Re: [Rd] R-forge, package dependencies
I have exactly the same issue with a pair of my packages on R-Forge. I've already notified Stefan, but I mentioned it wasn't urgent for me :) It must have something to do with the R check using a different environment than the build... So good hunting, Stefan! Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Uwe Ligges Sent: dinsdag 15 januari 2013 21:09 To: Thomas Lumley Cc: Stefan Theussl; R-devel Subject: Re: [Rd] R-forge, package dependencies On 15.01.2013 20:47, Thomas Lumley wrote: I have a project on R-forge (sqlsurvey.r-forge.r-project.org) with two packages, RMonetDB and sqlsurvey. At the moment, sqlsurvey is listed as failing to build. The error is on the Linux package check, which says that RMonetDB is not available: * checking package dependencies ... ERROR Package required but not available: 'RMonetDB' RMonetDB has built successfully: r-forge lists its status as 'current', with Linux, Windows, and Mac packages available for download. The package check for sqlsurvey on Windows and Mac finds RMonetDB without any problems, it's just on Linux that it appears to be unavailable. Any suggestions for how to fix this? I've tried uploading a new version of RMonetDB, but the situation didn't change: it built successfully, but the Linux check of sqlsurvey still couldn't find it. I think you have to ask Stefan to check the details. Best, Uwe -thomas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Dependencies on recommended packages
Dear all,
I've recently had some issues getting my package to successfully check.
This was on R-Forge, so it's not obvious for me to provide SessionInfo or
the likes (if necessary, Stefan can chime in?).
After some research (mainly by Stefan Theussler, driving force behind
R-Forge), this turned out to be the root cause:
On R-Forge, the version of R installed was the latest release (2.15.0),
which includes Matrix 1.0-5 as a recommended package.
My own package depends upon glmnet, which itself depends upon Matrix 1.0-6.
(Note: to avoid issues with that, as a test I've also included an explicit
dependency upon Matrix 1.0-6 in my own package, but this didn't change
anything).
During build and most of R CMD check (with the -as-cran flag), everything
worked out fine (which suggests to me that among others, Matrix 1.0-6 is
present and can be loaded, since one of the checks is that the package and
all its dependencies can be loaded), but while running the examples, somehow
loading of the package failed, with an error message that Matrix 1.0-6 could
not be loaded. Here's the relevant part of the log:
library('addendum')
Loading required package: glmnet
Error: package 'Matrix' 1.0-5 was found, but = 1.0.6 is required by
'glmnet'
Execution halted
Run time: 92.43 seconds.
There are some issues with this comparison, but in the Windows build/check
chain on R-Forge, R2.15.0 patched was installed (including Matrix 1.0-6) and
the build _was_ successful.
Stefan suspected this to be an artifact of Matrix being a recommended
package (so R CMD check would somehow prefer the version installed with R),
and to a certain degree the successful build/check with R patched confirms
this suspicion.
I've neither read up on this nor tried other options, but if this is indeed
the case then I suggest to alter this behaviour. Unless, of course, there is
any reason to treat recommended packages any different wrt versioning and
R CMD check.
I suspect other people may run into this sooner or later.
If not or if my/our analysis is wrong/incomplete I will gladly stand
corrected.
I'll leave it to you gurus to judge.
Thanks for R! (And another shout out to Stefan, who diligently helped me)
Nick Sabbe
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[Rd] plot(.xy) and add
I am still an avid user of R base plotting and fortunately so are a lot of
the interesting packages I use.
However, to this day, I am still annoyed by the fact that many functions do
not support the add parameter.
In many cases, this is caused by xy.plot not supporting it (because the
parameter is typically passed on to it through .)
It also requires lots of code constructs like
for(i in 1:10)
{
if(i==1)
{
plot(x,y[i,])
}
else
{
points(x,y[i,])
}
}
Now, I can understand that generally supporting add can have some unexpected
consequences in some cases (e.g. xlim and ylim should be ignored in these
cases), but I cannot imagine these truly to be worse than not supporting it.
Is there (still) a reason why this not supported and/or do people find this
as troublesome as I do?
