Chris Jean
WordPress developer for Automattic, Linux fan, and all-around nerd

Archive for Linux – Page 2

Find Which APT Package Provides a Specific Command

by Chris Jean
March 17th, 2014

I recently had to find out which APT package provided a specific command on one of my Ubuntu systems. After a bit of digging, I discovered that the dpkg command’s magical -S switch gives us a simple way to do this.

Per the dpkg-query man page, the -S switch (also valid as --search) does the following:

-S, --search filename-search-pattern...
    Search for packages that own files corresponding to the given pattern.  Standard shell wildchars can be used in the pattern.  This command will  not  list  extra  files  created  by  maintainer scripts, nor will it list alternatives.

In other words, it takes a file pattern (optionally including a path or portions of a path), searches the known packages to see if any have owned files that match the requested search, and lists any packages that contain a match.

For example:

[chris@home ~]$ dpkg -S /usr/bin/GET
libwww-perl: /usr/bin/GET
[chris@home ~]$ which ls
/bin/ls
[chris@home ~]$ dpkg --search /bin/ls
coreutils: /bin/ls
[chris@home ~]$ dpkg --search /etc/cron.d
sysstat, php5-common, cron, anacron, rsnapshot: /etc/cron.d
[chris@home ~]$ dpkg --search /etc/cron.d/*
anacron: /etc/cron.d/anacron
php5-common: /etc/cron.d/php5
rsnapshot: /etc/cron.d/rsnapshot
sysstat: /etc/cron.d/sysstat
[chris@home ~]$ dpkg --search /etc/cron.daily
google-chrome-beta, man-db, update-notifier-common, apt, popularity-contest, anacron, logrotate, aptitude, cracklib-runtime, dpkg, passwd, google-musicmanager-beta, sysstat, apache2, apache2.2-common, apport, google-talkplugin, cron, samba, bsdmainutils, ntp, mlocate: /etc/cron.daily
[chris@home ~]$ which which
/usr/bin/which
[chris@home ~]$ dpkg -S /usr/bin/which
debianutils: /usr/bin/which
[chris@home ~]$ which dpkg
/usr/bin/dpkg
[chris@home ~]$ dpkg -S /usr/bin/dpkg
dpkg: /usr/bin/dpkg
[chris@home ~]$

I added in the which command to show how you can retrieve the full path to specific commands.

Notice how supplying /etc/cron.d returned a listing of all matches for that specific string while searching for /etc/cron.d/* provides a separate match for each entry in the /etc/crond.d directory.

I really need to dig deeper into the dpkg command as it has a wealth of handy features that are just waiting to be used.

Categories Linux, Tips 'n Tricks
Comments (0)

Fix Missing Clock in Ubuntu’s Unity Panel

by Chris Jean
March 14th, 2014

I booted up my Ubuntu 13.10 system running Unity today to find that the clock was missing in the app panel.

Missing Clock App in Ubuntu 13.10

Fortunately this was easy to fix without having to reboot the system. I simply ran the following:

[chris@work ~]$ killall unity-panel-service
[chris@work ~]$

The clock instantly appeared.

Ubuntu 13.10 Clock App in Panel

If this doesn’t fix your problem, make sure that you have the indicator-datetime package installed. You can try installing it by running the following:

[gaarai@tenshi ~]$ sudo apt-get install indicator-datetime
The following NEW packages will be installed:
  gnome-control-center-datetime{a} indicator-datetime
0 packages upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/55.7 kB of archives. After unpacking 318 kB will be used.
Do you want to continue? [Y/n/?] y
Selecting previously unselected package indicator-datetime.
(Reading database ... 552412 files and directories currently installed.)
Unpacking indicator-datetime (from .../indicator-datetime_13.10.0+13.10.20131023.2-0ubuntu1_amd64.deb) ...
Selecting previously unselected package gnome-control-center-datetime.
Unpacking gnome-control-center-datetime (from .../gnome-control-center-datetime_13.10.0+13.10.20131023.2-0ubuntu1_amd64.deb) ...
Processing triggers for libglib2.0-0:amd64 ...
Processing triggers for libglib2.0-0:i386 ...
Processing triggers for bamfdaemon ...
Rebuilding /usr/share/applications/bamf-2.index...
Processing triggers for desktop-file-utils ...
Processing triggers for mime-support ...
Processing triggers for gnome-menus ...
Setting up indicator-datetime (13.10.0+13.10.20131023.2-0ubuntu1) ...
Setting up gnome-control-center-datetime (13.10.0+13.10.20131023.2-0ubuntu1) ...
Processing triggers for libc-bin ...

