Category: Gentoo

env python3.5: no such file or directory

The dependency conflicts may require a lot of time to resolve. On the contrary, uninstalling old software is easy, but it might lead to multiple broken programs and strange errors. Here is one of them, after removing the old python 3.4 and 3.5 (or whatever version it prints in your case) under Gentoo despite the rebuilding all dependencies as required by the emerge command for the new python 3.6 an error occurred trying to emerge the “app-misc/geoclue-2.5.3-r2”

[20/75] /usr/lib/python-exec/python3.6/meson --internal exe --unpickle /var/tmp/portage/app-misc/geoclue-2.5.3-r2/work/geoclue-2.5.3-build/meson-private/meson_exe_glib-mkenums_af4feac41c42ec7289410f8b20070c0528a3a7c0.dat
FAILED: public-api/gclue-enum-types.c 
/usr/lib/python-exec/python3.6/meson --internal exe --unpickle /var/tmp/portage/app-misc/geoclue-2.5.3-r2/work/geoclue-2.5.3-build/meson-private/meson_exe_glib-mkenums_af4feac41c42ec7289410f8b20070c0528a3a7c0.dat
/usr/bin/env: âpython3.5â: No such file or directory
ninja: build stopped: subcommand failed.
 * ERROR: app-misc/geoclue-2.5.3-r2::gentoo failed (compile phase):
 *   ninja -v -j15 -l14 -C /var/tmp/portage/app-misc/geoclue-2.5.3-r2/work/geoclue-2.5.3-build failed
 * 
 * Call stack:
 *     ebuild.sh, line  125:  Called src_compile
 *   environment, line 2847:  Called meson_src_compile
 *   environment, line 1904:  Called eninja '-C' '/var/tmp/portage/app-misc/geoclue-2.5.3-r2/work/geoclue-2.5.3-build'
 *   environment, line 1274:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 *

Despite the lines starting with “/usr/lib/python-exec/python3.6/meson”, there is an error for missing “python 3.5“.

Here is another example, just trying to execute the distcc-config and it immediately throws the error for missing “python 3.5“.

root@srv ~ # distcc-config 
/usr/bin/env: ‘python3.5’: No such file or directory

The python script distcc-config starts with:

root@srv ~ $ head /usr/bin/distcc-config
#!/usr/bin/env python3.5
# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

import os, re, signal, subprocess, sys

options=[
        '--get-hosts',
        '--set-hosts',
        '--get-verbose',

Apparently, multiple programs use this technic to explicitly put a specific version of python in the header of the python script to be used. Thus grantees the version in the header will be used even you change the system or user-preferred Python interpreter.

But uninstalling this python version all these programs will stop working till you rebuild them with emerge.
Keep on reading!

display packages from the Gentoo emerge resume list

A quick tip and an easy hack to see the emerge resume list, which will be used by the “emerge –resume” command. There are two resume lists – resume and resume_backup in the binary file /var/cache/edb/mtimedb.
The first two commands are python 3+.
The resume and resume_backup lists

python -c 'import portage; print(portage.mtimedb.get("resume", {}).get("mergelist"))'
python -c 'import portage; print(portage.mtimedb.get("resume_backup", {}).get("mergelist"))'

If you need the command for the python 2 you should use the following:

python -c 'import portage; print portage.mtimedb.get("resume", {}).get("mergelist")'
python -c 'import portage; print portage.mtimedb.get("resume_backup", {}).get("mergelist")'

Real world example

Resume list for

desktop ~ # emerge -v --nodeps $(qlist -IC|grep dev-qt)

These are the packages that would be merged, in order:

