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  • Generating EF Code First model classes from an existing database

    - by Jon Galloway
    Entity Framework Code First is a lightweight way to "turn on" data access for a simple CLR class. As the name implies, the intended use is that you're writing the code first and thinking about the database later. However, I really like the Entity Framework Code First works, and I want to use it in existing projects and projects with pre-existing databases. For example, MVC Music Store comes with a SQL Express database that's pre-loaded with a catalog of music (including genres, artists, and songs), and while it may eventually make sense to load that seed data from a different source, for the MVC 3 release we wanted to keep using the existing database. While I'm not getting the full benefit of Code First - writing code which drives the database schema - I can still benefit from the simplicity of the lightweight code approach. Scott Guthrie blogged about how to use entity framework with an existing database, looking at how you can override the Entity Framework Code First conventions so that it can work with a database which was created following other conventions. That gives you the information you need to create the model classes manually. However, it turns out that with Entity Framework 4 CTP 5, there's a way to generate the model classes from the database schema. Once the grunt work is done, of course, you can go in and modify the model classes as you'd like, but you can save the time and frustration of figuring out things like mapping SQL database types to .NET types. Note that this template requires Entity Framework 4 CTP 5 or later. You can install EF 4 CTP 5 here. Step One: Generate an EF Model from your existing database The code generation system in Entity Framework works from a model. You can add a model to your existing project and delete it when you're done, but I think it's simpler to just spin up a separate project to generate the model classes. When you're done, you can delete the project without affecting your application, or you may choose to keep it around in case you have other database schema updates which require model changes. I chose to add the Model classes to the Models folder of a new MVC 3 application. Right-click the folder and select "Add / New Item..."   Next, select ADO.NET Entity Data Model from the Data Templates list, and name it whatever you want (the name is unimportant).   Next, select "Generate from database." This is important - it's what kicks off the next few steps, which read your database's schema.   Now it's time to point the Entity Data Model Wizard at your existing database. I'll assume you know how to find your database - if not, I covered that a bit in the MVC Music Store tutorial section on Models and Data. Select your database, uncheck the "Save entity connection settings in Web.config" (since we won't be using them within the application), and click Next.   Now you can select the database objects you'd like modeled. I just selected all tables and clicked Finish.   And there's your model. If you want, you can make additional changes here before going on to generate the code.   Step Two: Add the DbContext Generator Like most code generation systems in Visual Studio lately, Entity Framework uses T4 templates which allow for some control over how the code is generated. K Scott Allen wrote a detailed article on T4 Templates and the Entity Framework on MSDN recently, if you'd like to know more. Fortunately for us, there's already a template that does just what we need without any customization. Right-click a blank space in the Entity Framework model surface and select "Add Code Generation Item..." Select the Code groupt in the Installed Templates section and pick the ADO.NET DbContext Generator. If you don't see this listed, make sure you've got EF 4 CTP 5 installed and that you're looking at the Code templates group. Note that the DbContext Generator template is similar to the EF POCO template which came out last year, but with "fix up" code (unnecessary in EF Code First) removed.   As soon as you do this, you'll two terrifying Security Warnings - unless you click the "Do not show this message again" checkbox the first time. It will also be displayed (twice) every time you rebuild the project, so I checked the box and no immediate harm befell my computer (fingers crossed!).   Here's the payoff: two templates (filenames ending with .tt) have been added to the project, and they've generated the code I needed.   The "MusicStoreEntities.Context.tt" template built a DbContext class which holds the entity collections, and the "MusicStoreEntities.tt" template build a separate class for each table I selected earlier. We'll customize them in the next step. I recommend copying all the generated .cs files into your application at this point, since accidentally rebuilding the generation project will overwrite your changes if you leave them there. Step Three: Modify and use your POCO entity classes Note: I made a bunch of tweaks to my POCO classes after they were generated. You don't have to do any of this, but I think it's important that you can - they're your classes, and EF Code First respects that. Modify them as you need for your application, or don't. The Context class derives from DbContext, which is what turns on the EF Code First features. It holds a DbSet for each entity. Think of DbSet as a simple List, but with Entity Framework features turned on.   //------------------------------------------------------------------------------ // <auto-generated> // This code was generated from a template. // // Changes to this file may cause incorrect behavior and will be lost if // the code is regenerated. // </auto-generated> //------------------------------------------------------------------------------ namespace EF_CodeFirst_From_Existing_Database.Models { using System; using System.Data.Entity; public partial class Entities : DbContext { public Entities() : base("name=Entities") { } public DbSet<Album> Albums { get; set; } public DbSet<Artist> Artists { get; set; } public DbSet<Cart> Carts { get; set; } public DbSet<Genre> Genres { get; set; } public DbSet<OrderDetail> OrderDetails { get; set; } public DbSet<Order> Orders { get; set; } } } It's a pretty lightweight class as generated, so I just took out the comments, set the namespace, removed the constructor, and formatted it a bit. Done. If I wanted, though, I could have added or removed DbSets, overridden conventions, etc. using System.Data.Entity; namespace MvcMusicStore.Models { public class MusicStoreEntities : DbContext { public DbSet Albums { get; set; } public DbSet Genres { get; set; } public DbSet Artists { get; set; } public DbSet Carts { get; set; } public DbSet Orders { get; set; } public DbSet OrderDetails { get; set; } } } Next, it's time to look at the individual classes. Some of mine were pretty simple - for the Cart class, I just need to remove the header and clean up the namespace. //------------------------------------------------------------------------------ // // This code was generated from a template. // // Changes to this file may cause incorrect behavior and will be lost if // the code is regenerated. // //------------------------------------------------------------------------------ namespace EF_CodeFirst_From_Existing_Database.Models { using System; using System.Collections.Generic; public partial class Cart { // Primitive properties public int RecordId { get; set; } public string CartId { get; set; } public int AlbumId { get; set; } public int Count { get; set; } public System.DateTime DateCreated { get; set; } // Navigation properties public virtual Album Album { get; set; } } } I did a bit more customization on the Album class. Here's what was generated: //------------------------------------------------------------------------------ // // This code was generated from a template. // // Changes to this file may cause incorrect behavior and will be lost if // the code is regenerated. // //------------------------------------------------------------------------------ namespace EF_CodeFirst_From_Existing_Database.Models { using System; using System.Collections.Generic; public partial class Album { public Album() { this.Carts = new HashSet(); this.OrderDetails = new HashSet(); } // Primitive properties public int AlbumId { get; set; } public int GenreId { get; set; } public int ArtistId { get; set; } public string Title { get; set; } public decimal Price { get; set; } public string AlbumArtUrl { get; set; } // Navigation properties public virtual Artist Artist { get; set; } public virtual Genre Genre { get; set; } public virtual ICollection Carts { get; set; } public virtual ICollection OrderDetails { get; set; } } } I removed the header, changed the namespace, and removed some of the navigation properties. One nice thing about EF Code First is that you don't have to have a property for each database column or foreign key. In the Music Store sample, for instance, we build the app up using code first and start with just a few columns, adding in fields and navigation properties as the application needs them. EF Code First handles the columsn we've told it about and doesn't complain about the others. Here's the basic class: using System.ComponentModel; using System.ComponentModel.DataAnnotations; using System.Web.Mvc; using System.Collections.Generic; namespace MvcMusicStore.Models { public class Album { public int AlbumId { get; set; } public int GenreId { get; set; } public int ArtistId { get; set; } public string Title { get; set; } public decimal Price { get; set; } public string AlbumArtUrl { get; set; } public virtual Genre Genre { get; set; } public virtual Artist Artist { get; set; } public virtual List OrderDetails { get; set; } } } It's my class, not Entity Framework's, so I'm free to do what I want with it. I added a bunch of MVC 3 annotations for scaffolding and validation support, as shown below: using System.ComponentModel; using System.ComponentModel.DataAnnotations; using System.Web.Mvc; using System.Collections.Generic; namespace MvcMusicStore.Models { [Bind(Exclude = "AlbumId")] public class Album { [ScaffoldColumn(false)] public int AlbumId { get; set; } [DisplayName("Genre")] public int GenreId { get; set; } [DisplayName("Artist")] public int ArtistId { get; set; } [Required(ErrorMessage = "An Album Title is required")] [StringLength(160)] public string Title { get; set; } [Required(ErrorMessage = "Price is required")] [Range(0.01, 100.00, ErrorMessage = "Price must be between 0.01 and 100.00")] public decimal Price { get; set; } [DisplayName("Album Art URL")] [StringLength(1024)] public string AlbumArtUrl { get; set; } public virtual Genre Genre { get; set; } public virtual Artist Artist { get; set; } public virtual List<OrderDetail> OrderDetails { get; set; } } } The end result was that I had working EF Code First model code for the finished application. You can follow along through the tutorial to see how I built up to the finished model classes, starting with simple 2-3 property classes and building up to the full working schema. Thanks to Diego Vega (on the Entity Framework team) for pointing me to the DbContext template.