Nick Sabbe
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Re: [Rd] NOTE: unstated dependencies in examples
So other people from the administration tell you which software to use for teaching? And what happens if they tell you only Excel is available? ... weird ... On the contrary, I should say: very common. We have hardly any control over what is installed on the application servers at our university (let alone how well it is installed). You can still use the old version there, if the new version depends on R = 2.14.0. The old version will stay in the binary repositories for old versions of R and in the package archives of the source repository as well. I think Duncan explained that already. Then what about new features that don't depend on parallel? Maintenance hell is born, just because you effectively force somebody to fork (True, the R builders are not the ones forcing people to stay on some old version, yet this scenario is not that strange that it should be ditched without regard). A second point is that the package would not *depend* or anything on R= 2.14.0. But it depends on it: it won't pass the checks for R 2.14.0. Somewhat silly if it only depends on it because of the check, no? Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check file issues
Here you go (though I doubt it will be actually helpful): R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252 LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Belgium.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] addendum_1.4 snowfall_1.84 snow_0.3-7 mgcv_1.7-6 rgl_0.92.798 glmnet_1.7 [7] Matrix_0.9996875-3 lattice_0.19-33svSocket_0.9-51TinnR_1.0.3 R2HTML_2.2 Hmisc_3.8-3 [13] survival_2.36-9 loaded via a namespace (and not attached): [1] cluster_1.14.0 grid_2.13.1nlme_3.1-102 svMisc_0.9-63 tools_2.13.1 Note that this is the sessionInfo from an interactive session. I don't know of an obvious way to provide you the sessionInfo of the session that is started by R CMD check (Assuming that at that point, an 'actual' R session has actually been started - it appears the error occurs before any 'real work' is started). Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: henrik.bengts...@gmail.com [mailto:henrik.bengts...@gmail.com] On Behalf Of Henrik Bengtsson Sent: donderdag 22 september 2011 17:59 To: Duncan Murdoch Cc: Nick Sabbe; r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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, 2011 at 5:33 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: 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 gone. By the time I reissue the command, the folder is truly gone, and the R CMD check can safely do its work. Is anyone else here using Win7 (32bit) and successfully building/checking R packages? Perhaps I'm the only one who has treaded this path :-) I do use Win7 on one machine, and have seen odd things happen, but not what you describe. I imagine a simple workaround for you would be to delete the folder before you call R CMD check (i.e. wrap R CMD check in a batch file to do that), but it would be nice if that were not necessary. Duncan Murdoch Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: donderdag 22 september 2011 14:20 To: Nick Sabbe Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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 for the same package. Not always, but _very_ often, I get the following error: C:\Users\nisabbe\Documents\@Doctoraat\RR CMD check addendum Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: Hmisc Loading required package: survival Loading required package: stats Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units Loading required package: R2HTML Warning in file(filename, wt) : cannot open file 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch eck.log': Permission denied Error in file(filename, wt) : cannot open the connection Execution halted If, after this, I immediately reissue the R CMD check command, it works, without the error. I think this has something to do with how Win7 processes file handling (there are known issues even noticeable in windows explorer), but perhaps there is a way of circumventing this? It would be greatly appreciated, as this issue is preventing automation of build/check/install scripts. Suggestions will be greatly appreciated. Nick Sabbe
Re: [Rd] R CMD check file issues
In my particular case, the antivirus appears irrelevant (turning it off does not change anything ; admittedly, turning 'off' an antivirus program through its user interface may still involve some background meddling - stubborn creatures they are, these AVs) Either way: since this is the only place I know of where R has problems with the slow filehandling in Win7, a solution may be to check repeatedly (with some delay and a timeout) after the delete calls whether the files are actually gone. Ugly, I admit, but since our Redmond friends don't provide it... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- project.org] On Behalf Of Prof Brian Ripley Sent: donderdag 22 september 2011 22:04 To: Henrik Bengtsson Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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 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, 2011 at 5:33 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: 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 gone. By the time I reissue the command, the folder is truly gone, and the R CMD check can safely do its work. Is anyone else here using Win7 (32bit) and successfully building/checking R packages? Perhaps I'm the only one who has treaded this path :-) I do use Win7 on one machine, and have seen odd things happen, but not what you describe. I imagine a simple workaround for you would be to delete the folder before you call R CMD check (i.e. wrap R CMD check in a batch file to do that), but it would be nice if that were not necessary. Duncan Murdoch Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: donderdag 22 september 2011 14:20 To: Nick Sabbe Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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 for the same package. Not always, but _very_ often, I get the following error: C:\Users\nisabbe\Documents\@Doctoraat\RR CMD check addendum Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: Hmisc Loading required package: survival Loading required package: stats Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units Loading required package: R2HTML Warning in file(filename, wt) : cannot open file 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch eck.log': Permission denied Error in file(filename, wt) : cannot open the connection Execution halted If, after this, I immediately reissue the R CMD check command, it works, without the error. I think this has something to do with how Win7 processes file handling (there are known issues even noticeable in windows explorer), but perhaps there is a way of circumventing this? It would be greatly appreciated, as this issue is preventing automation of build/check/install scripts. Suggestions will be greatly appreciated. Nick Sabbe -- ping: nick.sa...@ugent.be link:http://biomath.ugent.be/ http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove [[alternative HTML version deleted
