dependency conflict libxml2, itstool

engineer · May 2, 2019

One or more updates skipped due to dependency conflict:

dev-libs/libxml2-2.9.9-r1 conflicts with dev-util/itstool-2.0.6-r1

This was on 'emerge @system'

Anyone know the steps to resolve?

Tried --backtrack=500 and even removing both. Also tried --emptytree

engineer · May 3, 2019

Without my kernel working properly, I'm having trouble getting the output. Might take a picture of the screen.

But, what I did to try to get a kernel is to run a 'make clean' and 'make', then I was going to just genkernel and avoid the emerge.

But - I get the old: mpihelp_add_1 multiple definitions problem. Didn't this go away about a decade ago? It has something to do with 'extern' vs 'static'. Why is this still happening?!?

engineer · May 4, 2019

OK, got SSH working. Here's the output of emerge @world:

WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:

dev-libs/libxml2:2

  (dev-libs/libxml2-2.9.9-r1:2/2::core-kit, ebuild scheduled for merge) conflicts with
    dev-libs/libxml2[python,python_targets_python2_7(-),python_targets_python3_4(-),python_targets_python3_5(-),python_targets_python3_6(-),-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),python_single_target_python3_6(+)] required by (dev-util/itstool-2.0.6-r1:0/0::core-kit, installed)

engineer · May 4, 2019

[/etc/portage]-> emerge --rage-clean dev-util/itstool dev-libs/libxml2

dev-util/itstool

selected: 2.0.6-r1

protected: none

omitted: none

dev-libs/libxml2

selected: 2.9.8-r1

protected: none

omitted: none

All selected packages: =dev-libs/libxml2-2.9.8-r1 =dev-util/itstool-2.0.6-r1

>>> 'Selected' packages are slated for removal.

>>> 'Protected' and 'omitted' packages will not be removed.

>>> Unmerging (1 of 2) dev-util/itstool-2.0.6-r1...

>>> Unmerging (2 of 2) dev-libs/libxml2-2.9.8-r1...

>>> needed sym /usr/lib64/libxml2.so.2

>>> needed obj /usr/lib64/libxml2.so.2.9.8

* GNU info directory index is up-to-date.

!!! existing preserved libs:

>>> package: dev-libs/libxml2-2.9.8-r1

* - /usr/lib64/libxml2.so.2

* - /usr/lib64/libxml2.so.2.9.8

* used by /usr/bin/bijiben (app-misc/bijiben-3.30.3)

* used by /usr/bin/brasero (app-cdr/brasero-3.12.2-r1)

* used by /usr/bin/csslint-0.6 (dev-libs/libcroco-0.6.12-r1)

* used by 139 other files

Use emerge @preserved-rebuild to rebuild packages using these libraries

engineer · May 4, 2019

I did an emerge --depclean, then an emerge --backtrack=500 @world

>>> Installing (1 of 2) dev-libs/libxml2-2.9.8-r1::core-kit

>>> Emerging (2 of 2) dev-util/itstool-2.0.6-r1::core-kit

* itstool-2.0.6.tar.bz2 BLAKE2B SHA512 size ;-) ... [ ok ]

>>> Unpacking source...

>>> Unpacking itstool-2.0.6.tar.bz2 to /var/tmp/portage/dev-util/itstool-2.0.6-r1/work

>>> Source unpacked in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work

>>> Preparing source in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6 ...

* Fixing shebang in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/setup.py.

* Fixing shebang in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/setup.py.in.

* Fixing shebang in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/itstool.

>>> Source prepared.

>>> Configuring source in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6 ...

./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-silent-rules --docdir=/usr/share/doc/itstool-2.0.6-r1 --htmldir=/usr/share/doc/itstool-2.0.6-r1/html --libdir=/usr/lib64

checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /bin/mkdir -p

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

checking whether make supports nested variables... yes

checking whether /usr/bin/python3.6 version is >= 2.6... yes

checking for /usr/bin/python3.6 version... 3.6

checking for /usr/bin/python3.6 platform... linux

checking for /usr/bin/python3.6 script directory... ${prefix}/lib64/python3.6/site-packages

checking for /usr/bin/python3.6 extension module directory... ${exec_prefix}/lib64/python3.6/site-packages

checking for python module libxml2... found

checking that generated files are newer than configure... done

configure: creating ./config.status

config.status: creating Makefile

config.status: creating itstool

config.status: creating itstool.1

config.status: creating its/Makefile

config.status: creating setup.py

>>> Source configured.

