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jody
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Posts: 543
Location: Switzerland

PostPosted: Tue Jan 14, 2020 10:23 am    Post subject: Slot conflicts for perl, icu and qt, and no ebuild for vtk Reply with quote

When, after a sync, i run 'emerge --ask --update --newuse --deep @world', i get slot conflicts for perl, icu, python-exec, xorg-server, and several qt ebuilds, as well as an error referring to vtk:
Code:
  $ sudo emerge --ask --update --newuse --deep  @world

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

Calculating dependencies... done!

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:

dev-lang/perl:0

  (dev-lang/perl-5.30.1:0/5.30::gentoo, ebuild scheduled for merge) pulled in by
    (no parents that aren't satisfied by other packages in this slot)

  (dev-lang/perl-5.28.2-r1:0/5.28::gentoo, installed) pulled in by
    dev-lang/perl:0/5.28= required by (dev-perl/URI-1.730.0:0/0::gentoo, installed)
                 ^^^^^^^^                                                                                             
    (and 47 more with the same problem)

dev-libs/icu:0

  (dev-libs/icu-65.1:0/65.1::gentoo, ebuild scheduled for merge) pulled in by
    (no parents that aren't satisfied by other packages in this slot)

  (dev-libs/icu-64.2:0/64.2::gentoo, installed) pulled in by
    dev-libs/icu:0/64.2=[abi_x86_64(-)] required by (dev-libs/re2-0.2018.10.01:0/gentoo-2017-03-01::gentoo, installed)
                ^^^^^^^^                                                                                                                                 
    dev-libs/icu:0/64.2 required by (app-office/libreoffice-bin-6.2.8.2:0/0::gentoo, ebuild scheduled for merge)
                ^^^^^^^                                                                                                                             
    (and 13 more with the same problems)

dev-lang/python-exec:2

  (dev-lang/python-exec-2.4.6-r1:2/2::gentoo, ebuild scheduled for merge) pulled in by
    (no parents that aren't satisfied by other packages in this slot)

  (dev-lang/python-exec-2.4.6-r1:2/2::gentoo, installed) pulled in by
    >=dev-lang/python-exec-2:2/2=[python_targets_python2_7(-),python_targets_python3_5(-),python_targets_python3_6(-),-python_single_target_python2_7(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] required by (dev-python/netcdf4-python-1.2.2:0/0::gentoo, installed)
                                                                                                                                                                                                                                                                                                                     

x11-base/xorg-server:0

  (x11-base/xorg-server-1.20.6:0/1.20.6::gentoo, ebuild scheduled for merge) pulled in by
    (no parents that aren't satisfied by other packages in this slot)

  (x11-base/xorg-server-1.20.5:0/1.20.5::gentoo, installed) pulled in by
    x11-base/xorg-server:0/1.20.5= required by (x11-drivers/xf86-input-evdev-2.10.6:0/0::gentoo, installed)
                        ^^^^^^^^^^                                                                                                             

dev-qt/qtcore:5

  (dev-qt/qtcore-5.13.2-r1:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtcore-5.13.2 required by (dev-qt/qtsensors-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^              ^^^^^^                                                                                                                                       
    (and 18 more with the same problem)

  (dev-qt/qtcore-5.12.5-r1:5/5.12::gentoo, installed) pulled in by
    dev-qt/qtcore:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                 ^^^^^^^^                                                                                                         
    ~dev-qt/qtcore-5.12.5 required by (dev-qt/qtdbus-5.12.5:5/5.12::gentoo, installed)
    ^              ^^^^^^                                                                                                                   
    (and 5 more with the same problems)

dev-qt/qtgui:5

  (dev-qt/qtgui-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtgui-5.13.2[gles2=] required by (dev-qt/qtopengl-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^             ^^^^^^                                                                                                                                               
    (and 6 more with the same problem)

