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FreeBSD Ports — head/biology Makefile freebayes, head/biology/freebayes Makefile distinfo

biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15116

FreeBSD — stable/11 Makefile.inc1, stable/11/gnu/usr.bin/groff/tmac mdoc.local.in

Update stable/11 from 11.1-STABLE to 11.2-PRERELEASE, marking the
official start of the code slush.

Set the default mdoc(7) version to 11.2, and update the clang(1)
TARGET_TRIPLE to reflect 11.2.  While here, add missing FreeBSD
major versions to mdoc(7).

Approved by:        re (implicit)
Sponsored by:        The FreeBSD Foundation

FreeBSD — projects/pnfs-planb-server/sys/nfs nfs_nfssvc.c nfssvc.h

Update the nfssvc syscall to handle the mirrored DS recovery case.

FreeBSD — projects/pnfs-planb-server/sys/fs/nfs nfsport.h

Update nfsport.h for the mirror recovery code.

LLVM — cfe/trunk/lib/Analysis CFG.cpp, cfe/trunk/test/Analysis cfg-rich-constructors.cpp auto-obj-dtors-cfg-output.cpp

[CFG] [analyzer] Add construction contexts for loop condition variables.

Loop condition variables, eg.

  while (shared_ptr<int> P = getIntPtr()) { ... })

weren't handled in r324794 because they don't go through the common
CFGBuilder::VisitDeclStmt method. Which means that they regressed
after r324800.

Fix the regression by duplicating the necessary construction context scan in
the loop visiting code.

Differential Revision: https://reviews.llvm.org/D45706

LLVM — cfe/trunk/include/clang/StaticAnalyzer/Core/PathSensitive ExprEngine.h, cfe/trunk/lib/StaticAnalyzer/Core ExprEngine.cpp ExprEngineC.cpp

[analyzer] When we fail to evaluate a pointer cast, escape the pointer.

If a pointer cast fails (evaluates to an UnknownVal, i.e. not implemented in the
analyzer) and such cast is in fact the last use of the pointer, the pointer
symbol is no longer referenced by the program state and a leak is
(mis-)diagnosed.

"Escape" the pointer upon a failed cast, i.e. inform the checker that we can no
longer reliably track it.

Differential Revision: https://reviews.llvm.org/D45698

LLVM — lld/trunk/ELF InputFiles.h ScriptParser.cpp, lld/trunk/test/ELF warn-backrefs.s

[ELF] Increase NextGroupId with --end-group

Reviewers: ruiu, espindola

Subscribers: emaste, arichardson, llvm-commits

Differential Revision: https://reviews.llvm.org/D45846

FreeBSD — projects/pnfs-planb-server/sys/fs/nfsserver nfs_nfsdstate.c nfs_nfsdport.c

Update the last three kernel files for mirrored DS recovery.

LLVM — cfe/trunk/include/clang/Basic LangOptions.def, cfe/trunk/include/clang/Driver Options.td CC1Options.td

Implement proper support for `-falign-functions`

This implements support for the previously ignored flag
`-falign-functions`.  This allows the frontend to request alignment on
function definitions in the translation unit where they are not
explicitly requested in code.  This is compatible with the GCC behaviour
and the ICC behaviour.

The scalar value passed to `-falign-functions` aligns functions to a
power-of-two boundary.  If flag is used, the functions are aligned to
16-byte boundaries.  If the scalar is specified, it must be an integer
less than or equal to 4096.  If the value is not a power-of-two, the
driver will round it up to the nearest power of two.

LLVM — cfe/trunk/lib/Analysis CFG.cpp ConstructionContext.cpp, cfe/trunk/test/Analysis cfg-rich-constructors.cpp

[CFG] [analyzer] Don't treat argument constructors as temporary constructors.

Function argument constructors (that are used for passing objects into functions
by value) are completely unlike temporary object constructors, but we were
treating them as such because they are also wrapped into a CXXBindTemporaryExpr.

