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ixis 12-07-2005 07:22 PM

permission denied for root in FC4: why can't I modify own files?
 
ixis newbie needing some help... I am having a chronic “permission denied” problem here... since about some time and working as root all the time*. Some examples: I could not run java nor install a new one in my FC4. Ok, at the end I made some links and java was working (although is some times crashed my browser, oops), however the program I needed to install dependent on java, Apollo (fruitfly.org) failed to install due to permission problems with the java files. When I perform searches I don’t find files due to “permission denied” to some files. And the last program last night... EMBOSS (emboss.sourceforge.net), a pain in the ass... I keeps on creating files that I can not access during the installation process, at least not directly... and this ends up in error and stops the installation. I can go and change the permissions, and then it works, but then more and more “forbidden files” appear and I don’t understand why files created in my session are not accessible to me!!! Anyway, does not root have access to everything???
Strangely some time ago when I installed EMBOSS for the first time, I did not have direct access to internet through the network... and the installation went perfectly (only some errors due to no access to internet databases), EMBOSS programs worked.

*or is there a difference if I log in as root from a terminal within a user session or work directly on the root session???

Please help, linux is tricking me : (

ps: sorry I could not post the complete url's cause im too newbie...

Tinkster 12-08-2005 07:32 PM

G'day mate :}

Well, it would help if you could copy and paste the output of some of
those attempts, together with the actual output of ls -l of both the
directories content and an ls -ld from the affected directories parent.

Knowing what filesystem and mount-options have been used for the mount-point
you're trying to write stuff to might also be significant information.


Cheers,
Tink


P.S.: Whereabouts in NZ are you? :}

ixis 12-10-2005 07:02 PM

Hi Thinkster,

Thanks for the reply. Well I did not post any huge bunch of error messages cause I thought there might be some really “obvious” action that I should have performed and I did not. Mmm, I can not post my error messages because it's confused with urls... and I can not post urls till I have at least five posts... Well, this is one...

ixis 12-10-2005 07:03 PM

And this is another one... sorry, but I don't see any other way... hopefully the next post it accepts my message...

:)

ixis 12-10-2005 07:05 PM

Hi Thinkster,

Aha, now, this is the error message I obtain when trying to install Apollo:

[root@localhost pkg]# ./install.bin
Preparing to install...
Extracting the JRE from the installer archive...
Unpacking the JRE...
Extracting the installation resources from the installer archive...
Configuring the installer for this system's environment...
awk: cmd. line:6: warning: escape sequence `\.' treated as plain `.'

Launching installer...

IAResourceBundle: create resource bundle: en
seaFilename = install
Default properties location = /usr/local/pkg/
UI Mode set to 'SWING' UI not supported by VM. Reverting to AWT.
Default - AWT.
__________________________________________________________________________

__________________________________________________________________________

InstallAnywhere 6.1 Standard
__________________________________________________________________________

Sat Dec 10 23:27:45 NZDT 2005

Free memory = 15076 kB
Total memory = 16320 kB

No arguments.

java.class.path:
/tmp/install.dir.26376/InstallerData
/tmp/install.dir.26376/InstallerData/installer.zip

ZGUtil.CLASS_PATH:
/tmp/install.dir.26376/InstallerData
/tmp/install.dir.26376/InstallerData/installer.zip

sun.boot.class.path:
/tmp/install.dir.26376/Linux/resource/jre/lib/rt.jar
/tmp/install.dir.26376/Linux/resource/jre/lib/i18n.jar
/tmp/install.dir.26376/Linux/resource/jre/lib/sunrsasign.jar
/tmp/install.dir.26376/Linux/resource/jre/lib/jsse.jar
/tmp/install.dir.26376/Linux/resource/jre/lib/jce.jar
/tmp/install.dir.26376/Linux/resource/jre/lib/charsets.jar
/tmp/install.dir.26376/Linux/resource/jre/classes

java.ext.dirs:
/tmp/install.dir.26376/Linux/resource/jre/lib/ext

java.version == 1.4.2_07 (Java 2+)
java.vm.name == Java HotSpot(TM) Client VM
java.vm.vendor == Sun Microsystems Inc.
java.vm.version == 1.4.2_07-b05
java.vm.specification.name == Java Virtual Machine Specification
java.vm.specification.vendor == Sun Microsystems Inc.
java.vm.specification.version == 1.0
java.specification.name == Java Platform API Specification
java.specification.vendor == Sun Microsystems Inc.
java.specification.version == 1.4
java.vendor == Sun Microsystems Inc.
java.vendor.url == http://java.sun.com/
java.class.version == 48.0
java.compiler == null
java.home == /tmp/install.dir.26376/Linux/resource/jre
java.io.tmpdir == /tmp
os.name == Linux
os.arch == i386
os.version == 2.6.11-1.1369_FC4smp
path.separator == :
file.separator == /
file.encoding == UTF-8
user.name == root
user.home == /root
user.dir == /tmp/install.dir.26376
user.language == en
user.region == null
__________________________________________________________________________