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  • obiee memory usage

    - by user554629
    Heap memory is a frequent customer topic. Here's the quick refresher, oriented towards AIX, but the principles apply to other unix implementations. 1. 32-bit processes have a maximum addressability of 4GB; usable application heap size of 2-3 GB.  On AIX it is controlled by an environment variable: export LDR_CNTRL=....=MAXDATA=0x080000000   # 2GB ( The leading zero is deliberate, not required )   1a. It is  possible to get 3.25GB  heap size for a 32-bit process using @DSA (Discontiguous Segment Allocation)     export LDR_CNTRL=MAXDATA=0xd0000000@DSA  # 3.25 GB 32-bit only        One side-effect of using AIX segments "c" and "d" is that shared libraries will be loaded privately, and not shared.        If you need the additional heap space, this is worth the trade-off.  This option is frequently used for 32-bit java.   1b. 64-bit processes have no need for the @DSA option. 2. 64-bit processes can double the 32-bit heap size to 4GB using: export LDR_CNTRL=....=MAXDATA=0x100000000  # 1 with 8-zeros    2a. But this setting would place the same memory limitations on obiee as a 32-bit process    2b. The major benefit of 64-bit is to break the binds of 32-bit addressing.  At a minimum, use 8GB export LDR_CNTRL=....=MAXDATA=0x200000000  # 2 with 8-zeros    2c.  Many large customers are providing extra safety to their servers by using 16GB: export LDR_CNTRL=....=MAXDATA=0x400000000  # 4 with 8-zeros There is no performance penalty for providing virtual memory allocations larger than required by the application.  - If the server only uses 2GB of space in 64-bit ... specifying 16GB just provides an upper bound cushion.    When an unexpected user query causes a sudden memory surge, the extra memory keeps the server running. 3.  The next benefit to 64-bit is that you can provide huge thread stack sizes for      strange queries that might otherwise crash the server.      nqsserver uses fast recursive algorithms to traverse complicated control structures.    This means lots of thread space to hold the stack frames.    3a. Stack frames mostly contain register values;  64-bit registers are twice as large as 32-bit          At a minimum you should  quadruple the size of the server stack threads in NQSConfig.INI          when migrating from 32- to 64-bit, to prevent a rogue query from crashing the server.           Allocate more than is normally necessary for safety.    3b. There is no penalty for allocating more stack size than you need ...           it is just virtual memory;   no real resources  are consumed until the extra space is needed.    3c. Increasing thread stack sizes may require the process heap size (MAXDATA) to be increased.          Heap space is used for dynamic memory requests, and for thread stacks.          No performance penalty to run with large heap and thread stack sizes.           In a 32-bit world, this safety would require careful planning to avoid exceeding 2GM usable storage.     3d. Increasing the number of threads also may require additional heap storage.          Most thread stack frames on obiee are allocated when the server is started,          and the real memory usage increases as threads run work. Does 2.8GB sound like a lot of memory for an AIX application server? - I guess it is what you are accustomed to seeing from "grandpa's applications". - One of the primary design goals of obiee is to trade memory for services ( db, query caches, etc) - 2.8GB is still well under the 4GB heap size allocated with MAXDATA=0x100000000 - 2.8GB process size is also possible even on 32-bit Windows applications - It is not unusual to receive a sudden request for 30MB of contiguous storage on obiee.- This is not a memory leak;  eventually the nqsserver storage will stabilize, but it may take days to do so. vmstat is the tool of choice to observe memory usage.  On AIX vmstat will show  something that may be  startling to some people ... that available free memory ( the 2nd column ) is always  trending toward zero ... no available free memory.  Some customers have concluded that "nearly zero memory free" means it is time to upgrade the server with more real memory.   After the upgrade, the server again shows very little free memory available. Should you be concerned about this?   Many customers are !!  Here is what is happening: - AIX filesystems are built on a paging model.   If you read/write a  filesystem block it is paged into memory ( no read/write system calls ) - This filesystem "page" has its own "backing store" on disk, the original filesystem block.   When the system needs the real memory page holding the file block, there is no need to "page out".    The page can be stolen immediately, because the original is still on disk in the filesystem. - The filesystem  pages tend to collect ... every filesystem block that was ever seen since    system boot is available in memory.  If another application needs the file block, it is retrieved with no physical I/O. What happens if the system does need the memory ... to satisfy a 30MB heap request by nqsserver, for example? - Since the filesystem blocks have their own backing store ( not on a paging device )   the kernel can just steal any filesystem block ... on a least-recently-used basis   to satisfy a new real memory request for "computation pages". No cause for alarm.   vmstat is accurately displaying whether all filesystem blocks have been touched, and now reside in memory.   Back to nqsserver:  when should you be worried about its memory footprint? Answer:  Almost never.   Stop monitoring it ... stop fussing over it ... stop trying to optimize it. This is a production application, and nqsserver uses the memory it requires to accomplish the job, based on demand. C'mon ... never worry?   I'm from New York ... worry is what we do best. Ok, here is the metric you should be watching, using vmstat: - Are you paging ... there are several columns of vmstat outputbash-2.04$ vmstat 3 3 System configuration: lcpu=4 mem=4096MB kthr    memory              page              faults        cpu    ----- ------------ ------------------------ ------------ -----------  r  b    avm   fre  re  pi  po  fr   sr  cy  in   sy  cs us sy id wa  0  0 208492  2600   0   0   0   0    0   0  13   45  73  0  0 99  0  0  0 208492  2600   0   0   0   0    0   0   9   12  77  0  0 99  0  0  0 208492  2600   0   0   0   0    0   0   9   40  86  0  0 99  0 avm is the "available free memory" indicator that trends toward zerore   is "re-page".  The kernel steals a real memory page for one process;  immediately repages back to original processpi  "page in".   A process memory page previously paged out, now paged back in because the process needs itpo "page out" A process memory block was paged out, because it was needed by some other process Light paging activity ( re, pi, po ) is not a concern for worry.   Processes get started, need some memory, go away. Sustained paging activity  is cause for concern.   obiee users are having a terrible day if these counters are always changing. Hang on ... if nqsserver needs that memory and I reduce MAXDATA to keep the process under control, won't the nqsserver process crash when the memory is needed? Yes it will.   It means that nqsserver is configured to require too much memory and there are  lots of options to reduce the real memory requirement.  - number of threads  - size of query cache  - size of sort But I need nqsserver to keep running. Real memory is over-committed.    Many things can cause this:- running all application processes on a single server    ... DB server, web servers, WebLogic/WebSphere, sawserver, nqsserver, etc.   You could move some of those to another host machine and communicate over the network  The need for real memory doesn't go away, it's just distributed to other host machines. - AIX LPAR is configured with too little memory.     The AIX admin needs to provide more real memory to the LPAR running obiee. - More memory to this LPAR affects other partitions. Then it's time to visit your friendly IBM rep and buy more memory.

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  • SQLAuthority News – Job Interviewing the Right Way (and for the Right Reasons) – Guest Post by Feodor Georgiev

