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  • NHibernate / ORM - Child Update over Web Service

    - by tyndall
    What is the correct way to UPDATE a child object with NHibernate but not have to "awake" the parent object. Lets say you would like to try to avoid this because the parent object is large or expensive to initiate. Lets assume classes are called Author(parent) and Book(child). (still, trying to avoid instantiating Author) Book comes back over a web service as XML. It gets deserialized back into a CLR object. Book has an AuthorId property which allows this to happen. But it also has a Author property. Problem, comes when you try to SaveOrUpdate() Book and the author_id in the database gets wiped out because the Author was null when the object gets deserialized. This seems like this would be a common problem. What is the workaround? Also, if you instantiate the Author and it has a Books property. The book you are trying to update is already one of these books (List<Book>). We have also run into the "a different object with the same identifier value was already associated with the session" problems. What is the standard process to update a child over a web service?

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  • task_current redundant field

    - by user341940
    Hi, I'm writing a kernel module that reads from a /proc file. When someone writes into the /proc file the reader will read it, but if it reads again while there is no "new" write, it should be blocked. In order to remember if we already read, i need to keep a map of the latest buffer that process read. To avoid that, I was told that there might be some redundant field inside the current- (task_struct struct) that i can use to my benefits in order to save some states on the current process. How can I find such fields ? and how can i avoid them being overwritten ? I read somewhere that i can use the offset field inside the struct in order to save my information there and i need to block lseek operations so that field will stay untouched. How can I do so ? and where is that offset field, i can't find it inside the task_Struct. Thanks and I need to save for each process some information in order to map it against other information. I can write a ma

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  • Beware Sneaky Reads with Unique Indexes

