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• What is in your Mathematica tool bag?

  - by Timo

  We all know that Mathematica is great, but it also often lacks critical functionality. What kind of external packages / tools / resources do you use with Mathematica? I'll edit (and invite anyone else to do so too) this main post to include resources which are focused on general applicability in scientific research and which as many people as possible will find useful. Feel free to contribute anything, even small code snippets (as I did below for a timing routine). Also, undocumented and useful features in Mathematica 7 and beyond you found yourself, or dug up from some paper/site are most welcome. Please include a short description or comment on why something is great or what utility it provides. If you link to books on Amazon with affiliate links please mention it, e.g., by putting your name after the link. Packages: LevelScheme is a package that greatly expands Mathematica's capability to produce good looking plots. I use it if not for anything else then for the much, much improved control over frame/axes ticks. David Park's Presentation Package ($50 - no charge for updates) Tools: MASH is Daniel Reeves's excellent perl script essentially providing scripting support for Mathematica 7. (This is finally built in as of Mathematica 8 with the -script option.) Resources: Wolfram's own repository MathSource has a lot of useful if narrow notebooks for various applications. Also check out the other sections such as Current Documentation, Courseware for lectures, and Demos for, well, demos. Books: Mathematica programming: an advanced introduction by Leonid Shifrin (web, pdf) is a must read if you want to do anything more than For loops in Mathematica. Quantum Methods with Mathematica by James F. Feagin (amazon) The Mathematica Book by Stephen Wolfram (amazon) (web) Schaum's Outline (amazon) Mathematica in Action by Stan Wagon (amazon) - 600 pages of neat examples and goes up to Mathematica version 7. Visualization techniques are especially good, you can see some of them on the author's Demonstrations Page. Mathematica Programming Fundamentals by Richard Gaylord (pdf) - A good concise introduction to most of what you need to know about Mathematica programming. Undocumented (or scarcely documented) Features: How to customize Mathematica keyboard shortcuts. See this question. How to inspect patterns and functions used by Mathematica's own functions. See this answer How to achieve Consistent size for GraphPlots in Mathematica? See this question.

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• Log4r : logger inheritance, yaml configuration, alternatives ?

  - by devlearn

  Hello, I'm pretty new to ruby environments and I was looking for a nice logging framework to use it my ruby and rails applications. In my previous experiences I have successfully used log4j and log4p (the perl port) and was expecting the same level of usability (and maturity) with log4r. However I must say that there are a number of things that are not clear at all in the log4r framework. 1 Logger Inheritance The logger inheritance does not seem to be managed at all ! If I declare a logger named 'myapp' and then try to get a logger name 'myapp::engine', the lookup will end with a NameError. I would expect that the framework returns the root logger according to the naming scheme and to use the 'myapp' logger. Q1 : Of course I can work around this and manage the names by myself with a lookup method, however is there a cleaner way to do this without any extra coding ? 2 YAML configuration Second thing that confuses me is the yaml configuration. On the log4r site there are literally no information about this system, the doc links forward to missing pages, so all the info I can find about is contained in the examples directory of the gem. I was pretty confused with the fact that the yaml configuration must contain the pre_config section, and that I need to define my own levels. If I remove the pre_config secion, or replace all the “custom” levels by the standard ones ( debug, info, warn, fatal ) , the example will throw the following error : log4r/yamlconfigurator.rb:68:in `decode_yaml': Log level must be in 0..7 (ArgumentError) So there seems to be no way of using a simple file where we only declare the loggers and appenders for the framework. Q2 : I realy think that I missed something and that must be a way of providing a simple yaml conf file. Do you have any examples of such an usage ? 3 Variables substitution in XML file Q3 : The Yaml configuration system seems to provide such a feature however I was unable to find a similar feature with XML files. Any ideas ? 4 Alternatives ? I must say that I'm very disappointed by the feature level and the maturity of log4r compared to the log4j and other log4j ports. I run into this framework with a solid background of logging APIs in other languages and find myself working around in all kinds just to make 'basic things' running in a “real world application”. By that I mean a complex application composed of several gems, console/scripting apps, and a rails web front end where the configuration must be mutualized and where we make intensive usage of namespaces and inheritance. I've run several searches in order to find something more suitable or mature, but did not find anything similar. Q4 : Do you guys know any (serious) alternatives to log4r framework that could be used in a enterprise class app ? Thanks reading all of this ! I'd really appreciate any pointers, Kind Regards,

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• How do I verify a DKIM signature in PHP?

  - by angrychimp

  I'll admit I'm not very adept at key verification. What I have is a script that downloads messages from a POP3 server, and I'm attempting to verify the DKIM signatures in PHP. I've already figured out the body hash (bh) validation check, but I can't figure out the header validation. http://www.dkim.org/specs/rfc4871-dkimbase.html#rfc.section.6.1.3 Below is an example of my message headers. I've been able to use the Mail::DKIM package to validate the signature in Perl, so I know it's good. I just can't seem to figure out the instructions in the RFC and translate them into PHP code. DomainKey-Signature: q=dns; a=rsa-sha1; c=nofws; s=angrychimp-1.bh; d=angrychimp.net; h=From:X-Outgoing; b=RVkenibHQ7GwO5Y3tun2CNn5wSnooBSXPHA1Kmxsw6miJDnVp4XKmA9cUELwftf9 nGiRCd3rLc6eswAcVyNhQ6mRSsF55OkGJgDNHiwte/pP5Z47Lo/fd6m7rfCnYxq3 DKIM-Signature: v=1; a=rsa-sha1; d=angrychimp.net; s=angrychimp-1.bh; c=relaxed/simple; q=dns/txt; [email protected]; t=1268436255; h=From:Subject:X-Outgoing:Date; bh=gqhC2GEWbg1t7T3IfGMUKzt1NCc=; b=ZmeavryIfp5jNDIwbpifsy1UcavMnMwRL6Fy6axocQFDOBd2KjnjXpCkHxs6yBZn Wu+UCFeAP+1xwN80JW+4yOdAiK5+6IS8fiVa7TxdkFDKa0AhmJ1DTHXIlPjGE4n5; To: [email protected] Message-ID: From: DKIM Tester Reply-To: [email protected] Subject: Automated DKIM Testing (angrychimp.net) X-Outgoing: dhaka Date: Fri, 12 Mar 2010 15:24:15 -0800 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline MIME-Version: 1.0 Return-Path: [email protected] X-OriginalArrivalTime: 12 Mar 2010 23:25:50.0326 (UTC) FILETIME=[5A0ED160:01CAC23B] I can extract the public key from my DNS just fine, and I believe I'm canonicalizing the headers correctly, but I just can't get the signature validated. I don't think I'm preparing my key or computing the signature validation correctly. Is this something that's possible (do I need pear extensions or something?) or is manually validating a DKIM signature in PHP just not feasible?

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• Automatically generate table of function pointers in C.

