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Hardware problem?

Problems with emerge or ebuilds? Have a basic programming question about C, PHP, Perl, BASH or something else?
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rnd42
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Hardware problem?

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Post by rnd42 » Sat Dec 27, 2008 9:14 pm

Hi!

This all started this morning when I was trying to do 'emerge -e system'.
Problem is I can't get through all 98 ebuilds, but get stuck on any of them. It's a different ebuild every time so I guess it's more of a hardware problem than anything Gentoo. I always get stuck with an errorcode (unexpected end of file or syntax error near unexpected token) in the environment file (like /var/tmp/portage/sys-devel/patch-2.5.9/temp/environment this last time). If I check the environment file at the error I find an extra character there. What might cause this, memory, harddrive or motherboard? My Intel motherboard has been suspiciously slow to start up since the beginning... /var is a reiserfs on a raid1, I've also tried raid0 and ext2, but no difference.
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bunder
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Post by bunder » Sat Dec 27, 2008 9:27 pm

Moved from Off the Wall to Portage & Programming.

i'd be willing to bet its just portage, and not your system... if you specify what problems you're having in particular, maybe we can help you out a bit.

cheers
Neddyseagoon wrote:The problem with leaving is that you can only do it once and it reduces your influence.
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rnd42
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Post by rnd42 » Sat Dec 27, 2008 9:57 pm

Well, again tried 'emerge -e system'

This time I get stuck in app-arch/cpio-2.9-r1

Code: Select all

>>> Completed installing cpio-2.9-r1 into /var/tmp/portage/app-arch/cpio-2.9-r1/image/

ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/info
strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment
   bin/cpio
* checking 25 files for package collisions
>>> Merging app-arch/cpio-2.9-r1 to /
/var/tmp/portage/app-arch/cpio-2.9-r1/temp/environment: line 1729: syntax error near unexpected token `;'
/var/tmp/portage/app-arch/cpio-2.9-r1/temp/environment: line 1729: `                    ;
* 
 * ERROR: app-arch/cpio-2.9-r1 failed.
 * Call stack:
 *               ebuild.sh, line 1655:  Called die
 * The specific snippet of code:
 *      source "${T}"/environment || \
 *              die "error sourcing environment"
 *  The die message:
 *   error sourcing environment
 * 
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/tmp/portage/app-arch/cpio-2.9-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/app-arch/cpio-2.9-r1/temp/environment'.
 * 
!!! FAILED preinst: 1
Checking /var/tmp/portage/app-arch/cpio-2.9-r1/temp/environment line 1729 there's ;[ instead of ;; (the [ looks underscored). (I generally use joe for looking at and editing files)

Other times when I get end of file error I've seen an extra underscored @.
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bunder
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Post by bunder » Sat Dec 27, 2008 11:10 pm

can we see the output of:

emerge --info
env

thanks
Neddyseagoon wrote:The problem with leaving is that you can only do it once and it reduces your influence.
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rnd42
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Post by rnd42 » Sat Dec 27, 2008 11:31 pm

Certainly.

sabrina ~ # emerge --info
Portage 2.1.4.5 (default/linux/amd64/2008.0, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.27-gentoo-r7 x86_64)
=================================================================
System uname: 2.6.27-gentoo-r7 x86_64 Intel(R) Core(TM)2 Duo CPU E8400 @ 3.00GHz
Timestamp of tree: Sat, 27 Dec 2008 09:15:01 +0000
app-shells/bash: 3.2_p33
dev-lang/python: 2.5.2-r7
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox: 1.2.18.1-r2
sys-devel/autoconf: 2.61-r2
sys-devel/automake: 1.10.1-r1
sys-devel/binutils: 2.18-r3
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool: 1.5.26
virtual/os-headers: 2.6.23-r3
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-mtune=core2 -O3 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-mtune=core2 -O3 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="http://ftp.ing.umu.se/linux/gentoo/ ftp://ftp.ing.umu.se/linux/gentoo/ http://ftp.ds.karen.hj.se/gentoo/ ftp://ftp.ds.karen.hj.se/gentoo/ "
LDFLAGS="-Wl,-O1"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="acl amd64 berkdb bzip2 cli cracklib crypt cups dri fortran gdbm gmp gpm iconv ipv6 isdnlog ldap mailwrapper midi mmx mudflap multilib mysql ncurses nls nptl nptlonly openmp pam pcre perl pppd python readline
reflection session spl sse sse2 ssl sysfs tcpd unicode xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m
maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi
null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user
autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir
usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="fbdev
glint i810 intel mach64 mga neomagic nv r128 radeon savage sis tdfx trident vesa vga via vmware voodoo"
Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

