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• Adding a jar file to CLASSPATH is still not executable

  - by Simon O'Hanlon

  Perhaps I just don't understand how the whole CLASSPATH environment variable works when trying to find .jar files on your system. I thought if you specified it, you could launch .jar files with java in much the same way that you can launch executables that are on your path. I have an executable java archive (.jar file) on my system, that I stuck in /usr/local/bin/gatk/. I added this to my CLASSPATH via: export CLASSPATH=/usr/local/bin/gatk/GenomeAnalysisTK.jar I thought this would make the .jar file visible to my JVM. When I try to invoke it with java -jar GenomeAnalysisTK.jar #Error: Unable to access jarfile .gatk/GenomeAnalysisTK.jar I can invoke it setting the absolute path, e.g. java -jar /usr/local/bin/gatk/GenomeAnalysisTK.jar, however I'd rather not type the full path each time. I have read many of the linked tutorials but somehow I don't seem to be getting this right and I can't understand what I am doing wrong.

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• How to setup tomcat 7 as a server on windows 2008 server

  - by birdy

  I setup the tomcat7 as a service as below: c:\Program Files (x86)\Tomcat7\apache-tomcat-7.0.32\bin>service.bat install Installing the service 'Tomcat7' ... Using CATALINA_HOME: "C:\Program Files (x86)\Tomcat7\apache-tomcat-7.0.32" Using CATALINA_BASE: "C:\Program Files (x86)\Tomcat7\apache-tomcat-7.0.32" Using JAVA_HOME: "C:\Program Files (x86)\Java\jdk1.7.0_09" Using JRE_HOME: "C:\Program Files (x86)\Java\jdk1.7.0_09\jre" Using JVM: "C:\Program Files (x86)\Java\jdk1.7.0_09\jre\bin\server\ jvm.dll" However, when I try to start the service, I Get the error below: c:\Program Files (x86)\Tomcat7\apache-tomcat-7.0.32\bin>tomcat7.exe %1 is not a valid Win32 application. Failed to run service as console application This is the file I downloaded from apache: apache-tomcat-7.0.32-windows-x64.zip. I am able to successfully start tomcat on port 8080 as a standalong thing. Meaning I go to command prompt and type startup.bat and it starts up successfully. Question How can I resolve this and what are the things I should be troubleshooting for?

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• vPopmail / xinetd.

  - by Lorren Biffin

  I'm attempting to setup vpopmail on my CentOS server (Media Temple). Everything is working like a charm, with the exception that I cannot login to the server from any pop3 client. Upon trying to login I get the following error: Sending of password did not succeed. Mail server mail.(mydomain).com responded: Login failed. I'm running qmail (of course) with xinetd (not tcpserver). I've placed a file called pop3 into the folder /etc/xinetd.d with the content: service pop3 { disable = no socket_type = stream protocol = tcp wait = no user = root server = /var/qmail/bin/qmail-popup server_args = mail.(mydomain).com /home/vpopmail/bin/vchkpw /var/qmail/bin/qmail-pop3d Maildir log_type = FILE /var/log/xinetd.log log_on_success = HOST log_on_failure = HOST RECORD } Can anybody offer any guidance here? I've been unsuccessfully trying to make this happen for over a week.

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• Installing a program on Linux: providing a short command

  - by rwallace

  Suppose you're distributing a program to run on Linux, call it Foo, and the program executable is called foo.exe (because it's a CLR program so it runs under Mono) and it needs a couple of DLLs in the same directory and maybe a later version might need some data files that it reads on startup and whatever, so relocating it to a global bin directory is a bit of hassle and it really prefers to remain in its original directory... But the user would prefer to invoke the program by typing foo instead of mono /path/to/foo.exe. What's the best/most usual way to provide such a short command? Can/should an install script/makefile create a one line script called foo that invokes the full path, and put the one line script in a global bin directory? If so, what should be the target bin directory, and are there any directions about exactly how to do this? Or is there a preferred alternative?