  (dev-qt/qtgui-5.12.5:5/5.12::gentoo, installed) pulled in by
    ~dev-qt/qtgui-5.12.5 required by (dev-qt/qtsvg-5.12.5:5/5.12::gentoo, installed)
    ^             ^^^^^^                                                                                                                   
    dev-qt/qtgui:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                ^^^^^^^^                                                                                                         
    (and 3 more with the same problems)

dev-qt/qtnetwork:5

  (dev-qt/qtnetwork-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtnetwork-5.13.2 required by (dev-qt/qtxmlpatterns-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^                 ^^^^^^                                                                                                                                           
    (and 3 more with the same problem)

  (dev-qt/qtnetwork-5.12.5:5/5.12::gentoo, installed) pulled in by
    dev-qt/qtnetwork:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                    ^^^^^^^^                                                                                                         

dev-qt/qtprintsupport:5

  (dev-qt/qtprintsupport-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtprintsupport-5.13.2 required by (dev-qt/qtwebengine-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^                      ^^^^^^                                                                                                                                         

  (dev-qt/qtprintsupport-5.12.5:5/5.12::gentoo, installed) pulled in by
    dev-qt/qtprintsupport:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                         ^^^^^^^^                                                                                                         

dev-qt/qtsvg:5

  (dev-qt/qtsvg-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    (no parents that aren't satisfied by other packages in this slot)

  (dev-qt/qtsvg-5.12.5:5/5.12::gentoo, installed) pulled in by
    dev-qt/qtsvg:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                ^^^^^^^^                                                                                                         

dev-qt/qtwidgets:5

  (dev-qt/qtwidgets-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtwidgets-5.13.2[gles2=] required by (dev-qt/qtopengl-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^                 ^^^^^^                                                                                                                                               
    (and 4 more with the same problem)

  (dev-qt/qtwidgets-5.12.5-r1:5/5.12::gentoo, installed) pulled in by
    ~dev-qt/qtwidgets-5.12.5 required by (dev-qt/qtsvg-5.12.5:5/5.12::gentoo, installed)
    ^                 ^^^^^^                                                                                                                   
    dev-qt/qtwidgets:5/5.12= required by (sci-visualization/gnuplot-5.2.7:0/0::gentoo, installed)
                    ^^^^^^^^                                                                                                         
    (and 1 more with the same problems)

dev-qt/qtdbus:5

  (dev-qt/qtdbus-5.13.2:5/5.13::gentoo, ebuild scheduled for merge) pulled in by
    ~dev-qt/qtdbus-5.13.2 required by (dev-qt/qtsensors-5.13.2:5/5.13::gentoo, ebuild scheduled for merge)
    ^              ^^^^^^                                                                                                                                       
    (and 2 more with the same problem)

  (dev-qt/qtdbus-5.12.5:5/5.12::gentoo, installed) pulled in by
    ~dev-qt/qtdbus-5.12.5 required by (dev-qt/qtgui-5.12.5:5/5.12::gentoo, installed)
    ^              ^^^^^^                                                                                                                   

NOTE: Use the '--verbose-conflicts' option to display parents omitted above

It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.


emerge: there are no ebuilds to satisfy "=sci-libs/vtk-6.1.0*[imaging,-mpi,python,rendering,qt5,python_targets_python2_7(-),-python_single_target_jython2_7(-),-python_single_target_pypy(-),-python_single_target_pypy3(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-),-python_single_target_python3_7(-),python_single_target_python2_7(+)]".
(dependency required by "sci-visualization/visit-2.12.3-r1::gentoo" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])


The required ebuilds for sci-libs/vtk are masked
Code:
    Available versions:  (~)6.1.0-r4^t ~8.1.0-r3^t {R +X all-modules aqua boost cg doc examples ffmpeg gdal imaging java json kaapi mpi mysql odbc offscreen postgres python qt5 rendering smp tbb tcl test theora tk views web xdmf2 ELIBC="FreeBSD" PYTHON_SINGLE_TARGET="python2_7 python3_5 python3_6" PYTHON_TARGETS="python2_7 python3_5 python3_6" VIDEO_CARDS="nvidia"}
but i have unmasked vtk with the line
Code:
=sci-libs/vtk-6.1.0-r4
so i don't understand why i get the error message.

