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Bug 764110 - app-emulation/virtualbox-guest-additions: emerge hangs at "Extracting guest kernel module sources ..."
Summary: app-emulation/virtualbox-guest-additions: emerge hangs at "Extracting guest k...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Lars Wendler (Polynomial-C)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-01-06 12:45 UTC by Didier Colle
Modified: 2021-07-07 05:03 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Didier Colle 2021-01-06 12:45:37 UTC
Problem occurs with both versions currently available: 6.1.16-r1 and 6.0.24-r2

content of build.log:
 * Package:    app-emulation/virtualbox-guest-additions-6.1.16-r1
 * Repository: gentoo
 * Maintainer: polynomial-c@gentoo.org
 * USE:        X abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
 * Determining the location of the kernel source code
 * Found kernel source directory:
 *     /usr/src/linux
 * Found sources for kernel version:
 *     5.4.80-gentoo-r1-x86_64
 * Checking for suitable kernel configuration options...
 [ ok ]
>>> Unpacking source...
>>> Unpacking VirtualBox-6.1.16.tar.bz2 to /var/tmp/portage/app-emulation/virtualbox-guest-additions-6.1.16-r1/work
>>> Unpacking virtualbox-6.1.12-patches-01.tar.xz to /var/tmp/portage/app-emulation/virtualbox-guest-additions-6.1.16-r1/work
>>> Source unpacked in /var/tmp/portage/app-emulation/virtualbox-guest-additions-6.1.16-r1/work
>>> Preparing source in /var/tmp/portage/app-emulation/virtualbox-guest-additions-6.1.16-r1/work/VirtualBox-6.1.16 ...
 * Extracting guest kernel module sources ...


output of emerge --info:
Portage 3.0.12 (python 3.7.9-final-0, default/linux/amd64/17.1/desktop/gnome/systemd, gcc-9.3.0, glibc-2.32-r3, 5.4.80-gentoo-r1-x86_64 x86_64)
=================================================================
System uname: Linux-5.4.80-gentoo-r1-x86_64-x86_64-Intel-R-_Core-TM-_i7-4510U_CPU_@_2.00GHz-with-gentoo-2.7
KiB Mem:     4025524 total,    531920 free
KiB Swap:   33554428 total,  33529464 free
Timestamp of repository gentoo: Wed, 06 Jan 2021 10:05:01 +0000
Head commit of repository gentoo: 05f063dc477fdbb858b81e1bdf754e04594b133d
sh bash 5.0_p18
ld GNU ld (Gentoo 2.34 p6) 2.34.0
app-shells/bash:          5.0_p18::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.30.3::gentoo
dev-lang/python:          2.7.18-r4::gentoo, 3.7.9::gentoo, 3.8.6::gentoo, 3.9.0::gentoo
dev-util/cmake:           3.17.4-r1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.2-r1::gentoo
sys-devel/binutils:       2.34-r2::gentoo
sys-devel/gcc:            9.3.0-r2::gentoo
sys-devel/gcc-config:     2.3.2-r1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.4-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32-r3::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-jobs: 1
    sync-rsync-extra-opts: 
    sync-rsync-verify-metamanifest: yes

localrepo
    location: /var/db/repos/localrepo
    masters: gentoo

crossdev
    location: /var/db/repos/localrepo-crossdev
    masters: gentoo
    priority: 10

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 berkdb bindist branding bzip2 cairo cdda cdr cli colord crypt cups dbus dri dts dvd dvdr eds emboss encode evo exif flac fortran gdbm gif gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk gui iconv icu introspection ipv6 jpeg lcms libglvnd libnotify libsecret libtirpc mad mng mp3 mp4 mpeg multilib nautilus ncurses networkmanager nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio python_signle_target_python3_7 qt5 readline sdl seccomp spell split-usr ssl startup-notification svg sysprof systemd tcpd tiff tracker truetype udev udisks unicode upower usb vorbis wayland wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2 php7-3 php7-4" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python2_7 python3_8 python3_7" RUBY_TARGETS="ruby25 ruby26" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Lars Wendler (Polynomial-C) gentoo-dev 2021-01-06 16:25:33 UTC
Any chance you're trying to build this in a docker container?
Comment 2 Didier Colle 2021-01-07 09:30:36 UTC
(In reply to Lars Wendler (Polynomial-C) from comment #1)
> Any chance you're trying to build this in a docker container?

