Bug 273661 - freebsd-update install: ///usr/include/c++/v1/__string exists but is not a directory
Summary: freebsd-update install: ///usr/include/c++/v1/__string exists but is not a di...
Status: Closed FIXED
Alias: None
Product: Base System
Classification: Unclassified
Component: bin (show other bugs)
Version: 14.0-STABLE
Hardware: Any Any
: --- Affects Many People
Assignee: Ed Maste
URL: https://reviews.freebsd.org/D41893
Keywords:
Depends on:
Blocks: 14.0r
  Show dependency treegraph
 
Reported: 2023-09-09 16:44 UTC by Vedran Miletic
Modified: 2024-04-26 08:18 UTC (History)
16 users (show)

See Also:


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Description Vedran Miletic 2023-09-09 16:44:29 UTC
While upgrading 13.2-p3 to 14.0-BETA1 on amd64, after rebooting and during the second freebsd-update install I get:

# freebsd-update install
src component not installed, skipped
Creating snapshot of existing boot environment... done.
Installing updates...install: ///usr/include/c++/v1/__string exists but is not a directory
install: ///usr/include/c++/v1/__string/char_traits.h: Not a directory
install: ///usr/include/c++/v1/__string/extern_template_lists.h: Not a directory
Comment 1 Ed Maste freebsd_committer freebsd_triage 2023-09-09 19:09:19 UTC
@dim, do you know off hand of Clang changes that might have triggered this?
Comment 2 Dimitry Andric freebsd_committer freebsd_triage 2023-09-09 21:02:50 UTC
I'm unsure if freebsd-update can cope with it, but at some point during the llvm-15 import (which happened after 13.2 was released), the _file_ /usr/include/c++/v1/__string changed into a _directory_.

In https://cgit.freebsd.org/src/diff/etc/Makefile?id=fcaf7f8644a99 this is handled by the distrib-cleanup target: the old file is deleted before creating the new directory (which I assume is done by mtree).
Comment 3 Mark Dixon 2023-09-12 09:38:52 UTC
Confirmed, I see this also.
Comment 4 Michael Osipov 2023-09-13 07:43:33 UTC
I had similiar on 13-STABLE after a potionally upgrade from src. I have too boot from the ISO and copy the files over manually. I never investigated the cause.
Comment 5 Vedran Miletic 2023-09-13 07:57:46 UTC
(In reply to Michael Osipov from comment #4)
Sensible approach, I assume that's the way to fix it properly.

For those who are hit by this bug and don't want to search for install media, extract tarballs etc., here's a another, simpler approach that seems to work just as well. I can confirm that Clang is usable as I compiled GROMACS (C++) with several different CMake configurations just to verify that.

Assuming machine can access the internet, as root do the following:

# cd /usr/include/c++/v1
# mkdir __string
# cd __string
# fetch https://raw.githubusercontent.com/freebsd/freebsd-src/releng/14.0/contrib/llvm-project/libcxx/include/__string/char_traits.h
# fetch https://raw.githubusercontent.com/freebsd/freebsd-src/releng/14.0/contrib/llvm-project/libcxx/include/__string/extern_template_lists.h
Comment 6 Rene Ladan freebsd_committer freebsd_triage 2023-09-15 09:05:22 UTC
Upgrading a poudriere jail from src also gets bitten by this, but slightly different:

cd /zroot/poudriere/jails/14-amd64/usr/src; time env INSTALL="sh /zroot/poudriere/jails/14-amd64/usr/src/tools/install.sh"  TOOLS_PREFIX=/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64
.amd64/tmp  PATH=/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/legacy/usr/sbin:/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/legacy/usr/bin:/usr/obj/zroot
/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/legacy/bin:/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/legacy/usr/libexec:/sbin:/bin:/usr/sbin:/usr/bin  WORLDTMP=/usr/o
bj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp  MAKEFLAGS="-m /zroot/poudriere/jails/14-amd64/usr/src/tools/build/mk  -j 4 -J 15,16 -m /zroot/poudriere/jails/14-amd64/usr/src/shar
e/mk" make  -f Makefile.inc1  DESTDIR=  OBJTOP='/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools'  OBJROOT='${OBJTOP}/'  UNIVERSE_TOOLCHAIN_PATH=  MAKEOBJDIRPREFIX= 
 BOOTSTRAPPING=1400097  BWPHASE=bootstrap-tools  -DNO_CPU_CFLAGS  -DNO_LINT  -DNO_PIC  -DNO_SHARED  MK_ASAN=no  MK_CTF=no  MK_CLANG_EXTRAS=no  MK_CLANG_FORMAT=no  MK_CLANG_FULL=no  MK_HTML=n
o  MK_MAN=no  MK_PROFILE=no  MK_RETPOLINE=no  MK_SSP=no  MK_TESTS=no  MK_UBSAN=no  MK_WERROR=no  MK_INCLUDES=yes  MK_MAN_UTILS=yes MK_LLVM_TARGET_ALL=no bootstrap-tools
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/fortune/strfile/strfile.o
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/lib/clang/libclangminimal/Support/RISCVVIntrinsicUtils.o
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/dtc/dtc.o
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/lib/clang/libllvmminimal/Demangle/ItaniumDemangle.o
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/fortune/strfile/strfile.full
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/fortune/strfile/strfile.debug
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/fortune/strfile/strfile
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/fortune/strfile/_proginstall
Building /usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/dtc/input_buffer.o
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/llvm/lib/Demangle/ItaniumDemangle.cpp:13:
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/llvm/include/llvm/Demangle/Demangle.h:13:
/usr/include/c++/v1/string:561:10: fatal error: '__string/char_traits.h' file not found
#include <__string/char_traits.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /zroot/poudriere/jails/14-amd64/usr/src/usr.bin/dtc/dtc.cc:44:
In file included from /zroot/poudriere/jails/14-amd64/usr/src/usr.bin/dtc/fdt.hh:35:
In file included from /usr/include/c++/v1/algorithm:1913:
In file included from /usr/include/c++/v1/chrono:746:
In file included from /usr/include/c++/v1/__chrono/convert_to_tm.h:19:
In file included from /usr/include/c++/v1/__chrono/statically_widen.h:17:
In file included from /usr/include/c++/v1/__format/concepts.h:17:
In file included from /usr/include/c++/v1/__format/format_parse_context.h:15:
/usr/include/c++/v1/string_view:220:10: fatal error: '__string/char_traits.h' file not found
#include <__string/char_traits.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/clang/lib/Support/RISCVVIntrinsicUtils.cpp:9:
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/clang/include/clang/Support/RISCVVIntrinsicUtils.h:12:
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/llvm/include/llvm/ADT/ArrayRef.h:12:
In file included from /zroot/poudriere/jails/14-amd64/usr/src/contrib/llvm-project/llvm/include/llvm/ADT/Hashing.h:51:
In file included from /usr/include/c++/v1/algorithm:1913:
In file included from /usr/include/c++/v1/chrono:746:
In file included from /usr/include/c++/v1/__chrono/convert_to_tm.h:19:
In file included from /usr/include/c++/v1/__chrono/statically_widen.h:17:
In file included from /usr/include/c++/v1/__format/concepts.h:17:
In file included from /usr/include/c++/v1/__format/format_parse_context.h:15:
/usr/include/c++/v1/string_view:220:10: fatal error: '__string/char_traits.h' file not found
#include <__string/char_traits.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
*** [dtc.o] Error code 1

make[3]: stopped in /zroot/poudriere/jails/14-amd64/usr/src/usr.bin/dtc
.ERROR_TARGET='dtc.o'
.ERROR_META_FILE='/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/dtc/dtc.o.meta'
.MAKE.LEVEL='3'
MAKEFILE=''
.MAKE.MODE='meta missing-filemon=yes missing-meta=yes silent=yes verbose'
_ERROR_CMD='/usr/local/bin/ccache c++  -O2 -pipe -fno-common -g -gz=zlib -Wno-format-zero-length -Wsystem-headers -Wall -Wno-format-y2k -W -Wno-unused-parameter -Wpointer-arith -Wno-uninitia
lized -Wdate-time -Wno-empty-body -Wno-string-plus-int -Wno-unused-const-variable -Wno-error=unused-but-set-parameter -Wno-tautological-compare -Wno-unused-value -Wno-parentheses-equality -W
no-unused-function -Wno-enum-conversion -Wno-unused-local-typedef -Wno-address-of-packed-member -Qunused-arguments -I/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/legacy/us
r/include -fno-rtti -fno-exceptions  -std=c++11    -Wno-c++11-extensions   -c /zroot/poudriere/jails/14-amd64/usr/src/usr.bin/dtc/dtc.cc -o dtc.o;'
.CURDIR='/zroot/poudriere/jails/14-amd64/usr/src/usr.bin/dtc'
.MAKE='make'
.OBJDIR='/usr/obj/zroot/poudriere/jails/14-amd64/usr/src/amd64.amd64/tmp/obj-tools/usr.bin/dtc'
.TARGETS='all'
CPUTYPE=''
DESTDIR=''
LD_LIBRARY_PATH=''
MACHINE='amd64'
MACHINE_ARCH='amd64'
MACHINE_CPUARCH='amd64'
        0.92 real         0.47 user         0.14 sys

make[1]: stopped in /zroot/poudriere/jails/14-amd64/usr/src
Comment 7 Rene Ladan freebsd_committer freebsd_triage 2023-09-15 09:06:00 UTC
(In reply to Rene Ladan from comment #6)

