[Rd] names Rd see Also{slotNames}

2011-09-22 Thread Timothy Bates
Would anyone object to a suggestion that the names.Rd file could usefully point to seeAlso{slotNames}? cheers, tim -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __

[Rd] R check error / update.packages

2011-09-22 Thread Nick Sabbe
While building/checking a package of mine that depends on glmnet, I got the following message: * checking whether the name space can be loaded with stated dependencies ...Warn ing: running command 'C:/Users/nisabbe/Documents/R/R-2.13.1/bin/i386/Rterm.exe R_DEFAULT_PACKAGES=NULL --vanilla

[Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe
This problem is likely to be specific to Windows, and particularly Win7. After a successful build of a package (R CMD build addendum), I immediately run an R CMD check for the same package. Not always, but _very_ often, I get the following error: C:\Users\nisabbe\Documents\@Doctoraat\RR CMD

Re: [Rd] R check error / update.packages

2011-09-22 Thread Uwe Ligges
This is an infelicity in a recent glmnet release, I will follow up off list in a minute. Best, Uwe Ligges On 22.09.2011 13:16, Nick Sabbe wrote: While building/checking a package of mine that depends on glmnet, I got the following message: * checking whether the name space can be loaded

Re: [Rd] R CMD check file issues

2011-09-22 Thread Uwe Ligges
Are you sure there is no other check process or editor that locks the file? Uwe Ligges On 22.09.2011 13:53, Nick Sabbe wrote: This problem is likely to be specific to Windows, and particularly Win7. After a successful build of a package (R CMD build addendum), I immediately run an R CMD

Re: [Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe
Hello Uwe, and thanks for your interest in the issue. There is most certainly not another process that stops working between the two R CMD check calls (recently, I've made a habit out of being ready to press up arrow enter in the seconds after running my first R CMD check, to rerun it if it

Re: [Rd] R CMD check file issues

2011-09-22 Thread Uwe Ligges
On 22.09.2011 14:16, Nick Sabbe wrote: Hello Uwe, and thanks for your interest in the issue. There is most certainly not another process that stops working between the two R CMD check calls (recently, I've made a habit out of being ready to pressup arrow enter in the seconds after running

Re: [Rd] R CMD check file issues

2011-09-22 Thread Duncan Murdoch
On 11-09-22 7:53 AM, Nick Sabbe wrote: This problem is likely to be specific to Windows, and particularly Win7. The symptoms sound like interference from an anti-virus checker. Duncan Murdoch After a successful build of a package (R CMD build addendum), I immediately run an R CMD check

Re: [Rd] R CMD check file issues

2011-09-22 Thread Nick Sabbe
Hi Duncan (and others). I've just turned off my virus scanner (MS Forefront Endpoint Protection). The issue persists. It appears that the first time I call R CMD check, it deletes the previous rcheck folder, but tries to proceed before it is actually gone. By the time I reissue the command, the

Re: [Rd] R CMD check file issues

2011-09-22 Thread Duncan Murdoch
On 11-09-22 8:30 AM, Nick Sabbe wrote: Hi Duncan (and others). I've just turned off my virus scanner (MS Forefront Endpoint Protection). The issue persists. It appears that the first time I call R CMD check, it deletes the previous rcheck folder, but tries to proceed before it is actually

Re: [Rd] using R as SHELL in gnu make

2011-09-22 Thread Cook, Malcolm
OK, I now have a working version of setting SHELL=R in a GNU make script, allowing make’s recipes to be written in R, that works out most of the complications. I plan to clean it up a little more and blog about it soon here: http://malcook-gedanken.blogspot.com/ - I’ll follow up here when I

Re: [Rd] R CMD check file issues

2011-09-22 Thread Henrik Bengtsson
I'm on Windows 7 (64-bit) and everything works perfectly. Obviously, there is either another process locking down a file with the same name or the directory doesn't exist at the time of the file() call. Now to the most important question ...what's your sessionInfo()? /Henrik On Thu, Sep 22,

[Rd] How to call an MPI-enabled program from R?

2011-09-22 Thread Alireza Mahani
Conceptually, how is it possible to call an MPI-parallelized code in C from R? My experience with MPI so far indicates that one has to launch an MPI-enabled binary using a command like mpiexec -n number of processes name of binary In other words, I'm not sure how to create an MPI 'library' and

Re: [Rd] R CMD check file issues

2011-09-22 Thread Prof Brian Ripley
I do see this on Win7, and it is an antivirus issue (Sophos). Excluding the R check area solves it for me, as does an earlier delete. I have considered adding a delay in check.R, but it is not clear how long it would need to be. On Thu, 22 Sep 2011, Henrik Bengtsson wrote: I'm on Windows

[Rd] R-2.13.2 beta build for Windows

2011-09-22 Thread Dario Strbenac
Hello, I've had a look at a number of CRAN servers and all of them give a similar error, like : Not Found The requested URL /bin/windows/base/R-2.13.2beta-win.exe was not found on this server. Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle

Re: [Rd] R-2.13.2 beta build for Windows

2011-09-22 Thread Duncan Murdoch
On 11-09-22 8:00 PM, Dario Strbenac wrote: Hello, I've had a look at a number of CRAN servers and all of them give a similar error, like : Not Found The requested URL /bin/windows/base/R-2.13.2beta-win.exe was not found on this server. Additionally, a 404 Not Found error was encountered