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Which programming language could I use for Natural Language Processing to extract clinical words?

- by MACEE

I am going to do entity extraction (like Named Entity Recognition) from clinical free text (unstructured raw text such as discharge summaries) and these entities could be any medical problem, medical tests or treatments. I am going to use one of i2b2 datasets (https://www.i2b2.org/) if case you are familiar with that. I am new to the NLP(Natural Language Processing) field and I need a programming language to support NLP tasks and also easily connect to the available libraries of machine learning algorithms like CRF. I don't know much java and I heard about Python, Perl and Scala but I am not sure which one would be the best option for this task?

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Did You Know? I'm doing 3 more online seminars with SSWUG!

- by Kalen Delaney

As I told you in April , I recorded two more seminars with Stephen Wynkoop, on aspects of Query Processing. The first one will be broadcast on June 30 and the second on August 27. In between, we'll broadcast my Index Internals seminar, on July 23. Workshops can be replayed for up to a week after the broadcast, and you can even buy a DVD of the workshop. You can get more details by clicking on the workshop name, below, or check out the announcement on the SSWUG site at http://www.sswug.org/editorials/default.aspx?id=1948...(read more)

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Regain Sudo rights after removing from admin group

- by berkes

Hello, I accidentally removed myself from the admin group when editing the user. Now I can no longer use sudo. The error says: ber is not in the sudoers file. This incident will be reported. I booted up in rescue mode, but, when going into root prompt, it asks me for the root password. I don't have one, and providing with my own (first and only ubuntu-user) password, it won't allow entrance. My harddisk is encrypted, but only the /home/user part, not the entire disk, afaik. What can I do?

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When to reply 400 Bad Request

- by KajMagnus

According to www.w3.org, a Web server should reply with status code 400 Bad Request if: "The request could not be understood by the server due to malformed syntax. The client SHOULD NOT repeat the request without modifications" Does that mean only request that violates some HTTP spec? Or does it include a request that my particular Web app thinks is broken? When would you reply 400? For example, if my Web app expects a query string to always include a "function=..." parameter, would you reply code 400 Bad Request or 403 Forbidden? (403 means that "The server understood the request, but is refusing to fulfill it.")

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Frequent GUI pauses in Ubuntu 13.04 / Unity / Intel HD4000

- by Simon

I'm experiencing very frequent (and regular) GUI pauses on my system. Every 30 seconds (pretty much exactly) the GUI will freeze for maybe .25 to .5 seconds. The mouse stops moving, keys stop echoing and a stopwatch timer briefly pauses. I'm using the Intel Graphics driver available from: https://download.01.org/gfx/ubuntu/13.04/main I've looked in a few places and tried a few things for a solution: I've checked cron and anacron for scheduled processes. I've disabled background processes (eg mysql, postgres, apache) not that these were doing anything anyway I've checked the following posts and tried the suggestions there: Unity GUI pauses/freezes for less than a few seconds How to go about troubleshooting frequent system pauses I've watched the system using top and System Monitor and there are no spikes (or even blips) of cpu usage when the pauses occur. There are no obvious error messages in dmesg or syslog There is loads of free RAM (8GB+) and no swap usage If it helps it's a ZooStorm i5 laptop with a HD4000 GPU, 16GB Ram and an SSD. Any help / suggestions would be very gratefully received.

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Ubuntu will not start due to full partitions

- by mike

I left my computer downloading all the night and I did download 35 GB of movies (legal ...). I restarted the computed in the morning then I booted in my encrypted Windows partition for my work. I have left my computer downloading 35GB of files and when I restarted in the morning, I booted Windows. When I tried to access Ubuntu, it failed to boot and in low-graphic mode told me that it won't boot because the partition is full. I tried rescue and it reported 0 MB free. I also cannot delete files with sudo rm as all are impossible due to a read-only file system. I can mount it in Windows but there is a "write protection" there, also. Should I try a live USB?

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How do I install the Intel 82845 graphics driver -- videos are really slow?

