"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
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