From 72d675b23cf1c8326818499805ca7eca432d0cfe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= Date: Mon, 22 Jan 2018 18:27:50 +0000 Subject: [PATCH 01/13] star: init at 2.5.3a --- lib/maintainers.nix | 1 + .../science/biology/star/default.nix | 34 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 3 files changed, 37 insertions(+) create mode 100644 pkgs/applications/science/biology/star/default.nix diff --git a/lib/maintainers.nix b/lib/maintainers.nix index 9f9234f18a5..1e50e3d93f7 100644 --- a/lib/maintainers.nix +++ b/lib/maintainers.nix @@ -55,6 +55,7 @@ antonxy = "Anton Schirg "; apeschar = "Albert Peschar "; apeyroux = "Alexandre Peyroux "; + arcadio = "Arcadio Rubio García "; ardumont = "Antoine R. Dumont "; aristid = "Aristid Breitkreuz "; arobyn = "Alexei Robyn "; diff --git a/pkgs/applications/science/biology/star/default.nix b/pkgs/applications/science/biology/star/default.nix new file mode 100644 index 00000000000..1642739140d --- /dev/null +++ b/pkgs/applications/science/biology/star/default.nix @@ -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 ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6318a56fedf..186ce06978f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -18962,6 +18962,8 @@ 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 { }; From 1dd284ceb5a428e00049256a5a1b57350b15dc66 Mon Sep 17 00:00:00 2001 From: Daiderd Jordan Date: Wed, 24 Jan 2018 23:06:10 +0100 Subject: [PATCH 02/13] rust: disable another fragile test --- pkgs/development/compilers/rust/rustc.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/development/compilers/rust/rustc.nix b/pkgs/development/compilers/rust/rustc.nix index b7808ab6ec0..d3647971357 100644 --- a/pkgs/development/compilers/rust/rustc.nix +++ b/pkgs/development/compilers/rust/rustc.nix @@ -78,8 +78,9 @@ 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 From 7857399288e9c9e04569f777912789118b215a2a Mon Sep 17 00:00:00 2001 From: Andrew Childs Date: Wed, 24 Jan 2018 20:34:03 +0900 Subject: [PATCH 03/13] rustc: Fix corrupted .rlib files caused by stripping on Darwin --- pkgs/development/compilers/rust/rustc.nix | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pkgs/development/compilers/rust/rustc.nix b/pkgs/development/compilers/rust/rustc.nix index b7808ab6ec0..482f875054f 100644 --- a/pkgs/development/compilers/rust/rustc.nix +++ b/pkgs/development/compilers/rust/rustc.nix @@ -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 ${llvmShared}/lib"; # Enable nightly features in stable compiles (used for From 77a6cb32c67c7072297d2139ecff1fd467109fa2 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Sat, 27 Jan 2018 09:20:29 +0900 Subject: [PATCH 04/13] fac: 1.0.1 -> 1.0.4, add man page --- pkgs/development/tools/fac/default.nix | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/pkgs/development/tools/fac/default.nix b/pkgs/development/tools/fac/default.nix index 22b5ff4f086..c587505600c 100644 --- a/pkgs/development/tools/fac/default.nix +++ b/pkgs/development/tools/fac/default.nix @@ -1,8 +1,14 @@ -{ stdenv, buildGoPackage, fetchFromGitHub, makeWrapper, git }: +{ stdenv, buildGoPackage, fetchFromGitHub, fetchurl, makeWrapper, git }: -buildGoPackage rec { +let + # TODO: Remove this on next update, should be included + fac_1 = fetchurl { + url = https://raw.githubusercontent.com/mkchoi212/fac/0a500c2a2dba9017fe7c2a45f15c328755f561a6/doc/fac.1; + sha256 = "1fsyx9i20ryhpihdpvs2z7vccl13b9bnh5hcdxn7bvqjz78mbqhw"; + }; +in buildGoPackage rec { name = "fac-${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} $out/share/man/man1/fac.1 ''; meta = with stdenv.lib; { From 8b3e0561f5138050eb739569d1df1522380a7bbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Madrid=20Menc=C3=ADa?