[gaarai@tenshi ~]$
Categories Linux, Tips 'n Tricks
Comments (20)

Fix nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)

by Chris Jean
February 10th, 2014

My site is currently running off of an nginx HTTP server. In attempting to set up the site to respond to IPv6 requests, I ran into all sorts of problems. They all started off with the following error:

[gaarai@linode /etc/nginx]$ sudo service nginx restart
 * Restarting nginx nginx
nginx: [emerg] 807#0: no host in ":80" of the "listen" directive in /etc/nginx/sites-enabled/chrisjean.com:7

I poked around a bit more and ended up angering the nginx gods.

[gaarai@linode /etc/nginx]$ sudo service nginx restart
 * Restarting nginx nginx
nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:443 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:443 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:443 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:443 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:80 failed (98: Address already in use)
nginx: [emerg] bind() to [::]:443 failed (98: Address already in use)
nginx: [emerg] still could not bind()

I then found out that the guides I used were quite old and recommended an old syntax that no longer works. I used the following syntax as recommended in the guides:

server {
    listen :80;
    listen [::]:80;
}

This no longer works and will result in the problems listed above.

There are two solutions to the problem.

First Solution

The first solution is to remove the colon from in front of the IPv4 port and to specify ipv6only=on for the IPv6 port. It turns out that in Linux, binding to an IPv6 TCP port automatically binds to the IPv4 port as well. This explains the error messages about bind failures. Using ipv6only=on ensures that the IPv6 listen directive will only bind to IPv6 and not automatically to IPv4 as well.

server {
    listen 80;
    listen [::]:80 ipv6only=on;
}

Second Solution

The second solution is to change all of the listen directives for each server block to use the IPv6 format, for example:

server {
    listen [::]:80;
}

Note that there is just a single listen directive. Since by default, an IPv6 listen directive will bind to both IPv4 and IPv6 TCP ports, only the single listen directive is needed to cover both IPv4 and IPv6.

I list this solution second as 1) you may not want all of your server blocks to be available on both IPv4 and IPv6 (keeping them separate gives more control), 2) it may take a large amount of work to change all of the server blocks, and 3) if even one block is not updated properly, the server will be taken down. It is important to note that adding this listen directive is necessary even for server blocks that do not list a listen directive as the default is listen *:80, which only binds to IPv4.

Take the following block as an example.

server {
    server_name .gaarai.com;
    rewrite ^ http://chrisjean.com$request_uri? permanent;
}

This is a server block that causes redirection of one of my older domains to my current domain. This needs to be updated to the following:

server {
    listen [::]:80;
    
    server_name .gaarai.com;
    rewrite ^ http://chrisjean.com$request_uri? permanent;
}

Without this change, if I’m updating my server blocks to use the second method, restarting nginx will once again start spewing the messages about bind failures:

[gaarai@linode /etc/nginx]$ sudo service nginx restart
 * Restarting nginx nginx
nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use)
nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use)
nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use)
nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use)
nginx: [emerg] bind() to 0.0.0.0:80 failed (98: Address already in use)
nginx: [emerg] still could not bind()

Using Explicit Addresses

Some of you may wonder about server blocks that have to have explicit address designations. In situations such as these, using the first solution would be the best option as it gives you the most control over how to declare everything. This is how such a server block would look for my server:

server {
    listen 72.14.185.165:80;
    listen [2001:470:1f0e:4da::2]:80;
}

When using this method, you can’t use the listen [::]:80; directives as in the second solution since you’ll run into binding issues again.

Summary

First solution:

  • Pros
    • More flexibility
    • Easier to maintain with complex setups
    • Easier to maintain when listening to address-specific ports
  • Cons
    • Adds an extra line to each server block (I admit that it’s a sad excuse for a con)

Second solution:

  • Pros
    • Looks cleaner having just the one listen directive for each server block
    • Ensures that all the server blocks are configured on IPv6 and IPv4 as errors will occur if a single block is left in just IPv4
  • Cons
    • Can cause more headaches in complex setups as you won’t be able to use address-specific listen directives
    • Can cause many more errors than the first solution until all of the server blocks are updated to use the single listen directive properly

What am I using on my server? After ensuring that I understood both approaches, I went with the first solution. The idea of going through and reconfiguring everything later if/when I have to make some more complex changes doesn’t sound very appealing to me.

