Portage says "IndexError: list index out of range"

[adammorley]

Just rsync'ed, and got (this is after I tried rsync'ing again):

# emerge -pu world

These are the packages that I would merge, in order:

Calculating world dependencies \Traceback (most recent call last):
File "/usr/bin/emerge", line 1902, in ?
if not mydepgraph.xcreate(myaction):
File "/usr/bin/emerge", line 887, in xcreate
if not self.create(myk):
File "/usr/bin/emerge", line 637, in create
if not self.select_dep("/",mydep["/"],myparent=mp):
File "/usr/bin/emerge", line 735, in select_dep
mycheck=portage.dep_check(depstring,self.mydbapi[myroot])
File "/usr/lib/python2.2/site-packages/portage.py", line 2543, in dep_check
mylist=flatten(dep_listcleanup(dep_zapdeps(mysplit,mysplit2)))
File "/usr/lib/python2.2/site-packages/portage.py", line 2299, in dep_zapdeps
myresult=dep_zapdeps(unreduced[x],reduced[x])
File "/usr/lib/python2.2/site-packages/portage.py", line 2289, in dep_zapdeps
return unreduced[1]
IndexError: list index out of range


I have no idea what happend --- was working fine yesterday. Did my portage tree go south? Suggestions welcome.

I'll add:

# emerge info
Portage 2.0.48 (default-x86-1.4, gcc-3.2.2, glibc-2.3.1-r4)
=================================================================
System uname: 2.4.20-gentoo-r2 i686 Pentium III (Coppermine)
GENTOO_MIRRORS="http://gentoo.oregonstate.edu http://distro.ibiblio.org/pub/Linux/dis ... ons/gentoo"
CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share/config /usr/X11R6/lib/X11/xkb /opt/tomcat/conf /usr/kde/3.1/share/config /usr/share/config"
CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d"
PORTDIR="/usr/portage"
DISTDIR="/usr/portage/distfiles"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR_OVERLAY=""
USE="kde directfb alsa tetex aalib bonobo guile ruby mysql perl esd mozilla gphoto2 x86 oss 3dnow apm arts avi berkdb crypt cups encode gdbm gif gpm gtk imlib java jpeg gnome libg++ libwww mikmod mmx motif mpeg ncurses nls oggvorbis opengl pam pdflib png python qt qtmt quicktime readline sdl slang spell ssl svga tcpd truetype X xml2 xmms xv zlib"
COMPILER="gcc3"
CHOST="i686-pc-linux-gnu"
CFLAGS="-march=pentium3 -O3 -pipe"
CXXFLAGS="-march=pentium3 -O3 -pipe"
ACCEPT_KEYWORDS="x86"
MAKEOPTS="-j2"
AUTOCLEAN="yes"
SYNC="rsync://rsync.us.gentoo.org/gentoo-portage"
FEATURES="sandbox ccache"

And that /usr isn't full.

[greg]

Well you are not alone.. Did two rsyncs on different servers to see if one was bad? Reguardless the problem persists. For now I just plan to wait it out but figured I'd comment so you did not think that you were the only one... =_)

Greg

[d3c3it]

as bad as this sounds im glad im not the only 1 i thought i screwed up my system, so much so that i deleted my portage tree and synced it again but still came up with the same thing
ive no idea what it means, something to do with python thats all i know :/

[derheld42]

I'm getting the same thing..

