Solved: pacman - permissions differ on tmp/

Not sure if anyone else is seeing this because this may have been part of something I did a way back. I'm getting:
( 35/400) upgrading filesystem [######################] 100%
warning: directory permissions differ on tmp/
filesystem: 777 package: 1777
I know a bit about the filesystem package. If I remember correctly it contains files that are Arch specific like the boot scripts... Now if I'm reading this correctly the 777 permissions of "filesystem" is original directory and "package" is the package's permissions for the tmp directory. Here's my /tmp directory permissions after the update:
drwxrwxrwt 11 root root 4.0K Sep 13 11:41 tmp
Can anyone help me clarify this? Is the problem now fixed, or is there something I need to do?
Last edited by Gen2ly (2010-09-13 19:49:14)

I haven't seen pacman changing permission on directories yet, but according to the message, your /tmp didn't have the sticky bit set before the upgrade. Though things will work fine with just 777, not having the sticky bit on /tmp will mean that someone could delete and replace files owned by someone else, which is a security risk.

Similar Messages

[SOLVED] warning: directory permissions differ on var/log/wicd/

Hi,
I've seen several posts about this but I couldn't really figure out what's the appropriate action. Well, anyway I get the following error message when doing a pacman -Syu
warning: directory permissions differ on var/log/wicd/
filesystem: 1363 package: 755
Is it a bug? Should I change the filepermission of the directory, and if so to what?
Last edited by OMGitsUGOD (2009-09-18 10:38:32)

This is sort of related,
http://bbs.archlinux.org/viewtopic.php?pid=432588
or at least thats the post at the end has the same file permisions as I have in /var/log/wicd.
$ ls -la /var/log/ | grep wicd
d-wxrw--wt 2 root root 4096 2009-08-27 07:58 wicd
I'm pretty bad at this stuff, but isn't this rather 1361 than 1363, or am I totally wrong? And why not allow theowner to read the file?
Last edited by OMGitsUGOD (2009-09-17 08:43:32)

GDM update: directory permissions differ on /var/log/gdm/

Hello,
Running Arch 64Bits kernel 3.9.9-1 with systemd and i got the following warning during a gdm update today:
(1/6) upgrading libgdm [######################] 100%
(2/6) upgrading gdm [######################] 100%
warning: directory permissions differ on /var/log/gdm/
filesystem: 711 package: 1770
Why would gdm need some 1770 permissions for log files? Looks pretty suspicious to me, especially the sticky bit thing. What did i miss?
PS: BTW the update is successful (it's a warning afterall, not an error)
Thanks
EDIT:
Looks like the opposite situation than 3 years ago:
https://bbs.archlinux.org/viewtopic.php?id=94681
https://bugs.archlinux.org/task/19294
EDIT2: here's what i have in /var/log:
msytux666 var # ls -la
total 64
drwxr-xr-x 14 root root 4096 Jul 6 15:34 .
drwxr-xr-x 20 root root 4096 Jul 16 20:24 ..
-rwxrwxrwx 1 root root 4192 Jun 19 11:27 .com.zerog.registry.xml
drwxr-xr-x 7 root root 4096 Jul 7 00:07 abs
drwxr-xr-x 8 root root 4096 Jun 16 17:28 cache
drwxr-xr-x 3 root root 4096 Jun 17 19:07 db
drwxr-xr-x 2 root root 4096 May 31 20:40 empty
drwxrwxr-x 2 root games 4096 May 31 20:40 games
drwx--x--x 2 gdm gdm 4096 Jun 15 14:23 gdm
drwxr-xr-x 26 root root 4096 Jul 16 01:13 lib
drwxr-xr-x 2 root root 4096 May 31 20:40 local
lrwxrwxrwx 1 root root 11 May 31 20:40 lock -> ../run/lock
drwxr-xr-x 6 root root 4096 Jul 18 00:33 log
lrwxrwxrwx 1 root root 10 May 31 20:40 mail -> spool/mail
drwxr-xr-x 2 root root 4096 May 31 20:40 opt
lrwxrwxrwx 1 root root 6 May 31 20:40 run -> ../run
drwxr-xr-x 6 root root 4096 Jun 16 17:28 spool
drwxrwxrwt 8 root root 4096 Jul 18 00:33 tmp
gdm is owned by gdm, so why would it needs 1770 permissions?
EDIT3:
After further research i appear the way gdm is installed may matter.
Well i installed gdm through pacman and always update it with pacman as well. Never manually compiled/make_install'd it nor used abs for it.
Last edited by BGK (2013-07-19 21:37:13)