This patch adds a partial construction context layer for call argument values,
but doesn't proceed to transform it into an actual construction context yet.
This is tells the clients that we aren't supporting these constructors yet.

Differential Revision: https://reviews.llvm.org/D45650

DragonFlyBSD — etc/rc.d vknetd ip6fw

rc.d - Be quiet when check if modules are loaded
Delta File
+1 -1 etc/rc.d/vknetd
+1 -1 etc/rc.d/ip6fw
+1 -1 etc/rc.d/ipfw
+1 -1 etc/rc.d/mountcritremote
+1 -1 etc/rc.d/nfsclient
+1 -1 etc/rc.d/nfsserver
+3 -3 3 files not shown
+9 -9 9 files

LLVM — cfe/trunk/lib/StaticAnalyzer/Checkers RetainCountChecker.cpp, cfe/trunk/test/Analysis retain-release-safe.c

[analyzer] RetainCount: Accept more "safe" CFRetain wrappers.

r315736 added support for the misplaced CF_RETURNS_RETAINED annotation on
CFRetain() wrappers. It works by trusting the function's name (seeing if it
confirms to the CoreFoundation naming convention) rather than the annotation.

There are more false positives caused by users using a different naming
convention, namely starting the function name with "retain" or "release"
rather than suffixing it with "retain" or "release" respectively.

Because this isn't according to the naming convention, these functions
are usually inlined and the annotation is therefore ignored, which is correct.
But sometimes we run out of inlining stack depth and the function is
evaluated conservatively and then the annotation is trusted.

Add support for the "alternative" naming convention and test the situation when
we're running out of inlining stack depth.

rdar://problem/18270122

Differential Revision: https://reviews.llvm.org/D45117

LLVM — lld/trunk/test/wasm reloc-addend.ll, lld/trunk/wasm InputChunks.cpp

[WebAssembly] Fix bug where reloc addends were written as unsigned

Relocation addends can be negative so should be written as
signed LEBs. This bug meant that writing value between 64
and 128 would be incorrectly interpreted as negative by the
object file readers.

Differential Revision: https://reviews.llvm.org/D45825

FreeBSD — head/tools/diag/prtblknos prtblknos.c main.c

Fix incorrect output for a file consisting of a single full-size
block followed by a discontiguous fragment.

Add checks for unallocated inodes and inodes with unknown mode
types.

Cleanup variable declarations by changing from type `int' to types
like ufs_lbn_t, ufs2_daddr_t, etc.

Reported by: bde

FreeBSD — projects/pnfs-planb-server/sys/fs/nfs nfs_commonsubs.c nfs_var.h

Update three more files for mirrored DS recovery.

LLVM — llvm/trunk/include/llvm/CodeGen Passes.h, llvm/trunk/lib/CodeGen MachineOutliner.cpp TargetPassConfig.cpp

[MachineOutliner] NFC: Move EnableLinkOnceODROutlining into MachineOutliner.cpp

This moves the EnableLinkOnceODROutlining flag from TargetPassConfig.cpp into
MachineOutliner.cpp. It also removes OutlineFromLinkOnceODRs from the
MachineOutliner constructor. This is now handled by the moved command-line
flag.

FreeNAS — src/freenas-installer/etc install.sh, src/freenas/etc/ix.rc.d ix-loader

EFI uses "efi" for its video console, not "vidconsole".

FreeNAS — src/freenas-installer/etc install.sh, src/freenas/etc/ix.rc.d ix-loader

EFI uses "efi" for its video console, not "vidconsole".

LLVM — libcxx/trunk/include __config

Don't do aligned allocations on MSVCRT before 19.12 (update 15.3)

Reviewers: EricWF, pcc

Subscribers: christof, cfe-commits

Differential Revision: https://reviews.llvm.org/D45836
Delta File
+6 -0 libcxx/trunk/include/__config
+6 -0 1 file

LLVM — llvm/trunk/test/tools/llvm-mca/X86/BtVer2 resources-sse1.s

[llvm-mca][X86] Add prefetch instruction resource tests

LLVM — llvm/trunk/lib/MC/MCParser AsmParser.cpp, llvm/trunk/test/MC/WebAssembly basic-assembly.s

[WebAssembly] Enabled -triple=wasm32-unknown-unknown-wasm path using ELF directive parser.

