Running 'emerge -uvDN world' it complains about files not listed in Manifest: root@impala:/root(24)# emerge -uvDN world ... >>> Verifying ebuild manifests !!! A file is not listed in the Manifest: '/usr/portage_impala/sci-biology/rebase/rebase-1409.ebuild' !!! A file is not listed in the Manifest: '/usr/portage_impala/sci-chemistry/openbabel/openbabel-2.3.0.ebuild' If I checking one of these directories, I find: root@impala:/root(21)# ll /usr/portage_impala/sci-biology/rebase/ total 40 -rw-r--r-- 1 portage portage 17872 Jan 4 12:31 ChangeLog -rw-r--r-- 1 portage portage 4011 Jan 4 12:31 Manifest -rw-r--r-- 1 portage portage 813 Feb 28 2013 metadata.xml -rw-r--r-- 1 portage portage 1201 Aug 3 21:01 rebase-1403.ebuild -rw-r--r-- 1 portage portage 1205 Jun 4 2014 rebase-1406.ebuild -rw-r--r-- 1 portage portage 1205 Jul 31 10:44 rebase-1408.ebuild -rw-r--r-- 1 portage portage 1205 Sep 15 18:58 rebase-1409.ebuild -rw-r--r-- 1 portage portage 1201 Dec 31 17:01 rebase-1410.ebuild -rw-r--r-- 1 portage portage 1201 Dec 31 17:31 rebase-1411.ebuild -rw-r--r-- 1 portage portage 1205 Dec 2 11:28 rebase-1412.ebuild -rw-r--r-- 1 portage portage 1205 Jan 4 12:28 rebase-1501.ebuild Comparing with an other system: root@condor:/usr/local/portage(42)# ll /usr/portage/sci-biology/rebase/ total 30 -rw-r--r-- 1 root root 17872 Jan 4 12:31 ChangeLog -rw-r--r-- 1 root root 4011 Jan 4 12:31 Manifest -rw-r--r-- 1 root root 813 Feb 28 2013 metadata.xml -rw-r--r-- 1 root root 1201 Dec 31 17:31 rebase-1411.ebuild -rw-r--r-- 1 root root 1205 Dec 2 11:28 rebase-1412.ebuild -rw-r--r-- 1 root root 1205 Jan 4 12:28 rebase-1501.ebuild I see that I have old ebuilds in the /usr/portage_impala/sci-biology/rebase/. 'emerge --sync' or 'emaint all' does not help. Of course I can remove the old ebuilds manually. But what can be the reason? A crash during 'emerge --sync'? Reproducible: Always
Outdated rsync mirror? Filesystem errors? Whatever it is, you ought to try simply removing the files and running emerge --sync again.
Happens today again with wireshark: root@impala:/root(52)# emerge --update --newuse --deep --with-bdeps=y @world Calculating dependencies | * Missing digest for '/usr/portage_impala/net-analyzer/wireshark/wireshark-1.12.2-r1.ebuild' |... done! Exiting on signal 2 root@impala:/root(53)# ll /usr/portage_impala/net-analyzer/wireshark total 142 -rw-r--r-- 1 portage portage 99543 Jan 9 00:31 ChangeLog drwxr-xr-x 2 portage portage 1024 Dec 18 01:03 files/ -rw-r--r-- 1 portage portage 6385 Jan 9 00:31 Manifest -rw-r--r-- 1 portage portage 2551 Dec 17 16:31 metadata.xml -rw-r--r-- 1 portage portage 5978 Dec 3 11:01 wireshark-1.12.2.ebuild -rw-r--r-- 1 portage portage 6064 Dec 17 16:19 wireshark-1.12.2-r1.ebuild -rw-r--r-- 1 portage portage 6061 Jan 9 00:21 wireshark-1.12.3.ebuild -rw-r--r-- 1 portage portage 6158 Dec 17 16:31 wireshark-1.99.1.ebuild -rw-r--r-- 1 portage portage 6204 Dec 17 16:31 wireshark-99999999.ebuild root@impala:/root(54)# rm /usr/portage_impala/net-analyzer/wireshark/wireshark-1.12.2-r1.ebuild
