Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-09-01 Thread Davor Cubranic
emedy > applies (http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X): > > 'Configure option --with-internal-tzcode is the default on OS X, as the > system implementation of time zones does not work correctly for times > before 1902 or a

Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-09-01 Thread Davor Cubranic
dating the port to the current release: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195783. I've posted the summary of this thread there, thanks for your help. Davor Prof Brian Ripley writes: > On 31/08/2015 16:26, Davor Cubranic wrote: >> Prof Brian Ripley writes: >> >&

Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-08-31 Thread Davor Cubranic
Prof Brian Ripley writes: > Second, we don't have all the pertinent information such as the > configure options used and the architecture (x86_64?). I am going to > have to guess none as none were mentioned, but using --enable-R-shlib > would be pertinent. > > On

[Rd] Admin manual bug: packages installed on OS X

2014-03-03 Thread Davor Cubranic
The administration manual for the current release of R says in section 4.2, Uninstalling under OS X: "The installation consisted of three Apple packages: org.r-project.R.Leopard.fw.pkg, org.r-project.R.Leopard.GUI.pkg and org.r-project.x86_64.tcltk.x11”. This is not the case with R 3.0.2 on OS

Re: [Rd] How to debug an R package (with C code)

2014-01-19 Thread Davor Cubranic
: > On Sun, Jan 19, 2014 at 1:53 PM, Davor Cubranic wrote: > On Jan 17, 2014, at 6:17 AM, Gábor Csárdi wrote: > > > Small note: if you are using a recent version of OSX, then gdb is > > essentially useless, but you can use llvm, which is nicer in many respects, > >

Re: [Rd] How to debug an R package (with C code)

2014-01-19 Thread Davor Cubranic
On Jan 17, 2014, at 6:17 AM, Gábor Csárdi wrote: > Small note: if you are using a recent version of OSX, then gdb is > essentially useless, but you can use llvm, which is nicer in many respects, > anyway. What do you mean by this? Gdb is a debugger, and LLVM is a compiler infrastructure. Perha

Re: [Rd] eigen(symmetric=TRUE) for complex matrices

2013-06-18 Thread Davor Cubranic
On 13-06-18 12:57 AM, peter dalgaard wrote: Coercing A to a complex matrix should make no difference, but makes >eigen() return the wrong answer: > >>min(eigen(A+0i,T,T)$values) >[1] -0.359347 >> > >This is very, very wrong. Yep. I see this also on 10.6/7 (Snow Leopard, Lion) and 3.0.x, but

Re: [Rd] Recommended way to call/import functions from a Suggested package

2013-02-25 Thread Davor Cubranic
I don't see any warnings if MASS is listed in Suggests in the DESCRIPTION. Davor On 2013-02-25, at 1:28 PM, Hadley Wickham wrote: >> To summarize, it appears that the only way to call functions from a >> suggested package is by using either 'require' (which will dynamically >> attach it) or the

Re: [Rd] Recommended way to call/import functions from a Suggested package

2013-02-25 Thread Davor Cubranic
I haven't gotten any complaints from "R CMD check" when I used Simon's suggestion, even with "--as-cran" flag. Hadley's suggestion to use 'require' also works, and its side-effect of attaching the other package can in some applications be seen by the end user as a nice bonus, so I'll probably ha

Re: [Rd] Recommended way to call/import functions from a Suggested package

2013-02-25 Thread Davor Cubranic
On 2013-02-22, at 10:23 PM, Berwin A Turlach wrote: >> On Feb 22, 2013, at 6:39 PM, David Winsemius wrote: > [...] >>> I've always wondered: How does lattice manage to use grid functions >>> without putting them on the search path? > > Because lattice imports the grid package and has a NAMESPACE

[Rd] Recommended way to call/import functions from a Suggested package

2013-02-22 Thread Davor Cubranic
If in my package "Foo" I call a function from another package "Bar" if it's available, according to R-exts, this sounds like I should include "Suggests: Bar" in package Foo's description. But the manual is silent on how to treat Bar's namespace. Should I import it? If so, should this be conditio