sabrina ~ # env
MANPATH=/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.3.2/man
TERM=xterm
SHELL=/bin/bash
SSH_CLIENT=192.168.243.2 50721 22
SSH_TTY=/dev/pts/0
USER=root
LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:
*.svgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:
*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:
*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:
*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:
*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:
PAGER=/usr/bin/less
CONFIG_PROTECT_MASK=/etc/udev/rules.d /etc/terminfo /etc/ca-certificates.conf /etc/revdep-rebuild
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.3.2
PWD=/root
EDITOR=/bin/nano
SHLVL=1
HOME=/root
PYTHONPATH=/usr/lib64/portage/pym
LESS=-R -M --shift 5
LOGNAME=root
GCC_SPECS=
CVS_RSH=ssh
SSH_CONNECTION=192.168.243.2 50721 192.168.243.10 22
LESSOPEN=|lesspipe.sh %s
INFOPATH=/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.3.2/info
_=/usr/bin/env
sabrina ~ #
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legine
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Post by legine » Sun Dec 28, 2008 8:50 am

Heya,

I do not think it is a hardware Problem. Looks more like your compiler has swalloed some unwanted bits.
My guess would be that some low level librefernce doesnt work anymore as it should. Try to run, damn what was the name ;), ...

Damn I just remember the paludis name for it. ( reconcilio) I am sorry.
There is an emerge app that that checks for broken linkage. I post when I get the name or someone else is faster.

Out in the blue you could try reemerge glibc or something like it or it could be more simpler that gcc is looking in the wrong libraries. ( so. eselct could be another aproach to the problem.

Easiest way would be that emerge app thought.

[edit: revdep-rebuild is the name ... I knew I had to press the send button so it comes into my mind :) hehe]
quote from Spaceballs:
Dark Helmet:[...] we were told to comb the desert, so we're combing it! [puts down bullhorn] Find anything yet?!
Soldier: Nothing yet, sir.
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 9:08 am

Thanks, but revdep-rebuild finds nothing wrong;

sabrina ~ # revdep-rebuild
* Configuring search environment for revdep-rebuild

* Checking reverse dependencies
* Packages containing binaries and libraries broken by a package update
* will be emerged.

* Collecting system binaries and libraries
* Generated new 1_files.rr
* Collecting complete LD_LIBRARY_PATH
* Generated new 2_ldpath.rr
* Checking dynamic linking consistency
[ 100% ]

* Dynamic linking on your system is consistent... All done.
sabrina ~ #
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legine
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Post by legine » Sun Dec 28, 2008 9:43 am

hmmm,
not sure does emerge --update system --pretend give anything?
quote from Spaceballs:
Dark Helmet:[...] we were told to comb the desert, so we're combing it! [puts down bullhorn] Find anything yet?!
Soldier: Nothing yet, sir.
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 10:51 am

I also tried re-emerge glibc, but that didn't help so I also redid gcc and now I got through all 98 packages so I'm starting to wonder if I actually managed to forget to rebuild libtool last time I upgraded gcc...
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bunder
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Post by bunder » Sun Dec 28, 2008 11:54 am

at least you're getting somewhere... let us know how things turn out.

cheers
Neddyseagoon wrote:The problem with leaving is that you can only do it once and it reduces your influence.
banned from #gentoo since sept 2017
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 12:34 pm