= Date: Sat, 27 Jan 2018 08:38:31 +0100 Subject: [PATCH 05/13] mdp: 1.0.10 -> 1.0.12 --- pkgs/applications/misc/mdp/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/mdp/default.nix b/pkgs/applications/misc/mdp/default.nix index f627a3cda22..9e584217c59 100644 --- a/pkgs/applications/misc/mdp/default.nix +++ b/pkgs/applications/misc/mdp/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchFromGitHub, ncurses }: stdenv.mkDerivation rec { - version = "1.0.10"; + version = "1.0.12"; name = "mdp-${version}"; src = fetchFromGitHub { owner = "visit1985"; repo = "mdp"; rev = version; - sha256 = "1swp1hqryai84c8dpzsvjpgg5rz2vnn2vrp0dhwy8r0qgpmby2nn"; + sha256 = "04izj9i9rxmgswjh2iawqs6qglfv44zfv042smmcvfh1pm43361i"; }; makeFlags = [ "PREFIX=$(out)" ]; From cda71dc907af3552e45a31825943c1d528ef1b7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20Madrid=20Menc=C3=ADa?= Date: Sat, 27 Jan 2018 08:53:48 +0100 Subject: [PATCH 06/13] yq: 2.3.3 -> 2.3.4 --- pkgs/development/tools/yq/default.nix | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pkgs/development/tools/yq/default.nix b/pkgs/development/tools/yq/default.nix index 6ddea86f1a7..6fb7f8440ef 100644 --- a/pkgs/development/tools/yq/default.nix +++ b/pkgs/development/tools/yq/default.nix @@ -2,9 +2,8 @@ buildPythonApplication rec { - name = "${pname}-${version}"; pname = "yq"; - version = "2.3.3"; + version = "2.3.4"; propagatedBuildInputs = [ pyyaml jq ]; @@ -13,7 +12,7 @@ buildPythonApplication rec { src = fetchPypi { inherit pname version; - sha256 = "14ywdi464z68qclsqzb8r50rzmypknaz74zmpppkahjigfcfppm3"; + sha256 = "04ckrlmin8m176iicyfhddp4r0yry5hx306vhfglf8mcp1jkga78"; }; meta = with lib; { From 3d3acfaf276f227b7e787b4ba9ecdfea9cb29059 Mon Sep 17 00:00:00 2001 From: Gabriel Ebner Date: Sat, 27 Jan 2018 10:47:19 +0100 Subject: [PATCH 07/13] beets: ignore failing tests The unidecode 1.0.22 release changed the asciification slightly. --- pkgs/tools/audio/beets/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/audio/beets/default.nix b/pkgs/tools/audio/beets/default.nix index c711881d528..899845a044c 100644 --- a/pkgs/tools/audio/beets/default.nix +++ b/pkgs/tools/audio/beets/default.nix @@ -195,7 +195,7 @@ in pythonPackages.buildPythonApplication rec { BASH_COMPLETION_SCRIPT="${completion}" \ HOME="$(mktemp -d)" \ # Exclude failing test https://github.com/beetbox/beets/issues/2652 - nosetests -v --exclude="test_single_month_nonmatch_" + nosetests -v --exclude=test_single_month_nonmatch_ --exclude=test_asciify_variable --exclude=test_asciify_character_expanding_to_slash runHook postCheck ''; From 8fff34939050d80cc6a6545bb48a81a256d713eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Sat, 27 Jan 2018 08:43:16 +0100 Subject: [PATCH 08/13] spectre-meltdown-checker: 0.32 -> 0.33 --- pkgs/tools/security/spectre-meltdown-checker/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/security/spectre-meltdown-checker/default.nix b/pkgs/tools/security/spectre-meltdown-checker/default.nix index 9fa6307ebde..39770433ff3 100644 --- a/pkgs/tools/security/spectre-meltdown-checker/default.nix +++ b/pkgs/tools/security/spectre-meltdown-checker/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "spectre-meltdown-checker-${version}"; - version = "0.32"; + version = "0.33"; src = fetchFromGitHub { owner = "speed47"; repo = "spectre-meltdown-checker"; rev = "v${version}"; - sha256 = "1qd3cwmg3p309czmghczlacygiyngp2wcwdghacg0y4l9vrndg8c"; + sha256 = "0a0vbzjfmvcvak804y2s0301f9bcnr0nwg2piafx6i6ibisp917y"; }; prePatch = '' From e526128aed7b469559dd6b22e2196eb11d2a9ee7 Mon Sep 17 00:00:00 2001 From: zimbatm Date: Sat, 27 Jan 2018 12:57:11 +0000 Subject: [PATCH 09/13] packer: 1.1.0 -> 1.1.3 (#34329) --- pkgs/development/tools/packer/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/packer/default.nix b/pkgs/development/tools/packer/default.nix index f8dc96c2394..d97d67c9851 100644 --- a/pkgs/development/tools/packer/default.nix +++ b/pkgs/development/tools/packer/default.nix @@ -1,7 +1,7 @@ { stdenv, buildGoPackage, fetchFromGitHub }: buildGoPackage rec { name = "packer-${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${version}"; - sha256 = "09hwq6dxyzhpl97akwbb02bjrisz9rf296avg5zj2p5qdsf4y777"; + sha256 = "0bfjv4sqci10jzy11qg6q1xyik36v98vd6ck91sarawvgbaprsp2"; }; meta = with stdenv.lib; { From fff0daddce4999f0bdd428ee64be40cd8c26152e Mon Sep 17 00:00:00 2001 From: Tuomas Tynkkynen Date: Wed, 24 Jan 2018 00:21:16 +0200 Subject: [PATCH 10/13] streamlink: 0.9.0 -> 0.10.0 --- pkgs/applications/video/streamlink/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/video/streamlink/default.nix b/pkgs/applications/video/streamlink/default.nix index 9fd07febbfc..9ff54bd681f 100644 --- a/pkgs/applications/video/streamlink/default.nix +++ b/pkgs/applications/video/streamlink/default.nix @@ -1,17 +1,17 @@ { stdenv, pythonPackages, fetchFromGitHub, rtmpdump, ffmpeg }: pythonPackages.buildPythonApplication rec { - version = "0.9.0"; + version = "0.10.0"; name = "streamlink-${version}"; src = fetchFromGitHub { owner = "streamlink"; repo = "streamlink"; rev = "${version}"; - sha256 = "11jczkar3aqsbl5amkm7lsv4fz6xdaydd5izn222wjzsbvnzrcgd"; + sha256 = "1p9gkwcvqlnv09ihqh71nh82nnmq9ybp1v8d8kd2vhkg1vm5ximn"; }; - buildInputs = with pythonPackages; [ pytest mock ]; + checkInputs = with pythonPackages; [ pytest mock requests-mock ]; propagatedBuildInputs = (with pythonPackages; [ pycryptodome requests iso-639 iso3166 websocket_client ]) ++ [ rtmpdump ffmpeg ]; From eef3601b089782c70b66202c00f7adaa43f7a8a6 Mon Sep 17 00:00:00 2001 From: Tuomas Tynkkynen Date: Sat, 27 Jan 2018 16:22:11 +0200 Subject: [PATCH 11/13] Revert "ldb: 1.1.27 -> 1.3.1" MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This reverts commit bc474e2dd847776193678ef83143c92da4925d95. Source hash is incorrect: https://hydra.nixos.org/build/68234054 And even fixing it doesn't make it compile: Checking for system tdb (>=1.3.15) : not found ERROR: System library tdb of version 1.3.15 not found, and bundling disabled builder for ‘/nix/store/bxnawxa402vrv4qmcmj2hmp98a0bz7li-ldb-1.3.1.drv’ failed with exit code 1 error: build of ‘/nix/store/bxnawxa402vrv4qmcmj2hmp98a0bz7li-ldb-1.3.1.drv’ failed --- pkgs/development/libraries/ldb/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/ldb/default.nix b/pkgs/development/libraries/ldb/default.nix index f7da9e9140d..4f2785675f0 100644 --- a/pkgs/development/libraries/ldb/default.nix +++ b/pkgs/development/libraries/ldb/default.nix @@ -3,11 +3,11 @@ }: stdenv.mkDerivation rec { - name = "ldb-1.3.1"; + name = "ldb-1.1.27"; src = fetchurl { url = "mirror://samba/ldb/${name}.tar.gz"; - sha256 = "1b1mkggp8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d"; + sha256 = "1b1mkl5p8swb67s9aswavhzswlib34hpgsv66zgns009paf2df6d"; }; outputs = [ "out" "dev" ]; From 5925caf39daf0eda9b62067a78eff595636b8011 Mon Sep 17 00:00:00 2001 From: Tuomas Tynkkynen Date: Sat, 27 Jan 2018 16:11:52 +0200 Subject: [PATCH 12/13] libbsd: 0.8.6 -> 0.8.7 --- pkgs/development/libraries/libbsd/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/libbsd/default.nix b/pkgs/development/libraries/libbsd/default.nix index 7e112caf3c7..0e232a50e94 100644 --- a/pkgs/development/libraries/libbsd/default.nix +++ b/pkgs/development/libraries/libbsd/default.nix @@ -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 From 355a6ca18971b75219fa6bcf20902a2ac2d9b3e3 Mon Sep 17 00:00:00 2001 From: Tuomas Tynkkynen Date: Tue, 26 Dec 2017 18:25:27 +0200 Subject: [PATCH 13/13] diffoscope: 87 -> 90 --- pkgs/tools/misc/diffoscope/default.nix | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/pkgs/tools/misc/diffoscope/default.nix b/pkgs/tools/misc/diffoscope/default.nix index 5b42c811bd2..418d5e38fd7 100644 --- a/pkgs/tools/misc/diffoscope/default.nix +++ b/pkgs/tools/misc/diffoscope/default.nix @@ -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; {