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• X Session from Mac

  - by tekknolagi

  How can I log into an X server from Mac OS X? I know that ssh -X username@host will log me in and I will have the capability to run X applications. On Cygwin/X you can log in and have a whole X session from your computer... and it will look something like this: How can I replicate this? Using this batch script: @echo off SET DISPLAY=127.0.0.1:0.0 SET REMOTE_HOST=%1 IF "%REMOTE_HOST%" == "" SET REMOTE_HOST=10.0.0.1 SET CYGWIN_ROOT=\cygwin SET RUN=%CYGWIN_ROOT%\bin\run -p /usr/bin SET PATH=.;%CYGWIN_ROOT%\bin;%PATH% SET XAPPLRESDIR= SET XCMSDB= SET XKEYSYMDB= SET XNLSPATH= if not exist %CYGWIN_ROOT%\tmp\.X11-unix\X0 goto CLEANUP-FINISH attrib -s %CYGWIN_ROOT%\tmp\.X11-unix\X0 del %CYGWIN_ROOT%\tmp\.X11-unix\X0 :CLEANUP-FINISH if exist %CYGWIN_ROOT%\tmp\.X11-unix rmdir %CYGWIN_ROOT%\tmp\.X11-unix if "%OS%" == "Windows_NT" goto OS_NT echo startxdmcp.bat - Starting on Windows 95/98/Me goto STARTUP :OS_NT REM Windows NT/2000/XP echo startxdmcp.bat - Starting on Windows NT/2000/XP :STARTUP %RUN% XWin -query tekknolagi.dyndns.org -clipboard -lesspointer -scrollbars -screen 0 1050x1655@2 -screen 1 1680x985@1

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• store image installation error in UEC

  - by selvakumar

  to my college final year project we planned to setup the private cloud on the two machines. I recently installed Ubuntu Enterprise Cloud (UEC) on two of my machines . I was trying to install the store image through WebUI. I was able to download Ubuntu 10.04 - (i386) image but while installing, it's giving me following error: - Command 'euca-upload-bundle' returned status code 1: Checking bucket: image-store-1296600766 Traceback (most recent call last): File "/usr/bin/euca-upload-bundle", line 231, in main() File "/usr/bin/euca-upload-bundle", line 214, in main bucket_instance = ensure_bucket(conn, bucket, canned_acl) File "/usr/bin/euca-upload-bundle", line 87, in ensure_bucket bucket_instance = connection.get_bucket(bucket) File "/usr/lib/pymodules/python2.6/boto/s3/connection.py", line 275, in get_bucket rs = bucket.get_all_keys(headers, maxkeys=0) File "/usr/lib/pymodules/python2.6/boto/s3/bucket.py", line 204, in get_all_keys headers=headers, query_args=s) File "/usr/lib/pymodules/python2.6/boto/s3/connection.py", line 342, in make_request data, host, auth_path, sender) File "/usr/lib/pymodules/python2.6/boto/connection.py", line 459, in make_request return self._mexe(method, path, data, headers, host, sender) File "/usr/lib/pymodules/python2.6/boto/connection.py", line 437, in _mexe raise e socket.error: [Errno 110] Connection timed out could anyone please help me?

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• installing jdk1.7.0 on Ubuntu 11.04 machine

  - by Yogesh

  I am facing a problem while trying to install Java 7 on Ubuntu. The following are the steps that I performed for installing: I installed the setup file from the link given below: wget http://download.oracle.com/otn-pub/java/jdk/7u1-b08/jdk-7u1-linux-x64.tar.gz I have a file: jdk-7u1-linux-x64.tar.gz I Untared it: tar -xvf jdk-7u1-linux-x64.tar.gz sudo mv ./jdk1.7.0_01 /usr/lib/jvm/jdk1.7.0_01 sudo update-alternatives –config java Here it gave me the following output: There is only one alternative in link group java: /usr/lib/jvm/java-6-sun/jre/bin/java Nothing to configure. sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk1.7.0_01/jre/bin/java 1(I entered 1 here.) sudo update-alternatives --config java java -version. It showed the following output java version "1.6.0_26" Java(TM) SE Runtime Environment (build 1.6.0_26-b03) Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode) I am not sure if jdk1.7.0 is installed as its showing the version as 1.6.0_26.

