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dezgegdezgeg
committedJan 27, 2018
Merge remote-tracking branch 'upstream/master' into staging
·
branch-off-24.1118.03-beta
2 parents f968949 + 355a6ca commit c3a658d

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13 files changed

+80
-26
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13 files changed

+80
-26
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‎pkgs/applications/misc/mdp/default.nix

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,14 @@
11
{ stdenv, fetchFromGitHub, ncurses }:
22

33
stdenv.mkDerivation rec {
4-
version = "1.0.10";
4+
version = "1.0.12";
55
name = "mdp-${version}";
66

77
src = fetchFromGitHub {
88
owner = "visit1985";
99
repo = "mdp";
1010
rev = version;
11-
sha256 = "1swp1hqryai84c8dpzsvjpgg5rz2vnn2vrp0dhwy8r0qgpmby2nn";
11+
sha256 = "04izj9i9rxmgswjh2iawqs6qglfv44zfv042smmcvfh1pm43361i";
1212
};
1313

1414
makeFlags = [ "PREFIX=$(out)" ];

‎pkgs/applications/science/biology/star/default.nix

+34
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
{ stdenv, fetchFromGitHub, zlib }:
2+
3+
stdenv.mkDerivation rec {
4+
name = "star-${version}";
5+
version = "2.5.3a";
6+
7+
src = fetchFromGitHub {
8+
repo = "STAR";
9+
owner = "alexdobin";
10+
rev = version;
11+
sha256 = "1fd9xl7i1zxgsxn2qf6gz8s42g2djm29qmp6qb35d8nnxh8ns54x";
12+
};
13+
14+
sourceRoot = "source/source";
15+
16+
postPatch = "sed 's:/bin/rm:rm:g' -i Makefile";
17+
18+
buildInputs = [ zlib ];
19+
20+
buildPhase = "make STAR STARlong";
21+
22+
installPhase = ''
23+
mkdir -p $out/bin
24+
cp STAR STARlong $out/bin
25+
'';
26+
27+
meta = with stdenv.lib; {
28+
description = "Spliced Transcripts Alignment to a Reference";
29+
homepage = https://github.com/alexdobin/STAR;
30+
license = licenses.gpl3Plus;
31+
platforms = platforms.linux;
32+
maintainers = [ maintainers.arcadio ];
33+
};
34+
}

‎pkgs/applications/video/streamlink/default.nix

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,17 @@
11
{ stdenv, pythonPackages, fetchFromGitHub, rtmpdump, ffmpeg }:
22

33
pythonPackages.buildPythonApplication rec {
4-
version = "0.9.0";
4+
version = "0.10.0";
55
name = "streamlink-${version}";
66

77
src = fetchFromGitHub {
88
owner = "streamlink";
99
repo = "streamlink";
1010
rev = "${version}";
11-
sha256 = "11jczkar3aqsbl5amkm7lsv4fz6xdaydd5izn222wjzsbvnzrcgd";
11+
sha256 = "1p9gkwcvqlnv09ihqh71nh82nnmq9ybp1v8d8kd2vhkg1vm5ximn";
1212
};
1313

14-
buildInputs = with pythonPackages; [ pytest mock ];
14+
checkInputs = with pythonPackages; [ pytest mock requests-mock ];
1515

1616
propagatedBuildInputs = (with pythonPackages; [ pycryptodome requests iso-639 iso3166 websocket_client ]) ++ [ rtmpdump ffmpeg ];
1717

‎pkgs/development/compilers/rust/rustc.nix

+8-1
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,12 @@ stdenv.mkDerivation {
3737
# The build will fail at the very end on AArch64 without this.
3838
dontUpdateAutotoolsGnuConfigScripts = if stdenv.isAarch64 then true else null;
3939

40+
# Running the default `strip -S` command on Darwin corrupts the
41+
# .rlib files in "lib/".
42+
#
43+
# See https://github.com/NixOS/nixpkgs/pull/34227
44+
stripDebugList = if stdenv.isDarwin then [ "bin" ] else null;
45+
4046
NIX_LDFLAGS = optionalString stdenv.isDarwin "-rpath ${llvmShared}/lib";
4147

4248
# Enable nightly features in stable compiles (used for
@@ -78,8 +84,9 @@ stdenv.mkDerivation {
7884
#[ -f src/liballoc_jemalloc/lib.rs ] && sed -i 's,je_,,g' src/liballoc_jemalloc/lib.rs
7985
#[ -f src/liballoc/heap.rs ] && sed -i 's,je_,,g' src/liballoc/heap.rs # Remove for 1.4.0+
8086
81-
# Disable fragile linker-output-non-utf8 test
87+
# Disable fragile tests.
8288
rm -vr src/test/run-make/linker-output-non-utf8 || true
89+
rm -vr src/test/run-make/issue-26092.rs || true
8390
8491
# Remove test targeted at LLVM 3.9 - https://github.com/rust-lang/rust/issues/36835
8592
rm -vr src/test/run-pass/issue-36023.rs || true

