[Rd] Missing warning when NAs are generated during coercion to complex (PR#13942)

2009-09-03 Thread gmbecker
Hello all, I ran into this today and just thought you guys should know about it. Consider the following: as(c("TRUE", "TRUE"), "complex") #warning about NAs as(list("TRUE", "TRUE"), "complex") #no warning At first I thought that it was something about it being a list, but then I tried as(list("

[Rd] Missing warning when NAs are generated during coercion to complex

2009-09-03 Thread Gabriel Becker
Hello all, I ran into this today and just thought you guys should know about it. Consider the following: as(c("TRUE", "TRUE"), "complex") #warning about NAs as(list("TRUE", "TRUE"), "complex") #no warning At first I thought that it was something about it being a list, but then I tried as(list("

Re: [Rd] Running an expression 1MN times using embedded R

2009-09-03 Thread Saptarshi Guha
Oh!Thanks much. Worked perfectly. Hadn't realized the importance of -Wall. Regards saptarshi On Thu, Sep 3, 2009 at 7:27 PM, Simon Urbanek wrote: > > On Sep 3, 2009, at 7:15 PM, Saptarshi Guha wrote: > >> Hello, >> I'm evaluating this expression >> expression({ for(x in 1:5){ .Call('rh_status','

Re: [Rd] Rscript and default packages

2009-09-03 Thread Duncan Murdoch
On 03/09/2009 1:52 PM, Romain Francois wrote: On 09/03/2009 05:23 PM, Duncan Murdoch wrote: On 03/09/2009 9:53 AM, Romain Francois wrote: Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded when the script is invoked with Rscript. I know about the --d

Re: [Rd] Documentation for is.atomic and is.recursive

2009-09-03 Thread Duncan Murdoch
On 03/09/2009 5:36 PM, Stavros Macrakis wrote: On Wed, Sep 2, 2009 at 5:30 PM, Duncan Murdoch wrote: On 02/09/2009 4:10 PM, Stavros Macrakis wrote: ... I would nonetheless claim that the documentation as currently written is at best ambiguous and confusing, and would benefit from improved word

Re: [Rd] Running an expression 1MN times using embedded R

2009-09-03 Thread Simon Urbanek
On Sep 3, 2009, at 7:15 PM, Saptarshi Guha wrote: Hello, I'm evaluating this expression expression({ for(x in 1:5){ .Call('rh_status','x') }}) a million times from a program with R embedded in it. I have attached reproducible code that crashes with Program received signal SIGSEGV, Segmenta

[Rd] Running an expression 1MN times using embedded R

2009-09-03 Thread Saptarshi Guha
Hello, I'm evaluating this expression expression({ for(x in 1:5){ .Call('rh_status','x') }}) a million times from a program with R embedded in it. I have attached reproducible code that crashes with Program received signal SIGSEGV, Segmentation fault. 0x2b499ca40a6e in R_gc_internal (size

Re: [Rd] Including a binary Python Interpreter into a binary R-package for MS Windows

2009-09-03 Thread Guido van Steen
Sorry: I sent this email to r-de...@r-project.com. So that it got bounced. Hi Uwe, Thanks a lot for this answer. > Don't know Python on Windows so well, but why can't they > install it? You can also install R with limited user > privileges. The last time I worked with Python on MS Windows was

Re: [Rd] Documentation for is.atomic and is.recursive

2009-09-03 Thread Stavros Macrakis
On Wed, Sep 2, 2009 at 5:30 PM, Duncan Murdoch wrote: > On 02/09/2009 4:10 PM, Stavros Macrakis wrote: ... >> I would nonetheless claim that the documentation as currently written >> is at best ambiguous and confusing, and would benefit from improved >> wording. > > A claim that documentation would

Re: [Rd] R devel repository tarball naming issue

2009-09-03 Thread Hervé Pagès
Thanks Martin! The latest snapshot (R-devel_2009-09-03.tar.gz) looks OK. FYI the tarballs with a broken name are still here (ftp://ftp.stat.math.ethz.ch/Software/R/): R-devel_.tar.bz2 R-devel_.tar.gz Cheers, H. Martin Maechler wrote: "HP" == Hervé Pagès on Wed, 02 Sep 2009 15:21:11

