Merge branch 'master' into staging

20 files changed, 1189 insertions, 455 deletions

diff --git a/gnu/packages/patches/4store-unset-preprocessor-directive.patch b/gnu/packages/patches/4store-unset-preprocessor-directive.patch
new file mode 100644
index 0000000000..c4b1d6eda4
--- /dev/null
+++ b/gnu/packages/patches/4store-unset-preprocessor-directive.patch
@@ -0,0 +1,16 @@
+This patch removes the _XOPEN_SOURCE preprocessor directive as it does not seem to be needed.
+Setting it removes the definition of strdup, which is used in filter-datatypes.c.
+
+Patch by Roel Janssen <roel@gnu.org>
+*** a/src/frontend/filter-datatypes.c	1970-01-01 01:00:00.000000000 +0100
+--- b/src/frontend/filter-datatypes.c	2018-04-03 17:39:23.177905592 +0200
+***************
+*** 18,24 ****
+   *  Copyright (C) 2006 Steve Harris for Garlik
+   */
+  
+- #define _XOPEN_SOURCE
+  #include <stdlib.h>
+  #include <string.h>
+  #include <math.h>
+--- 18,23 ----
diff --git a/gnu/packages/patches/clang-libc-search-path.patch b/gnu/packages/patches/clang-3.5-libc-search-path.patch
index 50e4480239..50e4480239 100644
--- a/gnu/packages/patches/clang-libc-search-path.patch
+++ b/gnu/packages/patches/clang-3.5-libc-search-path.patch
diff --git a/gnu/packages/patches/clang-6.0-libc-search-path.patch b/gnu/packages/patches/clang-6.0-libc-search-path.patch
new file mode 100644
index 0000000000..a62e8063c2
--- /dev/null
+++ b/gnu/packages/patches/clang-6.0-libc-search-path.patch
@@ -0,0 +1,67 @@
+Clang attempts to guess file names based on the OS and distro (yes!),
+but unfortunately, that doesn't work for us.
+
+This patch makes it easy to insert libc's $libdir so that Clang passes the
+correct absolute file name of crt1.o etc. to 'ld'.  It also disables all
+the distro-specific stuff and removes the hard-coded FHS directory names
+to make sure Clang also works on non-GuixSD systems.
+
+--- cfe-6.0.0.src/lib/Driver/ToolChains/Linux.cpp
++++ cfe-6.0.0.src/lib/Driver/ToolChains/Linux.cpp
+@@ -207,7 +207,9 @@
+   PPaths.push_back(Twine(GCCInstallation.getParentLibPath() + "/../" +
+                          GCCInstallation.getTriple().str() + "/bin")
+                        .str());
+-
++  // Comment out the distro-specific tweaks so that they don't bite when
++  // using Guix on a foreign distro.
++#if 0
+   Distro Distro(D.getVFS());
+ 
+   if (Distro.IsAlpineLinux()) {
+@@ -255,6 +257,7 @@
+ 
+   if (IsAndroid || Distro.IsOpenSUSE())
+     ExtraOpts.push_back("--enable-new-dtags");
++#endif
+ 
+   // The selection of paths to try here is designed to match the patterns which
+   // the GCC driver itself uses, as this is part of the GCC-compatible driver.
+@@ -329,14 +332,12 @@
+     addPathIfExists(D, D.Dir + "/../" + OSLibDir, Paths);
+   }
+ 
+-  addPathIfExists(D, SysRoot + "/lib/" + MultiarchTriple, Paths);
+-  addPathIfExists(D, SysRoot + "/lib/../" + OSLibDir, Paths);
+-  addPathIfExists(D, SysRoot + "/usr/lib/" + MultiarchTriple, Paths);
+-  addPathIfExists(D, SysRoot + "/usr/lib/../" + OSLibDir, Paths);
+-
+   // Try walking via the GCC triple path in case of biarch or multiarch GCC
+   // installations with strange symlinks.
+   if (GCCInstallation.isValid()) {
++    // The following code would end up adding things like
++    // "/usr/lib/x86_64-unknown-linux-gnu/../../lib64" to the search path.
++#if 0
+     addPathIfExists(D,
+                     SysRoot + "/usr/lib/" + GCCInstallation.getTriple().str() +
+                         "/../../" + OSLibDir,
+@@ -349,6 +350,7 @@
+                              BiarchSibling.gccSuffix(),
+                       Paths);
+     }
++#endif
+ 
+     // See comments above on the multilib variant for details of why this is
+     // included even from outside the sysroot.
+@@ -373,8 +375,9 @@
+   if (StringRef(D.Dir).startswith(SysRoot))
+     addPathIfExists(D, D.Dir + "/../lib", Paths);
+ 
+-  addPathIfExists(D, SysRoot + "/lib", Paths);
+-  addPathIfExists(D, SysRoot + "/usr/lib", Paths);
++  // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
++  // and friends can be found.
++  addPathIfExists(D, "@GLIBC_LIBDIR@", Paths);
+ }
+ 
+ bool Linux::HasNativeLLVMSupport() const { return true; }
diff --git a/gnu/packages/patches/classpath-aarch64-support.patch b/gnu/packages/patches/classpath-aarch64-support.patch
new file mode 100644
index 0000000000..6fdac0c4fb
--- /dev/null
+++ b/gnu/packages/patches/classpath-aarch64-support.patch
@@ -0,0 +1,29 @@
+This is modeled after the ia64 support. Aarch64 can be either big endian
+or little endian, so we add the case for both.
+
+---
+ native/fdlibm/ieeefp.h | 8 ++++++++
+ 1 file changed, 8 insertions(+)
+
+diff --git a/native/fdlibm/ieeefp.h b/native/fdlibm/ieeefp.h
+index 1a9740f..73455c0 100644
+--- a/native/fdlibm/ieeefp.h
++++ b/native/fdlibm/ieeefp.h
+@@ -27,6 +27,14 @@
+ #endif
+ #endif
+ 
++#ifdef __aarch64__
++#ifdef __BIG_ENDIAN__
++#define __IEEE_BIG_ENDIAN
++#else
++#define __IEEE_LITTLE_ENDIAN
++#endif
++#endif
++
+ #ifdef __hppa__
+ #define __IEEE_BIG_ENDIAN
+ #endif
+-- 
+2.16.3
+
diff --git a/gnu/packages/patches/cool-retro-term-remove-non-free-fonts.patch b/gnu/packages/patches/cool-retro-term-remove-non-free-fonts.patch
deleted file mode 100644
index 7a033df413..0000000000
--- a/gnu/packages/patches/cool-retro-term-remove-non-free-fonts.patch
+++ /dev/null
@@ -1,205 +0,0 @@
-From 96ceffdfdcedd3ae33c46b11357aa2518e0a6152 Mon Sep 17 00:00:00 2001
-From: Petter <petter@mykolab.ch>
-Date: Thu, 27 Apr 2017 18:55:10 +0200
-Subject: [PATCH] Remove non-free fonts from settings menu
-
---- a/app/qml/ApplicationSettings.qml
-+++ b/app/qml/ApplicationSettings.qml
-@@ -409,7 +409,7 @@
-             obj_string: '{"ambientLight":0.16,"backgroundColor":"#000000","bloom":0.4,"brightness":0.5,"flickering":0.1,"contrast":0.85,"fontName":"TERMINUS_SCALED","fontColor":"#0ccc68","frameName":"SIMPLE_WHITE_FRAME","glowingLine":0.2,"horizontalSync":0.16,"jitter":0.18,"burnIn":0.45,"staticNoise":0.1,"rasterization":0,"screenCurvature":0.1,"windowOpacity":1,"chromaColor":0,"saturationColor":0,"rbgShift":0,"fontWidth":1.0,"useCustomCommand":false,"customCommand":""}'
-             builtin: true
-         }
--        ListElement{
-+        /*ListElement{
-             text: "Default Scanlines"
-             obj_string: '{"ambientLight":0.16,"backgroundColor":"#000000","bloom":0.4,"brightness":0.5,"flickering":0.1,"contrast":0.85,"fontName":"COMMODORE_PET","fontColor":"#00ff5b","frameName":"SIMPLE_WHITE_FRAME","glowingLine":0.2,"horizontalSync":0.14,"jitter":0.11,"burnIn":0.4,"staticNoise":0.05,"rasterization":1,"screenCurvature":0.1,"windowOpacity":1,"chromaColor":0,"saturationColor":0,"rbgShift":0,"fontWidth":1.0,"useCustomCommand":false,"customCommand":""}'
-             builtin: true
-@@ -433,7 +433,7 @@
-             text: "IBM Dos"
-             obj_string: '{"ambientLight":0.16,"backgroundColor":"#000000","bloom":0.4,"brightness":0.5,"flickering":0.07,"contrast":0.85,"fontName":"IBM_DOS","fontColor":"#ffffff","frameName":"SIMPLE_WHITE_FRAME","glowingLine":0.13,"horizontalSync":0,"jitter":0.16,"burnIn":0.3,"staticNoise":0.03,"rasterization":0,"screenCurvature":0.1,"windowOpacity":1,"chromaColor":1,"saturationColor":0,"rbgShift":0.35,"fontWidth":1.0,"useCustomCommand":false,"customCommand":""}'
-             builtin: true
--        }
-+        }*/
-         ListElement{
-             text: "IBM 3278"
-             obj_string: '{"ambientLight":0.1,"backgroundColor":"#000000","bloom":0.15,"brightness":0.5,"flickering":0,"contrast":0.85,"fontName":"IBM_3278","fontColor":"#0ccc68","frameName":"SIMPLE_WHITE_FRAME","glowingLine":0,"horizontalSync":0,"jitter":0,"burnIn":0.6,"staticNoise":0,"rasterization":0,"screenCurvature":0.1,"windowOpacity":1,"chromaColor":0,"saturationColor":0,"rbgShift":0,"fontWidth":1.0,"useCustomCommand":false,"customCommand":""}'
