NixOS · Mar 2, 2020 · Mar 2, 2020 · Mar 2, 2020 · Mar 2, 2020 · Mar 2, 2020
diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix
@@ -5,13 +5,13 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "truvari";
-  version = "1.3.2";
+  version = "1.3.4";
 
   src = fetchFromGitHub {
     owner = "spiralgenetics";
     repo = "truvari";
     rev = "v${version}";
-    sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1";
+    sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v";
   };
 
   propagatedBuildInputs = with python3Packages; [
@@ -25,8 +25,9 @@ python3Packages.buildPythonApplication rec {
 
   prePatch = ''
     substituteInPlace ./setup.py \
-      --replace '"progressbar2==3.41.0",' "" \
-      --replace '"pysam==0.15.2",' ""
+      --replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \
+      --replace '"pysam==0.15.2",' '"pysam==0.15.4",' \
+      --replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",'
   '';
 
   meta = with lib; {

diff --git a/pkgs/build-support/build-bazel-package/default.nix b/pkgs/build-support/build-bazel-package/default.nix
@@ -4,8 +4,13 @@
 , lib
 }:
 
+let
+  bazelPkg = bazel;
+in
+
 args@{
   name
+, bazel ? bazelPkg
 , bazelFlags ? []
 , bazelBuildFlags ? []
 , bazelFetchFlags ? []

diff --git a/pkgs/development/compilers/llvm/5/compiler-rt-sys-ustat.patch b/pkgs/development/compilers/llvm/5/compiler-rt-sys-ustat.patch
@@ -0,0 +1,58 @@
+From 521935db9de17ad08748fd050137ac83b7734835 Mon Sep 17 00:00:00 2001
+From: Craig Topper <craig.topper@intel.com>
+Date: Thu, 24 May 2018 17:59:47 +0000
+Subject: [PATCH] sanitizer: Use pre-computed size of struct ustat for Linux
+
+<sys/ustat.h> has been removed from glibc 2.28 by:
+
+commit cf2478d53ad7071e84c724a986b56fe17f4f4ca7
+Author: Adhemerval Zanella <adhemerval.zanella@linaro.org>
+Date: Sun Mar 18 11:28:59 2018 +0800
+
+Deprecate ustat syscall interface
+This patch uses pre-computed size of struct ustat for Linux to fix
+
+https://bugs.llvm.org/show_bug.cgi?id=37418
+
+Patch by H.J. Lu.
+
+Differential Revision: https://reviews.llvm.org/D47281
+
+git-svn-id: https://llvm.org/svn/llvm-project/compiler-rt/trunk@333213 91177308-0d34-0410-b5e6-96231b3b80d8
+---
+ .../sanitizer_platform_limits_posix.cc            | 15 +++++++++++++--
+ 1 file changed, 13 insertions(+), 2 deletions(-)
+
+diff --git a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
+index 94b8f3f627..936d818673 100644
+--- a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
++++ b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
+@@ -159,7 +159,6 @@ typedef struct user_fpregs elf_fpregset_t;
+ # include <sys/procfs.h>
+ #endif
+ #include <sys/user.h>
+-#include <sys/ustat.h>
+ #include <linux/cyclades.h>
+ #include <linux/if_eql.h>
+ #include <linux/if_plip.h>
+@@ -253,7 +252,19 @@ namespace __sanitizer {
+ #endif // SANITIZER_LINUX || SANITIZER_FREEBSD
+
+ #if SANITIZER_LINUX && !SANITIZER_ANDROID
+-  unsigned struct_ustat_sz = sizeof(struct ustat);
++  // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which
++  // has been removed from glibc 2.28.
++#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \
++  || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \
++  || defined(__x86_64__)
++#define SIZEOF_STRUCT_USTAT 32
++#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \
++  || defined(__powerpc__) || defined(__s390__)
++#define SIZEOF_STRUCT_USTAT 20
++#else
++#error Unknown size of struct ustat
++#endif
++  unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;
+   unsigned struct_rlimit64_sz = sizeof(struct rlimit64);
+   unsigned struct_statvfs64_sz = sizeof(struct statvfs64);
+ #endif // SANITIZER_LINUX && !SANITIZER_ANDROID
diff --git a/pkgs/development/compilers/llvm/5/compiler-rt.nix b/pkgs/development/compilers/llvm/5/compiler-rt.nix
@@ -16,7 +16,8 @@ stdenv.mkDerivation {
 
   patches = [
     ./compiler-rt-codesign.patch # Revert compiler-rt commit that makes codesign mandatory
-  ] ++ optional stdenv.hostPlatform.isMusl ./sanitizers-nongnu.patch;
+  ] ++ optional stdenv.hostPlatform.isMusl ./sanitizers-nongnu.patch
+    ++ optional (stdenv.hostPlatform.libc == "glibc") ./compiler-rt-sys-ustat.patch;
 