Re: [Rd] Suggestion: Allow packages to add additional information to sessionInfo()

2009-09-03 Thread Henrik Bengtsson
On Thu, Sep 3, 2009 at 10:38 AM, Kevin R. Coombes wrote: > [1] I agree that sessionInfo() can be taken further. > [2] I even more strongly agree that it would be a bad idea to allow packages > to add features that cause the base sessionInfo() function to fail. > > Why not add an extra function call

Re: [Rd] Rscript and default packages

2009-09-03 Thread Romain Francois
On 09/03/2009 05:23 PM, Duncan Murdoch wrote: On 03/09/2009 9:53 AM, Romain Francois wrote: Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded when the script is invoked with Rscript. I know about the --default-packages argument, but I was wondering

Re: [Rd] Suggestion: Allow packages to add additional information to sessionInfo()

2009-09-03 Thread Kevin R. Coombes
[1] I agree that sessionInfo() can be taken further. [2] I even more strongly agree that it would be a bad idea to allow packages to add features that cause the base sessionInfo() function to fail. Why not add an extra function called something like "packageSessionInfo()" that would provide th

Re: [Rd] Suggestion: Allow packages to add additional information to sessionInfo()

2009-09-03 Thread Henrik Bengtsson
On Thu, Sep 3, 2009 at 10:16 AM, Gabor Grothendieck wrote: > The danger is that it could introduce bugs into the process > of reporting bugs. If you mean that sessionInfo() will result in an error, that is easily solved by a tryCatch() statement. Timeouts are harder. One can also consider provid

Re: [Rd] Suggestion: Allow packages to add additional information to sessionInfo()

2009-09-03 Thread Gabor Grothendieck
The danger is that it could introduce bugs into the process of reporting bugs. On Thu, Sep 3, 2009 at 1:05 PM, Henrik Bengtsson wrote: > Hi, > > sessionInfo() has been proven really useful, but you still often have > to ask for additional information in order to help troubleshooting. > For instanc

[Rd] Suggestion: Allow packages to add additional information to sessionInfo()

2009-09-03 Thread Henrik Bengtsson
Hi, sessionInfo() has been proven really useful, but you still often have to ask for additional information in order to help troubleshooting. For instance, for troubleshooting the aroma.affymetrix, it is very helpful to know what the current working directory is, for other packages certain system

[Rd] Turn of -O2 during package build

2009-09-03 Thread Saptarshi Guha
Hello, I'm using a Makevars.in file and running my code through gdb. I understand i should turn of -O2, but R's makeconf overrides my settings /ln/meraki/custom/lib64/R/etc/Makeconf:112: warning: overriding commands for target `.cc.o' in Makevars.in .cc.o: g++ -g ${PKG_CXXFLAGS} ${PKG_LI

Re: [Rd] Turn of -O2 during package build

2009-09-03 Thread Saptarshi Guha
My own response: use %.o: %.cc and not the form given below. Regards S On Thu, Sep 3, 2009 at 12:59 PM, Saptarshi Guha wrote: > Hello, > I'm using a Makevars.in file and running my code through gdb. I > understand i should turn of -O2, but R's makeconf overrides my > settings > > /ln/meraki/custom

Re: [Rd] clearNames and unname

2009-09-03 Thread Douglas Bates
On Thu, Sep 3, 2009 at 10:02 AM, Martin Maechler wrote: >> "MM" == Martin Maechler >>     on Thu, 3 Sep 2009 16:14:24 +0200 writes: > >> "HW" == Hadley Wickham >>     on Thu, 3 Sep 2009 08:16:27 -0500 writes: > >    HW> Just noticed these two functions (clearNames is stats and unn

Re: [Rd] force & identity

2009-09-03 Thread Roger Peng
Given that the two functions (although identical) serve different purposes and are in a sense unrelated, it's not clear that a See Also is needed (and in fact might be confusing). -roger On Thu, Sep 3, 2009 at 9:17 AM, Hadley Wickham wrote: > Similarly, force & identity are identical (although wi

Re: [Rd] --enable-memory-profiling at configuration (compilation) time?