  - by jeremytrimble

  I'm looking for a way to automatically (as part of the compilation/build process) generate a "table" of function pointers in C. Specifically, I want to generate an array of structures something like: typedef struct { void (*p_func)(void); char * funcName; } funcRecord; /* Automatically generate the lines below: */ extern void func1(void); extern void func2(void); /* ... */ funcRecord funcTable[] = { { .p_func = &func1, .funcName = "func1" }, { .p_func = &func2, .funcName = "func2" } /* ... */ }; /* End automatically-generated code. */ ...where func1 and func2 are defined in other source files. So, given a set of source files, each of which which contain a single function that takes no arguments and returns void, how would one automatically (as part of the build process) generate an array like the one above that contains each of the functions from the files? I'd like to be able to add new files and have them automatically inserted into the table when I re-compile. I realize that this probably isn't achievable using the C language or preprocessor alone, so consider any common *nix-style tools fair game (e.g. make, perl, shell scripts (if you have to)). But Why? You're probably wondering why anyone would want to do this. I'm creating a small test framework for a library of common mathematical routines. Under this framework, there will be many small "test cases," each of which has only a few lines of code that will exercise each math function. I'd like each test case to live in its own source file as a short function. All of the test cases will get built into a single executable, and the test case(s) to be run can be specified on the command line when invoking the executable. The main() function will search through the table and, if it finds a match, jump to the test case function. Automating the process of building up the "catalog" of test cases ensures that test cases don't get left out (for instance, because someone forgets to add it to the table) and makes it very simple for maintainers to add new test cases in the future (just create a new source file in the correct directory, for instance). Hopefully someone out there has done something like this before. Thanks, StackOverflow community!

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• Personal Project - Next practical language/tech to learn

  - by Paul Nathan

  I'm working on a personal project doing some finance analysis. It's a totally new field for me, and I'm really having fun with it so far, plus working in the high-level language arena is a great break from my embedded systems daytime work. I have a MySQL backend on a non-local server with a pile of stock data. My task now is to do some analysis of the stocks and produce something approximating a useful result. There are a couple technical difficulties. (1) I have a lot of records. To be precise, I believe I'm near 100K records right now, and this number grows by 6.1K each weekday. I need to create a way to rummage through these fields and do data analysis - based on a given computation, go look at this other set. Fine and dandy, nothing too outre. But this means I could really use a straightforward API for talking to MySQL. (2) Ideally, it runs on OS X 10.4.11. No Windows/Linux machine at home. (3) I can use PHP, C++, Perl, etc. I even have an R installation. I'm pretty flexible with stuff, so long as it runs on OS X. (Lots of options here, pick water, H20, or dihydrogen monoxide ;-) ) (4)Lack of hassle. While I like clever and fun ways of doing things, I'm trying to get some analysis done, not spend ten hours doing installation work and scratching my head figuring out a theoretical syntax question needed to spout out "hello world". What's the question? I'd like to dig into something different than my usual PHP/C++/C toolset. I'm looking for recommendations for languages/technologies that will assist me and meet the above requirements. In particular, I've heard a lot of buzz about F# and Python on SO. I've used CLISP for small problems before, and kinda liked it. I'm seeking opinions about those in particular. edit:since I rent the DB server and have a limited amount of CPU time online, I'm trying to do the analysis on a local machine.

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• ImageMagick on Mac OSX Snow Leopard. Is there any way to get it to work?

  - by ?????

  It seems that I have more trouble getting standard Unix things to run on Snow Leopard than any other platform--including Windows cygwin For the past couple of days, I've been trying to get ImageMagick to run on Snow Leopard. The most obvious way, Mac Ports, fails: tppllc-Mac-Pro:ImageMagick-sl swirsky$ sudo port install imagemagick ---> Computing dependencies for p5-locale-gettext ---> Configuring p5-locale-gettext Error: Target org.macports.configure returned: configure failure: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_perl_p5-locale-gettext/work/gettext-1.05" && /opt/local/bin/perl Makefile.PL INSTALLDIRS=vendor " returned error 2 Command output: checking for gettext... no checking for gettext in -I/opt/local/include -arch i386 -L/opt/local/lib -lintl...gettext function not found. Please install libintl at Makefile.PL line 18. no Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade xorg-libXt failed Before reporting a bug, first run the command again with the -d flag to get complete output. tppllc-Mac-Pro:ImageMagick-sl swirsky$ Not wanting to spend another two days figuring out why my libintl doesn't have a "gettext" function, I tried a different route: the script mentioned here: http://github.com/masterkain/ImageMagick-sl This script downloads and installs an ImageMagic independently of MacPorts issues tppllc-Mac-Pro:ImageMagick-sl swirsky$ /usr/local/bin/convert dyld: Library not loaded: /opt/local/lib/libiconv.2.dylib Referenced from: /opt/local/lib/libfontconfig.1.dylib Reason: Incompatible library version: libfontconfig.1.dylib requires version 8.0.0 or later, but libiconv.2.dylib provides version 7.0.0 Trace/BPT trap It downloads everything and compiles fine, but fails when I try to run it, with the message above. So now I'm two steps away from ImageMagick, trying to get a newer libiconv on my machine. I downloaded the latest libiconv, compiled and built it. I put the resulting library in /opt/local/lib, and I still get the same error message: tppllc-Mac-Pro:.libs swirsky$ sudo mv libiconv.2.dylib /opt/local/lib/libiconv.2.dylib tppllc-Mac-Pro:.libs swirsky$ convert dyld: Library not loaded: /opt/local/lib/libiconv.2.dylib Referenced from: /opt/local/lib/libfontconfig.1.dylib Reason: Incompatible library version: libfontconfig.1.dylib requires version 8.0.0 or later, but libiconv.2.dylib provides version 7.0.0 Trace/BPT trap So here's my question: Is it possible to get ImageMagick to run on OSX Snow Leopard? Are there any binary distributions that have static libraries baked in so I don't have to worry about these issue/

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• What are five things you hate about your favorite language?

  - by brian d foy

  There's been a cluster of Perl-hate on Stackoverflow lately, so I thought I'd bring my "Five things you hate about your favorite language" question to StackOverflow. Take your favorite language and tell me five things you hate about it. Those might be things that just annoy you, admitted design flaws, recognized performance problems, or any other category. You just have to hate it, and it has to be your favorite language. Don't compare it to another language, and don't talk about languages that you already hate. Don't talk about the things you like in your favorite language. I just want to hear the things that you hate but tolerate so you can use all of the other stuff, and I want to hear it about the language you wished other people would use. I ask this whenever someone tries to push their favorite language on me, and sometimes as an interview question. If someone can't find five things to hate about his favorite tool, he don't know it well enough to either advocate it or pull in the big dollars using it. He hasn't used it in enough different situations to fully explore it. He's advocating it as a culture or religion, which means that if I don't choose his favorite technology, I'm wrong. I don't care that much which language you use. Don't want to use a particular language? Then don't. You go through due diligence to make an informed choice and still don't use it? Fine. Sometimes the right answer is "You have a strong programming team with good practices and a lot of experience in Bar. Changing to Foo would be stupid." This is a good question for code reviews too. People who really know a codebase will have all sorts of suggestions for it, and those who don't know it so well have non-specific complaints. I ask things like "If you could start over on this project, what would you do differently?" In this fantasy land, users and programmers get to complain about anything and everything they don't like. "I want a better interface", "I want to separate the model from the view", "I'd use this module instead of this other one", "I'd rename this set of methods", or whatever they really don't like about the current situation. That's how I get a handle on how much a particular developer knows about the codebase. It's also a clue about how much of the programmer's ego is tied up in what he's telling me. Hate isn't the only dimension of figuring out how much people know, but I've found it to be a pretty good one. The things that they hate also give me a clue how well they are thinking about the subject.