‎pkgs/development/libraries/ldb/default.nix

+2-2
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,11 @@
33
}:
44

55
stdenv.mkDerivation rec {
6-
name = "ldb-1.3.1";
6+
name = "ldb-1.1.27";
77

88
src = fetchurl {
99
url = "mirror://samba/ldb/${name}.tar.gz";
10-
sha256 = "1b1mkggp8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
10+
sha256 = "1b1mkl5p8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d";
1111
};
1212

1313
outputs = [ "out" "dev" ];

‎pkgs/development/libraries/libbsd/default.nix

+2-2
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@
22

33
stdenv.mkDerivation rec {
44
name = "libbsd-${version}";
5-
version = "0.8.6";
5+
version = "0.8.7";
66

77
src = fetchurl {
88
url = "http://libbsd.freedesktop.org/releases/${name}.tar.xz";
9-
sha256 = "11wnkzims5grprvhb1ssmq9pc2lcgh2r2rk8gwgz36ply6fvyzs6";
9+
sha256 = "0c9bl49zs0xdddcwj5dh0lay9sxi2m1yi74848g8p87mb87g2j7m";
1010
};
1111

1212
# darwin changes configure.ac which means we need to regenerate

‎pkgs/development/tools/fac/default.nix

+12-4
Original file line numberDiff line numberDiff line change
@@ -1,23 +1,31 @@
1-
{ stdenv, buildGoPackage, fetchFromGitHub, makeWrapper, git }:
1+
{ stdenv, buildGoPackage, fetchFromGitHub, fetchurl, makeWrapper, git }:
22

3-
buildGoPackage rec {
3+
let
4+
# TODO: Remove this on next update, should be included
5+
fac_1 = fetchurl {
6+
url = https://raw.githubusercontent.com/mkchoi212/fac/0a500c2a2dba9017fe7c2a45f15c328755f561a6/doc/fac.1;
7+
sha256 = "1fsyx9i20ryhpihdpvs2z7vccl13b9bnh5hcdxn7bvqjz78mbqhw";
8+
};
9+
in buildGoPackage rec {
410
name = "fac-${version}";
5-
version = "1.0.1";
11+
version = "1.0.4";
612

713
goPackagePath = "github.com/mkchoi212/fac";
814

915
src = fetchFromGitHub {
1016
owner = "mkchoi212";
1117
repo = "fac";
1218
rev = "v${version}";
13-
sha256 = "1j5kip3l3p9qlly03pih905sdz3ncvpj7135jpnfhckbk1s5x9dc";
19+
sha256 = "0jhx80jbkxfxj95hmdpb9wwwya064xpfkaa218l1lwm3qwfbpk95";
1420
};
1521

1622
nativeBuildInputs = [ makeWrapper ];
1723

1824
postInstall = ''
1925
wrapProgram $bin/bin/fac \
2026
--prefix PATH : ${git}/bin
27+
28+
install -D ${fac_1} $out/share/man/man1/fac.1
2129
'';
2230

2331
meta = with stdenv.lib; {

‎pkgs/development/tools/packer/default.nix

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
{ stdenv, buildGoPackage, fetchFromGitHub }:
22
buildGoPackage rec {
33
name = "packer-${version}";
4-
version = "1.1.0";
4+
version = "1.1.3";
55

66
goPackagePath = "github.com/hashicorp/packer";
77

@@ -11,7 +11,7 @@ buildGoPackage rec {
1111
owner = "hashicorp";
1212
repo = "packer";
1313
rev = "v${version}";
14-
sha256 = "09hwq6dxyzhpl97akwbb02bjrisz9rf296avg5zj2p5qdsf4y777";
14+
sha256 = "0bfjv4sqci10jzy11qg6q1xyik36v98vd6ck91sarawvgbaprsp2";
1515
};
1616

1717
meta = with stdenv.lib; {

‎pkgs/development/tools/yq/default.nix

+2-3
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,8 @@
22

33
buildPythonApplication rec {
44

5-
name = "${pname}-${version}";
65
pname = "yq";
7-
version = "2.3.3";
6+
version = "2.3.4";
87