[ebuild     U  ] dev-qt/designer-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="declarative webkit -debug -test" 8,493 KiB
[ebuild     U  ] dev-qt/linguist-tools-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="qml -debug -test" 0 KiB
[ebuild     U  ] dev-qt/qdbus-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qtbluetooth-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -qml -test" 2,727 KiB
[ebuild   R    ] dev-qt/qtchooser-66::gentoo  USE="-test" 32 KiB
[ebuild     U  ] dev-qt/qtconcurrent-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 48,549 KiB
[ebuild     U  ] dev-qt/qtcore-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="icu -debug (-systemd) -test" 0 KiB
[ebuild     U  ] dev-qt/qtdbus-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qtdeclarative-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="jit widgets -debug -gles2 -localstorage -test" 20,753 KiB
[ebuild     U  ] dev-qt/qtgraphicaleffects-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 13,713 KiB
[ebuild     U  ] dev-qt/qtgui-5.14.0-r1:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="accessibility dbus egl evdev gif ibus jpeg libinput png udev vnc wayland%* xcb -debug -eglfs -gles2 -test -tslib -tuio" 0 KiB
[ebuild     U  ] dev-qt/qthelp-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qtimageformats-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="mng -debug -test (-jpeg2k%)" 1,768 KiB
[ebuild     U  ] dev-qt/qtlocation-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 5,974 KiB
[ebuild   R    ] dev-qt/qtlockedfile-2.4.1_p20171024::gentoo  USE="-doc" 694 KiB
[ebuild     U  ] dev-qt/qtmultimedia-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="alsa gstreamer openal pulseaudio qml widgets -debug -gles2 -test" 3,671 KiB
[ebuild     U  ] dev-qt/qtnetwork-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="libproxy networkmanager ssl -bindist -connman -debug -sctp -test" 0 KiB
[ebuild     U  ] dev-qt/qtopengl-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -gles2 -test" 0 KiB
[ebuild     U  ] dev-qt/qtpaths-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qtpositioning-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="qml -debug -geoclue -test" 0 KiB
[ebuild     U  ] dev-qt/qtprintsupport-5.14.0-r1:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="cups -debug -gles2 -test" 0 KiB
[ebuild     U  ] dev-qt/qtquickcontrols2-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test -widgets" 7,947 KiB
[ebuild     U  ] dev-qt/qtquickcontrols-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="widgets -debug -test" 5,843 KiB
[ebuild     U  ] dev-qt/qtscript-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="jit scripttools -debug -test" 2,584 KiB
[ebuild     U  ] dev-qt/qtsensors-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -qml -test" 1,996 KiB
[ebuild   R    ] dev-qt/qtsingleapplication-2.6.1_p20171024::gentoo  USE="X -doc" 0 KiB
[ebuild     U  ] dev-qt/qtspeech-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 99 KiB
[ebuild     U  ] dev-qt/qtsql-5.14.0:5/5.14.0::gentoo [5.12.2:5/5.12.2::gentoo] USE="mysql sqlite -debug -freetds -oci8 -odbc -postgres -test" 0 KiB
[ebuild     U  ] dev-qt/qtsvg-5.14.0-r1:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 1,822 KiB
[ebuild     U  ] dev-qt/qttest-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qttranslations-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 1,302 KiB
[ebuild     U  ] dev-qt/qtvirtualkeyboard-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="spell xcb -debug -handwriting -test" 10,705 KiB
[ebuild     U  ] dev-qt/qtwayland-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="libinput xcomposite -debug -test" 532 KiB
[ebuild     U  ] dev-qt/qtwebchannel-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="qml -debug -test" 192 KiB
[ebuild     U  ] dev-qt/qtwebengine-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="alsa pulseaudio system-icu widgets -bindist -debug -designer -jumbo-build -pax_kernel -system-ffmpeg -test (-geolocation%*)" 235,904 KiB
[ebuild     U  ] dev-qt/qtwebkit-5.212.0_pre20190629:5/5.212::gentoo [5.212.0_pre20180120:5/5.212::gentoo] USE="X geolocation hyphen jit multimedia opengl printsupport qml -gles2 -gstreamer -nsplugin -orientation -webp" 12,166 KiB
[ebuild     U  ] dev-qt/qtwidgets-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="gtk png xcb -debug -gles2 -test" 0 KiB
[ebuild     U  ] dev-qt/qtx11extras-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 125 KiB
[ebuild     U  ] dev-qt/qtxml-5.14.0:5/5.14::gentoo [5.12.2:5/5.12::gentoo] USE="-debug -test" 0 KiB
[ebuild     U  ] dev-qt/qtxmlpatterns-5.14.0:5/5.14::gentoo [5.11.1:5/5.11::gentoo] USE="-debug -qml% -test" 1,362 KiB

Total: 40 packages (37 upgrades, 3 reinstalls), Size of downloads: 388,941 KiB


>>> Verifying ebuild manifests
>>> Running pre-merge checks for dev-qt/qtwebkit-5.212.0_pre20190629

>>> Emerging (1 of 40) dev-qt/designer-5.14.0::gentoo
 * Fetching files in the background.
 * To view fetch progress, run in another terminal:
 * tail -f /var/log/emerge-fetch.log
 * qttools-everywhere-src-5.14.0.tar.xz BLAKE2B SHA512 size ;-) ...                                                                                                  [ ok ]
!!! Failed to set new SELinux execution context. Is your current SELinux context allowed to run Portage?
>>> Unpacking source...
>>> Unpacking qttools-everywhere-src-5.14.0.tar.xz to /var/tmp/portage/dev-qt/designer-5.14.0/work
^C

Exiting on signal 2
sandbox:stop  caught signal 2 in pid 22886
sandbox:stop  Send signal 4 more times to force SIGKILL
Sandboxed process killed by signal: Interrupt
^C * The ebuild phase 'die_hooks' has been killed by signal 2.