I'm trying to
emerge -up php

Here's my output:

Code: Select all

These are the packages that I would merge, in order:

Calculating dependencies
!!! Problem in dev-php/php dependencies.
!!! list index out of range

Here's my emerge info

Code: Select all

Portage 2.0.48-r1 (default-x86-1.4, gcc-3.2.2, glibc-2.3.1-r4)
=================================================================
System uname: 2.4.21_rc8-gss i686 AMD Athlon(tm) XP 1600+
GENTOO_MIRRORS="http://gentoo.oregonstate.edu http://distro.ibiblio.org/pub/Linux/distributions/gentoo"
CONFIG_PROTECT="/etc /var/qmail/control /usr/share/config /usr/kde/2/share/config /usr/kde/3/share/config"
CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d"
PORTDIR="/usr/portage"
DISTDIR="/usr/portage/distfiles"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR_OVERLAY=""
USE="x86 oss 3dnow apm arts avi crypt cups encode gif gpm imlib jpeg libg++ libwww mikmod mmx motif mpeg ncurses nls oggvorbis opengl pdflib png quicktime sdl spell svga truetype X xml2 xmms xv zlib gdbm berkdb slang readline tcpd pam ssl perl python qt -kde -gnome gtk -java ufed mysql php"
COMPILER="gcc3"
CHOST="i686-pc-linux-gnu"
CFLAGS="-march=athlon-xp -O2 -pipe"
CXXFLAGS="-march=athlon-xp -O2 -pipe"
ACCEPT_KEYWORDS="x86"
MAKEOPTS="-j2"
AUTOCLEAN="yes"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
FEATURES="sandbox ccache"

[col]

yes same here, worked fine yesterday when a new portage was installed....now it has broken

[G_Man]

This looks like it is only happening to people that have

ACCEPT_KEYWORDS="x86"

active. When I do:

emerge -pU world,
This works fine, but:

ACCEPT_KEYWORDS="x86" emerge -pU world,
Gives this error

Code: Select all

Calculating world dependencies /Traceback (most recent call last):
  File "/usr/bin/emerge", line 1902, in ?
    if not mydepgraph.xcreate(myaction):
  File "/usr/bin/emerge", line 887, in xcreate
    if not self.create(myk):
  File "/usr/bin/emerge", line 637, in create
    if not self.select_dep("/",mydep["/"],myparent=mp):
  File "/usr/bin/emerge", line 795, in select_dep
    if not self.create(myk,myparent):
  File "/usr/bin/emerge", line 637, in create
    if not self.select_dep("/",mydep["/"],myparent=mp):
  File "/usr/bin/emerge", line 735, in select_dep
    mycheck=portage.dep_check(depstring,self.mydbapi[myroot])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2543, in dep_check
    mylist=flatten(dep_listcleanup(dep_zapdeps(mysplit,mysplit2)))
  File "/usr/lib/python2.2/site-packages/portage.py", line 2299, in dep_zapdeps
    myresult=dep_zapdeps(unreduced[x],reduced[x])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2289, in dep_zapdeps
    return unreduced[1]
IndexError: list index out of range

Can the portage programers have a look at this?

[Mr.Gone]

Yep.. Ran into the same problem, for me with mod_php.

Code: Select all

These are the packages that I would merge, in order:

Calculating dependencies \
!!! Problem in dev-php/mod_php dependencies.
!!! list index out of range

...and portage info:

Code: Select all

Portage 2.0.48-r1 (default-x86-1.4, gcc-3.2.2, glibc-2.3.1-r4)
=================================================================
System uname: 2.4.20-gam-catalyst-1 i686 Intel(R) Pentium(R) 4 CPU 2.40GHz
GENTOO_MIRRORS="ftp://ftp.ussg.iu.edu/pub/linux/gentoo http://gentoo.oregonstate.edu/ http://www.ibiblio.org/pub/Linux/distributions/gentoo"
CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share/config /usr/X11R6/lib/X11/xkb /usr/kde/3.1/share/config /usr/share/config"
CONFIG_PROTECT_MASK="/etc/init.d /etc/wget /etc/gconf /etc/env.d"
PORTDIR="/usr/portage"
DISTDIR="/usr/portage/distfiles"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR_OVERLAY=""
USE="x86 oss 3dnow apm arts avi crypt cups encode gif jpeg kde libg++ mikmod mmx mpeg ncurses nls pdflib png quicktime spell truetype xmms xv zlib gtkhtml gdbm berkdb slang readline bonobo svga java guile sdl gpm tcpd pam libwww ssl perl esd imlib oggvorbis qt motif opengl mozilla X gtk gnome python xml xml2 php mysql"
COMPILER="gcc3"
CHOST="i686-pc-linux-gnu"
CFLAGS="-march=pentium3 -O3 -pipe -foptimize-sibling-calls -fomit-frame-pointer"
CXXFLAGS="-march=pentium3 -O3 -pipe -foptimize-sibling-calls -fomit-frame-pointer"
ACCEPT_KEYWORDS="x86"
MAKEOPTS="-j6"
AUTOCLEAN="yes"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
FEATURES="sandbox ccache"