2009-09-03 Thread Dirk Eddelbuettel
On 3 September 2009 at 13:40, Corrado wrote: | Dear Rfriends, | | what is the option --enable-memory-profiling at configuration (just before build | + install) time? | | I did not find mention of it in the R admin manual (http://cran.r- | project.org/doc/manuals/R-admin.html). Try the 'R Exte

Re: [Rd] Rscript and default packages

2009-09-03 Thread Duncan Murdoch
On 03/09/2009 9:53 AM, Romain Francois wrote: Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded when the script is invoked with Rscript. I know about the --default-packages argument, but I was wondering if there was a mechanism to embed this inform

Re: [Rd] clearNames and unname

2009-09-03 Thread Martin Maechler
> "MM" == Martin Maechler > on Thu, 3 Sep 2009 16:14:24 +0200 writes: > "HW" == Hadley Wickham > on Thu, 3 Sep 2009 08:16:27 -0500 writes: HW> Just noticed these two functions (clearNames is stats and unname in HW> base) that do the same thing. MM> clearName

Re: [Rd] clearNames and unname

2009-09-03 Thread Martin Maechler
> "HW" == Hadley Wickham > on Thu, 3 Sep 2009 08:16:27 -0500 writes: HW> Just noticed these two functions (clearNames is stats and unname in HW> base) that do the same thing. clearNames looks like an accident. unname() has existed for much longer {and as someone else said},

[Rd] Rscript and default packages

2009-09-03 Thread Romain Francois
Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded when the script is invoked with Rscript. I know about the --default-packages argument, but I was wondering if there was a mechanism to embed this information within the script itself Romain -- Rom

Re: [Rd] clearNames and unname

2009-09-03 Thread Henrique Dallazuanna
Hadley, clearNames don't work with matrices: m <- matrix(1:9, ncol = 3, dimnames = list(letters[1:3], letters[1:3])) clearNames(m) unname(m) On Thu, Sep 3, 2009 at 10:16 AM, Hadley Wickham wrote: > Just noticed these two functions (clearNames is stats and unname in > base) that do the same t

Re: [Rd] Package names

2009-09-03 Thread Henrik Bengtsson
2009/9/3 Uwe Ligges : > > > Hadley Wickham wrote: >> >> Currently, writing R extensions states: "The ‘Package’ and ‘Version’ >> fields give the name and the version of the package, respectively. The >> name should consist of letters, numbers, and the dot character and >> start with a letter. " >> >

Re: [Rd] Package names

2009-09-03 Thread Uwe Ligges
Hadley Wickham wrote: Currently, writing R extensions states: "The ‘Package’ and ‘Version’ fields give the name and the version of the package, respectively. The name should consist of letters, numbers, and the dot character and start with a letter. " Now that _ is no longer an assignment oper

Re: [Rd] Package names

2009-09-03 Thread Hadley Wickham
>> Currently, writing R extensions states: "The ‘Package’ and ‘Version’ >> fields give the name and the version of the package, respectively. The >> name should consist of letters, numbers, and the dot character and >> start with a letter. " > >> Now that _ is no longer an assignment operator, coul

Re: [Rd] Package names

2009-09-03 Thread Kurt Hornik
> Hadley Wickham writes: > Currently, writing R extensions states: "The ‘Package’ and ‘Version’ > fields give the name and the version of the package, respectively. The > name should consist of letters, numbers, and the dot character and > start with a letter. " > Now that _ is no longer an a

[Rd] force & identity

2009-09-03 Thread Hadley Wickham
Similarly, force & identity are identical (although with different semantic connotations). Would be nice to have a see also from each. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] clearNames and unname

2009-09-03 Thread Hadley Wickham
Just noticed these two functions (clearNames is stats and unname in base) that do the same thing. Hadley -- http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Package names

2009-09-03 Thread Hadley Wickham
Currently, writing R extensions states: "The ‘Package’ and ‘Version’ fields give the name and the version of the package, respectively. The name should consist of letters, numbers, and the dot character and start with a letter. " Now that _ is no longer an assignment operator, could it be added to

Re: [Rd] Depth of protection stack?