 * Messages for package dev-qt/designer-5.14.0:

We interrupted it on purpose with Ctrl+C.

The output of the above python command:

desktop ~ # python -c 'import portage; print(portage.mtimedb.get("resume", {}).get("mergelist"))'
[['ebuild', '/', 'dev-qt/designer-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/linguist-tools-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qdbus-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtbluetooth-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtchooser-66', 'merge'], ['ebuild', '/', 'dev-qt/qtconcurrent-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtcore-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtdbus-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtdeclarative-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtgraphicaleffects-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtgui-5.14.0-r1', 'merge'], ['ebuild', '/', 'dev-qt/qthelp-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtimageformats-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtlocation-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtlockedfile-2.4.1_p20171024', 'merge'], ['ebuild', '/', 'dev-qt/qtmultimedia-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtnetwork-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtopengl-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtpaths-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtpositioning-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtprintsupport-5.14.0-r1', 'merge'], ['ebuild', '/', 'dev-qt/qtquickcontrols2-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtquickcontrols-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtscript-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtsensors-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtsingleapplication-2.6.1_p20171024', 'merge'], ['ebuild', '/', 'dev-qt/qtspeech-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtsql-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtsvg-5.14.0-r1', 'merge'], ['ebuild', '/', 'dev-qt/qttest-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qttranslations-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtvirtualkeyboard-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtwayland-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtwebchannel-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtwebengine-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtwebkit-5.212.0_pre20190629', 'merge'], ['ebuild', '/', 'dev-qt/qtwidgets-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtx11extras-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtxml-5.14.0', 'merge'], ['ebuild', '/', 'dev-qt/qtxmlpatterns-5.14.0', 'merge']]
desktop ~ # python -c 'import portage; print(portage.mtimedb.get("resume_backup", {}).get("mergelist"))'
None

gentoo emerge resume – Invalid resume list and clean the list

Under Gentoo and emerge it will eventually end up using “–resume” paired with “–skipfirst” emerge command, which should resume last list of packages to build without the first one. Each execution of emerge command should reset the list but apparently it might not be the case (in fact two lists are kept – resume and resume_backup, read below).
The command just reads a list of packages and emerges them – it’s fast and it does not go through the whole process of dependancy check! But sometimes the list could be old or get corrupted or it just throws errors for “Invalid resume list“:

dekstop ~ # emerge --resume --skipfirst

These are the packages that would be merged, in order:

Calculating dependencies... done!
 * Invalid resume list:
 * 
 *   ('ebuild', '/', 'kde-frameworks/kpty-5.66.0', 'merge')
 *   ('ebuild', '/', 'kde-plasma/libkscreen-5.17.5', 'merge')
 *   ('ebuild', '/', 'kde-apps/kmbox-19.12.1', 'merge')
 *   ('ebuild', '/', 'kde-frameworks/kdesignerplugin-5.66.0', 'merge')
 *   ('ebuild', '/', 'kde-plasma/kwayland-integration-5.17.5', 'merge')
 *   ('ebuild', '/', 'kde-plasma/xembed-sni-proxy-5.17.5', 'merge')
 *   ('ebuild', '/', 'net-libs/accounts-qml-0.7-r1', 'merge')
 *   ('ebuild', '/', 'kde-apps/akonadi-notes-19.12.1', 'merge')
....
....
 * One or more packages are either masked or have missing dependencies:
 * 
 *   dev-lang/python:3.4[xml(+)] pulled in by:
 *     (dev-python/setuptools-40.6.2:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.5[xml(+)] pulled in by:
 *     (dev-python/setuptools-40.6.2:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.4 pulled in by:
 *     (dev-python/certifi-2018.8.24:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.5 pulled in by:
 *     (dev-python/certifi-2018.8.24:0/0::gentoo, installed)
 * 
 *   dev-libs/openssl:0/0= pulled in by:
 *     (dev-lang/python-2.7.17-r1:2.7/2.7::gentoo, installed)
 * 
 *   dev-lang/python:3.5 pulled in by:
 *     (dev-util/glib-utils-2.56.2:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.4 pulled in by:
 *     (sys-apps/file-5.35:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.5 pulled in by:
 *     (sys-apps/file-5.35:0/0::gentoo, installed)
 * 
 *   >=dev-libs/icu-58.1:0/60.2= pulled in by:
 *     (dev-lang/spidermonkey-52.9.1_pre1:52/52::gentoo, installed)
....
....
 *   dev-lang/python:3.4 pulled in by:
 *     (virtual/python-enum34-1:0/0::gentoo, installed)
 * 
 *   dev-lang/python:3.5 pulled in by:
 *     (virtual/python-enum34-1:0/0::gentoo, installed)
 * 
 *   dev-libs/openssl:0/0= pulled in by:
 *     (dev-lang/python-3.7.6:3.7/3.7m::gentoo, installed)
 * 
 * The resume list contains packages that are either masked or have
 * unsatisfied dependencies. Please restart/continue the operation
 * manually, or use --skipfirst to skip the first package in the list and
 * any other packages that may be masked or have missing dependencies.