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• PL/SQL pre-compile and Code Quality checks in an automatted build environment?

  - by Lars Corneliussen

  We build software using Hudson and Maven. We have C#, java and last, but not least PL/SQL sources (sprocs, packages, DDL, crud) For C# and Java we do unit tests and code analysis, but we don't really know the health of our PL/SQL sources before we actually publish them to the target database. Requirements There are a couple of things we wan't to test in the following priority: Are the sources valid, hence "compilable"? For packages, with respect to a certain database, would they compile? Code Quality: Do we have code flaws like duplicates, too complex methods or other violations to a defined set of rules? Also, the tool must run head-less (commandline, ant, ...) we wan't to do analysis on a partial code base (changed sources only) Tools We did a little research and found the following tools that could potencially help: Cast Application Intelligence Platform (AIP): Seems to be a server that grasps information about "anything". Couldn't find a console version that would export in readable format. Toad for Oracle: The Professional version is said to include something called Xpert validates a set of rules against a code base. Sonar + PL/SQL-Plugin: Uses Toad for Oracle to display code-health the sonar-way. This is for browsing the current state of the code base. Semantic Designs DMSToolkit: Quite general analysis of source code base. Commandline available? Semantic Designs Clones Detector: Detects clones. But also via command line? Fortify Source Code Analyzer: Seems to be focussed on security issues. But maybe it is extensible? more... So far, Toad for Oracle together with Sonar seems to be an elegant solution. But may be we are missing something here? Any ideas? Other products? Experiences? Related Questions on SO: http://stackoverflow.com/questions/531430/any-static-code-analysis-tools-for-stored-procedures http://stackoverflow.com/questions/839707/any-code-quality-tool-for-pl-sql http://stackoverflow.com/questions/956104/is-there-a-static-analysis-tool-for-python-ruby-sql-cobol-perl-and-pl-sql

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• jquerymobile conflict with autocomplete : $this.attr("href") is undefined

  - by sweets-BlingBling

  When I use jquery ui autocomplete version 1.8.5 with jquery mobile alpha 2. I get an error when I click an item from the autocomplete list: $this.attr("href") is undefined. Does anyone know any fix for it? EDITED: <html> <head> <link rel="stylesheet" type="text/css" href="css/ui-lightness/jquery-ui-1.8.custom.css"> <link rel="stylesheet" type="text/css" href="css/autocomplete.css"> </head> <body> <div id="formWrap"> <form id="messageForm" action="#"> <fieldset> <label id="toLabel">select:</label> <div id="friends" class="ui-helper-clearfix"> <input id="to" type="text"> </div> </fieldset> </form> </div> <script type="text/javascript" src="js/jquery-1.4.2.min.js"></script> <script type="text/javascript" src="js/jquery.mobile-1.0a2.js"></script> <script type="text/javascript" src="js/jquery-ui-1.8.custom.min.js"></script> <script type="text/javascript"> $(function(){ var availableTags = [ "ActionScript", "AppleScript", "Asp", "BASIC", "C", "C++", "Clojure", "COBOL", "ColdFusion", "Erlang", "Fortran", "Groovy", "Haskell", "Java", "JavaScript", "Lisp", "Perl", "PHP", "Python", "Ruby", "Scala", "Scheme" ]; //attach autocomplete $("#to").autocomplete({ source:availableTags , //define select handler select: function(e, ui) { var contact = ui.item.value; createSpan(contact); $("#to").val("").css("top", 2); return false; } }); }); function createSpan(contact){ //create formatted friend span = $("<span>").text(contact) //add contact to contact div span.insertBefore("#to"); } </script> </body> </html>

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• Classifying captured data in unknown format?

  - by monch1962

  I've got a large set of captured data (potentially hundreds of thousands of records), and I need to be able to break it down so I can both classify it and also produce "typical" data myself. Let me explain further... If I have the following strings of data: 132T339G1P112S 164T897F5A498S 144T989B9B223T 155T928X9Z554T ... you might start to infer the following: possibly all strings are 14 characters long the 4th, 8th, 10th and 14th characters may always be alphas, while the rest are numeric the first character may always be a '1' the 4th character may always be the letter 'T' the 14th character may be limited to only being 'S' or 'T' and so on... As you get more and more samples of real data, some of these "rules" might disappear; if you see a 15 character long string, then you have evidence that the 1st "rule" is incorrect. However, given a sufficiently large sample of strings that are exactly 14 characters long, you can start to assume that "all strings are 14 characters long" and assign a numeric figure to your degree of confidence (with an appropriate set of assumptions around the fact that you're seeing a suitably random set of all possible captured data). As you can probably tell, a human can do a lot of this classification by eye, but I'm not aware of libraries or algorithms that would allow a computer to do it. Given a set of captured data (significantly more complex than the above...), are there libraries that I can apply in my code to do this sort of classification for me, that will identify "rules" with a given degree of confidence? As a next step, I need to be able to take those rules, and use them to create my own data that conforms to these rules. I assume this is a significantly easier step than the classification, but I've never had to perform a task like this before so I'm really not sure how complex it is. At a guess, Python or Java (or possibly Perl or R) are possibly the "common" languages most likely to have these sorts of libraries, and maybe some of the bioinformatic libraries do this sort of thing. I really don't care which language I have to use; I need to solve the problem in whatever way I can. Any sort of pointer to information would be very useful. As you can probably tell, I'm struggling to describe this problem clearly, and there may be a set of appropriate keywords I can plug into Google that will point me towards the solution. Thanks in advance

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• [NEWVERSION]algorithm || method to write prog[UNSOLVED] [closed]

  - by fatai

  I am one of the computer science student. Everyone solve problem with a different or same method, ( but actually I dont know whether they use method or I dont know whether there are such common method to approach problem.) if there are common method, What is it ? If there are different method, which method are you using ? All teacher give us problem which in simple form sometimes, but they donot introduce any approach or method(s) so that we cannot make a decision to choose the method then apply that one to problem , afterward find solution then write code.No help from teacher , push us to find method to solve homework. Ex: my friend is using no method , he says "I start to construct algorithm while I try to write prog." I have found one method when I failed the course, More accurately, my method: When I counter problem in language , I will get more paper and then ; first, input/ output step ; my prog will take this / these there argument(s) and return namely X , ex : in c, input length is not known and at same type , so I must use pointer desired output is in form of package , so use structure second, execution part ; in that step , I am writing all step which are goes to final output ex : in python ; 1.) [ + , [- , 4 , [ * , 1 , 2 ]], 5] 2.) [ + , [- , 4 , 2 ],5 ] 3.) [ + , 2 , 5] 4.) 7 ==> return 7 third, I will write test code ex : in c++ input : append 3 4 5 6 vector_x remove 0 1 desired output vector_x holds : 5 6 now, my other question is ; What is/are other method(s) which have/has been; used to construct class :::: for c++ , python, java used to communicate classes / computers used for solving embedded system problem ::::: for c by other user? Some programmer uses generalized method without considering prog-language(java , perl .. ), what is this method ? Why I wonder , because I learn if you dont costruct algorithm on paper, you may achieve your goal. Like no money no lunch , I can say no algorithm no prog therefore , feel free when you write your own method , a way which is introduced by someone else but you are using and you find it is so efficient