-diff --git a/app/qml/FontPixels.qml b/app/qml/FontPixels.qml
-index 6ff85da..6f0d0ba 100644
---- a/app/qml/FontPixels.qml
-+++ b/app/qml/FontPixels.qml
-@@ -32,7 +32,7 @@ QtObject{
-     property bool lowResolutionFont: true
- 
-     property ListModel fontlist: ListModel{
--        ListElement{
-+        /*ListElement{
-             name: "COMMODORE_PET"
-             text: "Commodore PET (1977)"
-             source: "fonts/1977-commodore-pet/COMMODORE_PET.ttf"
-@@ -40,7 +40,7 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.8
--        }
-+        }*/
-         ListElement{
-             name: "PROGGY_TINY"
-             text: "Proggy Tiny (Modern)"
-@@ -68,7 +68,7 @@ QtObject{
-             baseScaling: 3.0
-             fontWidth: 1.0
-         }
--        ListElement{
-+        /*ListElement{
-             name: "APPLE_II"
-             text: "Apple ][ (1977)"
-             source: "fonts/1977-apple2/PrintChar21.ttf"
-@@ -76,8 +76,8 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.9
--        }
--        ListElement{
-+        }*/
-+        /*ListElement{
-             name: "ATARI_400"
-             text: "Atari 400-800 (1979)"
-             source: "fonts/1979-atari-400-800/ATARI400800_original.TTF"
-@@ -85,8 +85,8 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.8
--        }
--        ListElement{
-+        }*/
-+        /*ListElement{
-             name: "COMMODORE_64"
-             text: "Commodore 64 (1982)"
-             source: "fonts/1982-commodore64/C64_Pro_Mono_v1.0-STYLE.ttf"
-@@ -94,6 +94,6 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.8
--        }
-+        }*/
-     }
- }
-diff --git a/app/qml/FontScanlines.qml b/app/qml/FontScanlines.qml
-index eebf00b..410d7b6 100644
---- a/app/qml/FontScanlines.qml
-+++ b/app/qml/FontScanlines.qml
-@@ -32,7 +32,7 @@ QtObject{
-     property bool lowResolutionFont: true
- 
-     property ListModel fontlist: ListModel{
--        ListElement{
-+        /*ListElement{
-             name: "COMMODORE_PET"
-             text: "Commodore PET (1977)"
-             source: "fonts/1977-commodore-pet/COMMODORE_PET.ttf"
-@@ -40,7 +40,7 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.7
--        }
-+        }*/
-         ListElement{
-             name: "PROGGY_TINY"
-             text: "Proggy Tiny (Modern)"
-@@ -68,7 +68,7 @@ QtObject{
-             baseScaling: 3.0
-             fontWidth: 1.0
-         }
--        ListElement{
-+        /*ListElement{
-             name: "APPLE_II"
-             text: "Apple ][ (1977)"
-             source: "fonts/1977-apple2/PrintChar21.ttf"
-@@ -76,8 +76,8 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.8
--        }
--        ListElement{
-+        }*/
-+        /*ListElement{
-             name: "ATARI_400"
-             text: "Atari 400-800 (1979)"
-             source: "fonts/1979-atari-400-800/ATARI400800_original.TTF"
-@@ -85,8 +85,8 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.7
--        }
--        ListElement{
-+        }*/
-+        /*ListElement{
-             name: "COMMODORE_64"
-             text: "Commodore 64 (1982)"
-             source: "fonts/1982-commodore64/C64_Pro_Mono_v1.0-STYLE.ttf"
-@@ -94,6 +94,6 @@ QtObject{
-             pixelSize: 8
-             baseScaling: 4.0
-             fontWidth: 0.7
--        }
-+        }*/
-     }
- }
-diff --git a/app/qml/Fonts.qml b/app/qml/Fonts.qml
-index ad20844..882808a 100644
---- a/app/qml/Fonts.qml
-+++ b/app/qml/Fonts.qml
-@@ -80,7 +80,7 @@
-             fontWidth: 1.0
-             lowResolutionFont: true
-         }
--        ListElement{
-+        /*ListElement{
-             name: "COMMODORE_PET_SCALED"
-             text: "Commodore PET (1977)"
-             source: "fonts/1977-commodore-pet/COMMODORE_PET.ttf"
-@@ -89,7 +89,7 @@
-             baseScaling: 3.5
-             fontWidth: 0.7
-             lowResolutionFont: true
--        }
-+        }*/
-         ListElement{
-             name: "PROGGY_TINY_SCALED"
-             text: "Proggy Tiny (Modern)"
-@@ -100,7 +100,7 @@
-             fontWidth: 0.9
-             lowResolutionFont: true
-         }
--        ListElement{
-+        /*ListElement{
-             name: "APPLE_II_SCALED"
-             text: "Apple ][ (1977)"
-             source: "fonts/1977-apple2/PrintChar21.ttf"
-@@ -149,7 +149,7 @@
-             baseScaling: 2.0
-             fontWidth: 1.0
-             lowResolutionFont: true
--        }
-+        }*/
-         ListElement{
-             name: "HERMIT"
-             text: "HD: Hermit (Modern)"
-@@ -177,7 +177,7 @@
-             fontWidth: 1.0
-             lowResolutionFont: false
-         }
--        ListElement{
-+        /*ListElement{
-             name: "MONACO"
-             text: "HD: Monaco (Modern)"
-             source: "fonts/modern-monaco/monaco.ttf"
-@@ -185,7 +185,7 @@
-             pixelSize: 30
-             fontWidth: 1.0
-             lowResolutionFont: false
--        }
-+        }*/
-         ListElement{
-             name: "INCONSOLATA"
-             text: "HD: Inconsolata (Modern)"
diff --git a/gnu/packages/patches/datamash-arm-tests.patch b/gnu/packages/patches/datamash-arm-tests.patch
new file mode 100644
index 0000000000..a24c5320ad
--- /dev/null
+++ b/gnu/packages/patches/datamash-arm-tests.patch
@@ -0,0 +1,71 @@
+See https://lists.gnu.org/archive/html/bug-datamash/2018-03/msg00003.html and
+https://lists.gnu.org/archive/html/bug-datamash/2018-03/txt4DmvR7p6J9.txt
+
+From d446dba317aa067440d6312d955d523129949327 Mon Sep 17 00:00:00 2001
+From: Assaf Gordon <address@hidden>
+Date: Thu, 22 Mar 2018 11:00:34 -0600
+Subject: [PATCH 1/2] tests: fix --format='%4000f' expected output
+
+Can be 1.000009... or 1.000008999, depending on representation.
+
+* tests/datamash-output-format.pl: Check only the first 5 digits.
+---
+ tests/datamash-output-format.pl | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/tests/datamash-output-format.pl b/tests/datamash-output-format.pl
+index 52c68a2..ca99bb0 100755
+--- a/tests/datamash-output-format.pl
++++ b/tests/datamash-output-format.pl
+@@ -98,12 +98,13 @@ my @Tests =
+    {OUT => "0" x 3999 . "1\n"}],
+ 
+   # due to binary floating representation, some decimal point digits won't be
+-  # zero (e.g. 1.0000090000000000000000000000000523453254320000000...).
+-  # The OUT_SUBST replaces exactly 3994 digits (as expected from the format)
++  # zero (e.g. 1.0000090000000000000000000000000523453254320000000... or
++  # 1.000008999999...).
++  # The OUT_SUBST replaces exactly 3995 digits (as expected from the format)
+   # with an "X".
+   ['m2', '--format "%.4000f"   sum 1',  {IN_PIPE=>$in1},
+-   {OUT => "1.000009X\n"},
+-   {OUT_SUBST => 's/^(1\.000009)([0-9]{3994})$/\1X/'}],
++   {OUT => "1.00000X\n"},
++   {OUT_SUBST => 's/^(1\.00000)([0-9]{3995})$/\1X/'}],
+ 
+ );
+ 
+-- 
+2.7.4
+
+
+From f4871963974a96d6e69cb80b9c2fac7ff0c1d472 Mon Sep 17 00:00:00 2001
+From: Assaf Gordon <address@hidden>
+Date: Thu, 22 Mar 2018 11:18:13 -0600
+Subject: [PATCH 2/2] tests: disable --format="%a" test
+
+Valid output can differ (e.g. 0x8.000p-3 vs 0x1.000p+0).
+
+* tests/datamash-output-format.pl: Disable 'a1' test.
+---
+ tests/datamash-output-format.pl | 4 +++-
+ 1 file changed, 3 insertions(+), 1 deletion(-)
+
+diff --git a/tests/datamash-output-format.pl b/tests/datamash-output-format.pl
+index ca99bb0..5e90ae0 100755
+--- a/tests/datamash-output-format.pl
++++ b/tests/datamash-output-format.pl
+@@ -90,7 +90,9 @@ my @Tests =
+   ['e2', '--format "%.3e"  sum 1', {IN_PIPE=>$in1}, {OUT=>"1.000e+00\n"}],
+ 
+   # Test Custom formats: %a
+-  ['a1', '--format "%0.3a" sum 1', {IN_PIPE=>$in1}, {OUT=>"0x8.000p-3\n"}],
++  # Disable the test for now. Valid output can differ (e.g. 0x8.000p-3 and
++  # 0x1.000p0 ).
