[Solved] Getting "Permission denied" when applying patches

Message

Javran · Post by **Javran** » Thu Dec 26, 2019 7:45 pm

By patches I mean those shipped with ebuild, I've removed my /etc/portage/patches while troubleshotting.
Not sure what happened but suddenly all packages with patches are failing with error messages like this:

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 * Package:    media-video/smplayer-19.10.2
 * Repository: gentoo
 * Maintainer: qt@gentoo.org media-video@gentoo.org
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking smplayer-19.10.2.tar.bz2 to /var/tmp/portage/media-video/smplayer-19.10.2/work
>>> Source unpacked in /var/tmp/portage/media-video/smplayer-19.10.2/work
>>> Preparing source in /var/tmp/portage/media-video/smplayer-19.10.2/work/smplayer-19.10.2 ...
 * Applying smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch ...
/var/tmp/portage/media-video/smplayer-19.10.2/temp/environment: line 429: /var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch: Permission denied
 *     /var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch: patch failed to apply without a fuzz factor, please rebase
/var/tmp/portage/media-video/smplayer-19.10.2/temp/environment: line 434: /var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch: Permission denied
 [ !! ]
 * ERROR: media-video/smplayer-19.10.2::gentoo failed (prepare phase):
 *   patch -p1  failed with /var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch
 * 
 * Call stack:
 *               ebuild.sh, line  125:  Called src_prepare
 *             environment, line 1469:  Called default
 *      phase-functions.sh, line  855:  Called default_src_prepare
 *      phase-functions.sh, line  920:  Called __eapi6_src_prepare
 *             environment, line  237:  Called eapply '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch' '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-17.1.0-advertisement_crap.patch' '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-18.2.0-jobserver.patch' '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-18.3.0-disable-werror.patch' '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-16.4.0-zero-bidi.patch'
 *             environment, line  499:  Called _eapply_patch '/var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch'
 *             environment, line  437:  Called __helpers_die 'patch -p1  failed with /var/tmp/portage/media-video/smplayer-19.10.2/files/smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch'
 *   isolated-functions.sh, line  112:  Called die
 * The specific snippet of code:
 *   		die "$@"
 * 
 * If you need support, post the output of `emerge --info '=media-video/smplayer-19.10.2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=media-video/smplayer-19.10.2::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/media-video/smplayer-19.10.2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/media-video/smplayer-19.10.2/temp/environment'.
 * Working directory: '/var/tmp/portage/media-video/smplayer-19.10.2/work/smplayer-19.10.2'
 * S: '/var/tmp/portage/media-video/smplayer-19.10.2/work/smplayer-19.10.2'

The command was simply "emerge -av1 media-video/smplayer" and I've have the exact same version successfully emerged previously.
EDIT: I'm only picking some random package that has this problem. I'm experiencing the same problem with "dev-lang/python-3.8.1" and (it seems like) all other packages that require patching.

emerge --info '=media-video/smplayer-19.10.2::gentoo'

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Portage 2.3.82 (python 3.6.10-final-0, default/linux/amd64/17.1/desktop, gcc-9.2.0, glibc-2.30-r3, 5.4.4-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.4.4-gentoo-x86_64-AMD_Ryzen_9_3900X_12-Core_Processor-with-gentoo-2.6
KiB Mem:    32899564 total,  30328696 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Wed, 25 Dec 2019 00:45:01 +0000
Head commit of repository gentoo: 3428f827643b9460f7c0b15f4c64025349ab8fe1
Head commit of repository steam-overlay: 5b099b835b5b8dc7f37390e37e44cebba7cc315d

sh bash 5.0_p11
ld GNU ld (Gentoo 2.33.1 p1) 2.33.1
app-shells/bash:          5.0_p11::gentoo
dev-lang/perl:            5.30.1::gentoo
dev-lang/python:          2.7.17::gentoo, 3.6.10::gentoo, 3.7.5-r1::gentoo
dev-util/cmake:           3.16.1::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.1-r2::gentoo
sys-devel/binutils:       2.33.1::gentoo
sys-devel/gcc:            9.2.0-r2::gentoo
sys-devel/gcc-config:     2.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.4::gentoo (virtual/os-headers)
sys-libs/glibc:           2.30-r3::gentoo
Repositories:

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

steam-overlay
    location: /usr/local/portage/steam-overlay
    sync-type: git
    sync-uri: https://github.com/anyc/steam-overlay.git
    masters: gentoo
    priority: 50

Installed sets: @my-themes, @steam
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -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="-march=native -O2 -pipe"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going --quiet-build --autounmask-write"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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="-march=native -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs candy 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 sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://mirror.sjc02.svwh.net/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j25"
PKGDIR="/var/cache/binpkgs"
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 bluetooth branding bzip2 cairo cdda cdr cli consolekit crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam ffmpeg flac fortran gdbm gif gpm gtk iconv icu ipv6 jpeg lcms ldap libnotify libtirpc mad mng mp3 mp4 mpeg multilib ncurses networkmanager nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt5 readline sdl seccomp split-usr ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wifi wxwidgets x264 xattr xcb xft 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="mmx mmxext sse sse2 aes avx avx2 f16c fma3 pclmul popcnt sha sse3 sse4_1 sse4_2 sse4a 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" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

media-video/smplayer-19.10.2::gentoo was built with the following:
USE="-autoshutdown -bidi -debug -mpris" ABI_X86="(64)"

Some stuff that I merged today in case you can spot anything (output of "genlop -l"):

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     Thu Dec 26 10:56:58 2019 >>> sys-devel/llvm-common-9.0.1
     Thu Dec 26 10:57:04 2019 >>> sys-fs/fuse-common-3.9.0
     Thu Dec 26 10:57:15 2019 >>> sys-apps/file-5.38
     Thu Dec 26 10:57:23 2019 >>> sys-power/acpid-2.0.32-r1
     Thu Dec 26 10:57:28 2019 >>> app-eselect/eselect-ruby-20191222
     Thu Dec 26 10:57:34 2019 >>> sys-libs/efivar-37
     Thu Dec 26 10:58:13 2019 >>> sys-kernel/gentoo-sources-5.4.6
     Thu Dec 26 10:58:28 2019 >>> dev-ruby/racc-1.4.16-r1
     Thu Dec 26 10:58:49 2019 >>> net-libs/libtirpc-1.2.5
     Thu Dec 26 11:00:15 2019 >>> dev-qt/qtcore-5.14.0
     Thu Dec 26 11:00:36 2019 >>> dev-qt/qtxml-5.14.0
     Thu Dec 26 11:00:48 2019 >>> dev-qt/linguist-tools-5.14.0
     Thu Dec 26 11:01:10 2019 >>> dev-qt/qttest-5.14.0
     Thu Dec 26 11:01:32 2019 >>> dev-qt/qtscript-5.14.0
     Thu Dec 26 11:02:07 2019 >>> dev-qt/qtdbus-5.14.0
     Thu Dec 26 11:02:22 2019 >>> xfce-base/exo-0.12.11
     Thu Dec 26 11:02:31 2019 >>> net-im/skypeforlinux-8.55.0.123
     Thu Dec 26 11:02:41 2019 >>> www-client/vivaldi-2.10.1745.23_p1
     Thu Dec 26 11:02:46 2019 >>> virtual/editor-0-r3
     Thu Dec 26 11:03:41 2019 >>> dev-lang/python-3.6.10
     Thu Dec 26 11:03:56 2019 >>> sys-apps/portage-2.3.83
     Thu Dec 26 11:12:38 2019 >>> dev-libs/jsoncpp-1.9.2-r2
     Thu Dec 26 11:26:34 2019 >>> sys-apps/portage-2.3.82

Post by **Banana** » Thu Dec 26, 2019 7:55 pm

Hello Javran.