    - by pinaldave
    Feodor Georgiev is a SQL Server database specialist with extensive experience of thinking both within and outside the box. He has wide experience of different systems and solutions in the fields of architecture, scalability, performance, etc. Feodor has experience with SQL Server 2000 and later versions, and is certified in SQL Server 2008. Feodor has written excellent article on Job Interviewing the Right Way. Here is his article in his own language. A while back I was thinking to start a blog post series on interviewing and employing IT personnel. At that time I had just read the ‘Smart and gets things done’ book (http://www.joelonsoftware.com/items/2007/06/05.html) and I was hyped up on some debatable topics regarding finding and employing the best people in the branch. I have no problem with hiring the best of the best; it’s just the definition of ‘the best of the best’ that makes things a bit more complicated. One of the fundamental books one can read on the topic of interviewing is the one mentioned above. If you have not read it, then you must do so; not because it contains the ultimate truth, and not because it gives the answers to most questions on the subject, but because the book contains an extensive set of questions about interviewing and employing people. Of course, a big part of these questions have different answers, depending on location, culture, available funds and so on. (What works in the US may not necessarily work in the Nordic countries or India, or it may work in a different way). The only thing that is valid regardless of any external factor is this: curiosity. In my belief there are two kinds of people – curious and not-so-curious; regardless of profession. Think about it – professional success is directly proportional to the individual’s curiosity + time of active experience in the field. (I say ‘active experience’ because vacations and any distractions do not count as experience :)  ) So, curiosity is the factor which will distinguish a good employee from the not-so-good one. But let’s shift our attention to something else for now: a few tips and tricks for successful interviews. Tip and trick #1: get your priorities straight. Your status usually dictates your priorities; for example, if the person looking for a job has just relocated to a new country, they might tend to ignore some of their priorities and overload others. In other words, setting priorities straight means to define the personal criteria by which the interview process is lead. For example, similar to the following questions can help define the criteria for someone looking for a job: How badly do I need a (any) job? Is it more important to work in a clean and quiet environment or is it important to get paid well (or both, if possible)? And so on… Furthermore, before going to the interview, the candidate should have a list of priorities, sorted by the most importance: e.g. I want a quiet environment, x amount of money, great helping boss, a desk next to a window and so on. Also it is a good idea to be prepared and know which factors can be compromised and to what extent. Tip and trick #2: the interview is a two-way street. A job candidate should not forget that the interview process is not a one-way street. What I mean by this is that while the employer is interviewing the potential candidate, the job seeker should not miss the chance to interview the employer. Usually, the employer and the candidate will meet for an interview and talk about a variety of topics. In a quality interview the candidate will be presented to key members of the team and will have the opportunity to ask them questions. By asking the right questions both parties will define their opinion about each other. For example, if the candidate talks to one of the potential bosses during the interview process and they notice that the potential manager has a hard time formulating a question, then it is up to the candidate to decide whether working with such person is a red flag for them. There are as many interview processes out there as there are companies and each one is different. Some bigger companies and corporates can afford pre-selection processes, 3 or even 4 stages of interviews, small companies usually settle with one interview. Some companies even give cognitive tests on the interview. Why not? In his book Joel suggests that a good candidate should be pampered and spoiled beyond belief with a week-long vacation in New York, fancy hotels, food and who knows what. For all I can imagine, an interview might even take place at the top of the Eifel tower (right, Mr. Joel, right?) I doubt, however, that this is the optimal way to capture the attention of a good employee. The ‘curiosity’ topic What I have learned so far in my professional experience is that opinions can be subjective. Plus, opinions on technology subjects can also be subjective. According to Joel, only hiring the best of the best is worth it. If you ask me, there is no such thing as best of the best, simply because human nature (well, aside from some physical limitations, like putting your pants on through your head :) ) has no boundaries. And why would it have boundaries? I have seen many curious and interesting people, naturally good at technology, though uninterested in it as one  can possibly be; I have also seen plenty of people interested in technology, who (in an ideal world) should have stayed far from it. At any rate, all of this sums up at the end to the ‘supply and demand’ factor. The interview process big-bang boils down to this: If there is a mutual benefit for both the employer and the potential employee to work together, then it all sorts out nicely. If there is no benefit, then it is much harder to get to a common place. Tip and trick #3: word-of-mouth is worth a thousand words Here I would just mention that the best thing a job candidate can get during the interview process is access to future team members or other employees of the new company. Nowadays the world has become quite small and everyone knows everyone. Look at LinkedIn, look at other professional networks and you will realize how small the world really is. Knowing people is a good way to become more approachable and to approach them. Tip and trick #4: Be confident. It is true that for some people confidence is as natural as breathing and others have to work hard to express it. Confidence is, however, a key factor in convincing the other side (potential employer or employee) that there is a great chance for success by working together. But it cannot get you very far if it’s not backed up by talent, curiosity and knowledge. Tip and trick #5: The right reasons What really bothers me in Sweden (and I am sure that there are similar situations in other countries) is that there is a tendency to fill quotas and to filter out candidates by criteria different from their skill and knowledge. In job ads I see quite often the phrases ‘positive thinker’, ‘team player’ and many similar hints about personality features. So my guess here is that discrimination has evolved to a new level. Let me clear up the definition of discrimination: ‘unfair treatment of a person or group on the basis of prejudice’. And prejudice is the ‘partiality that prevents objective consideration of an issue or situation’. In other words, there is not much difference whether a job candidate is filtered out by race, gender or by personality features – it is all a bad habit. And in reality, there is no proven correlation between the technology knowledge paired with skills and the personal features (gender, race, age, optimism). It is true that a significantly greater number of Darwin awards were given to men than to women, but I am sure that somewhere there is a paper or theory explaining the genetics behind this. J This topic actually brings to mind one of my favorite work related stories. A while back I was working for a big company with many teams involved in their processes. One of the teams was occupying 2 rooms – one had the team members and was full of light, colorful posters, chit-chats and giggles, whereas the other room was dark, lighted only by a single monitor with a quiet person in front of it. Later on I realized that the ‘dark room’ person was the guru and the ultimate problem-solving-brain who did not like the chats and giggles and hence was in a separate room. In reality, all severe problems which the chatty and cheerful team members could not solve and all emergencies were directed to ‘the dark room’. And thus all worked out well. The moral of the story: Personality has nothing to do with technology knowledge and skills. End of story. Summary: I’d like to stress the fact that there is no ultimately perfect candidate for a job, and there is no such thing as ‘best-of-the-best’. From my personal experience, the main criteria by which I measure people (co-workers and bosses) is the curiosity factor; I know from experience that the more curious and inventive a person is, the better chances there are for great achievements in their field. Related stories: (for extra credit) 1) Get your priorities straight. A while back as a consultant I was working for a few days at a time at different offices and for different clients, and so I was able to compare and analyze the work environments. There were two different places which I compared and recently I asked a friend of mine the following question: “Which one would you prefer as a work environment: a noisy office full of people, or a quiet office full of faulty smells because the office is rarely cleaned?” My friend was puzzled for a while, thought about it and said: “Hmm, you are talking about two different kinds of pollution… I will probably choose the second, since I can clean the workplace myself a bit…” 2) The interview is a two-way street. One time, during a job interview, I met a potential boss that had a hard time phrasing a question. At that particular time it was clear to me that I would not have liked to work under this person. According to my work religion, the properly asked question contains at least half of the answer. And if I work with someone who cannot ask a question… then I’d be doing double or triple work. At another interview, after the technical part with the team leader of the department, I was introduced to one of the team members and we were left alone for 5 minutes. I immediately jumped on the occasion and asked the blunt question: ‘What have you learned here for the past year and how do you like your job?’ The team member looked at me and said ‘Nothing really. I like playing with my cats at home, so I am out of here at 5pm and I don’t have time for much.’ I was disappointed at the time and I did not take the job offer. I wasn’t that shocked a few months later when the company went bankrupt. 3) The right reasons to take a job: personality check. A while back I was asked to serve as a job reference for a coworker. I agreed, and after some weeks I got a phone call from the company where my colleague was applying for a job. The conversation started with the manager’s question about my colleague’s personality and about their social skills. (You can probably guess what my internal reaction was… J ) So, after 30 minutes of pouring common sense into the interviewer’s head, we finally agreed on the fact that a shy or quiet personality has nothing to do with work skills and knowledge. Some years down the road my former colleague is taking the manager’s position as the manager is demoted to a different department. Reference: Feodor Georgiev, Pinal Dave (http://blog.SQLAuthority.com) Filed under: PostADay, Readers Contribution, SQL, SQL Authority, SQL Query, SQL Server, SQL Tips and Tricks, T SQL, Technology