++  # ['a1', '--format "%0.3a" sum 1', {IN_PIPE=>$in1}, {OUT=>"0x8.000p-3\n"}],
+ 
+ 
+   # Custom formats can use lots of memory
+-- 
+2.7.4
+
diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch
new file mode 100644
index 0000000000..3315c2a176
--- /dev/null
+++ b/gnu/packages/patches/delly-use-system-libraries.patch
@@ -0,0 +1,56 @@
+--- a/Makefile	2017-04-09 12:48:15.000000000 +0200
++++ b/Makefile	2017-06-21 14:26:02.749282787 +0200
+@@ -9,8 +9,8 @@
+ 
+ # Flags
+ CXX=g++
+-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
+-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
++CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
++LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
+ 
+ # Additional flags for release/debug
+ ifeq (${PARALLEL}, 1)
+@@ -23,7 +23,7 @@
+ ifeq (${STATIC}, 1)
+ 	LDFLAGS += -static -static-libgcc -pthread -lhts -lz
+ else
+-	LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
++	LDFLAGS += -lhts -lz
+ endif
+ ifeq (${DEBUG}, 1)
+ 	CXXFLAGS += -g -O0 -fno-inline -DDEBUG
+@@ -41,29 +41,17 @@
+ DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
+ 
+ # Targets
+-TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe
++TARGETS = src/delly src/cov src/dpe
+ 
+ all:   	$(TARGETS)
+ 
+-.htslib: $(HTSLIBSOURCES)
+-	cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
+-
+-.bcftools: $(HTSLIBSOURCES)
+-	cd src/bcftools && make && cd ../../ && touch .bcftools
+-
+-.boost: $(BOOSTSOURCES)
+-	cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
+-
+-src/delly: .htslib .bcftools .boost $(DELLYSOURCES)
+-	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+-
+-src/cov: .htslib .bcftools .boost $(DELLYSOURCES)
++src/cov: $(DELLYSOURCES)
+ 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+ 
+-src/dpe: .htslib .bcftools .boost $(DELLYSOURCES)
++src/dpe: $(DELLYSOURCES)
+ 	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+ 
+ clean:
+ 	cd src/htslib && make clean
+ 	cd src/modular-boost && ./b2 --clean-all
+-	rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools
++	rm -f $(TARGETS) $(TARGETS:=.o)
diff --git a/gnu/packages/patches/freeimage-unbundle.patch b/gnu/packages/patches/freeimage-unbundle.patch
new file mode 100644
index 0000000000..2727d9fbda
--- /dev/null
+++ b/gnu/packages/patches/freeimage-unbundle.patch
@@ -0,0 +1,550 @@
+https://src.fedoraproject.org/cgit/rpms/freeimage.git/tree/FreeImage-3.17.0_unbundle.patch
+
+diff -rupN FreeImage/genfipsrclist.sh FreeImage-new/genfipsrclist.sh
+--- FreeImage/genfipsrclist.sh	2015-02-20 10:52:16.000000000 +0100
++++ FreeImage-new/genfipsrclist.sh	2015-09-05 02:13:52.041353305 +0200
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJPEG Source/LibPNG Source/LibTIFF4 Source/ZLib Source/LibOpenJPEG Source/OpenEXR Source/OpenEXR/Half Source/OpenEXR/Iex Source/OpenEXR/IlmImf Source/OpenEXR/IlmThread Source/OpenEXR/Imath Source/OpenEXR/IexMath Source/LibRawLite Source/LibRawLite/dcraw Source/LibRawLite/internal Source/LibRawLite/libraw Source/LibRawLite/src Source/LibWebP Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib Wrapper/FreeImagePlus"
++DIRLIST="Wrapper/FreeImagePlus"
+ 
+ 
+ echo "VER_MAJOR = 3" > fipMakefile.srcs
+@@ -19,5 +19,6 @@ echo -n "INCLUDE =" >> fipMakefile.srcs
+ for DIR in $DIRLIST; do
+ 	echo -n " -I$DIR" >> fipMakefile.srcs
+ done
++echo -n " -IDist" >> fipMakefile.srcs
+ echo >> fipMakefile.srcs
+ 
+diff -rupN FreeImage/gensrclist.sh FreeImage-new/gensrclist.sh
+--- FreeImage/gensrclist.sh	2015-02-20 10:51:50.000000000 +0100
++++ FreeImage-new/gensrclist.sh	2015-09-05 02:13:52.041353305 +0200
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-DIRLIST=". Source Source/Metadata Source/FreeImageToolkit Source/LibJPEG Source/LibPNG Source/LibTIFF4 Source/ZLib Source/LibOpenJPEG Source/OpenEXR Source/OpenEXR/Half Source/OpenEXR/Iex Source/OpenEXR/IlmImf Source/OpenEXR/IlmThread Source/OpenEXR/Imath Source/OpenEXR/IexMath Source/LibRawLite Source/LibRawLite/dcraw Source/LibRawLite/internal Source/LibRawLite/libraw Source/LibRawLite/src Source/LibWebP Source/LibJXR Source/LibJXR/common/include Source/LibJXR/image/sys Source/LibJXR/jxrgluelib"
++DIRLIST=". Source Source/Metadata Source/FreeImageToolkit"
+ 
+ echo "VER_MAJOR = 3" > Makefile.srcs
+ echo "VER_MINOR = 17.0" >> Makefile.srcs
+diff -rupN FreeImage/Makefile.fip FreeImage-new/Makefile.fip
+--- FreeImage/Makefile.fip	2015-03-08 18:03:56.000000000 +0100
++++ FreeImage-new/Makefile.fip	2015-09-05 02:14:09.212684028 +0200
+@@ -17,20 +17,22 @@ MODULES = $(SRCS:.c=.o)
+ MODULES := $(MODULES:.cpp=.o)
+ CFLAGS ?= -O3 -fPIC -fexceptions -fvisibility=hidden
+ # OpenJPEG
+-CFLAGS += -DOPJ_STATIC
++override CFLAGS += -DOPJ_STATIC
+ # LibRaw
+-CFLAGS += -DNO_LCMS
++override CFLAGS += -DNO_LCMS
+ # LibJXR
+-CFLAGS += -DDISABLE_PERF_MEASUREMENT -D__ANSI__
+-CFLAGS += $(INCLUDE)
++override CFLAGS += -DDISABLE_PERF_MEASUREMENT -D__ANSI__
++override CFLAGS += $(INCLUDE)
+ CXXFLAGS ?= -O3 -fPIC -fexceptions -fvisibility=hidden -Wno-ctor-dtor-privacy
+ # LibJXR
+-CXXFLAGS += -D__ANSI__
+-CXXFLAGS += $(INCLUDE)
++override CXXFLAGS += -D__ANSI__
++override CXXFLAGS += $(INCLUDE)
++LDFLAGS ?=
++override LDFLAGS += -LDist -lfreeimage-$(VER_MAJOR).$(VER_MINOR)
+ 
+ ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),x86_64)
+-	CFLAGS += -fPIC
+-	CXXFLAGS += -fPIC
++	override CFLAGS += -fPIC
++	override CXXFLAGS += -fPIC
+ endif
+ 
+ TARGET  = freeimageplus
+@@ -68,7 +70,7 @@ $(STATICLIB): $(MODULES)
+ 	$(AR) r $@ $(MODULES)
+ 
+ $(SHAREDLIB): $(MODULES)
+-	$(CC) -s -shared -Wl,-soname,$(VERLIBNAME) $(LDFLAGS) -o $@ $(MODULES) $(LIBRARIES)
++	$(CC) -shared -Wl,-soname,$(VERLIBNAME) $(LDFLAGS) -o $@ $(MODULES) $(LIBRARIES)
+ 
+ install:
+ 	install -d $(INCDIR) $(INSTALLDIR)
+diff -rupN FreeImage/Makefile.gnu FreeImage-new/Makefile.gnu
+--- FreeImage/Makefile.gnu	2015-03-08 18:04:00.000000000 +0100
++++ FreeImage-new/Makefile.gnu	2015-09-05 02:14:04.810599259 +0200
+@@ -16,21 +16,11 @@ LIBRARIES = -lstdc++
+ MODULES = $(SRCS:.c=.o)
+ MODULES := $(MODULES:.cpp=.o)
+ CFLAGS ?= -O3 -fPIC -fexceptions -fvisibility=hidden
+-# OpenJPEG
+-CFLAGS += -DOPJ_STATIC
+-# LibRaw
+-CFLAGS += -DNO_LCMS
+-# LibJXR
+-CFLAGS += -DDISABLE_PERF_MEASUREMENT -D__ANSI__
+-CFLAGS += $(INCLUDE)
+-CXXFLAGS ?= -O3 -fPIC -fexceptions -fvisibility=hidden -Wno-ctor-dtor-privacy
+-# LibJXR
+-CXXFLAGS += -D__ANSI__
+-CXXFLAGS += $(INCLUDE)
++override CFLAGS += $(INCLUDE) -D__ANSI__ -I/usr/include/jxrlib $(shell pkg-config --cflags OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
++override LDFLAGS += -ljpeg -ljpegxr -ljxrglue $(shell pkg-config --libs OpenEXR libopenjp2 libraw libpng libtiff-4 libwebp libwebpmux zlib)
+ 
+ ifeq ($(shell sh -c 'uname -m 2>/dev/null || echo not'),x86_64)
+-	CFLAGS += -fPIC
+-	CXXFLAGS += -fPIC
++	override CFLAGS += -fPIC
+ endif
+ 
+ TARGET  = freeimage
+@@ -61,13 +51,13 @@ FreeImage: $(STATICLIB) $(SHAREDLIB)
+ 	$(CC) $(CFLAGS) -c $< -o $@
+ 
+ .cpp.o:
+-	$(CXX) $(CXXFLAGS) -c $< -o $@
++	$(CXX) $(CFLAGS) -c $< -o $@
+ 
+ $(STATICLIB): $(MODULES)
+ 	$(AR) r $@ $(MODULES)
+ 
+ $(SHAREDLIB): $(MODULES)
+-	$(CC) -s -shared -Wl,-soname,$(VERLIBNAME) $(LDFLAGS) -o $@ $(MODULES) $(LIBRARIES)
++	$(CC) -shared -Wl,-soname,$(VERLIBNAME) $(LDFLAGS) -o $@ $(MODULES) $(LIBRARIES)
+ 
+ install:
+ 	install -d $(INCDIR) $(INSTALLDIR)
+diff -rupN FreeImage/Source/FreeImage/J2KHelper.cpp FreeImage-new/Source/FreeImage/J2KHelper.cpp
+--- FreeImage/Source/FreeImage/J2KHelper.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/J2KHelper.cpp	2015-09-05 02:13:52.042353324 +0200
+@@ -21,7 +21,7 @@
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+-#include "../LibOpenJPEG/openjpeg.h"
++#include <openjpeg.h>
+ #include "J2KHelper.h"
+ 
+ // --------------------------------------------------------------------------
+diff -rupN FreeImage/Source/FreeImage/Plugin.cpp FreeImage-new/Source/FreeImage/Plugin.cpp
+--- FreeImage/Source/FreeImage/Plugin.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/Plugin.cpp	2015-09-05 02:13:52.042353324 +0200
+@@ -263,7 +263,12 @@ FreeImage_Initialise(BOOL load_local_plu
+ 			s_plugins->AddNode(InitDDS);
+ 	        s_plugins->AddNode(InitGIF);
+ 	        s_plugins->AddNode(InitHDR);
+-			s_plugins->AddNode(InitG3);
++/* The G3 fax format plugin is deliberately disabled in the Fedora build of
++   FreeImage as it requires that FreeImage uses a private copy of libtiff
++   which is a no no because of security reasons. */
++#if 0
++ 			s_plugins->AddNode(InitG3);
++#endif
+ 			s_plugins->AddNode(InitSGI);
+ 			s_plugins->AddNode(InitEXR);
+ 			s_plugins->AddNode(InitJ2K);
+diff -rupN FreeImage/Source/FreeImage/PluginEXR.cpp FreeImage-new/Source/FreeImage/PluginEXR.cpp
+--- FreeImage/Source/FreeImage/PluginEXR.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginEXR.cpp	2015-09-05 02:13:52.042353324 +0200
+@@ -28,16 +28,16 @@
+ #pragma warning (disable : 4800) // ImfVersion.h - 'const int' : forcing value to bool 'true' or 'false' (performance warning)
+ #endif 
+ 
+-#include "../OpenEXR/IlmImf/ImfIO.h"
+-#include "../OpenEXR/Iex/Iex.h"
+-#include "../OpenEXR/IlmImf/ImfOutputFile.h"
+-#include "../OpenEXR/IlmImf/ImfInputFile.h"
+-#include "../OpenEXR/IlmImf/ImfRgbaFile.h"
+-#include "../OpenEXR/IlmImf/ImfChannelList.h"
+-#include "../OpenEXR/IlmImf/ImfRgba.h"
+-#include "../OpenEXR/IlmImf/ImfArray.h"
+-#include "../OpenEXR/IlmImf/ImfPreviewImage.h"
+-#include "../OpenEXR/Half/half.h"
++#include <OpenEXR/ImfIO.h>
++#include <OpenEXR/Iex.h>
++#include <OpenEXR/ImfOutputFile.h>
++#include <OpenEXR/ImfInputFile.h>
++#include <OpenEXR/ImfRgbaFile.h>
++#include <OpenEXR/ImfChannelList.h>
++#include <OpenEXR/ImfRgba.h>
++#include <OpenEXR/ImfArray.h>
++#include <OpenEXR/ImfPreviewImage.h>
++#include <OpenEXR/half.h>
+ 
+ 
+ // ==========================================================
+diff -rupN FreeImage/Source/FreeImage/PluginJ2K.cpp FreeImage-new/Source/FreeImage/PluginJ2K.cpp
+--- FreeImage/Source/FreeImage/PluginJ2K.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginJ2K.cpp	2015-09-05 02:13:52.043353343 +0200
+@@ -21,7 +21,7 @@
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+-#include "../LibOpenJPEG/openjpeg.h"
++#include <openjpeg.h>
+ #include "J2KHelper.h"
+ 
+ // ==========================================================
+diff -rupN FreeImage/Source/FreeImage/PluginJP2.cpp FreeImage-new/Source/FreeImage/PluginJP2.cpp
+--- FreeImage/Source/FreeImage/PluginJP2.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginJP2.cpp	2015-09-05 02:13:52.043353343 +0200
+@@ -21,7 +21,7 @@
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+-#include "../LibOpenJPEG/openjpeg.h"
++#include <openjpeg.h>
+ #include "J2KHelper.h"
+ 
+ // ==========================================================
+diff -rupN FreeImage/Source/FreeImage/PluginJPEG.cpp FreeImage-new/Source/FreeImage/PluginJPEG.cpp
+--- FreeImage/Source/FreeImage/PluginJPEG.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginJPEG.cpp	2015-09-05 02:13:52.043353343 +0200
+@@ -35,9 +35,9 @@ extern "C" {
+ #undef FAR
+ #include <setjmp.h>
+ 
+-#include "../LibJPEG/jinclude.h"
+-#include "../LibJPEG/jpeglib.h"
+-#include "../LibJPEG/jerror.h"
++#include <stdio.h>
++#include <jpeglib.h>
++#include <jerror.h>
+ }
+ 
+ #include "FreeImage.h"
+diff -rupN FreeImage/Source/FreeImage/PluginJXR.cpp FreeImage-new/Source/FreeImage/PluginJXR.cpp
+--- FreeImage/Source/FreeImage/PluginJXR.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginJXR.cpp	2015-09-05 02:13:52.043353343 +0200
+@@ -23,7 +23,7 @@
+ #include "Utilities.h"
+ #include "../Metadata/FreeImageTag.h"
+ 
+-#include "../LibJXR/jxrgluelib/JXRGlue.h"
++#include <JXRGlue.h>
+ 
+ // ==========================================================
+ // Plugin Interface
+diff -rupN FreeImage/Source/FreeImage/PluginPNG.cpp FreeImage-new/Source/FreeImage/PluginPNG.cpp
+--- FreeImage/Source/FreeImage/PluginPNG.cpp	2015-03-10 20:16:12.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginPNG.cpp	2015-09-05 02:13:52.044353363 +0200
+@@ -40,8 +40,8 @@
+ 
+ // ----------------------------------------------------------
+ 
+-#include "../ZLib/zlib.h"
+-#include "../LibPNG/png.h"
++#include <zlib.h>
++#include <png.h>
+ 
+ // ----------------------------------------------------------
+ 
+diff -rupN FreeImage/Source/FreeImage/PluginRAW.cpp FreeImage-new/Source/FreeImage/PluginRAW.cpp
+--- FreeImage/Source/FreeImage/PluginRAW.cpp	2015-03-08 20:12:04.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginRAW.cpp	2015-09-05 02:13:52.044353363 +0200
+@@ -19,7 +19,7 @@
+ // Use at your own risk!