I can mask perl and icu:
Code:
>dev-lang/perl-5.28.2-r1
>dev-libs/icu-64.2
without new error messages (and no messages for python-exec and xorg-server).

But it looks like i can't mask the mentioned qt ebuilds without running into a different problem:
Code:
 $ sudo emerge --ask --update --newuse --deep  @world

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

Calculating dependencies... done!

!!! All ebuilds that could satisfy "~dev-qt/qtcore-5.13.2" have been masked.
!!! One of the following masked packages is required to complete your request:
- dev-qt/qtcore-5.13.2-r1::gentoo (masked by: package.mask)

(dependency required by "dev-qt/qtsvg-5.13.2::gentoo" [ebuild])
(dependency required by "dev-python/PyQt5-5.13.2::gentoo[svg]" [ebuild])
(dependency required by "dev-python/matplotlib-2.2.2-r1::gentoo[qt5]" [ebuild])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])
For more information, see the MASKED PACKAGES section in the emerge
man page or refer to the Gentoo Handbook.


What steps can i take to make emerge --ask --update --newuse --deep @world work properly?
And what do i have to do to make vtk emergeable?
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charles17
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Joined: 02 Mar 2008
Posts: 2901

PostPosted: Tue Jan 14, 2020 10:58 am    Post subject: Reply with quote

jody wrote:
What steps can i take to make emerge --ask --update --newuse --deep @world work properly?

Replace --newuse with --changed-use and add --with-bdeps=y --complete-graph.
And ensure to have your world file cleaned, see https://wiki.gentoo.org/wiki/Selected-packages_set_%28Portage%29#Keeping_the_world_file_clean

For vtk: emerge --autounmask -pvt sci-libs/vtk
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asturm
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Posts: 7331
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PostPosted: Tue Jan 14, 2020 12:40 pm    Post subject: Reply with quote

Masking solves no problems. Old vtk is simply gone. visit is also gone.
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ulenrich
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Joined: 10 Oct 2010
Posts: 1405

PostPosted: Tue Jan 14, 2020 1:40 pm    Post subject: Reply with quote

@Jody , a lot issues for you now:

1)dev-libs/icu-65.1
isn't working yet with libreoffice-bin, despite it is stable

2) all of
dev-qt/* ~unstable OR stable
(if you have libressl you have to use one unstable qt ebuild from the libressl overlay)

3)python2 - your serious challenge here - is dying now. Try to disable python2 where ever you can, even when you loose calibre (paid by an agency to become exploitable). I only need python2 for:
Code:
# emerge -cpv =dev-lang/python-2.7.17-r1

Calculating dependencies  ....... done!
  dev-lang/python-2.7.17-r1 pulled in by:
    dev-lang/spidermonkey-60.5.2_p0-r2 requires >=dev-lang/python-2.7.5-r2:2.7
    dev-qt/qtwebengine-5.13.2 requires >=dev-lang/python-2.7.5-r2:2.7
    media-libs/clutter-gst-3.0.27 requires >=dev-lang/python-2.7.5-r2:2.7
Make shure you have at least one python3 (python3.8 not works for all yet).

4)perl
try to purge with brute force dev-perl modules which offend you (you'll get them back automatically)

Only mask:
>dev-libs/icu-65
>dev-lang/python-3.8

EDIT: asturm corrected me on icu


Last edited by ulenrich on Tue Jan 14, 2020 2:31 pm; edited 3 times in total
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asturm
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PostPosted: Tue Jan 14, 2020 2:13 pm    Post subject: Reply with quote

ulenrich wrote:
1)dev-libs/icu-65.1
isn't working yet with quiet a lot, despite it is stable
I have never experienced such with any stable before - special icu - but not so important

BS, libreoffice-bin is the only package relevant there, not a single bug otherwise.
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pourpier
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Joined: 27 Sep 2017
Posts: 148

PostPosted: Tue Jan 14, 2020 8:19 pm    Post subject: Reply with quote

asturm wrote:
ulenrich wrote:
1)dev-libs/icu-65.1
isn't working yet with quiet a lot, despite it is stable
I have never experienced such with any stable before - special icu - but not so important

BS, libreoffice-bin is the only package relevant there, not a single bug otherwise.


