Open yurivict opened 1 year ago
This is the behavior caused by 'Disk full' condition. fsck has accidentally left the UFS snapshot (which I didn't notice in time) which caused a lingering 'Disk full' condition. The above symptoms are a result of some bug in pkg that is triggered by the 'Disk full' condition.
Please make the pkg behavior reasonable. It looks like some SQLite 'prepare' statements failed and weren't reported. Also 'Disk full' should be part of the log, and it isn't.
pkg
does this w/out Disk Full condition as well:
$ sudo pkg autoremove
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 106 packages:
Installed packages to be REMOVED:
akonadi: 22.08.3
arb: 2.23.0
autoconf-switch: 20220527
chmlib: 0.40_1
discount: 2.2.7b
ebook-tools: 0.2.2_8
gl2ps: 1.4.2_1
googletest: 1.12.1
java-zoneinfo: 2021.e
javavmwrapper: 2.7.9
kdegraphics-mobipocket: 22.08.3
kf5-kactivities: 5.99.0
kf5-kdelibs4support: 5.99.0
kf5-khtml: 5.99.0
kf5-kinit: 5.99.0
kf5-kpty: 5.99.0
kf5-purpose: 5.99.0
kf5-threadweaver: 5.99.0
libfmt: 8.1.1
libkexiv2: 22.08.3
liblas: 1.8.1_21
libmicrohttpd: 0.9.75
libspectre: 0.2.11
llvm15: 15.0.6_1
m4: 1.4.19,1
mfem: 4.4_6
mpir: 3.0.0_1
netpbm: 10.91.01_1
node16: 16.19.0
openturns: 1.20_1
p5-Locale-gettext: 1.07
p5-Text-Unidecode: 1.30
p5-Unicode-EastAsianWidth: 12.0
pdal: 2.3.0_9
poppler-qt5: 22.12.0
pugixml: 1.13
py27-setuptools44: 44.1.1
py310-setuptools: 63.1.0
py311-setuptools: 63.1.0
py37-setuptools: 63.1.0
py38-setuptools: 63.1.0
py39-Shapely: 1.8.5
py39-appdirs: 1.4.4
py39-atomicwrites: 1.4.1
py39-attrs: 22.1.0
py39-bcrypt: 3.2.2
py39-beaker: 1.11.0
py39-beautifulsoup: 4.11.1
py39-chardet: 4.0.0,1
py39-colorlog: 6.7.0
py39-constantly: 15.1.0
py39-django32: 3.2.16
py39-dpcontracts: 0.6.0
py39-filelock: 3.8.2
py39-gast: 0.5.3
py39-h11: 0.14.0
py39-httpcore: 0.15.0_1
py39-hyperlink: 21.0.0
py39-itsdangerous: 2.1.2
py39-jaraco: 1
py39-jaraco.context: 4.1.2
py39-jaraco.functools: 3.5.2
py39-jsonschema: 4.14.0
py39-lark: 1.1.3
py39-libcst: 0.3.23
py39-markdown-it-py: 2.1.0
py39-mccabe: 0.7.0
py39-mdit-py-plugins: 0.3.1
py39-mistune0: 0.8.4
py39-mpmath: 1.2.1
py39-msgpack: 1.0.4
py39-mypy: 0.991
py39-pep517: 0.13.0
py39-ply: 3.11
py39-priority1: 1.3.0
py39-ptyprocess: 0.7.0
py39-pycodestyle: 2.10.0
py39-pycollada: 0.6_3
py39-pyflakes: 3.0.1
py39-pyglet1: 1.5.27
py39-pyserial: 3.5_2
py39-pytest-black: 0.3.12
py39-pytest-forked: 1.4.0
py39-python-fcl: 0.0.12_2
py39-python-multipart: 0.0.5
py39-redis: 3.5.3_1
py39-rfc3986: 1.5.0,1
py39-rtree: 1.0.1
py39-scikit-image: 0.19.3
py39-service_identity: 18.1.0
py39-sortedcontainers: 2.4.0
py39-sphinx-basic-ng: 0.0.1a12
py39-svg_path: 4.0.2
py39-sympy: 1.11.1_1
py39-towncrier: 22.8.0
py39-traceback2: 1.4.0_2
py39-triangle: 20200424
py39-xxhash: 3.1.0
py39-zope.interface: 5.3.0
qt5-scripttools: 5.15.10p0
qt5-webengine: 5.15.2_7
qt5-xmlpatterns: 5.15.5p0
suitesparse-klu: 2.0.0
texlive-base: 20210325_12
verdict: 1.4.1
xtl-quant-stack: 0.7.4
Number of packages to be removed: 106
The operation will free 2 GiB.