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• Can't run command with sudo, even with the full path, I got an error

  - by Keating Wang

  the command starling is /home/keating/.rvm/gems/ruby-1.9.2-p290/bin/starling when run starling, get the error Permission denied when run rvmsudo starling, works well when run sudo starling, get the error sudo: starling: command not found when run sudo /home/keating/.rvm/gems/ruby-1.9.2-p290/bin/starling, get the error: /home/keating/.rvm/rubies/ruby-1.9.2-p290/lib/ruby/site_ruby/1.9.1/rubygems/dependency.rb:247:in to_specs': Could not find starling (>= 0) amongst [minitest-1.6.0, rake-0.8.7, rdoc-2.5.8] (Gem::LoadError) from /home/keating/.rvm/rubies/ruby-1.9.2-p290/lib/ruby/site_ruby/1.9.1/rubygems/dependency.rb:256:into_spec' from /home/keating/.rvm/rubies/ruby-1.9.2-p290/lib/ruby/site_ruby/1.9.1/rubygems.rb:1229:in gem' from /home/keating/.rvm/gems/ruby-1.9.2-p290/bin/starling:18:in' I really want to run the command with sudo, because the error above is the same as running rvmsudo service starling start(I had set starling as a service of the os)

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• Where is php executable on Ubuntu?

  - by user601L

  I have installed apache and php. I know php works as I have tested a simple php file on apache server. I'm writing a simple webserver which should be able to process php files. So what I want to do is once I get a request for a php file, something like 'exec php test.php' and get the output and pass it to the client. As I'm not much into Ubuntu, I don't know where is the php executable (should be in \bin right?) to do it. But there is no php file inside \bin or \usr\bin. When I run 'which php' it shows nothing. How do I do this?

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• KDE on Windows won't download/install

  - by endolith

  No matter which mirror I use, I get this error. I've tried a few times over the last several weeks. Download failed --------------------------- The download of ftp://kde.mirrors.tds.net/pub/kde/stable/4.5.4/win32/libopensp-vc100-1.5.2-bin.tar.bz2 failed with error: archive downloaded from ftp://kde.mirrors.tds.net/pub/kde/stable/4.5.4/win32/libopensp-vc100-1.5.2-bin.tar.bz2 checksum error --------------------------- Retry Ignore Cancel Should I just ignore this and let it continue? Update: I ran as administrator, changed the install directory to C:\KDE, and ignored this error, and it seemed to install, but then gave me a different error, same file: Error --------------------------- Internal Error - File C:/Temp/KDE/libopensp-vc100-1.5.2-bin.tar.bz2 does not exist --------------------------- Cancel But now programs seem to work! Should I just ignore this error? I can't even find a plain English explanation of what libopensp is.

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• Creepy MySQL error during hard work

  - by Kiewic

  Hi, I have a MySQL database installed on a OpenSuse 11.1 server (it is a Bitnami image). The database works fine, it can stay many days without any error, but when MySQL receives a huge amount of transactions, it dies immediately. The next screen shows the error: Moreover, I don't know how to restart MySQL. I have tried this: /opt/bitnami/mysql/bin/mysqld start But it doesn't work, that gives me the next output: 110209 17:09:01 [ERROR] Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root! 110209 17:09:01 [ERROR] Aborting 110209 17:09:01 [Note] /opt/bitnami/mysql/bin/mysqld.bin: Shutdown complete It doesn't matter which kind of statements are executing, if they are a huge amount, MySQL dies. The MySQL server version is 5.1.30 What can be causing these sudden failures?

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• Git can no longer open emacs as its editor

