I am trying to compile the alignment program AQUA with a .tcl script. I have compiled the programs and set the environmental variables in the .tcl file but I am still getting the following error;
tclsh AQUA.tcl mtDNA.fas
stderr couldn't execute "/home/shump/AQUA/muscle": permission denied
couldn't execute "/home/shump/AQUA/rascal": permission denied
couldn't execute "/home/shump/AQUA/normd": permission denied
One normd file does not exists yet (mtDNA.fas.muscle.normd), full stop
If anyone could put me in the right direction to solve this issue, I would appreciate it.
P
Most likely you need to set the execute bit permission on the files mentioned, using:
chmod +x /home/shump/AQUA/muscle /home/shump/AQUA/rascal /home/shump/AQUA/normd
Related
I am setting up a spring boot application and when running it, it should generate a folder in the source directory (see step 3: https://www.baeldung.com/spring-boot-h2-database)
But when running the application I receive the following error:
org.h2.message.DbException: Log file error: "/data/sample.trace.db", cause: "org.h2.message.DbException: Error while creating file ""/data"" [90062-200]" [90034-200]
at org.h2.message.DbException.get(DbException.java:194)
at org.h2.message.TraceSystem.logWritingError(TraceSystem.java:294)
at org.h2.message.TraceSystem.openWriter(TraceSystem.java:315)
at org.h2.message.TraceSystem.writeFile(TraceSystem.java:263)
at org.h2.message.TraceSystem.write(TraceSystem.java:247)
at org.h2.message.Trace.error(Trace.java:194)
it seems to be a permission problem but I do not understand why. My current user, has admin permissons. What am I missing here?
When I encounter this problem on my machine I proceed through following steps:
If I don't know what user & group I am right now: $whoami && groups
What user is the program executed with (I'm not into Java so eg. PHP "echo exec('whoami');")
Who has access to the directory: $ls -la
3.1 If only owner has access and you are not the owner: $chown user:group file
3.2 If group and owner should have access consider: $chmod 770 file
Log rotate doesn't work very well.
So, when i execute command, I got a below error first time.
$ logrotate /etc/logrotate.d/systemname
error: error creating output file /var/lib/logrotate/logrotate.status.tmp: Permission denied
then i changed /var/lib/logrotate/ to 666
Error message change like below.
$ logrotate -f /etc/logrotate.d/systemname
error: error stat()ing state file /var/lib/logrotate/logrotate.status: Permission denied
Help me, how to solve this problem?
thanks.
I am assuming that you tried to run logrotate as unprivileged user ($ in the prompt), so you had no permissions for /var/lib/logrotate/.
I'm trying to import an Oracle dump file, and despite granting global rwx permissions on the files, I'm still getting a permission errors when running the import.
Here's the whole process I've run through:
# Create the dump directory with the dump file, and grant 777 permissions
mkidr -p /home/vagrant/dump
mv /home/vagrant/data.dmp /home/vagrant/dump
chmod -R 777 /home/vagrant/dump
# Check the file permissions
# drwsrwsrwx. vagrant vagrant dump
# -rwxrwxrwx. vagrant vagrant dump/data.dmp
# Add the directory to Oracle
sqlplus system/vagrant
CREATE DIRECTORY DUMP_DIR AS '/home/vagrant/dump';
exit
# Try importing the data
impdp system/vagrant dumpfile=data.dmp directory=DUMP_DIR nologfile=y
And let the keyboard smashing begin...
Connected to: Oracle Database 11g Express Edition Release 11.2.0.2.0 - 64bit Production
ORA-39001: invalid argument value
ORA-39000: bad dump file specification
ORA-31640: unable to open dump file "/home/vagrant/dump/data.dmp" for read
ORA-27037: unable to obtain file status
Linux-x86_64 Error: 13: Permission denied
Additional information: 3
Note: I'm entirely aware that these permissions and passwords are terrible for security, but since I'm just trying to run some experimental analysis on a publicly available data set, I don't really care.
I think the problem is that your script says mkidr instead of mkdir.
This way, you don't create the directory, when you move the file to the supposed dir, it only renames the file, making it appear (as a file, not a directory) /home/vagrant/dump with the right permissions (except the d char at the beginning) and, of course, you cannot search it for files, as it's not a directory, but a file. This will also impede oracle to execute successfully the CREATE DIRECTORY DUMP_DIR AS '/home/vagrant/dump'; as there's a file there with that name.
By the way, to access a file, you don't only need read access in the file inode, but also execute permission x in all the directories followed along the path (in this case /home, /home/vagrant and /home/vagrant/dump ---this last one is a file, not a directory---). In this case, it's ora (the user oracle runs as) the user that must be checked.
I suggest you to impersonate as the user ora and try to read the file if that doesn't work, from the same directory where the database runs, and using the same path as it uses to open the file.
'/usr/bin/myapp' is a link to '/usr/bin/consolehelper'.
When non-root user try to run '/usr/bin/myapp' on command prompt, it shows 'userhelper must be setuid root'. But running with 'sudo /usr/bin/myapp' it works fine.
While using with GUI, it shows 'Insufficient rights' popup. I tried by changing permissions of related files '/etc/security/console.apps/myapp' and '/etc/pam.d/myapp'.
I am getting same popup while opening 'System->Administration->Users and Groups'.
I got the solution! The problem was absence of setuid bit for /usr/sbin/userhelper. I set this using following command:
chmod u+s /usr/sbin/userhelper
This changed the permissions from '-rwx--x--x' to '-rws--x--x'
Today I tried to my USVN on http://192.168.1.2/usvn/ but unfotunately I get this shocking message !!!
Zend_Session::start() - /var/www/usvn/library/Zend/Session.php(Line:438): Error #2 session_start(): open(/var/lib/php5/sess_o58dtec91alc8r5q8821to20h0, O_RDWR) failed: Permission denied (13) Array /var/www/usvn/library/Zend/Session.php(Line:442): Error #2 session_write_close(): open(/var/lib/php5/sess_o58dtec91alc8r5q8821to20h0, O_RDWR) failed: Permission denied (13) Array /var/www/usvn/library/Zend/Session.php(Line:442): Error #2 session_write_close(): Failed to write session data (files). Please verify that the current setting of session.save_path is correct (/var/lib/php5) Array
Trace:
/var/www/usvn/library/Zend/Session/Namespace.php:124 Zend_Session::start
/var/www/usvn/library/Zend/Auth/Storage/Session.php:87 Zend_Session_Namespace::__construct
/var/www/usvn/library/Zend/Auth.php:91 Zend_Auth_Storage_Session::__construct
/var/www/usvn/library/Zend/Auth.php:143 Zend_Auth::getStorage
/var/www/usvn/library/USVN/Controller.php:83 Zend_Auth::getIdentity
/var/www/usvn/library/Zend/Controller/Action.php:492 USVN_Controller::preDispatch
/var/www/usvn/library/Zend/Controller/Dispatcher/Standard.php:285 Zend_Controller_Action::dispatch
/var/www/usvn/library/Zend/Controller/Front.php:934 Zend_Controller_Dispatcher_Standard::dispatch
/var/www/usvn/public/index.php:5 Zend_Controller_Front::dispatch
So Can you please help!
Your apache/php installation is not able to write files in the session.save_path.
Make sure that the user under which apache runs has permissions to read and write in /var/lib/php5/.
Normally in every apache installation this should be true by default unless you messed up something with permissions.
After fixing that you're likely to encounter the same issue for usvn repository path. So keep that in mind. The php/apache user is NOT your shell user, so you should check for that user permissions, usually it's www-data or apache.