    - by Paul White NZ
    A few days ago, Sandra Mueller (twitter | blog) asked a question using twitter’s #sqlhelp hash tag: “Might SQL Server retrieve (out-of-row) LOB data from a table, even if the column isn’t referenced in the query?” Leaving aside trivial cases (like selecting a computed column that does reference the LOB data), one might be tempted to say that no, SQL Server does not read data you haven’t asked for.  In general, that’s quite correct; however there are cases where SQL Server might sneakily retrieve a LOB column… Example Table Here’s a T-SQL script to create that table and populate it with 1,000 rows: CREATE TABLE dbo.LOBtest ( pk INTEGER IDENTITY NOT NULL, some_value INTEGER NULL, lob_data VARCHAR(MAX) NULL, another_column CHAR(5) NULL, CONSTRAINT [PK dbo.LOBtest pk] PRIMARY KEY CLUSTERED (pk ASC) ); GO DECLARE @Data VARCHAR(MAX); SET @Data = REPLICATE(CONVERT(VARCHAR(MAX), 'x'), 65540);   WITH Numbers (n) AS ( SELECT ROW_NUMBER() OVER (ORDER BY (SELECT 0)) FROM master.sys.columns C1, master.sys.columns C2 ) INSERT LOBtest WITH (TABLOCKX) ( some_value, lob_data ) SELECT TOP (1000) N.n, @Data FROM Numbers N WHERE N.n <= 1000; Test 1: A Simple Update Let’s run a query to subtract one from every value in the some_value column: UPDATE dbo.LOBtest WITH (TABLOCKX) SET some_value = some_value - 1; As you might expect, modifying this integer column in 1,000 rows doesn’t take very long, or use many resources.  The STATITICS IO and TIME output shows a total of 9 logical reads, and 25ms elapsed time.  The query plan is also very simple: Looking at the Clustered Index Scan, we can see that SQL Server only retrieves the pk and some_value columns during the scan: The pk column is needed by the Clustered Index Update operator to uniquely identify the row that is being changed.  The some_value column is used by the Compute Scalar to calculate the new value.  (In case you are wondering what the Top operator is for, it is used to enforce SET ROWCOUNT). Test 2: Simple Update with an Index Now let’s create a nonclustered index keyed on the some_value column, with lob_data as an included column: CREATE NONCLUSTERED INDEX [IX dbo.LOBtest some_value (lob_data)] ON dbo.LOBtest (some_value) INCLUDE ( lob_data ) WITH ( FILLFACTOR = 100, MAXDOP = 1, SORT_IN_TEMPDB = ON ); This is not a useful index for our simple update query; imagine that someone else created it for a different purpose.  Let’s run our update query again: UPDATE dbo.LOBtest WITH (TABLOCKX) SET some_value = some_value - 1; We find that it now requires 4,014 logical reads and the elapsed query time has increased to around 100ms.  The extra logical reads (4 per row) are an expected consequence of maintaining the nonclustered index. The query plan is very similar to before (click to enlarge): The Clustered Index Update operator picks up the extra work of maintaining the nonclustered index. The new Compute Scalar operators detect whether the value in the some_value column has actually been changed by the update.  SQL Server may be able to skip maintaining the nonclustered index if the value hasn’t changed (see my previous post on non-updating updates for details).  Our simple query does change the value of some_data in every row, so this optimization doesn’t add any value in this specific case. The output list of columns from the Clustered Index Scan hasn’t changed from the one shown previously: SQL Server still just reads the pk and some_data columns.  Cool. Overall then, adding the nonclustered index hasn’t had any startling effects, and the LOB column data still isn’t being read from the table.  Let’s see what happens if we make the nonclustered index unique. Test 3: Simple Update with a Unique Index Here’s the script to create a new unique index, and drop the old one: CREATE UNIQUE NONCLUSTERED INDEX [UQ dbo.LOBtest some_value (lob_data)] ON dbo.LOBtest (some_value) INCLUDE ( lob_data ) WITH ( FILLFACTOR = 100, MAXDOP = 1, SORT_IN_TEMPDB = ON ); GO DROP INDEX [IX dbo.LOBtest some_value (lob_data)] ON dbo.LOBtest; Remember that SQL Server only enforces uniqueness on index keys (the some_data column).  The lob_data column is simply stored at the leaf-level of the non-clustered index.  With that in mind, we might expect this change to make very little difference.  Let’s see: UPDATE dbo.LOBtest WITH (TABLOCKX) SET some_value = some_value - 1; Whoa!  Now look at the elapsed time and logical reads: Scan count 1, logical reads 2016, physical reads 0, read-ahead reads 0, lob logical reads 36015, lob physical reads 0, lob read-ahead reads 15992.   