(In reply to Jeroen Roovers from comment #1) > Outdated rsync mirror? Filesystem errors? > Whatever it is, you ought to try simply removing the files and running > emerge --sync again. And it happens today with other packages: root@impala:/root(55)# emerge --update --newuse --deep --with-bdeps=y @world Calculating dependencies \ * Missing digest for '/usr/portage_impala/x11-libs/gtk+/gtk+-3.4.4.ebuild' \ * Missing digest for '/usr/portage_impala/x11-libs/gtk+/gtk+-2.24.24.ebuild' \ * Missing digest for '/usr/portage_impala/sci-chemistry/pdb2pqr/pdb2pqr-1.8.0-r1.ebuild' * Missing digest for '/usr/portage_impala/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0-r2.ebuild' * Missing digest for '/usr/portage_impala/sci-chemistry/pdb2pqr/pdb2pqr-1.7.0.ebuild' * Missing digest for '/usr/portage_impala/sci-libs/colamd/colamd-2.7.4.ebuild' * Missing digest for '/usr/portage_impala/sci-libs/amd/amd-2.2.3.ebuild' * Missing digest for '/usr/portage_impala/sci-libs/umfpack/umfpack-5.6.1-r1.ebuild' ... done! [ebuild U ] sys-devel/automake-wrapper-10 [9] [ebuild U ] media-libs/freetype-2.5.5 [2.5.4-r1] [ebuild U ] media-libs/exiftool-9.80 [9.79] [ebuild U ] dev-perl/Inline-0.780.0 [0.530.0] [ebuild NS ] sys-devel/automake-1.15 [1.10.3-r1, 1.11.6-r1, 1.12.6, 1.14.1] [ebuild N ] net-dialup/rp-pppoe-3.11-r3 USE="tk" [ebuild U ] sys-apps/hwids-20150107 [20141214] [ebuild r U ] dev-lisp/sbcl-1.2.7 [1.2.6] [ebuild rR ] sci-mathematics/maxima-5.35.1-r1 [ebuild U ] net-analyzer/wireshark-1.12.3 [1.12.2-r1] [ebuild R ] gnome-base/libgnome-2.32.1-r1 USE="(-doc%*)" [ebuild U ] dev-libs/openssl-1.0.1k [1.0.1j] [ebuild U ] x11-base/xorg-server-1.16.3-r1 [1.16.2.901-r1] [ebuild U ] net-analyzer/tcpdump-4.6.2-r1 [4.6.2] [ebuild U ] dev-python/ssl-fetch-0.3 [0.2.1] [ebuild N ] sci-libs/vtk-6.1.0-r1 USE="R X boost cg doc examples ffmpeg gdal java mpi mysql odbc postgres python qt4 rendering smp tbb tcl theora tk -all-modules (-aqua) -imaging -json -kaapi -offscreen {-test} -views -web -xdmf2" PYTHON_TARGETS="python2_7" VIDEO_CARDS="-nvidia" [ebuild U ] sci-mathematics/freemat-4.2 [4.0] USE="vtk%*" [ebuild U #] dev-python/PyQt5-5.4 [5.3.2] [ebuild U ] media-sound/pulseaudio-5.0-r7 [5.0-r6] ... so I am afraid that some of my portage settings or my filesystem is responsible. If my filesystem is responsible, what should I check. I have a seperate /var and a seperate /var/tmp partition. Is it enough, to check the /var partition?
I have alsa a seperate /usr/portage partition.
(In reply to Juergen Rose from comment #4) > I have alsa a seperate /usr/portage partition. I just checked /usr/portage, found and corrected some issues. I will see, what happens now.
I had for one week no further issues.