Okay I'm confused ...
Commit:https://projects.archlinux.org/svntogit … 92c38d536d
@@ -68,8 +68,7 @@ package_gdm() {
cd $pkgbase-$pkgver
make DESTDIR="$pkgdir" install
- chmod 1770 "$pkgdir/var/log/gdm"
- chmod 700 "$pkgdir/var/lib/gdm/.config/dconf"
+ chmod 711 "$pkgdir/var/log/gdm"
rm -r "$pkgdir/var/run" "$pkgdir/var/gdm"
### Split libgdm
so that takes away the 1770 permissions, and replaces them with 711.
@@ -5,6 +5,7 @@ post_install() {
getent passwd gdm > /dev/null 2>&1 || usr/sbin/useradd -c 'Gnome Display Manager' -u 120 -g gdm -d /var/lib/gdm -s /sbin/nologin gdm
passwd -l gdm > /dev/null
chown -R gdm:gdm /var/lib/gdm > /dev/null
+ chown root:gdm /var/log/gdm > /dev/null
glib-compile-schemas /usr/share/glib-2.0/schemas
gtk-update-icon-cache -q -t -f /usr/share/icons/hicolor
however:
chown root:gdm /var/log/gdm > /dev/null
.. is where I get confused. This command makes root and the group gdm the new owners of /var/log/gdm, or did I go wrong somewhere?

[SOLVED]pacman fails to upgrade... /usr/bin/vercmp: cannot execute bin

Proceed with installation? [Y/n] y
:: Retrieving packages from core...
pacman-3.2.1-1-x86_64 491.3K 1850.7K/s 00:00:00 [########################################################################################################] 100%
checking package integrity...
(1/1) checking for file conflicts [########################################################################################################] 100%
(1/1) upgrading pacman [########################################################################################################] 100%
warning: /etc/pacman.d/mirrorlist installed as /etc/pacman.d/mirrorlist.pacnew
/tmp/alpm_eT02H1/.INSTALL: line 5: /usr/bin/vercmp: cannot execute binary file
/tmp/alpm_eT02H1/.INSTALL: line 5: [: : integer expression expected
Here is more info on my system and the file vermcp is installed and permissions seem correct.
http://rafb.net/p/MYk3pO21.html
HELP?
Last edited by rooloo (2008-09-09 00:07:09)

Ok, this was my dumb mistake again. I was testing out powerpill on my server which is a 32 bit machine. I tried copying my 64 bit mirrorlist to my 32 bit server because I have it ranked and slimmed down to only the essential servers.

Permissions differ not being fixed...

Hi Everyone,
I run "verify permissions" time to time and the permissions stated below always pops out even though i have run "repair permissions" several times on them. It appears again the next time i do the testing again. So it appears that they are not fixed. Does anyone have an answer for this and how to solve this issue?
Thanks.
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/DVD.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSettings.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSources.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Movies.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Music.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Photos.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Podcasts.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/TV.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/BackRow.framework/Versions/A/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "Applications/iTunes.app/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "Applications/iTunes.app/Contents/Frameworks/InternetUtilities.bundle/Contents/ CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "Applications/iTunes.app/Contents/Resources/iTunesHelper.app/Contents/CodeResou rces", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "System/Library/CoreServices/RawCamera.bundle/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/CodeResourc es", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/BlackAndWhiteEffect.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/CubeTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/DissolveTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/DropletTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/FadeThroughBlackTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/FlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/MosaicFlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/MosaicFlipTransitionSmall.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/PageFlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/PushTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/RevealTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/SepiaEffect.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/TwirlTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/WipeTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
-------------------------------------------------------------