I just got home and tried 'emerge -eav world' as well, but got unexpected-end-of-file in an environment file again so gcc was unfortunately not the problem. :?

sabrina ~ # emerge --update --pretend system

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

Calculating system dependencies... done!
sabrina ~ # emerge --update --pretend world

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

Calculating world dependencies... done!
sabrina ~ #
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Polynomial-C
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Post by Polynomial-C » Sun Dec 28, 2008 12:50 pm

Just a wild guess. Do you have a file /etc/portage/bashrc? If yes, please post it here...
The manual said "Requires Windows10 or better" so I installed GNU/Linux...

my portage overlay

Need a stage1 tarball? (Unofficial builds)
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 1:21 pm

Nope. No /etc/portage/bashrc.
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legine
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Post by legine » Sun Dec 28, 2008 1:50 pm

Hmpf, bugger :P

Well, is it now at least the same file or still Random?

If it is the same file you may want to try to sync again.

I am pretty out of Ideas atm. :(
quote from Spaceballs:
Dark Helmet:[...] we were told to comb the desert, so we're combing it! [puts down bullhorn] Find anything yet?!
Soldier: Nothing yet, sir.
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Post by Nerevar » Sun Dec 28, 2008 2:45 pm

Shot in the dark: try reinstalling portage and then running dispatch-conf or etc-update
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 3:16 pm

legine: Still random. :?

DarrenSmith: Thanks. emerge -e system and emerge -e world both start by re-emerging portage so I tried both dispatch-conf and etc-update. Unfortunatley neither changed the behaviour.


What utility/How is this environtment file created?
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Nerevar
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Post by Nerevar » Sun Dec 28, 2008 4:06 pm

This might provide some more details:

Code: Select all

PORTAGE_DEBUG=1 emerge -e system 2>&1 | tee /tmp/build.log
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legine
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Post by legine » Sun Dec 28, 2008 4:14 pm

Can it be a freespace Problem?

I mean
>>> Completed installing cpio-2.9-r1 into /var/tmp/portage/app-arch/cpio-2.9-r1/image/

Does look like the compilation of the app is finished in the sandbox. Now should come some sort of cleanup and copy. Or am I wrong.
I go check it out. (hehe lets hope emerge still works on my box. Since I use paludis for a long time now.)

[edit] HA!

Code: Select all

>>> Completed installing cpio-2.9-r1 into /var/tmp/portage/app-arch/cpio-2.9-r1/image/

ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/info
strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment
   bin/cpio
* checking 25 files for package collisions
>>> Merging app-arch/cpio-2.9-r1 to /
--- /usr/
--- /usr/share/
--- /usr/share/info/
>>> /usr/share/info/cpio.info.bz2
yes, I would check your hd space next. df -h / should do. That would explain this randomness. :)
Ofc haveing more info with that debug option is agreat idea, too... :-D
[/edit]
quote from Spaceballs:
Dark Helmet:[...] we were told to comb the desert, so we're combing it! [puts down bullhorn] Find anything yet?!
Soldier: Nothing yet, sir.
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 7:16 pm

Don't think it's diskspace;

Code: Select all

sabrina ~ # df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/md/6              47G  2.8G   44G   6% /
udev                   10M  300K  9.8M   3% /dev
/dev/md/1             950M  6.9M  895M   1% /boot
/dev/md/3              24G   68M   24G   1% /tmp
/dev/md/5              46G  2.0G   42G   5% /var
/dev/md/7              47G   33M   47G   1% /home
shm                   2.0G     0  2.0G   0% /dev/shm
sabrina ~ #
Finally got an error with the debug on, only that package part is still quite a lot of text though, doesn't feel good to just paste it here. What would be the best way of sharing it?