Misc Details

My server is hosted at Linode and is currently running Ubuntu Server 13.10 with nginx version 1.4.1. Since Linode supports IPv6, my server was already configured to have IPv6 addresses available. If you have a server that does not have IPv6 allocations yet, you can use Hurricane Electric’s Tunnel Broker to get an IPv6 tunnel that directs IPv6 traffic to your server’s IPv4 address.

More details about nginx’s listen directive can be found in the official documentation.

Categories Linux
Comments (7)

Restart Ubuntu’s Unity Without Logging Out

by Chris Jean
February 13th, 2013

Sometimes when you change a configuration in Unity that is based on configuration files, you need to force Unity to reload. In most guides that I’ve found, the recommendation is to simply log out and log in again. While this works, losing everything that you have open just to force a reloading of configuration files is a bit much. Fortunately, there is a very easy way to force Unity to reload.

These details are specific to Unity running in Ubuntu 12.10, but should work as long as your system is running Unity.

  1. Load a run dialog by pressing Alt+F2
  2. Type unity --replace
  3. Press the Enter key

The screen will flicker and things will start to look normal again in a few seconds. This is due to the entire desktop reloading. The end result is that the configuration files will have reloaded. The only side effects are that your windows may be reordered in the alt-tab listing and some windows may switch their desktop (typically, I have at least one window from my second desktop switch over to my first desktop).

Categories Linux, Tips 'n Tricks
Comments (5)

Upgrade PHP 5.1/5.2 to 5.3 on CentOS

by Chris Jean
June 24th, 2011

I’m finding that more and more software developers are being quite inconsiderate and are making code that requires PHP 5.3. Since many server-based and long-term support distros are still on PHP 5.2, this can make things difficult quickly.

I’ll share how I upgraded one of my servers, but I do need to let you know about some specifics about my setup as your setup may be different and require different steps to upgrade.

When I started, my system ran CentOS 5.5 and PHP 5.2.16. Now it is running CentOS 5.6 and PHP 5.3.3.

You won’t be able to follow these steps without root access, so that is definitely a requirement. I’m also running Apache. You may be using a different web server, but if you don’t know what I’m talking about, you are running Apache. I assume that if you run a different server, you will know what to change in my steps.

Read More→

Categories Linux, Tips 'n Tricks
Comments (98)

PHP 5.3 and “It is not safe to rely on the system’s timezone settings”

by Chris Jean
June 24th, 2011

I just updated one of my CentOS systems to PHP 5.3 (a chore best reserved for another blog post), and started to see the following warning popping up:

PHP Notice: in file index.php on line 15: date(): It is not safe to rely on the system’s timezone settings. You are *required* to use the date.timezone setting or the date_default_timezone_set() function. In case you used any of those methods and you are still getting this warning, you most likely misspelled the timezone identifier. We selected ‘America/Chicago’ for ‘CDT/-5.0/DST’ instead

Annoying to say the least. The fix is much easier than the message makes it seem.

PHP 5.3 now requires that you either have a timezone set in your php.ini file or that you pass the desired timezone via the date_default_timezone_set() function before calling the date() function.

I opened my server’s /etc/php.ini file and searched for timezone. My ini file had a section like the following:

[Date]
; Defines the default timezone used by the date functions
; http://www.php.net/manual/en/datetime.configuration.php#ini.date.timezone
; date.timezone =

I uncommented the date.timezone line and added the timezone I wanted.

[Date]
; Defines the default timezone used by the date functions
; http://www.php.net/manual/en/datetime.configuration.php#ini.date.timezone
date.timezone = 'America/Chicago'

There are two very important things to do in order for this to work properly for you:

  1. Use a timezone that is appropriate for your needs. Use PHP’s List of Supported Timezones to find the timezone that works for you.
  2. Since your server is likely to cache the PHP configuration, you will want to restart your web server process in order for the change to be recognized. The command to execute varies by system, but for most systems, the following will work: 
    [user@server /etc]$ sudo service httpd restart
[sudo] password for user:
Stopping httpd:                          [  OK  ]
Starting httpd:                          [  OK  ]
[user@server /etc]$

    Of course, if you are already root, you won’t need to use sudo:

    [root@server /etc]# service httpd restart
Stopping httpd:                          [  OK  ]
Starting httpd:                          [  OK  ]
[root@server /etc]#
Categories Linux, Tips 'n Tricks
Comments (10)

View CSV Data from the Command Line

by Chris Jean
June 17th, 2011

I recently wrote a script to dump data into CSV files. The CSV files work well for using in other scripts, but they are a bit difficult to read in order to verify that the data looks good. Sure, I could transfer the files to my local system and open them up in OpenOffice Spreadsheet or a similar program, but I want to do quick checks of the generated data and constantly copying the data and opening it up again in a program would just slow me down. Fortunately, there is a better way.

