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nelsonwcf Tux's lil' helper
Joined: 31 Oct 2012 Posts: 112
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Posted: Thu Jul 21, 2016 1:54 am Post subject: Lots of issues after emerging testing R package: |
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Hi guys,
Since I've tried to emerge the latest version of R package, my system go all messed up and I don't know how fix many of the conflicts that started to appear in portage. I returned the previous settings to packages.{keywords, accept_keywords, use} but even so I can't seem find a way to fix the conflicts.
Can someone help me fix my portage build?
Code: | Calculating dependencies ..... done!
[ebuild R ] x11-libs/libX11-1.6.3 ABI_X86="32*"
WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:
x11-proto/inputproto:0
(x11-proto/inputproto-2.3.1:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/inputproto-2.3[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
x11-libs/libXdmcp:0
(x11-libs/libXdmcp-1.1.2:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libXdmcp-1.1.1-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
net-fs/samba:0
(net-fs/samba-4.2.11:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=net-fs/samba-4.0.0_alpha1[client] required by (kde-apps/kio-extras-15.12.3:5/5::gentoo, installed)
^^^^^^
>=net-fs/samba-4.0.0_alpha1:0[client] required by (media-video/vlc-2.2.1-r1:0/5-8::gentoo, installed)
^^^^^^
x11-proto/xextproto:0
(x11-proto/xextproto-7.3.0:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xextproto-7.2.1-r1:0/0=[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXext-1.3.3:0/0::gentoo, installed)
>=x11-proto/xextproto-7.2.1-r1:=[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXext-1.3.3:0/0::gentoo, installed)
>=x11-proto/xextproto-7.2.1-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
x11-libs/libXext:0
(x11-libs/libXext-1.3.3:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libXext-1.3.2[abi_x86_32] required by (x11-drivers/nvidia-drivers-361.28:0/361::gentoo, installed)
^^^^^^^^^^
x11-proto/xproto:0
(x11-proto/xproto-7.0.28:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xproto-7.0.24[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXau-1.0.8:0/0::gentoo, installed)
>=x11-proto/xproto-7.0.24[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
x11-proto/kbproto:0
(x11-proto/kbproto-1.0.7:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/kbproto-1.0.6-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
dev-libs/libpthread-stubs:0
(dev-libs/libpthread-stubs-0.3-r1:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=dev-libs/libpthread-stubs-0.3-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
x11-proto/xf86bigfontproto:0
(x11-proto/xf86bigfontproto-1.2.0-r1:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xf86bigfontproto-1.2.0-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
sys-libs/tevent:0
(sys-libs/tevent-0.9.28:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=sys-libs/tevent-0.9.27[python(+),abi_x86_64(-)] required by (sys-libs/ldb-1.1.26:0/1.1.26::gentoo, installed)
x11-proto/xcb-proto:0
(x11-proto/xcb-proto-1.11:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xcb-proto-1.11[abi_x86_32(-),abi_x86_64(-),python_targets_python3_4(-),python_single_target_python3_4(+)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
x11-libs/libxcb:0
(x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libxcb-1.9.3[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, ebuild scheduled for merge)
x11-libs/libXau:0
(x11-libs/libXau-1.0.8:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libXau-1.0.7-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
The following USE changes are necessary to proceed:
(see "package.use" in the portage(5) man page for more details)
# required by x11-libs/libXext-1.3.3::gentoo
# required by www-client/firefox-bin-45.2.0::gentoo
# required by @selected
# required by @world (argument)
>=x11-libs/libX11-1.6.3 abi_x86_32
Use --autounmask-write to write changes to config files (honoring
CONFIG_PROTECT). Carefully examine the list of proposed changes,
paying special attention to mask or keyword changes that may expose
experimental or unstable packages.
emerge: there are no ebuilds built with USE flags to satisfy ">=x11-libs/libX11-1.6.2[abi_x86_32]".
!!! One of the following packages is required to complete your request:
- x11-libs/libX11-1.6.2::gentoo (Change USE: +abi_x86_32)
(dependency required by "x11-drivers/nvidia-drivers-361.28::gentoo[X,multilib]" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument]) |
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DONAHUE Watchman
Joined: 09 Dec 2006 Posts: 7651 Location: Goose Creek SC
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Posted: Thu Jul 21, 2016 1:18 pm Post subject: |
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run eselect news read all
take action as recommended in items:
2015-03-28-true-multilib
2015-10-22-gcc-5-new-c++11-abi
2015-12-16-python-abiflags-rebuild-needed
then, if you haven't, emerge python-updater and perl-cleaner and run python-updater and perl-cleaner all _________________ Defund the FCC. |
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nelsonwcf Tux's lil' helper
Joined: 31 Oct 2012 Posts: 112
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Posted: Fri Jul 22, 2016 1:56 am Post subject: |
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DONAHUE wrote: | run eselect news read all
take action as recommended in items:
2015-03-28-true-multilib
2015-10-22-gcc-5-new-c++11-abi
2015-12-16-python-abiflags-rebuild-needed
then, if you haven't, emerge python-updater and perl-cleaner and run python-updater and perl-cleaner all |
my select news read all returned no messages (I think I purged all messages that I've read last year).