Re: [Rd] Depends/Imports/Suggest/Enhence

2012-11-06 Thread Davor Cubranic
On 2012-11-06, at 9:49 AM, Uwe Ligges wrote: > On 06.11.2012 17:55, Christophe Genolini wrote: >> >>> "Imports" means that symbols are imported form the namespace, so they >>> are mandatory for the package to operate. "Suggests" means that >>> symbols from the package are not required, but they a

Re: [Rd] x11 icon and class

2012-06-12 Thread Davor Cubranic
On 2012-06-07, at 12:05 PM, Philip Johnson wrote: > The X11 device driver does not provide the X window manager with an icon > (_NET_WM_ICON) or, under some circumstances, with a class (WM_CLASS). This > hinders usability under the new stable version of Ubuntu, which has a (new) > user interfac

Re: [Rd] [R] Version control (git, mercurial) for R packages

2012-02-10 Thread Davor Cubranic
On February 10, 2012 09:11:35 AM Rainer M Krug wrote: > But what I was thinking about (in my other post as well) is to include > github (or any other git repo provider) into r-forge for the automatic > creation of packages. > > So is there an easy way to kind of push a certain revision up to > r-f

Re: [Rd] Best practices for writing R functions

2011-07-26 Thread Davor Cubranic
On 2011-07-23, at 5:57 AM, Alireza Mahani wrote: > Another trick to reduce verbosity of code (and focus on algorithm logic > rather than boilerplate code) is to maintain a global copy of variables (in > the global environment) which makes them visible to all functions (where > appropriate, of cour

Re: [Rd] Fwd: Understanding R's "Environment" concept

2011-07-18 Thread Davor Cubranic
On 2011-07-18, at 11:52 AM, Nipesh Bajaj wrote: > Hi all, I am trying to understand the R's "environment" concept > however the underlying help files look quite technical to me. Can > experts here provide me some more intuitive ideas behind this concept > like, why it is there, what exactly it is

Re: [Rd] Syntactically valid names

2011-07-05 Thread Davor Cubranic
On July 5, 2011 04:59:16 PM Hadley Wickham wrote: > That's not a syntactically valid name - you use backticks to refer to > names that are not syntactically valid. I was too loose in my terminology: I meant that `x prime` is a valid name, but as you said, it is not syntactically valid. Davor __

Re: [Rd] Syntactically valid names

2011-07-05 Thread Davor Cubranic
On June 30, 2011 01:37:57 PM Hadley Wickham wrote: > Is there any easy way to tell if a string is a syntactically valid name? [...] > > One implementation would be: > > is.syntactic <- function(x) x == make.names(x) > > but I wonder if there's a more elegant way. This is without quoting, right

Re: [Rd] cerr and cout not working calling c++ from R

2011-05-06 Thread Davor Cubranic
On 2011-05-06, at 11:41 AM, Dirk Eddelbuettel wrote: > | I¹m trying to call some of my c++ code from R and seem to be having an issue > | with streams, although that¹s just one obvious sign of something different > | in performance between calling the same function from main in c++ vs. > | calling

Re: [Rd] Wish there were a "strict mode" for R interpreter. What

2011-04-11 Thread Davor Cubranic
On 2011-04-09, at 2:08 PM, Ted Harding wrote: > I think the right thing to so is to introduce the students to the > basics of scoping, early in the process of learning R. I know the basics of scoping perfectly well, but that doesn't stop me from occasionally misspelling a variable name that only

Re: [Rd] Phrase "package writer" in R-exts

2011-04-01 Thread Davor Cubranic
On 2011-04-01, at 12:17 PM, Ted Byers wrote: > Note, while I see the author's > responsibility to write perfectly (or at least try), the reader also has a > responsibility to work at determining what the author meant by what he or > she wrote. Most people don't read reference manuals to engage wi

[Rd] Phrase "package writer" in R-exts

2011-04-01 Thread Davor Cubranic
In a conversation with a programmer new to writing R packages, he mentioned that he was very confused by phrase "package writer" used in the document, and said that he "[was] literally imagining some sort of function that writes something related to packages". I can see his point: not only is i

