Merge pull request #18478 from JuliaLang/tk/backports-0.4.7

[release-0.4] backports for 0.4.7

.travis.yml

@@ -28,6 +28,7 @@ matrix:
             - gfortran
     - os: osx
       env: ARCH="x86_64"
+      osx_image: xcode7
 cache:
   directories:
     - $TRAVIS_BUILD_DIR/deps-i686
@@ -64,6 +65,7 @@ before_install:
         contrib/travis_fastfail.sh || exit 1;
         brew tap staticfloat/julia;
         brew rm --force $(brew deps julia);
+        brew install -v cmake staticfloat/juliadeps/libgfortran;
         brew install -v --only-dependencies julia;
         BUILDOPTS="-j3 USECLANG=1 LLVM_CONFIG=$(brew --prefix llvm33-julia)/bin/llvm-config-3.3 VERBOSE=1 USE_BLAS64=0 SUITESPARSE_INC=-I$(brew --prefix suite-sparse-julia)/include FORCE_ASSERTIONS=1 STAGE2_DEPS=utf8proc";
         BUILDOPTS="$BUILDOPTS LIBBLAS=-lopenblas LIBBLASNAME=libopenblas LIBLAPACK=-lopenblas LIBLAPACKNAME=libopenblas";

CONTRIBUTING.md

@@ -136,6 +136,7 @@ Make sure that [Travis](http://www.travis-ci.org) greenlights the pull request w
  - try to adhere to a 92 character line length limit
  - use upper camel case convention for modules, type names
  - use lower case with underscores for method names
+ - in docstring refer to the language as "Julia" and the executable as "`julia`"
 
 #### General Formatting Guidelines For C code contributions
 

Makefile

@@ -563,11 +563,11 @@ ifneq (,$(filter $(ARCH), i386 i486 i586 i686))
 	7z x -y 7z920.exe 7z.exe 7z.dll && \
 	../contrib/windows/winrpm.sh http://download.opensuse.org/repositories/windows:/mingw:/win32/openSUSE_13.2 \
 		"mingw32-libexpat1 mingw32-zlib1" && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw32-libgfortran3-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw32-libquadmath0-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw32-libstdc++6-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw32-libgcc_s_sjlj1-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw32-libssp0-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw32-libgfortran3-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw32-libquadmath0-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw32-libstdc++6-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw32-libgcc_s_sjlj1-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw32-libssp0-5.3.0-1.1.noarch.rpm && \
 	for i in *.rpm; do 7z x -y $$i; done && \
 	for i in *.cpio; do 7z x -y $$i; done && \
 	cp usr/i686-w64-mingw32/sys-root/mingw/bin/*.dll . && \
@@ -580,11 +580,11 @@ else ifeq ($(ARCH),x86_64)
 	mv _7z.exe 7z.exe && \
 	../contrib/windows/winrpm.sh http://download.opensuse.org/repositories/windows:/mingw:/win64/openSUSE_13.2 \
 		"mingw64-libexpat1 mingw64-zlib1" && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw64-libgfortran3-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw64-libquadmath0-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw64-libstdc++6-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw64-libgcc_s_seh1-5.3.0-1.1.noarch.rpm && \
-	$(JLDOWNLOAD) https://juliacache.s3.amazonaws.com/mingw64-libssp0-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw64-libgfortran3-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw64-libquadmath0-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw64-libstdc++6-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw64-libgcc_s_seh1-5.3.0-1.1.noarch.rpm && \
+	$(JLDOWNLOAD) https://julialang.s3.amazonaws.com/bin/winnt/extras/mingw64-libssp0-5.3.0-1.1.noarch.rpm && \
 	for i in *.rpm; do 7z x -y $$i; done && \
 	for i in *.cpio; do 7z x -y $$i; done && \
 	cp usr/x86_64-w64-mingw32/sys-root/mingw/bin/*.dll . && \

base/channels.jl

@@ -49,7 +49,6 @@ function fetch(c::Channel)
 end
 
 function take!(c::Channel)
-    !isopen(c) && !isready(c) && throw(closed_exception())
     wait(c)
     v = shift!(c.data)
     notify(c.cond_put, nothing, false, false) # notify only one, since only one slot has become available for a put!.
@@ -60,6 +59,7 @@ isready(c::Channel) = n_avail(c) > 0
 
 function wait(c::Channel)
     while !isready(c)
+        !isopen(c) && throw(closed_exception())
         wait(c.cond_take)
     end
     nothing

base/docs/helpdb.jl

@@ -918,7 +918,7 @@ typeintersect
 doc"""
     pointer(array [, index])
 
-Get the native address of an array or string element. Be careful to ensure that a julia reference to `a` exists as long as this pointer will be used. This function is "unsafe" like `unsafe_convert`.
+Get the native address of an array or string element. Be careful to ensure that a Julia reference to `a` exists as long as this pointer will be used. This function is "unsafe" like `unsafe_convert`.
 