This is a temporary solution until a proper WASM implementation of
MCAsmParserExtension is in place, but at least for now will unblock this
path.

Added test to make sure this path works with the WASM Assembler.

Patch By Wouter van Oortmerssen!

Differential Revision: https://reviews.llvm.org/D45386

LLVM — lld/trunk/test/ELF merge-to-non-alloc.s

Add a test. NFC.

We have relatively few tests on the contents of non alloc
sections. This one would have found a bug in a patch I am working on.

LLVM — llvm/trunk/test/Transforms/Reassociate matching-binops.ll

[Reassociate] add baseline tests for binop swapping; NFC

Similar to rL330086, I don't know if we want to do these 
transforms here, but we might as well have the tests
here either way to show that this pass is missing 
potential functionality (intentionally or not).

FreeBSD — head/tools/tools sortbench, head/tools/tools/sortbench sort_bench.c bench.py

Add sortbench.

This is a set of benchmarks of qsort, mergesort, heapsort, and
optionally wikisort and a script to run them.

Submitted by:        Miles Fertel <milesfertel at college.harvard.edu>
Sponsored by:        Google Summer of Code 2017
Differential Revision:        https://reviews.freebsd.org/D12677

HardenedBSD — tools/tools/sortbench sort_bench.c bench.py

Add sortbench.

This is a set of benchmarks of qsort, mergesort, heapsort, and
optionally wikisort and a script to run them.

Submitted by:        Miles Fertel <milesfertel at college.harvard.edu>
Sponsored by:        Google Summer of Code 2017
Differential Revision:        https://reviews.freebsd.org/D12677

LLVM — lld/trunk/COFF Writer.cpp PDB.cpp

COFF: Remove OutputSection::getPermissions() and getCharacteristics().

All callers can just access the header directly.

Differential Revision: https://reviews.llvm.org/D45800

LLVM — llvm/trunk/test/tools/llvm-mca/X86/Broadwell resources-fma.s, llvm/trunk/test/tools/llvm-mca/X86/Haswell resources-fma.s

[llvm-mca][FMA] Add FMA resource tests

LLVM — llvm/trunk/lib/Target/AMDGPU SIFoldOperands.cpp SIInstrInfo.cpp, llvm/trunk/test/CodeGen/AMDGPU pk_max_f16_literal.ll add.v2i16.ll

[AMDGPU] Use packed literals with zero either lower or hi part

Differential Revision: https://reviews.llvm.org/D45790

FreeBSD — projects/pnfs-planb-server/sys/fs/nfs nfs_commonkrpc.c nfs.h

Update the first two files for mirrored recovery.

FreeBSD — head/share/mk bsd.sys.mk, head/stand/i386 Makefile.inc

Add support for linker-type-specific flags

r332090 added a LINKER_TYPE test to add the --no-rosegment flag when
linking the i386 loader components with lld.  Instead, introduce a
general mechanism for setting LDFLAGS for a specific linker type,
and use it for --no-rosegment.

Sponsored by:        The FreeBSD Foundation
Differential Revision:        https://reviews.freebsd.org/D14998

HardenedBSD — share/mk bsd.sys.mk, stand/i386 Makefile.inc

Add support for linker-type-specific flags

r332090 added a LINKER_TYPE test to add the --no-rosegment flag when
linking the i386 loader components with lld.  Instead, introduce a
general mechanism for setting LDFLAGS for a specific linker type,
and use it for --no-rosegment.