Could it be possible to create a package like the icu4c-compat of Alien Bob? http://www.slackware.com/~alien/slackbuilds/icu4c-compat/pkg64/current/
Whenever icu gets an upgrade Alien Bob updates that package so that LibreOffice is not broken.
I was obliged to mask dev-libs/icu to keep libreoffice-bin-6.2.8.2
I would have thought the new version 6.3.4.2 of libreoffice-bin would have solved this but unfortunately it still depends on dev-libs/icu-64.2 and this is quite annoying!
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asturm
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PostPosted: Tue Jan 14, 2020 8:20 pm    Post subject: Reply with quote

No it is not possible.

There is no libreoffice-bin-6.3.4.2.
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pourpier
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PostPosted: Tue Jan 14, 2020 8:37 pm    Post subject: Reply with quote

asturm wrote:
No it is not possible.

There is no libreoffice-bin-6.3.4.2.


Here eix libreoffice-bin
Code:
[I] app-office/libreoffice-bin
     Available versions:  6.2.8.2^st ~6.3.4.2^st {gnome java kde ELIBC="FreeBSD" PYTHON_SINGLE_TARGET="+python3_6" PYTHON_TARGETS="+python3_6"}
     Installed versions:  6.2.8.2^st(14:01:45 08/12/19)(java -gnome -kde ELIBC="-FreeBSD" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python3_6")
     Homepage:            https://www.libreoffice.org
     Description:         A full office productivity suite. Binary package


[Moderator edit: added [code] tags to preserve output layout. -Hu]
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asturm
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PostPosted: Tue Jan 14, 2020 9:08 pm    Post subject: Reply with quote

Oh, this just appeared on latest sync. Yes that is a mistake.
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jody
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PostPosted: Wed Jan 15, 2020 9:50 am    Post subject: Reply with quote

Following charles17's suggestions i cleaned my world file a little bit and ran the command
Code:
 $ sudo emerge --ask --update --changed-use --with-bdeps=y --complete-graph  --deep  @world
which ran through without any complaints (all perl an qt issues disappeared). When i ran the command again (after masking icu-65), i got the following:
Code:
WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:

dev-lang/python-exec:2

  (dev-lang/python-exec-2.4.6-r1:2/2::gentoo, ebuild scheduled for merge) conflicts with
    >=dev-lang/python-exec-2:2/2=[python_targets_python2_7(-),python_targets_python3_5(-),python_targets_python3_6(-),-python_single_target_python2_7(-),-python_single_target_python3_5(-),-python_single_target_python3_6(-)] required by (dev-python/netcdf4-python-1.2.2:0/0::gentoo, installed)

!!! Problems have been detected with your world file
!!! Please run emaint --check world

The suggested 'emaint' command didn't report anything.

@ulenrich:
Quote:
3)python2 - your serious challenge here - is dying now. Try to disable python2 where ever you can, even when you loose calibre (paid by an agency to become exploitable).

Looking at the dependencies on python 2.7 i see mostly other python 2.7 modules, but also some packages i do want to keep, for instance inkscape, scipy, revelation.
When i look at these packages with eix they mostly seem to allow python 3, for example inkscape:
Code:
 $ eix inkscape
[I] media-gfx/inkscape
     Available versions:  0.92.4^t ~1.0_beta2^t **9999*l^t {cdr dbus dia exif gnome graphicsmagick imagemagick inkjar jemalloc jpeg latex lcms nls openmp postscript spell static-libs svg2 visio wpg PYTHON_SINGLE_TARGET="+python2_7 python3_6 python3_7" PYTHON_TARGETS="+python2_7 python3_6 python3_7"}
     Installed versions:  0.92.4^t(10:04:44 PM 01/02/2020)(cdr dbus exif jpeg lcms nls openmp spell -dia -gnome -imagemagick -inkjar -latex -postscript -static-libs -visio -wpg PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7")
     Homepage:            https://inkscape.org/
     Description:         SVG based generic vector-drawing program

How can i force these packages to use python 3.6?