[Rd] R check error / update.packages
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 --slave -f C:\Users\nisabbe\AppData\Local\Tem p\RtmpZpjj07\Rin121ae93' had status 1 WARNING Error: .onLoad failed in loadNamespace() for 'glmnet', details: call: cat(Loaded glmnet, installed.packages()[glmnet, Version], error: could not find function installed.packages Execution halted A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. I have not changed anything to my dependencies (since my last successful build the day before yesterday), and to my knowledge, I have not changed anything relevant. I am using R 2.13.1 (unchanged since the last successful build) on Windows 7 32bit. When starting a vanilla R terminal, the function installed.packages is present and can be run. Apart from this, I do not get any warnings or errors (e.g. the examples run fine). Also, as far as I can tell, I've never had the warning wrt status 1 (up to today), but it is unclear whether one is just the consequence of the other. Note: the sources for this package can be found on R-Forge: https://r-forge.r-project.org/R/?group_id=1130 The namespace itself contains as its import statement: import(glmnet, rgl, Matrix, snowfall) Can someone please help me avoid this warning, as I prefer 0 errors 0 warnings. On a related note, while trying to alleviate the problem, I ran update.packages, which led me to another problem: apparently, packages that are loaded at the time of update.packages are not updated and may end up broken (this was the case for lattice and Hmisc, for me). Luckily my colleague had gone through the same troubles and pointed me to the solution. I can imagine it to be hard to define exactly which packages should or shouldn't be updated, but it would be nice if the update.packages at least issued a warning against this. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be/ http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check file issues
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 check addendum Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: Hmisc Loading required package: survival Loading required package: stats Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units Loading required package: R2HTML Warning in file(filename, wt) : cannot open file 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch eck.log': Permission denied Error in file(filename, wt) : cannot open the connection Execution halted If, after this, I immediately reissue the R CMD check command, it works, without the error. I think this has something to do with how Win7 processes file handling (there are known issues even noticeable in windows explorer), but perhaps there is a way of circumventing this? It would be greatly appreciated, as this issue is preventing automation of build/check/install scripts. Suggestions will be greatly appreciated. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be/ http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check file issues
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 fails). At worst, there may ever have been an explorer window open, but this is definitely not always the case, and I'm sure this window was not closed then, between the calls. I'm really quite afraid it is more of a windows issue than an R issue, but I was hoping you wizards might have a workaround (apart from the obvious suggestion to install Linux), as it is immensely annoying... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: donderdag 22 september 2011 13:58 To: Nick Sabbe Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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 check for the same package. Not always, but _very_ often, I get the following error: C:\Users\nisabbe\Documents\@Doctoraat\RR CMD check addendum Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: Hmisc Loading required package: survival Loading required package: stats Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units Loading required package: R2HTML Warning in file(filename, wt) : cannot open file 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch eck.log': Permission denied Error in file(filename, wt) : cannot open the connection Execution halted If, after this, I immediately reissue the R CMD check command, it works, without the error. I think this has something to do with how Win7 processes file handling (there are known issues even noticeable in windows explorer), but perhaps there is a way of circumventing this? It would be greatly appreciated, as this issue is preventing automation of build/check/install scripts. Suggestions will be greatly appreciated. Nick Sabbe -- ping: nick.sa...@ugent.be link:http://biomath.ugent.be/ http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check file issues
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 folder is truly gone, and the R CMD check can safely do its work. Is anyone else here using Win7 (32bit) and successfully building/checking R packages? Perhaps I'm the only one who has treaded this path :-) Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: donderdag 22 september 2011 14:20 To: Nick Sabbe Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check file issues 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 for the same package. Not always, but _very_ often, I get the following error: C:\Users\nisabbe\Documents\@Doctoraat\RR CMD check addendum Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: Hmisc Loading required package: survival Loading required package: stats Loading required package: graphics Loading required package: splines Attaching package: 'Hmisc' The following object(s) are masked from 'package:survival': untangle.specials The following object(s) are masked from 'package:base': format.pval, round.POSIXt, trunc.POSIXt, units Loading required package: R2HTML Warning in file(filename, wt) : cannot open file 'C:/Users/nisabbe/Documents/@Doctoraat/R/addendum.Rcheck/00ch eck.log': Permission denied Error in file(filename, wt) : cannot open the connection Execution halted If, after this, I immediately reissue the R CMD check command, it works, without the error. I think this has something to do with how Win7 processes file handling (there are known issues even noticeable in windows explorer), but perhaps there is a way of circumventing this? It would be greatly appreciated, as this issue is preventing automation of build/check/install scripts. Suggestions will be greatly appreciated. Nick Sabbe -- ping: nick.sa...@ugent.be link:http://biomath.ugent.be/ http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] do.call and sys.call: suggestion for improval?
