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Bug 670484

Summary: /apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
Product: Portage Development Reporter: Martin Mokrejš <mmokrejs>
Component: CoreAssignee: Portage team <dev-portage>
Severity: normal Keywords: InVCS, REGRESSION
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
See Also:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 671498    

Description Martin Mokrejš 2018-11-06 12:15:08 UTC
  on Gentoo-Prefix installation I see the following:

make[2]: Nothing to be done for 'install-exec-am'.
 /apps/gentoo/bin/mkdir -p '/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.2/image//apps/gentoo/usr/share/doc/abyss-2.1.2'
 /apps/gentoo/usr/bin/install -c -m 644 ChangeLog CITATION.bib COPYRIGHT LICENSE '/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.2/image//apps/gentoo/usr/share/doc/abyss-2.1.2'
make[2]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.2/work/abyss-2.1.2'
make[1]: Leaving directory '/apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.2/work/abyss-2.1.2'
>>> Completed installing abyss-2.1.2 into /apps/gentoo/var/tmp/portage/sci-biology/abyss-2.1.2/image/

 * Final size of build directory: 28772 KiB (28.0 MiB)
 * Final size of installed tree:   8864 KiB ( 8.6 MiB)

/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found

>>> Installing (1 of 1) sci-biology/abyss-2.1.2::science

$ emerge --info
!!! Repository 'x-portage' is missing masters attribute in '/apps/gentoo/usr/local/portage/metadata/layout.conf'
!!! Set 'masters = gentoo' in this file for future compatibility
WARNING: One or more repositories have missing repo_name entries:


NOTE: Each repo_name entry should be a plain text file containing a
unique name for the repository on the first line.

Portage 2.3.51 (python 3.5.5-final-0, default/linux/amd64/17.0/no-multilib/prefix/kernel-2.6.32+, gcc-7.3.0, glibc-2.25-r11, 2.6.32-696.20.1.el6.x86_64 x86_64)
System uname: Linux-2.6.32-696.20.1.el6.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-4627_v2_@_3.30GHz-with-redhat-6.9-Santiago
KiB Mem:  3333628636 total,3024192908 free
KiB Swap:    7812028 total,   7812028 free
Timestamp of repository gentoo: Sun, 04 Nov 2018 22:00:01 +0000
Head commit of repository gentoo: 6a18bb60f924dc63b74598375d6d06aee73ff08c
sh bash 4.4_p23
ld GNU ld (Gentoo 2.30 p2) 2.30.0
app-shells/bash:          4.4_p23::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.26.2::gentoo
dev-lang/python:          2.7.14-r2::gentoo, 3.5.5-r1::gentoo
dev-util/cmake:           3.11.1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.30-r2::gentoo, 2.31.1-r1::gentoo
sys-devel/gcc:            5.4.0-r4::gentoo, 6.4.0-r5::gentoo, 7.3.0-r6::gentoo, 8.2.0-r4::gentoo
sys-devel/gcc-config:     1.9.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.16-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.25-r11::gentoo

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

    location: /apps/gentoo/usr/local/portage
    masters: gentoo
    priority: 0

    location: /apps/gentoo/var/lib/layman/haskell
    masters: gentoo
    priority: 50

    location: /apps/gentoo/var/lib/layman/science
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype- AdobeFlash-11.x Intel-SDP OPERA-2014"
CFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf"
CONFIG_PROTECT_MASK="/apps/gentoo/etc/gentoo-release /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
FCFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged"
FFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize"
GENTOO_MIRRORS=" rsync://"
LINGUAS="en_US en_GB en cs"
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"
USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify libtirpc lm_sensors mad mmx mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit postscript ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sparsehash sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 static-libs suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" 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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx f16c mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-1" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby24 ruby25" 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"
Comment 1 Martin Mokrejš 2018-11-06 12:26:36 UTC
Another example:

>>> Completed installing oracle-jre-bin- into /apps/gentoo/var/tmp/portage/dev-java/oracle-jre-bin-

 * Final size of build directory: 379152 KiB (370.2 MiB)
 * Final size of installed tree:  409568 KiB (399.9 MiB)

grep: /apps/gentoo/var/tmp/portage/dev-java/oracle-jre-bin- Is a directory
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 54: canonicalize: command not found
/apps/gentoo/usr/lib/portage/python3.5/install-qa-check.d/05prefix: line 63: canonicalize: command not found

>>> Installing (1 of 3) dev-java/oracle-jre-bin-
Comment 2 Zac Medico gentoo-dev 2018-11-06 18:00:47 UTC
The canonicalize function was removed in this commit:
Comment 3 James R Larrowe 2019-01-13 22:57:22 UTC
I have the same issue. It's blocking a Prefix install. Is this going to be fixed any time soon?
Comment 4 Larry the Git Cow gentoo-dev 2019-01-13 23:38:21 UTC
The bug has been referenced in the following commit(s):

commit 8463281f6a6daec64a976693447c240f0d669f08
Author:     Zac Medico <>
AuthorDate: 2019-01-13 23:11:40 +0000
Commit:     Zac Medico <>
CommitDate: 2019-01-13 23:17:32 +0000 restore canonicalize func (bug 675284)
    The canonicalize function is required by install-qa-check.d/05prefix.
    Fixes: aa0a94198794 ("ecompress: Replace with implementation from portage[mgorny]")
    Signed-off-by: Zac Medico <>

 bin/                            | 34 ++++++++++++++++++++++++
 lib/portage/tests/resolver/ |  1 +
 2 files changed, 35 insertions(+)
Comment 5 Fabian Groffen gentoo-dev 2019-01-14 08:54:13 UTC
Hmmm, Prefix had this restored already since

I guess you're not using the Prefix branch then.
Comment 6 Larry the Git Cow gentoo-dev 2019-01-15 06:22:33 UTC
The bug has been referenced in the following commit(s):

commit 4c7debeccab9d1ea546ffbd6cbb9ff352aba8f63
Author:     Zac Medico <>
AuthorDate: 2019-01-15 06:13:54 +0000
Commit:     Zac Medico <>
CommitDate: 2019-01-15 06:22:23 +0000

    sys-apps/portage: version bump to 2.3.56
     #675284 restore canonicalize func
     #675312 pid-sandbox: execute pid-ns-init as pid 1
    Package-Manager: Portage-2.3.56, Repoman-2.3.12
    Signed-off-by: Zac Medico <>

 sys-apps/portage/Manifest              |   1 +
 sys-apps/portage/portage-2.3.56.ebuild | 271 +++++++++++++++++++++++++++++++++
 2 files changed, 272 insertions(+)
Comment 7 Guilherme Amadio gentoo-dev 2019-01-23 08:45:43 UTC
@grobian on prefix-standalone we use vanilla portage, not the prefix branch.
Comment 8 Guilherme Amadio gentoo-dev 2019-01-23 08:48:16 UTC
I just tested this with portage 2.3.58. I think this can be closed. Thanks!
Comment 9 Martin Mokrejš 2019-02-05 16:26:32 UTC
Right, works for me too with sys-apps/portage-2.3.59-r1::gentoo as of now.