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  • Alternative to BerkeleyDB?

    - by John
    I'm looking for a dbm-like library that I can use in place of Berkeley DB, which I'm currently using. My main reason for switching is the licensing fees for BDB are pretty high (free for open source apps, but my employer does not want to open source this particular app for various reasons). I've looked briefly at qdbm but it doesn't look like it will fill my needs -- lots of keys (several million) and large data items ( 1-5 megabytes). Before I continue my search I figured I'd ask because it seems there are tons of dbm-like libraries out there.

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  • Calculating a Sample Covariance Matrix for Groups with plyr

    - by John A. Ramey
    I'm going to use the sample code from http://gettinggeneticsdone.blogspot.com/2009/11/split-apply-and-combine-in-r-using-plyr.html for this example. So, first, let's copy their example data: mydata=data.frame(X1=rnorm(30), X2=rnorm(30,5,2), SNP1=c(rep("AA",10), rep("Aa",10), rep("aa",10)), SNP2=c(rep("BB",10), rep("Bb",10), rep("bb",10))) I am going to ignore SNP2 in this example and just pretend the values in SNP1 denote group membership. So then, I may want some summary statistics about each group in SNP1: "AA", "Aa", "aa". Then if I want to calculate the means for each variable, it makes sense (modifying their code slightly) to use: > ddply(mydata, c("SNP1"), function(df) data.frame(meanX1=mean(df$X1), meanX2=mean(df$X2))) SNP1 meanX1 meanX2 1 aa 0.05178028 4.812302 2 Aa 0.30586206 4.820739 3 AA -0.26862500 4.856006 But what if I want the sample covariance matrix for each group? Ideally, I would like a 3D array, where the I have the covariance matrix for each group, and the third dimension denotes the corresponding group. I tried a modified version of the previous code and got the following results that have convinced me that I'm doing something wrong. > daply(mydata, c("SNP1"), function(df) cov(cbind(df$X1, df$X2))) , , = 1 SNP1 1 2 aa 1.4961210 -0.9496134 Aa 0.8833190 -0.1640711 AA 0.9942357 -0.9955837 , , = 2 SNP1 1 2 aa -0.9496134 2.881515 Aa -0.1640711 2.466105 AA -0.9955837 4.938320 I was thinking that the dim() of the 3rd dimension would be 3, but instead, it is 2. Really this is a sliced up version of the covariance matrix for each group. If we manually compute the sample covariance matrix for aa, we get: [,1] [,2] [1,] 1.4961210 -0.9496134 [2,] -0.9496134 2.8815146 Using plyr, the following gives me what I want in list() form: > dlply(mydata, c("SNP1"), function(df) cov(cbind(df$X1, df$X2))) $aa [,1] [,2] [1,] 1.4961210 -0.9496134 [2,] -0.9496134 2.8815146 $Aa [,1] [,2] [1,] 0.8833190 -0.1640711 [2,] -0.1640711 2.4661046 $AA [,1] [,2] [1,] 0.9942357 -0.9955837 [2,] -0.9955837 4.9383196 attr(,"split_type") [1] "data.frame" attr(,"split_labels") SNP1 1 aa 2 Aa 3 AA But like I said earlier, I would really like this in a 3D array. Any thoughts on where I went wrong with daply() or suggestions? Of course, I could typecast the list from dlply() to a 3D array, but I'd rather not do this because I will be repeating this process many times in a simulation. As a side note, I found one method (http://www.mail-archive.com/[email protected]/msg86328.html) that provides the sample covariance matrix for each group, but the outputted object is bloated. Thanks in advance.

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  • Writing a simple RSpec test to check that Rake tasks are correct

    - by John Feminella
    I'm trying to be diligent about checking my rake tasks with RSpec tests, but in the process of feeling my way around I seem to have hit a wall. I've got a really simple RSpec test that looks like this: # ./test/meta_spec.rb describe "Rake tasks" do require 'rake' before(:each) do @rake = Rake::Application.new @rake.load_rakefile # => Error here! Rake.application = @rake end after(:each) do Rake.application = nil end it "should have at least one RSpec test to execute" do Rake.application["specs"].spec_files.size.should > 0 end end I have a simple task called "specs" defined in ./Rakefile.rb which has an RSpec task that includes all the *_spec.rb files. If I put the @rake.load_rakefile method in, I want that Rakefile to load. But instead it just bombs out. If I comment it out, however, the test fails because the "specs" task is (understandably) not defined. Where am I going wrong?