- by Mahesh Bhat

I installed lubuntu on my machine and seems Intel 82845 graphics wasn't installed. Videos are showing frame by frame. Many says ubuntu kernel has built in support for it. but seems it is not. There is a website www.intellinuxgraphics.org has drivers for many kinds of linux distributions. But I find it difficult how to install them on my lubuntu. Can anyone elabroate on how that can be installed ? Output of the command dmesg http://paste.ubuntu.com/1058720/ Output of the command lsmod http://paste.ubuntu.com/1058724/

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Wubi downloaded and installed 64bit 12.10 on my 32bit netbook

- by Troy

I downloaded the Wubi installer on my atom N450 netbook. When I started up Ubuntu I got an error that read failed to change the mode of /ect/passwd- to 0600. Then while it booted it froze and several strange characters filled the screen. Finally it loaded it ran pretty slow, and I could connect to my router, but not to the internet. Ping 8.8.8.8 showed no server found. So I checked the about computer and it said I was running the 64 bit installation. Now I know that my computer has a low power 32 bit chip and even the Ubuntu iso download suggested a 32 bit installation. So I went to double check and see if I just missed the option for a 32 bit Wubi install and I did not. There was no option. Is there any way to download a 32 bit version of 12.10 through the Wubi?

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Aren't there compilers better at telling the programmer what's wrong in a code ?

- by jokoon

I have worked a little while with the Microsoft compiler from Visual C++ but I worked a long time with G++, and I remember often having bad times understanding what was wrong in my code with the former. Beside binary code generation and optimisation, I think this is a very important feature of a C++ compiler: giving the programmer a clue that makes him understand as fast as possible what is wrong with his/her code. I can understand some programmers understand programming as some sort of "competition" to make less errors, but to me that's a counter productive opinion. I once tried Clang compiler for C from the LLVM thingie, I didn't use it for a long time, but I was impressed on how explicit and easy to understand the error messages were. What are your experiences, and how do you think this matters ? Some WIP of C++ Clang: http://clang.llvm.org/cxx_status.html

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Xubuntu, LXDE, USB Booting

- by Kosciak

Welcome, My problem appeared today - I was using Xubuntu for a long time, but find out that LXDE should be faster than Xfce, so I installed it. After installing I followed tutorial for removing Xfce, cause disk in my computer is very small and I wanted to release some free space. I used command from this tutorial: How to remove xubuntu-desktop? but instead of remove I entered purge command… and rebooted at the end. And I uninstalled whole my things. The problem is in installing system again - it's old Sony Vaio laptop (PCG-GR250) and I have broken CD-DVD drive. It's possible to boot from USB? I can access recovery mode, will this help me? Please answer fast, because it's my brother computer, and his going to kill me if I won't fix this fast :(

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Profiling Startup Of VS2012 – YourKit Profiler