I indeed have docker installed inside this vbox guest.
I did however NOT launch this emerge command inside a docker container.
Comment 3 Lars Wendler (Polynomial-C) gentoo-dev 2021-01-07 15:40:50 UTC
Can you check if the error persists when you uninstall docker? You can make a backup of the docker package with /usr/bin/quickpkg:

  quickpkg app-emulation/docker

and later re-install it with

  emerge -1OKv app-emulation/docker
Comment 4 Didier Colle 2021-01-07 18:58:40 UTC
(In reply to Lars Wendler (Polynomial-C) from comment #3)
> Can you check if the error persists when you uninstall docker? 

I tried this. Without success (was hanging at same point for more than half an hour), unfortunately.
Comment 5 Lars Wendler (Polynomial-C) gentoo-dev 2021-01-07 19:03:26 UTC
Plaese check if something is locking your /dev/null device. bug #748984 had been filed for the very same reason and there the offending blocker process was docker.
Comment 6 Joakim Tjernlund 2021-01-07 21:23:01 UTC
(In reply to Didier Colle from comment #2)
> (In reply to Lars Wendler (Polynomial-C) from comment #1)
> > Any chance you're trying to build this in a docker container?
> 
> I indeed have docker installed inside this vbox guest.
> I did however NOT launch this emerge command inside a docker container.

I think you need to stop the docker daemon where you run the emerge cmd
Comment 7 Didier Colle 2021-01-08 11:52:09 UTC
(In reply to Lars Wendler (Polynomial-C) from comment #5)
> Plaese check if something is locking your /dev/null device. bug #748984 had
> been filed for the very same reason and there the offending blocker process
> was docker.

my apologies for the stupid question: how can I confirm there is no such lock?
I thought using flock -u in case such lock exists, but either I don't understand the flock command or it is not reliable:
> dcolle@localhost ~ $ flock -n -E 200 -x /dev/null echo; echo $?
> 
> 0
> dcolle@localhost ~ $ flock -n -E 200 -x /dev/null echo; echo $?
> 
> 0
Should the output of the second run not result in 200 instead of 0 after a blank line???
Comment 8 Lars Wendler (Polynomial-C) gentoo-dev 2021-01-13 09:42:03 UTC
AFAIK, /usr/bin/flock is not the right tool for checking if a file is locked from some application. Better use one of the following two tools for this:

  /bin/fuser (sys-process/psmisc package)
  /usr/bin/lsof (sys-process/lsof package)
Comment 9 Didier Colle 2021-01-19 17:14:48 UTC
(In reply to Lars Wendler (Polynomial-C) from comment #8)
> AFAIK, /usr/bin/flock is not the right tool for checking if a file is locked
> from some application. Better use one of the following two tools for this:
> 
>   /bin/fuser (sys-process/psmisc package)
>   /usr/bin/lsof (sys-process/lsof package)


Thanks for the pointers.

The good news: in the meantime, I could emerge the virtualbox-guest-additions package.
The bad news: I am not sure what solved the problem; executing fuser -k /dev/null was a bit too drastic which terminated my emacs over ssh session and was not able to restore that session and consequently rebooted my headless vm.

Is the conclusion that the docker package should block the virtualbox-guet-additions package? (no issue for my day to day work, but sporadically I need the docker stuff in that vm, thus both packages blocking each other would be a pity)
Comment 10 timemars 2021-07-07 05:03:25 UTC
(In reply to Lars Wendler (Polynomial-C) from comment #5)
> Plaese check if something is locking your /dev/null device. bug #748984 had
> been filed for the very same reason and there the offending blocker process
> was docker.

Hi Lars,

I don't use docker but cri-o. Once I disable cri-o (systemctl disable cri-o) the issue disappears. I believe I am hitting the same issue.

I understand that after removing "&>/dev/null" the kmk command will become too verbose, but will the -s option work? Below is what I get from kmk --help:

-s, --silent, --quiet       Don't echo recipes.