Does anyone have an answer for this
Apple changed the structure of some of its packages without updating the repair permissions mechanism.
how to solve this issue?
Wait for Apple to release a patch and then install it. It can't be fixed by customers.
(43344)

Libvirt permissions differ on upgrade

(12/16) upgrading libvirt [--------------------------------] 100%
warning: /etc/libvirt/qemu/networks/default.xml installed as /etc/libvirt/qemu/networks/default.xml.pacnew
warning: directory permissions differ on /var/lib/libvirt/qemu/
filesystem: 755 package: 770
>>> You may need to run 'rm -rf ~/.libvirt'
Does pacman just never update permissions automatically? Anyway I just manually changed it with the following command. Hope that was the right call.
$ sudo chmod 770 /var/lib/libvirt/qemu/

Directory permissions are never changed automatically. A directory could be part of two different packages, with each package specifying different permissions. To make the job easier pacman only warns about changed directory permissions. File permissions are another matter, they will be modified.
You did the right thing with changing the permissions if the 755 wasn't set by you manually.

Directory permissions differ on var/

When upgrading packages with pacman, I've been getting a warning that "directory permissions differ on var/ filesystem 775 package 755
This most recently was during my upgrade of xorg-server
I'm not sure what causes this warning, or whether some action needs to be taken, and if so, which way to change things.....:(

http://bbs.archlinux.org/viewtopic.php?id=42314

Warning: directory permissions differ

I am getting an error when downloading and installing packages with pacman.
This is what I get:
$ sudo pacman -S nitrogen
warning: nitrogen-1.2-1 is up to date -- reinstalling
resolving dependencies...
looking for inter-conflicts...
Targets: nitrogen-1.2-1
Total Download Size: 0.00 MB
Total Installed Size: 0.13 MB
Proceed with installation? [Y/n]
checking package integrity...
(1/1) checking for file conflicts [#####################] 100%
(1/1) upgrading nitrogen [#####################] 100%
warning: directory permissions differ on usr/man/man1/
filesystem: 755 package: 700
I don't know if that has a serious impact, but I am sure it shouldn't be like that...

Snowman wrote:Submit a bug report.
This is one way and i hope it helps you and the other devs. But what do you think about that the systems can repair this by itselfs? On my opensuse server i have a tool named chkstat which runs as a cronjob and set the file permissions as loaded from a file.
Source: http://ftp.gwdg.de/pub/opensuse/distrib … 11.src.rpm
manpage: http://www.trinler.de/de/linux/man.html?command=chkstat
The advantage from my side is that one or a group of devs define the file permissions standard for arch linux and everyone can choose to use it or to append own more or less secure/paranoid settings. Another sideeffect is that every dev can take a look inside this config file to see what permission the own PKGBUILD need so that in the best case we will not see such messages in the future. The source includes config files so there is no need to restyle this all from zero.

"Permissions differ" on exactly 80 paths

If I repair my disk permissions on my Mac its permissions differ on 80 paths, reaching from AirPort over QuickTime to iPhoto...
What's the problem and how can I solve it?

As long as you end up with the message 'permission repairs complete' you are OK.
Permissions you can ignore on 10.5:
http://support.apple.com/kb/TS1448?viewlocale=en_US
using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard changed the location of a number of system components.

I have to keep going back to utilities first aid and do a disck permission repair because my monitor keeps going to sleep. this is the message i get.Permissions differ on "System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resourc es/

I have to keep going to disk repair to correct an issue that makes my monitor go to sleep the message i get is
Permissions differ on “System/Library/PreferencePanes/.Displays/V1/Displays.prefPane/Contents/Resourc es/pt.lproj/DisplaysPref.nib”; should be -rw-r--r-- ; they are -rwxr-xr-x .