Not all packages are included above, but it is clear that the list includes packages not only from the last emerge command. The list includes multiple old packages and dependencies about python:3.4, python:3.5, openssl:0/0.
The list is located in the binary file: /var/cache/edb/mtimedb and to clean the list you should execute:

desktop ~ # emaint --fix cleanresume
Emaint: fix cleanresume    100% [============================================>]

It is safe to the directory, too:

rm -Rf /var/cache/edb/

emaint is part of the sys-apps/portage package, so the program should always be available in the system.

*Bonus 1 – old packages

There is one more problem in the above example! In fact, you may clear the resume list with emaint or remove the whole directory “/var/cache/edb”, but still to receive such errors let’s say resuming log lists like KDE, gnome, qt packages (packages with many dependencies).

This problem persists not only with “–resume”, but also with “–keep-going” option!

When using “–keep-going” option you’ll get the same errors after the line “One or more packages are either masked or have missing dependencies”. So it is not an option, which may replace the “–resume” option.

Even all dependencies were resolved when the emerge list was generated when resuming a list of packages may throw errors for packages, which pull old packages because they had not been rebuilt against the updated of some of their dependencies. For example, simple enough from the above emerge resume command:
Some packages of our KDE resume list depends on the “dev-python/setuptools”, which has not been rebuilt against the new python (or after a removed old version python 3.4 and 3.5 or even another [old] package depends on the old python 3.5 and dev-python/setuptools, which has not been rebuilt after the python 3.4/3.5 removal!) and now this is a problem to resume the emerge list.

The solution is to take all those packages (after the line “One or more packages are either masked or have missing dependencies”) and rebuild or remove them.

Keep on reading!

meson.build – ERROR: Dependency “x11” not found, tried pkgconfig and cmake

Another day and another major update exposed an error of missing the “x11” library. Apparently, the pkg-config got corrupted for X11 library. Most of the time the error is self-explanatory, but sometimes it is too generic like: 

Run-time dependency x11 found: NO (tried pkgconfig and cmake)

meson.build:412:2: ERROR: Dependency "x11" not found, tried pkgconfig and cmake

The name “x11” is a part of multiple libraries:

srv ~ # pkg-config --list-all |grep x11

gdkglext-1.0                               GdkGLExt - OpenGL Extension to GDK (x11 target)
gdk-2.0                                    GDK - GTK+ Drawing Kit (x11 target)
gtk+-2.0                                   GTK+ - GTK+ Graphical UI Library (x11 target)
gdkglext-x11-1.0                           GdkGLExt - OpenGL Extension to GDK (x11 target)
x11-xcb                                    X11 XCB - X Library XCB interface
gdk-x11-3.0                                GDK - GTK+ Drawing Kit
gdk-x11-2.0                                GDK - GTK+ Drawing Kit (x11 target)
gtkglext-1.0                               GtkGLExt - OpenGL Extension to GTK+ (x11 target)
x11                                        X11 - X Library
xkbcommon-x11                              xkbcommon-x11 - XKB API common to servers and clients - X11 support
scim-x11utils                              scim-x11utils - X11 Utilities for Smart Common Input Method platform
clutter-x11-1.0                            Clutter - Clutter Core Library
gtk+-x11-3.0                               GTK+ - GTK+ Graphical UI Library
libva-x11                                  libva-x11 - Userspace Video Acceleration (VA) x11 interface
gtkglext-x11-1.0                           GtkGLExt - OpenGL Extension to GTK+ (x11 target)
gtk+-x11-2.0                               GTK+ - GTK+ Graphical UI Library (x11 target)

The above example is of working x11 library pkg-config. In our broken system the 10th line was missing.
Keep on reading!

libselinux – undefined reference to pcre_version

Emerging the “sys-libs/libselinux-2.9-r1” failed with this link errors of undefined references