Using a combination of the cat, column, and less commands that are available from most *nix shells, the CSV data can be rendered into a nice table and quickly navigated. Here is an example:

[chris@host data]$ cat file.csv | sed -e 's/,,/, ,/g' | column -s, -t | less -#5 -N -S
      1 number_of_tests  execution_time min  execution_time max  execution_time avg  execution_time std_dev  peak_memory_usage min  peak_memory_usage max  peak_memory_usage avg  peak_memory_usage std_dev  real_memory_usage min
      2 449              0.2421700954        0.2522599697        0.24422667392717    0.0013405194115834      22062656               22067696               22062951.732739        552.24028841091            22282240
      3 416              0.2449610233        0.2619900703        0.24721734340337    0.0015257664849685      21295528               21300888               21295541.019231        262.48728836508            21495808
      4 446              0.2286360264        0.2422661781        0.23043336515404    0.001174508347353       20895976               20900800               20895987.03139         228.20177111936            20971520
      5 428              0.1955471039        0.2902140617        0.1981168762521     0.0046106433816399      18045464               18048784               18045487.271028        276.98063531264            18087936
      6 436              0.2208828926        0.2558329105        0.22297720351353    0.0021463518368546      18717960               18723192               18718020.238532        557.06025400191            18874368

The output is easy to navigate with the cursor keys and is perfect for quickly verifying the generated data.

To use for your files, simply replace file.csv in the above example with your file’s name. The -#5 determines how many columns to scroll when using the left and right arrow keys. You can increase or decrease this as needed to make navigating easier.

For those interested, I’ve tested this on Debian-based (Ubuntu, Mint, etc) and Redhat-based (CentOS) systems, and it works on all of them.

Since I’m tying together various command line tools that have no concept of the CSV format, there are some contents that this does not handle well. For example, all commas will be treated as separating out columns, even if the comma is escaped by quotes or a backslash.

I updated the command to fix a problem with handling empty entries, such as “…,data,,data,…”. The sed command takes care of changing those empty values to a space.

Categories Linux, Tips 'n Tricks
Comments (8)

Fix “Insecure $ENV{PATH} while running setuid”

by Chris Jean
June 6th, 2011

Yet another tale from trying to run a Perl script with the setuid bit turned on. See my earlier post on fixing “Can’t do setuid (cannot exec sperl)” for details about why running perl scripts with setuid bits is a special case.

I tried to run my script and I got the following message:

[user@server ~]$ run-script
Insecure $ENV{PATH} while running setuid at ~/run-script line 4.

The basic idea that this message is trying to get across is that an environment variable that is being used may contain data that could open up an attack vector. The way to fix this is by setting the variable to a set of defaults that don’t come from the user and thus are less susceptible to being manipulated by someone in order to break the security of the system.

In this case, my script executed a program on the shell. Since shell interpretation comes into play, the $PATH variable is looked at to decide where the program could be located. This is an attack vector as someone could just change that variable to cause their own code to be called, thus escalating their code’s privileges without your knowledge.

In order to avoid this, I set the $PATH variable to a restricted set for use in the script by adding the following in the script before my shell call:

$ENV{"PATH"} = "/usr/bin";

This may need to be modified to meet your specific needs. In addition to making this change, I went ahead and changed the call to the shell program to be an absolute reference to the program in order to further mitigate any potential issue, such as aliases.

Categories Linux, Tips 'n Tricks
Comments (2)

Fix “Can’t do setuid (cannot exec sperl)”

by Chris Jean
June 6th, 2011

I recently needed to run a perl script with setuid bit set. This allows the script to run as the user the script’s file is owned by. In this case, I needed the script to run as root.

Since doing this can be very dangerous, Perl does something very nice by default: If you have the setuid bit set on the script, it forces the script to run in Taint Mode which helps to ensure proper sanitation of the environment and inputs. By doing this, Perl can help lock down possible attack vectors that can compromise the security of your script. This isn’t perfect however, so I do recommend that you read up on Perl’s security measures.

