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chi86
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PostPosted: Sun Nov 23, 2014 10:46 am    Post subject: emerge of most package fails after I restored a backup Reply with quote

Hi,
I have a problem with my Mathematica (https://forums.gentoo.org/viewtopic-t-997008.html) and for that reason I resored a backup of a version where mathematica stilled worked and now i cant emerge most package due to errors!

I did the backup with: tar -cvpf /backup/fullbackup.tar --directory=/ --exclude=proc --exclude=sys --exclude=dev/pts --exclude=backup --exclude=mnt --exclude=home .

everthing worked fine and it looked good because i could start gentoo/gnome but when I have to emerge something it fails:

Code:
 * Messages for package app-portage/eix-0.30.4:

 * ERROR: app-portage/eix-0.30.4::gentoo failed (configure phase):
 *   econf failed
 *
 * Call stack:
 *          ebuild.sh, line   93:  Called src_configure
 *        environment, line 2010:  Called econf '--without-sqlite' '--without-extra-doc' '--enable-nls' '--disable-separate-tools' '--disable-security' '--disable-optimization' '--disable-strong-security' '--disable-strong-optimization' '--disable-debugging' '--disable-swap-remote' '--without-always-accept-keywords' '--with-dep-default' '--with-zsh-completion' '--with-portage-rootpath=/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.8.3' '--with-eprefix-default=' '--docdir=/usr/share/doc/eix-0.30.4' '--htmldir=/usr/share/doc/eix-0.30.4/html'
 *   phase-helpers.sh, line  584:  Called die
 * The specific snippet of code:
 *            die "econf failed"
 *
 * If you need support, post the output of `emerge --info '=app-portage/eix-0.30.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=app-portage/eix-0.30.4::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/app-portage/eix-0.30.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/app-portage/eix-0.30.4/temp/environment'.
 * Working directory: '/var/tmp/portage/app-portage/eix-0.30.4/work/eix-0.30.4'
 * S: '/var/tmp/portage/app-portage/eix-0.30.4/work/eix-0.30.4'


Code:
 * Messages for package sys-devel/gcc-4.8.3:

 * ERROR: sys-devel/gcc-4.8.3::gentoo failed (compile phase):
 *   emake failed
 *
 * If you need support, post the output of `emerge --info '=sys-devel/gcc-4.8.3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-devel/gcc-4.8.3::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-devel/gcc-4.8.3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-devel/gcc-4.8.3/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-devel/gcc-4.8.3/work/build'
 * S: '/var/tmp/portage/sys-devel/gcc-4.8.3/work/gcc-4.8.3'
 *
 * Please include /var/tmp/portage/sys-devel/gcc-4.8.3/work/gcc-build-logs.tar.bz2 in your bug report.
 *


the packaged that worked where: gentoo-sources and firefox-bin!!

Did I maybe mess something up with the permissions? But I thought by using the -p flag in tar that sould work fine?
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NeddySeagoon
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PostPosted: Sun Nov 23, 2014 12:31 pm    Post subject: Reply with quote

chi86,

Since configue failed we need lo see the configure.log file.
The build log at /var/tmp/portage/app-portage/eix-0.30.4/temp/build.log will tell where it is.

Both files are fairly big. Use a pasebin and post links.
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Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail.
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Hu
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PostPosted: Sun Nov 23, 2014 3:50 pm    Post subject: Reply with quote

How did you restore the backup? Did you wipe out the directories that would be restored prior to unpacking? If not, you may now have orphan files from the pre-restore state.
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chi86
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PostPosted: Sun Nov 23, 2014 7:10 pm    Post subject: Reply with quote

Quote:
Since configue failed we need lo see the configure.log file.


eix:
http://pastebin.com/73d9wYmb

gcc:
http://pastebin.com/HdSqG086

Quote:
How did you restore the backup? Did you wipe out the directories that would be restored prior to unpacking? If not, you may now have orphan files from the pre-restore state.


yes i deleted all directories before I restored the tar!
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NeddySeagoon
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PostPosted: Sun Nov 23, 2014 7:26 pm    Post subject: Reply with quote

chi86,

Code:
checking whether we are cross compiling... configure: error: in `/var/tmp/portage/app-portage/eix-0.30.4/work/eix-0.30.4':
configure: error: cannot run C++ compiled programs.
See `config.log' for more details


Code:
checking how to run the C preprocessor... /lib/cpp
configure: error: in `/var/tmp/portage/sys-devel/gcc-4.8.3/work/build/lto-plugin':
configure: error: C preprocessor "/lib/cpp" fails sanity check
See `config.log' for more details.