- by Alois Kraus

The YourKit (v7.0.5) profiler is interesting in terms of price (79€ single place license, 409€ + 1 year support and upgrades) and feature set. You do get a performance and memory profiler in one package for which you normally need also to pay extra from the other vendors. As an interesting side note the profiler UI is written in Java because they do also sell Java profilers with the same feature set. To get all methods of a VS startup you need first to configure it to include System* in the profiled methods and you need to configure * to measure wall clock time. By default it does record only CPU times which allows you to optimize CPU hungry operations. But you will never see a Thread.Sleep(10000) in the profiler blocking the UI in this mode. It can profile as all others processes started from within the profiler but it can also profile the next or all started processes. As usual it can profile in sampling and tracing mode. But since it is a memory profiler as well it does by default also record all object allocations > 1MB. With allocation recording enabled VS2012 did crash but without allocation recording there were no problems. The CPU tab contains the time line of the application and when you click in the graph you the call stacks of all threads at this time. This is really a nice feature. When you select a time region you the CPU Usage estimation for this time window. I have seen many applications consuming 100% CPU only because they did create garbage like crazy. For this is the Garbage Collection tab interesting in conjunction with a time range. This view is like the CPU table only that the CPU graph (green) is missing. All relevant information except for GCs/s is already visible in the CPU tab. Very handy to pinpoint excessive GC or CPU bound issues. The Threads tab does show the thread names and their lifetime. This is useful to see thread interactions or which thread is hottest in terms of CPU consumption. On the CPU tab the call tree does exist in a merged and thread specific view. When you click on a method you get below a list of all called methods. There you can sort for methods with a high own time which are worth optimizing. In the Method List you can select which scope you want to see. Back Traces are the methods which did call you. Callees ist the list of methods called directly or indirectly by your method as a flat list. This is not a call stack but still very useful to see which methods were slow so you can see the “root” cause quite quickly without the need to click trough long call stacks. The last view Merged Calles is a call stacked view of the previous view. This does help a lot to understand did call each method at run time. You would get the same view with a debugger for one call invocation but here you get the full statistics (invocation count) as well. Since YourKit is also a memory profiler you can directly see which objects you have on your managed heap and which objects do hold most of your precious memory. You can in in the Object Explorer view also examine the contents of your objects (strings or whatsoever) to get a better understanding which objects where potentially allocating this stuff. YourKit is a very easy to use combined memory and performance profiler in one product. The unbeatable single license price makes it very attractive to straightly buy it. Although it is a Java UI it is very responsive and the memory consumption is considerably lower compared to dotTrace and ANTS profiler. What I do really like is to start the YourKit ui and then start the processes I want to profile as usual. There is no need to alter your own application code to be able to inject a profiler into your new started processes. For performance and memory profiling you can simply select the process you want to investigate from the list of started processes. That's the way I like to use profilers. Just get out of the way and let the application run without any special preparations. Next: Telerik JustTrace

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Using EPEL repos with Oracle Linux

- by wcoekaer

There's a Fedora project called EPEL which hosts a set of additional packages that can be installed on top of various distributions such as Red Hat Enterprise Linux, CentOS, Scientific Linux and of course also Oracle Linux. These packages are not distributed by the distribution vendor and as such also not supported by the vendors (including Oracle) however for users that want to pick up some extras that are useful, it's very easy to do this. All you need to do is download the EPEL RPM from the website, install it on Oracle Linux 5 or Oracle Linux 6 and run yum install or yum search to get the packages. example : # wget http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-5.noarch.rpm # rpm -ivh epel-release-6-5.noarch.rpm # yum repolist Loaded plugins: refresh-packagekit, rhnplugin repo id repo name status epel Extra Packages for Enterprise Linux 6 - x86_64 7,124 The folks that build these repositories are doing a great job at adding very useful packages. They are free, but also unsupported of course.

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How to make Firefox windows style less space consuming?

- by chocobai

Firefox takes up so much space on small screens, so I'm searching for solutions that make firefox' interface less space consuming on ubuntu 12.04 with gnome3. Good examples are the chromium-style, but chromium is kind of slow in gnome3. Chromium does it, firefox on osx does it. Is this also possible on ubuntu via a custom modification or something? Here a screenshot of what I am thinking about: Firefox on OSX: https://wiki.mozilla.org/images/5/50/Firefox-4-Mockup-i06-%28OSX%29-%28TabsTop%29-%28Persona%29.png Thanks for your help.

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ANTLRWorks 2: Early Access Preview 10

- by Geertjan

I took a quick look at how the ANTLRWorks 2 project is getting on... and discovered that today, March 23, the new early access preview 10 has been released: http://www.antlr.org/wiki/display/ANTLR4/1.+Overview Downloaded it immediately and was impressed when browsing through the Java.g file that I also found on the Antlr site: (Click to enlarge the image above.) On the page above, the following enhancements are listed: Add tooltips for rule references Finally fixed the navigator update bug Major improvements to code completion Fix legacy mode Many performance and stability updates I've blogged before about how the developers on the above project consider their code completion to be "scary fast". Some discussions have taken place about how code developed by the ANTLRWorks team could be contributed to the NetBeans project, since NetBeans IDE and ANTLRWorks 2 are both based on the NetBeans Platform.