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• gcc/g++: error when compiling large file

  - by Alexander

  Hi, I have a auto-generated C++ source file, around 40 MB in size. It largely consists of push_back commands for some vectors and string constants that shall be pushed. When I try to compile this file, g++ exits and says that it couldn't reserve enough virtual memory (around 3 GB). Googling this problem, I found that using the command line switches --param ggc-min-expand=0 --param ggc-min-heapsize=4096 may solve the problem. They, however, only seem to work when optimization is turned on. 1) Is this really the solution that I am looking for? 2) Or is there a faster, better (compiling takes ages with these options acitvated) way to do this? Best wishes, Alexander Update: Thanks for all the good ideas. I tried most of them. Using an array instead of several push_back() operations reduced memory usage, but as the file that I was trying to compile was so big, it still crashed, only later. In a way, this behaviour is really interesting, as there is not much to optimize in such a setting -- what does the GCC do behind the scenes that costs so much memory? (I compiled with deactivating all optimizations as well and got the same results) The solution that I switched to now is reading in the original data from a binary object file that I created from the original file using objcopy. This is what I originally did not want to do, because creating the data structures in a higher-level language (in this case Perl) was more convenient than having to do this in C++. However, getting this running under Win32 was more complicated than expected. objcopy seems to generate files in the ELF format, and it seems that some of the problems I had disappeared when I manually set the output format to pe-i386. The symbols in the object file are by standard named after the file name, e.g. converting the file inbuilt_training_data.bin would result in these two symbols: binary_inbuilt_training_data_bin_start and binary_inbuilt_training_data_bin_end. I found some tutorials on the web which claim that these symbols should be declared as extern char _binary_inbuilt_training_data_bin_start;, but this does not seem to be right -- only extern char binary_inbuilt_training_data_bin_start; worked for me.

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• ImageMagick on Mac OSX Snow Leopard. Is there any way to get it to compile and run?

  - by ?????

  It seems that I have more trouble getting standard Unix things to run on Snow Leopard than any other platform--including Windows cygwin For the past couple of days, I've been trying to get ImageMagick to run on Snow Leopard. The most obvious way, Mac Ports, fails: tppllc-Mac-Pro:ImageMagick-sl swirsky$ sudo port install imagemagick ---> Computing dependencies for p5-locale-gettext ---> Configuring p5-locale-gettext Error: Target org.macports.configure returned: configure failure: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_perl_p5-locale-gettext/work/gettext-1.05" && /opt/local/bin/perl Makefile.PL INSTALLDIRS=vendor " returned error 2 Command output: checking for gettext... no checking for gettext in -I/opt/local/include -arch i386 -L/opt/local/lib -lintl...gettext function not found. Please install libintl at Makefile.PL line 18. no Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade xorg-libXt failed Before reporting a bug, first run the command again with the -d flag to get complete output. tppllc-Mac-Pro:ImageMagick-sl swirsky$ Not wanting to spend another two days figuring out why my libintl doesn't have a "gettext" function, I tried a different route: the script mentioned here: http://github.com/masterkain/ImageMagick-sl This script downloads and installs an ImageMagic independently of MacPorts issues tppllc-Mac-Pro:ImageMagick-sl swirsky$ /usr/local/bin/convert dyld: Library not loaded: /opt/local/lib/libiconv.2.dylib Referenced from: /opt/local/lib/libfontconfig.1.dylib Reason: Incompatible library version: libfontconfig.1.dylib requires version 8.0.0 or later, but libiconv.2.dylib provides version 7.0.0 Trace/BPT trap It downloads everything and compiles fine, but fails when I try to run it, with the message above. So now I'm two steps away from ImageMagick, trying to get a newer libiconv on my machine. I downloaded the latest libiconv, compiled and built it. I put the resulting library in /opt/local/lib, and I still get the same error message: tppllc-Mac-Pro:.libs swirsky$ sudo mv libiconv.2.dylib /opt/local/lib/libiconv.2.dylib tppllc-Mac-Pro:.libs swirsky$ convert dyld: Library not loaded: /opt/local/lib/libiconv.2.dylib Referenced from: /opt/local/lib/libfontconfig.1.dylib Reason: Incompatible library version: libfontconfig.1.dylib requires version 8.0.0 or later, but libiconv.2.dylib provides version 7.0.0 Trace/BPT trap Now here's something interesting. The error message shows it's looking in /opt/local/lib/libiconv.2.dylib. otools -L shows that this does implement 8.0.0: tppllc-Mac-Pro:.libs swirsky$ otool -L /opt/local/lib/libiconv.2.dylib /opt/local/lib/libiconv.2.dylib: /usr/local/lib/libiconv.2.dylib (compatibility version 8.0.0, current version 8.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.0.0) tppllc-Mac-Pro:.libs swirsky$ And, for good measure, I set the DYLD_LIBRARY_PATH to make sure this directory is the one for dynamic libraries. So even though I do have a library that provides 8.0.0, it's being seen as 7.0.0! Any ideas why this would happen? So here's my question: Is it possible to get ImageMagick to run on OSX Snow Leopard? Are there any binary distributions that have static libraries baked in so I don't have to worry about these issue/

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• Escaping Code for Different Shells

  - by Jon Purdy

  Question: What characters do I need to escape in a user-entered string to securely pass it into shells on Windows and Unix? What shell differences and version differences should be taken into account? Can I use printf "%q" somehow, and is that reliable across shells? Backstory (a.k.a. Shameless Self-Promotion): I made a little DSL, the Vision Web Template Language, which allows the user to create templates for X(HT)ML documents and fragments, then automatically fill them in with content. It's designed to separate template logic from dynamic content generation, in the same way that CSS is used to separate markup from presentation. In order to generate dynamic content, a Vision script must defer to a program written in a language that can handle the generation logic, such as Perl or Python. (Aside: using PHP is also possible, but Vision is intended to solve some of the very problems that PHP perpetuates.) In order to do this, the script makes use of the @system directive, which executes a shell command and expands to its output. (Platform-specific generation can be handled using @unix or @windows, which only expand on the proper platform.) The problem is obvious, I should think: test.htm: <!-- ... --> <form action="login.vis" method="POST"> <input type="text" name="USERNAME"/> <input type="password" name="PASSWORD"/> </form> <!-- ... --> login.vis: #!/usr/bin/vision # Think USERNAME = ";rm -f;" @system './login.pl' { USERNAME; PASSWORD } One way to safeguard against this kind of attack is to set proper permissions on scripts and directories, but Web developers may not always set things up correctly, and the naive developer should get just as much security as the experienced one. The solution, logically, is to include a @quote directive that produces a properly escaped string for the current platform. @system './login.pl' { @quote : USERNAME; @quote : PASSWORD } But what should @quote actually do? It needs to be both cross-platform and secure, and I don't want to create terrible problems with a naive implementation. Any thoughts?