So now down to the main point of this post. I tried to run the script with the setuid bit set, and I got the following error message:

[user@server ~]$ run-script
Can't do setuid (cannot exec sperl)

Well that certainly puts a damper on things. Fortunately, the solution is easy. There is simply an additional package that needs to be installed to provide the wrapper program that puts this Perl security in place.

For Debian (Ubuntu, Mint, etc as well), run the following:

[user@server ~]$ sudo apt-get install perl-suid

For CentOS, run the following:

[user@server ~]$ sudo yum install perl-suidperl
Categories Linux, Tips 'n Tricks
Comments (3)

Fix “WordPress database error Table … is marked as crashed and should be repaired”

by Chris Jean
August 30th, 2010

All the content on my site was gone. When I went to investigate, I found my error log was filled with the following error:

WordPress database error Table './database_name/prefix_posts' is marked as crashed and should be repaired for query SELECT YEAR(post_date) AS `year`, MONTH(post_date) AS `month`, count(ID) as posts FROM prefix_posts  WHERE post_type = 'post' AND post_status = 'publish' GROUP BY YEAR(post_date), MONTH(post_date) ORDER BY post_date DESC  made by require, require_once, include, do_action, call_user_func_array, flexx_after_content, get_sidebar, locate_template, load_template, require_once, dynamic_sidebar, call_user_func_array, WP_Widget->display_callback, WP_Widget_Archives->widget, wp_get_archives

A very scary looking error, but it was easy to fix.

My Preferred Repair Method

[user@server ~/public_html]$ mysql -u user -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 1120449
Server version: 5.1.48 MySQL Community Server (GPL)

Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved.
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL v2 license

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> connect database
Connection id:    1120477
Current database: database

mysql> select * from prefix_posts limit 1;
ERROR 2006 (HY000): MySQL server has gone away
No connection. Trying to reconnect...
Connection id:    1120568
Current database: database

ERROR 145 (HY000): Table './database/prefix_posts' is marked as crashed and should be repaired
mysql> repair table prefix_posts;
+-----------------------+--------+----------+----------+
| Table                 | Op     | Msg_type | Msg_text |
+-----------------------+--------+----------+----------+
| database.prefix_posts | repair | status   | OK       |
+-----------------------+--------+----------+----------+
1 row in set (3.56 sec)

mysql> select * from prefix_posts limit 1;
+----+-------------+---------------------+---------------------+--------------+------------+---------------+--------------+-------------+----------------+-------------+---------------+-----------+---------+--------+---------------------+---------------------+-----------------------+-------------+------------------------------------------------------------+------------+------------+----------------+---------------+
| ID | post_author | post_date           | post_date_gmt       | post_content | post_title | post_category | post_excerpt | post_status | comment_status | ping_status | post_password | post_name | to_ping | pinged | post_modified       | post_modified_gmt   | post_content_filtered | post_parent | guid                                                       | menu_order | post_type  | post_mime_type | comment_count |
+----+-------------+---------------------+---------------------+--------------+------------+---------------+--------------+-------------+----------------+-------------+---------------+-----------+---------+--------+---------------------+---------------------+-----------------------+-------------+------------------------------------------------------------+------------+------------+----------------+---------------+
| 12 |           8 | 2008-05-20 10:09:49 | 2008-05-20 15:09:49 |              | 308image1  |             0 |              | inherit     | open           | open        |               | 308image1 |         |        | 2008-05-20 10:09:49 | 2008-05-20 15:09:49 |                       |           0 | http://gaarai.com/wp-content/uploads/2008/05/308image1.gif |          0 | attachment | image/gif      |             0 |
+----+-------------+---------------------+---------------------+--------------+------------+---------------+--------------+-------------+----------------+-------------+---------------+-----------+---------+--------+---------------------+---------------------+-----------------------+-------------+------------------------------------------------------------+------------+------------+----------------+---------------+
1 row in set (0.00 sec)

mysql> exit
Bye
[user@server ~/public_html]$

For me, this was the easiest and quickest way to repair the table.

Repairing Tables with phpMyAdmin

For you, you might prefer to use phpMyAdmin. Fortunately, repairing a table with phpMyAdmin is easy.

  1. Log in to your phpMyAdmin or connect to it via your cPanel back-end.
  2. Select the database with the crashed table.
  3. Put a checkmark next to each crashed table.
  4. Select “Repair table” from the “With selected:” drop down at the bottom of the list.
  5. Let phpMyAdmin do its thing.
Categories Linux, Tips 'n Tricks, WordPress
Comments (15)
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