 Calling `Ref(array[, index])` is generally preferable to this function.
 """
@@ -1388,7 +1388,7 @@ valtype
 doc"""
     edit(path::AbstractString, [line])
 
-Edit a file or directory optionally providing a line number to edit the file at. Returns to the julia prompt when you quit the editor.
+Edit a file or directory optionally providing a line number to edit the file at. Returns to the `julia` prompt when you quit the editor.
 """
 edit(path::AbstractString, line=?)
 
@@ -4009,7 +4009,7 @@ addprocs()
 addprocs(machines; keyword_args...) -> List of process identifiers
 ```
 
-Add processes on remote machines via SSH. Requires julia to be installed in the same
+Add processes on remote machines via SSH. Requires `julia` to be installed in the same
 location on each node, or to be available via a shared file system.
 
 `machines` is a vector of machine specifications.  Worker are started for each specification.
@@ -4039,7 +4039,7 @@ Keyword arguments:
 * `dir`: specifies the working directory on the workers. Defaults to the host's current
          directory (as found by `pwd()`)
 
-* `exename`: name of the julia executable. Defaults to `"\$JULIA_HOME/julia"` or
+* `exename`: name of the `julia` executable. Defaults to `"\$JULIA_HOME/julia"` or
              `"\$JULIA_HOME/julia-debug"` as the case may be.
 
 * `exeflags`: additional flags passed to the worker processes.
@@ -4455,7 +4455,7 @@ Convert `x` to a value of type `T`
 
 In cases where `convert` would need to take a Julia object and turn it into a `Ptr`, this function should be used to define and perform that conversion.
 
-Be careful to ensure that a julia reference to `x` exists as long as the result of this function will be used. Accordingly, the argument `x` to this function should never be an expression, only a variable name or field reference. For example, `x=a.b.c` is acceptable, but `x=[a,b,c]` is not.
+Be careful to ensure that a Julia reference to `x` exists as long as the result of this function will be used. Accordingly, the argument `x` to this function should never be an expression, only a variable name or field reference. For example, `x=a.b.c` is acceptable, but `x=[a,b,c]` is not.
 
 The `unsafe` prefix on this function indicates that using the result of this function after the `x` argument to this function is no longer accessible to the program may cause undefined behavior, including program corruption or segfaults, at any later time.
 """
@@ -7761,7 +7761,7 @@ error
 doc"""
     less(file::AbstractString, [line])
 
-Show a file using the default pager, optionally providing a starting line number. Returns to the julia prompt when you quit the pager.
+Show a file using the default pager, optionally providing a starting line number. Returns to the `julia` prompt when you quit the pager.
 """
 less(f::AbstractString, ?)
 
@@ -8686,7 +8686,7 @@ listenany
 doc"""
     getpid() -> Int32
 
-Get julia's process ID.
+Get Julia's process ID.
 """
 getpid
 
@@ -10227,7 +10227,7 @@ redirect_stdout
 doc"""
     redirect_stdout(stream)
 
-Replace `STDOUT` by stream for all C and julia level output to `STDOUT`. Note that `stream` must be a TTY, a `Pipe` or a `TCPSocket`.
+Replace `STDOUT` by stream for all C and Julia level output to `STDOUT`. Note that `stream` must be a TTY, a `Pipe` or a `TCPSocket`.
 """
 redirect_stdout(stream)
 

base/float16.jl

@@ -154,7 +154,7 @@ end
 
 for func in (:div,:fld,:cld,:rem,:mod,:atan2,:hypot)
     @eval begin
-        $func(a::Float16,b::Float16) = Float16($func(Float32(a),Float32(a)))
