failing test https://github.com/beetbox/beets/issues/2652
nosetests -v --exclude="test_single_month_nonmatch_"
nosetests -v --exclude=test_single_month_nonmatch_ --exclude=test_asciify_variable --exclude=test_asciify_character_expanding_to_slash
runHook postCheck
'';

12
pkgs/tools/misc/diffoscope/default.nix
View File

@ -1,4 +1,4 @@
{ lib, stdenv, fetchgit, python3Packages, docutils
{ lib, stdenv, fetchgit, python3Packages, docutils, help2man
, acl, apktool, libbfd, bzip2, cbfstool, cdrkit, colord, colordiff, coreutils, cpio, diffutils, dtc
, e2fsprogs, file, findutils, fontforge-fonttools, fpc, gettext, ghc, ghostscriptX, giflib, gnupg1, gnutar
, gzip, imagemagick, jdk, libarchive, libcaca, llvm, mono, openssh, pdftk, pgpdump, poppler_utils, sng, sqlite
@ -8,12 +8,12 @@
python3Packages.buildPythonApplication rec {
name = "diffoscope-${version}";
version = "87";
version = "90";
src = fetchgit {
url = "git://anonscm.debian.org/reproducible/diffoscope.git";
rev = "refs/tags/${version}";
sha256 = "0j3pljwmggrpaghbamvr24x4cg5yj7hl2ll27405p7970scnpngv";
sha256 = "1w16667j6ag2iim1xcy8y9v9965mq50k64wnf693mivddll62704";
};
patches = [
@ -25,6 +25,8 @@ python3Packages.buildPythonApplication rec {
sed -i setup.py -e "/'rpm-python',/d"
'';
nativeBuildInputs = [ docutils help2man ];
# Still missing these tools: docx2txt enjarify js-beautify oggDump Rscript
# Also these libraries: python3-guestfs
pythonPath = with python3Packages; [ debian libarchive-c python_magic tlsh rpm ] ++ [
@ -37,10 +39,12 @@ python3Packages.buildPythonApplication rec {
];
doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
checkInputs = with python3Packages; [ pytest ];
postInstall = ''
make -C doc
mkdir -p $out/share/man/man1
${docutils}/bin/rst2man.py debian/diffoscope.1.rst $out/share/man/man1/diffoscope.1
cp doc/diffoscope.1 $out/share/man/man1/diffoscope.1
'';
meta = with stdenv.lib; {

4
pkgs/tools/security/spectre-meltdown-checker/default.nix
View File

@ -2,13 +2,13 @@
stdenv.mkDerivation rec {
name = "spectre-meltdown-checker-${version}";
version = "0.32";
version = "0.33";
src = fetchFromGitHub {
owner = "speed47";
repo = "spectre-meltdown-checker";
rev = "v${version}";
sha256 = "1qd3cwmg3p309czmghczlacygiyngp2wcwdghacg0y4l9vrndg8c";
sha256 = "0a0vbzjfmvcvak804y2s0301f9bcnr0nwg2piafx6i6ibisp917y";
};
prePatch = ''

2
pkgs/top-level/all-packages.nix
View File

@ -18995,6 +18995,8 @@ with pkgs;
snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
star = callPackage ../applications/science/biology/star { };
varscan = callPackage ../applications/science/biology/varscan/default.nix { };
bwa = callPackage ../applications/science/biology/bwa/default.nix { };