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Bug 508312 - "emerge --update --newuse --deep --with-bdeps=y @world" does not finish,
Summary: "emerge --update --newuse --deep --with-bdeps=y @world" does not finish,
Status: UNCONFIRMED
Alias: None
Product: Portage Development
Classification: Unclassified
Component: Core - Interface (emerge) (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Portage team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-04-21 09:36 UTC by Juergen Rose
Modified: 2014-11-14 08:54 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


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Description Juergen Rose 2014-04-21 09:36:54 UTC
"emerge --update --newuse --deep --with-bdeps=y @world" seems to hang at:

root@lynx:/usr/src/linux(53)# emerge --update --newuse --deep --with-bdeps=y  @world
Calculating dependencies... done!
[ebuild     U  ] dev-lang/php-5.5.11 [5.5.10]
[ebuild     U  ] dev-ruby/rake-10.3.1 [0.9.6-r1]
[ebuild     U  ] sci-libs/shogun-3.2.0 [2.0.0] PYTHON_SINGLE_TARGET="python2_7%* -python3_3%" PYTHON_TARGETS="python2_7%* python3_3%*" 
[ebuild   R    ] sci-biology/emboss-6.3.1_p4-r1 [6.3.1_p4-r1] USE="doc%*" 

WARNING: One or more updates/rebuilds have been skipped due to a dependency conflict:

dev-libs/liborcus:0

  (dev-libs/liborcus-0.7.0:0/0.5::gentoo, ebuild scheduled for merge) conflicts with
    =dev-libs/liborcus-0.5*:0/0.5= required by (app-office/libreoffice-4.2.3.3:0/0::gentoo, installed)
    ^                  ^^^^       
    =dev-libs/liborcus-0.5*:= required by (app-office/libreoffice-4.2.3.3:0/0::gentoo, installed)
    ^                  ^^^^  

dev-lang/parrot:0

  (dev-lang/parrot-6.3.0:0/6.1.0::gentoo, ebuild scheduled for merge) conflicts with
    <dev-lang/parrot-6.2.0 required by (dev-lang/nqp-2014.04:0/0::gentoo, installed)
    ^                ^^^^^

dev-libs/libixion:0

  (dev-libs/libixion-0.7.0:0/0.7::gentoo, ebuild scheduled for merge) conflicts with
    <dev-libs/libixion-0.7:= required by (dev-libs/liborcus-0.5.1:0/0.5::gentoo, ebuild scheduled for merge)
    ^                  ^^^  


!!! The following installed packages are masked:
- sci-biology/embassy-cbstools-1.0.0-r3::science (masked by: package.mask)
/var/lib/layman/science/profiles/package.mask:
# Justin Lecher <jlec@gentoo.org> (20 Feb 2012)
# They are broken in one or the other way
# Need to be bumped to emboss-6.4.0

- sci-biology/embassy-domainatrix-0.1.0-r6::science (masked by: package.mask)
For more information, see the MASKED PACKAGES section in the emerge
man page or refer to the Gentoo Handbook.


>>> Verifying ebuild manifests

It is running already running one and a half hour and I get no further output:

ps shows me that it is running with 40-60% CPU utilization and 24% memory usage, but it is not show by top:
rose@lynx:/home/rose/Pictures(17)$ /bin/ps waux | grep "USER\|emerge" | grep -v grep
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root      8392 58.4 24.4 1095864 976060 pts/0  S+   09:55  36:24 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
rose@lynx:/home/rose/Pictures(18)$ date
Mon Apr 21 10:57:28 CEST 2014
rose@lynx:/home/rose/Pictures(19)$ /bin/ps waux | grep "USER\|emerge" | grep -v grep
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root      8392 55.8 24.4 1095864 976060 pts/0  S+   09:55  36:24 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
rose@lynx:/home/rose/Pictures(20)$ /bin/ps waux | grep "USER\|emerge" | grep -v grep
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
root      8392 42.7 24.4 1095864 976060 pts/0  S+   09:55  36:24 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
rose@lynx:/home/rose/Pictures(21)$ date
Mon Apr 21 11:20:12 CEST 2014



root@lynx:/root(9)# date
Mon Apr 21 11:30:15 CEST 2014
root@lynx:/root(10)# top | grep emerge

root@lynx:/root(11)# date
Mon Apr 21 11:36:26 CEST 2014
Comment 1 Juergen Rose 2014-04-21 10:42:15 UTC
I killed the running emerge process and start it once more:
The first ~35 minutes I see the rotation bar of Calculating dependencies.
Then I see "Calculating dependencies... done!" and emerge starts to try to emerge some packages. I have 759 packages in /var/lib/portage/world and with my USE flags in /etc/make.conf 3677 packages are installed. The processor is Core(TM)2 Duo CPU T9500@2.60GHz.  Is it to expect, that "emerge --update --newuse --deep --with-bdeps=y @world" needs so long to calculate dependencies? Or is it the consequence of some misconfiguration?

In first terminal window runs:

root@lynx:/usr/src/linux(54)# emerge --update --newuse --deep --with-bdeps=y  @world
Calculating dependencies /


In a second terminal window I run top, and see almost 100% CPU and 25% MEM usage:

root@lynx:/root(13)# top -b | grep USER
  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
root@lynx:/root(14)# top -b | grep emerge
 9934 root      20   0  784884 669392   4016 R  45.0 16.8   1:57.27 emerge
 9934 root      20   0  789868 674048   4016 R  70.8 16.9   1:59.40 emerge
 9934 root      20   0  794108 678452   4016 R  81.7 17.0   2:01.86 emerge
...
 9934 root      20   0 1092776 977300   4016 R  99.6 24.5  35:24.86 emerge
 9934 root      20   0 1092776 977300   4016 R 100.0 24.5  35:27.87 emerge
...
 9934 root      20   0 1097344 977552   4232 S  27.6 24.5  35:46.76 emerge
 9934 root      20   0 1097344 977552   4232 D   0.0 24.5  35:46.76 emerge
 9934 root      20   0 1097348 977648   4328 S  24.9 24.5  35:47.51 emerge
 9934 root      20   0 1097348 977648   4328 S   0.0 24.5  35:47.51 emerge


In the third terminal window runs ps and shows the following:

rose@lynx:/home/rose/Pictures(22)$/bin/ps waux | grep USER
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
rose@lynx:/home/rose/Pictures(23)$ while true ; do  /bin/ps waux | grep "emerge" | grep -v grep ; sleep 1; done
root      9934 81.1 10.6 540836 425364 pts/0   R+   11:37   0:56 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 81.3 10.7 544584 428728 pts/0   R+   11:37   0:57 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
...
root      9934 97.6 24.5 1097344 977508 pts/0  R+   11:37  35:44 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.6 24.5 1097344 977508 pts/0  R+   11:37  35:45 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.6 24.5 1097344 977552 pts/0  S+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.6 24.5 1097344 977552 pts/0  S+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.5 24.5 1097344 977552 pts/0  S+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.5 24.5 1097344 977552 pts/0  S+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.4 24.5 1097344 977552 pts/0  S+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.4 24.5 1098368 977552 pts/0  D+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.4 24.5 1098368 978576 pts/0  D+   11:37  35:46 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.3 24.5 1097348 977648 pts/0  S+   11:37  35:47 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.3 24.5 1097348 977648 pts/0  S+   11:37  35:47 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.3 24.5 1097348 977648 pts/0  S+   11:37  35:47 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world
root      9934 97.2 24.5 1097348 977648 pts/0  S+   11:37  35:47 /usr/bin/python2.7 -b /usr/bin/emerge --update --newuse --deep --with-bdeps=y @world