+        $func(a::Float16,b::Float16) = Float16($func(Float32(a),Float32(b)))
     end
 end
 

base/linalg/arnoldi.jl

@@ -117,7 +117,7 @@ function _eigs(A, B;
     T = eltype(A)
     iscmplx = T <: Complex
     isgeneral = B !== I
-    sym = issym(A) && !iscmplx
+    sym = issym(A) && issym(B) && !iscmplx
     nevmax=sym ? n-1 : n-2
     if nevmax <= 0
         throw(ArgumentError("Input matrix A is too small. Use eigfact instead."))
@@ -135,9 +135,6 @@ function _eigs(A, B;
         ncv = ncvmin
     end
     ncv = BlasInt(min(ncv, n))
-    if isgeneral && !isposdef(B)
-        throw(PosDefException(0))
-    end
     bmat = isgeneral ? "G" : "I"
     isshift = sigma !== nothing
 
@@ -208,7 +205,7 @@ function _eigs(A, B;
             solveSI(x) = x
         else                #    Shift-invert mode
             mode       = 3
-            F = factorize(sigma==zero(T) ? A : A - UniformScaling(sigma))
+            F = factorize(A - UniformScaling(sigma))
             solveSI(x) = F \ x
         end
     else                    # Generalized eigenproblem
@@ -219,7 +216,7 @@ function _eigs(A, B;
             solveSI(x) = F \ x
         else                #    Shift-invert mode
             mode       = 3
-            F = factorize(sigma==zero(T) ? A : A-sigma*B)
+            F = factorize(A - sigma*B)
             solveSI(x) = F \ x
         end
     end

base/linalg/lapack.jl

@@ -1504,7 +1504,12 @@ for (geev, gesvd, gesdd, ggsvd, elty, relty) in
                 end
                 @lapackerror
                 if lwork < 0
-                    lwork = BlasInt(real(work[1]))
+                    # Work around issue with truncated Float32 representation of lwork in
+                    # sgesdd by using nextfloat. See
+                    # http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=13&t=4587&p=11036&hilit=sgesdd#p11036
+                    # and
+                    # https://github.com/scipy/scipy/issues/5401
+                    lwork = round(BlasInt, nextfloat(real(work[1])))
                     work = Array($elty, lwork)
                 end
             end

base/linalg/symmetric.jl

@@ -56,6 +56,9 @@ end
 ctranspose(A::Hermitian) = A
 trace(A::Hermitian) = real(trace(A.data))
 
+Base.conj(A::HermOrSym) = typeof(A)(conj(A.data), A.uplo)
+Base.conj!(A::HermOrSym) = typeof(A)(conj!(A.data), A.uplo)
+
 #tril/triu
 function tril(A::Hermitian, k::Integer=0)
     if A.uplo == 'U' && k <= 0

base/linalg/uniformscaling.jl

@@ -24,6 +24,11 @@ one{T}(J::UniformScaling{T}) = one(UniformScaling{T})
 zero{T}(::Type{UniformScaling{T}}) = UniformScaling(zero(T))
 zero{T}(J::UniformScaling{T}) = zero(UniformScaling{T})
 
+istriu(::UniformScaling) = true
+istril(::UniformScaling) = true
+issym(::UniformScaling) = true
+ishermitian(J::UniformScaling) = isreal(J.λ)
+
 (+)(J1::UniformScaling, J2::UniformScaling) = UniformScaling(J1.λ+J2.λ)
 (+){T}(B::BitArray{2},J::UniformScaling{T}) = bitunpack(B) + J
 (+)(J::UniformScaling, B::BitArray{2})      = J + bitunpack(B)
@@ -121,9 +126,8 @@ inv(J::UniformScaling) = UniformScaling(inv(J.λ))
 *(J1::UniformScaling, J2::UniformScaling) = UniformScaling(J1.λ*J2.λ)
 *(B::BitArray{2}, J::UniformScaling) = *(bitunpack(B), J::UniformScaling)
 *(J::UniformScaling, B::BitArray{2}) = *(J::UniformScaling, bitunpack(B))
-*(A::AbstractMatrix, J::UniformScaling) = J.λ == 1 ? A : J.λ*A
-*(J::UniformScaling, A::AbstractVecOrMat) = J.λ == 1 ? A : J.λ*A
-
+*(A::AbstractMatrix, J::UniformScaling) = A*J.λ
+*(J::UniformScaling, A::AbstractVecOrMat) = J.λ*A