+ // ==========================================================
+ 
+-#include "../LibRawLite/libraw/libraw.h"
++#include <libraw/libraw.h>
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+diff -rupN FreeImage/Source/FreeImage/PluginTIFF.cpp FreeImage-new/Source/FreeImage/PluginTIFF.cpp
+--- FreeImage/Source/FreeImage/PluginTIFF.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginTIFF.cpp	2015-09-05 02:13:52.044353363 +0200
+@@ -37,9 +37,9 @@
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+-#include "../LibTIFF4/tiffiop.h"
++#include <tiffio.h>
+ #include "../Metadata/FreeImageTag.h"
+-#include "../OpenEXR/Half/half.h"
++#include <OpenEXR/half.h>
+ 
+ #include "FreeImageIO.h"
+ #include "PSDParser.h"
+@@ -194,16 +194,6 @@ TIFFFdOpen(thandle_t handle, const char
+ 	return tif;
+ }
+ 
+-/**
+-Open a TIFF file for reading or writing
+-@param name
+-@param mode
+-*/
+-TIFF*
+-TIFFOpen(const char* name, const char* mode) {
+-	return 0;
+-}
+-
+ // ----------------------------------------------------------
+ //   TIFF library FreeImage-specific routines.
+ // ----------------------------------------------------------
+diff -rupN FreeImage/Source/FreeImage/PluginWebP.cpp FreeImage-new/Source/FreeImage/PluginWebP.cpp
+--- FreeImage/Source/FreeImage/PluginWebP.cpp	2015-03-02 02:07:08.000000000 +0100
++++ FreeImage-new/Source/FreeImage/PluginWebP.cpp	2015-09-05 02:13:52.044353363 +0200
+@@ -24,10 +24,10 @@
+ 
+ #include "../Metadata/FreeImageTag.h"
+ 
+-#include "../LibWebP/src/webp/decode.h"
+-#include "../LibWebP/src/webp/encode.h"
+-#include "../LibWebP/src/enc/vp8enci.h"
+-#include "../LibWebP/src/webp/mux.h"
++#include <webp/decode.h>
++#include <webp/encode.h>
++// #include "../LibWebP/src/enc/vp8enci.h"
++#include <webp/mux.h>
+ 
+ // ==========================================================
+ // Plugin Interface
+diff -rupN FreeImage/Source/FreeImage/ZLibInterface.cpp FreeImage-new/Source/FreeImage/ZLibInterface.cpp
+--- FreeImage/Source/FreeImage/ZLibInterface.cpp	2015-03-02 02:07:10.000000000 +0100
++++ FreeImage-new/Source/FreeImage/ZLibInterface.cpp	2015-09-05 02:13:52.044353363 +0200
+@@ -19,10 +19,9 @@
+ // Use at your own risk!
+ // ==========================================================
+ 
+-#include "../ZLib/zlib.h"
++#include <zlib.h>
+ #include "FreeImage.h"
+ #include "Utilities.h"
+-#include "../ZLib/zutil.h"	/* must be the last header because of error C3163 in VS2008 (_vsnprintf defined in stdio.h) */
+ 
+ /**
+ Compresses a source buffer into a target buffer, using the ZLib library. 
+@@ -115,7 +114,7 @@ FreeImage_ZLibGZip(BYTE *target, DWORD t
+ 			return 0;
+         case Z_OK: {
+             // patch header, setup crc and length (stolen from mod_trace_output)
+-            BYTE *p = target + 8; *p++ = 2; *p = OS_CODE; // xflags, os_code
++            BYTE *p = target + 8; *p++ = 2; *p = 0x03; // xflags, os_code (unix)
+  	        crc = crc32(crc, source, source_size);
+ 	        memcpy(target + 4 + dest_len, &crc, 4);
+ 	        memcpy(target + 8 + dest_len, &source_size, 4);
+diff -rupN FreeImage/Source/FreeImage.h FreeImage-new/Source/FreeImage.h
+--- FreeImage/Source/FreeImage.h	2015-03-04 02:17:54.000000000 +0100
++++ FreeImage-new/Source/FreeImage.h	2015-09-05 02:13:52.045353382 +0200
+@@ -155,8 +155,11 @@ typedef uint8_t BYTE;
+ typedef uint16_t WORD;
+ typedef uint32_t DWORD;
+ typedef int32_t LONG;
++// Disable these, they conflict with the (wrong) ones of libraw
++#if 0
+ typedef int64_t INT64;
+ typedef uint64_t UINT64;
++#endif
+ #else
+ // MS is not C99 ISO compliant
+ typedef long BOOL;
+@@ -410,7 +413,12 @@ FI_ENUM(FREE_IMAGE_FORMAT) {
+ 	FIF_DDS		= 24,
+ 	FIF_GIF     = 25,
+ 	FIF_HDR		= 26,
+-	FIF_FAXG3	= 27,
++/* The G3 fax format plugin is deliberately disabled in the Fedora build of
++   FreeImage as it requires that FreeImage uses a private copy of libtiff
++   which is a no no because of security reasons. */
++#if 0
++ 	FIF_FAXG3	= 27,
++#endif
+ 	FIF_SGI		= 28,
+ 	FIF_EXR		= 29,
+ 	FIF_J2K		= 30,
+@@ -473,6 +481,10 @@ FI_ENUM(FREE_IMAGE_DITHER) {
+ 	FID_BAYER16x16	= 6		//! Bayer ordered dispersed dot dithering (order 4 dithering matrix)
+ };
+ 
++/* The FreeImage_JPEGTransform functions are deliberately disabled in the
++   Fedora build of FreeImage as they require that FreeImage uses a private copy
++   of libjpeg which is a no no because of security reasons. */
++#if 0
+ /** Lossless JPEG transformations
+ Constants used in FreeImage_JPEGTransform
+ */
+@@ -486,6 +498,7 @@ FI_ENUM(FREE_IMAGE_JPEG_OPERATION) {
+ 	FIJPEG_OP_ROTATE_180	= 6,	//! 180-degree rotation
+ 	FIJPEG_OP_ROTATE_270	= 7		//! 270-degree clockwise (or 90 ccw)
+ };
++#endif
+ 
+ /** Tone mapping operators.
+ Constants used in FreeImage_ToneMapping.