Hi all. I'll start by introducing the origin of the problem, although it appears to me that it goes beyond my specific setting. I'm currently working on a method for finding the 'lowest named function call' on the call stack. I am aware that the name of a function is not uniquely defined, but for most reasonable cases, the intended name can be easily induced. You can see some of the specific issues here: http://stackoverflow.com/questions/7307987/logging-current-function-name if you like. After some fidgeting and great help by Andrie (see the SO link; sorry I don't know his last name), it works rather well. There are, however, issues wrt do.call. Typical usage would then be: do.call(some.named.function, some.list) Now, when I look at the stackframe inside this some.named.function (or a function that is called from it), more or less like this: funcs - sapply(2+1:sys.nframe(), function(i) sys.call(sys.parent(n=i))[[1]] ) I get strange results: contrary to the 'normal' named function calls, I don't get the function name, but I get back a closure, that is really just (a copy of) my original some.named.function. On the other hand, the do.call call itself is _not_ on the stackframe. The good news is: this makes do.call still reasonably identifiable (I'm willing to assume this closure returning in sys.call is unique to do.call). The bad news is, that there is, as of now, no way to retrieve the name of the function as it was passed to do.call. So, my questions: * why is the do.call call itself not on the stackframe? (I could hope to extract the name there somehow) * why is the result of sys.call not consistent with normal function calls? I am aware of the warning in the help for do.call that the precise semantics are currently undefined and subject to change, but I was hoping this could be (easily) altered? I believe it is in the best interest of the R community that calls through do.call are as close as possible to 'normal' calls, and this is rather a big difference. * does anybody have other suggestions on how to obtain the name of the function in that case? I'm also willing to accept that I may need to change my own implementation after 'the specific semantics' change somewhere in the future. If there is a reason behind the difference (besides something like it's not so easy to code that), I would be very interested in learning about it. Also, if I have completely misunderstood how things work, I will gladly accept redirections and/or flames. Thanks in advance (well, not for potential flames), Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Linking to lapack
Hello all. I'm developing a package for R holding a Gibbs sampler, which tends to have better performance when written in C than in R. During each iteration in the Gibbs sampler, I need the inverse of a symmetric matrix. For this, I wish to use lapack, as is concisely suggested in Writing R extensions, since this will have better performance than I could ever write myself. After some twiddling I have got my code to compile by including R_ext/Lapack.h and using F77_CALL(dpotrf), but unfortunately, I don't get this to link properly. I get this message: testc.o:testc.c:(.text+0x255): undefined reference to `dpotrf_' which seems logical to me as far as my understanding of C reaches, but I don't know how to resolve it. I'm quite sure I need some extra parameters in my makefile, but as I come from a world where all these complexities are happily abstracted away for me by an IDE, I have no actual clue on how to surmount this. However: when I'm done with all my code, I wish to build a package for publication on CRAN, so I want to be sure that not only I can build it on my system, but it will also work well when distributed to other computers (if I understand the package process well, source files are compiled and linked during installation of the package), so I would also like to know how to do this. It should not be relevant, but either way: I'm doing all this on a Windows 7 machine, though the package will probably be used on Linux-based servers eventually. Finally: I have found no comprehensive list of the functions available to an R package developer, nor, strangely, questions about that. Does such a thing exist, or are we up to hoping we find what we are looking for in the header files? If it does not exist already, I would surely be willing to work on it. Thanks for any input. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