BTW, is it normal to have

Code: Select all

ACCEPT_KEYWORDS="x86"

when that's neither in my environment variables nor in /etc/make.conf?

peas..

[adammorley]

I thought the accept_keywords jobbie was important. But I don't know. Has anybody filed a bug? I don't file bugs anymore, because I don't know what the proper channels are for elevation of issues with gentoo, and its bit me before.

[col]

this is what I get:

Code: Select all

emerge -up world

portage: 'portage' user or group missing. Please update baselayout
         and merge portage user(250) and group(250) into your passwd
         and group files. Non-root compilation is disabled until then.
         Also note that non-root/wheel users will need to be added to
         the portage group to do portage commands.

         For the defaults, line 1 goes into passwd, and 2 into group.
         portage:x:250:250:portage:/var/tmp/portage:/bin/false
         portage::250:portage


These are the packages that I would merge, in order:

Calculating world dependencies |Traceback (most recent call last):
  File "/usr/bin/emerge", line 1902, in ?
    if not mydepgraph.xcreate(myaction):
  File "/usr/bin/emerge", line 887, in xcreate
    if not self.create(myk):
  File "/usr/bin/emerge", line 637, in create
    if not self.select_dep("/",mydep["/"],myparent=mp):
  File "/usr/bin/emerge", line 735, in select_dep
    mycheck=portage.dep_check(depstring,self.mydbapi[myroot])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2543, in dep_check
    mylist=flatten(dep_listcleanup(dep_zapdeps(mysplit,mysplit2)))
  File "/usr/lib/python2.2/site-packages/portage.py", line 2299, in dep_zapdeps
    myresult=dep_zapdeps(unreduced[x],reduced[x])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2289, in dep_zapdeps
    return unreduced[1]
IndexError: list index out of range

[Mr.Gone]

..is there any reason I would have

Code: Select all

ACCEPT_KEYWORDS="x86"

in the output from "emerge info" when it's not in my /etc/make.conf nor is it set as an environment variable? I didn't know there was another place that emerge looked..

[Mr.Gone]

Ah. I found the problem. Someone posted a typo'd ebuild.
My particular problem is that the tildes were left out of the KEWORDS="~x86 [...]" string.

I wouldn't be surprised if your problems were right nearly the same thing, if not the exact same thing (as someone mentioned they were emerging php, not mod_php).

To fix:

Code: Select all

cd /usr/portage/dev-php/mod_php/

Using your favorite editor, edit mod_php-4.3.2.ebuild (or whatever ebuild is giving you hell, and has this problem. If you're unsure, choose the most recent one that doesn't have an r1, r2, r3, etc behind it.
For example:

Code: Select all

nano mod_php-4.3.2.ebuild

Then, change

Code: Select all

KEYWORDS="x86 sparc ppc alpha hppa ~arm ~sparc"

to

Code: Select all

KEYWORDS="~x86 ~sparc ~ppc ~alpha ~hppa ~arm ~sparc"

save and try emerging again.
-gone

[derheld42]

It looks like the /etc/make.profile directory has your missing x86.