CPU time = 172 ms, elapsed time = 16172 ms. Even with all the data and index pages in memory, the query took over 16 seconds to update just 1,000 rows, performing over 52,000 LOB logical reads (nearly 16,000 of those using read-ahead). Why on earth is SQL Server reading LOB data in a query that only updates a single integer column? The Query Plan The query plan for test 3 looks a bit more complex than before: In fact, the bottom level is exactly the same as we saw with the non-unique index.  The top level has heaps of new stuff though, which I’ll come to in a moment. You might be expecting to find that the Clustered Index Scan is now reading the lob_data column (for some reason).  After all, we need to explain where all the LOB logical reads are coming from.  Sadly, when we look at the properties of the Clustered Index Scan, we see exactly the same as before: SQL Server is still only reading the pk and some_value columns – so what’s doing the LOB reads? Updates that Sneakily Read Data We have to go as far as the Clustered Index Update operator before we see LOB data in the output list: [Expr1020] is a bit flag added by an earlier Compute Scalar.  It is set true if the some_value column has not been changed (part of the non-updating updates optimization I mentioned earlier). The Clustered Index Update operator adds two new columns: the lob_data column, and some_value_OLD.  The some_value_OLD column, as the name suggests, is the pre-update value of the some_value column.  At this point, the clustered index has already been updated with the new value, but we haven’t touched the nonclustered index yet. An interesting observation here is that the Clustered Index Update operator can read a column into the data flow as part of its update operation.  SQL Server could have read the LOB data as part of the initial Clustered Index Scan, but that would mean carrying the data through all the operations that occur prior to the Clustered Index Update.  The server knows it will have to go back to the clustered index row to update it, so it delays reading the LOB data until then.  Sneaky! Why the LOB Data Is Needed This is all very interesting (I hope), but why is SQL Server reading the LOB data?  For that matter, why does it need to pass the pre-update value of the some_value column out of the Clustered Index Update? The answer relates to the top row of the query plan for test 3.  I’ll reproduce it here for convenience: Notice that this is a wide (per-index) update plan.  SQL Server used a narrow (per-row) update plan in test 2, where the Clustered Index Update took care of maintaining the nonclustered index too.  I’ll talk more about this difference shortly. The Split/Sort/Collapse combination is an optimization, which aims to make per-index update plans more efficient.  It does this by breaking each update into a delete/insert pair, reordering the operations, removing any redundant operations, and finally applying the net effect of all the changes to the nonclustered index. Imagine we had a unique index which currently holds three rows with the values 1, 2, and 3.  If we run a query that adds 1 to each row value, we would end up with values 2, 3, and 4.  The net effect of all the changes is the same as if we simply deleted the value 1, and added a new value 4. By applying net changes, SQL Server can also avoid false unique-key violations.  If we tried to immediately update the value 1 to a 2, it would conflict with the existing value 2 (which would soon be updated to 3 of course) and the query would fail.  You might argue that SQL Server could avoid the uniqueness violation by starting with the highest value (3) and working down.  That’s fine, but it’s not possible to generalize this logic to work with every possible update query. SQL Server has to use a wide update plan if it sees any risk of false uniqueness violations.  It’s worth noting that the logic SQL Server uses to detect whether these violations are possible has definite limits.  As a result, you will often receive a wide update plan, even when you can see that no violations are possible. Another benefit of this optimization is that it includes a sort on the index key as part of its work.  Processing the index changes in index key order promotes sequential I/O against the nonclustered index. A side-effect of all this is that the net changes might include one or more inserts.  In order to insert a new row in the index, SQL Server obviously needs all the columns – the key column and the included LOB column.  