Have you done a PRAM reset, CMD+Option+p+r...
http://support.apple.com/kb/HT1379
In fact, do 3 in a row, takes a bit of time.
Intel-based Macs: Resetting the System Management Controller (SMC)...
http://support.apple.com/kb/HT3964

Permissions differ but don't seem to repair

Hello,
When I run verify permissions a long list of things pop up saying the permissions differ. But when I run repair permissions the same things pop up as differing permissions. I thought maybe it was just the computer telling me it was fixing the problem, but, out of curiosity, I ran verify permissions again. The same things popped up in the window. I've also got a problem with Safari, Mail, and iTunes hanging and when I try to force quit the application it won't actually force quit and the blue on light in the dock stays lit. I also noticed that one of the messages in verify permissions said something about iTunes. Could these two things possibly be connected. I was just about to run an archive install because I read in a thread that this would fix the latter problem of applications not quitting. But I also keep reading about verifying permissions before doing that, and I don't think I've had a successful verify and repair yet. Any and every piece of help is appreciated
Edit-now it's saying that one thing is irreparable. Answers?
Message was edited by: MichaelJZilla

HI,
The permissions issues and Safari/Mail and iTunes issues are NOT related.
First. You can safely ignore the messages when you repair disk permissions. They are a result of recent software updates. As long as you see these words at the bottom of the window;
Permissions repair complete, you have nothing to worry about.
Now, applications that freeze or crash and you can't quit.. that's different. Might be an underlying problem. Boot from your install disk and check the hard disk for errors.
*"and I don't think I've had a successful verify and repair yet."*
Do you mean you've run Disk Utility and it's reported errors and they aren't repaired? Here's how to do that.
Insert the installer disk and Restart, holding down the "C" key until grey Apple appears.
Go to Installer menu (Panther and earlier) or Utilities menu (Tiger and later) and launch Disk Utility.
Select your HDD (manufacturer ID) in the left panel.
Select First Aid in the Main panel.
*(Check S.M.A.R.T Status of HDD at the bottom of right panel. It should say: Verified)*
Click Repair Disk on the bottom right.
If DU reports disk does not need repairs quit DU and restart.
If DU reports errors Repair again and again until DU reports disk is repaired.
When you are finished with DU, from the Menu Bar, select Utilities/Startup Manager.
Select your start up disk and click Restart
Check to see how much free disk space there is. Right or control click the MacintoshHD icon. Click Get Info. In the Get Info window you will see Capacity and Available. Make sure you always have a minimum of 10% to 15% free disk space at all times.
Carolyn

Disk Utility - Disk Permissions Differ and Warnings?

Dear Forum,
I have a screen freeze problem with my G5 DP. I've tried various ways to cure it like running OmniDiskSweeper to no avail.
In Disk Utility when I run Repair Permissions there are some Permissions Differ and unresolved Warnings listed. Please see below.
Permissions differ on "private/var/log/secure.log", should be -rw------- , they are -rw-r----- .
Permissions differ on "Library/Application Support/ProApps/Internal Plug-Ins/BrowserKit/iLife.bkplugin/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "System/Library/PrivateFrameworks/BrowserKit.framework/Versions/A/CodeResources ", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/DVD.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSettings.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSources.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Movies.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Music.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Photos.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Podcasts.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/TV.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/BackRow.framework/Versions/A/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/ProKit.framework/Versions/A/Resources/Leopard Panels.bundle/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/
Resources/DiskManagementTool" has been modified and will not be repaired.
Permissions differ on "System/Library/Extensions/AppleNDRV/ATIDriver.bundle/Contents/MacOS/ATIDriver" , should be -rwxr-xr-x , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/AppleNDRV/ATIRuntimeDriver.bundle/Contents/MacOS/ATI RuntimeDriver", should be -rwxr-xr-x , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/ATIRadeon8500VADriver.bundle/Contents/MacOS/ATIRadeo n8500VADriver", should be -rwxr-xr-x , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/ATIRadeon9700VADriver.bundle/Contents/MacOS/ATIRadeo n9700VADriver", should be -rwxr-xr-x , they are -rw-r--r-- .
Warning: SUID file "usr/sbin/pppd" has been modified and will not be repaired.
Warning: SUID file "usr/sbin/vpnd" has been modified and will not be repaired.
Can anybody advise me on how to resolve these permissions differ and Warnings in the hope that it will fix my screen freeze problem.
Sincerely,