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  • Compiled Haskell libraries with FFI imports are invalid when imported into GHCI

    - by John Millikin
    I am using GHC 6.12.1, in Ubuntu 10.04 When I try to use the FFI syntax for static storage, only modules running in interpreted mode (ie GHCI) work properly. Compiled modules have invalid pointers, and do not work. I'd like to know whether anybody can reproduce the problem, whether this an error in my code or GHC, and (if the latter) whether it's a known issue. I'm using sys_siglist because it's present in a standard library on my system, but I don't believe the actual storage used matters (I discovered this while writing a binding to libidn). If it helps, sys_siglist is defined in <signal.h> as: extern __const char *__const sys_siglist[_NSIG]; I thought this type might be the problem, so I also tried wrapping it in a plain C procedure: #include<stdio.h> const char **test_ffi_import() { printf("C think sys_siglist = %X\n", sys_siglist); return sys_siglist; } However, importing that doesn't change the result, and the printf() call prints the same pointer value as show siglist_a. My suspicion is that it's something to do with static and dynamic library loading. Update: somebody in #haskell suggested this might be 64-bit specific; if anybody tries to reproduce it, can you mention your architecture and whether it worked in a comment? Code as follows: -- A.hs {-# LANGUAGE ForeignFunctionInterface #-} module A where import Foreign import Foreign.C foreign import ccall "&sys_siglist" siglist_a :: Ptr CString -- -- B.hs {-# LANGUAGE ForeignFunctionInterface #-} module B where import Foreign import Foreign.C foreign import ccall "&sys_siglist" siglist_b :: Ptr CString -- -- Main.hs {-# LANGUAGE ForeignFunctionInterface #-} module Main where import Foreign import Foreign.C import A import B foreign import ccall "&sys_siglist" siglist_main :: Ptr CString main = do putStrLn $ "siglist_a = " ++ show siglist_a putStrLn $ "siglist_b = " ++ show siglist_b putStrLn $ "siglist_main = " ++ show siglist_main peekSiglist "a " siglist_a peekSiglist "b " siglist_b peekSiglist "main" siglist_main peekSiglist name siglist = do ptr <- peekElemOff siglist 2 str <- maybePeek peekCString ptr putStrLn $ "siglist_" ++ name ++ "[2] = " ++ show str I would expect something like this output, where all pointer values identical and valid: $ runhaskell Main.hs siglist_a = 0x00007f53a948fe00 siglist_b = 0x00007f53a948fe00 siglist_main = 0x00007f53a948fe00 siglist_a [2] = Just "Interrupt" siglist_b [2] = Just "Interrupt" siglist_main[2] = Just "Interrupt" However, if I compile A.hs (with ghc -c A.hs), then the output changes to: $ runhaskell Main.hs siglist_a = 0x0000000040378918 siglist_b = 0x00007fe7c029ce00 siglist_main = 0x00007fe7c029ce00 siglist_a [2] = Nothing siglist_b [2] = Just "Interrupt" siglist_main[2] = Just "Interrupt"

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  • Set title of SplitViewController

    - by John
    I am using the SplitViewController template. How do I set the title on the topbar in the detailview? Been trying to work this out for hours. Tried simple: detailViewController.title = @"String"; but no luck. Any help appreciated. Thanks.

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  • .hgignore whole directory tree excepting one specific file

    - by John Mee
    Can anyone tell me the .hgignore pattern to track one specific file in a directory and to ignore everything else? I have a "media" directory which contains a "default.png", for obvious purposes, and the rest of the directory will hold user media. We want hg to ignore everything in the media directory excepting the default file.