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Support for non-english characters?

- by TomJ

Is support for non-english characters common in programming languages? I mean, technically, I would think it is feasable, but I don't have any experience in anything other than english, so I don't know how common it is. I know that there are non-english based programming languages, but can something like C#, C++, C, Java, or Python support non-english classes/methods/variables? Example in go (url, http://play.golang.org/p/wRYCNVdbjC) package main import "fmt" type ?? struct { ?? string } func main() { fmt.Println("Hello, ??") ?? := new(??) ??.?? = "hello world" fmt.Println(??.??) }

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Wifi problem in ubuntu using macbook pro when it restart

- by Amro

I was read that subject : http://ubuntuforums.org/showthread.php?t=2011756 and i follow it step by step in the page n 1 , then i was connect but after i restart my macbook again , i was lost the wifi connection.i dont know why or whats the problem exactly. every time I run this command: dmesg | grep -e b43 -e bcma I get this output: [ 2012.769684] bcma-pci-bridge 0000:02:00.0: PCI INT A -> GSI 17 (level, low) -> IRQ 17 [ 2012.769701] bcma-pci-bridge 0000:02:00.0: setting latency timer to 64 [ 2012.769775] bcma: Core 0 found: ChipCommon (manuf 0x4BF, id 0x800, rev 0x25, class 0x0) [ 2012.769808] bcma: Core 1 found: IEEE 802.11 (manuf 0x4BF, id 0x812, rev 0x1D, class 0x0) [ 2012.769889] bcma: Core 2 found: PCIe (manuf 0x4BF, id 0x820, rev 0x13, class 0x0) [ 2012.770175] bcma: PMU resource config unknown for device 0x4331 [ 2012.824527] bcma: Bus registered [ 2012.831744] b43-phy0: Broadcom 4331 WLAN found (core revision 29) [ 2013.371031] b43-phy0: Loading firmware version 666.2 (2011-02-23 01:15:07) and to get the connection again every time i must entery that code in the step of reload driver. How i can let the ubuntu see my wifi and wireless device automatically when i reboot my computer????

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Live Webcasts of the Transit of Venus

- by TATWORTH

Space.com have published a list of webcams for the Transit of Venus at http://www.space.com/14568-venus-transits-sun-2012-skywatching.htmlLive Webcasts Around the World Here is a list of observatories and organizations providing live webcasts on June 5 of the Venus transit of 2012: NASA webcast from Mauna Kea, Hawaii: http://venustransit.nasa.gov/2012/transit/webcast.php Exploratorium (in San Francisco, Calif.) webcast from Mauna Loa, Hawaii: http://www.exploratorium.edu/venus/ Slooh Space Camera telescope feed from around the world: http://www.slooh.com/transit-of-venus/ Astronomers Without Borders webcast from the Mount Wilson Observatory in California: http://www.astronomerswithoutborders.org/projects/transit-of-venus.htmlI intend to publish a single list later.

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Desktop does not show when I installed nvidia drivers!

- by Levan

The desktop does not show after I installed nvidia experimental drivers. I tried nvidia simple proprietary drivers, and they did not work either. Here is how it looks. This is not cropped or any thing. This is how it looks, after the installation of the drivers the desktop resolution decreased from 1440X900 to 1024X768 The desktop only shows desh and panels when I use the open source drivers. Is there any way to fix this so I can get better performance? Thank you in advance. Thanks to rft183 who provided the solution here is another link to the post that states that he found a solution http://ubuntuforums.org/showthread.php?p=12303179#post12303179

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Shadowmap first phase and shaders

- by KaiserJohaan

I am using OpenGL 3.3 and am tryin to implement shadow mapping using cube maps. I have a framebuffer with a depth attachment and a cube map texture. My question is how to design the shaders for the first pass, when creating the shadowmap. This is my vertex shader: in vec3 position; uniform mat4 lightWVP; void main() { gl_Position = lightWVP * vec4(position, 1.0); } Now, do I even need a fragment shader in this shader pass? from what I understand after reading http://www.opengl.org/wiki/Fragment_Shader, by default gl_FragCoord.z is written to the currently attached depth component (to which my cubemap texture is bound to). Thus I shouldnt even need a fragment shader for this pass and from what I understand, there is no other work to do in the fragment shader other than writing this value. Is this correct?