>>> Compiling source in /var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6 ...

make -j5

Making all in its

make[1]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[1]: Nothing to be done for 'all'.

make[1]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[1]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

make[1]: Nothing to be done for 'all-am'.

make[1]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

>>> Source compiled.

>>> Test phase [not enabled]: dev-util/itstool-2.0.6-r1

>>> Install itstool-2.0.6-r1 into /var/tmp/portage/dev-util/itstool-2.0.6-r1/image category dev-util

make -j5 DESTDIR=/var/tmp/portage/dev-util/itstool-2.0.6-r1/image install

Making install in its

make[1]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[2]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[2]: Nothing to be done for 'install-exec-am'.

/bin/mkdir -p '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/share/itstool/its'

/usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c -m 644 docbook.its docbook5.its its.its mallard.its ttml.its xhtml.its '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/share/itstool/its'

make[2]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[1]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6/its'

make[1]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

make[2]: Entering directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

/bin/mkdir -p '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/bin'

/bin/mkdir -p '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/share/man/man1'

/usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c itstool '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/bin'

/usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c -m 644 itstool.1 '/var/tmp/portage/dev-util/itstool-2.0.6-r1/image/usr/share/man/man1'

make[2]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

make[1]: Leaving directory '/var/tmp/portage/dev-util/itstool-2.0.6-r1/work/itstool-2.0.6'

>>> Completed installing itstool-2.0.6-r1 into /var/tmp/portage/dev-util/itstool-2.0.6-r1/image

* Final size of build directory: 680 KiB

* Final size of installed tree: 252 KiB

ecompressdir: bzip2 -9 /usr/share/doc

ecompressdir: bzip2 -9 /usr/share/man

>>> Installing (2 of 2) dev-util/itstool-2.0.6-r1::core-kit

>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

* GNU info directory index is up-to-date.

* After world updates, it is important to remove obsolete packages with

* emerge --depclean. Refer to `man emerge` for more information.

[/usr/src/linux]-> emerge --depclean

* Always study the list of packages to be cleaned for any obvious

* mistakes. Packages that are part of the world set will always

* be kept. They can be manually added to this set with

* `emerge --noreplace <atom>`. Packages that are listed in

* package.provided (see portage(5)) will be removed by

* depclean, even if they are part of the world set.

*

* As a safety measure, depclean will not remove any packages

* unless *all* required dependencies have been resolved. As a

* consequence of this, it often becomes necessary to run

* `emerge --update --newuse --deep @world` prior to depclean.

Calculating dependencies... done!

>>> Calculating removal order...

sys-kernel/debian-sources-lts

selected: 4.9.161_p1

protected: none

omitted: 4.9.168_p1

All selected packages: =sys-kernel/debian-sources-lts-4.9.161_p1

>>> 'Selected' packages are slated for removal.

>>> 'Protected' and 'omitted' packages will not be removed.

>>> Waiting 5 seconds before starting...

>>> (Control-C to abort)...

>>> Unmerging in: 5 4 3 2 1

>>> Unmerging (1 of 1) sys-kernel/debian-sources-lts-4.9.161_p1...

*

* To avoid automounting and auto(un)installing with /boot,

* just export the DONT_MOUNT_BOOT variable.

*

* Your boot partition was detected as being mounted as /boot.

* Files will be installed there for debian-sources-lts to function correctly.

*

Packages installed: 1728

Packages in world: 68

Packages in system: 81

Required packages: 1728

Number removed: 1

* Messages for package sys-kernel/debian-sources-lts-4.9.161_p1:

*

* To avoid automounting and auto(un)installing with /boot,

* just export the DONT_MOUNT_BOOT variable.

*

* GNU info directory index is up-to-date.

[/usr/src/linux]-> emerge @world

Calculating dependencies... done!

WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:

dev-libs/libxml2:2

(dev-libs/libxml2-2.9.9-r1:2/2::core-kit, ebuild scheduled for merge) conflicts with

dev-libs/libxml2[python,python_targets_python2_7(-),python_targets_python3_4(-),python_targets_python3_5(-),python_targets_python3_6(-),-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),python_single_target_python3_6(+)] required by (dev-util/itstool-2.0.6-r1:0/0::core-kit, installed)

>>> Auto-cleaning packages...