Code: Select all

$cd /etc/make.profile
$grep x86 *
make.defaults:USE="x86 oss 3dnow apm arts avi berkdb crypt cups encode gdbm gif gpm gtk imlib
make.defaults:ARCH="x86"
make.defaults:ACCEPT_KEYWORDS="x86"

[Mr.Gone]

Thanks.. ..but, for now, since I'm not really sure whether it's supposed to be there or not, and since I've already kinda wrapped up what was causing me the problem, I'll go ahead and leave it there. It occurs to me the make flags might work like 'x86' just indicates the arch, and '~x86' indicates that it's experimental.. ..I'm sure I've got it wrong to some degree, but.. thanks for the help.

~gone

[quag7]

I tried several of the possible fixes suggested. What finally fixed the problem was just deleting everything in /var/cache.

What other effects this has I don't know but now it's working.

When surgical troubleshooting fails, a reckless and ignorant scorched-earth outburst at the peak of a temper tantrum will see us through.

[Krisserferson]

If this occurs, you might just want to try running the emerge command with the additional --debug parameter.. In my case, this pointed out that /usr/portage/dev-php/php/php-4.3.2.ebuild was the culprit.. Just deleting the ebuild was enough for me..

[gegen]

With
# emerge -p `cat /var/cache/edb/world`
i found that dev-php/mod_php was the ebuild that started the problem, so i commented it on world file and uptated all other ebuild except that one.
Hope it helps.

[bridenour]

For me, php and mod_php were the problems, although I don't know what the specific problem is. I resolved the issue by changing the entries in my /var/cache/edb/world file to:

<dev-php/php-4.3.2
<dev-php/mod_php-4.3.2

This should restrict these packages to versions earlier than the ones causing the problem.


- Bob

[deathbaz]

Hi all

I don't think the root cause of the problem here are the KEYWORD flags, since KEYWORD="~86" in the ebuild file would indicate that this particular ebuild is not considered stable for that architecture - which would be odd since there was a GLSA distributed on June 9th advising people to upgrade to this version. I think that rules out the possibility that there is a typo (in the KEYWORD line anyway).

Also locking portage to versions <4.3.2 is going to leave you vulnerable to the exploits mentioned in the GLSA. I guess thats up to you, but its not really the go if you are seeing this problem on production server.

Its also interesting to note that there have been no new GLSA's posted to the News and Announcements forum since 3rd June too.

[Genone]

So it seems that the problem is in the php eclass as the mod_php ebuild has not been modified in the last 5 days but there were 5 commits for the eclass since the last modifcation of mod_php.

[Byte]

Running: emerge -DUupv world:

Code: Select all

Parent:    ebuild / dev-php/php-4.3.2 nomerge
Depstring: >=sys-libs/cracklib-2.7-r7 sys-apps/bzip2 X? ( virtual/x11 ) crypt? ( >=dev-libs/libmcrypt-2.4 >=app-crypt/mhash-0.8 ) curl? ( >=net-ftp/curl-7.10.2 ) firebird? ( >=dev-db/firebird-1.0 ) flash? ( media-libs/libswf >=media-libs/ming-0.2a ) freetds? ( >=dev-db/freetds-0.53 ) || ( gd-bundled? () gd? ( media-libs/libgd >=media-libs/jpeg-6b >=media-libs/libpng-1.2.5 ) ) gdbm? ( >=sys-libs/gdbm-1.8.0 ) java? ( =virtual/jdk-1.4* dev-java/java-config ) jpeg? ( >=media-libs/jpeg-6b ) ldap? ( >=net-nds/openldap-1.2.11 ) mysql? ( >=dev-db/mysql-3.23.26 ) nls? ( sys-devel/gettext ) odbc? ( >=dev-db/unixODBC-1.8.13 ) pam? ( >=sys-libs/pam-0.75 ) pdflib? ( >=media-libs/pdflib-4.0.3 >=media-libs/jpeg-6b >=media-libs/libpng-1.2.5 ) png? ( >=media-libs/libpng-1.2.5 ) postgres? ( >=dev-db/postgresql-7.1 ) qt? ( >=x11-libs/qt-2.3.0 ) snmp? ( || ( >=net-analyzer/net-snmp-5.0.6-r1 net-analyzer/ucd-snmp ) ) spell? ( app-text/aspell ) ssl? ( >=dev-libs/openssl-0.9.5 ) tiff? ( >=media-libs/tiff-3.5.5 ) xml2? ( dev-libs/libxml2 >=dev-libs/libxslt-1.0.30 ) >=net-libs/libwww-5.3.2 >=app-text/sablotron-0.97 dev-libs/expat sys-libs/zlib virtual/mta truetype? ( ~media-libs/freetype-1.3.1 >=media-libs/t1lib-1.3.1 ) !bootstrap? ( sys-devel/patch ) imap? ( >=net-mail/uw-imap-2001a-r1 ) mcal? ( dev-libs/libmcal ) !dev-libs/9libs !bootstrap? ( sys-devel/patch ) readline? ( >=sys-libs/ncurses-5.1 >=sys-libs/readline-4.1 ) >=sys-libs/cracklib-2.7-r7 sys-apps/bzip2 X? ( virtual/x11 ) crypt? ( >=dev-libs/libmcrypt-2.4 >=app-crypt/mhash-0.8 ) curl? ( >=net-ftp/curl-7.10.2 ) firebird? ( >=dev-db/firebird-1.0 ) flash? ( media-libs/libswf >=media-libs/ming-0.2a ) freetds? ( >=dev-db/freetds-0.53 ) || ( gd-bundled? () gd? ( media-libs/libgd >=media-libs/jpeg-6b >=media-libs/libpng-1.2.5 ) ) gdbm? ( >=sys-libs/gdbm-1.8.0 ) java? ( =virtual/jdk-1.4* dev-java/java-config ) jpeg? ( >=media-libs/jpeg-6b ) ldap? ( >=net-nds/openldap-1.2.11 ) mysql? ( >=dev-db/mysql-3.23.26 ) nls? ( sys-devel/gettext ) odbc? ( >=dev-db/unixODBC-1.8.13 ) pam? ( >=sys-libs/pam-0.75 ) pdflib? ( >=media-libs/pdflib-4.0.3 >=media-libs/jpeg-6b >=media-libs/libpng-1.2.5 ) png? ( >=media-libs/libpng-1.2.5 ) postgres? ( >=dev-db/postgresql-7.1 ) qt? ( >=x11-libs/qt-2.3.0 ) snmp? ( || ( >=net-analyzer/net-snmp-5.0.6-r1 net-analyzer/ucd-snmp ) ) spell? ( app-text/aspell ) ssl? ( >=dev-libs/openssl-0.9.5 ) tiff? ( >=media-libs/tiff-3.5.5 ) xml2? ( dev-libs/libxml2 >=dev-libs/libxslt-1.0.30 ) >=net-libs/libwww-5.3.2 >=app-text/sablotron-0.97 dev-libs/expat sys-libs/zlib virtual/mta truetype? ( ~media-libs/freetype-1.3.1 >=media-libs/t1lib-1.3.1 )
Traceback (most recent call last):
  File "/usr/bin/emerge", line 1902, in ?
    if not mydepgraph.xcreate(myaction):
  File "/usr/bin/emerge", line 887, in xcreate
    if not self.create(myk):
  File "/usr/bin/emerge", line 637, in create
    if not self.select_dep("/",mydep["/"],myparent=mp):
  File "/usr/bin/emerge", line 735, in select_dep
    mycheck=portage.dep_check(depstring,self.mydbapi[myroot])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2543, in dep_check
    mylist=flatten(dep_listcleanup(dep_zapdeps(mysplit,mysplit2)))
  File "/usr/lib/python2.2/site-packages/portage.py", line 2299, in dep_zapdeps
    myresult=dep_zapdeps(unreduced[x],reduced[x])
  File "/usr/lib/python2.2/site-packages/portage.py", line 2289, in dep_zapdeps
    return unreduced[1]
IndexError: list index out of range