/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_version':
regex.c:(.text+0x30): undefined reference to `pcre_version'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_writef':
regex.c:(.text+0x95): undefined reference to `pcre_fullinfo'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.c:(.text+0xf6): undefined reference to `pcre_fullinfo'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_data_free':
regex.c:(.text+0x1eb): undefined reference to `pcre_free'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.c:(.text+0x200): undefined reference to `pcre_free_study'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_prepare_data':
regex.c:(.text+0x26d): undefined reference to `pcre_compile'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.c:(.text+0x28f): undefined reference to `pcre_study'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_load_mmap':
regex.c:(.text+0x385): undefined reference to `pcre_fullinfo'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.c:(.text+0x3ed): undefined reference to `pcre_fullinfo'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_match':
regex.c:(.text+0x494): undefined reference to `pcre_exec'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.lo: in function `regex_cmp':
regex.c:(.text+0x502): undefined reference to `pcre_fullinfo'
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: regex.c:(.text+0x51a): undefined reference to `pcre_fullinfo'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:148: libselinux.so.1] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/var/tmp/portage/sys-libs/libselinux-2.9-r1/work/libselinux-2.9-abi_x86_32.x86/src'
make: *** [Makefile:44: all] Error 1
 * ERROR: sys-libs/libselinux-2.9-r1::gentoo failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=sys-libs/libselinux-2.9-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/libselinux-2.9-r1::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-libs/libselinux-2.9-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/libselinux-2.9-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-libs/libselinux-2.9-r1/work/libselinux-2.9-abi_x86_32.x86'
 * S: '/var/tmp/portage/sys-libs/libselinux-2.9-r1/work/libselinux-2.9'

>>> Failed to emerge sys-libs/libselinux-2.9-r1, Log file:

>>>  '/var/tmp/portage/sys-libs/libselinux-2.9-r1/temp/build.log'

 * Messages for package sys-libs/libselinux-2.9-r1:

 * ERROR: sys-libs/libselinux-2.9-r1::gentoo failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=sys-libs/libselinux-2.9-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/libselinux-2.9-r1::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-libs/libselinux-2.9-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/libselinux-2.9-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-libs/libselinux-2.9-r1/work/libselinux-2.9-abi_x86_32.x86'
 * S: '/var/tmp/portage/sys-libs/libselinux-2.9-r1/work/libselinux-2.9'

The solution was to rebuild the dev-libs/libpcre and dev-libs/libpcre2 libraries.

emerge -va dev-libs/libpcre dev-libs/libpcre2

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U  ] dev-libs/libpcre-8.43:3::gentoo [8.42:3::gentoo] USE="bzip2 cxx jit pcre16 readline recursion-limit (split-usr%*) (static-libs) (unicode) zlib -libedit -pcre32" ABI_X86="32 (64) (-x32)" 1540 KiB
[ebuild     U  ] dev-libs/libpcre2-10.34::gentoo [10.32::gentoo] USE="bzip2 jit pcre16 pcre32* readline recursion-limit (split-usr%*) unicode zlib -libedit -static-libs" ABI_X86="32 (64) (-x32)" 1676 KiB

Total: 2 packages (2 upgrades), Size of downloads: 3216 KiB

if you encounter the error above even you are not using Gentoo probably the problem is your libpcre/libpcre2 library and try to rebuild it or include the proper path to the library and its headers.

Gentoo – UnicodeEncodeError: ‘ascii’ codec can’t encode character ‘\xc4’ in position 83: ordinal not in range(128)

Recently emerging package =dev-lang/go-1.13.4 under Gentoo failed on one of our virtual servers with:

--- /usr/lib/go/test/fixedbugs/issue27836.dir/
Traceback (most recent call last):
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/_MergeProcess.py", line 234, in _spawn
    prev_mtimes=self.prev_mtimes, counter=counter)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 1788, in wrapper
    return f(self, *args, **kwargs)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 5385, in merge
    counter=counter)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 4548, in treewalk
    rval = self._merge_contents(srcroot, destroot, cfgfiledict)
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 4828, in _merge_contents
    self.settings["EPREFIX"].lstrip(os.sep), cfgfiledict, mymtime):
  File "/usr/lib64/python3.6/site-packages/portage/dbapi/vartree.py", line 5225, in mergeme
    encoding=_encodings['merge'])
  File "/usr/lib64/python3.6/site-packages/portage/util/movefile.py", line 256, in movefile
    selinux.rename(src, dest)
  File "/usr/lib64/python3.6/site-packages/portage/__init__.py", line 246, in __call__
    rval = self._func(*wrapped_args, **wrapped_kwargs)
  File "/usr/lib64/python3.6/site-packages/portage/_selinux.py", line 71, in rename
    os.rename(src, dest)
UnicodeEncodeError: 'ascii' codec can't encode character '\xc4' in position 83: ordinal not in range(128)

>>> Failed to install dev-lang/go-1.13.4, Log file:

>>>  '/var/tmp/portage/dev-lang/go-1.13.4/temp/build.log'

The above log shows that the emerge fails in the installation phase when moving the files to the proper path in the system. The problem there is a non-ASCII character in the file name or path, but the environment is set to use ASCII as language.