>>> No outdated packages were found on your system.

engineer · May 4, 2019

My package.use

[/etc/portage]-> cat package.use

>=app-misc/pax-utils-0.1.10

>=app-text/asciidoc-8.6.10 python_single_target_python2_7 python_targets_python2_7

>=app-text/poppler-0.74.0

>=dev-libs/glib-2.44.0

>=dev-libs/liborcus-0.13

>=dev-libs/xmlsec-1.2.26 nss

>=dev-libs/libxml2-2.9.9-r1

>=dev-util/itstool-2.0.6-r1

>=media-libs/gd-2.2.5-r1 fontconfig

>=media-libs/lensfun-0.2.5

>=media-libs/mlt-6.12.0-r1 sdl frei0r

>=media-video/ffmpeg-3.4.5 sdl

>=sys-boot/grub-2.02-r3 mount

>=virtual/ffmpeg-9-r2 sdl

>=x11-libs/cairo-1.14.12 X

app-office/libreoffice firebird googledrive

kde-apps/kde-apps-meta nls

kde-plasma/plasma-meta gtk kde

media-libs/gegl -amd64 cairo ffmpeg lensfun openexr umfpack v4l vala

sys-devel/gdb

x11-apps/xinit

cardinal · May 5, 2019

python_single_target is a subset of python_targets and requires a matching version of python_targets

itstool python_targets_python3_6 must be enabled for python_single_target_python3_6

rj@funtoo ~ $ emerge -pv itstool

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

Calculating dependencies... done!

[ebuild   R    ] dev-util/itstool-2.0.6-r1::core-kit  PYTHON_SINGLE_TARGET="python3_6 -python2_7 -python3_4 -python3_5 -python3_7" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5 -python3_7" 0 KiB

Total: 1 packages (1 reinstall), Size of downloads: 0 KiB

Reference: https://wiki.gentoo.org/wiki/Project:Python/PYTHON_TARGETS

The PYTHON_SINGLE_TARGET variable is used for packages that are built for a single implementation of choice only. It may contain only a single implementation. Due to technical limitations, the implementation specified as PYTHON_SINGLE_TARGET must also be included in PYTHON_TARGETS for the package in question.

engineer · May 6, 2019

>=app-misc/pax-utils-0.1.10
>=app-text/asciidoc-8.6.10 python_single_target_python2_7 python_targets_python2_7
>=app-text/poppler-0.74.0
>=dev-libs/glib-2.44.0
>=dev-libs/liborcus-0.13
>=dev-libs/xmlsec-1.2.26 nss

>=dev-libs/libxml2-2.9.9-r1 python_single_target_python3_6 python_targets_python3_6
>=dev-util/itstool-2.0.6-r1 python_single_target_python3_6 python_targets_python3_6

>=media-libs/gd-2.2.5-r1 fontconfig
>=media-libs/lensfun-0.2.5
>=media-libs/mlt-6.12.0-r1 sdl frei0r
>=media-video/ffmpeg-3.4.5 sdl
>=sys-boot/grub-2.02-r3 mount
>=virtual/ffmpeg-9-r2 sdl
>=x11-libs/cairo-1.14.12 X
app-office/libreoffice firebird googledrive
kde-apps/kde-apps-meta nls
kde-plasma/plasma-meta gtk kde
media-libs/gegl -amd64 cairo ffmpeg lensfun openexr umfpack v4l vala
sys-devel/gdb
x11-apps/xinit

[/etc/portage]-> emerge @world
Calculating dependencies... done!

WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:

dev-libs/libxml2:2

  (dev-libs/libxml2-2.9.9-r1:2/2::core-kit, ebuild scheduled for merge) conflicts with
    dev-libs/libxml2[python,python_targets_python2_7(-),python_targets_python3_4(-),python_targets_python3_5(-),python_targets_python3_6(-),-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),python_single_target_python3_6(+)] required by (dev-util/itstool-2.0.6-r1:0/0::core-kit, installed)

I put them in package.use, but nothing changes: python_targets_python3_6 is still (-).

How to override?

cardinal · May 6, 2019

Add to package.use

dev-util/itstool PYTHON_TARGETS: -* python3_6 PYTHON_SINGLE_TARGET: -* python3_6
dev-libs/libxml2 PYTHON_TARGETS: -* python3_6

I don't specify >=< and package version when overriding default USE flags in package.use

Reference: https://wiki.gentoo.org/wiki/Project:Python/PYTHON_TARGETS

https://wiki.gentoo.org/wiki/Handbook:Parts/Working/USE

engineer · May 22, 2019

Thanks guys - I've put all three way to override python in my package.use!!

# package.use
#
# three ways to select python version
>=app-text/asciidoc-8.6.10 python_single_target_python2_7 python_targets_python2_7
dev-util/itstool PYTHON_TARGETS: -* python3_6 PYTHON_SINGLE_TARGET: -* python3_6
dev-libs/libxml2 python_targets_python*

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dependency conflict libxml2, itstool

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