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• Overloading framework methods in objective-c, or retaining local changes with framework updates.

  - by Jeff B

  I am using cocos2d to build an iPhone game. It's mostly done, but along the way I came across some things that I would like to handle better. I am fairly new to Objective C, and honestly I do more Perl scripting in my day-to-day job than anything, so my C skills are a little rusty. One of them is the fact that I have modified cocos2d files for some specific cases in my game. However, when I update to a new version, I have to manually pull my changes forward. So, the question is, what is the best way to deal with this? Some options I have thought of: Overload/redefine the cocos2d classes. I was under the impression that I cannot overload existing class functions, so I don't think this will work. Create patches that I re-apply after library updates. I don't think this will work as the new files won't necessarily be the same as the old ones, and if they were, I could just copy the whole file forward. Turn in my changes to Cocos2d. Not an option as my changes are very specific to my application. Am I missing something obvious? UPDATE: I will explain what I am doing to be more clear. Cocos2d has a CCNode object, which can contain children, etc. I added a shadow, which is very similar to a child, but handled a little differently. The shadow has an offset from the parent, and translates with it's parent, rotates around it's own center when the parent rotates, etc. The shadow is not included as a true child, however, so given the correct z-index, the shadows can render under ALL other objects, but still move with the parent. To do this I added addShadow functions to CCNode, and modified the setPosition and setRotate functions to move the shadowSprite: CCNode.m: -(id) init { if ((self=[super init]) ) { ... shadowSprite_ = nil; ... } } ... -(BOOL) addShadow: (CCNode*) child offset: (CGPoint) offset { shadowSprite_ = child; shadowSprite_.position = CGPointMake(position_.x+offset.x, position_.y+offset.y); return YES; } ... -(void) setRotation: (float)newRotation { rotation_ = newRotation; isTransformDirty_ = isInverseDirty_ = YES; if(shadowSprite_) { [shadowSprite_ setRotation: newRotation]; } } There is more, of course, including the prototypes in the .h file, but that is the basics. I don't think I need shadowSprite to be a property, because I don't need to access it after it has been added.

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• Question about DBD::CSB Statement-Functions

  - by sid_com

  From the SQL::Statement::Functions documentation: Function syntax When using SQL::Statement/SQL::Parser directly to parse SQL, functions (either built-in or user-defined) may occur anywhere in a SQL statement that values, column names, table names, or predicates may occur. When using the modules through a DBD or in any other context in which the SQL is both parsed and executed, functions can occur in the same places except that they can not occur in the column selection clause of a SELECT statement that contains a FROM clause. # valid for both parsing and executing SELECT MyFunc(args); SELECT * FROM MyFunc(args); SELECT * FROM x WHERE MyFuncs(args); SELECT * FROM x WHERE y < MyFuncs(args); # valid only for parsing (won't work from a DBD) SELECT MyFunc(args) FROM x WHERE y; Reading this I would expect that the first SELECT-statement of my example shouldn't work and the second should but it is quite the contrary. #!/usr/bin/env perl use warnings; use strict; use 5.010; use DBI; open my $fh, '>', 'test.csv' or die $!; say $fh "id,name"; say $fh "1,Brown"; say $fh "2,Smith"; say $fh "7,Smith"; say $fh "8,Green"; close $fh; my $dbh = DBI->connect ( 'dbi:CSV:', undef, undef, { RaiseError => 1, f_ext => '.csv', }); my $table = 'test'; say "\nSELECT 1"; my $sth = $dbh->prepare ( "SELECT MAX( id ) FROM $table WHERE name LIKE 'Smith'" ); $sth->execute (); $sth->dump_results(); say "\nSELECT 2"; $sth = $dbh->prepare ( "SELECT * FROM $table WHERE id = MAX( id )" ); $sth->execute (); $sth->dump_results(); outputs: SELECT 1 '7' 1 rows SELECT 2 Unknown function 'MAX' at /usr/lib/perl5/site_perl/5.10.0/SQL/Parser.pm line 2893. DBD::CSV::db prepare failed: Unknown function 'MAX' at /usr/lib/perl5/site_perl/5.10.0/SQL/Parser.pm line 2894. [for Statement "SELECT * FROM test WHERE id = MAX( id )"] at ./so_3.pl line 30. DBD::CSV::db prepare failed: Unknown function 'MAX' at /usr/lib/perl5/site_perl/5.10.0/SQL/Parser.pm line 2894. [for Statement "SELECT * FROM test WHERE id = MAX( id )"] at ./so_3.pl line 30. Could someone explaine me this behavior?

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• WndProc(ref Message m), Prevent minimize Games, Send key strokes.

  - by Stanomatic

  Overview: I am going to create a touch application that interfaces with games and other apps. This concept is similar to the app found on touch-buddy.com but I will be using C# and WPF instead of how the application is written in Perl. I have a few challenges I would like to evaluate. The touch-buddy app uses two approaches while interacting with games; 1. Client mode (Same machine runs both game and touch-buddy). 2. Server / Client mode where a separate box sends commands to the game machine. The reason I believe for this method was to circumvent the issue with games minimizing. In Client only mode I am faced with the issue where I touch a screen OTHER than the main screen where the game is viewed and then the game minimizes. Not all games have this behavior but I would like to conquer the games that do minimize and prevent it. Is it possible to keep a game front and center Focused and prevent minimizing utilizing C# WndProc(ref Message m)? I have been experimenting with WndProc(ref Message m) where I created a win form and when I press minimize on my own Win form and it will close an instance of notepad. This proves to me that I can capture a message, prevent that message from bubbling up and then send a message to another application. I then tried to click on notepad with my touch screen and keep my win form application in focus and not minimize. At this point I am unsuccessful. I need more time understanding message codes. Is this the right approach? Can it be done? Should I look at other libraries such as Windows Automation? Key input is my other concern. What is the best way to send key strokes to other apps/games. Should I tap into DirectX, use some kind of send key, Automation Framework? Can any of these handle the multiple key strokes that some simulation games require? I appreciate any links and or insight you may have. If you have gone down this path for any reason I would love to hear your comments. Stan

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• L-Soft LISTSERV TCPGUI Interface for PHP Creation