[edit]
Found a place to put it;
http://user1.netatonce.com/~u46621/coreutilserror.txt
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Post by MotivatedTea » Sun Dec 28, 2008 10:12 pm

The error is always in a ..../temp/environment file for each package, but in a different place each time. I don't know how this file is generated. In the output you posted, it says "The ebuild environment file is located at '/var/tmp/portage/sys-apps/coreutils-6.10-r2/temp/environment'". Could you also post that file, especially the lines around 1519?
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rnd42
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Post by rnd42 » Sun Dec 28, 2008 11:07 pm

For that error, no. Here's another one, complete with environment file;

http://user1.netatonce.com/~u46621/lvm2_error.zip

[edit]
Second one
http://user1.netatonce.com/~u46621/bzip2_error.zip
[/edit]
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Post by MotivatedTea » Sun Dec 28, 2008 11:29 pm

In the files you just posted, the error says there is an unexpected end of file at line 1767 while sourcing the environment. Well, the environment file is longer than that, but it looks corrupted: on line 1766, the 7th character is a null character. There's another null character on line 1770. I don't know how this environment file is being created, but I would guess that it's being generated by concatenating some other file that exist somewhere else on your system. You'll have to track down the file that this is coming from and "fix" it: either by removing the null characters, or, preferably, getting a fresh copy somehow.

Here is what lines 1763-1771 of lvm2_environment from your zipfile look like to me:

Code: Select all

                    physics)
                        type=Physics
                    ;;
      <nul>             visual*)
                        type=DataVisualization
                    ;;
                    *)
            <nul>           type=
                    ;;
                esac;
                type="Science;${type}"
            ;;
Note that those "<nul>"s are actually single null characters.
[edit]
Your bzip2 environment file has even more nul characters, again starting one line before the reported location of the error.
[/edit]

Does anyone else know where these environment files come from or how they're generated?

By the way, whether or not the <nul> characters are visible depends on your editor. In nano, they appear as ^@; in nedit they appear as <nul>.
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Post by legine » Mon Dec 29, 2008 12:08 am

Honestly at this point I would file a bug. Thats way to deep in the system, you are better off consulting a dev that knows how emerge is written to track this further. :?
Or MotivatedTea you think you can dig that further?

At least this is beyond what I know. I am sorry. whished I could do more. Good Luck :-D
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Soldier: Nothing yet, sir.
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Nerevar
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Post by Nerevar » Mon Dec 29, 2008 12:58 am

I'm also out of ideas regarding portage. That code is way too "complex". The only thing I can think of left to do would be to boot to single user mode and run an fsck of your /var file system. Random NULs like that could be a sign of corruption although it's not typically single NULs. Good luck!
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Post by MotivatedTea » Mon Dec 29, 2008 1:09 am

The null characters are showing up inside what look like a function called make_desktop_entry () (scroll up from the line the error is on). I can see a function with the same name, but different indentation, in /usr/portage/eclass/eutils.eclass. I would check to see if that file also contains null characters, because it if does, you have a problem with portage.

Code: Select all

grep -a -P '\000' /usr/portage/eclass/eutils.eclass
If there aren't any nulls in there (if the grep command above produces no output), then something's going wrong somwhere else.

I agree with legine: it does look like you might need a portage dev to help track this down. It looks to me like the problem is in one of three places:
1) some file in your portage has gotten corrupted
2) some utility that portage uses to manipulate files has gotten corrupted
3) some other configuration file on your system is being used by portage, and it's corrupted.
fsck'ing your system, as DarrenSmith suggests, isn't a bad idea; at least it can't hurt. (Well, it can't hurt if you do a read-only check, and it shouldn't make things worse to repair any errors found...)

As a last-ditch effort, you could try downloading and unpacking a fresh portage snapshot, then re-installing portage. (I.e., overwrite the portage tree and portage itself with a fresh copy.) Also, if you're using any overlays, disable them temporarily. I believe overlays can override/extend parts portage's eclasses. I'm just guessing here, though. You'll probably need to contact a dev. In the meantime, you could also try searching your harddrive for text files that contain the tring "make_desktop_entry" and also contain null characters.
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