  - by mwilliams

  I'm running Git version 1.7.3.2 that I built from source, zsh is my shell, and emacs is my editor. Recently I started seeing the following: /usr/local/Cellar/git/1.7.3.2/libexec/git-core/git-sh-setup: line 106: emacs: command not found Could not execute editor My zshrc looks like the following so I can use the Cocoa build and the console binary provided with it. EMACS_HOME="/Applications/Emacs.app/Contents/MacOS" function e() { PATH=$EMACS_HOME/bin:$PATH $EMACS_HOME/Emacs -nw $@ } function ec() { PATH=$EMACS_HOME/bin:$PATH emacsclient -t $@ } function es() { e --daemon=$1 && ec -s $1 } function el() { ps ax|grep Emacs } function ek() { $EMACS_HOME/bin/emacsclient -e '(kill-emacs)' -s $1 } function ecompile() { e -eval "(setq load-path (cons (expand-file-name \".\") load-path))" \ -batch -f batch-byte-compile $@ } alias emacs=e alias emacsclient=ec And I also have export EDITOR="emacs" and have tried adding export GIT_EDITOR="emacs" (and swapping that out with "e") But whatever I try I can't get git to open emacs whenever I need to do a commit or an interactive rebase, etc etc...

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• client denied by server configuration , Options ExecCGI is off in this directory

  - by John Smiith

  Error log [Wed Jul 04 06:01:54 2012] [error] [client 127.0.0.1] File does not exist: C:/xampp/www/htdocs/localhost/favicon.ico [Wed Jul 04 06:01:54 2012] [error] [client 127.0.0.1] client denied by server configuration: C:/xampp/Bin/apache [Wed Jul 04 06:01:58 2012] [error] [client 127.0.0.1] Options ExecCGI is off in this directory: C:/xampp/www/htdocs/wsgi_app/wsgi_handler.py [Wed Jul 04 06:01:58 2012] [error] [client 127.0.0.1] client denied by server configuration: C:/xampp/Bin/apache [Wed Jul 04 06:01:58 2012] [error] [client 127.0.0.1] File does not exist: C:/xampp/www/htdocs/localhost/favicon.ico [Wed Jul 04 06:01:58 2012] [error] [client 127.0.0.1] client denied by server configuration: C:/xampp/Bin/apache Virtual host <VirtualHost *:80> ServerAdmin [email protected] DocumentRoot "C:/xampp/www/htdocs/localhost" ServerName localhost ServerAlias www.localhost ErrorLog "logs/localhost-error.log" CustomLog "logs/localhost-access.log" combined </VirtualHost> mod_wsgi httpdconf WSGIScriptAlias /wsgi "C:/xampp/www/htdocs/wsgi_app/wsgi_handler.py" <Directory "C:/xampp/www/htdocs/wsgi_app/"> AllowOverride None Options None Order deny,allow Allow from all </Directory> http://localhost/wsgi giving 403 error

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• Ubuntu can't install an older version of a package

  - by Trevor Newhook

  When I try to do an apt-get install, I keep getting an error: Depends: libgtk-3-common (= 3.4.1-0ubuntu1) but 3.4.2-0ubuntu0.4 is to be installed when I run sudo apt-get -f install, I get several dpkg: warning: files list file for package 'XXX' missing, assuming package has no files currently installed. then Preparing to replace libgtk-3-bin 3.4.1-0ubuntu1 (using .../libgtk-3-bin_3.4.2-0ubuntu0.4_i386.deb) ... Adding 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin' dpkg-divert: error: rename involves overwriting `/usr/sbin/update-icon-caches.gtk2' with different file `/usr/sbin/update-icon-caches', not allowed dpkg: error processing /var/cache/apt/archives/libgtk-3-bin_3.4.2-0ubuntu0.4_i386.deb (--unpack): subprocess new pre-installation script returned error exit status 2 Errors were encountered while processing: /var/cache/apt/archives/libgtk-3-bin_3.4.2-0ubuntu0.4_i386.deb E: Sub-process /usr/bin/dpkg returned an error code (1) I'm not sure why it's complaining about a newer version of a package, but any help would be appreciated

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• winrar command line folder stucture

  - by Lee Hull

  I am trying to zip up a folder.. Example: C:\Test*.* C:\Test\bin*.* I want to be able to zip up the Test folder with bin subfolder, however, I need the Test folder contents in the zip root. I am trying to do this using the WinRar command line (rar.exe) I've tried using rar.exe a "C:\File.zip" -ep "C:\Test" but it puts all the folder contents in root... Tried rar.exe a "C:\File.zip" -ep "C:\Test*.*" "C:\Test\bin" same thing.. any ideas?