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  • All words in a trie data-structure

    - by John Smith
    I'm trying to put all words in a trie in a string, a word is detonated by the eow field being true for a certain character in the trie data structure, hence a trie can could have letters than lead up to no word, for ex "abc" is in the trie but "c"'s eow field is false so "abc" is not a word Here is my Data structure struct Trie { bool eow; //when a Trie field isWord = true, hence there is a word char letter; Trie *letters[27]; }; and here is my attemped print-all function, basically trying to return all words in one string seperated by spaces for words string printAll( string word, Trie& data) { if (data.eow == 1) return word + " "; for (int i = 0; i < 26; i++) { if (data.letters[i] != NULL) printAll( word + data.letters[i]->letter, *(data.letters[i])); } return ""; } Its not outputting what i want, any suggestions?

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  • DB2 ZOS String Comparison Problem

    - by John
    I am comparing some CHAR data in a where clause in my sql like this, where PRI_CODE < PriCode The problem I am having is when the CHAR values are of different lengths. So if PRI_CODE = '0800' and PriCode = '20' it is returning true instead of false. It looks like it is comparing it like this '08' < '20' instead of like '0800' < '20' Does a CHAR comparison start from the Left until one or the other values end? If so how do I fix this? My values can have letters in it so convering to numeric is not an option.

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  • C# vs C - Big performance difference

    - by John
    I'm finding massive performance differences between similar code in C anc C#. The C code is: #include <stdio.h> #include <time.h> #include <math.h> main() { int i; double root; clock_t start = clock(); for (i = 0 ; i <= 100000000; i++){ root = sqrt(i); } printf("Time elapsed: %f\n", ((double)clock() - start) / CLOCKS_PER_SEC); } And the C# (console app) is: using System; using System.Collections.Generic; using System.Text; namespace ConsoleApplication2 { class Program { static void Main(string[] args) { DateTime startTime = DateTime.Now; double root; for (int i = 0; i <= 100000000; i++) { root = Math.Sqrt(i); } TimeSpan runTime = DateTime.Now - startTime; Console.WriteLine("Time elapsed: " + Convert.ToString(runTime.TotalMilliseconds/1000)); } } } With the above code, the C# completes in 0.328125 seconds (release version) and the C takes 11.14 seconds to run. The c is being compiled to a windows executable using mingw. I've always been under the assumption that C/C++ were faster or at least comparable to C#.net. What exactly is causing the C to run over 30 times slower? EDIT: It does appear that the C# optimizer was removing the root as it wasn't being used. I changed the root assignment to root += and printed out the total at the end. I've also compiled the C using cl.exe with the /O2 flag set for max speed. The results are now: 3.75 seconds for the C 2.61 seconds for the C# The C is still taking longer, but this is acceptable

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  • unable to get into windows 7 or ubuntu after system file back on a dual boot system

    - by John Jiang
    I installed ubuntu on my dell xps 9000 which originally has a window 7 installed. So after I did system file back up as told by windows 7 and restarted my computer, I received the following message right after restarting in the black screen: roughly like this: ubuntu grub error, " " symbol cannot be found. I was wondering how I can get access into windows 7 and uninstall ubuntu all together. I actually had the same booting problem after system backup before and the solution was to install two extra ubuntus but I'd prefer not to do that. I'd highly appreciate any help!

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  • I want to combine my www and non www and keep the link jucie from both.

    - by John Ray
    My website shows up for some keywords in the www and some in the non www. Seaquake shows more links to the non www version. It is a PR2 either way. I would like to combine the link juice of the two versions into the non www version. Does anyone know the best way to combine the two and keep the link juice of both. It is as simple as a 301 redirect and if so does the 301 need to be handled in any specific way.

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  • PHP - Looking for an HTML Generator/Manager

    - by John Himmelman
    I'm trying to find a tool that I can use to generate markup programatically (non-irl word). Here is an example of what I'm trying to accomplish in pseudo-code... $htmlDoc = new HTML_Document(); $htmlDoc->setTitle('Cool Title'); $htmlDoc->addJs('some_js_file.js'); $htmlDoc->addStylesheet('some_css_file.css'); $divElement = new HTML_Element_Div(); $htmlDoc->append('body', $divElement); $output = $htmlDoc->generate(); What is the best tool for this?