@asturm: do you know why visit has been removed from portage?
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fedeliallalinea
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PostPosted: Wed Jan 15, 2020 10:06 am    Post subject: Reply with quote

jody wrote:
When i look at these packages with eix they mostly seem to allow python 3, for example inkscape:
Code:
 $ eix inkscape
[I] media-gfx/inkscape
     Available versions:  0.92.4^t ~1.0_beta2^t **9999*l^t {cdr dbus dia exif gnome graphicsmagick imagemagick inkjar jemalloc jpeg latex lcms nls openmp postscript spell static-libs svg2 visio wpg PYTHON_SINGLE_TARGET="+python2_7 python3_6 python3_7" PYTHON_TARGETS="+python2_7 python3_6 python3_7"}
     Installed versions:  0.92.4^t(10:04:44 PM 01/02/2020)(cdr dbus exif jpeg lcms nls openmp spell -dia -gnome -imagemagick -inkjar -latex -postscript -static-libs -visio -wpg PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7")
     Homepage:            https://inkscape.org/
     Description:         SVG based generic vector-drawing program

How can i force these packages to use python 3.6?

You can't force python3_6 for version 0.92.4 because use flag not exists, for use inkscape with python3 support you should unmask 1.0_beta2.
Eix output show all merged use flags available, this means that a use flag can be present in a specific version only
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charles17
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Joined: 02 Mar 2008
Posts: 2901

PostPosted: Wed Jan 15, 2020 11:26 am    Post subject: Reply with quote

jody wrote:
Following charles17's suggestions i cleaned my world file a little bit and ran the command
Code:
 $ sudo emerge --ask --update --changed-use --with-bdeps=y --complete-graph  --deep  @world
which ran through without any complaints (all perl an qt issues disappeared). When i ran the command again (after masking icu-65), i got the following:

<EDIT>
   For icu-65 see https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fc70a4c39488da
</EDIT>

jody wrote:
@ulenrich:
Quote:
3)python2 - your serious challenge here - is dying now. Try to disable python2 where ever you can, even when you loose calibre (paid by an agency to become exploitable).

Looking at the dependencies on python 2.7 i see mostly other python 2.7 modules, but also some packages i do want to keep, for instance inkscape, scipy, revelation.
When i look at these packages with eix they mostly seem to allow python 3, for example inkscape:
Code:
 $ eix inkscape
[I] media-gfx/inkscape
     Available versions:  0.92.4^t ~1.0_beta2^t **9999*l^t {cdr dbus dia exif gnome graphicsmagick imagemagick inkjar jemalloc jpeg latex lcms nls openmp postscript spell static-libs svg2 visio wpg PYTHON_SINGLE_TARGET="+python2_7 python3_6 python3_7" PYTHON_TARGETS="+python2_7 python3_6 python3_7"}
     Installed versions:  0.92.4^t(10:04:44 PM 01/02/2020)(cdr dbus exif jpeg lcms nls openmp spell -dia -gnome -imagemagick -inkjar -latex -postscript -static-libs -visio -wpg PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7")
     Homepage:            https://inkscape.org/
     Description:         SVG based generic vector-drawing program

How can i force these packages to use python 3.6?

For inkscape see bug 696794


Last edited by charles17 on Wed Jan 15, 2020 1:17 pm; edited 1 time in total
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asturm
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Joined: 05 Apr 2007
Posts: 7331
Location: Austria

PostPosted: Wed Jan 15, 2020 11:40 am    Post subject: Reply with quote

jody wrote:
@asturm: do you know why visit has been removed from portage?

Yes, I removed it. No bump in a long time, no maintainer, a horrible build system, single-handedly blocking old vtk-6 cleanup (which had a load of unfixed bugs), which itself was unable to build already.
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