Sorry!
If you were having any serious problems with your Mac you might as well complete the exercise by repairing your hard disk as well. You cannot do this from the same start-up disk. Reboot from your install disk (holding down the C key). Once it opens, select your language, and then go to Disk Utility from the Utilities menu. Select your hard disk as before and click Repair.
Once that is complete reboot again from your usual start-up disk.
More useful reading here:
Resolve startup issues and perform disk maintenance with Disk Utility and fsck
http://support.apple.com/kb/TS1417?viewlocale=en_US
For a full description of how to resolve Disk, Permission and Cache Corruption, you should read this FAQ from the X Lab:
http://www.thexlab.com/faqs/repairprocess.html

Disk Permissions differ after a day

Hi,
Just in the past couple of days my computer has been running very slowly. It has been taking 15 minutes to log in, so I fire up Disk Utility, Verify permissions and there are a heap of differing permissions. I repair permissions and the machine runs fine. The next day the computer is back to being slow. I go through verifying permissions and there are a heap of differing permissions again.
My Hard Drive is farily full, I have 2 partitions, the Macintosh HD partition is running at 7gb free and the extended partition has 32gb free. I don't know if a full disk would be causing these errors.
Here is a log of the disk utility.
Any help would be greatly appreciated.
Thanks
===========================
2009-03-14 09:12:43 +0900: Repairing permissions for “Macintosh HD”
2009-03-14 09:12:43 +0900: Reading permissions database.
2009-03-14 09:12:43 +0900: Reading the permissions database can take several minutes.
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/DVD.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSettings.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSources.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Movies.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Music.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Photos.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Podcasts.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/TV.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:48 +0900: Permissions differ on "System/Library/PrivateFrameworks/BackRow.framework/Versions/A/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:20:56 +0900: Permissions differ on "private/var/spool/cups/cache/rss", should be drwxr-xr-x , they are drwxrwxr-x .
2009-03-14 09:22:35 +0900: Permissions differ on "Applications/iTunes.app/Contents/CodeResources", should be -rw-rw-r-- , they are lrwxr-xr-x .
2009-03-14 09:22:35 +0900: Permissions differ on "Applications/iTunes.app/Contents/Frameworks/InternetUtilities.bundle/Contents/ CodeResources", should be -rw-rw-r-- , they are lrwxr-xr-x .
2009-03-14 09:22:40 +0900: Permissions differ on "Applications/iTunes.app/Contents/Resources/iTunesHelper.app/Contents/CodeResou rces", should be -rw-rw-r-- , they are lrwxr-xr-x .
2009-03-14 09:22:48 +0900: Permissions differ on "System/Library/LaunchDaemons/com.apple.usbmuxd.plist", should be -rw-r--r-- , they are -rwxr-xr-x .
2009-03-14 09:36:46 +0900: Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
2009-03-14 09:36:47 +0900: Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.
2009-03-14 09:37:08 +0900: Permissions differ on "System/Library/CoreServices/RawCamera.bundle/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
2009-03-14 09:37:13 +0900: Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
2009-03-14 09:37:13 +0900: Warning: SUID file "System/Library/Printers/IOMs/LPRIOM.plugin/Contents/MacOS/LPRIOMHelper" has been modified and will not be repaired.
2009-03-14 09:37:14 +0900: Group differs on "private/etc/cups", should be 0, group is 26.
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iLifeMediaBrowser.framework/Versions/A/CodeRe sources", should be -rw-r--r-- , they are lrw-r--r-- .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/CodeResourc es", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/BlackAndWhiteEffect.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/CubeTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/DissolveTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/DropletTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/FadeThroughBlackTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/FlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/MosaicFlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/MosaicFlipTransitionSmall.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/PageFlipTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/PushTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/RevealTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/SepiaEffect.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/TwirlTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:20 +0900: Permissions differ on "System/Library/PrivateFrameworks/iPhotoAccess.framework/Versions/A/Resources/P lugins/WipeTransition.IAPlugin/Contents/CodeResources", should be -rw-r--r-- , they are lrwxr-xr-x .
2009-03-14 09:37:27 +0900:
2009-03-14 09:37:27 +0900: Permissions repair complete
2009-03-14 09:37:27 +0900:
2009-03-14 09:37:27 +0900:

I have no idea but repairing permissions or not would not likely have any impact on the computer's login time (do you actually mean login as in entering your username and password or do you simply mean boot time?)
If your computer runs slow look for other possible causes such as incompatible third-party software you have installed or corrupted caches and/or preference files. See the following:
Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility. For situations DU cannot handle the best third-party utilities are: Disk Warrior; DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. TechTool Pro provides additional repair options including file repair and recovery, system diagnostics, and disk defragmentation. TechTool Pro 4.5.1 or higher are Intel Mac compatible; Drive Genius is similar to TechTool Pro in terms of the various repair services provided. Versions 1.5.1 or later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep. Dependence upon third-party utilities to run the periodic maintenance scripts had been significantly reduced in Tiger and Leopard.
OS X automatically defrags files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems.
I would also recommend downloading the shareware utility TinkerTool System that you can use for periodic maintenance such as removing old logfiles and archives, clearing caches, etc.
For emergency repairs install the freeware utility Applejack. If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the commandline. Note that AppleJack 1.5 is required for Leopard.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
1. Retrospect Desktop (Commercial - not yet universal binary)
2. Synchronize! Pro X (Commercial)
3. Synk (Backup, Standard, or Pro)
4. Deja Vu (Shareware)
5. Carbon Copy Cloner (Donationware)
6. SuperDuper! (Commercial)
7. Intego Personal Backup (Commercial)
8. Data Backup (Commercial)
9. SilverKeeper 2.0 (Freeware)
10. MimMac (Commercial)
11. CloneTool Hatchery (Shareware)
12. Clone X (Commercial)
The following utilities can also be used for backup, but cannot create bootable clones:
1. Backup (requires a .Mac account with Apple both to get the software and to use it.)
2. Toast
3. Impression
4. arRSync
Apple's Backup is a full backup tool capable of also backing up across multiple media such as CD/DVD. However, it cannot create bootable backups. It is primarily an "archiving" utility as are the other two.
Impression and Toast are disk image based backups, only. Particularly useful if you need to backup to CD/DVD across multiple media.
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at www.versiontracker.com and www.macupdate.com.

When I repair disk permissions I get the following:Repairing permissions for "MacIntosh HD" Determining correct file permissions. Permissions differ on ./Library/Widgets, should be drwxr-xr-x , they are drwxrwxr-x Owner and group corrected on ./Library/W