This is the reason SQL Server reads the LOB data as part of the Clustered Index Update. In addition, the some_value_OLD column is required by the Split operator (it turns updates into delete/insert pairs).  In order to generate the correct index key delete operation, it needs the old key value. The irony is that in this case the Split/Sort/Collapse optimization is anything but.  Reading all that LOB data is extremely expensive, so it is sad that the current version of SQL Server has no way to avoid it. Finally, for completeness, I should mention that the Filter operator is there to filter out the non-updating updates. Beating the Set-Based Update with a Cursor One situation where SQL Server can see that false unique-key violations aren’t possible is where it can guarantee that only one row is being updated.  Armed with this knowledge, we can write a cursor (or the WHILE-loop equivalent) that updates one row at a time, and so avoids reading the LOB data: SET NOCOUNT ON; SET STATISTICS XML, IO, TIME OFF;   DECLARE @PK INTEGER, @StartTime DATETIME; SET @StartTime = GETUTCDATE();   DECLARE curUpdate CURSOR LOCAL FORWARD_ONLY KEYSET SCROLL_LOCKS FOR SELECT L.pk FROM LOBtest L ORDER BY L.pk ASC;   OPEN curUpdate;   WHILE (1 = 1) BEGIN FETCH NEXT FROM curUpdate INTO @PK;   IF @@FETCH_STATUS = -1 BREAK; IF @@FETCH_STATUS = -2 CONTINUE;   UPDATE dbo.LOBtest SET some_value = some_value - 1 WHERE CURRENT OF curUpdate; END;   CLOSE curUpdate; DEALLOCATE curUpdate;   SELECT DATEDIFF(MILLISECOND, @StartTime, GETUTCDATE()); That completes the update in 1280 milliseconds (remember test 3 took over 16 seconds!) I used the WHERE CURRENT OF syntax there and a KEYSET cursor, just for the fun of it.  One could just as well use a WHERE clause that specified the primary key value instead. Clustered Indexes A clustered index is the ultimate index with included columns: all non-key columns are included columns in a clustered index.  Let’s re-create the test table and data with an updatable primary key, and without any non-clustered indexes: IF OBJECT_ID(N'dbo.LOBtest', N'U') IS NOT NULL DROP TABLE dbo.LOBtest; GO CREATE TABLE dbo.LOBtest ( pk INTEGER NOT NULL, some_value INTEGER NULL, lob_data VARCHAR(MAX) NULL, another_column CHAR(5) NULL, CONSTRAINT [PK dbo.LOBtest pk] PRIMARY KEY CLUSTERED (pk ASC) ); GO DECLARE @Data VARCHAR(MAX); SET @Data = REPLICATE(CONVERT(VARCHAR(MAX), 'x'), 65540);   WITH Numbers (n) AS ( SELECT ROW_NUMBER() OVER (ORDER BY (SELECT 0)) FROM master.sys.columns C1, master.sys.columns C2 ) INSERT LOBtest WITH (TABLOCKX) ( pk, some_value, lob_data ) SELECT TOP (1000) N.n, N.n, @Data FROM Numbers N WHERE N.n <= 1000; Now here’s a query to modify the cluster keys: UPDATE dbo.LOBtest SET pk = pk + 1; The query plan is: As you can see, the Split/Sort/Collapse optimization is present, and we also gain an Eager Table Spool, for Halloween protection.  In addition, SQL Server now has no choice but to read the LOB data in the Clustered Index Scan: The performance is not great, as you might expect (even though there is no non-clustered index to maintain): Table 'LOBtest'. Scan count 1, logical reads 2011, physical reads 0, read-ahead reads 0, lob logical reads 36015, lob physical reads 0, lob read-ahead reads 15992.   Table 'Worktable'. Scan count 1, logical reads 2040, physical reads 0, read-ahead reads 0, lob logical reads 34000, lob physical reads 0, lob read-ahead reads 8000.   SQL Server Execution Times: CPU time = 483 ms, elapsed time = 17884 ms. Notice how the LOB data is read twice: once from the Clustered Index Scan, and again from the work table in tempdb used by the Eager Spool. If you try the same test with a non-unique clustered index (rather than a primary key), you’ll get a much more efficient plan that just passes the cluster key (including uniqueifier) around (no LOB data or other non-key columns): A unique non-clustered index (on a heap) works well too: Both those queries complete in a few tens of milliseconds, with no LOB reads, and just a few thousand logical reads.  (In fact the heap is rather more efficient). There are lots more fun combinations to try that I don’t have space for here. Final Thoughts The behaviour shown in this post is not limited to LOB data by any means.  If the conditions are met, any unique index that has included columns can produce similar behaviour – something to bear in mind when adding large INCLUDE columns to achieve covering queries, perhaps. Paul White Email: [email protected] Twitter: @PaulWhiteNZ