The solution is to check if the environment LANG is set and what it contains. In this case, we should set the LANG environment to utf8.

export LANG=en_US.UTF-8

Most of the cases this kind of error could occur with virtual servers, docker (or the other kind of containers like lxc, podman and so on) containers and chroot jails or screens with changed user with su or sudo! In our case, the LANG just got missed because of a switch user procedure in a container and the emerge failed with the above error. When the LANG is missing probably the default value is “C”. In fact, check not only LANG but also the “LC_ALL” environment variable (it may have different value, which is wrong!), which also should be “en_US.UTF-8”:

export LC_ALL=en_US.UTF-8

Or try removing it at all with 

unset LC_ALL

Keep on reading!

Gentoo – updating perl and problems like perl-core/ is blocking virtual/perl-

When upgrading Perl under Gentoo it’s almost typical to have blocks of the kind:

[blocks B      ] <perl-core/File-Path-2.160.0 ("<perl-core/File-Path-2.160.0" is blocking virtual/perl-File-Path-2.160.0)
[blocks B      ] <perl-core/Module-CoreList-5.201.905.220 ("<perl-core/Module-CoreList-5.201.905.220" is blocking virtual/perl-Module-CoreList-5.201.905.220)
[blocks B      ] <perl-core/Archive-Tar-2.320.0 ("<perl-core/Archive-Tar-2.320.0" is blocking virtual/perl-Archive-Tar-2.320.0)

These blocks appeared when we tried updaring the Perl 5.26 to 5.30 (dev-lang/perl-5.30.0:0/5.30::gentoo from dev-lang/perl-5.26.2:0). This update is a major update.
So what does it mean?
The virtual package and the perl-core package should be the same version, but it appears there are no corresponding same versions to the virtual package versions (). The problem is that the update depends on a newer version of File-Path, Module-CoreList, and Archive-Tar but there are only virtual packages with the required versions. Virtual packages are just meta-packages and they do not install any module. First, what are the virtual/[perl-module] and perl-core/[perl-module]:

  • perl-core/[perl-module] – perl independent modules. In fact, the same module may be independent and it may be part of the build-in packages from the Perl main package – dev-lang/perl. Sometimes you may choose the independent package, because of a newer version than the version included in the dev-lang/perl package.
  • virtual/[perl-module] – perl meta-package, which ensures the installation of the module. The module could be an independent package from above or module, which is included in the main Perl package (in dev-lang/perl)

To solve the blocks of this kind “perl-core/ is blocking virtual/perl-” you must check for a newer version of perl-core/* if there is no newer version, just to remove the package and let the setup (emerge) use the module included in dev-lang/perl.

In our case, there are no newer versions of the three packages and we remove them with:

emerge -Cv perl-core/File-Path perl-core/Module-CoreList perl-core/Archive-Tar

And then emerge with no problems the new version of Perl with:

emerge --verbose --verbose-conflicts --backtrack=200000 $(qlist -IC|grep perl|sort|uniq) media-gfx/inkscape media-gfx/imagemagick dev-php/pecl-imagick

For detail explaination of why we use verbose-conflicts, backtrack, qlist and three excplicitly added packages you may read our article on similar subject – Gentoo updating perl with many masked and blocked packages
You may read the offcial documentation for more information – https://wiki.gentoo.org/wiki/Perl#Introduction

Updating our Perl from dev-lang/perl-5.26.2:0 to dev-lang/perl-5.30.0:0/5.30

Keep on reading!

emerge – ERROR: 17.1 migration has not been performed – upgrade from 13 to 17.1

When upgrading to 17.1 profile you need to perform additional steps to get to a healthy Gentoo portage system using profile 17.1.
Here what we stumbled when we tried to upgrade from 13 to 17.1:

>>> Emerging (1 of 3) dev-libs/elfutils-0.177::gentoo
 * Fetching files in the background.
 * To view fetch progress, run in another terminal:
 * tail -f /var/log/emerge-fetch.log
 * elfutils-0.177.tar.bz2 BLAKE2B SHA512 size ;-) ...                                                                                                                [ ok ]
 * Please follow the instructions in the news item:
 * 2019-06-05-amd64-17-1-profiles-are-now-stable
 * or choose the 17.0 profile.
 * ERROR: dev-libs/elfutils-0.177::gentoo failed (setup phase):
 *   ERROR: 17.1 migration has not been performed!!
 * 
 * Call stack:
 *        ebuild.sh, line 591:  Called __source_all_bashrcs
 *        ebuild.sh, line 410:  Called __try_source '/usr/portage/profiles/default/linux/amd64/17.1/profile.bashrc'
 *        ebuild.sh, line 467:  Called __qa_source '/usr/portage/profiles/default/linux/amd64/17.1/profile.bashrc'
 *        ebuild.sh, line 112:  Called source '/usr/portage/profiles/default/linux/amd64/17.1/profile.bashrc'
 *   profile.bashrc, line   6:  Called die
 * The specific snippet of code:
 *              die "ERROR: 17.1 migration has not been performed!!"
 * 
 * If you need support, post the output of `emerge --info '=dev-libs/elfutils-0.177::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-libs/elfutils-0.177::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/dev-libs/elfutils-0.177/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-libs/elfutils-0.177/temp/die.env'.
 * Working directory: '/var/tmp/portage/dev-libs/elfutils-0.177/homedir'
 * S: '/var/tmp/portage/dev-libs/elfutils-0.177/work/elfutils-0.177'