Sponsored by:        The FreeBSD Foundation
Differential Revision:        https://reviews.freebsd.org/D14998
Delta File
+1 -5 stand/i386/Makefile.inc
+2 -0 share/mk/bsd.sys.mk
+3 -5 2 files

FreeBSD Ports — head/sysutils Makefile py-hpilo, head/sysutils/py-hpilo Makefile pkg-descr

sysutils/py-hpilo: Add python tool for HP iLO

This port add a python library and a command-line tool to interact with
the iLO, the management interface provided by HP

LLVM — llvm/trunk/tools/llvm-objdump MachODump.cpp

[llvm-objdump] Issue error message when object file cannot be created

FreeBSD — projects/pnfs-planb-server/sys/amd64/acpica acpi_machdep.c acpi_wakecode.S, projects/pnfs-planb-server/sys/amd64/amd64 pmap.c exception.S

Merge in an up to date kernel from head.

LLVM — llvm/trunk/utils/TableGen X86DisassemblerTables.cpp

[X86] Remove non-existant instruction name from X86DisassemblerTables.cpp.

This instruction was removed a long time so we don't need to check for it here.

FreeBSD Ports — head/www/yarn distinfo Makefile

www/yarn: Update to 1.6.0

Changelog: https://github.com/yarnpkg/yarn/releases/tag/v1.6.0

FreeBSD — head/lib/libc/riscv Makefile.inc, head/lib/libc/riscv/gen _setjmp.S flt_rounds.c

Replace SOFTFLOAT with __riscv_float_abi_*.

With SOFTFLOAT, libc and libm were built correctly, but any program
including fenv.h itself assumed it was on a hardfloat systen and emitted
inline fpu instructions for fedisableexcept() and friends.

Unlike r315424 which did this for MIPS, I've used riscv_float_abi_soft
and riscv_float_abi_double macros as appropriate rather than using
__riscv_float_abi_soft exclusively.  This ensures that attempts to use an
unsupported hardfloat ABI will fail.

Reviewed by:        br
Sponsored by:        DARPA, AFRL
Differential Revision:        https://reviews.freebsd.org/D10039

HardenedBSD — lib/libc/riscv Makefile.inc, lib/libc/riscv/gen _setjmp.S flt_rounds.c

Replace SOFTFLOAT with __riscv_float_abi_*.

With SOFTFLOAT, libc and libm were built correctly, but any program
including fenv.h itself assumed it was on a hardfloat systen and emitted
inline fpu instructions for fedisableexcept() and friends.

Unlike r315424 which did this for MIPS, I've used riscv_float_abi_soft
and riscv_float_abi_double macros as appropriate rather than using
__riscv_float_abi_soft exclusively.  This ensures that attempts to use an
unsupported hardfloat ABI will fail.

Reviewed by:        br
Sponsored by:        DARPA, AFRL
Differential Revision:        https://reviews.freebsd.org/D10039

FreeBSD — head/sys/modules random

Remove empty dir no longer required.

Reported by:        Jung-uk Kim
Delta File
+0 -0 head/sys/modules/random/
+0 -0 1 file

HardenedBSD — sys/fs/nfsserver nfs_nfsdserv.c

Remove empty dir no longer required.

Reported by:        Jung-uk Kim
∈ rmacklem - 8cd51ec4 - 2018-04-19 20:30:33
Fix OpenDowngrade for NFSv4.1 if a client sets the OPEN_SHARE_ACCESS_WANT* bits.

The NFSv4.1 RFC specifies that the OPEN_SHARE_ACCESS_WANT bits can be set
in the OpenDowngrade share_access argument and are basically ignored.
I do not know of a extant NFSv4.1 client that does this, but this little
patch fixes it just in case.
It also changes the error from NFSERR_BADXDR to NFSERR_INVAL since the NFSv4.1
RFC specifies this as the error to be returned if bogus bits are set.
(The NFSv4.0 RFC didn't specify any error for this, so the error reply can
 be changed for NFSv4.0 as well.)
Found by inspection while looking at a problem with OpenDowngrade reported
for the ESXi 6.5 NFSv4.1 client.