+@@ -1076,7 +1089,10 @@ DLL_API const char* DLL_CALLCONV FreeIma
+ // --------------------------------------------------------------------------
+ // JPEG lossless transformation routines
+ // --------------------------------------------------------------------------
+-
++/* The FreeImage_JPEGTransform functions are deliberately disabled in the
+++   Fedora build of FreeImage as they require that FreeImage uses a private copy
+++   of libjpeg which is a no no because of security reasons. */
++#if 0
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGTransform(const char *src_file, const char *dst_file, FREE_IMAGE_JPEG_OPERATION operation, BOOL perfect FI_DEFAULT(TRUE));
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGTransformU(const wchar_t *src_file, const wchar_t *dst_file, FREE_IMAGE_JPEG_OPERATION operation, BOOL perfect FI_DEFAULT(TRUE));
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGCrop(const char *src_file, const char *dst_file, int left, int top, int right, int bottom);
+@@ -1085,6 +1101,7 @@ DLL_API BOOL DLL_CALLCONV FreeImage_JPEG
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGTransformCombined(const char *src_file, const char *dst_file, FREE_IMAGE_JPEG_OPERATION operation, int* left, int* top, int* right, int* bottom, BOOL perfect FI_DEFAULT(TRUE));
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGTransformCombinedU(const wchar_t *src_file, const wchar_t *dst_file, FREE_IMAGE_JPEG_OPERATION operation, int* left, int* top, int* right, int* bottom, BOOL perfect FI_DEFAULT(TRUE));
+ DLL_API BOOL DLL_CALLCONV FreeImage_JPEGTransformCombinedFromMemory(FIMEMORY* src_stream, FIMEMORY* dst_stream, FREE_IMAGE_JPEG_OPERATION operation, int* left, int* top, int* right, int* bottom, BOOL perfect FI_DEFAULT(TRUE));
++#endif
+ 
+ 
+ // --------------------------------------------------------------------------
+diff -rupN FreeImage/Source/FreeImageToolkit/JPEGTransform.cpp FreeImage-new/Source/FreeImageToolkit/JPEGTransform.cpp
+--- FreeImage/Source/FreeImageToolkit/JPEGTransform.cpp	2015-03-02 02:07:10.000000000 +0100
++++ FreeImage-new/Source/FreeImageToolkit/JPEGTransform.cpp	2015-09-05 02:13:52.045353382 +0200
+@@ -26,10 +26,10 @@ extern "C" {
+ #undef FAR
+ #include <setjmp.h>
+ 
+-#include "../LibJPEG/jinclude.h"
+-#include "../LibJPEG/jpeglib.h"
+-#include "../LibJPEG/jerror.h"
+-#include "../LibJPEG/transupp.h"
++#include <jinclude.h>
++#include <jpeglib.h>
++#include <jerror.h>
++#include <transupp.h>
+ }
+ 
+ #include "FreeImage.h"
+diff -rupN FreeImage/Source/Metadata/TagConversion.cpp FreeImage-new/Source/Metadata/TagConversion.cpp
+--- FreeImage/Source/Metadata/TagConversion.cpp	2015-03-02 02:07:10.000000000 +0100
++++ FreeImage-new/Source/Metadata/TagConversion.cpp	2015-09-05 02:13:52.045353382 +0200
+@@ -30,6 +30,11 @@
+ 
+ #define MAX_TEXT_EXTENT	512
+ 
++// These were in FreeImage.h, but are moved here to avoid conflicts (see note in FreeImage.h)
++typedef int64_t INT64;
++typedef uint64_t UINT64;
++
++
+ /**
+ Convert a tag to a C string
+ */
+diff -rupN FreeImage/Source/Metadata/XTIFF.cpp FreeImage-new/Source/Metadata/XTIFF.cpp
+--- FreeImage/Source/Metadata/XTIFF.cpp	2015-03-02 02:07:10.000000000 +0100
++++ FreeImage-new/Source/Metadata/XTIFF.cpp	2015-09-05 02:13:52.045353382 +0200
+@@ -29,13 +29,18 @@
+ #pragma warning (disable : 4786) // identifier was truncated to 'number' characters
+ #endif
+ 
+-#include "../LibTIFF4/tiffiop.h"
++#include <tiffio.h>
+ 
+ #include "FreeImage.h"
+ #include "Utilities.h"
+ #include "FreeImageTag.h"
+ #include "FIRational.h"
+ 
++extern "C"
++{
++    int _TIFFDataSize(TIFFDataType type);
++}
++
+ // ----------------------------------------------------------
+ //   Extended TIFF Directory GEO Tag Support
+ // ----------------------------------------------------------
+@@ -224,6 +229,33 @@ tiff_write_geotiff_profile(TIFF *tif, FI
+ //   TIFF EXIF tag reading & writing
+ // ----------------------------------------------------------
+ 
++static uint32 exif_tag_ids[] = {
++  EXIFTAG_EXPOSURETIME, EXIFTAG_FNUMBER, EXIFTAG_EXPOSUREPROGRAM,
++  EXIFTAG_SPECTRALSENSITIVITY, EXIFTAG_ISOSPEEDRATINGS, EXIFTAG_OECF,
++  EXIFTAG_EXIFVERSION, EXIFTAG_DATETIMEORIGINAL, EXIFTAG_DATETIMEDIGITIZED,
++  EXIFTAG_COMPONENTSCONFIGURATION, EXIFTAG_COMPRESSEDBITSPERPIXEL,
++  EXIFTAG_SHUTTERSPEEDVALUE, EXIFTAG_APERTUREVALUE,
++  EXIFTAG_BRIGHTNESSVALUE, EXIFTAG_EXPOSUREBIASVALUE,
++  EXIFTAG_MAXAPERTUREVALUE, EXIFTAG_SUBJECTDISTANCE, EXIFTAG_METERINGMODE,
++  EXIFTAG_LIGHTSOURCE, EXIFTAG_FLASH, EXIFTAG_FOCALLENGTH,
++  EXIFTAG_SUBJECTAREA, EXIFTAG_MAKERNOTE, EXIFTAG_USERCOMMENT,
++  EXIFTAG_SUBSECTIME, EXIFTAG_SUBSECTIMEORIGINAL,
++  EXIFTAG_SUBSECTIMEDIGITIZED, EXIFTAG_FLASHPIXVERSION, EXIFTAG_COLORSPACE,
++  EXIFTAG_PIXELXDIMENSION, EXIFTAG_PIXELYDIMENSION,
++  EXIFTAG_RELATEDSOUNDFILE, EXIFTAG_FLASHENERGY,
++  EXIFTAG_SPATIALFREQUENCYRESPONSE, EXIFTAG_FOCALPLANEXRESOLUTION,
++  EXIFTAG_FOCALPLANEYRESOLUTION, EXIFTAG_FOCALPLANERESOLUTIONUNIT,
++  EXIFTAG_SUBJECTLOCATION, EXIFTAG_EXPOSUREINDEX, EXIFTAG_SENSINGMETHOD,
++  EXIFTAG_FILESOURCE, EXIFTAG_SCENETYPE, EXIFTAG_CFAPATTERN,
++  EXIFTAG_CUSTOMRENDERED, EXIFTAG_EXPOSUREMODE, EXIFTAG_WHITEBALANCE,
++  EXIFTAG_DIGITALZOOMRATIO, EXIFTAG_FOCALLENGTHIN35MMFILM,
++  EXIFTAG_SCENECAPTURETYPE, EXIFTAG_GAINCONTROL, EXIFTAG_CONTRAST,
++  EXIFTAG_SATURATION, EXIFTAG_SHARPNESS, EXIFTAG_DEVICESETTINGDESCRIPTION,
++  EXIFTAG_SUBJECTDISTANCERANGE, EXIFTAG_GAINCONTROL, EXIFTAG_GAINCONTROL,
++  EXIFTAG_IMAGEUNIQUEID
++};
++static int nExifTags = sizeof(exif_tag_ids) / sizeof(exif_tag_ids[0]);
++
+ /**
+ Read a single Exif tag
+ 
+@@ -575,45 +607,11 @@ tiff_read_exif_tags(TIFF *tif, TagLib::M
+ 
+ 	// loop over all Core Directory Tags
+ 	// ### uses private data, but there is no other way
++	// -> Fedora: Best we can do without private headers is to hard-code a list of known EXIF tags and read those
+ 	if(md_model == TagLib::EXIF_MAIN) {
+-		const TIFFDirectory *td = &tif->tif_dir;
+-
+-		uint32 lastTag = 0;	//<- used to prevent reading some tags twice (as stored in tif_fieldinfo)
+-
+-		for (int fi = 0, nfi = (int)tif->tif_nfields; nfi > 0; nfi--, fi++) {
+-			const TIFFField *fld = tif->tif_fields[fi];
+-
+-			const uint32 tag_id = TIFFFieldTag(fld);
+-
+-			if(tag_id == lastTag) {
+-				continue;
+-			}
+-
+-			// test if tag value is set
+-			// (lifted directly from LibTiff _TIFFWriteDirectory)
+-
+-			if( fld->field_bit == FIELD_CUSTOM ) {
+-				int is_set = FALSE;
+-
+-				for(int ci = 0; ci < td->td_customValueCount; ci++ ) {
+-					is_set |= (td->td_customValues[ci].info == fld);
+-				}
+-
+-				if( !is_set ) {
+-					continue;
+-				}
+-
+-			} else if(!TIFFFieldSet(tif, fld->field_bit)) {
+-				continue;
+-			}
+-
+-			// process *all* other tags (some will be ignored)
+-
+-			tiff_read_exif_tag(tif, tag_id, dib, md_model);
+-
+-			lastTag = tag_id;
++		for (int i = 0; i < nExifTags; ++i) {
++			tiff_read_exif_tag(tif, exif_tag_ids[i], dib, md_model);
+ 		}
+-
+ 	}
+ 
+ 	return TRUE;
+@@ -723,10 +721,9 @@ tiff_write_exif_tags(TIFF *tif, TagLib::
+ 	
+ 	TagLib& tag_lib = TagLib::instance();
+ 	
+-	for (int fi = 0, nfi = (int)tif->tif_nfields; nfi > 0; nfi--, fi++) {
+-		const TIFFField *fld = tif->tif_fields[fi];
+-		
+-		const uint32 tag_id = TIFFFieldTag(fld);
++	for (int fi = 0; fi < nExifTags; fi++) {
++		const uint32 tag_id = exif_tag_ids[fi];
++		const TIFFField *fld = TIFFFieldWithTag(tif, tag_id);
+ 
+ 		if(skip_write_field(tif, tag_id)) {
+ 			// skip tags that are already handled by the LibTIFF writing process
diff --git a/gnu/packages/patches/htop-fix-process-tree.patch b/gnu/packages/patches/htop-fix-process-tree.patch
deleted file mode 100644
index d8e5e2ccac..0000000000
--- a/gnu/packages/patches/htop-fix-process-tree.patch
+++ /dev/null
@@ -1,99 +0,0 @@
-From 2971a187551e062ffefdab965f55377b36cd94eb Mon Sep 17 00:00:00 2001
-From: Tobias Geerinckx-Rice <me@tobias.gr>
-Date: Wed, 21 Feb 2018 06:00:50 +0100
-Subject: [PATCH] Fix process tree
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-This manually reverts:
-
-  commit 584a9bceab948590dabd189d234a86e6bf4ec3f4
-  Author: wangqr <wangqr@wangqr.tk>
-  Date:   Fri Sep 1 21:27:24 2017 +0800
-
-  Find roots when constructing process tree, fix #587
-
-which breaks the process tree (‘t’) view in at least some cases.
-I will investigate further...
----
- ProcessList.c | 63 +++++++++++++++++------------------------------------------
- 1 file changed, 18 insertions(+), 45 deletions(-)
-
-diff --git a/ProcessList.c b/ProcessList.c
-index 48b2d95..225253d 100644
---- a/ProcessList.c
-+++ b/ProcessList.c
-@@ -213,51 +213,24 @@ void ProcessList_sort(ProcessList* this) {
-       // Restore settings
-       this->settings->sortKey = sortKey;
-       this->settings->direction = direction;
--      int vsize = Vector_size(this->processes);
--      // Find all processes whose parent is not visible
--      int size;
--      while ((size = Vector_size(this->processes))) {
--         int i;
--         for (i = 0; i < size; i++) {
--            Process* process = (Process*)(Vector_get(this->processes, i));
--            // Immediately consume not shown processes
--            if (!process->show) {
--               process = (Process*)(Vector_take(this->processes, i));
--               process->indent = 0;
--               Vector_add(this->processes2, process);
--               ProcessList_buildTree(this, process->pid, 0, 0, direction, false);
--               break;
--            }
--            pid_t ppid = process->tgid == process->pid ? process->ppid : process->tgid;
--            // Bisect the process vector to find parent
--            int l = 0, r = size;
--            // If PID corresponds with PPID (e.g. "kernel_task" (PID:0, PPID:0)
--            // on Mac OS X 10.11.6) cancel bisecting and regard this process as
--            // root.