As you can see there is news, which consists of 12 steps to perform a successful upgrade to profile 17.1.
You can read the news with (the news output is included at the end of this article, just for completeness):

eselect news read 28

Specific note for our upgrade – in fact, our Gentoo installation was a chroot and it had not been updated for three years. The profile was 13.0 and portage supported only EAPI 5, which is a real problem. The new portage tree (we installed the latest) has no profile 13.0 and our emerge was half broken. We have preliminary steps described in Failed to install sys-apps/portage – Called pkg_preinst – portage._compat_upgrade.default_locations

Because we upgrade from 13.0 to 17.1, first, we need to perform the 17.0 upgrade (check the original steps here – https://gentoo.org/support/news-items/2017-11-30-new-17-profiles.html)

STEP 1) Select the previous profile 17.0 temporarily.

srv ~ # eselect profile set default/linux/amd64/17.0

You won’t be able to build any GNU GCC and you cannot continue with the next step.

STEP 2) Upgrade to GNU GCC 6.4.0 or later.

Our current GNU GCC is really old – 4.9.3. The latest version is gcc-9.2.0-r1 and we are going to use it.
Keep on reading!

Failed to install sys-apps/portage – Called pkg_preinst – portage._compat_upgrade.default_locations

Recently there was a problem with one compute node servers, which Gentoo (in fact, the chroot environment had not been updated for 3 years) could not emerge the new portage because it kept failing in the pkg_preinst with:

srv ~ # USE="-rsync-verify" emerge -va '=sys-apps/portage-2.3.76::gentoo'
.....
.....
>>> Installing (1 of 1) sys-apps/portage-2.3.76::gentoo
 * checking 1999 files for package collisions
1000 files checked ...
^[[B>>> Merging sys-apps/portage-2.3.76 to /
/usr/bin/python2.7: No module named _compat_upgrade
 * ERROR: sys-apps/portage-2.3.76::gentoo failed (preinst phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line 133:  Called pkg_preinst
 *   environment, line 3238:  Called die
 * The specific snippet of code:
 *       env -u DISTDIR -u PORTAGE_OVERRIDE_EPREFIX -u PORTAGE_REPOSITORIES -u PORTDIR -u PORTDIR_OVERLAY PYTHONPATH="${D%/}${PYTHON_SITEDIR}${PYTHONPATH:+:${PYTHONPATH}}" "${PYTHON}" -m portage._compat_upgrade.default_locations || die;
 * 
 * If you need support, post the output of `emerge --info '=sys-apps/portage-2.3.76::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-apps/portage-2.3.76::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-apps/portage-2.3.76/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-apps/portage-2.3.76/temp/environment'.
 * Working directory: '/var/tmp/portage/._portage_reinstall_.RKkxLW/pym'
 * S: '/var/tmp/portage/sys-apps/portage-2.3.76/work/portage-2.3.76'
!!! FAILED preinst: 1

>>> Failed to install sys-apps/portage-2.3.76, Log file:

>>>  '/var/tmp/portage/sys-apps/portage-2.3.76/temp/build.log'

Note this is the installation phase, where everything from the build process passes smoothly, but it fails to install it with some vague error of a dying line with a couple of python and portage environments. The problem is the current portage does not support EAPI 6 and 7 and some packages were unable to be installed!

And we fixed the issue by just using the method described in our previous article – Fix your broken or old portage in Gentoo, fix the emerge command
Cloning a new portage software and using it to emerge (install) a newer (or reinstall the current) portage in the system to fix the system’s portage and the emerge command:

cd /root
git clone https://anongit.gentoo.org/git/proj/portage.git
/root/portage/bin/emerge --sync
eselect profile set default/linux/amd64/17.1
/root/portage/bin/emerge -v portage

Now the latest and stable Gentoo profile is 17.1, so we set it to be sure we use it (in future this may change).
Keep on reading!

Fix your broken or old portage in Gentoo, fix the emerge command

Using Gentoo for servers and chroots it might happen to deal with old and not regularly updated Gentoo environment, which in some cases is completely non-updatable using the regular process with emerge command. And no emerge means no installs from the Gentoo packaging system. Or you maybe have a broken portage after failed update with missing emerge command or missing or broken portage modules

In general, this article is for those, who cannot update their “sys-apps/portage” or even the emerge command exits with errors and is of no use.