I ran python-updater and perl-cleaner all but nothing changed.
I believe I forgot to tell something: When installing R and R Studio, I've added the ~amd64 flag. During the emerge, one of the packages failed to compile. After that, I removed the ~amd64 flag and re-emerged. This issue started to appear after that. |
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DONAHUE Watchman
Joined: 09 Dec 2006 Posts: 7651 Location: Goose Creek SC
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Posted: Fri Jul 22, 2016 2:49 am Post subject: |
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eselect news read all not select news read all
if you still get no news with eselect, browse to https://www.gentoo.org/support/news-items/
better to leave the global keyword alone and add the defective package to package.mask _________________ Defund the FCC. |
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nelsonwcf Tux's lil' helper
Joined: 31 Oct 2012 Posts: 112
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Posted: Fri Jul 22, 2016 11:03 pm Post subject: |
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Hi,
Well, I followed the advice in the three news, then ran python-updater and perl-cleaner all. However, it didn't solve the problem.
How do I find the defective package? After I ran emerge --depclean once the package failed, it removed it (because the dependent software, R, was never installed) so it is not in the system anymore.
Any other ideas of what may be causing this issue?
Below more information about my system:
Code: | emerge --update --newuse --with-bdeps=y --deeo @world
WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:
x11-proto/inputproto:0
(x11-proto/inputproto-2.3.1:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/inputproto-2.3[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, installed)
x11-proto/xextproto:0
(x11-proto/xextproto-7.3.0:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xextproto-7.2.1-r1:=[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXext-1.3.3:0/0::gentoo, installed)
>=x11-proto/xextproto-7.2.1-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, installed)
>=x11-proto/xextproto-7.2.1-r1:0/0=[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXext-1.3.3:0/0::gentoo, installed)
x11-proto/xproto:0
(x11-proto/xproto-7.0.28:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/xproto-7.0.24[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, installed)
>=x11-proto/xproto-7.0.24[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libXau-1.0.8:0/0::gentoo, installed)
x11-libs/libXau:0
(x11-libs/libXau-1.0.8:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libXau-1.0.7-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
x11-proto/kbproto:0
(x11-proto/kbproto-1.0.7:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-proto/kbproto-1.0.6-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, installed)
x11-libs/libxcb:0
(x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libxcb-1.9.3[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libX11-1.6.3:0/0::gentoo, installed)
x11-libs/libXdmcp:0
(x11-libs/libXdmcp-1.1.2:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=x11-libs/libXdmcp-1.1.1-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
dev-libs/libpthread-stubs:0
(dev-libs/libpthread-stubs-0.3-r1:0/0::gentoo, ebuild scheduled for merge) conflicts with
>=dev-libs/libpthread-stubs-0.3-r1[abi_x86_32(-),abi_x86_64(-)] required by (x11-libs/libxcb-1.11.1:0/1.11.1::gentoo, installed)
>>> Auto-cleaning packages...
>>> No outdated packages were found on your system.
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Below my make.conf:
Code: | # These settings were set by the catalyst build script that automatically
# built this stage.
# Please consult /usr/share/portage/config/make.conf.example for a more
# detailed example.
CFLAGS="-march=native -O2 -pipe"
CXXFLAGS="${CFLAGS}"
MAKEOPTS="-j4"
# WARNING: Changing your CHOST is not something that should be done lightly.
# Please consult http://www.gentoo.org/doc/en/change-chost.xml before changing.
CHOST="x86_64-pc-linux-gnu"