java.lang.UnsatisfiedLinkError: /tmp/install.dir.26376/Linux/resource/jre/lib/i386/libawt.so: /tmp/install.dir.26376/Linux/resource/jre/lib/i386/libawt.so: cannot restore segment prot after reloc: Permission denied
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.NativeLibLoader.loadLibraries(Unknown Source)
at sun.awt.DebugHelper.<clinit>(Unknown Source)
at java.awt.Component.<clinit>(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.f(DashoA8113)
at com.zerog.ia.installer.LifeCycleManager.g(DashoA8113)
at com.zerog.ia.installer.LifeCycleManager.a(DashoA8113)
at com.zerog.ia.installer.Main.main(DashoA8113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.zerog.lax.LAX.launch(DashoA8113)
at com.zerog.lax.LAX.main(DashoA8113)
Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)

Stack Trace:
java.lang.UnsatisfiedLinkError: /tmp/install.dir.26376/Linux/resource/jre/lib/i386/libawt.so: /tmp/install.dir.26376/Linux/resource/jre/lib/i386/libawt.so: cannot restore segment prot after reloc: Permission denied
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.NativeLibLoader.loadLibraries(Unknown Source)
at sun.awt.DebugHelper.<clinit>(Unknown Source)
at java.awt.Component.<clinit>(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.f(DashoA8113)
at com.zerog.ia.installer.LifeCycleManager.g(DashoA8113)
at com.zerog.ia.installer.LifeCycleManager.a(DashoA8113)
at com.zerog.ia.installer.Main.main(DashoA8113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.zerog.lax.LAX.launch(DashoA8113)
at com.zerog.lax.LAX.main(DashoA8113)
This Application has Unexpectedly Quit: Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)


The permission information you asked for:

[root@localhost pkg]# ls -l
total 74752
drwxrwxrwx 11 ixis iris 4096 Dec 10 23:14 EMBOSS-3.0.0
-rwxr-xr-x 1 ixis iris 55504250 Nov 21 10:06 install.bin
-rwxr-xr-x 1 ixis iris 16517969 Nov 21 14:04 jre-1_5_0_01-linux-i586.bin
-rwxr-xr-x 1 ixis iris 3069437 Aug 10 10:23 MUMmer3.18.tar.gz
-rwxr-xr-x 1 ixis iris 1331611 Aug 16 13:37 pipmaker-2005-08-03-01.tar.tar
[root@localhost pkg]# cd ..
[root@localhost local]# ls -ld
drwxr-xr-x 12 root root 4096 Dec 8 01:01 .


And I’m afraid I’m not sure what you mean by “mount points”. The only thing I can thing of is my fstab file, here it is:

# This file is edited by fstab-sync - see 'man fstab-sync' for details
/dev/VolGroup00/LogVol00 / ext3 defaults 1 1
LABEL=/boot /boot ext3 defaults 1 2
/dev/devpts /dev/pts devpts gid=5,mode=620 0 0
/dev/shm /dev/shm tmpfs defaults 0 0
/dev/sdb2 /opt vfat defaults 0 0
/dev/proc /proc proc defaults 0 0
/dev/sys /sys sysfs defaults 0 0
/dev/VolGroup00/LogVol01 swap swap defaults 0 0
/dev/fd0 /media/floppy auto pamconsole,exec,noauto,managed 0 0
/dev/hdb /media/cdrecorder auto pamconsole,exec,noauto,managed 0 0
/dev/hda /media/cdrecorder1 auto pamconsole,exec,noauto,managed 0 0
/dev/sdc1 /media/IRIS vfat pamconsole,exec,noauto,fscontext=system_u:object_r:removable_t,managed 0 0
/dev/sdd5 /media/DISK3_VOL2 ntfs pamconsole,exec,noauto,fscontext=system_u:object_r:removable_t,managed 0 0
/dev/sdd1 /media/DISK3_VOL1 vfat pamconsole,exec,noauto,fscontext=system_u:object_r:removable_t,managed 0 0
/dev/sdd6 /media/DISK3_VOL3 ntfs pamconsole,exec,noauto,fscontext=system_u:object_r:removable_t,managed 0 0

Please let me know any more information you need. By the way I am in Christchurch... Uni of Canterbury.

Cheers,

Iris


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