Are you using tmpfs? What does a

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ls -l of /var/tmp/portage/media-video/smplayer-19.10.2/files/

show?

What happens after you delete everything in /var/tmp/portage/* and run an emerge again?

Gatak · Post by **Gatak** » Thu Dec 26, 2019 8:03 pm

I have seen this on a few packages recently. The problem seems to be wrong permission on the source files when unpacked to /var/tmp/portage/, so the patch can't be applied.

My solution was to use "ebuild theapp-1.2.3.ebuild unpack", then do a "chmod a+rw /var/tmp/portage -R". Then continue with "ebuild theapp-1.2.3.ebuild merge"

Javran · Post by **Javran** » Thu Dec 26, 2019 8:04 pm

*_-=Banana=-_* wrote:Hello Javran.

Are you using tmpfs? What does a
Code: Select all
ls -l of /var/tmp/portage/media-video/smplayer-19.10.2/files/
show?

What happens after you delete everything in /var/tmp/portage/* and run an emerge again?

Yes, my /var/tmp/portage is mounted as tmpfs.

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# ls -l /var/tmp/portage/media-video/smplayer-19.10.2/files/
total 24
-rw-r--r-- 1 root root  566 Aug  8  2015 smplayer-14.9.0.6966-unbundle-qtsingleapplication.patch
-rw-r--r-- 1 root root  489 Mar 31  2016 smplayer-16.4.0-zero-bidi.patch
-rw-r--r-- 1 root root 1982 Oct  6  2017 smplayer-17.1.0-advertisement_crap.patch
-rw-r--r-- 1 root root  423 Feb 10  2018 smplayer-18.2.0-jobserver.patch
-rw-r--r-- 1 root root  367 May  7  2018 smplayer-18.3.0-disable-werror.patch
-rw-r--r-- 1 root root  969 Oct 28 03:39 smplayer-19.5.0-mpv-0.30.0.patch

Same thing happens after I removed everything in /var/tmp/portage/*.

Post by **Ionen** » Thu Dec 26, 2019 8:08 pm

Are you able to access /var/db/repos/media-video/smplayer/files/ as non-root? (or /usr/portage/media-video/smplayer/files/, wherever your gentoo repos is stored).

Maybe one of the directory within the path is not world readable and be an issue when emerge drops root privileges.

Edit: /var/tmp/portage/media-video/smplayer-19.10.2/files/ should just be a symbolic link to that location, so the problem shouldn't be in /var/tmp/portage

Post by **Banana** » Thu Dec 26, 2019 8:18 pm

Gatak wrote:I have seen this on a few packages recently. The problem seems to be wrong permission on the source files when unpacked to /var/tmp/portage/, so the patch can't be applied.
...

maybe a clean of the disfiles directory could help.

You are on tmpfs, does the tmpfs size is enough to run the emerge process?

Javran · Post by **Javran** » Thu Dec 26, 2019 8:24 pm

Gatak wrote:I have seen this on a few packages recently. The problem seems to be wrong permission on the source files when unpacked to /var/tmp/portage/, so the patch can't be applied.

My solution was to use "ebuild theapp-1.2.3.ebuild unpack", then do a "chmod a+rw /var/tmp/portage -R". Then continue with "ebuild theapp-1.2.3.ebuild merge"

I just tried that and it didn't work, "chmod -R" doesn't seem to propagate though symbol links, and I'm still seeing write permission unset in /var/tmp/portage/media-video/smplayer-19.10.2/files.
I've also tried "chown portage.portage" on all patches under /var/db/repos/gentoo/media-video/smplayer/files, which didn't seem to make a difference.

If this is a known issue, is there a bug tracking that? Prior to this post I did try to peek a bit in bugzilla but didn't find anything of interest.

Javran · Post by **Javran** » Thu Dec 26, 2019 8:27 pm

Ionen wrote:Are you able to access /var/db/repos/media-video/smplayer/files/ as non-root? (or /usr/portage/media-video/smplayer/files/, wherever your gentoo repos is stored).