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  • R Package Installation with Oracle R Enterprise

    - by Sherry LaMonica-Oracle
    Normal 0 false false false EN-US X-NONE X-NONE Programming languages give developers the opportunity to write reusable functions and to bundle those functions into logical deployable entities. In R, these are called packages. R has thousands of such packages provided by an almost equally large group of third-party contributors. To allow others to benefit from these packages, users can share packages on the CRAN system for use by the vast R development community worldwide. R's package system along with the CRAN framework provides a process for authoring, documenting and distributing packages to millions of users. In this post, we'll illustrate the various ways in which such R packages can be installed for use with R and together with Oracle R Enterprise. In the following, the same instructions apply when using either open source R or Oracle R Distribution. In this post, we cover the following package installation scenarios for: R command line Linux shell command line Use with Oracle R Enterprise Installation on Exadata or RAC Installing all packages in a CRAN Task View Troubleshooting common errors 1. R Package Installation BasicsR package installation basics are outlined in Chapter 6 of the R Installation and Administration Guide. There are two ways to install packages from the command line: from the R command line and from the shell command line. For this first example on Oracle Linux using Oracle R Distribution, we’ll install the arules package as root so that packages will be installed in the default R system-wide location where all users can access it, /usr/lib64/R/library.Within R, using the install.packages function always attempts to install the latest version of the requested package available on CRAN:R> install.packages("arules")If the arules package depends upon other packages that are not already installed locally, the R installer automatically downloads and installs those required packages. This is a huge benefit that frees users from the task of identifying and resolving those dependencies.You can also install R from the shell command line. This is useful for some packages when an internet connection is not available or for installing packages not uploaded to CRAN. To install packages this way, first locate the package on CRAN and then download the package source to your local machine. For example:$ wget http://cran.r-project.org/src/contrib/arules_1.1-2.tar.gz Then, install the package using the command R CMD INSTALL:$ R CMD INSTALL arules_1.1-2.tar.gzA major difference between installing R packages using the R package installer at the R command line and shell command line is that package dependencies must be resolved manually at the shell command line. Package dependencies are listed in the Depends section of the package’s CRAN site. If dependencies are not identified and installed prior to the package’s installation, you will see an error similar to:ERROR: dependency ‘xxx’ is not available for package ‘yyy’As a best practice and to save time, always refer to the package’s CRAN site to understand the package dependencies prior to attempting an installation. If you don’t run R as root, you won’t have permission to write packages into the default system-wide location and you will be prompted to create a personal library accessible by your userid. You can accept the personal library path chosen by R, or specify the library location by passing parameters to the install.packages function. For example, to create an R package repository in your home directory: R> install.packages("arules", lib="/home/username/Rpackages")or$ R CMD INSTALL arules_1.1-2.tar.gz --library=/home/username/RpackagesRefer to the install.packages help file in R or execute R CMD INSTALL --help at the shell command line for a full list of command line options.To set the library location and avoid having to specify this at every package install, simply create the R startup environment file .Renviron in your home area if it does not already exist, and add the following piece of code to it:R_LIBS_USER = "/home/username/Rpackages" 2. Setting the RepositoryEach time you install an R package from the R command line, you are asked which CRAN mirror, or server, R should use. To set the repository and avoid having to specify this during every package installation, create the R startup command file .Rprofile in your home directory and add the following R code to it:cat("Setting Seattle repository")r = getOption("repos") r["CRAN"] = "http://cran.fhcrc.org/"options(repos = r)rm(r) This code snippet sets the R package repository to the Seattle CRAN mirror at the start of each R session. 3. Installing R Packages for use with Oracle R EnterpriseEmbedded R execution with Oracle R Enterprise allows the use of CRAN or other third-party R packages in user-defined R functions executed on the Oracle Database server. The steps for installing and configuring packages for use with Oracle R Enterprise are the same as for open source R. The database-side R engine just needs to know where to find the R packages.The Oracle R Enterprise installation is performed by user oracle, which typically does not have write permission to the default site-wide library, /usr/lib64/R/library. On Linux and UNIX platforms, the Oracle R Enterprise Server installation provides the ORE script, which is executed from the operating system shell to install R packages and to start R. The ORE script is a wrapper for the default R script, a shell wrapper for the R executable. It can be used to start R, run batch scripts, and build or install R packages. Unlike the default R script, the ORE script installs packages to a location writable by user oracle and accessible by all ORE users - $ORACLE_HOME/R/library.To install a package on the database server so that it can be used by any R user and for use in embedded R execution, an Oracle DBA would typically download the package source from CRAN using wget. If the package depends on any packages that are not in the R distribution in use, download the sources for those packages, also.  For a single Oracle Database instance, replace the R script with ORE to install the packages in the same location as the Oracle R Enterprise packages. $ wget http://cran.r-project.org/src/contrib/arules_1.1-2.tar.gz$ ORE CMD INSTALL arules_1.1-2.tar.gzBehind the scenes, the ORE script performs the equivalent of setting R_LIBS_USER to the value of $ORACLE_HOME/R/library, and all R packages installed with the ORE script are installed to this location. For installing a package on multiple database servers, such as those in an Oracle Real Application Clusters (Oracle RAC) or a multinode Oracle Exadata Database Machine environment, use the ORE script in conjunction with the Exadata Distributed Command Line Interface (DCLI) utility.