--            if (process->pid == ppid)
--               r = 0;
--            while (l < r) {
--               int c = (l + r) / 2;
--               pid_t pid = ((Process*)(Vector_get(this->processes, c)))->pid;
--               if (ppid == pid) {
--                  break;
--               } else if (ppid < pid) {
--                  r = c;
--               } else {
--                  l = c + 1;
--               }
--            }
--            // If parent not found, then construct the tree with this root
--            if (l >= r) {
--               process = (Process*)(Vector_take(this->processes, i));
--               process->indent = 0;
--               Vector_add(this->processes2, process);
--               ProcessList_buildTree(this, process->pid, 0, 0, direction, process->showChildren);
--               break;
--            }
--         }
--         // There should be no loop in the process tree
--         assert(i < size);
-+
-+      // Take PID 1 as root and add to the new listing
-+       int vsize = Vector_size(this->processes);
-+      Process* init = (Process*) (Vector_take(this->processes, 0));
-+      if (!init) return;
-+      // This assertion crashes on hardened kernels.
-+      // I wonder how well tree view works on those systems.
-+      // assert(init->pid == 1);
-+      init->indent = 0;
-+      Vector_add(this->processes2, init);
-+      // Recursively empty list
-+      ProcessList_buildTree(this, init->pid, 0, 0, direction, true);
-+      // Add leftovers
-+      while (Vector_size(this->processes)) {
-+         Process* p = (Process*) (Vector_take(this->processes, 0));
-+         p->indent = 0;
-+         Vector_add(this->processes2, p);
-+         ProcessList_buildTree(this, p->pid, 0, 0, direction, p->showChildren);
-       }
-       assert(Vector_size(this->processes2) == vsize); (void)vsize;
-       assert(Vector_size(this->processes) == 0);
--- 
-2.16.2
-
diff --git a/gnu/packages/patches/hwloc-tests-without-sysfs.patch b/gnu/packages/patches/hwloc-tests-without-sysfs.patch
deleted file mode 100644
index ea6ec41616..0000000000
--- a/gnu/packages/patches/hwloc-tests-without-sysfs.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Fix a test failure in the build environment, where /sys is missing.
-From <https://github.com/bgoglin/hwloc/commit/a2cc4f2e2bf4a8bbdd61b578a62e27e7482799cf.patch>.
-
-From a2cc4f2e2bf4a8bbdd61b578a62e27e7482799cf Mon Sep 17 00:00:00 2001
-From: Brice Goglin <Brice.Goglin@inria.fr>
-Date: Tue, 6 Feb 2018 17:13:26 +0100
-Subject: [PATCH] linux: honor the filtering cores and packages when reading
- topology from cpuinfo
-
-Caused a make check crash in lstopo --filter all:none in chroot without sysfs.
-
-Thanks to Ludovic Courtes for the report.
-
-Signed-off-by: Brice Goglin <Brice.Goglin@inria.fr>
----
- hwloc/topology-linux.c | 6 ++++--
- 1 file changed, 4 insertions(+), 2 deletions(-)
-
-diff --git a/hwloc/topology-linux.c b/hwloc/topology-linux.c
-index 290da0d72..e1bbf94e1 100644
---- a/hwloc/topology-linux.c
-+++ b/hwloc/topology-linux.c
-@@ -4101,7 +4101,8 @@ look_cpuinfo(struct hwloc_topology *topology,
-     }
-   /* create package objects */
-   hwloc_debug("%u pkgs%s\n", numpkgs, missingpkg ? ", but some missing package" : "");
--  if (!missingpkg && numpkgs>0) {
-+  if (!missingpkg && numpkgs>0
-+      && hwloc_filter_check_keep_object_type(topology, HWLOC_OBJ_PACKAGE)) {
-     for (i = 0; i < numpkgs; i++) {
-       struct hwloc_obj *obj = hwloc_alloc_setup_object(topology, HWLOC_OBJ_PACKAGE, Lpkg_to_Ppkg[i]);
-       int doneinfos = 0;
-@@ -4145,7 +4146,8 @@ look_cpuinfo(struct hwloc_topology *topology,
-     }
-   /* create Core objects */
-   hwloc_debug("%u cores%s\n", numcores, missingcore ? ", but some missing core" : "");
--  if (!missingcore && numcores>0) {
-+  if (!missingcore && numcores>0
-+      && hwloc_filter_check_keep_object_type(topology, HWLOC_OBJ_CORE)) {
-     for (i = 0; i < numcores; i++) {
-       struct hwloc_obj *obj = hwloc_alloc_setup_object(topology, HWLOC_OBJ_CORE, Lcore_to_Pcore[i]);
-       obj->cpuset = hwloc_bitmap_alloc();
diff --git a/gnu/packages/patches/libgnomeui-utf8.patch b/gnu/packages/patches/libgnomeui-utf8.patch
index 304d74e1e2..11622b21ee 100644
--- a/gnu/packages/patches/libgnomeui-utf8.patch
+++ b/gnu/packages/patches/libgnomeui-utf8.patch
@@ -8,11 +8,11 @@ make[2]: Entering directory '/tmp/guix-build-libgnomeui-2.24.5.drv-0/libgnomeui-
 INFO: Reading ./gnome-marshal.list...
   GEN    gnome-marshal.h
 Traceback (most recent call last):
-  File "/gnu/store/azh1is0xknn4xphwj33iqcb5ic9qhk8l-glib-2.54.2-bin/bin/glib-mkenums", line 688, in <module>
+  File "/gnu/store/...-glib-2.54.2-bin/bin/glib-mkenums", line 688, in <module>
     process_file(fname)
-  File "/gnu/store/azh1is0xknn4xphwj33iqcb5ic9qhk8l-glib-2.54.2-bin/bin/glib-mkenums", line 420, in process_file
+  File "/gnu/store/...-glib-2.54.2-bin/bin/glib-mkenums", line 420, in process_file
     line = curfile.readline()
-  File "/gnu/store/3lkypf5wnsnvkaidhw0pv7k3yjfh1r9g-python-3.6.3/lib/python3.6/codecs.py", line 321, in decode
+  File "/gnu/store/...-python-3.6.3/lib/python3.6/codecs.py", line 321, in decode
     (result, consumed) = self._buffer_decode(data, self.errors, final)
 UnicodeDecodeError: 'utf-8' codec can't decode byte 0xf1 in position 1009: invalid continuation byte
 make[2]: *** [Makefile:1109: stamp-gnometypebuiltins.h] Error 1
diff --git a/gnu/packages/patches/libusb-for-axoloti.patch b/gnu/packages/patches/libusb-for-axoloti.patch
index 2c07d767d9..76a45e801d 100644
--- a/gnu/packages/patches/libusb-for-axoloti.patch
+++ b/gnu/packages/patches/libusb-for-axoloti.patch
@@ -1,14 +1,14 @@
-diff -rp -u4 libusb-1.0.19-orig/libusb/descriptor.c libusb-1.0.19/libusb/descriptor.c
---- libusb-1.0.19-orig/libusb/descriptor.c	2015-05-12 00:15:19 +0200
-+++ libusb-1.0.19/libusb/descriptor.c	2015-05-12 00:17:09 +0200
-@@ -1181,9 +1181,9 @@ int API_EXPORTED libusb_get_string_descr
+diff -rpu4 libusb-1.0.22.orig/libusb/descriptor.c libusb-1.0.22/libusb/descriptor.c
+--- libusb-1.0.22.orig/libusb/descriptor.c	2018-03-17 08:23:37.000000000 +0100
++++ libusb-1.0.22/libusb/descriptor.c	2018-03-29 10:36:09.968429473 +0200
+@@ -1173,9 +1173,9 @@ int API_EXPORTED libusb_get_string_descr
  	if (tbuf[1] != LIBUSB_DT_STRING)
  		return LIBUSB_ERROR_IO;
  
  	if (tbuf[0] > r)
 -		return LIBUSB_ERROR_IO;
-+            tbuf[0] = r;
++		tbuf[0] = r;
  
- 	for (di = 0, si = 2; si < tbuf[0]; si += 2) {
+ 	di = 0;
+ 	for (si = 2; si < tbuf[0]; si += 2) {
  		if (di >= (length - 1))
- 			break;
diff --git a/gnu/packages/patches/links-CVE-2017-11114.patch b/gnu/packages/patches/links-CVE-2017-11114.patch
deleted file mode 100644
index c5ac9884b5..0000000000
--- a/gnu/packages/patches/links-CVE-2017-11114.patch
+++ /dev/null
@@ -1,99 +0,0 @@
-Fix CVE-2017-11114:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-11114
-http://seclists.org/fulldisclosure/2017/Jul/76
-
-Patch copied from Debian:
-
-https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=870299#12
-
-Origin: upstream, commit: fee5dca79a93a37024e494b985386a5fe60bc1b7
-Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=870299#12
-Author: Mikulas Patocka <mikulas@twibright.com>
-Date:   Wed Aug 2 20:13:29 2017 +0200
-Subject: Fix read out of memory in case of corrupted UTF-8 data
-
----
- charsets.c |   37 +------------------------------------
- links.h    |    9 ++++-----
- 2 files changed, 5 insertions(+), 41 deletions(-)
-
-Index: links-2.14/charsets.c
-===================================================================
---- links-2.14.orig/charsets.c
-+++ links-2.14/charsets.c
-@@ -215,41 +215,6 @@ static struct conv_table *get_translatio
- 	return utf_table;
- }
- 
--unsigned short int utf8_2_uni_table[0x200] = {
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 128,	0, 0, 0, 192,	0,
--	0, 0, 256,	0, 0, 0, 320,	0, 0, 0, 384,	0, 0, 0, 448,	0,
--	0, 0, 512,	0, 0, 0, 576,	0, 0, 0, 640,	0, 0, 0, 704,	0,
--	0, 0, 768,	0, 0, 0, 832,	0, 0, 0, 896,	0, 0, 0, 960,	0,
--	0, 0, 1024,	0, 0, 0, 1088,	0, 0, 0, 1152,	0, 0, 0, 1216,	0,
--	0, 0, 1280,	0, 0, 0, 1344,	0, 0, 0, 1408,	0, 0, 0, 1472,	0,
--	0, 0, 1536,	0, 0, 0, 1600,	0, 0, 0, 1664,	0, 0, 0, 1728,	0,
--	0, 0, 1792,	0, 0, 0, 1856,	0, 0, 0, 1920,	0, 0, 0, 1984,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--	0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0, 0, 0, 0,	0,
--};
--
- unsigned char utf_8_1[256] = {
- 	6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
- 	7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
-@@ -269,7 +234,7 @@ unsigned char utf_8_1[256] = {
- 	3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 6, 6,
- };
- 
--static_const unsigned min_utf_8[9] = {
-+static_const unsigned min_utf_8[8] = {
- 	0, 0x4000000, 0x200000, 0x10000, 0x800, 0x80, 0x100, 0x1,
- };
- 
-Index: links-2.14/links.h
-===================================================================
---- links-2.14.orig/links.h
-+++ links-2.14/links.h
-@@ -3906,15 +3906,14 @@ unsigned char *cp_strchr(int charset, un
- void init_charset(void);
- 
- unsigned get_utf_8(unsigned char **p);
--extern unsigned short int utf8_2_uni_table[0x200];
- #define GET_UTF_8(s, c)							\
- do {									\
- 	if ((unsigned char)(s)[0] < 0x80)				\
- 		(c) = (s)++[0];						\
--	else if (((c) = utf8_2_uni_table[((unsigned char)(s)[0] << 2) +	\
--				((unsigned char)(s)[1] >> 6) - 0x200]))	\
--		(c) += (unsigned char)(s)[1] & 0x3f, (s) += 2;		\
--	else								\
-+	else if ((unsigned char)(s)[0] >= 0xc2 && (unsigned char)(s)[0] < 0xe0 &&\
-+	         ((unsigned char)(s)[1] & 0xc0) == 0x80) {		\
-+		(c) = (unsigned char)(s)[0] * 0x40 + (unsigned char)(s)[1], (c) -= 0x3080, (s) += 2;\
-+	} else								\
- 		(c) = get_utf_8(&(s));					\
- } while (0)
- #define FWD_UTF_8(s)							\
diff --git a/gnu/packages/patches/lyx-2.2.3-fix-test.patch b/gnu/packages/patches/lyx-2.2.3-fix-test.patch
new file mode 100644
index 0000000000..10b7d2a3a9
--- /dev/null
+++ b/gnu/packages/patches/lyx-2.2.3-fix-test.patch
@@ -0,0 +1,13 @@
+See https://www.lyx.org/trac/ticket/10800#comment:17
+diff --git a/src/tex2lyx/test/test-structure.lyx.lyx b/src/tex2lyx/test/test-structure.lyx.lyx
+index feff755cd2..2c7f2ace5c 100644
+--- a/src/tex2lyx/test/test-structure.lyx.lyx
++++ b/src/tex2lyx/test/test-structure.lyx.lyx
+@@ -212,7 +212,7 @@ This causes the
+ \begin_inset Flex Flex:Strong
+ status collapsed
+ 
+-\begin_layout Standard
++\begin_layout Plain Layout
+ logikalmkup
+ \end_layout
diff --git a/gnu/packages/patches/mupdf-CVE-2018-1000051.patch b/gnu/packages/patches/mupdf-CVE-2018-1000051.patch
new file mode 100644
index 0000000000..bb78c46f80
--- /dev/null
+++ b/gnu/packages/patches/mupdf-CVE-2018-1000051.patch
@@ -0,0 +1,88 @@
+Fix CVE-2018-1000051:
+
+https://bugs.ghostscript.com/show_bug.cgi?id=698873
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1000051
+
+Patch copied from upstream source repository:
+
+https://git.ghostscript.com/?p=mupdf.git;a=commit;h=321ba1de287016b0036bf4a56ce774ad11763384
+
+From 321ba1de287016b0036bf4a56ce774ad11763384 Mon Sep 17 00:00:00 2001
+From: Sebastian Rasmussen <sebras@gmail.com>
+Date: Tue, 19 Dec 2017 23:47:47 +0100
+Subject: [PATCH] Bug 698825: Do not drop borrowed colorspaces.