# These are the USE flags that were used in addition to what is provided by the
# profile used for building.
USE="dbus bindist mmx sse sse2 alsa consolekit libinput"
INPUT_DEVICES="libinput"
PORTDIR="/usr/portage"
DISTDIR="${PORTDIR}/distfiles"
PKGDIR="${PORTDIR}/packages"
LINGUAS="en"
VIDEO_CARDS="nvidia" |
package.accept_keywords:
Code: | sys-boot/refind ~amd64 |
package.keywords:
Code: | cross-armv7a-hardfloat-linux-gnueabi/binutils arm -amd64 -~amd64
cross-armv7a-hardfloat-linux-gnueabi/gcc arm -amd64 -~amd64
cross-armv7a-hardfloat-linux-gnueabi/linux-headers arm -amd64 -~amd64
cross-armv7a-hardfloat-linux-gnueabi/glibc arm -amd64 -~amd64
cross-armv7a-hardfloat-linux-gnueabi/gdb arm ~arm -amd64 -~amd64
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package.use:
Code: | cross-armv7a-hardfloat-linux-gnueabi/binutils -selinux -multilib
cross-armv7a-hardfloat-linux-gnueabi/linux-headers -selinux -multilib
cross-armv7a-hardfloat-linux-gnueabi/glibc -selinux -multilib
cross-armv7a-hardfloat-linux-gnueabi/gcc -selinux -boundschecking -d -gcj -gtk -libffi -mudflap -objc -objc++ -objc-gc -multilib
net-misc/iputils -caps -filecaps
dev-python/pyudev pyqt4
sys-boot/refind ~amd64 ext4
# required by x11-drivers/nvidia-drivers-361.28::gentoo[X,multilib]
# required by x11-base/xorg-drivers-1.17::gentoo[video_cards_nvidia]
# required by @selected
# required by @world (argument)
>=x11-libs/libX11-1.6.3 abi_x86_32
# required by x11-drivers/nvidia-drivers-361.28::gentoo[X,multilib]
# required by x11-base/xorg-drivers-1.17::gentoo[video_cards_nvidia]
# required by @selected
# required by @world (argument)
>=x11-libs/libXext-1.3.3 abi_x86_32
# required by sys-libs/ldb-1.1.26::gentoo
# required by net-fs/samba-4.2.11::gentoo
# required by net-libs/libsoup-2.52.2::gentoo[samba]
# required by net-misc/networkmanager-1.0.12-r1::gentoo
# required by kde-frameworks/networkmanager-qt-5.21.0::gentoo
# required by kde-plasma/plasma-workspace-5.5.5-r2::gentoo[geolocation]
# required by kde-plasma/powerdevil-5.5.5::gentoo
# required by kde-plasma/plasma-meta-5.5.5::gentoo
# required by @selected
# required by @world (argument)
>=sys-libs/tevent-0.9.28 python
# required by media-video/vlc-2.2.1-r1::gentoo[samba]
# required by media-libs/phonon-vlc-0.7.2::gentoo
# required by media-libs/phonon-4.7.2::gentoo[vlc]
# required by kde-frameworks/knotifyconfig-5.21.0::gentoo[phonon]
# required by kde-apps/kdenlive-15.12.3::gentoo
# required by kde-apps/kdemultimedia-meta-15.12.3::gentoo
# required by kde-apps/kde-apps-meta-15.12.3-r3::gentoo
# required by @selected
# required by @world (argument)
>=net-fs/samba-4.2.11 client | [/code]
There must be some way to fix this issue without having to reinstall everything.
Also, when I try to uninstall many libs, emerge says that the lib is being used and don't unmerge it. I really don't know how to deal with this problem and reading the portage guides didn't shed light on the subject.
Thank you,
Nelson |
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DONAHUE Watchman
Joined: 09 Dec 2006 Posts: 7651 Location: Goose Creek SC
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Posted: Sat Jul 23, 2016 2:26 am Post subject: |
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if needed, then
Run: Code: | wgetpaste -t -s dpaste -c "emerge --info" | Code: | wgetpaste -t -s dpaste -c "emerge -pv dev-lang/R" | and/or Code: | wgetpaste -t -s dpaste -c "emerge -pvuND world" | Post the url's returned _________________ Defund the FCC. |
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DONAHUE Watchman
Joined: 09 Dec 2006 Posts: 7651 Location: Goose Creek SC
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Posted: Sat Jul 23, 2016 2:39 pm Post subject: |
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try placing in /etc/portage/package.use followed by emerge -avuND world. BTW, the troublemaker appears to be nvidia-drivers. I don't use nvidia-drivers; tried an emerge -pv nvidia-drivers and received a huge number of abi_x86 blockers. added */* abi_x86_32 to /etc/portage/package.use and the mess cleared. _________________ Defund the FCC. |
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Syl20 l33t
Joined: 04 Aug 2005 Posts: 619 Location: France
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Posted: Tue Jul 26, 2016 12:25 pm Post subject: |
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nelsonwcf wrote: | There must be some way to fix this issue without having to reinstall everything. |
Yes. Add this in your package.use file :
Code: | >=x11-proto/inputproto-2.3 abi_x86_32
>=x11-proto/xextproto-7.2.1-r1 abi_x86_32
>=x11-proto/xproto-7.0.24 abi_x86_32
>=x11-libs/libXau-1.0.7-r1 abi_x86_32
>=x11-proto/kbproto-1.0.6-r1 abi_x86_32
>=x11-libs/libxcb-1.9.3 abi_x86_32
>=x11-libs/libXdmcp-1.1.1-r1 abi_x86_32
>=dev-libs/libpthread-stubs-0.3-r1 abi_x86_32 |
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sabayonino Veteran
Joined: 03 Jan 2012 Posts: 1012
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Posted: Tue Jul 26, 2016 6:36 pm Post subject: |
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DONAHUE wrote: | try placing in /etc/portage/package.use followed by emerge -avuND world. BTW, the troublemaker appears to be nvidia-drivers. I don't use nvidia-drivers; tried an emerge -pv nvidia-drivers and received a huge number of abi_x86 blockers. added */* abi_x86_32 to /etc/portage/package.use and the mess cleared. |
can also run
Code: | # emerge dev-lang/R --autounmask-write || etc-update |
(then type -5 to write config file)
and he can compile only packages with "abi_x86_32" flag needed _________________ LRS i586 on G.Drive
LRS x86-64 EFI on MEGA |
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