$ dcli -g nodes -l oracle ORE CMD INSTALL arules_1.1-1.tar.gz The DCLI -g flag designates a file containing a list of nodes to install on, and the -l flag specifies the user id to use when executing the commands. For more information on using DCLI with Oracle R Enterprise, see Chapter 5 in the Oracle R Enterprise Installation Guide.If you are using an Oracle R Enterprise client, install the package the same as any R package, bearing in mind that you must install the same version of the package on both the client and server machines to avoid incompatibilities. 4. CRAN Task ViewsCRAN also maintains a set of Task Views that identify packages associated with a particular task or methodology. Task Views are helpful in guiding users through the huge set of available R packages. They are actively maintained by volunteers who include detailed annotations for routines and packages. If you find one of the task views is a perfect match, you can install every package in that view using the ctv package - an R package for automating package installation. To use the ctv package to install a task view, first, install and load the ctv package.R> install.packages("ctv")R> library(ctv)Then query the names of the available task views and install the view you choose.R> available.views() R> install.views("TimeSeries") 5. Using and Managing R packages To use a package, start up R and load packages one at a time with the library command.Load the arules package in your R session. R> library(arules)Verify the version of arules installed.R> packageVersion("arules")[1] '1.1.2'Verify the version of arules installed on the database server using embedded R execution.R> ore.doEval(function() packageVersion("arules"))View the help file for the apropos function in the arules packageR> ?aproposOver time, your package repository will contain more and more packages, especially if you are using the system-wide repository where others are adding additional packages. It’s good to know the entire set of R packages accessible in your environment. To list all available packages in your local R session, use the installed.packages command:R> myLocalPackages <- row.names(installed.packages())R> myLocalPackagesTo access the list of available packages on the ORE database server from the ORE client, use the following embedded R syntax: R> myServerPackages <- ore.doEval(function() row.names(installed.packages()) R> myServerPackages 6. Troubleshooting Common ProblemsInstalling Older Versions of R packagesIf you immediately upgrade to the latest version of R, you will have no problem installing the most recent versions of R packages. However, if your version of R is older, some of the more recent package releases will not work and install.packages will generate a message such as: Warning message: In install.packages("arules") : package ‘arules’ is not availableThis is when you have to go to the Old sources link on the CRAN page for the arules package and determine which version is compatible with your version of R.Begin by determining what version of R you are using:$ R --versionOracle Distribution of R version 3.0.1 (--) -- "Good Sport" Copyright (C) The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit)Given that R-3.0.1 was released May 16, 2013, any version of the arules package released after this date may work. Scanning the arules archive, we might try installing version 0.1.1-1, released in January of 2014:$ wget http://cran.r-project.org/src/contrib/Archive/arules/arules_1.1-1.tar.gz$ R CMD INSTALL arules_1.1-1.tar.gzFor use with ORE:$ ORE CMD INSTALL arules_1.1-1.tar.gzThe "package not available" error can also be thrown if the package you’re trying to install lives elsewhere, either another R package site, or it’s been removed from CRAN. A quick Google search usually leads to more information on the package’s location and status.Oracle R Enterprise is not in the R library pathOn Linux hosts, after installing the ORE server components, starting R, and attempting to load the ORE packages, you may receive the error:R> library(ORE)Error in library(ORE) : there is no package called ‘ORE’If you know the ORE packages have been installed and you receive this error, this is the result of not starting R with the ORE script. To resolve this problem, exit R and restart using the ORE script. After restarting R and ">running the command to load the ORE packages, you should not receive any errors.$ ORER> library(ORE)On Windows servers, the solution is to make the location of the ORE packages visible to R by adding them to the R library paths. To accomplish this, exit R, then add the following lines to the .Rprofile file. On Windows, the .Rprofile file is located in R\etc directory C:\Program Files\R\R-<version>\etc. Add the following lines:.libPaths("<path to $ORACLE_HOME>/R/library")The above line will tell R to include the R directory in the Oracle home as part of its search path. When you start R, the path above will be included, and future R package installations will also be saved to $ORACLE_HOME/R/library. This path should be writable by the user oracle, or the userid for the DBA tasked with installing R packages.Binary package compiled with different version of RBy default, R will install pre-compiled versions of packages if they are found. If the version of R under which the package was compiled does not match your installed version of R you will get an error message:Warning message: package ‘xxx’ was built under R version 3.0.0The solution is to download the package source and build it for your version of R.$ wget http://cran.r-project.org/src/contrib/Archive/arules/arules_1.1-1.tar.gz$ R CMD INSTALL arules_1.1-1.tar.gzFor use with ORE:$ ORE CMD INSTALL arules_1.1-1.tar.gzUnable to execute files in /tmp directoryBy default, R uses the /tmp directory to install packages. On security conscious machines, the /tmp directory is often marked as "noexec" in the /etc/fstab file. This means that no file under /tmp can ever be executed, and users who attempt to install R package will receive an error:ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual’The solution is to set the TMP and TMPDIR environment variables to a location which R will use as the compilation directory. For example:$ mkdir <some path>/tmp$ export TMPDIR= <some path>/tmp$ export TMP= <some path>/tmpThis error typically appears on Linux client machines and not database servers, as Oracle Database writes to the value of the TMP environment variable for several tasks, including holding temporary files during database installation. 7. Creating your own R packageCreating your own package and submitting to CRAN is for advanced users, but it is not difficult. The procedure to follow, along with details of R's package system, is detailed in the Writing R Extensions manual.