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  • How Do You Profile & Optimize CUDA Kernels?

    - by John Dibling
    I am somewhat familiar with the CUDA visual profiler and the occupancy spreadsheet, although I am probably not leveraging them as well as I could. Profiling & optimizing CUDA code is not like profiling & optimizing code that runs on a CPU. So I am hoping to learn from your experiences about how to get the most out of my code. There was a post recently looking for the fastest possible code to identify self numbers, and I provided a CUDA implementation. I'm not satisfied that this code is as fast as it can be, but I'm at a loss as to figure out both what the right questions are and what tool I can get the answers from. How do you identify ways to make your CUDA kernels perform faster?

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  • Load a controller into an other controller in cakephp

    - by john
    im developing a web application, using multiple pages, each with their own controller. The problem now is that there are some variables in a controller, created for one page, that are required for an other page ( with a different controller). Therefor i need to load one controller into the other one. I did this by adding App::import('Controller', 'sections'); $sections= new sectionsController; $sections-constructClasses(); to the controller, but this doens't seem to work.. Maybe u guys have some ideas? Thnx in advance!

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  • How would you go about parsing markdown?

    - by John Leidegren
    You can find the syntax here. The thing is, the source that follows with the download is written in perl. Which I have no intentions of honoring. It is riddled with regex and it relies on MD5 hashes to escape certain characters. Something is just wrong about that! I'm about to hard code a parser for markdown and I'm wonder if someone had some experience with this? Edit: If you don't have anything meaningful to say about the actual parsing of markdown, spare me the time. (This might sound harsh, but yes, I'm looking for insight, not a solution i.e. third-party library). To help a bit with the answers, regex are meant to identify patterns! NOT to parse an entire grammar. That people consider doing so is foobar. If you think about markdown, it's fundamentally based around the concept of paragraphs. As such, a reasonable approach might be to split the input into paragraphs. There are many kinds of paragraphs e.g. heading, text, list, blockquote, code. The challenge is thus to identify these paragraphs and in what context they occur. I'll be back with a solution, once I find it's worthy to be shared.

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  • UNIX-style RegExp Replace running extremely slowly under windows. Help? EDIT: Negative lookahead ass

    - by John Sullivan
    I'm trying to run a unix regEXP on every log file in a 1.12 GB directory, then replace the matched pattern with ''. Test run on a 4 meg file is took about 10 minutes, but worked. Obviously something is murdering performance by several orders of magnitude. Find: ^(?!.*155[0-2][0-9]{4}\s.*).*$ -- NOTE: match any line NOT starting 155[0-2]NNNN where in is a number 0-9. Replace with: ''. Is there some justifiable reason for my regExp to take this long to replace matching text, or is the program I am using (this is windows / a program called "grepWin") most likely poorly optimized? Thanks. UPDATE: I am noticing that searching for ^(155[0-2]).$ takes ~7 seconds in a 5.6 MB file with 77 matches. Adding the Negative Lookahead Assertion, ?=, so that the regExp becomes ^(?!155[0-2]).$ is causing it to take at least 5-10 minutes; granted, there will be thousands and thousands of matches. Should the negative lookahead assertion be extremely detrimental to performance, and/or a large quantity of matches?

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  • Conventions for the behavior of double or triple "click to select text" features?

    - by John Sullivan
    Almost any mature program that involves text implements "double click to select the word" and, in some cases, "triple click to select additional stuff like an entire line" as a feature. I find these features useful but they are often inconsistent between programs. Example - some programs' double clicks do not select the ending space after a word, but most do. Some recognize the - character as the end of a word, others do not. SO likes to select the entire paragraph as I write this post when I triple click it, VS web developer 2005 has no triple click support, and ultra-edit 32 will select one line upon triple clicking. We could come up with innumerable inconsistencies about how double and triple click pattern matching is implemented across programs. I am concerned about how to implement this behavior in my program if nobody else has achieved a convention about how the pattern matching should work. My question is, does a convention (conventions? maybe an MS or Linux convention?) exist that dictates how these features are supposed to behave to the end user? What, if any, are they?