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Inside the Raspberry Pi Factory

- by Jason Fitzpatrick

Curious where your pint-sized Raspberry Pi came from? You might be surprised to learn it was built, tested, and packaged all in an equally pint-sized factory in South Wales. Nick Heath of Tech Republic takes us on a photo tour of the Raspberry Pi factory with a stop at each stage of production and testing. The photo above shows one of the manual construction steps, the insertion of the large components such as the USB and Ethernet ports. Hit up the link below for the full tour. Raspberry Pi: Inside the Pi Factory [Tech Republic] Our Geek Trivia App for Windows 8 is Now Available Everywhere How To Boot Your Android Phone or Tablet Into Safe Mode HTG Explains: Does Your Android Phone Need an Antivirus?

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Alternative way of developing for ASP.NET to WebForms - Any problems with this?

- by John

So I have been developing in ASP.NET WebForms for some time now but often get annoyed with all the overhead (like ViewState and all the JavaScript it generates), and the way WebForms takes over a lot of the HTML generation. Sometimes I just want full control over the markup and produce efficient HTML of my own so I have been experimenting with what I like to call HtmlForms. Essentially this is using ASP.NET WebForms but without the form runat="server" tag. Without this tag, ASP.NET does not seem to add anything to the page at all. From some basic tests it seems that it runs well and you still have the ability to use code-behind pages, and many ASP.NET controls such as repeaters. Of course without the form runat="server" many controls won't work. A post at Enterprise Software Development lists the controls that do require the tag. From that list you will see that all of the form elements like TextBoxes, DropDownLists, RadioButtons, etc cannot be used. Instead you use normal HTML form controls. But how do you access these HTML controls from the code behind? Retrieving values on post back is easy, you just use Request.QueryString or Request.Form. But passing data to the control could be a little messy. Do you use a ASP.NET Literal control in the value field or do you use <%= value % in the markup page? I found it best to add runat="server" to my HTML controls and then you can access the control in your code-behind like this: ((HtmlInputText)txtName).Value = "blah"; Here's a example that shows what you can do with a textbox and drop down list: Default.aspx <%@ Page Language="C#" AutoEventWireup="true" CodeBehind="Default.aspx.cs" Inherits="NoForm.Default" %> <%@ Page Language="C#" AutoEventWireup="true" CodeBehind="Default.aspx.cs" Inherits="NoForm.Default" %> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN""http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head runat="server"> <title></title> </head> <body> <form action="" method="post"> <label for="txtName">Name:</label> <input id="txtName" name="txtName" runat="server" /><br /> <label for="ddlState">State:</label> <select id="ddlState" name="ddlState" runat="server"> <option value=""></option> </select><br /> <input type="submit" value="Submit" /> </form> </body> </html> Default.aspx.cs using System; using System.Web.UI.HtmlControls; using System.Web.UI.WebControls; namespace NoForm { public partial class Default : System.Web.UI.Page { protected void Page_Load(object sender, EventArgs e) { //Default values string name = string.Empty; string state = string.Empty; if (Request.RequestType == "POST") { //If form submitted (post back) name = Request.Form["txtName"]; state = Request.Form["ddlState"]; //Server side form validation would go here //and actions to process form and redirect } ((HtmlInputText)txtName).Value = name; ((HtmlSelect)ddlState).Items.Add(new ListItem("ACT")); ((HtmlSelect)ddlState).Items.Add(new ListItem("NSW")); ((HtmlSelect)ddlState).Items.Add(new ListItem("NT")); ((HtmlSelect)ddlState).Items.Add(new ListItem("QLD")); ((HtmlSelect)ddlState).Items.Add(new ListItem("SA")); ((HtmlSelect)ddlState).Items.Add(new ListItem("TAS")); ((HtmlSelect)ddlState).Items.Add(new ListItem("VIC")); ((HtmlSelect)ddlState).Items.Add(new ListItem("WA")); if (((HtmlSelect)ddlState).Items.FindByValue(state) != null) ((HtmlSelect)ddlState).Value = state; } } } As you can see, you have similar functionality to ASP.NET server controls but more control over the final markup, and less overhead like ViewState and all the JavaScript ASP.NET adds. Interestingly you can also use HttpPostedFile to handle file uploads using your own input type="file" control (and necessary form enctype="multipart/form-data"). So my question is can you see any problems with this method, and any thoughts on it's usefulness? I have further details and tests on my blog.

