update soft libxml2 FAILED Applying FreeBSD patch-CVE-2019-20388

Hello.
Updating programs on the server.
An incomprehensible situation for me.
my system FreeBSD 11.4-RELEASE-p10 amd64
I updated ports, created indexes to ports.
Code:
root@test:/usr/ports/textproc/libxslt # make reinstall clean
===>  Deinstalling for libxslt
===>   Deinstalling libxslt-1.1.34_1
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):

Installed packages to be REMOVED:
    libxslt: 1.1.34_1

Number of packages to be removed: 1

The operation will free 1 MiB.
[test] [1/1] Deinstalling libxslt-1.1.34_1...
[test] [1/1] Deleting files for libxslt-1.1.34_1: 100%
===>  License MIT accepted by the user
===>   libxslt-1.1.34_2 depends on file: /usr/local/sbin/pkg - found
=> libxslt-1.1.34.tar.gz doesn't seem to exist in /usr/ports/distfiles/gnome2.
=> Attempting to fetch [URL]http://xmlsoft.org/sources/libxslt-1.1.34.tar.gz[/URL]
libxslt-1.1.34.tar.gz                                 3469 kB   10 MBps    01s
===> Fetching all distfiles required by libxslt-1.1.34_2 for building
===>  Extracting for libxslt-1.1.34_2
=> SHA256 Checksum OK for gnome2/libxslt-1.1.34.tar.gz.
===>  Patching for libxslt-1.1.34_2
===>  Applying FreeBSD patches for libxslt-1.1.34_2 from /usr/ports/textproc/libxslt/files
===>   libxslt-1.1.34_2 depends on package: gmake>=4.3 - found
===>   libxslt-1.1.34_2 depends on package: pkgconf>=1.3.0_1 - found
===>   libxslt-1.1.34_2 depends on shared library: libgcrypt.so - found (/usr/local/lib/libgcrypt.so)
===>   libxslt-1.1.34_2 depends on shared library: libgpg-error.so - found (/usr/local/lib/libgpg-error.so)
===>   libxslt-1.1.34_2 depends on shared library: libxml2.so - not found
===>  Deinstalling for libxml2
===>   libxml2 not installed, skipping
===>  Patching for libxml2-2.9.12
===>  Applying FreeBSD patches for libxml2-2.9.12 from /usr/ports/textproc/libxml2/files
Ignoring previously applied (or reversed) patch.
1 out of 1 hunks ignored--saving rejects to xmlschemas.c.rej
===>  FAILED Applying FreeBSD patch-CVE-2019-20388
===> FAILED to apply cleanly FreeBSD patch(es)  patch-CVE-2019-20388
*** Error code 1

Stop.
make[5]: stopped in /usr/ports/textproc/libxml2
*** Error code 1

Stop.
make[4]: stopped in /usr/ports/textproc/libxml2
*** Error code 1

Stop.
make[3]: stopped in /usr/ports/textproc/libxml2
*** Error code 1

Stop.
make[2]: stopped in /usr/ports/textproc/libxslt
*** Error code 1

Stop.
make[1]: stopped in /usr/ports/textproc/libxslt
*** Error code 1

Stop.
make: stopped in /usr/ports/textproc/libxslt
How to fix it?
Code:
===>  Patching for libxml2-2.9.12
===>  Applying FreeBSD patches for libxml2-2.9.12 from /usr/ports/textproc/libxml2/files
Ignoring previously applied (or reversed) patch.
1 out of 1 hunks ignored--saving rejects to xmlschemas.c.rej
===>  FAILED Applying FreeBSD patch-CVE-2019-20388
===> FAILED to apply cleanly FreeBSD patch(es)  patch-CVE-2019-20388
 
That's how you upgrade the ports themselves, I'm asking how you update your ports tree.
 
That's how you upgrade the ports themselves, I'm asking how you update your ports tree.
gitup ports
and
cd /usr/ports/ && make index

nano /usr/local/etc/gitup.conf
# $FreeBSD$
#
# Default configuration options for gitup.conf.
{
"defaults" : {
"host" : "git.freebsd.org",
"port" : 443,
"verbosity" : 1,
"work_directory" : "/var/db/gitup",
},

"ports" : {
"host" : "git.freebsd.org",
"repository" : "/ports.git",
"branch" : "main",
"target" : "/usr/ports",
"ignores" : [
"distfiles",
"packages",
"INDEX-11",
],
},

"quarterly" : {
"repository_path" : "/ports.git",
"branch" : "quarterly",
"target_directory" : "/usr/ports",
"ignores" : [
"distfiles",
"packages",
"INDEX-11",
],
},
}
 
Right, it seems like gitup(1) fails to remove files when they're deleted from git. Simplest solution is to remove /usr/ports/* and do a fresh checkout.
 
Yes, there's no telling what more files it kept that should have been removed. So to be sure you have a good, clean ports tree I would just wipe it and do a fresh checkout.
 
Yes, there's no telling what more files it kept that should have been removed. So to be sure you have a good, clean ports tree I would just wipe it and do a fresh checkout.
And in the future be like?
Each time to remove all of the ports tree is not the case.
 
rm -rf /usr/ports/*
gitup ports
gitup: build_repair_command: There are too many files to repair -- please re-clone the repository: Argument list too long
It is better to install the full git port rather than gitup.
 
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