 *(x::Number, J::UniformScaling) = UniformScaling(x*J.λ)
 *(J::UniformScaling, x::Number) = UniformScaling(J.λ*x)
 

base/mmap.jl

@@ -203,9 +203,11 @@ const MS_INVALIDATE = 2
 const MS_SYNC = 4
 
 function sync!{T}(m::Array{T}, flags::Integer=MS_SYNC)
-    @unix_only systemerror("msync", ccall(:msync, Cint, (Ptr{Void}, Csize_t, Cint), pointer(m), length(m)*sizeof(T), flags) != 0)
+    offset = rem(UInt(pointer(m)), PAGESIZE)
+    ptr = pointer(m) - offset
+    @unix_only systemerror("msync", ccall(:msync, Cint, (Ptr{Void}, Csize_t, Cint), ptr, length(m)*sizeof(T), flags) != 0)
     @windows_only systemerror("could not FlushViewOfFile: $(Libc.FormatMessage())",
-                    ccall(:FlushViewOfFile, stdcall, Cint, (Ptr{Void}, Csize_t), pointer(m), length(m)) == 0)
+                    ccall(:FlushViewOfFile, stdcall, Cint, (Ptr{Void}, Csize_t), ptr, length(m)) == 0)
 end
 sync!(B::BitArray, flags::Integer=MS_SYNC) = sync!(B.chunks, flags)
 

base/sharedarray.jl

@@ -75,7 +75,7 @@ function SharedArray(T::Type, dims::NTuple; init=false, pids=Int[])
         end
 
         # All good, immediately unlink the segment.
-        if prod(dims) > 0
+        if (prod(dims) > 0) && (sizeof(T) > 0)
             if onlocalhost
                 rc = shm_unlink(shm_seg_name)
             else
@@ -218,7 +218,6 @@ function finalize_refs{T,N}(S::SharedArray{T,N})
         empty!(S.pids)
         empty!(S.refs)
         init_loc_flds(S)
-        finalize(S.s)
         S.s = Array(T, ntuple(d->0,N))
     end
     S
@@ -480,7 +479,7 @@ function shm_mmap_array(T, dims, shm_seg_name, mode)
     local s = nothing
     local A = nothing
 
-    if prod(dims) == 0
+    if (prod(dims) == 0) || (sizeof(T) == 0)
         return Array(T, dims)
     end
 

base/sparse/linalg.jl

@@ -18,11 +18,6 @@ function increment!{T<:Integer}(A::AbstractArray{T})
 end
 increment{T<:Integer}(A::AbstractArray{T}) = increment!(copy(A))
 
-## Multiplication with UniformScaling (scaled identity matrices)
-
-(*)(S::SparseMatrixCSC, J::UniformScaling) = J.λ == 1 ? S : J.λ*S
-(*){Tv,Ti}(J::UniformScaling, S::SparseMatrixCSC{Tv,Ti}) = J.λ == 1 ? S : S*J.λ
-
 ## sparse matrix multiplication
 
 function (*){TvA,TiA,TvB,TiB}(A::SparseMatrixCSC{TvA,TiA}, B::SparseMatrixCSC{TvB,TiB})

contrib/install.sh

@@ -26,3 +26,5 @@ for SRC in $ARGS; do
     # Do the chmod dance, and ignore errors on platforms that don't like setting permissions of symlinks
     chmod $PERMS $DESTFILE 2>/dev/null
 done
+
+exit 0

contrib/prepare_release.sh

@@ -14,6 +14,8 @@ if [ -z "$tag" ]; then
 fi
 version=$(cat VERSION)
 majmin=$(cut -d. -f1-2 VERSION)
+# remove -rc# if present
+majminpatch=$(cut -d- -f1 VERSION)
 if [ "$tag" != "v$version" ]; then
   echo "error: tagged commit does not match content of VERSION file" >&2
   exit 1
@@ -33,28 +35,35 @@ rm -rf julia-$version
 # download and rename binaries, with -latest copies
 julianightlies="https://s3.amazonaws.com/julianightlies/bin"
 curl -L -o julia-$version-linux-x86_64.tar.gz \
-  $julianightlies/linux/x64/$majmin/julia-$version-$shashort-linux64.tar.gz
+  $julianightlies/linux/x64/$majmin/julia-$majminpatch-$shashort-linux64.tar.gz
 cp julia-$version-linux-x86_64.tar.gz julia-$majmin-latest-linux-x86_64.tar.gz
 curl -L -o julia-$version-linux-i686.tar.gz \
-  $julianightlies/linux/x86/$majmin/julia-$version-$shashort-linux32.tar.gz
+  $julianightlies/linux/x86/$majmin/julia-$majminpatch-$shashort-linux32.tar.gz
 cp julia-$version-linux-i686.tar.gz julia-$majmin-latest-linux-i686.tar.gz
