biology/diamond: Update to 2.2.5 and fix deepclust crash
Initialize the seed_only member in the Hsp constructor that takes an
ApproxHsp. deepclust builds Hsps through this constructor for its
approximate alignments, so seed_only was left uninitialized. When it
evaluated to true, the SEED_ONLY flag was set on an otherwise
full-length intermediate output record. The multiblock join later
parsed that record as seed-only, stopped four bytes short, and aborted
with "Unexpected end of file", failing the deepclust-multiblock
regression test.
On Linux, the uninitialized member consistently evaluated to false,
masking the bug. On FreeBSD, it evaluated to true, and triggered the
crash.
Release notes: https://github.com/bbuchfink/diamond/releases/tag/v2.2.5
Sponsored by: The FreeBSD Foundation
stand: consume UEFI PXE Base Code cache to seed DHCP
Populate stand/libsa/bootp.c's bootp_response global from the UEFI PXE
Base Code Protocol's cached DhcpAck, so bootp() can enter RFC 2131
INIT-REBOOT and skip DISCOVER/OFFER instead of running a fresh DHCP
transaction after the firmware has already done one.
manuals: Fix Fx and nearby mechanical typos
Fix compiler warnings related to the Fx macro, as well as all other
mechanical typos that were visible within one screenful of them. These
cause rendering glitches on various toolchains with various of the five
and a half decades of rich output formats and tooling manpages scale to.
The *x macro set specifies operating systems. These macros take the rest
of the line as an argument. Sometimes, a space was not used to separate
the argument of Fx and the trailing period. Another, FreeBSD Foundation
was misrepresented as an operating system version instead of an author.
Two more had other parts of the sentence supplied as an argument to Fx.
While I had those open, fix the other mechancial typos visible on those
specific screenfulls. Fix a list width glitch, correct section typo
AUTHOR to AUTHORS, and switch AUTHORS sections containing prose to
prose-mode so that they wrap freely when rendered.
PR: 297248
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nfs_commonkrpc.c: Fix recovery that was broken by 4d80d4913e79
Commit 4d80d4913e79 added a check for nfsess_defunct already
being set. This was incorrect because, once set, nfsess_defunct
remains set and an additional recovery might be needed.
This patch reverts this part of 4d80d4913e79.
PR: 297252
Suggested by: olivier
MFC after: 3 days
Fixes: 4d80d4913e79 ("nfs: Fix argument typo to avoid a crash")
ng_ipfw: provide a tree for faster hook lookup
This should assist setups that connect a lot of nodes to ipfw: and then
distribute traffic with ipfw(4) tablearg feature.
Reviewed by: pouria
Differential Revision: https://reviews.freebsd.org/D58547
uexterr_gettext(3): support dynamic kernel categories
Add an uncached sysctl based implementation which retrieves individual
categories. A cache would be an obvious extension should this optional
feature that can only be enabled by an environmental varible have a
noticable performance impact in a case that matters.
Reviewed by: kib
Sponsored by: Innovate UK
Differential Revision: https://reviews.freebsd.org/D58238
kdump(1): minimally adapt to exterror category sources
Add some minimal handling of category sources other than static kernel
sources. We don't actually look up dynamic sources yet (that would
require extended trace records to add the file names to the trace file
since we can't assume the trace file is running on a kernel with the
same numbers.)
Make the decision to append a "src/" prefix to each file name
dependent on the category source.
Reviewed by: kib
Sponsored by: Innovate UK
Differential Revision: https://reviews.freebsd.org/D58412
exterror(9): dynamic kernel categories
Make it possible to define categories without compiling their
paths into libc (important for third-party modules). The
EXTERR_CATEGORY_DYNAMIC macro can be defined to a string describing the
compilation unit (generally the path relative to src/sys) which takes
the place of EXTERR_CATEGORY.
These strings are assembled in linker sets with category numbers
assigned at system startup or module load time. The strings can be
retrieved from the kern.exterr.categories.<category> sysctl.
Reviewed by: kib
Sponsored by: Innovate UK
Differential Revision: https://reviews.freebsd.org/D58237
exterror(9): split category into multiple sources
The static, global index into an array of strings is simple, cheap,
and works for the base kernel, but is unworkable for (potentially
third-party) kernel modules or for arbitrary userspace code. Swipe a
few of the top bits of category to indicate a source with all-zeros
being the current model (EXTERR_CAT_SRC_KERN_STATIC). Add two
additional sources EXTERR_CAT_SRC_KERN_DYNAMIC and EXTERR_CAT_SRC_USER
with stub implementations.
Reviewed by: kib
Sponsored by: Innovate UK
Differential Revision: https://reviews.freebsd.org/D58236
bin/sh: Fix history long line truncation/corruption
When reading from standard input with editline history enabled, increase
buffer size to accomodate long lines so that history is recorded
correctly. Cleanup el_gets() handling avoiding potentially dangerous
retention of pointers to editline buffers across calls. Ensure struct
parsefile objects are properly zero initialised when created. Remove
push argument from setinputstring() and simplify logic as it was always
called with a value of one and as was written was potentially dangerous
if ever called with a value of zero.
This commit does not fix long lines when history is enabled but editing
is not (e.g. if there is no terminal).
MFC after: 3 weeks
Pull Request: https://github.com/freebsd/freebsd-src/pull/2028
Signed-off-by: Kristofer Peterson <kris at tranception.com>
(cherry picked from commit 95e4fce8f0c4fc6bf828288b1d63faf0f1300198)