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• All terminal commands (like ls, cd, edit, open) are returning errors on my Mac

  - by park

  From what I can tell from reading other questions/answers is that my .bash_profile file may be corrupt. If I type echo $PATH in terminal the result is: /usr/local/git/bin From what I've read, that's not what the result is supposed to be. But I also can't get any of the commands (like edit or subl, for Sublime Text 2) to open the .bash_profile file to edit it. I was able to open the file in TextEdit using "cmd-shift-.", and here's what's in the file: [[ -s "$HOME/.rvm/scripts/rvm" ]] && source "$HOME/.rvm/scripts/rvm" PATH=$PATH:~/bin export PATH export PATH=/usr/local/git/bin But the file is LOCKED, so I can't edit it there either. I'm very new to programming and in the middle of trying to install everything on my Mac to go through a Ruby on Rails tutorial. I can't even check my version of ruby, since even ruby -v returns -bash: ruby: command not found Any help would be greatly appreciated. Thanks.

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• add script on boot linux machine

  - by user1546679

  I have one script to start a service on my ubuntu. I added it on boot machine using "# update-rc.d projeto defaults". But it still doesn't start with the boot machine. I think is because I am using other user to start the script "su - www-data -c ...". But I am not sure, because I run the update-rc.d command as root. When I execute the script from a terminal, it asks the password of the user www-data. Does anyone know what is happening? Thanks a lot! Felipe #!/bin/bash # /var/www/boinc/projeto/bin/start function action { su - www-data -c "/var/www/boinc/projeto/bin/$1" } case $1 in start|stop|status) action $1 ;; *) echo "ERRO: usar $0 (start|stop|status)" exit 1 ;; esac

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• How do I run Munin plugins written in Ruby, using RVM?

  - by hlg

  Hi! I try to run some Munin plugins written in Ruby. I would like to use RVM, so Munin needs to know where to find Ruby. I tried to change the line calling munin-cron in the cron file as follows: */5 * * * * munin bash -c 'source /usr/local/lib/rvm && rvm 1.9.2@munin && /usr/bin/munin-cron' This leads to error messages in munin-node.log, saying /usr/bin/env: ruby: No such file or directory When I change the plugins' shebangs to the actual path of the Ruby executable it works, but the RVM environment should be set so that '/usr/bin/env ruby' works. It does when I execute the plugins as root. Any ideas?

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• Adding cygwin on right click on windows explorer

  - by PushpRaj

  I wish to add a command on right click menu in explorer that opens current directory with cygwin. For same I have successfully added these registries: [HKEY_CURRENT_USER\software\classes\directory\shell\cygwin] @="c:\\cygwin\\bin\\bash.exe --login -i -c \"cd '%1'; bash\"" [HKEY_CURRENT_USER\software\classes\drive\shell\cygwin] @="c:\\cygwin\\bin\\bash.exe --login -i -c \"cd '%1'; bash\"" but this adds the command only when on some folder or drive. I want generic right click on explorer, on which, search gives me this registry to edit: [HKEY_CLASSES_ROOT\Directory\Background\shell\cygwin] @="c:\\cygwin\\bin\\bash.exe --login -i -c \"cd '%1'; bash\"" My problem lies with the value of the key, which doesnt work on %1 but on some static value like /cygdrive/c Could someone please tell me the proper way to pass current directory to the command, also please refer me some basic and advanced pages for same. Thank you.

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• what is the best setting for using lighttpd on 8G ram?

  - by user39639

  I have running 8GB ram and 8 x Xeon 3361 system! What is the best setting for running simultaneous connection! What is the maximum? Is setting like this correct? server.max-keep-alive-requests = 0 server.max-keep-alive-idle = 10 server.max-read-idle = 60 server.max-write-idle = 60 server.event-handler = "linux-sysepoll" server.max-fds = 2048 fastcgi.server = ( ".php" = ( "localhost" = ( "socket" = "/tmp/php-fastcgi.socket", "bin-path" = "/usr/bin/php-cgi", "max-procs" = 20, "bin-environment" = ( "PHP_FCGI_CHILDREN" = "40", "PHP_FCGI_MAX_REQUESTS" = "800" ), "broken-scriptfilename" = "enable" ) ) ) please help me!