Proceed with deinstalling packages? [y/N]: y
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Generating GTK icon cache for /usr/local/share/icons/hicolor
Building the Shared MIME-Info database cache
pkg: sqlite error while executing VACUUM; in file pkgdb.c:2333: cannot VACUUM - SQL statements in progress
[yuri@yv /usr/ports/science/dynare]$ sudo pkg autoremove
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 63 packages:
Installed packages to be REMOVED:
c-ares: 1.18.1_1
ceres-solver: 2.1.0_1
cminpack: 1.3.6_4
coin-or-bonmin: 1.8.8_5
dlib-cpp: 19.24
fcl05: 0.5.0_2
flint2: 2.9.0
hypre: 2.26.0
kaccounts-integration: 22.08.3
kf5-kdesignerplugin: 5.99.0
kf5-kemoticons: 5.99.0
kf5-kirigami2: 5.99.0
kf5-kitemmodels: 5.99.0
kf5-kjs: 5.99.0
kf5-kunitconversion: 5.99.0
laszip: 3.4.3
lazperf: 2.0.0
libpotrace: 1.16
llvm12: 12.0.1_10
mysql57-server: 5.7.40
p5-File-HomeDir: 1.006
p5-YAML-Tiny: 1.73
pagmo2: 2.18.0_8
primesieve: 8.0
py39-PyWavelets: 1.4.1
py39-black: 22.10.0_2
py39-chaospy: 4.3.8
py39-click-default-group: 1.2.2
py39-cloudpickle: 2.2.0
py39-dill: 0.3.4
py39-exceptiongroup: 1.0.0rc9
py39-h2: 4.0.0
py39-html5lib: 1.0.1
py39-imageio: 2.22.1
py39-incremental: 21.3.0
py39-mdurl: 0.1.2
py39-more-itertools: 8.14.0
py39-networkx: 2.8.8,1
py39-pyasn1: 0.4.8
py39-pyasn1-modules: 0.2.8
py39-pyrsistent: 0.18.1
py39-pytest: 7.2.0,1
py39-sniffio: 1.3.0
py39-soupsieve: 2.0.1
py39-sphinx: 4.5.0,1
py39-sqlparse: 0.4.3
py39-tifffile: 2022.7.28
py39-toml: 0.10.2
py39-typing-inspect: 0.8.0
python27: 2.7.18_2
python310: 3.10.9_1
python311: 3.11.1
python37: 3.7.16
python38: 3.8.16
qt5-sqldrivers-mysql: 5.15.5p165
spatialindex: 1.8.5
suitesparse-btf: 2.0.0
superlu-dist: 8.1.2
t1lib: 5.1.2_5,1
teckit: 2.5.11
tex-web2c: 20210325
texlive-tlmgr: 20210325_1
xpdfopen: 0.86_1
Number of packages to be removed: 63
The operation will free 2 GiB.
Proceed with deinstalling packages? [y/N]: y
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[14/63] Deinstalling mysql57-server-5.7.40...
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==> You should manually remove the "mysql" user.
==> You should manually remove the "mysql" group
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pkg: sqlite error while executing VACUUM; in file pkgdb.c:2333: cannot VACUUM - SQL statements in progress
root@clamav:~ # pkg autoremove Checking integrity... done (0 conflicting) Deinstallation has been requested for the following 3 packages:
Installed packages to be REMOVED: libiconv: 1.17 perl5: 5.32.1_3 python39: 3.9.16
Number of packages to be removed: 3
The operation will free 181 MiB.