This is from 14.0-ALPHA3 to todays stable/14
Comment 8 Dimitry Andric freebsd_committer freebsd_triage 2023-09-15 13:02:08 UTC
(In reply to Rene Ladan from comment #6)
That means that for some reason the headers didn't get installed, but the directory does seem to have been made? You should probably look at the installworld log for the jail.
Comment 9 Joshua Kinard 2023-09-18 17:31:11 UTC
Semi-related, the third invocation of freebsd-update fails to complete at least two file moves in the OpenZFS contrib code:

> # freebsd-update install
> Installing updates...rmdir: ///usr/src/sys/contrib/openzfs/cmd/zvol_wait: Directory not empty
> rmdir: ///usr/src/sys/contrib/openzfs/cmd/arc_summary: Directory not empty
>  done.
> 
> # ls ///usr/src/sys/contrib/openzfs/cmd/zvol_wait
> b3433d339ca5398071ebb49e801b32f541c1f3f95b5c76ca8dbdf1888faec897*
> 
> # ls ///usr/src/sys/contrib/openzfs/cmd/arc_summary
> 81fc104da57777f45c931c9c2f425f1fe219d12dc61a9d2928a1b03561f9aecb*

Both are executable scripts, one shell, the other python.  Quick fix is to mv the file out of the directory, rmdir the directory, then change that file's name to be that of the directory.  Neither script is actually installed into the base system, but arc_summary is available as a port under sysutils.

Not sure if a new bug should be opened for this, or if any/all issues w/ freebsd-update itself failing to complete file updates should go into this bug.  A quick way to find these missed files may be to look for a file with a name 64 characters long in hex via 'find . -type f | grep -E "[a-f0-9]{64}"'
Comment 10 Rene Ladan freebsd_committer freebsd_triage 2023-09-25 07:40:42 UTC
Perhaps related, after doing a freebsd-update from 13.2-R to 14.0-BETA1 (I believe this is a continued upgrade from earlier from when upgrading userland took to long and I had to catch a train to Coimbra), I see this in the third `freebsd-update install` after upgrading all ports packages:

``
Creating snapshot of existing boot environment... done.
Installing updates...rmdir: ///usr/tests/usr.bin/uuencode: Directory not empty
rmdir: ///usr/tests/usr.bin/uudecode: Directory not empty
rmdir: ///usr/src/sys/contrib/openzfs/cmd/zvol_wait: Directory not empty
rmdir: ///usr/src/sys/contirb/openzfs/cmd/arc_summary: Directory not empty
```

But perhaps this is because I might have downloaded patches for BETA3 too, not sure where they went though.
Comment 11 commit-hook freebsd_committer freebsd_triage 2023-09-27 19:24:20 UTC
A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85

commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Ed Maste <emaste@FreeBSD.org>
CommitDate: 2023-09-27 19:23:08 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 12 Ed Maste freebsd_committer freebsd_triage 2023-09-27 19:35:34 UTC
A change to handle the file->directory case is now committed to main. Note that rollback will not yet work because we don't handle the directory->file case, in addition to preexisting issues with rollback (PR256252, PR273950).

You can try fetching freebsd-update from main and using it to upgrade to 14.0-BETA3 with something like:

$ fetch -o freebsd-update https://cgit.freebsd.org/src/plain/usr.sbin/freebsd-update/freebsd-update.sh
$ sha256 freebsd-update
SHA256 (freebsd-update) = cf4f38fb2ccc32236be9ec2300a21dcb02a1520d26f82479355b55508dd8598f
$ chmod a+x freebsd-update

then carry on with usual freebsd-update steps:

# ./freebsd-update -r 14.0-BETA3 upgrade
...
Comment 13 Ed Maste freebsd_committer freebsd_triage 2023-09-29 15:12:19 UTC
At present a warning will still be emitted during the upgrade:
rm: ///usr/include/c++/v1/__string: is a directory

Despite this the on-disk install will be correct. The warning can be ignored.
Comment 14 commit-hook freebsd_committer freebsd_triage 2023-10-01 13:07:26 UTC
A commit in branch stable/14 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=bc412215646cbb21529156d08fbbb7bbf5028c26

commit bc412215646cbb21529156d08fbbb7bbf5028c26
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Ed Maste <emaste@FreeBSD.org>
CommitDate: 2023-10-01 13:06:44 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 15 commit-hook freebsd_committer freebsd_triage 2023-10-01 16:32:02 UTC
A commit in branch releng/14.0 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=4719202d8cffdcae1645b2bf508ba6097e912b77

commit 4719202d8cffdcae1645b2bf508ba6097e912b77
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Ed Maste <emaste@FreeBSD.org>
CommitDate: 2023-10-01 16:28:04 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)
    (cherry picked from commit bc412215646cbb21529156d08fbbb7bbf5028c26)

    Approved by:    re (gjb)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 16 commit-hook freebsd_committer freebsd_triage 2023-10-01 16:34:04 UTC
A commit in branch stable/13 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=774cc6348a50c13b952e9f36ef8395f9b48733db

commit 774cc6348a50c13b952e9f36ef8395f9b48733db
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Ed Maste <emaste@FreeBSD.org>
CommitDate: 2023-10-01 16:33:03 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 17 commit-hook freebsd_committer freebsd_triage 2023-10-01 16:35:06 UTC
A commit in branch stable/12 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=274281864fc03c62443677751bf3036fbbf9d778

commit 274281864fc03c62443677751bf3036fbbf9d778
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Ed Maste <emaste@FreeBSD.org>
CommitDate: 2023-10-01 16:33:56 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 18 Ed Maste freebsd_committer freebsd_triage 2023-10-01 19:14:35 UTC
Screen recordings of upgrades from 12.3 and from 13.2, fetching freebsd-update per comment #12

12.3 https://asciinema.org/a/611456
13.2 https://asciinema.org/a/611461
Comment 19 Ed Maste freebsd_committer freebsd_triage 2023-10-03 00:29:06 UTC
Fix is merged into all stable branches and 14.0 releng branch, and being prepared for an EN for 12.4 and 13.2.

(In reply to Rene Ladan from comment #10)
> Installing updates...rmdir: ///usr/tests/usr.bin/uuencode: Directory not empty
> rmdir: ///usr/tests/usr.bin/uudecode: Directory not empty
> rmdir: ///usr/src/sys/contrib/openzfs/cmd/zvol_wait: Directory not empty
> rmdir: ///usr/src/sys/contirb/openzfs/cmd/arc_summary: Directory not empty

I did not observe any similar errors while testing this change; if you happy to see this again please open a new bug with the details.
Comment 20 commit-hook freebsd_committer freebsd_triage 2023-10-03 22:14:13 UTC
A commit in branch releng/13.2 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=cfb624d7e2507c81441bb01e0078abad25ef235d

commit cfb624d7e2507c81441bb01e0078abad25ef235d
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Gordon Tetlow <gordon@FreeBSD.org>
CommitDate: 2023-10-03 21:22:19 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Approved by:    so
    Security:       FreeBSD-EN-23:12.freebsd-update
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)
    (cherry picked from commit 774cc6348a50c13b952e9f36ef8395f9b48733db)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 21 commit-hook freebsd_committer freebsd_triage 2023-10-03 22:15:16 UTC
A commit in branch releng/12.4 references this bug:

URL: https://cgit.FreeBSD.org/src/commit/?id=0eb6c273622d77a89115e7d4f01609eefc50b33c

commit 0eb6c273622d77a89115e7d4f01609eefc50b33c
Author:     Ed Maste <emaste@FreeBSD.org>
AuthorDate: 2023-09-27 13:36:33 +0000
Commit:     Gordon Tetlow <gordon@FreeBSD.org>
CommitDate: 2023-10-03 21:10:42 +0000

    freebsd-update: handle file -> directory on upgrade

    Upgrading from FreeBSD 13.2 to 14.0 failed with
      install: ///usr/include/c++/v1/__string exists but is not a directory
    because __string changed from a file to a directory with an LLVM
    upgrade.

    Now, remove the existing file when the type conflicts.  Note that this
    is only an interim fix to facilitate upgrades from 13.2 for 14.0 BETA
    testing.  This change does not handle the directory -> file case and
    further work is needed.

    PR:             273661
    Reviewed by:    dim, gordon
    Approved by:    so
    Security:       FreeBSD-EN-23:12.freebsd-update
    Sponsored by:   The FreeBSD Foundation
    Differential Revision:  https://reviews.freebsd.org/D41893

    (cherry picked from commit f6d37c9ca13f8ab0ef32cf5344daecb8122d1e85)
    (cherry picked from commit 274281864fc03c62443677751bf3036fbbf9d778)

 usr.sbin/freebsd-update/freebsd-update.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)
Comment 22 bergerkos 2023-11-18 20:59:01 UTC
The same in 14.0-RELEASE. By the end of the upgrade via freebsd-update  /usr/include/c++/v1/__strings is just missing. I had to fix it by extracting it directly from base.txz:
#tar -C / -xzvf share/TEMP/base.txz './usr/include/c++/v1/__string'
Comment 23 bergerkos 2023-11-18 21:14:00 UTC
And mine is a system CONTINUALLY upgraded via freebsd-update. So if freebsd-update is supposed to work, this needs to be fixed.
Comment 24 Vedran Miletic 2023-11-18 21:53:35 UTC
(In reply to bergerkos from comment #22)
Did you upgrade from 13.2-RELEASE-p5 or newer? Working freebsd-update was shipped in the errata for 13.2-RELEASE: https://www.freebsd.org/releases/13.2R/errata/
Comment 25 Nino 2023-11-26 22:45:57 UTC
I've just updated system from 13.2 to 14.0 and got the following error messages which led me to this bug:

# freebsd-update install
src component not installed, skipped
Installing updates...rmdir: ///usr/tests/usr.bin/uuencode: Directory not empty
rmdir: ///usr/tests/usr.bin/uudecode: Directory not empty

This particular error message was mentioned in comment #10, though comment #19 suggested it was not reproducible. It is also the entire error (no c++ or zfs errors that seem to be the more relevant errors tackled in this bug report).

System was upgraded per instructions on https://www.freebsd.org/releases/14.0R/installation/ including the initial:

# freebsd-update fetch
# freebsd-update install

The system seems to work fine after the final restart, so I'm posting it just in case someone gets a chance to look at it. 

tl;dr as of 2023-11-26 a clean upgrade from 13.2 to 14.0 still emits an error.
Comment 26 Nhan Ho 2023-12-29 13:36:43 UTC
Upgrading from 13.2-p9 to 14.0-RELEASE, I'm still getting the error 
Installing updates...rm: ///usr/src/contrib/llvm-project/libcxx/include/__string: is a directory
rm: ///usr/include/c++/v1/__string: is a directory

Though everything looks fine afterward
Comment 27 dereckson 2024-01-17 10:37:03 UTC
On 14.0 system upgraded with freebsd-update from 13.2, I've also the end /usr/include/c++/v1/string still as a file.

When trying to build a software with include <string>, I've the error noted above:

In file included from ./Column.h:33:
/usr/include/c++/v1/string:561:10: fatal error: '__string/char_traits.h' file not found
#include <__string/char_traits.h>
         ^~~~~~~~~~~~~~~~~~~~~~~~

So a verification for 14.0 in the next patch to supersede the file by the directory would be welcome in 14.0-RELEASE-p5 for example.
Comment 28 Ed Maste freebsd_committer freebsd_triage 2024-03-23 13:41:36 UTC
(In reply to dereckson from comment #27)
> On 14.0 system upgraded with freebsd-update from 13.2

What exact version (patch level) of 13.2 did you upgrade from?
Comment 29 spork 2024-04-03 00:51:23 UTC
Going from 13.2-p11 to 13.3-RELEASE, this file vs. directory issue still seems to be here:

# /usr/sbin/freebsd-update install
src component not installed, skipped
Creating snapshot of existing boot environment... done.
Installing updates...install: ///usr/include/c++/v1/__string exists but is not a directory
install: ///usr/include/c++/v1/__tuple exists but is not a directory
install: ///usr/include/c++/v1/__string/char_traits.h: Not a directory
install: ///usr/include/c++/v1/__string/constexpr_c_functions.h: Not a directory
install: ///usr/include/c++/v1/__string/extern_template_lists.h: Not a directory
install: ///usr/include/c++/v1/__tuple/make_tuple_types.h: Not a directory
install: ///usr/include/c++/v1/__tuple/pair_like.h: Not a directory
install: ///usr/include/c++/v1/__tuple/sfinae_helpers.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_element.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_indices.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_like.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_like_ext.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_size.h: Not a directory
install: ///usr/include/c++/v1/__tuple/tuple_types.h: Not a directory

Restarting sshd after upgrade