98
propagatedBuildInputs = [ pyyaml jq ];
109

@@ -13,7 +12,7 @@ buildPythonApplication rec {
1312

1413
src = fetchPypi {
1514
inherit pname version;
16-
sha256 = "14ywdi464z68qclsqzb8r50rzmypknaz74zmpppkahjigfcfppm3";
15+
sha256 = "04ckrlmin8m176iicyfhddp4r0yry5hx306vhfglf8mcp1jkga78";
1716
};
1817

1918
meta = with lib; {

‎pkgs/tools/audio/beets/default.nix

+1-1
Original file line numberDiff line numberDiff line change
@@ -195,7 +195,7 @@ in pythonPackages.buildPythonApplication rec {
195195
BASH_COMPLETION_SCRIPT="${completion}" \
196196
HOME="$(mktemp -d)" \
197197
# Exclude failing test https://github.com/beetbox/beets/issues/2652
198-
nosetests -v --exclude="test_single_month_nonmatch_"
198+
nosetests -v --exclude=test_single_month_nonmatch_ --exclude=test_asciify_variable --exclude=test_asciify_character_expanding_to_slash
199199
200200
runHook postCheck
201201
'';

‎pkgs/tools/misc/diffoscope/default.nix

+8-4
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
{ lib, stdenv, fetchgit, python3Packages, docutils
1+
{ lib, stdenv, fetchgit, python3Packages, docutils, help2man
22
, acl, apktool, libbfd, bzip2, cbfstool, cdrkit, colord, colordiff, coreutils, cpio, diffutils, dtc
33
, e2fsprogs, file, findutils, fontforge-fonttools, fpc, gettext, ghc, ghostscriptX, giflib, gnupg1, gnutar
44
, gzip, imagemagick, jdk, libarchive, libcaca, llvm, mono, openssh, pdftk, pgpdump, poppler_utils, sng, sqlite
@@ -8,12 +8,12 @@
88

99
python3Packages.buildPythonApplication rec {
1010
name = "diffoscope-${version}";
11-
version = "87";
11+
version = "90";
1212

1313
src = fetchgit {
1414
url = "git://anonscm.debian.org/reproducible/diffoscope.git";
1515
rev = "refs/tags/${version}";
16-
sha256 = "0j3pljwmggrpaghbamvr24x4cg5yj7hl2ll27405p7970scnpngv";
16+
sha256 = "1w16667j6ag2iim1xcy8y9v9965mq50k64wnf693mivddll62704";
1717
};
1818

1919
patches = [
@@ -25,6 +25,8 @@ python3Packages.buildPythonApplication rec {
2525
sed -i setup.py -e "/'rpm-python',/d"
2626
'';
2727

28+
nativeBuildInputs = [ docutils help2man ];
29+
2830
# Still missing these tools: docx2txt enjarify js-beautify oggDump Rscript
2931
# Also these libraries: python3-guestfs
3032
pythonPath = with python3Packages; [ debian libarchive-c python_magic tlsh rpm ] ++ [
@@ -37,10 +39,12 @@ python3Packages.buildPythonApplication rec {
3739
];
3840

3941
doCheck = false; # Calls 'mknod' in squashfs tests, which needs root
42+
checkInputs = with python3Packages; [ pytest ];
4043

4144
postInstall = ''
45+
make -C doc
4246
mkdir -p $out/share/man/man1
43-
${docutils}/bin/rst2man.py debian/diffoscope.1.rst $out/share/man/man1/diffoscope.1
47+
cp doc/diffoscope.1 $out/share/man/man1/diffoscope.1
4448
'';
4549

4650
meta = with stdenv.lib; {

‎pkgs/tools/security/spectre-meltdown-checker/default.nix

+2-2
Original file line numberDiff line numberDiff line change
@@ -2,13 +2,13 @@
22

33
stdenv.mkDerivation rec {
44
name = "spectre-meltdown-checker-${version}";
5-
version = "0.32";
5+
version = "0.33";
66

77
src = fetchFromGitHub {
88
owner = "speed47";
99
repo = "spectre-meltdown-checker";
1010
rev = "v${version}";
11-
sha256 = "1qd3cwmg3p309czmghczlacygiyngp2wcwdghacg0y4l9vrndg8c";
11+
sha256 = "0a0vbzjfmvcvak804y2s0301f9bcnr0nwg2piafx6i6ibisp917y";
1212
};
1313

1414
prePatch = ''

‎pkgs/top-level/all-packages.nix

+2
Original file line numberDiff line numberDiff line change
@@ -18995,6 +18995,8 @@ with pkgs;
1899518995

1899618996
snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
1899718997

18998+
star = callPackage ../applications/science/biology/star { };
18999+
1899819000
varscan = callPackage ../applications/science/biology/varscan/default.nix { };
1899919001

1900019002
bwa = callPackage ../applications/science/biology/bwa/default.nix { };

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