Proceed with deinstalling packages? [y/N]: y [clamav] [1/3] Deinstalling python39-3.9.16... [clamav] [1/3] Deleting files for python39-3.9.16: 100% [clamav] [2/3] Deinstalling perl5-5.32.1_3... [clamav] [2/3] Deleting files for perl5-5.32.1_3: 100% [clamav] [3/3] Deinstalling libiconv-1.17... [clamav] [3/3] Deleting files for libiconv-1.17: 100% pkg: sqlite error while executing VACUUM; in file pkgdb.c:2333: cannot VACUUM - SQL statements in progress
In a next "pkg autoremove" it shows no error.
pkg autoremove Checking integrity... done (0 conflicting) Deinstallation has been requested for the following 3 packages:
Installed packages to be REMOVED: http-parser: 2.9.4 libssh2: 1.10.0_1,3 python39: 3.9.16
Number of packages to be removed: 3
The operation will free 120 MiB.
Proceed with deinstalling packages? [y/N]: y [1/3] Deinstalling http-parser-2.9.4... [1/3] Deleting files for http-parser-2.9.4: 100% [2/3] Deinstalling python39-3.9.16... [2/3] Deleting files for python39-3.9.16: 100% [3/3] Deinstalling libssh2-1.10.0_1,3... [3/3] Deleting files for libssh2-1.10.0_1,3: 100% pkg: sqlite error while executing VACUUM; in file pkgdb.c:2333: cannot VACUUM - SQL statements in progress
This just hit me as well:
# pkg autoremove -y
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
Checking for upgrades (1 candidates): 100%
Processing candidates (1 candidates): 100%
Checking integrity... done (0 conflicting)
Your packages are up to date.
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 21 packages:
Installed packages to be REMOVED:
aom: 3.5.0_1
cairo: 1.17.4_2,3
cups: 2.4.2
dav1d: 1.0.0_3
dejavu: 2.37_1
fribidi: 1.0.12
harfbuzz: 6.0.0
jbig2dec: 0.19
libXft: 2.3.7
libXmu: 1.1.3,1
libXpm: 3.5.13
libde265: 1.0.9
libidn: 1.38
openjpeg: 2.5.0
php81-xml: 8.1.14
php81-zlib: 8.1.14
poppler-data: 0.4.11
svt-av1: 1.4.1
webp: 1.2.4_1
x265: 3.4_2
xorg-fonts-truetype: 7.7_1
Number of packages to be removed: 21
The operation will free 112 MiB.
[1/21] Deinstalling xorg-fonts-truetype-7.7_1...
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[2/21] Deinstalling cairo-1.17.4_2,3...
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[3/21] Deinstalling dejavu-2.37_1...
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[4/21] Deinstalling x265-3.4_2...
[4/21] Deleting files for x265-3.4_2: 100%
[5/21] Deinstalling cups-2.4.2...
[5/21] Deleting files for cups-2.4.2: 100%
==> You should manually remove the "cups" user.
==> You should manually remove the "cups" group
[6/21] Deinstalling libde265-1.0.9...
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[7/21] Deinstalling php81-zlib-8.1.14...
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[9/21] Deinstalling svt-av1-1.4.1...
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[10/21] Deinstalling libidn-1.38...
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[12/21] Deinstalling jbig2dec-0.19...
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[13/21] Deinstalling libXmu-1.1.3,1...
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[14/21] Deinstalling aom-3.5.0_1...
[14/21] Deleting files for aom-3.5.0_1: 100%
[15/21] Deinstalling dav1d-1.0.0_3...
[15/21] Deleting files for dav1d-1.0.0_3: 100%
[16/21] Deinstalling php81-xml-8.1.14...
[16/21] Deleting files for php81-xml-8.1.14: 100%
[17/21] Deinstalling libXft-2.3.7...
[17/21] Deleting files for libXft-2.3.7: 100%
[18/21] Deinstalling webp-1.2.4_1...
[18/21] Deleting files for webp-1.2.4_1: 100%
[19/21] Deinstalling libXpm-3.5.13...
[19/21] Deleting files for libXpm-3.5.13: 100%
[20/21] Deinstalling harfbuzz-6.0.0...
[20/21] Deleting files for harfbuzz-6.0.0: 100%
[21/21] Deinstalling poppler-data-0.4.11...
[21/21] Deleting files for poppler-data-0.4.11: 100%
Running fc-cache to build fontconfig cache...
pkg: sqlite error while executing VACUUM; in file pkgdb.c:2333: cannot VACUUM - SQL statements in progress
BTW, this happens without Disk Full as well.
It looks like some SQLite related object isn't released when vacuuming is attempted.
Here is how the session went:
Please note that pkg succeeded in the end, which it shouldn't.