Reported by:        andreas.nagy at frequentis.com
PR:                227214
MFC after:        1 week
Delta File
+4 -2 sys/fs/nfsserver/nfs_nfsdserv.c
+4 -2 1 file

FreeBSD — head/sys/fs/nfsserver nfs_nfsdserv.c

Fix OpenDowngrade for NFSv4.1 if a client sets the OPEN_SHARE_ACCESS_WANT* bits.

The NFSv4.1 RFC specifies that the OPEN_SHARE_ACCESS_WANT bits can be set
in the OpenDowngrade share_access argument and are basically ignored.
I do not know of a extant NFSv4.1 client that does this, but this little
patch fixes it just in case.
It also changes the error from NFSERR_BADXDR to NFSERR_INVAL since the NFSv4.1
RFC specifies this as the error to be returned if bogus bits are set.
(The NFSv4.0 RFC didn't specify any error for this, so the error reply can
 be changed for NFSv4.0 as well.)
Found by inspection while looking at a problem with OpenDowngrade reported
for the ESXi 6.5 NFSv4.1 client.

Reported by:        andreas.nagy at frequentis.com
PR:                227214
MFC after:        1 week

LLVM — llvm/trunk/include/llvm/Transforms/Utils LoopRotationUtils.h, llvm/trunk/lib/Transforms/Scalar LoopRotation.cpp

Refine the loop rotation's API

Summary:
The following changes addresses the following two issues.

1) The existing loop rotation pass contains both loop latch simplification and loop 
rotation. So one flag RotationOnly is added to be passed to the loop rotation pass.
2) The threshold value is initialized with MAX_UINT since the loop rotation utility should 
not have threshold limit.

Reviewers: dmgreen, efriedma

Reviewed By: efriedma

Differential Revision: https://reviews.llvm.org/D45582

FreeBSD Ports — head/benchmarks/stress-ng distinfo Makefile

benchmarks/stressng: Update to 0.09.25

Changelog:
http://kernel.ubuntu.com/git/cking/stress-ng.git/log/?h=V0.09.25

HardenedBSD — usr.sbin/pwd_mkdb pwd_mkdb.c

pwd_mkdb: warn that legacy support is deprecated (if specified)

r283981 switched pwd_mkdb to emit only v4 database entries by default,
and introduced a -l (legacy) option emit v3 entries in addition.  The
commit message claims that legacy support will be removed in 12.0, so
emit a warning now if it is used.
Delta File
+2 -0 usr.sbin/pwd_mkdb/pwd_mkdb.c
+2 -0 1 file

FreeBSD — head/usr.sbin/pwd_mkdb pwd_mkdb.c

pwd_mkdb: warn that legacy support is deprecated (if specified)

r283981 switched pwd_mkdb to emit only v4 database entries by default,
and introduced a -l (legacy) option emit v3 entries in addition.  The
commit message claims that legacy support will be removed in 12.0, so
emit a warning now if it is used.
Delta File
+2 -0 head/usr.sbin/pwd_mkdb/pwd_mkdb.c
+2 -0 1 file

FreeNAS — gui choices.py, gui/sharing forms.py

Address William's review

FreeNAS — gui/sharing forms.py, src/middlewared/middlewared/plugins smb.py

Address William's review

LLVM — lld/trunk/COFF Chunks.h ICF.cpp

COFF: Rename Chunk::getPermissions to getOutputCharacteristics.

In an upcoming change I will need to make a distinction between section
type (code, data, bss) and permissions. The term that I use for both
of these things is "output characteristics".

Differential Revision: https://reviews.llvm.org/D45799

FreeBSD Ports — head/devel/libuv distinfo Makefile

Upgrade to v1.20.1.

Release notes at https://github.com/libuv/libuv/releases/tag/v1.20.1

FreeBSD Ports — head/sysutils/ansible distinfo Makefile