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• Command output as string

  - by rik

  I want to get output from command C:\Program Files (x86)\Java\jre7\bin\java.exe" -version as string variable. I tried this way: $out = &"C:\Program Files (x86)\Java\jre7\bin\java.exe" -version but it gives error message: java.exe : java version "1.7.0_05" At line:1 char:9 + $out = & <<<< "C:\Program Files (x86)\Java\jre7\bin\java.exe" -version + CategoryInfo : NotSpecified: (java version "1.7.0_05":String) [], RemoteException + FullyQualifiedErrorId : NativeCommandError Java(TM) SE Runtime Environment (build 1.7.0_05-b05) Java HotSpot(TM) Client VM (build 23.1-b03, mixed mode, sharing) $out variable seems empty. What am I doing wrong?

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• Mac OS X 10.6 executable not found without full path

  - by Danack

  I just installed Apache via MacPorts. It seems that my Mac was absolutely confused about which version of the Apache executables to run. After moving the Apache executables that ship with the Mac to a directory that is not listed in the PATH variable, trying to run the httpd built by MacPorts fails even though the correct directory (/opt/local/apache2/bin) is listed in the PATH variable. If I navigate to the directory /opt/local/apache2/bin and type the command httpd I still get the error message -bash: httpd: command not found If I type the command with the full path /opt/local/apache2/bin/httpd it works fine. I've run the command alias to see if something was clashing but the only thing listed is: alias wget='curl -O' How do I find what is intercepting the command and preventing the executable being found in the directory, even when I'm inside the same directory? By the way, the httpd file is executable: -rwxr-xr-x 1 root admin 442496 9 May 2012 httpd

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• How do I install the latest Sun Java JRE on Ubuntu Server 9.10?

  - by blackrobot

  Unfortunately, if I try to install sun-java via apt-get, it's not found in the repositories. # apt-get install sun-java6-jre Reading package lists... Done Building dependency tree Reading state information... Done Package sun-java6-jre is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source E: Package sun-java6-jre has no installation candidate If I try to install it using the bin from Sun's website, here's the issue: # ./jre-6u18-linux-i586.bin (license agreement...) Do you agree to the above license terms? [yes or no] yes Unpacking... Checksumming... Extracting... ./jre-6u18-linux-i586.bin: 366: ./install.sfx.10648: not found Failed to extract the files. Please refer to the Troubleshooting section of the Installation Instructions on the download page for more information. Thanks for the help.

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• `wget` is not recognized or either can't find the file

  - by clankill3r

  if i use cd C:\Program Files (x86)\GnuWin32\bin then i'm able to use wget commands for example: wget http://www.ultralightnews.com/trikes/images/trikes/dfs-singletrike.jpg but i can't find the file back, i looked in c:\ and in the bin folder mentioned above and in GnuWin32\etc If i try wget -O C:\Users\clankill3r\Downloads\wgetfolder wget http://www.ultralightnews.com/trikes/images/trikes/dfs-singletrike.jpg then it says Permision denied, i did allow all permisions possible for every group / user. Some people say it downloads to the current folder your working in (that's why i looked in the bin). But i thought let's try to run the command from another folder so i used: 'cd C:\Users\clankill3r\Downloads\wgetfolderand then the wget comman but then it says thewget` command is not recognized. can someone help?

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• How to run long time process on Udev event?

  - by neclude

  (sorry for my bad english) I want run ppp connection when my usb modem is connect. so i use next udev rule: ACTION=="add", SUBSYSTEM=="tty", ATTRS{idVendor}=="16d8",\ RUN+="/usr/local/bin/newPPP.sh $env{DEVNAME}" (my modem appear in /dev as ttyACM0) newPPP.sh: #!/bin/bash /usr/bin/pon prov $1 >/dev/null 2>&1 & Problem: udev event fire, newPPP.sh running, BUT newPPP.sh process will be killed after ~4-5s. ppp not have time to connect. (in it params is timeout 10s for dial up). How can i run long time process, that will not be killed? (I was try nohup. It don't work too.) System: Arch Linux

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