+curl -L -o julia-$version-linux-arm.tar.gz \
+  $julianightlies/linux/arm/$majmin/julia-$majminpatch-$shashort-linuxarm.tar.gz
+cp julia-$version-linux-arm.tar.gz julia-$majmin-latest-linux-arm.tar.gz
 curl -L -o "julia-$version-osx10.7 .dmg" \
-  $julianightlies/osx/x64/$majmin/julia-$version-$shashort-osx.dmg
+  $julianightlies/osx/x64/$majmin/julia-$majminpatch-$shashort-osx.dmg
 cp "julia-$version-osx10.7 .dmg" "julia-$majmin-latest-osx10.7 .dmg"
 curl -L -o julia-$version-win64.exe \
-  $julianightlies/winnt/x64/$majmin/julia-$version-$shashort-win64.exe
+  $julianightlies/winnt/x64/$majmin/julia-$majminpatch-$shashort-win64.exe
 cp julia-$version-win64.exe julia-$majmin-latest-win64.exe
 curl -L -o julia-$version-win32.exe \
-  $julianightlies/winnt/x86/$majmin/julia-$version-$shashort-win32.exe
+  $julianightlies/winnt/x86/$majmin/julia-$majminpatch-$shashort-win32.exe
 cp julia-$version-win32.exe julia-$majmin-latest-win32.exe
 
-shasum -a 256 julia-$version* | grep -v sha256 | grep -v md5 > julia-$version.sha256
-md5sum julia-$version* | grep -v sha256 | grep -v md5 > julia-$version.md5
+echo "Note: if windows code signing is not working on the buildbots, then the"
+echo "checksums need to be re-calculated after the binaries are manually signed!"
+
+shasum -a 256 julia-$version* | grep -v -e sha256 -e md5 -e asc > julia-$version.sha256
+md5sum julia-$version* | grep -v -e sha256 -e md5 -e asc > julia-$version.md5
 
 gpg -u julia --armor --detach-sig julia-$version-full.tar.gz
 gpg -u julia --armor --detach-sig julia-$version.tar.gz
 gpg -u julia --armor --detach-sig julia-$version-linux-x86_64.tar.gz
 gpg -u julia --armor --detach-sig julia-$version-linux-i686.tar.gz
+gpg -u julia --armor --detach-sig julia-$version-linux-arm.tar.gz
 
 echo "All files prepared. Attach julia-$version.tar.gz and julia-$version-full.tar.gz"
 echo "to github releases, upload all binaries and checksums to julialang S3. Be sure"

contrib/windows/julia-manifest.xml

@@ -7,11 +7,6 @@
       </requestedPrivileges>
     </security>
   </trustInfo>
-  <dependency>
-    <dependentAssembly>
-      <assemblyIdentity type="win32" name="Microsoft.VC90.CRT" version="9.0.21022.8" processorArchitecture="amd64" publicKeyToken="1fc8b3b9a1e18e3b"></assemblyIdentity>
-    </dependentAssembly>
-  </dependency>
   <compatibility xmlns="urn:schemas-microsoft-com:compatibility.v1">
     <application>
       <!--The ID below indicates application support for Windows Vista -->

contrib/windows/msys_build.sh

@@ -103,6 +103,11 @@ mkdir -p usr/Git/tmp
 # Remove libjulia.dll if it was copied from downloaded binary
 rm -f usr/bin/libjulia.dll
 rm -f usr/bin/libjulia-debug.dll
+rm -f usr/bin/libgcc_s_s*-1.dll
+rm -f usr/bin/libgfortran-3.dll
+rm -f usr/bin/libquadmath-0.dll
+rm -f usr/bin/libssp-0.dll
+rm -f usr/bin/libstdc++-6.dll
 
 if [ -z "$USEMSVC" ]; then
   if [ -z "`which ${CROSS_COMPILE}gcc 2>/dev/null`" ]; then

doc/Makefile

@@ -24,7 +24,7 @@ $(ACTIVATE):
 	touch -c $@
 
 $(SPHINX_BUILD): $(ACTIVATE) requirements.txt
-	. $(ACTIVATE) && pip install sphinx==1.3.1 \
+	. $(ACTIVATE) && pip install sphinx==1.4.5 \
 	              && pip install -r requirements.txt
 	touch -c $@
 

doc/conf.py

@@ -96,6 +96,9 @@
 primary_domain = 'jl'
 highlight_language = 'julia'
 
+# Flaky links to ignore in linkcheck - permissions or empty returns
+linkcheck_ignore = ['https://www.appveyor.com',
+    'https://bugs.kde.org/show_bug.cgi\?id=136779']
 
 # -- Options for HTML output ---------------------------------------------------