  - by poolnoodl

  I'm trying to use LISTSERV's "API" in PHP. L-Soft calls this TCPGUI, and essentially, you can request data like over Telnet. To do this, I'm using PHP's TCP socket functions. I've seen this done in other languages but can't quite convert it to PHP. I can connect, I can change set ASCII or BINARY mode. But I can never quite craft the header packet the way I need to authenticate, so I'm thinking I'm messing up my conversion. C: http://www.lsoft.com/manuals/16.0/htmlhelp/advanced%20topics/TCPGUI.html#2334328 $origin = '[email protected]'; $pwd = 'password'; $host = "example.com"; $port = 2306; $email = "[email protected]"; $list = "mailinglist"; $command = "Query $list FOR $email"; $fp = stream_socket_client("tcp://$host:$port", $errno, $errstr, 30); $cmd = $command . " PW=" . $pwd; $len = strlen($cmd); $orglen = strlen($origin); $n = $len + $orglen + 1; $headerPacket[0] = "1"; $headerPacket[1] = "B"; $headerPacket[2] = "\r"; $headerPacket[3] = "\n"; $headerPacket[4] = ord($n / 256); $headerPacket[5] = ord($n + 255); $headerPacket[6] = ord($orglen); for ($i = 0; $i < $orglen; $i++) { $headerPacket[$i + 7] = ord($origin[$i]); } for ($i = 0; $i < $len; $i++) { $cmdPacket[$i] = ord($cmd[$i]); } fwrite($fp, implode($headerPacket)); while (!feof($fp)) { echo fgets($fp, 1024); } Any thoughts on where I'm going wrong? I'd much appreciate it if anyone could point me toward some code to do this, days of googling and searching here on SO has only lead me to examples in other languages. Of course, if you know C (or Java or Perl as linked below in my comment to bypass the spam filter), PHP, and socket programming fairly well, you could probably rewrite the whole of the code in an hour, maybe a few minutes. You'd have my eternal thanks for that.

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• Binding on a port with netpipes/netcat

  - by mindas

  I am trying to write a simple bash script that is listening on a port and responding with a trivial HTTP response. My specific issue is that I am not sure if the port is available and in case of bind failure I fall back to next port until bind succeeds. So far to me the easiest way to achieve this was something like: for (( i=$PORT_BASE; i < $(($PORT_BASE+$PORT_RANGE)); i++ )) do if [ $DEBUG -eq 1 ] ; then echo trying to bind on $i fi /usr/bin/faucet $i --out --daemon echo test 2>/dev/null if [ $? -eq 0 ] ; then #success? port=$i if [ $DEBUG -eq 1 ] ; then echo "bound on port $port" fi break fi done Here I am using faucet from netpipes Ubuntu package. The problem with this is that if I simply print "test" to the output, curl complains about non-standard HTTP response (error code 18). That's fair enough as I don't print HTTP-compatible response. If I replace echo test with echo -ne "HTTP/1.0 200 OK\r\n\r\ntest", curl still complains: user@server:$ faucet 10020 --out --daemon echo -ne "HTTP/1.0 200 OK\r\n\r\ntest" ... user@client:$ curl ip.of.the.server:10020 curl: (56) Failure when receiving data from the peer I think the problem lies in how faucet is printing the response and handling the connection. For example if I do the server side in netcat, curl works fine: user@server:$ echo -ne "HTTP/1.0 200 OK\r\n\r\ntest\r\n" | nc -l 10020 ... user@client:$ curl ip.of.the.server:10020 test user@client:$ I would be more than happy to replace faucet with netcat in my main script, but the problem is that I want to spawn independent server process to be able to run client from the same base shell. faucet has a very handy --daemon parameter as it forks to background and I can use $? (exit status code) to check if bind succeeded. If I was to use netcat for a similar purpose, I would have to fork it using & and $? would not work. Does anybody know why faucet isn't responding correctly in this particular case and/or can suggest a solution to this problem. I am not married neither to faucet nor netcat but would like the solution to be implemented using bash or it's utilities (as opposed to write something in yet another scripting language, such as Perl or Python).

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• Where can I find "canonical" sample programs that give quick refreshers for any given language? [on hold]

  - by acheong87

  Note to those close-voting this question: I understand this isn't a conventional programming question and I can agree with the reasoning that it's in the subjective domain (like best-of lists). In other ways though I think it's appropriate because, though it's not a "a specific programming problem," nor concerning "a software algorithm", nor (strictly) concerning "software tools commonly used by programmers", I think it is a "practical, answerable [problem that is] unique to the programming profession," and I think it is "based on an actual [problem I] face." I've been wanting this for some time now, because both approaches of (a) Googling for samples as I write every other line of code and (b) just winging it and seeing what errors crop up, distract me from coding efficiently. This note will be removed if the question gains popularity; this question will be deleted otherwise. I spend most of my time developing in C++, PHP, or Javascript, and every once in a while I have to do something in, say, VBA. In those times, it'd be convenient if I could just put up some sample code on a second monitor, something in between a cheat sheet (often too compact; and doesn't resemble anything that could actually compile/run), and a language reference (often too verbose, or segmented; requires extra steps to search or click through an index), so I can just glance at it and recall things, like how to loop through non-empty cells in a column. I think there's a hidden benefit to seeing formed code, that triggers the right spots in our brains to get back into a language we only need to brush up on. Similar in spirit is how http://ideone.com lets you click "Template" in any given language so you can get started without even doing a search. That template alone tells a lot, sometimes! Case-sensitivity, whitespace conventions, identifier conventions, the spelling of certain types, etc. I couldn't find a resource that pulled together such samples, so if there indeed doesn't exist such a repository, I was hoping this question would inspire professionals and experts to contribute links to the most useful sample code they've used for just this purpose: a keep-on-the-side, form-as-well-as-content, compilable/executable, reminder of a language's basic and oft-used features. Personally I am interested in seeing "samplers" for: VBA, Perl, Python, Java, C# (though for some of these autocompleters in Eclipse, Visual Studio, etc. help enough), awk, and sed. I'm tagging c++, php, and javascript because these are languages for which I'd best be able to evaluate whether proffered sample code matches what I had in mind.