2009-09-03 Thread Simon Urbanek
On Sep 2, 2009, at 22:28 , Saptarshi Guha wrote: Hello, Is there a way, in C, to find how deep my current protection stack is(apart from keeping a count). I know the default nested size is 50,000 and because of some coding error i think i'm reaching it. Is there a way to find out the curr

Re: [Rd] How to ship R scripts with R packages ?

2009-09-03 Thread Romain Francois
On 09/03/2009 02:46 PM, Duncan Murdoch wrote: On 03/09/2009 7:47 AM, Romain Francois wrote: On 09/02/2009 01:13 PM, Duncan Murdoch wrote: Romain Francois wrote: Hello, (This is a remix of this previous thread: https://stat.ethz.ch/pipermail/r-devel/2009-August/054264.html , but with a concre

Re: [Rd] How to ship R scripts with R packages ?

2009-09-03 Thread Duncan Murdoch
On 03/09/2009 7:47 AM, Romain Francois wrote: On 09/02/2009 01:13 PM, Duncan Murdoch wrote: Romain Francois wrote: Hello, (This is a remix of this previous thread: https://stat.ethz.ch/pipermail/r-devel/2009-August/054264.html , but with a concrete example) I am developing some packages that

Re: [Rd] How to ship R scripts with R packages ?

2009-09-03 Thread Dirk Eddelbuettel
On 3 September 2009 at 13:47, Romain Francois wrote: | On 09/02/2009 01:13 PM, Duncan Murdoch wrote: | > I think exec is a reasonable place to put the script. If you don't want | > to type that long command above, why not put it in a small function in | > the package? E.g. define | > | > antR <- f

[Rd] --enable-memory-profiling at configuration (compilation) time?

2009-09-03 Thread Corrado
Dear Rfriends, what is the option --enable-memory-profiling at configuration (just before build + install) time? I did not find mention of it in the R admin manual (http://cran.r- project.org/doc/manuals/R-admin.html). Regards -- Corrado Topi Global Climate Change & Biodiversity Indicators A

Re: [Rd] How to ship R scripts with R packages ?

2009-09-03 Thread Romain Francois
On 09/02/2009 01:13 PM, Duncan Murdoch wrote: Romain Francois wrote: Hello, (This is a remix of this previous thread: https://stat.ethz.ch/pipermail/r-devel/2009-August/054264.html , but with a concrete example) I am developing some packages that contain scripts (for Rscript) and would like t

Re: [Rd] names<- in data.frame (PR#13916)

2009-09-03 Thread ripley
It does work correctly: > names(tdf) [1] "" "" The thing you have overlooked is that data frames are required to have non-empty (not 'zero-length': yours has length 2) names, and the print method has created some (as data.frame will if you give unnamed arguments). Please be careful to disting

Re: [Rd] S4 Generics and NAMESPACE : justified warning ?

2009-09-03 Thread Yohan Chalabi
"MM" == Martin Maechler on Mon, 31 Aug 2009 14:51:16 +0200 MM> Yes, I agree, unjustified in your case. MM> The question is: is there a patch which does differentiate MM> between your situation and Martin's scenario -- or does your MM> patch already do that? Hi Martin, Tha

Re: [Rd] R devel repository tarball naming issue

2009-09-03 Thread Martin Maechler
> "HP" == Hervé Pagès > on Wed, 02 Sep 2009 15:21:11 -0700 writes: HP> Hi, HP> Same here, we rely on these snapshots for the Bioconductor build system. HP> ftp://ftp.stat.math.ethz.ch/Software/R/ HP> Now there seems to be a file (or symlink) named R-devel.tar.gz (not

Re: [Rd] Including a binary Python Interpreter into a binary R-package for MS Windows

2009-09-03 Thread Uwe Ligges
gvst...@yahoo.com wrote: 2009/8/30 Uwe Ligges : [snip] Guido van Steen wrote: [snip] Something that interests me too: What about R's policy with respect to including binary files? I saw that developers should include a file [snip] Please do not include binary files and carefully watch for