Maybe one of the directory within the path is not world readable and be an issue when emerge drops root privileges.

Edit: /var/tmp/portage/media-video/smplayer-19.10.2/files/ should just be a symbolic link to that location, so the problem shouldn't be in /var/tmp/portage

I guess you meant "/var/db/repos/gentoo/media-video/smplayer/files"? No, my non-root account got permission denied when accessing "/var/db/repos/gentoo".

Post by **Banana** » Thu Dec 26, 2019 8:32 pm

doesn't the rights be portage:portage and not root:root?

see here: viewtopic-p-7576334.html

Post by **Ionen** » Thu Dec 26, 2019 8:35 pm

Javran wrote:I guess you meant "/var/db/repos/gentoo/media-video/smplayer/files"? No, my non-root account got permission denied when accessing "/var/db/repos/gentoo".

Yeah I did. Well, that's the issue...

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chmod 755 /var/db/repos/gentoo

will likely fix this assuming no other directory with wrong permissions in the path.

But why is it not world readable in the first place? This isn't something that needs to be hidden from non-root/portage (Edit: notably because it's needed to use things like equery as normal user). I've seen another user have the same issue recently (I assumed user error back then).

Javran · Post by **Javran** » Thu Dec 26, 2019 8:37 pm

*_-=Banana=-_* wrote:
Gatak wrote:I have seen this on a few packages recently. The problem seems to be wrong permission on the source files when unpacked to /var/tmp/portage/, so the patch can't be applied.
...
maybe a clean of the disfiles directory could help.

You are on tmpfs, does the tmpfs size is enough to run the emerge process?

As long as all checksums match, I don't think this is related to distfiles (I'll try to avoid cleaning that if possible in case I need to downgrade something to resolve this).
/var/tmp/portage is mounted with size=8192M, ought to be enough for anybody.

Javran · Post by **Javran** » Thu Dec 26, 2019 8:45 pm

Ionen wrote:
Javran wrote:I guess you meant "/var/db/repos/gentoo/media-video/smplayer/files"? No, my non-root account got permission denied when accessing "/var/db/repos/gentoo".
Yeah I did. Well, that's the issue...
Code: Select all
chmod 755 /var/db/repos/gentoo
will likely fix this assuming no other directory with wrong permissions in the path.

But why is it not world readable in the first place? This isn't something that needs to be hidden from non-root/portage (Edit: notably because it's needed to use things like equery as normal user). I've seen another user have the same issue recently (I assumed user error back then).

Indeed, my /var/db/repos/gentoo was 700, setting it to 755 seems to get rid of the permission issue, thanks!
That's weird, could this be some upgrade automation script? I don't recall making any permission changes recently. In fact I've been assuming my ebuild files were still in /usr/portage until like an hour ago.

Post by **Ionen** » Thu Dec 26, 2019 8:52 pm

Could be related to the sync method, some specific condition, or maybe a temporary bug that only affected people that sync at the wrong moment (it doesn't sound that widespread), and it's technically maybe fixed save for a few poor souls that got unlucky.

And yeah, /var/db/repos/gentoo is the new location, personally never liked /usr/portage (already used a different location) and I guess gentoo agrees with that now.
Edit: And I'll probably move it to this new location, it makes sense to me. Funny enough I already used /var/cache/distfiles and /var/cache/packages(binpkgs) as my defaults before gentoo made the move (see this for new paths).

Edit2: Also the other user I talked about had 0700 on /usr/portage rather than /var/db/repos/gentoo, so I don't "think" it's related to the move.

Javran · Post by **Javran** » Thu Dec 26, 2019 9:02 pm

Thank you all for the help, I'll mark this as solved.
(for the record I also have a custom DISTFILES setup on my old machine, but well I've been lazy with my new machine

)
tldr: If you ran into issues with apply patches getting permission denied, check permission of /var/db/repos/gentoo, if it's 700 (drwx------), you can set it to 755.