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• Can't install MySQL

  - by James Marthenal

  I have a Debian machine that I have previously installed MySQL on. In an attempt to delete it, I stupidly deleted the directories/files /etc/mysql/, /etc/init.d/mysql, /usr/lib/mysql/, /var/lib/mysql/. I then later did sudo apt-get purge mysql-server mysql-server-5.0. Now, when I try to install mysql-server, I get: $ sudo apt-get install mysql-server Reading package lists... Done Building dependency tree Reading state information... Done The following extra packages will be installed: mysql-server-5.0 The following NEW packages will be installed: mysql-server mysql-server-5.0 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 0B/27.4MB of archives. After this operation, 86.6MB of additional disk space will be used. Do you want to continue [Y/n]? y WARNING: The following packages cannot be authenticated! mysql-server-5.0 mysql-server Authentication warning overridden. Preconfiguring packages ... Can't exec "/tmp/mysql-server-5.0.config.122781": Permission denied at /usr/share/perl/5.10/IPC/Open3.pm line 168. open2: exec of /tmp/mysql-server-5.0.config.122781 configure failed at /usr/share/perl5/Debconf/ConfModule.pm line 59 mysql-server-5.0 failed to preconfigure, with exit status 255 Selecting previously deselected package mysql-server-5.0. (Reading database ... 158138 files and directories currently installed.) Unpacking mysql-server-5.0 (from .../mysql-server-5.0_5.0.51a-24+lenny5_amd64.deb) ... Selecting previously deselected package mysql-server. Unpacking mysql-server (from .../mysql-server_5.0.51a-24+lenny5_all.deb) ... Processing triggers for man-db ... Setting up mysql-server-5.0 (5.0.51a-24+lenny5) ... Stopping MySQL database server: mysqld. 110206 19:31:13 [ERROR] /usr/sbin/mysqld: Can't find file: './mysql/user.frm' (errno: 13) 110206 19:31:13 [ERROR] /usr/sbin/mysqld: Can't find file: './mysql/user.frm' (errno: 13) ERROR: 1017 Can't find file: './mysql/user.frm' (errno: 13) 110206 19:31:13 [ERROR] Aborting 110206 19:31:13 [Note] /usr/sbin/mysqld: Shutdown complete /etc/init.d/mysql: WARNING: /etc/mysql/my.cnf cannot be read. See README.Debian.gz (warning). Starting MySQL database server: mysqld . . . . . . . . . . . . . . failed! invoke-rc.d: initscript mysql, action "start" failed. dpkg: error processing mysql-server-5.0 (--configure): subprocess post-installation script returned error exit status 1 dpkg: dependency problems prevent configuration of mysql-server: mysql-server depends on mysql-server-5.0; however: Package mysql-server-5.0 is not configured yet. dpkg: error processing mysql-server (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: mysql-server-5.0 mysql-server E: Sub-process /usr/bin/dpkg returned an error code (1) I have tried to search for a solution via Google and have found lots of suggestions for this problem, but ultimately it seems like the problem is that by deleting the files manually, I messed up the mysql-common package. I have tried to do sudo apt-get install --reinstall mysql-common followed by installing mysql-server, but it does the exact same thing. I previously had MySQL working great, I just want to get it back to that state. Thanks so much for your help.

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• iproute2 not functioning ("RTNETLINK answers: Operation not supported")

  - by James Watt

  The command and error message: gtwy ~ # ip rule add from 64.251.23.186 table t1 RTNETLINK answers: Operation not supported Older article of the same problem, but it did not help me: http://forums.gentoo.org/viewtopic-t-696982-start-0-postdays-0-postorder-asc-highlight-.html I have looked on google at great lengths to try to find a solution. It seems that my kernel configuration is missing something? Any help or ideas would be appreciated. My system/kernel is: 2.6.36-gentoo-r5 #3 SMP Thu Jan 13 10:49:06 EST 2011 x86_64 Intel(R) Xeon(R) CPU X3220 @ 2.40GHz GenuineIntel GNU/Linux. I am posting this on SuperUser since this system is used as a workstation and this problem is unrelated to specific tasks that are handled exclusively by servers. iproute2 is installed: gtwy etc # emerge --search iproute2 Searching... [ Results for search key : iproute2 ] [ Applications found : 1 ] * sys-apps/iproute2 Latest version available: 2.6.35-r2 Latest version installed: 2.6.35-r2 Size of files: 378 kB Homepage: http://www.linuxfoundation.org/collaborate/workgroups/networking/iproute2 Description: kernel routing and traffic control utilities License: GPL-2 A small snippet of my kernel .config (view entire .config): gtwy linux # cat .config | grep NETLINK CONFIG_NETFILTER_NETLINK=y CONFIG_NETFILTER_NETLINK_QUEUE=y CONFIG_NETFILTER_NETLINK_LOG=y CONFIG_NF_CT_NETLINK=y CONFIG_SCSI_NETLINK=y gtwy linux # cat .config | grep IP_ADVANCED_ROUTER CONFIG_IP_ADVANCED_ROUTER=y gtwy linux # cat .config | grep INGRESS CONFIG_NET_SCH_INGRESS=y gtwy linux # cat .config | grep NET_SCHED CONFIG_NET_SCHED=y emerge --info Portage 2.1.9.25 (default/linux/amd64/10.0, gcc-4.1.2, glibc-2.10.1-r1, 2.6.36-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.36-gentoo-r5-x86_64-Intel-R-_Xeon-R-_CPU_X3220_@_2.40GHz-with-gentoo-1.12.13 Timestamp of tree: Thu, 13 Jan 2011 01:15:01 +0000 app-shells/bash: 4.0_p37 dev-java/java-config: 1.3.7-r1, 2.1.10 dev-lang/python: 2.4.6, 2.5.4-r4, 2.6.5-r2, 3.1.2-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.9.6-r2::<unknown repository>, 1.10.2, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.1.2, 4.3.4, 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b sys-devel/make: 3.81 virtual/os-headers: 2.6.30-r1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=nocona -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.chem.wisc.edu/gentoo" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="acl amd64 apache2 berkdb bzip2 cli cracklib crypt ctype cups curl cxx dri fortran gdbm gpm iconv jpeg jpeg2k libwww mmx modules mudflap multilib mysql ncurses nls nptl nptlonly openmp pam pcre perl php png pppd python readline session sockets sse sse2 ssl symlink sysfs tcpd threads unicode vhosts xml xorg xsl zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga neomagic nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

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• Having problems with high CPU usage and apparent memory leak of Exim

  - by Dancrumb

  I'm having problems with my server and am hoping you can help. The culprit appears to be exim. The CPU usage is consistently high and the memory usage trends up and up and up for no apparent reason (this is not a heavily used server). To demonstrate the issue, I ran the following: root@server [/var/log]# service exim restart; for iter in `seq 0 9`; do date; top -n1 | grep exim; sleep 10; done Shutting down exim: [ OK ] Shutting down spamd: [ OK ] Starting exim: [ OK ] Sun Jun 6 18:12:07 CDT 2010 62592 root 25 0 11400 6572 2356 R 51.5 1.3 0:00.92 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim Sun Jun 6 18:12:18 CDT 2010 62592 root 25 0 28768 23m 2356 R 57.4 4.6 0:06.75 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:12:28 CDT 2010 62592 root 25 0 36408 30m 2356 R 55.5 6.0 0:12.59 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:12:39 CDT 2010 62592 root 25 0 41396 35m 2356 R 53.5 7.0 0:18.35 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:12:49 CDT 2010 62592 root 25 0 45868 40m 2356 R 47.5 7.8 0:24.06 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:13:00 CDT 2010 62592 root 25 0 50056 44m 2356 R 55.3 8.6 0:29.84 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:13:10 CDT 2010 62592 root 25 0 53888 47m 2356 R 55.2 9.4 0:35.63 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:13:21 CDT 2010 62592 root 20 0 56920 50m 2356 R 55.3 9.9 0:41.15 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:13:31 CDT 2010 62592 root 25 0 60380 54m 2356 R 53.4 10.6 0:46.98 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim Sun Jun 6 18:13:42 CDT 2010 62592 root 22 0 63400 57m 2356 R 49.5 11.2 0:52.74 exim 62587 mailnull 18 0 7548 1212 792 S 0.0 0.2 0:00.00 exim 62588 root 18 0 7536 2052 1648 S 0.0 0.4 0:00.00 exim After some time, it gets to a rate of picking up an extra MB every 10s. I've checked the exim logs and there are no messages coming in there. exim -bV shows: Exim version 4.69 #1 built 16-Mar-2009 14:44:43 Copyright (c) University of Cambridge 2006 Berkeley DB: Sleepycat Software: Berkeley DB 4.2.52: (February 22, 2005) Support for: crypteq iconv() IPv6 PAM Perl OpenSSL Content_Scanning Old_Demime Experimental_SPF Experimental_SRS Experimental_DomainKeys Lookups: lsearch wildlsearch nwildlsearch iplsearch dbm dbmnz passwd Authenticators: cram_md5 dovecot plaintext spa Routers: accept dnslookup ipliteral manualroute queryprogram redirect Transports: appendfile/maildir autoreply pipe smtp Size of off_t: 8 Configuration file is /etc/exim.conf I'm at something of a loss as to how to proceed. Any recommendations would be well received!