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  • Should I add the vcxproj.filter files to source control

    - by jschroedl
    While evaluating Visual Studio 2010 Beta 2, I see that in the converted directory my vcproj files have become vcxproj files. There are also vcxproj.filter files alongside each project which appear to contain a description of the folder structure (\Source Files, \Header Files, etc.). Do you think these filter files should be kept per-user or should the be shared across the whole dev group and checked into SCC? My current thinking is to check them in but wondered if there's any reasons not to do that or perhaps good reasons that I should definitely check them in. The obvious benefit is that the folder structures will match if I'm looking at someone else's machine but maybe they'd like to reorganize things logically??

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  • AVerMedia A309-B mini-PCI to AVerMedia A317 Mini PCI card

    - by Chris
    I got an HP pavilion hdx 16 1060ED laptop (Windows Vista) with a a DVB-T tuner card Now I would like a hybrid or analog turner card in it. According to the HP data of a more expensive variant, a AVerMedia A317 Mini PCI card installed is installed. My system has a AVerMedia A309-B mini-PCI placed in the system. my questions: 1 - is it possible to replace it with a expensive one? (AVerMedia A317 Mini PCI card) and 2 - what will this cost? 3 - I can build it myself and what can I do with the old card I like to hear from you.

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  • CUDA Driver API vs. CUDA runtime

    - by Morten Christiansen
    When writing CUDA applications, you can either work at the driver level or at the runtime level as illustrated on this image (The libraries are CUFFT and CUBLAS for advanced math): I assume the tradeoff between the two are increased performance for the low-evel API but at the cost of increased complexity of code. What are the concrete differences and are there any significant things which you cannot do with the high-level API? I am using CUDA.net for interop with C# and it is built as a copy of the driver API. This encourages writing a lot of rather complex code in C# while the C++ equivalent would be more simple using the runtime API. Is there anything to win by doing it this way? The one benefit I can see is that it is easier to integrate intelligent error handling with the rest of the C# code.

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  • Amazon EC2 spot instances - is there a catch ?

    - by gareth_bowles
    I needed to start a new EC2 instance today and decided to try out the new spot instances, where you can reduce your instance cost by bidding on the maximum per-hour price you're prepared to pay. Since today's spot price was only 3.5c / hour, compared with 8.5c / hour for an on-demand instance, I was wondering: if I just bid a really high price, say 10c / hour, can I effectively be sure of getting a much cheaper long-running instance than an on-demand instance (since the spot instances are only charged by the current spot price) ? I suppose it's theoretically possible for the spot price to go over the on-demand price, but as far as I can tell from the data on the AWS site, the spot price has always been well below that.

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  • Amazon EC2 spot instances - is there a catch ?

    - by gareth_bowles
    I needed to start a new EC2 instance today and decided to try out the new spot instances, where you can reduce your instance cost by bidding on the maximum per-hour price you're prepared to pay. Since today's spot price was only 35c / hour, compared with 85c / hour for an on-demand instance, I was wondering: if I just bid a really high price, say $1 / hour, can I effectively be sure of getting a much cheaper long-running instance than an on-demand instance (since the spot instances are only charged by the current spot price) ? I suppose it's theoretically possible for the spot price to go over the on-demand price, but as far as I can tell from the data on the AWS site, the spot price has always been well below that.

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  • GWT layout panels vs. CSS layout

    - by David
    I read an article entitled "Tags First GWT", in which the writer suggests using GWT for event-handling, and CSS for layout. I just don't know whether the benefit of GWT's cross-browser compatibility goodness outweighs the flexibility offered by pure CSS layout. GWT GWT 2.0 has some snazzy layout panels, but to get them to resize properly you really need to build the entire panel containment tree from the root panel down. It's an all-or-nothing thing, it seems. CSS You can use CSS to layout an application too, and I'm inclined to do just that, if only to justify my purchase of several books touting the 'semantic markup' gospel. The downside might be cross-browser incompatibilities, the prevalence of which I have yet to determine. Which way to go? What is your opinion? Are cross-browser problems bad enough, and prevalent enough, to warrant ditching my CSS books, and building with GWT layout panels?

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  • Started a Forum Board (with phpBB), but Now Rethinking Choice of Board App - Security

    - by nicorellius
    The main reason I even started participating on Superuser.com is because a friend ripped me a new one for using phpBB. He said, "check out StackExchange, they have their act together!" I did, and it's true. So now, after learning phpBB and implementing the board (it's still new and in its infancy), I feel slightly regretful. I would love to use the Stack Exchange tool, but the cost will eventually be the main deterrent. The attractive thing about phpBB is that it's free and open. However, I have heard that it lacks security. Has anyone had this experience, that phpBB is not secure, such that they changed board software? And, I wonder if Stack Exchange is going to introduce a cheaper option for low traffic users? Does this question belong on meta?

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  • What is the advantage of WSDualHttpBinding in WCF?

    - by schmoopy
    How much benefit would there be to using WSDualHttpBinding with IIS hosted service vs. a client poll that calls the WCF service, assuming in the latter the service cached the data in question? This scenerio would be for a notify type of service where the clients need to be notified by the service when an event occurs. Specifically, what advantages would WSDualHttpBinding provide over polling? ie: Less network traffic, faster to design, easier to maintain, more control ??? From what i understand, WSDualHttpBinding is less scalable than client polling, so why use it at all? Edit: As Matt supplied, time critical can be one reason for the duplex binding. Here is what i have so far: WSDualHttpBinding adv: can get immediate response w/o waiting on polling timer dis: less scalable than WsHttpBinding dis: less firewall friendly I'll add to this based on comments, please let me know if i state anything incorrectly. thanks for you input :-)

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  • Inner synchronization on the same object as the outer synchronization

    - by Yaneeve
    Recently I attended a lecture concerning some design patterns: The following code had been displayed: public static Singleton getInstance() { if (instance == null) { synchronized(Singleton.class) { //1 Singleton inst = instance; //2 if (inst == null) { synchronized(Singleton.class) { //3 inst = new Singleton(); //4 } instance = inst; //5 } } } return instance; } taken from: Double-checked locking: Take two My question has nothing to do with the above mentioned pattern but with the synchronized block: Is there any benefit whatsoever to the double synchronization done in lines 1 & 3 with regards to the fact that the synchronize operation is done on the same Object?

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  • Cheap dvr media server

    - by Tester101
    I would like to build a new computer to be used as a DVR and media server. I am thinking of using mythtv as the DVR software, but short of that decision I am completely open to suggestions. Requirements: Must be cheap. Must have low power consumption (since it will always be on). Should be quiet. Should be small. I'm really not sure where to start with this project, and am open to any hardware/software suggestions. Is it possible to build a small quiet and cheap system? *Keep in mind I am working on this project because I am tired of Cable rate increases, but I can't imagine living without a DVR so cost is very important and I would like the system to be sub $200.00. The system also needs to handle the new digital broadcast system. Thanks for the help,

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  • Amazon EC2 EBS volume scheduled backup/snapshots using puppet

    - by Ehrann Mehdan
    I am not a Linux admin, although I wish I was, and I have seen these questions Amazon EC2 Backup Strategy Amazon EC2 + EBS:: Regular backup plan? Simple Backup Strategy for Amazon EC2 instances / volumes? And this suggestion http://alestic.com/2009/09/ec2-consistent-snapshot I tried using command line + crontab (the command line works, but crontab for some reason, doesn't) But I'm still pretty lost, all I want is an automated, rolling backup of my amazon EC2 (EBS) data (by rolling I mean keep 3-4 weeks back, but delete old snapshots as new ones come for cost control) And as things usually go, if there is something that is hard and painful, someone creates a solution for it. My question is simple, is there a way using a tool like Puppet to do it without a painful learning curve? (or via other tools like http://ylastic.com) If yes, how?