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  • Stored Procedures with SSRS? Hmm… not so much

    - by Rob Farley
    Little Bobby Tables’ mother says you should always sanitise your data input. Except that I think she’s wrong. The SQL Injection aspect is for another post, where I’ll show you why I think SQL Injection is the same kind of attack as many other attacks, such as the old buffer overflow, but here I want to have a bit of a whinge about the way that some people sanitise data input, and even have a whinge about people who insist on using stored procedures for SSRS reports. Let me say that again, in case you missed it the first time: I want to have a whinge about people who insist on using stored procedures for SSRS reports. Let’s look at the data input sanitisation aspect – except that I’m going to call it ‘parameter validation’. I’m talking about code that looks like this: create procedure dbo.GetMonthSummaryPerSalesPerson(@eomdate datetime) as begin     /* First check that @eomdate is a valid date */     if isdate(@eomdate) != 1     begin         select 'Please enter a valid date' as ErrorMessage;         return;     end     /* Then check that time has passed since @eomdate */     if datediff(day,@eomdate,sysdatetime()) < 5     begin         select 'Sorry - EOM is not complete yet' as ErrorMessage;         return;     end         /* If those checks have succeeded, return the data */     select SalesPersonID, count(*) as NumSales, sum(TotalDue) as TotalSales     from Sales.SalesOrderHeader     where OrderDate >= dateadd(month,-1,@eomdate)         and OrderDate < @eomdate     group by SalesPersonID     order by SalesPersonID; end Notice that the code checks that a date has been entered. Seriously??!! This must only be to check for NULL values being passed in, because anything else would have to be a valid datetime to avoid an error. The other check is maybe fair enough, but I still don’t like it. The two problems I have with this stored procedure are the result sets and the small fact that the stored procedure even exists in the first place. But let’s consider the first one of these problems for starters. I’ll get to the second one in a moment. If you read Jes Borland (@grrl_geek)’s recent post about returning multiple result sets in Reporting Services, you’ll be aware that Reporting Services doesn’t support multiple results sets from a single query. And when it says ‘single query’, it includes ‘stored procedure call’. It’ll only handle the first result set that comes back. But that’s okay – we have RETURN statements, so our stored procedure will only ever return a single result set.  Sometimes that result set might contain a single field called ErrorMessage, but it’s still only one result set. Except that it’s not okay, because Reporting Services needs to know what fields to expect. Your report needs to hook into your fields, so SSRS needs to have a way to get that information. For stored procs, it uses an option called FMTONLY. When Reporting Services tries to figure out what fields are going to be returned by a query (or stored procedure call), it doesn’t want to have to run the whole thing. That could take ages. (Maybe it’s seen some of the stored procedures I’ve had to deal with over the years!) So it turns on FMTONLY before it makes the call (and turns it off again afterwards). FMTONLY is designed to be able to figure out the shape of the output, without actually running the contents. It’s very useful, you might think. set fmtonly on exec dbo.GetMonthSummaryPerSalesPerson '20030401'; set fmtonly off Without the FMTONLY lines, this stored procedure returns a result set that has three columns and fourteen rows. But with FMTONLY turned on, those rows don’t come back. But what I do get back hurts Reporting Services. It doesn’t run the stored procedure at all. It just looks for anything that could be returned and pushes out a result set in that shape. Despite the fact that I’ve made sure that the logic will only ever return a single result set, the FMTONLY option kills me by returning three of them. It would have been much better to push these checks down into the query itself. alter procedure dbo.GetMonthSummaryPerSalesPerson(@eomdate datetime) as begin     select SalesPersonID, count(*) as NumSales, sum(TotalDue) as TotalSales     from Sales.SalesOrderHeader     where     /* Make sure that @eomdate is valid */         isdate(@eomdate) = 1     /* And that it's sufficiently past */     and datediff(day,@eomdate,sysdatetime()) >= 5     /* And now use it in the filter as appropriate */     and OrderDate >= dateadd(month,-1,@eomdate)     and OrderDate < @eomdate     group by SalesPersonID     order by SalesPersonID; end Now if we run it with FMTONLY turned on, we get the single result set back. But let’s consider the execution plan when we pass in an invalid date. First let’s look at one that returns data. I’ve got a semi-useful index in place on OrderDate, which includes the SalesPersonID and TotalDue fields. It does the job, despite a hefty Sort operation. …compared to one that uses a future date: You might notice that the estimated costs are similar – the Index Seek is still 28%, the Sort is still 71%. But the size of that arrow coming out of the Index Seek is a whole bunch smaller. The coolest thing here is what’s going on with that Index Seek. Let’s look at some of the properties of it. Glance down it with me… Estimated CPU cost of 0.0005728, 387 estimated rows, estimated subtree cost of 0.0044385, ForceSeek false, Number of Executions 0. That’s right – it doesn’t run. So much for reading plans right-to-left... The key is the Filter on the left of it. It has a Startup Expression Predicate in it, which means that it doesn’t call anything further down the plan (to the right) if the predicate evaluates to false. Using this method, we can make sure that our stored procedure contains a single query, and therefore avoid any problems with multiple result sets. If we wanted, we could always use UNION ALL to make sure that we can return an appropriate error message. alter procedure dbo.GetMonthSummaryPerSalesPerson(@eomdate datetime) as begin     select SalesPersonID, count(*) as NumSales, sum(TotalDue) as TotalSales, /*Placeholder: */ '' as ErrorMessage     from Sales.SalesOrderHeader     where     /* Make sure that @eomdate is valid */         isdate(@eomdate) = 1     /* And that it's sufficiently past */     and datediff(day,@eomdate,sysdatetime()) >= 5     /* And now use it in the filter as appropriate */     and OrderDate >= dateadd(month,-1,@eomdate)     and OrderDate < @eomdate     group by SalesPersonID     /* Now include the error messages */     union all     select 0, 0, 0, 'Please enter a valid date' as ErrorMessage     where isdate(@eomdate) != 1     union all     select 0, 0, 0, 'Sorry - EOM is not complete yet' as ErrorMessage     where datediff(day,@eomdate,sysdatetime()) < 5     order by SalesPersonID; end But still I don’t like it, because it’s now a stored procedure with a single query. And I don’t like stored procedures that should be functions. That’s right – I think this should be a function, and SSRS should call the function. And I apologise to those of you who are now planning a bonfire for me. Guy Fawkes’ night has already passed this year, so I think you miss out. (And I’m not going to remind you about when the PASS Summit is in 2012.) create function dbo.GetMonthSummaryPerSalesPerson(@eomdate datetime) returns table as return (     select SalesPersonID, count(*) as NumSales, sum(TotalDue) as TotalSales, '' as ErrorMessage     from Sales.SalesOrderHeader     where     /* Make sure that @eomdate is valid */         isdate(@eomdate) = 1     /* And that it's sufficiently past */     and datediff(day,@eomdate,sysdatetime()) >= 5     /* And now use it in the filter as appropriate */     and OrderDate >= dateadd(month,-1,@eomdate)     and OrderDate < @eomdate     group by SalesPersonID     union all     select 0, 0, 0, 'Please enter a valid date' as ErrorMessage     where isdate(@eomdate) != 1     union all     select 0, 0, 0, 'Sorry - EOM is not complete yet' as ErrorMessage     where datediff(day,@eomdate,sysdatetime()) < 5 ); We’ve had to lose the ORDER BY – but that’s fine, as that’s a client thing anyway. We can have our reports leverage this stored query still, but we’re recognising that it’s a query, not a procedure. A procedure is designed to DO stuff, not just return data. We even get entries in sys.columns that confirm what the shape of the result set actually is, which makes sense, because a table-valued function is the right mechanism to return data. And we get so much more flexibility with this. If you haven’t seen the simplification stuff that I’ve preached on before, jump over to http://bit.ly/SimpleRob and watch the video of when I broke a microphone and nearly fell off the stage in Wales. You’ll see the impact of being able to have a simplifiable query. You can also read the procedural functions post I wrote recently, if you didn’t follow the link from a few paragraphs ago. So if we want the list of SalesPeople that made any kind of sales in a given month, we can do something like: select SalesPersonID from dbo.GetMonthSummaryPerSalesPerson(@eomonth) order by SalesPersonID; This doesn’t need to look up the TotalDue field, which makes a simpler plan. select * from dbo.GetMonthSummaryPerSalesPerson(@eomonth) where SalesPersonID is not null order by SalesPersonID; This one can avoid having to do the work on the rows that don’t have a SalesPersonID value, pushing the predicate into the Index Seek rather than filtering the results that come back to the report. If we had joins involved, we might see some of those being simplified out. We also get the ability to include query hints in individual reports. We shift from having a single-use stored procedure to having a reusable stored query – and isn’t that one of the main points of modularisation? Stored procedures in Reporting Services are just a bit limited for my liking. They’re useful in plenty of ways, but if you insist on using stored procedures all the time rather that queries that use functions – that’s rubbish. @rob_farley