C++ is broken it both cases. We need to see the config.log file. The eix one will do, it will be the same cause in both places.
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chi86
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PostPosted: Sun Nov 23, 2014 7:28 pm    Post subject: Reply with quote

eix config.log:

http://pastebin.com/GHVLY2kM
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NeddySeagoon
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PostPosted: Sun Nov 23, 2014 7:35 pm    Post subject: Reply with quote

[chi86,

code]/usr/include/features.h:379:25: fatal error: sys/cdefs.h: No such file or directory
# include <sys/cdefs.h>[/code]

Code:
$ equery b sys/cdefs.h
 * Searching for sys/cdefs.h ...
sys-devel/dev86-0.16.21 (/usr/lib64/bcc/include/sys/cdefs.h)
sys-libs/glibc-2.20 (/usr/include/sys/cdefs.h)


It looks like glibc has a bit missing. You might be abe to build that. I don't think it needs C++
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chi86
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PostPosted: Sun Nov 23, 2014 7:46 pm    Post subject: Reply with quote

No that fails aswell:

Code:
* Messages for package sys-libs/glibc-2.19-r1:

 * Simple build failed ... assuming this is desired #324685
 * Simple build failed ... assuming this is desired #324685
 * ERROR: sys-libs/glibc-2.19-r1::gentoo failed (compile phase):
 *   make nptl for x86 failed
 *
 * Call stack:
 *           ebuild.sh, line   93:  Called src_compile
 *         environment, line 3221:  Called eblit-run 'src_compile'
 *         environment, line  955:  Called eblit-glibc-src_compile
 *   src_compile.eblit, line   23:  Called foreach_abi 'toolchain-glibc_src_compile'
 *        common.eblit, line  326:  Called toolchain-glibc_src_compile
 *   src_compile.eblit, line   12:  Called die
 * The specific snippet of code:
 *            emake -C "$(builddir ${t})" || die "make ${t} for ${ABI} failed"
 *
 * If you need support, post the output of `emerge --info '=sys-libs/glibc-2.19-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.19-r1::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.19-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.19-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-libs/glibc-2.19-r1/work/build-x86-x86_64-pc-linux-gnu-nptl'
 * S: '/var/tmp/portage/sys-libs/glibc-2.19-r1/work/glibc-2.19'



I can post the log file but it is huge ;(
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NeddySeagoon
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PostPosted: Sun Nov 23, 2014 8:03 pm    Post subject: Reply with quote

chi86,

Its a bit longwined but its safe and it works.

Both links describe the same process.
https://forums.gentoo.org/viewtopic-p-7476018.html#7476018
https://forums.gentoo.org/viewtopic-p-7358388.html#7358388
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mv
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PostPosted: Sun Nov 23, 2014 8:04 pm    Post subject: Reply with quote

You can unpack glibc and copy the missing file from misc/sys/cdefs.h into /usr/include/sys/cdefs.h
Perhaps afterwards you can recompile glibc successfully. If you not, you have a serious problem...

Edit: NeddySeagoon's suggestion is probably best if this one file copy does not help to reemerge glibc.
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NeddySeagoon
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PostPosted: Sun Nov 23, 2014 8:11 pm    Post subject: Reply with quote

mv,

I did consider that approach and its probably worth a try.
However, we don't know that its is only a single file, so where do you stop?
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chi86
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PostPosted: Mon Dec 01, 2014 5:41 pm    Post subject: Reply with quote

Sorry for the long delay but i had an internet problem. I'm just started recompiling glibc as suggested in (https://forums.gentoo.org/viewtopic-p-7358388.html#7358388) and it failed aswell ;(

glibc:

>>> '/var/tmp/portage/sys-libs/glibc-2.19-r1/temp/build.log'

* Messages for package sys-libs/glibc-2.19-r1:

* ERROR: sys-libs/glibc-2.19-r1::gentoo failed (install phase):
* (no error message)
*
* Call stack:
* ebuild.sh, line 93: Called src_install
* environment, line 3340: Called eblit-run 'src_install'
* environment, line 993: Called eblit-glibc-src_install
* src_install.eblit, line 242: Called foreach_abi 'toolchain-glibc_src_install'
* common.eblit, line 326: Called toolchain-glibc_src_install
* src_install.eblit, line 9: Called die
* The specific snippet of code:
* emake install_root="${D}$(alt_prefix)" install || die
*
* If you need support, post the output of `emerge --info '=sys-libs/glibc-2.19-r1::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sys-libs/glibc-2.19-r1::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sys-libs/glibc-2.19-r1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sys-libs/glibc-2.19-r1/temp/environment'.
* Working directory: '/var/tmp/portage/sys-libs/glibc-2.19-r1/work/build-x86-x86_64-pc-linux-gnu-nptl'
* S: '/var/tmp/portage/sys-libs/glibc-2.19-r1/work/glibc-2.19'

the build log is huge should i post that as well?
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steveL
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PostPosted: Mon Dec 01, 2014 7:12 pm    Post subject: Re: emerge of most package fails after I restored a backup Reply with quote

chi86 wrote:
I did the backup with: tar -cvpf /backup/fullbackup.tar --directory=/ --exclude=proc --exclude=sys --exclude=dev/pts --exclude=backup --exclude=mnt --exclude=home

I don't think those excludes are what you wanted; eg --exclude=/proc iirc. Someone will correct me if I'm wrong. ;)
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NeddySeagoon
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PostPosted: Mon Dec 01, 2014 7:46 pm    Post subject: Reply with quote

steveL,

Well, it would be good to see dev in the excludes list. I'm not sure if leading / are required or not, since I would not try tarring up a live root fs.
There are too many breakages due to files open for writing.
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steveL
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PostPosted: Tue Dec 02, 2014 5:35 pm    Post subject: Reply with quote

NeddySeagoon wrote:
Well, it would be good to see dev in the excludes list. I'm not sure if leading / are required or not, since I would not try tarring up a live root fs.
There are too many breakages due to files open for writing.

Yeah fair enough; pretty sure the leading / is required, or it'll try to match anywhere in the path. It came up on another thread a while ago, but don't ask me where. ;-)
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