In cases such as:

  • Missing portage files (broken portage)
  • Broken emerge command (broken portage)
  • no update of new portage is possible – very very old portage, which does not support EAPI of all current “sys-apps/portage” (now is EAPI=5) and you do not have old portage ebuild files
  • Easy update the portage to the newest in an old Gentoo system.

A real world errors are included at the bottom for each case above.

You need just a working python 2.7.x and git to clone “https://anongit.gentoo.org/git/proj/portage.git” or at least some tool to download the portage package.

Unpack to a globally accessible directory, DO NOT USE “/root“, because emerge changes user to non-privileges and needs execute permission for other for the all the path to the directory of emerge. Look below for more details.

Our example is to repair a completely broken portage with error:

srv ~ # emerge -va portage
Traceback (most recent call last):
  File "/usr/lib/python-exec/python2.7/emerge", line 42, in <module>
    import portage
ImportError: No module named portage

STEP 1) Clone the portage package from the git or download the portage tarball.

If you do not have a git client you can always check the URL in the sys-app/portage ebuild and download the URL. Still, if you cannot find the tarball’s URL, you can just simply get a mirror such as https://mirror.leaseweb.com/gentoo/distfiles, wait for the loading of the page (12Mbytes, it’s huge, all Gentoo tarball files’ names are here) and grep in it by the name “portage”. Or you can check here https://dev.gentoo.org/~zmedico/portage/archives/. Download the latest tarball and unpack it in the /opt directory.
Using git is the easiest method, but it is the same with downloading and unpacking the tarball in the “/opt”.

srv opt # git clone https://anongit.gentoo.org/git/proj/portage.git
Cloning into 'portage'...
remote: Enumerating objects: 151654, done.
remote: Counting objects: 100% (151654/151654), done.
remote: Compressing objects: 100% (39915/39915), done.
remote: Total 151654 (delta 112542), reused 149864 (delta 111349)
Receiving objects: 100% (151654/151654), 22.38 MiB | 550.00 KiB/s, done.
Resolving deltas: 100% (112542/112542), done.
srv opt # cd portage/
srv portage # ls -al
total 232
drwxr-xr-x. 11 root root  4096 Oct  6 04:52 .
drwx------.  4 root root  4096 Oct  6 04:51 ..
drwxr-xr-x.  6 root root  4096 Oct  6 04:52 bin
drwxr-xr-x.  5 root root  4096 Oct  6 04:52 cnf
-rw-r--r--.  1 root root  1840 Oct  6 04:52 COPYING
-rw-r--r--.  1 root root  6646 Oct  6 04:52 DEVELOPING
drwxr-xr-x.  5 root root  4096 Oct  6 04:52 doc
-rw-r--r--.  1 root root   200 Oct  6 04:52 .editorconfig
drwxr-xr-x.  7 root root  4096 Oct  6 04:52 .git
-rw-r--r--.  1 root root    80 Oct  6 04:52 .gitignore
drwxr-xr-x.  4 root root  4096 Oct  6 04:52 lib
-rw-r--r--.  1 root root 18092 Oct  6 04:52 LICENSE
-rwxr-xr-x.  1 root root  1272 Oct  6 04:52 make.conf.example-repatch.sh
drwxr-xr-x.  3 root root  4096 Oct  6 04:52 man
-rw-r--r--.  1 root root   290 Oct  6 04:52 MANIFEST.in
drwxr-xr-x.  2 root root  4096 Oct  6 04:52 misc
-rw-r--r--.  1 root root 17845 Oct  6 04:52 NEWS
-rw-r--r--.  1 root root     0 Oct  6 04:52 .portage_not_installed
-rw-r--r--.  1 root root  2246 Oct  6 04:52 README
-rw-r--r--.  1 root root 68122 Oct  6 04:52 RELEASE-NOTES
drwxr-xr-x.  6 root root  4096 Oct  6 04:52 repoman
-rwxr-xr-x.  1 root root  4889 Oct  6 04:52 runtests
-rwxr-xr-x.  1 root root 19743 Oct  6 04:52 setup.py
drwxr-xr-x.  2 root root  4096 Oct  6 04:52 src
-rwxr-xr-x.  1 root root    81 Oct  6 04:52 tabcheck.py
-rw-r--r--.  1 root root  1864 Oct  6 04:52 TEST-NOTES
-rw-r--r--.  1 root root   571 Oct  6 04:52 testpath
-rw-r--r--.  1 root root   348 Oct  6 04:52 tox.ini
-rw-r--r--.  1 root root   584 Oct  6 04:52 .travis.yml

This is the latest portage with working emerge command in the bin sub-directory.
Keep on reading!