Okay, here goes. Hopefully I'm not "n00b"ed to death here. The other night, I unmerged mplayer, since I no longer desired to have it installed on my system. During the unmerging process, it took the bio2jack and win32codecs packages along with it, which I have since remerged. I then did an emerge --sync and noticed the following error during the process: delete_file: unlink "/usr/portage/app-text/a2ps/files/digest-a2ps-4.13c-r2" failed: Operation not permitted I went and took a look the directory and noticed an interesting anomaly: the "digest-a2ps-4.13c-r2" file is reported to be over a GB in size, is now somehow being read as a sticky socket, and has some rather interesting stats when looked at with a ls -al sr-----rwt 21505 2292203972 1074004386 1281306068 Sep 8 2016 digest-a2ps-4.13c-r2 This is also affecting "/etc/xdg/menus". My system currently is reading it as a 2.8 GB file of unknown type with the following stats when looked at with ls -al ?r----xr-x 9209 3912526490 3741581311 3025156755 Jun 9 1915 menus The main problem with this particular file is that "menus" is supposed to be a DIRECTORY, not a 2.8 GB file. In the case of both of these files, I cannot manipulate them in any way, shape or form, nor at any init level. I can't change their permissions even as root, portage can't do anything with "menus" when I try to remerge gnome-menus, and my main menu in gnome is missing every entry in it under the "Applications" heading, save for 'Run Application'. An e2fsck run on the root filesystem via knoppix shows that it's clean as a whistle, with no errors of any kind reported. I'm convinced that if I could just delete these two problems, I could remerge gnome-menus and update my portage tree. Any and all help would be so beyond appreciated. Reproducible: Always Steps to Reproduce: 1. 2. 3.
Looks like it could be filesystem problems to me. You didn't say what filesystem you're using and didn't include the output of emerge --info as directed on the bug submission page though so there's not really enough information.
yeah, sounds like filesystem corruption reboot and run fsck