It stops after "Parent: ebuild / dev-php/php-4.3.2 nomerge", so:

Code: Select all

# cd /usr/portage/dev-php/php
# ls
ChangeLog  files                php-4.3.0-r4.ebuild  php-4.3.1-r2.ebuild  php-4.3.2.ebuild
Manifest   php-4.3.0-r3.ebuild  php-4.3.1-r1.ebuild  php-4.3.1.ebuild
# nano php-4.3.2.ebuild
# nano php-4.3.1.ebuild

looking at the two files,

Code: Select all

PROVIDE="virtual/php"

is missing from 4.3.2 (but is in 4.3.1)

I thought that adding that line to the 4.3.2 ebuild would fix it.
It doesn't.

Someone has seriously messed up the 4.3.2 ebuild:
(part of a diff between 4.3.1 and 4.3.2):

Code: Select all

4.3.1:
! IUSE="truetype postgres tiff libwww nls jpeg readline ssl oci8 mysql X gdbm curl imap xml2 xml cjk pdflib qt snmp crypt flash odb$

- MY_P=php-${PV}
- S=${WORKDIR}/${MY_P}
  DESCRIPTION="PHP Shell Interpreter"
- SRC_URI="http://us3.php.net/distributions/${MY_P}.tar.bz2"
- HOMEPAGE="http://www.php.net/"
- LICENSE="PHP"
  SLOT="0"
  PROVIDE="virtual/php"
- KEYWORDS="x86 ppc sparc"

4.3.2:
! inherit php eutils
!
! IUSE="${IUSE} readline"

  DESCRIPTION="PHP Shell Interpreter"
  SLOT="0"
+ KEYWORDS="x86 ppc sparc ~alpha ~arm ~hppa ~mips"
  PROVIDE="virtual/php"

! DEPEND="${DEPEND}
!       readline? ( >=sys-libs/ncurses-5.1 >=sys-libs/readline-4.1 ) "

+ RDEPEND="${RDEPEND}"

! EXCLUDE_DB4_FIX=1
! EXCLUDE_PEAR_FIX=1

I now notice it inherits the php eclass:
"inherit php eutils"

Looking in the php.eclasss:

Code: Select all

# This EBUILD is totally masked presently. Use it at your own risk.  I know it
# is severely broken, but I needed to get a copy into CVS to pass around and
# repoman was complaining at me too much

oops.
looks like someone tried to use an eclass that isn't ready
so the posted fix is needed, mask php-4.3.2. (and the same for mod_php)

[Byte]

so the posted fix is needed, mask php-4.3.2. (and the same for mod_php)

Except I can't seem to mask it properly, ">dev-php/php-4.3.1" and "=dev-php/php-4.3.2" don't work

[d3c3it]

so the posted fix is needed, mask php-4.3.2. (and the same for mod_php)

Except I can't seem to mask it properly, ">dev-php/php-4.3.1" and "=dev-php/php-4.3.2" don't work

ditto
rsync doesnt seem to do poop. ive tired all the ideas here but nothing
wish i could program id have ago at fixing it

[solatis]

Same problem here... and waiting for a fix

[grimlog]

Hello,

Same problem here... and waiting for a fix

I edited /var/cache/edb/world like this:

<=dev-php/mod_php-4.3.1
<=dev-php/php-4.3.1

and it worked.

HTH
Michael

[d3c3it]

Hello,

Same problem here... and waiting for a fix

I edited /var/cache/edb/world like this:

<=dev-php/mod_php-4.3.1
<=dev-php/php-4.3.1

and it worked.

HTH
Michael

WOOO emerge -Dup world works again, im downgrading both mod_php and php it seems its very br0ke right now but that fixed it for now:)