+
+Previously the borrowed colorspace was dropped when updating annotation
+appearances, leading to use after free warnings from valgrind/ASAN.
+---
+ source/pdf/pdf-appearance.c | 8 ++------
+ 1 file changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/source/pdf/pdf-appearance.c b/source/pdf/pdf-appearance.c
+index 70f684f4..d7a1dddd 100644
+--- a/source/pdf/pdf-appearance.c
++++ b/source/pdf/pdf-appearance.c
+@@ -2170,7 +2170,6 @@ void pdf_update_free_text_annot_appearance(fz_context *ctx, pdf_document *doc, p
+ 	fz_device *dev = NULL;
+ 	font_info font_rec;
+ 	fz_text *text = NULL;
+-	fz_colorspace *cs = NULL;
+ 	fz_matrix page_ctm;
+ 
+ 	pdf_page_transform(ctx, annot->page, NULL, &page_ctm);
+@@ -2184,11 +2183,11 @@ void pdf_update_free_text_annot_appearance(fz_context *ctx, pdf_document *doc, p
+ 	fz_var(dlist);
+ 	fz_var(dev);
+ 	fz_var(text);
+-	fz_var(cs);
+ 	fz_try(ctx)
+ 	{
+ 		char *contents = pdf_to_str_buf(ctx, pdf_dict_get(ctx, obj, PDF_NAME_Contents));
+ 		char *da = pdf_to_str_buf(ctx, pdf_dict_get(ctx, obj, PDF_NAME_DA));
++		fz_colorspace *cs;
+ 		fz_point pos;
+ 		fz_rect rect;
+ 
+@@ -2223,7 +2222,6 @@ void pdf_update_free_text_annot_appearance(fz_context *ctx, pdf_document *doc, p
+ 		fz_drop_display_list(ctx, dlist);
+ 		font_info_fin(ctx, &font_rec);
+ 		fz_drop_text(ctx, text);
+-		fz_drop_colorspace(ctx, cs);
+ 	}
+ 	fz_catch(ctx)
+ 	{
+@@ -2359,7 +2357,6 @@ void pdf_set_signature_appearance(fz_context *ctx, pdf_document *doc, pdf_annot
+ 	fz_device *dev = NULL;
+ 	font_info font_rec;
+ 	fz_text *text = NULL;
+-	fz_colorspace *cs = NULL;
+ 	fz_path *path = NULL;
+ 	fz_buffer *fzbuf = NULL;
+ 	fz_matrix page_ctm;
+@@ -2375,7 +2372,6 @@ void pdf_set_signature_appearance(fz_context *ctx, pdf_document *doc, pdf_annot
+ 	fz_var(dlist);
+ 	fz_var(dev);
+ 	fz_var(text);
+-	fz_var(cs);
+ 	fz_var(fzbuf);
+ 	fz_try(ctx)
+ 	{
+@@ -2384,6 +2380,7 @@ void pdf_set_signature_appearance(fz_context *ctx, pdf_document *doc, pdf_annot
+ 		fz_rect logo_bounds;
+ 		fz_matrix logo_tm;
+ 		fz_rect rect;
++		fz_colorspace *cs = fz_device_rgb(ctx); /* Borrowed reference */
+ 
+ 		pdf_to_rect(ctx, pdf_dict_get(ctx, annot->obj, PDF_NAME_Rect), &annot_rect);
+ 		rect = annot_rect;
+@@ -2396,7 +2393,6 @@ void pdf_set_signature_appearance(fz_context *ctx, pdf_document *doc, pdf_annot
+ 		fz_bound_path(ctx, path, NULL, &fz_identity, &logo_bounds);
+ 		center_rect_within_rect(&logo_bounds, &rect, &logo_tm);
+ 		fz_concat(&logo_tm, &logo_tm, &page_ctm);
+-		cs = fz_device_rgb(ctx); /* Borrowed reference */
+ 		fz_fill_path(ctx, dev, path, 0, &logo_tm, cs, logo_color, 1.0f, NULL);
+ 
+ 		get_font_info(ctx, doc, dr, da, &font_rec);
+-- 
+2.16.3
+
diff --git a/gnu/packages/patches/mupdf-CVE-2018-6544.patch b/gnu/packages/patches/mupdf-CVE-2018-6544.patch
new file mode 100644
index 0000000000..b2c8f849f3
--- /dev/null
+++ b/gnu/packages/patches/mupdf-CVE-2018-6544.patch
@@ -0,0 +1,109 @@
+Fix CVE-2018-6544:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-6544
+https://bugs.ghostscript.com/show_bug.cgi?id=698830
+https://bugs.ghostscript.com/show_bug.cgi?id=698965 
+
+Patches copied from upstream source repository:
+
+https://git.ghostscript.com/?p=mupdf.git;h=26527eef77b3e51c2258c8e40845bfbc015e405d
+https://git.ghostscript.com/?p=mupdf.git;h=b03def134988da8c800adac1a38a41a1f09a1d89
+
+From b03def134988da8c800adac1a38a41a1f09a1d89 Mon Sep 17 00:00:00 2001
+From: Sebastian Rasmussen <sebras@gmail.com>
+Date: Thu, 1 Feb 2018 16:36:14 +0100
+Subject: [PATCH] Bug 698830: Avoid recursion when loading object streams
+ objects.
+
+If there were indirect references in the object stream dictionary and
+one of those indirect references referred to an object inside the object
+stream itself, mupdf would previously enter recursion only bounded by the
+exception stack. After this commit the object stream is checked if it is
+marked immediately after being loaded. If it is marked then we terminate
+the recursion at this point, if it is not marked then mark it and
+attempt to load the desired object within. We also take care to unmark
+the stream object when done or upon exception.
+---
+ source/pdf/pdf-xref.c | 14 ++++++++++++++
+ 1 file changed, 14 insertions(+)
+
+diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c
+index 723b543c..ed09094c 100644
+--- a/source/pdf/pdf-xref.c
++++ b/source/pdf/pdf-xref.c
+@@ -1576,6 +1576,19 @@ pdf_load_obj_stm(fz_context *ctx, pdf_document *doc, int num, pdf_lexbuf *buf, i
+ 	{
+ 		objstm = pdf_load_object(ctx, doc, num);
+ 
++		if (pdf_obj_marked(ctx, objstm))
++			fz_throw(ctx, FZ_ERROR_GENERIC, "recursive object stream lookup");
++	}
++	fz_catch(ctx)
++	{
++		pdf_drop_obj(ctx, objstm);
++		fz_rethrow(ctx);
++	}
++
++	fz_try(ctx)
++	{
++		pdf_mark_obj(ctx, objstm);
++
+ 		count = pdf_to_int(ctx, pdf_dict_get(ctx, objstm, PDF_NAME_N));
+ 		first = pdf_to_int(ctx, pdf_dict_get(ctx, objstm, PDF_NAME_First));
+ 
+@@ -1655,6 +1668,7 @@ pdf_load_obj_stm(fz_context *ctx, pdf_document *doc, int num, pdf_lexbuf *buf, i
+ 		fz_drop_stream(ctx, stm);
+ 		fz_free(ctx, ofsbuf);
+ 		fz_free(ctx, numbuf);
++		pdf_unmark_obj(ctx, objstm);
+ 		pdf_drop_obj(ctx, objstm);
+ 	}
+ 	fz_catch(ctx)
+-- 
+2.16.3
+
+From 26527eef77b3e51c2258c8e40845bfbc015e405d Mon Sep 17 00:00:00 2001
+From: Sebastian Rasmussen <sebras@gmail.com>
+Date: Mon, 29 Jan 2018 02:00:48 +0100
+Subject: [PATCH] Bug 698830: Don't drop unkept stream if running out of error
+ stack.
+
+Under normal conditions where fz_keep_stream() is called inside
+fz_try() we may call fz_drop_stream() in fz_catch() upon exceptions.