   # TSAN requires XPC on Darwin, which we have no public/free source files for. We can depend on the Apple frameworks
   # to get it, but they're unfree. Since LLVM is rather central to the stdenv, we patch out TSAN support so that Hydra

diff --git a/pkgs/development/compilers/polyml/5.7-new-libffi-FFI_SYSV.patch b/pkgs/development/compilers/polyml/5.7-new-libffi-FFI_SYSV.patch
@@ -0,0 +1,34 @@
+For 5.7 the copyright header is different.
+
+From ad32de7f181acaffaba78d5c3d9e5aa6b84a741c Mon Sep 17 00:00:00 2001
+From: David Matthews <dm@prolingua.co.uk>
+Date: Sun, 7 Apr 2019 13:41:33 +0100
+Subject: [PATCH] Remove FFI_SYSV from abi table for X86/64 Unix.  It appears
+ that this has been removed in upstream versions of libffi and causes problems
+ when building using the system libffi.
+
+---
+ libpolyml/polyffi.cpp | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/libpolyml/polyffi.cpp b/libpolyml/polyffi.cpp
+index 5424dd84..3dc9cc7c 100644
+--- a/libpolyml/polyffi.cpp
++++ b/libpolyml/polyffi.cpp
+@@ -1,7 +1,7 @@
+ /*
+     Title:  New Foreign Function Interface
+
+-    Copyright (c) 2015  David C.J. Matthews
++    Copyright (c) 2015, 2019  David C.J. Matthews
+
+     This library is free software; you can redistribute it and/or
+     modify it under the terms of the GNU Lesser General Public
+@@ -109,7 +109,6 @@ static struct _abiTable { const char *abiName; ffi_abi abiCode; } abiTable[] =
+ #elif defined(X86_WIN64)
+     {"win64", FFI_WIN64},
+ #elif defined(X86_ANY)
+-    {"sysv", FFI_SYSV},
+     {"unix64", FFI_UNIX64},
+ #endif
+     { "default", FFI_DEFAULT_ABI}
diff --git a/pkgs/development/compilers/polyml/5.7.nix b/pkgs/development/compilers/polyml/5.7.nix
@@ -8,6 +8,8 @@ stdenv.mkDerivation rec {
     substituteInPlace configure.ac --replace stdc++ c++
   '';
 
+  patches = [ ./5.7-new-libffi-FFI_SYSV.patch ];
+
   buildInputs = [ libffi gmp ];
 
   nativeBuildInputs = stdenv.lib.optional stdenv.isDarwin autoreconfHook;
@@ -33,6 +35,6 @@ stdenv.mkDerivation rec {
     homepage = https://www.polyml.org/;
     license = licenses.lgpl21;
     platforms = with platforms; (linux ++ darwin);
-    maintainers = with maintainers; [ maggesi yurrriq ];
+    maintainers = with maintainers; [ maggesi ];
   };
 }
diff --git a/pkgs/development/compilers/polyml/default.nix b/pkgs/development/compilers/polyml/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, autoreconfHook, gmp, libffi }:
+{ stdenv, fetchFromGitHub, fetchpatch, autoreconfHook, gmp, libffi }:
 
 stdenv.mkDerivation rec {
   pname = "polyml";
@@ -8,6 +8,14 @@ stdenv.mkDerivation rec {
     substituteInPlace configure.ac --replace stdc++ c++
   '';
 
+  patches = [
+    (fetchpatch {
+      name = "new-libffi-FFI_SYSV.patch";
+      url = "https://github.com/polyml/polyml/commit/ad32de7f181acaffaba78d5c3d9e5aa6b84a741c.patch";
+      sha256 = "007q3r2h9kfh3c1nv0dyhipmak44q468ab9bwnz4kk4a2dq76n8v";
+    })
+  ];
+
   buildInputs = [ libffi gmp ];
 
   nativeBuildInputs = stdenv.lib.optional stdenv.isDarwin autoreconfHook;
@@ -33,6 +41,6 @@ stdenv.mkDerivation rec {
     homepage = https://www.polyml.org/;
     license = licenses.lgpl21;
     platforms = with platforms; (linux ++ darwin);
-    maintainers = with maintainers; [ maggesi yurrriq ];
+    maintainers = with maintainers; [ maggesi kovirobi ];
   };
 }
diff --git a/pkgs/development/interpreters/icon-lang/default.nix b/pkgs/development/interpreters/icon-lang/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, libX11, libXt , withGraphics ? true }:
+{ stdenv, fetchFromGitHub, fetchpatch, libX11, libXt, withGraphics ? true }:
 
 stdenv.mkDerivation rec {
   pname = "icon-lang";
@@ -12,6 +12,18 @@ stdenv.mkDerivation rec {
 
   buildInputs = stdenv.lib.optionals withGraphics [ libX11 libXt ];
 