Re: [Rd] another import puzzle

2011-03-27 Thread Davor Cubranic
On 03/26/2011 12:19 PM, Ben Bolker wrote: > ["Namespace dependency not required: lme4a"] > I think "dependence" works better than "dependency" in English, too I'm not a native English speaker, but "dependency" is a pretty standard software engineering term for this kind of relationship. I.e., "lm

Re: [Rd] "+" operator on characters revisited

2011-01-24 Thread Davor Cubranic
On 2011-01-23, at 4:34 AM, Gabor Grothendieck wrote: > On Sun, Jan 23, 2011 at 6:56 AM, Vitalie S. wrote: >> Gabor Grothendieck writes: >> >>> Also the gsubfn supports quasi perl style string interpolation that >>> can sometimes be used to avoid the use of paste in the first place. >>> Just pre

Re: [Rd] R5 reference classes: how to initialize exactly?

2010-11-22 Thread Davor Cubranic
>> Just a clarification for posterity - R5 has nothing to do with the new >> reference classes. It's not even an official name, but informally it's a >> collection of ideas for an entirely new object system that can replace >> both S3 and S4 (not that it will but it should be seen as having the >>

Re: [Rd] gomp library with Rtools212

2010-11-19 Thread Davor Cubranic
On November 19, 2010 07:58:40 am Marko Robnik-Šikonja wrote: > Dear developers, > > I am a maintainer of the CORElearn package which uses OpenMP > multithreading to speed up some computations. When producing a new > release we tested the package with the latest R 2.12.0. On Linux the > package wor

Re: [Rd] problem building R from svn repo

2010-11-14 Thread Davor Cubranic
> > You should not run configure or make with sudo. If you need to > > install system-wide, you only need to run make install under sudo, > > like > > ./configure > > make > > sudo make install > > I thougt so, and did so first. But that generated other errors!, > which was killed by using sudo.

Re: [Rd] LAPACK libraries improperly linked

2010-11-14 Thread Davor Cubranic
On November 14, 2010 10:05:24 am Ron Burns wrote: > [ 41 ] (ron) ls /usr/lib/libatlas* > /usr/lib/libatlas.so.3gf@ > [ 42 ] (ron) ls /usr/lib/libf77blas* > /usr/lib/libf77blas.so.3gf@ > > so these are there and linked OK and there is no Rlapack. These are soft links. Could you do an 'l

Re: [Rd] Missing libpthread in RTools

2010-10-19 Thread Davor Cubranic
On 2010-10-15, at 4:39 PM, Duncan Murdoch wrote: > On 15/10/2010 4:53 PM, Davor Cubranic wrote: >> It appears that Mingw gcc included in RTools is missing a dependent >> library. If I compile a program with '-lgomp' switch (for OpenMP >> support), I get a error

[Rd] Missing libpthread in RTools

2010-10-15 Thread Davor Cubranic
It appears that Mingw gcc included in RTools is missing a dependent library. If I compile a program with '-lgomp' switch (for OpenMP support), I get a errors about undefined references to functions like '_imp__pthread_mutex_destroy'. Adding the '-static' switch, I get the following error:

Re: [Rd] small syntax suggestion

2010-08-24 Thread Davor Cubranic
On August 23, 2010 01:27:24 pm Philippe Grosjean wrote: > They have to write such a code like this: > > if (x < -3) do_something > > That way, there is no ambiguity. Don't you think it's important to > write clear code, including by using spaces where it makes it easier > to read,... and less amb

Re: [Rd] small syntax suggestion

2010-08-23 Thread Davor Cubranic
On 2010-08-23, at 6:15 AM, Barry Rowlingson wrote: > On Sun, Aug 22, 2010 at 4:33 PM, ivo welch wrote: >> I have found that my students often make the mistake of >> mixing up comparisons and assignments with negative numbers: >> >> if (x<-3) do_something; > > If you tell your students not to u