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  • How to update a custom dependency property when the datasource list changes

    - by John
    Hi We have a user control with a custom dependency property (DP). The DP is bound to an ObservableCollection. When a new item is added to the collection programatically, the databinding does not update the target DP. Why? We think it's because, unfortunately, in our case the target is not a ListBox or ListView, but a Canvas. The DP, when changed or initialized, is supposed to draw a Shape (!) onto the Canvas, and the shape's position and size is bound to the collection item's two properties: WIDTH, LEFT. Ideally we don't want to clear the Canvas and redraw all items just becasue one has been added (or deleted). But how? So: How can the custom DP take care of drawing the shape for the new collection item? What callback do we need, at what point in time does this have to happen, and what specific MetaDataOptions might there? Also, are there any good resources out there concerning all these dependency property options. They are quite confusing. MSDN does not really help with what we're trying to do. Thanks!

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  • How can I send an automated reply to the sender and all recipients with Procmail?

    - by jchong
    I'd like to create a procmail recipe or Perl or shell script that will send an auto response to the original sender as well as anybody that was copied (either To: or cc:) on the original email. Example: [email protected] writes an email to [email protected] and [email protected] (in the To: field). Copies are sent via cc: to [email protected] and [email protected]. I'd like the script to send an auto response to the original sender ([email protected]) and everybody else that was sent a copy of the email ([email protected], [email protected], [email protected] and [email protected]). Thanks

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  • Looking for Fiddler2 help. connection to gateway refused? Just got rid of a virus

    - by John Mackey
    I use Fiddler2 for facebook game items, and it's been a great success. I accessed a website to download some dat files I needed. I think it was eshare, ziddu or megaupload, one of those. Anyway, even before the rar file had downloaded, I got this weird green shield in the bottom right hand corner of my computer. It said a Trojan was trying to access my computer, or something to that extent. It prompted me to click the shield to begin anti-virus scanning. It turns out this rogue program is called Antivirus System Pro and is pretty hard to get rid of. After discovering the rogue program, I tried using Fiddler and got the following error: [Fiddler] Connection to Gateway failed.Exception Text: No connection could be made because the target machine actively refused it 127.0.0.1:5555 I ended up purchasing SpyDoctor + Antivirus, which I'm told is designed specifically for getting rid of these types of programs. Anyway, I did a quick-scan last night with spydoctor and malware bytes. Malware picked up 2 files, and Spydoctor found 4. Most were insignificant, but it did find a worm called Worm.Alcra.F, which was labeled high-priority. I don’t know if that’s the Anti-Virus Pro or not, but SpyDoctor said it got rid of all of those successfully. I tried to run Fiddler again before leaving home, but was still getting the "gateway failed" error. Im using the newest version of firefox. When I initially set up the Fiddler 2.2.8.6, I couldn’t get it to run at first, so I found this faq on the internet that said I needed to go through ToolsOptionsSettings and set up an HTTP Proxy to 127.0.0.1 and my Port to 8888. Once I set that up and downloaded this fiddler helper as a firefox add-on, it worked fine. When I turn on fiddler, it automatically takes my proxy setting from no proxy (default) to the 127.0.0.1 with Port 8888 set up. It worked fine until my computer detected this virus. Anyway, hopefully I've given you sufficient information to offer me your best advice here. Like I said, Spydoctor says the bad stuff is gone, so maybe the rogue program made some type of change in my fiddler that I could just reset or uncheck or something like that? Or will I need to completely remove fiddler and those dat files and rar files I downloaded? Any help would be greatly appreciated. Thanks for your time.

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  • Superfish drop down menu, how to fix z-index in ie6 and ie7?

    - by John Isaacks
    I am using the superfish plugin for jquery here: clicky it works fine in all modern browsers FF,Safari, Chrome, IE8 but it seems like the z-index is not working in ie6 and 7 you can see the menu is appearing, but being cut off by the elements below it. I have tried adding a z-index everywhere I can think of but nothing seems to fix this. How can I fix this? Thanks!!!

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