+  patches = [
+    # Patch on git master, likely won't be necessary in future release
+    (fetchpatch {
+      url = "https://github.com/gtownsend/icon/commit/bfc4a6004d0d3984c8066289b8d8e563640c4ddd.patch";
+      sha256 = "1pqapjghk10rb73a1mfflki2wipjy4kvnravhmrilkqzb9hd6v8m";
+      excludes = [
+        "doc/relnotes.htm"
+        "src/h/version.h"
+      ];
+    })
+  ];
+
   configurePhase =
     let
       _name = if stdenv.isDarwin then "macintosh" else "linux";

diff --git a/pkgs/development/python-modules/tensorflow/default.nix b/pkgs/development/python-modules/tensorflow/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, pkgs, buildBazelPackage, lib, fetchFromGitHub, fetchpatch, symlinkJoin
+{ stdenv, pkgs, bazel_1, buildBazelPackage, lib, fetchFromGitHub, fetchpatch, symlinkJoin
 , addOpenGLRunpath
 # Python deps
 , buildPythonPackage, isPy3k, pythonOlder, pythonAtLeast, python
@@ -69,7 +69,7 @@ let
 
   tfFeature = x: if x then "1" else "0";
 
-  version = "1.15.0";
+  version = "1.15.1";
   variant = if cudaSupport then "-gpu" else "";
   pname = "tensorflow${variant}";
 
@@ -94,6 +94,7 @@ let
 
   bazel-build = buildBazelPackage {
     name = "${pname}-${version}";
+    bazel = bazel_1;
 
     src = fetchFromGitHub {
       owner = "tensorflow";
@@ -114,6 +115,11 @@ let
         url = "https://github.com/tensorflow/tensorflow/pull/29673/commits/498e35a3bfe38dd75cf1416a1a23c07c3b59e6af.patch";
         sha256 = "1m2qmwv1ysqa61z6255xggwbq6mnxbig749bdvrhnch4zydxb4di";
       })
+      (fetchpatch {
+        name = "backport-pr-18950.patch";
+        url = "https://github.com/tensorflow/tensorflow/commit/73640aaec2ab0234d9fff138e3c9833695570c0a.patch";
+        sha256 = "1n9ypbrx36fc1kc9cz5b3p9qhg15xxhq4nz6ap3hwqba535nakfz";
+      })
 
       ./tf-1.15-bazel-1.0.patch
 
@@ -291,9 +297,9 @@ let
 
       # cudaSupport causes fetch of ncclArchive, resulting in different hashes
       sha256 = if cudaSupport then
-        "1rbg8w8pjf15hpvzrclsi19lhsrwdns6f8psb1wz35ay0ggdw8c0"
+        "1p544yk7jcspgc4qr4amw11ds16c2an5yxvagx5pmwawz0s083pf"
       else
-        "0d8wq89iz9vrzvr971mgdclxxjcjr32r7aj817h019x3pc53qnwx";
+        "1dqbw3k3avqiy9xpgs44l6z65ab5rjjlxwig8z7gcl7fw9h6sbq9";
     };
 
     buildAttrs = {

diff --git a/...nt/tools/build-managers/bazel/default.nix → ...d-managers/bazel/bazel-latest/default.nix b/...nt/tools/build-managers/bazel/default.nix → ...d-managers/bazel/bazel-latest/default.nix
@@ -159,7 +159,7 @@ stdenv.mkDerivation rec {
     # On Darwin, the last argument to gcc is coming up as an empty string. i.e: ''
     # This is breaking the build of any C target. This patch removes the last
     # argument if it's found to be an empty string.
-    ./trim-last-argument-to-gcc-if-empty.patch
+    ../trim-last-argument-to-gcc-if-empty.patch
 
     # --experimental_strict_action_env (which may one day become the default
     # see bazelbuild/bazel#2574) hardcodes the default
@@ -168,17 +168,17 @@ stdenv.mkDerivation rec {
     # So we are replacing this bazel paths by defaultShellPath,
     # improving hermeticity and making it work in nixos.
     (substituteAll {
-      src = ./strict_action_env.patch;
+      src = ../strict_action_env.patch;
       strictActionEnvPatch = defaultShellPath;
     })
 
     # bazel reads its system bazelrc in /etc
     # override this path to a builtin one
     (substituteAll {
-      src = ./bazel_rc.patch;
+      src = ../bazel_rc.patch;
       bazelSystemBazelRCPath = bazelRC;
     })
-  ] ++ lib.optional enableNixHacks ./nix-hacks.patch;
+  ] ++ lib.optional enableNixHacks ../nix-hacks.patch;
 
 
   # Additional tests that check bazel’s functionality. Execute
@@ -289,7 +289,7 @@ stdenv.mkDerivation rec {
     #!${runtimeShell}
     cat ${runCommand "bazel-deps.json" {} ''
         ${unzip}/bin/unzip ${src} WORKSPACE
-        ${python3}/bin/python3 ${./update-srcDeps.py} ./WORKSPACE > $out
+        ${python3}/bin/python3 ${../update-srcDeps.py} ./WORKSPACE > $out
     ''} > ${builtins.toString ./src-deps.json}
   '';
 

diff --git a/.../tools/build-managers/bazel/src-deps.json → ...managers/bazel/bazel-latest/src-deps.json b/.../tools/build-managers/bazel/src-deps.json → ...managers/bazel/bazel-latest/src-deps.json