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What's New & Cool in NetBeans IDE 7.x

- by Geertjan

Loads of new features have been added to NetBeans IDE during the NetBeans IDE 7.x release cycle, i.e., 7.0 together with all the minor releases that have come after that, up to 7.4, which was released during the last few days. Hard to keep track of everything added over all those releases, so instead of making a "What's New in NetBeans IDE 7.4" slide deck (which would only cover the highlights of the NetBeans IDE 7.4 Release Notes), as we would normally do, we've instead produced "What's New in NetBeans IDE 7.x", which is around 50 slides presenting all the key features of the IDE, together with all the key newest features. Here it is: If you want to present the wonderful world that is the NetBeans ecosystem to your JUG or school or university or colleagues in your company, just download the above slide deck (either PDF or the PowerPoint sources) here: https://netbeans.org/community/teams/evangelism And happy NetBeans IDE 7.4 to everyone using NetBeans IDE everywhere in the world!

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My ubuntuone is broken, what is the problem?

- by user6962

I am on 10.10 and u1sdtool seems to be completely broken. I reinstalled it, no change. I can add my PC to the account, but it is added twice(!) every time I tried. So I have my netbook and two times my PC in the account. The netbook with 10.04 has no problems. Below is the error msg I get when attempting to startup Ubuntu One on the command line. desktop:~$ u1sdtool --status Oops, an error ocurred: Traceback (most recent call last): Failure: dbus.exceptions.DBusException: org.freedesktop.DBus.Error.NoReply: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken. desktop:~$ Starting it from the Me Menu has the same effect, the HDD will get really busy for a minute and then nothing happens, the client will not start. Nothing in the syslog or anywhere.

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AHCI Hotswap in Lucid Server

- by chong

Does Lucid support hotswapping of AHCI devices? Is there anything more to it than simply unmounting all filesystems on the drive to be disconnected and plugging in the new disk? 00:1f.2 SATA controller: Intel Corporation 82801IR/IO/IH (ICH9R/DO/DH) 6 port SATA AHCI Controller (rev 02) is the controller I'm working with. BIOS is set to AHCI. I also tried simply unmounting and unplugging. That seemed to work fine. Plugging in a new drive locked up the system. AHCI kernel module is also loaded. I've also looked at the Raid WIKI on kernel.org which talks about hardware requirements for AHCI HotSwapping of disks. My drives and cables all appear to meet the criteria, but most of that info pertains to the electrical side (grounding, etc...).

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How can menu bars that require a right click be activated?

- by Amos Annoy

I've noticed that NetworkManager only has a single, left or right, click menu and no longer has an About menu option to show it's splash screen. In fact all the top bar mini short cut icons have been amputated and crippled leaving them with no rights. This severely impacts on our custom aps., similar to FireFox bookmarks, which can no longer be right clicked to bring up a context menu. It is possible to disengage FF's File|Edit|... menu bar from the top by running it in safe-mode so the menu bar is resident in a window, restoring right clicks, but our aps. do not have "safe modes". How can right clicks in menu bars be restored? reference

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