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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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  • How do I create Tetris Blocks in XNA with C#?

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    I'm making a Tetris Clone in C# with XNA, and I'm unsure of how to actually implement the blocks. I don't think that making the shapes as images will work (because parts are removed when lines are formed), so I Have blocks to make up the pieces like This. Unfortunately, I don't know how to actually define the blocks to make the pieces, nor do I know how to manipulate them to make them rotate, etc. Edit: I would also need assistance in learning how to make the Tetris Grid too.

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  • JQuery Internals Documentation

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    Is there any documentation available that explains the internals of JQuery and JQuery UI? I have been looking through the source code, and while much of it makes sense, I was still hoping for an overview to help speed up my learning process. Thanks

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  • SIM Application Toolkit development

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  • How do I configure Mercurial to use environment variables in mercurial.ini

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  • Want to learn Microsoft-Dynamics CRM. Please suggest for Dynamics Beginners?

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  • How to build a dotnetnuke module from source i.e blog module

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  • Becoming a better Android programmer

    - by Drew Dara-Abrams
    Any suggestions on how to become a better Android programmer? I'm past intro tutorials, which mainly focus on how to use pieces of the SDK, but I still struggle to structure big Android apps. Obviously the best use of my time is continuing with my coding projects, but I'm wondering if I should be learning more about Android particulars, solidifying my somewhat shaky Java knowledge, going back to object-oriented fundamentals or patterns...? Pointers to resources (books, example apps, sites) you've found helpful would be great.

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  • How Drupal works?

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    I have yet to see a comprehensive overview about how Drupal really works. Most of the tutorials are about lame things, like adding a module or configuring a site. Where is a flowchart about how the page gets generated? Most of the documentation is clumsy too. What's the best resource for learning how Drupal really works?

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  • General Purpose Language to build a compiler for

    - by Brownie
    Inspired by Eric Sink's interview on the stackoverflow podcast I would like to build a full compiler in my spare time for the learning experience. My initial thought was to build a C compiler but I'm not sure whether it would take too much time. I am wondering if there is a smaller general purpose language that would be more appropriate to implement as a first compiler effort? Or is a C implementation doable on a reasonable timescale (200 hrs)? It is my intention to target the CLR.

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  • Coldfusion popularity

    - by jrharshath
    Hi, I've heard of Coldfusion being a server side technology for web app dev. Are there any statistics as to how widely it is used as opposed to PHP, Java Servlets and JSP or ASP.NET? Are there any special features in coldfusion that make learning it worth the while? Thanks, jrh PS: please don't close this question as argumentative. I'm looking for statistics and real answers. Thanks for understanding.

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    i want to use one of these to describe my xml document. i've read that xsd is better than the older dtd since it supports namespaces and data types. does this mean that i should only use xsd for all future needs and totally ignore dtd and don´t even have to bother learning its structure?

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    Climbing the learning mountain of TVirtualTreeView, I'm attempting to create a custom descendant that ensures that, when the control is resized, the width of the last column exactly fills control's width without requiring a horizontal scroll bar. I see a number of items (a method and a number of events) pertaining to "AutoFitColumns", but not documentation covering this feature. Can I use AutoFitColumns to automatically resize my last column and if so, how.

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  • Is it necessary to know flash designing for flex3 ?

    - by Srinivas Iyer
    I am from a programming background ,and newbie to flex3 . i would like to learn flex3 and develop some application using rails and flex3 . Is it necessary to know flash in order to learn flex3 or just learning Action script 3 would do ? .Can anybody tell what are the prerequisites to learn flex3 . Thanks in Advance.

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  • Browser not loading Php pages

    - by ihaveitnow
    Im using a linux machine, and I followed the instructions seen on http://jm2.php.net/manual/en/install.php to setup php, apache and my sql. I did exactly what it said and nothing more, but when I try to open a .php file with firefox or chrome, it downloads...? Im following a tutorial on learning php seen here: http://devzone.zend.com/node/view/id/625 Is there something im not doing or doing wrong? All answers are appreciated.

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  • The Programmer's Bill of Rights

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    I know Jeff has written about this subject on his coding horror blog in the past but I am interested in learning the opinions of a broad set of developers. I agree wholeheartedly with his statement: I propose we adopt a Programmer's Bill of Rights, protecting the rights of programmers by preventing companies from denying them the fundamentals they need to be successful. So, if you could propose one item to the bill of rights, what would it be?

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  • voice recognition in android

    - by jaymin
    Hi, I am an android application developer. I was curious as to how does voice recognition could be implemented using android. There is inbuilt support for speech recognition in android, but how can it be used to implement voice recognition...Are there any links which would help me in learning on this topic.. Thanks

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  • vb classic coder to android how to transition?

    - by user366654
    Hi guys. I'm a VB/vba coder and would like to start android dev. Currently I'm learning Java from scratch and. Its quite tough. I've read about oop but never actually written any OO code. Java syntax is also quite foreign but I'm getting the hang of it. My question is, which is absolutely the best transition path for a vb old dog to writing for froyo?

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