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• GNU/Linux swapping blocks system

  - by Ole Tange

  I have used GNU/Linux on systems from 4 MB RAM to 512 GB RAM. When they start swapping, most of the time you can still log in and kill off the offending process - you just have to be 100-1000 times more patient. On my new 32 GB system that has changed: It blocks when it starts swapping. Sometimes with full disk activity but other times with no disk activity. To examine what might be the issue I have written this program. The idea is: 1 grab 3% of the memory free right now 2 if that caused swap to increase: stop 3 keep the chunk used for 30 seconds by forking off 4 goto 1 - #!/usr/bin/perl sub freekb { my $free = `free|grep buffers/cache`; my @a=split / +/,$free; return $a[3]; } sub swapkb { my $swap = `free|grep Swap:`; my @a=split / +/,$swap; return $a[2]; } my $swap = swapkb(); my $lastswap = $swap; my $free; while($lastswap >= $swap) { print "$swap $free"; $lastswap = $swap; $swap = swapkb(); $free = freekb(); my $used_mem = "x"x(1024 * $free * 0.03); if(not fork()) { sleep 30; exit(); } } print "Swap increased $swap $lastswap\n"; Running the program forever ought to keep the system at the limit of swapping, but only grabbing a minimal amount of swap and do that very slowly (i.e. a few MB at a time at most). If I run: forever free | stdbuf -o0 timestamp > freelog I ought to see swap slowly rising every second. (forever and timestamp from https://github.com/ole-tange/tangetools). But that is not the behaviour I see: I see swap increasing in jumps and that the system is completely blocked during these jumps. Here the system is blocked for 30 seconds with the swap usage increases with 1 GB: secs 169.527 Swap: 18440184 154184 18286000 170.531 Swap: 18440184 154184 18286000 200.630 Swap: 18440184 1134240 17305944 210.259 Swap: 18440184 1076228 17363956 Blocked: 21 secs. Swap increase 2400 MB: 307.773 Swap: 18440184 581324 17858860 308.799 Swap: 18440184 597676 17842508 330.103 Swap: 18440184 2503020 15937164 331.106 Swap: 18440184 2502936 15937248 Blocked: 20 secs. Swap increase 2200 MB: 751.283 Swap: 18440184 885288 17554896 752.286 Swap: 18440184 911676 17528508 772.331 Swap: 18440184 3193532 15246652 773.333 Swap: 18440184 1404540 17035644 Blocked: 37 secs. Swap increase 2400 MB: 904.068 Swap: 18440184 613108 17827076 905.072 Swap: 18440184 610368 17829816 942.424 Swap: 18440184 3014668 15425516 942.610 Swap: 18440184 2073580 16366604 This is bad enough, but what is even worse is that the system sometimes stops responding at all - even if I wait for hours. I have the feeling it is related to the swapping issue, but I cannot tell for sure. My first idea was to tweak /proc/sys/vm/swappiness from 60 to 0 or 100, just to see if that had any effect at all. 0 did not have an effect, but 100 did cause the problem to arise less often. How can I prevent the system from blocking for such a long time? Why does it decide to swapout 1-3 GB when less than 10 MB would suffice?

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• Changing User/Group to allow PHP to chmod/rename and move_upload_file()

  - by moe

  It seems like I cannot do anything with my PHP script on my VPS. It returns 'Permission denied' when I try to upload something to a directory. Yes, I have changed the permission to 777, and it works, but I do not like the insecurity When running the command: ps axu|grep apache|grep -v grep It returns nobody 7689 0.1 3.8 50604 20036 ? S 21:38 0:00 /usr/local/apache/bin/httpd -k start -DSSL root 13600 0.0 3.8 50304 20348 ? Ss Jun06 0:46 /usr/local/apache/bin/httpd -k start -DSSL nobody 15733 0.1 3.8 50700 20156 ? S 21:39 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 15818 0.1 3.8 51492 20180 ? S 21:39 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 23843 0.1 3.7 51336 19592 ? S 21:40 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30335 0.0 3.5 50436 18496 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30406 0.0 3.5 50444 18544 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30407 0.0 3.5 50556 18696 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30472 0.0 3.6 50828 19348 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30474 0.0 3.5 50668 18868 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30476 0.0 3.6 50532 19064 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 30501 0.0 3.8 50556 20080 ? S 21:36 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32341 0.0 3.5 50444 18492 ? S 21:41 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32370 0.0 3.5 50444 18476 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32414 0.1 3.7 51336 19524 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32416 0.1 3.5 50668 18816 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32457 0.1 3.6 50828 19320 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32458 0.1 3.6 50772 19276 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32459 0.0 3.5 50444 18504 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32460 0.2 3.6 50828 19320 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32463 0.0 3.5 50444 18472 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL nobody 32466 0.0 3.4 50436 17960 ? S 21:42 0:00 /usr/local/apache/bin/httpd -k start -DSSL The owner of the directory is 'user [505]' and the group is 'user[508]' (as seen in WinSCP) What can I do to change the Apache Handler to the right owner and group to allow my PHP scripts to work? P.S My PHP is not set to safe mode, and the open_basedir is set to no value EDIT: This is what my httpd.conf looks like (for the associative domain) <VirtualHost *:80> ServerName domain.com ServerAlias www.domain.com DocumentRoot /home/domain/public_html ServerAdmin info@domain ## User <theUsername> # Needed for Cpanel::ApacheConf <IfModule mod_userdir.c> Userdir disabled Userdir enabled <userName> </IfModule> <IfModule mod_suphp.c> suPHP_UserGroup <userName> <userName> </IfModule> <IfModule !mod_disable_suexec.c> SuexecUserGroup <userName> <userName> </IfModule> CustomLog /usr/local/apache/domlogs/domain.com-bytes_log "%{%s}t %I .\n%{%s}t %O ." CustomLog /usr/local/apache/domlogs/domain.com combined ScriptAlias /cgi-bin/ /home/domain/public_html/cgi-bin/ #Options -ExecCGI -Includes #RemoveHandler cgi-script .cgi .pl .plx .ppl .perl

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