+The issue comes when fz_keep_stream() has not yet been called but is
+dropped in fz_catch(). This happens in the PDF from the bug when
+fz_try() runs out of exception stack, and next the code in fz_catch()
+runs, dropping the caller's reference to the filter chain stream!
+
+The simplest way of fixing this it to always keep the filter chain
+stream before fz_try() is called. That way fz_catch() may drop the
+stream whether an exception has occurred or if the fz_try() ran out of
+exception stack.
+---
+ source/pdf/pdf-stream.c | 5 ++---
+ 1 file changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/source/pdf/pdf-stream.c b/source/pdf/pdf-stream.c
+index c89da5c4..c6ba7ad3 100644
+--- a/source/pdf/pdf-stream.c
++++ b/source/pdf/pdf-stream.c
+@@ -303,14 +303,13 @@ pdf_open_raw_filter(fz_context *ctx, fz_stream *chain, pdf_document *doc, pdf_ob
+ 		*orig_gen = 0;
+ 	}
+ 
+-	fz_var(chain);
++	chain = fz_keep_stream(ctx, chain);
+ 
+ 	fz_try(ctx)
+ 	{
+ 		len = pdf_to_int(ctx, pdf_dict_get(ctx, stmobj, PDF_NAME_Length));
+ 
+-		/* don't close chain when we close this filter */
+-		chain2 = fz_keep_stream(ctx, chain);
++		chain2 = chain;
+ 		chain = NULL;
+ 		chain = fz_open_null(ctx, chain2, len, offset);
+ 
+-- 
+2.16.3
+
diff --git a/gnu/packages/patches/mupen64plus-video-z64-glew-correct-path.patch b/gnu/packages/patches/mupen64plus-video-z64-glew-correct-path.patch
new file mode 100644
index 0000000000..c3fcfbbd0e
--- /dev/null
+++ b/gnu/packages/patches/mupen64plus-video-z64-glew-correct-path.patch
@@ -0,0 +1,36 @@
+From 21507b3600c616bca7049004eb518cf11f45f299 Mon Sep 17 00:00:00 2001
+From: "Anthony J. Bentley" <anthony@cathet.us>
+Date: Sun, 7 Jun 2015 02:41:28 -0600
+Subject: [PATCH] Correct the path to the GLEW header.
+
+---
+ src/glshader.cpp | 2 +-
+ src/rgl.h        | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/glshader.cpp b/src/glshader.cpp
+index 4729945..a8947ea 100644
+--- a/src/glshader.cpp
++++ b/src/glshader.cpp
+@@ -23,7 +23,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include "rgl_assert.h"
+-#include <glew.h>
++#include <GL/glew.h>
+ #if defined(__MACOSX__)
+ #include <OpenGL/gl.h>
+ #include <OpenGL/glext.h>
+diff --git a/src/rgl.h b/src/rgl.h
+index c15f93f..1748406 100644
+--- a/src/rgl.h
++++ b/src/rgl.h
+@@ -26,7 +26,7 @@
+ #include "rgl_assert.h"
+ #include "rdp.h"
+ 
+-#include <glew.h>
++#include <GL/glew.h>
+ #if defined(__MACOSX__)
+ #include <OpenGL/gl.h>
+ #elif defined(__MACOS__)
diff --git a/gnu/packages/patches/racket-fix-xform-issue.patch b/gnu/packages/patches/racket-fix-xform-issue.patch
new file mode 100644
index 0000000000..0a1640ee51
--- /dev/null
+++ b/gnu/packages/patches/racket-fix-xform-issue.patch
@@ -0,0 +1,63 @@
+050cdb59839896b41431791f8ee0ef2564231b8f
+Author:     Matthew Flatt <mflatt@racket-lang.org>
+AuthorDate: Tue Mar 6 09:05:08 2018 -0700
+Commit:     Matthew Flatt <mflatt@racket-lang.org>
+CommitDate: Tue Mar 6 09:05:08 2018 -0700
+
+Parent:     efb9a919fc ffi docs: clarification on `unsafe-socket->port`
+Containing: master
+Follows:    v5.0.1 (21612)
+
+xform: avoid problems with `__signbitf128`
+
+Closes #1962 and uses the suggested patch there, among other changes.
+
+2 files changed, 6 insertions(+), 3 deletions(-)
+racket/collects/compiler/private/xform.rkt | 2 +-
+racket/src/racket/src/number.c             | 7 +++++--
+
+diff --git a/racket/collects/compiler/private/xform.rkt b/racket/collects/compiler/private/xform.rkt
+index 28a425c057..89ae848f9c 100644
+--- a/collects/compiler/private/xform.rkt
++++ b/collects/compiler/private/xform.rkt
+@@ -904,7 +904,7 @@
+ 
+                strlen cos cosl sin sinl exp expl pow powl log logl sqrt sqrtl atan2 atan2l frexp
+                isnan isinf fpclass signbit _signbit _fpclass __fpclassify __fpclassifyf __fpclassifyl
+-	       _isnan __isfinited __isnanl __isnan __signbit __signbitf __signbitd __signbitl
++	       _isnan __isfinited __isnanl __isnan __signbit __signbitf __signbitd __signbitl __signbitf128
+                __isinff __isinfl isnanf isinff __isinfd __isnanf __isnand __isinf __isinff128
+                __inline_isnanl __inline_isnan __inline_signbit __inline_signbitf __inline_signbitd __inline_signbitl
+                __builtin_popcount __builtin_clz __builtin_isnan __builtin_isinf __builtin_signbit
+diff --git a/racket/src/racket/src/number.c b/racket/src/racket/src/number.c
+index 71f42aaf3c..3bbad3ba83 100644
+--- a/src/racket/src/number.c
++++ b/src/racket/src/number.c
+@@ -1796,6 +1796,7 @@ double scheme_real_to_double(Scheme_Object *r)
+ }
+ 
+ XFORM_NONGCING static MZ_INLINE int minus_zero_p(double d)
++  XFORM_SKIP_PROC
+ {
+ #ifdef MZ_IS_NEG_ZERO
+   return MZ_IS_NEG_ZERO(d);
+@@ -1809,7 +1810,9 @@ int scheme_minus_zero_p(double d)
+   return minus_zero_p(d);
+ }
+ 
+-static int rational_dbl_p(double f) {
++XFORM_NONGCING static int rational_dbl_p(double f)
++  XFORM_SKIP_PROC
++{
+   return !(MZ_IS_NAN(f)
+            || MZ_IS_INFINITY(f));
+ }
+@@ -1955,7 +1958,7 @@ real_p(int argc, Scheme_Object *argv[])
+   return (SCHEME_REALP(o) ? scheme_true : scheme_false);
+ }
+ 
+-static int is_rational(const Scheme_Object *o)
++XFORM_NONGCING static int is_rational(const Scheme_Object *o)
+ {
+   if (SCHEME_FLOATP(o))
+     return rational_dbl_p(SCHEME_FLOAT_VAL(o));
\ No newline at end of file
diff --git a/gnu/packages/patches/sharutils-CVE-2018-1000097.patch b/gnu/packages/patches/sharutils-CVE-2018-1000097.patch
new file mode 100644
index 0000000000..8d58218184
--- /dev/null
+++ b/gnu/packages/patches/sharutils-CVE-2018-1000097.patch
@@ -0,0 +1,21 @@
+Fix CVE-2018-1000097:
+
+https://security-tracker.debian.org/tracker/CVE-2018-1000097
+https://nvd.nist.gov/vuln/detail/CVE-2018-1000097
+
+Patch taken from upstream bug report:
+https://lists.gnu.org/archive/html/bug-gnu-utils/2018-02/msg00005.html
+
+diff --git a/src/unshar.c b/src/unshar.c
+index 80bc3a9..0fc3773 100644
+--- a/src/unshar.c
++++ b/src/unshar.c
+@@ -240,7 +240,7 @@ find_archive (char const * name, FILE * file, off_t start)
+       off_t position = ftello (file);
+ 
+       /* Read next line, fail if no more and no previous process.  */
+-      if (!fgets (rw_buffer, BUFSIZ, file))
++      if (!fgets (rw_buffer, rw_base_size, file))
+ 	{
+ 	  if (!start)
+ 	    error (0, 0, _("Found no shell commands in %s"), name);
diff --git a/gnu/packages/patches/translate-shell-fix-curl-tests.patch b/gnu/packages/patches/translate-shell-fix-curl-tests.patch
new file mode 100644
index 0000000000..33731462b8
--- /dev/null
+++ b/gnu/packages/patches/translate-shell-fix-curl-tests.patch
@@ -0,0 +1,60 @@
+This patch fixes Curl related tests for 'translate-shell'.
+
+Upstream bug URL:
+
+https://github.com/soimort/translate-shell/issues/221
+
+From bb9f32d3145125ba664b6b05bf0a2fd34108e9d2 Mon Sep 17 00:00:00 2001
+From: Mort Yao <soi@mort.ninja>
+Date: Sun, 25 Mar 2018 03:14:33 +0200
+Subject: [PATCH] TestUtils: perform curl-related tests only if NETWORK_ACCESS
+ is set to yes (#221)
+
+---
+ test/TestUtils.awk | 32 +++++++++++++++++---------------
+ 1 file changed, 17 insertions(+), 15 deletions(-)
+
+diff --git a/test/TestUtils.awk b/test/TestUtils.awk
+index 08bb2e9..1c141e5 100644
+--- a/test/TestUtils.awk
++++ b/test/TestUtils.awk
+@@ -30,22 +30,24 @@ BEGIN {
+         assertTrue(newerVersion("2", "1.9.9999"))
+     }
+ 
+-    T("curl()", 1)
+-    {
+-        delete tokens; delete ast
+-        tokenize(tokens, curl("https://httpbin.org/get"))
+-        parseJson(ast, tokens)
+-        assertEqual(unparameterize(ast[0 SUBSEP "url"]),
+-                    "https://httpbin.org/get")
+-    }
++    if (yn(ENVIRON["NETWORK_ACCESS"])) { # if network access enabled
++        T("curl()", 1)
++        {
++            delete tokens; delete ast
++            tokenize(tokens, curl("https://httpbin.org/get"))
++            parseJson(ast, tokens)
++            assertEqual(unparameterize(ast[0 SUBSEP "url"]),
++                        "https://httpbin.org/get")
++        }
+ 
+-    T("curlPost()", 1)
+-    {
+-        delete tokens; delete ast
+-        tokenize(tokens, curlPost("https://httpbin.org/post", "fizz=buzz"))
+-        parseJson(ast, tokens)
+-        assertEqual(unparameterize(ast[0 SUBSEP "url"]),
+-                    "https://httpbin.org/post")
++        T("curlPost()", 1)
++        {
++            delete tokens; delete ast
++            tokenize(tokens, curlPost("https://httpbin.org/post", "fizz=buzz"))
++            parseJson(ast, tokens)
++            assertEqual(unparameterize(ast[0 SUBSEP "url"]),
++                        "https://httpbin.org/post")
++        }
+     }
+ 
+     T("dump()", 3)