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  • C# System.Data.SQLite Designer Code

    - by Nathan
    I've been messing around with the SQLite Designer in Visual Studio 2008 and I have noticed that when I use the generated Insert/Update statements they run extremely slow. Example: I have a data table with four columns and 5700 rows it took ~5 mins to insert the data into the database table However, I wrote my own database connection and insert methods using parameters and a single transaction and the same 5700 rows were inserted in under 1 second. Why is the generated code so slow and what is benefit to even using it? Thanks. Nathan

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  • 64-bit Cisco VPN client (IPsec) ?

    - by mika
    Cisco VPN client (IPsec) does not support 64bit Windows. Worse, Cisco does not even plan to release a 64-bit version, instead they say that "For x64 (64-bit) Windows support, you must utilize Cisco's next-generation Cisco AnyConnect VPN Client." Cisco VPN Client Introduction Cisco VPN Client FAQ But SSL VPN licences cost extra. For example, most new ASA firewalls come with plenty of IPSec VPN licences but only a few SSL VPN licences. What alternatives do you have for 64-bit Windows? So far, I know two: 32-bit Cisco VPN Client on a virtual machine NCP Secure Entry Client on 64-bit Windows Any other suggestions or experiences? -mika-

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  • Developing online invoicing and inventory application.

    - by Rohit
    My clients are using a desktop version of my inventory solution that I developed using .NET. I want to make an online version so that data is available centrally and clients can work from any location. I searched using Google to find similar tools and found few. I want to know what type of security considerations to take while designing such an application? Some clients can't afford dedicated server cost. What if I use shared hosting only? What are the risks of shared hosting?

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  • Developing online invoicing and inventory application.

    - by Rohit
    My clients are using a desktop version of my inventory solution that I developed using .NET. I want to make an online version so that data is available centrally and clients can work from any location. I searched using Google to find similar tools and found few. I want to know what type of security considerations to take while designing such an application? Some clients can't afford dedicated server cost. What if I use shared hosting only? What are the risks of shared hosting?

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  • java annotations: library to override annotations with xml files

    - by flybywire
    Java has annotations and that is good. However, some developers feel that it is best to annotate code with metadata using xml files - others prefer annotations but would use metadata to override annotations in source code. I am writing a Java framework that uses annotations. The question is: is there a standard way to define and parse metadata from xml files. I think this is something every framework that uses annotations could benefit from but I can seem to find something like this on the Internet. Must I roll my own xml parsing/validation or has someone already done something like this?

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  • IMAP Idle Timeout

    - by Paul
    Lets say I am using IMAP IDLE to monitor changes in a mail folder. The IMAP spec says that IDLE connections should only stay alive for 30 minutes max, but it is recommended that a lower number of minutes is selected - say 20 minutes, then cancel the idle and restart. I am wondering what would happen if the mail contents changed between the idle canceling, and the new idle being created. An email could potentially be missed. Given that RECENT is a bit vague, this could lead to getting a message list before the old idle ends, and a new idle starts. But this is almost the same as polling every 20 minutes, and defeats some of the benefit of idle. Alternatively, a new idle session could be started prior to terminating the expiring one. But in any case, I think this problem has already been solved so here I am asking for recommendations. Thanks, Paul

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  • Comparison of the multiprocessing module and pyro?

    - by fivebells
    I use pyro for basic management of parallel jobs on a compute cluster. I just moved to a cluster where I will be responsible for using all the cores on each compute node. (On previous clusters, each core has been a separate node.) The python multiprocessing module seems like a good fit for this. I notice it can also be used for remote-process communication. If anyone has used both frameworks for remote-process communication, I'd be grateful to hear how they stack up against each other. The obvious benefit of the multiprocessing module is that it's built-in from 2.6. Apart from that, it's hard for me to tell which is better.

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  • Adaboost algorithm and its usage in face detection

    - by Hani
    I am trying to understand Adaboost algorithm but i have some troubles. After reading about Adaboost i realized that it is a classification algorithm(somehow like neural network). But i could not know how the weak classifiers are chosen (i think they are haar-like features for face detection) and how finally the H result which is the final strong classifier can be used. I mean if i found the alpha values and compute the H ,how am i going to benefit from it as a value (one or zero) for new images. Please is there an example describes it in a perfect way? i found the plus and minus example that is found in most adaboost tutorials but i did not know how exactly hi is chosen and how to adopt the same concept on face detection. I read many papers and i had many ideas but until now my ideas are not well arranged. Thanks....

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  • Silverlight Threading and its usage

    - by Harryboy
    Hello Experts, Scenario : I am working on LOB application, as in silverlight every call to service is Async so automatically UI is not blocked when the request is processed at server side. Silverlight also supports threading as per my understanding if you are developing LOB application threads are most useful when you need to do some IO operation but as i am not using OOB application it is not possible to access client resource and for all server request it is by default Async. In above scenario is there any usage of Threading or can anyone provide some good example where by using threading we can improve performance. I have tried to search a lot on this topic but everywhere i have identified some simple threading example from which it is very difficult to understand the real benefit. Thanks for help

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  • How to Deserialize XMLDocument to object in C#?

    - by Deepfreezed
    I have a .Net webserivce that accepts XML in string format. XML String sent into the webserivce can represent any Object in the system. I need to check the first node to figure out what object to deserialize the XML string. For this I will have to load the XML into an XMLDocument (Don't want to use RegEx or string compare). I am wondering if there is a way to Deserialize the XMLDocument/XMLNode rather that deserializing the string to save some performance? Is there going to be any performance benefit serializing the XMLNode rather that the string? Method to Load XMLDocument public void LoadFromString(String s) { m_XmlDoc = new XmlDocument(); m_XmlDoc.LoadXml(s); } Thanks

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