Repairing permissions for “MacIntosh HD”
Determining correct file permissions.
Permissions differ on ./Library/Widgets, should be drwxr-xr-x , they are drwxrwxr-x
Owner and group corrected on ./Library/Widgets
Permissions corrected on ./Library/Widgets
Permissions differ on ./System/Library/User Template, should be drwx------ , they are drwxr-xr-x
Owner and group corrected on ./System/Library/User Template
Permissions corrected on ./System/Library/User Template
Group differs on ./usr/bin/fetchmail, should be 0, group is 6
Permissions differ on ./usr/bin/fetchmail, should be -rwxr-xr-x , they are -rwxr-sr-x
Owner and group corrected on ./usr/bin/fetchmail
Permissions corrected on ./usr/bin/fetchmail
Permissions differ on ./usr/lib/php/build/Makefile.global, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/Makefile.global
Permissions corrected on ./usr/lib/php/build/Makefile.global
Permissions differ on ./usr/lib/php/build/acinclude.m4, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/acinclude.m4
Permissions corrected on ./usr/lib/php/build/acinclude.m4
Permissions differ on ./usr/lib/php/build/mkdep.awk, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/mkdep.awk
Permissions corrected on ./usr/lib/php/build/mkdep.awk
Permissions differ on ./usr/lib/php/build/phpize.m4, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/phpize.m4
Permissions corrected on ./usr/lib/php/build/phpize.m4
Permissions differ on ./usr/lib/php/build/scan_makefile_in.awk, should be -r--r--r-- , they are -r-xr-xr-x
Owner and group corrected on ./usr/lib/php/build/scan_makefile_in.awk
Permissions corrected on ./usr/lib/php/build/scan_makefile_in.awk
Permissions differ on ./usr/lib/system/libmathCommon.A.dylib, should be -r-xr-xr-x , they are -rwxr-xr-x
Owner and group corrected on ./usr/lib/system/libmathCommon.A.dylib
Permissions corrected on ./usr/lib/system/libmathCommon.A.dylib
Permissions differ on ./usr/libexec/dumpemacs, should be -r-sr-xr-x , they are -r-xr-xr-x
Owner and group corrected on ./usr/libexec/dumpemacs
Permissions corrected on ./usr/libexec/dumpemacs
Permissions repair complete
The privileges have been verified or repaired on the selected volume
Then I sometimes get the brown screen that states,You must re-start your computer.
I have already zeroed out the hard drive and re-installed Panther and the upgrade Tiger disc.
I repair permissions using the Tiger disc upgrade.
Can anyone help me with this??

> I repair permissions using the Tiger disc upgrade.
One thing to note... When running Repair Disk Permissions, it is best to run it while started up normally, from your normal startup disk, not from a Mac OS X installation disc. The only time you should run it while started up from an installation disc is if some problem is preventing you from starting up normally. OTOH, Repair Disk can only be used when starting up from a different disk (such as an installation disc).
So, I would start up normally, run Disk Utility, and use Repair Disk Permissions on your normal startup disk.
NOTE: Repair Disk Permissions often gives alerts messages that can be ignored. They are more "informational," not serious errors.
http://support.apple.com/kb/TS1448
You should still run it periodically. When you run it, what needs to be repaired has been repaired; consider the rest of it an FYI. I've never experience a problem, where a Repair Disk Permissions message actually caused a problem. But, if you ever get an error while running Repair Disk (or Verify Disk), that is usually a serious problem.

Disk permissions do not repair: Verify permissions for "Macintosh HD" Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar", should be lrwxr-xr-x , they are lrw-r--r-- . Permissions differ on "System/Library/Jav

Disk Utility does not repair Permissions (shows repaired but just come back up again). See problems:
Verify permissions for “Macintosh HD”
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib", should be 0, user is 95.
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist", should be lrwxr-xr-x , they are lrw-r--r-- .
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries", should be 0, user is 95.
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Home/lib/security/cacerts", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_CN.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/ko.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/ko.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Dutch.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Dutch.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Italian.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Spanish.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Spanish.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/French.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/French.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/German.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/German.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Japanese.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Japanese.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/dt.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle", should be drwxr-xr-x , they are lrwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Home/lib/security/cacerts", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/English.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/English.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .

Ignore all these.
http://support.apple.com/kb/TS1448?viewlocale=en_US

Solved: pacman - permissions differ on tmp/

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