On 28 January 2012 at 16:52, Uwe Ligges wrote:
|
|
| On 27.01.2012 15:57, Dirk Eddelbuettel wrote:
| >
| > On 12 January 2012 at 12:12, Hervé Pagès wrote:
| > | Hi Dirk,
| > |
| > | On 01/11/2012 11:42 AM, Dirk Eddelbuettel wrote:
| > |>
| > |> R CMD check real
R> seq(as.Date(Sys.Date()), by="-1 months", length=6)
[1] "2012-01-31" "2011-12-31" "2011-12-01" "2011-10-31" "2011-10-01"
"2011-08-31"
R>
Notice how October appears twice.
Now, date arithmetic is gruesome but the documentation for seq.Date et al
does not hint it wouldn't honour the by= argume
On 31 January 2012 at 15:17, Duncan Murdoch wrote:
| On 12-01-31 2:56 PM, Dirk Eddelbuettel wrote:
| >
| > R> seq(as.Date(Sys.Date()), by="-1 months", length=6)
| > [1] "2012-01-31" "2011-12-31" "2011-12-01" "2011-10-31" "2011-1
On 31 January 2012 at 15:28, Sarah Goslee wrote:
| As Duncan pointed out, this is documented in ?seq.POSIXt:
|
| Using ‘"month"’ first advances the month without changing the day:
| if this results in an invalid day of the month, it is counted
| forward into the next month: see the
On 1 February 2012 at 10:24, Dave Pugmire wrote:
| Hi,
| I'm new to R, and am trying to embed R into another application.
| I'm calling gev.fit() from the ismev package, and it is crashing somewhere
| inside it.
| gdb is not catching it, and valgrind is not showing any memory corruption
| issues.
On 1 February 2012 at 20:23, Uwe Ligges wrote:
|
|
| On 01.02.2012 20:10, Robert M. Flight wrote:
| > Doing package development on a Windows 7 machine, and I want to tell R
| > check not to worry about the "suggested" packages.
| >
| > I realize this can be done using the ~/.R/check.Renviron fil
On 6 February 2012 at 12:45, Jeroen Ooms wrote:
| After upgrading my servers to 2.14, log files were filled warnings
| that 'mem.limits' has been deprecated and to use gc instead. After
| reading the NEWS for R 2.14.0 and PR#14795 I learned that it is
| actually deprecated without replacement.
|
On 8 February 2012 at 19:26, Uwe Ligges wrote:
|
|
| On 07.02.2012 19:13, Hadley Wickham wrote:
| > Hi all,
| >
| > Am I using the correct syntax to set a custom R_LIBS when running R
| > CMD INSTALL from the command line?
| >
| > I get:
| >
| > R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rap
On 8 February 2012 at 20:05, Uwe Ligges wrote:
| Anyway, this won't work under a Windows shell, I believe. At least, I do
| not know how to set an env variable and run RCMD INSTALL in a Windows
| shell as a one liner - independent of R.
FWIW this issue was addressed by Oleg years ago in cfuncti
Trevor,
On 10 February 2012 at 15:04, Trevor Davis wrote:
| > So is there a safe fallback or not? Should I install texlive-fonts-extra
too
| > when building?
| >
| > Dirk
| >
You quoted a message (skipping its date) that is rather old,
R> difftime(Sys.Date()-1, as.Date("2011-09-23"))
On 13 February 2012 at 16:09, Lorenzo wrote:
| Hello all,
|
| I'm trying hard to make R CMD SHLIB work on Windows XP (32-bit) - please
Have a look at the countless examples and hundreds of unit tests in the Rcpp
package. Almost all of them work by using the inline package to compile,
link and l
Ben,
On 17 February 2012 at 11:31, Ben Bolker wrote:
|
| I'm sure I'm being an absolute bonehead (again), but can someone
| suggest what I might be doing wrong?
|
| Trying to build latest r-devel on Ubuntu 10.04; as recommended in
Happy to take this off-list --- I do build every now and the
On 19 February 2012 at 14:45, Paul Gilbert wrote:
| I am trying to add
|
| #include
|
| to a .c file in one of my package, so I can call error() without a
You may want to turn 'remapping' on which hides all R functions behind a
prefix of Rf_ so that error() becomes Rf_error(). Define R_NO_RE
On 19 February 2012 at 15:08, Paul Gilbert wrote:
|
|
| On 12-02-19 02:59 PM, Dirk Eddelbuettel wrote:
| >
| > On 19 February 2012 at 14:45, Paul Gilbert wrote:
| > | I am trying to add
| > |
| > | #include
| > |
| > | to a .c file in one of my package, so I can c
On 24 February 2012 at 00:27, Suraj Gupta wrote:
| I don't think that is it. My startup message is currently in .onAttach and I
| still see startup message from packages that I have moved from Imports to
| Depends.
| Dirk?
There are / were are few issues intertwined in my case, and yours may dif
Hi Pratibha,
May I suggest to move this over to the rcpp-devel list (where you need to be
subscribed to post)? I am setting an appropriate Reply-To: now, we should
then also remove the CC for r-devel.
On 1 March 2012 at 11:05, Pratibha Rana wrote:
| Hi,
|
| I am using RInside for one of the a
Justin,
On 8 March 2012 at 11:06, Justin Talbot wrote:
| I've been working on an R performance academic project for the last
| couple years which has involved writing an interpreter for R from
| scratch and a JIT for R vector operations.
Cool. I think John mention that once or twice and I promp
On 18 March 2012 at 03:30, oliver wrote:
| Hello,
|
| when looking at "Writing R Extensions"
| with mem-allocation in mind, I wondered,
| which functions to use to substitute
| malloc(), calloc(), realloc() and strdup() and free().
|
| It looked like Calloc() or R_Calloc() might be useful for
|
On 18 March 2012 at 06:16, oliver wrote:
| > R> library(inline)
| > R>
| > R> f <- cfunction(signature(), verbose=TRUE, body='
| > +double *p = Calloc(5, double);
| [...]
|
| That line cleared the issue.
| Thank you for providing an example.
|
| When reading in the documentation I was not s
Awesome. I love the reference card. This will be useful.
But I couldn't resist recasting your final "silly" example into
a) inline use which I find generally easier than having to do R CMD SHLIB
followed by dyn.load()
b) a comparison with Rcpp which looks just about the same minus so
On 29 March 2012 at 07:58, Brian G. Peterson wrote:
| On Thu, 2012-03-29 at 16:52 +1300, Thomas Lumley wrote:
| > The 'No visible binding for global variable" is a good example. This
| > found some bugs in my 'survey' package, which I removed. There is
| > still one note of this type, which arise
On 7 April 2012 at 16:27, Thomas J. Leeper wrote:
| I'm currently working on a new package for R that interfaces with an API.
| Most of the package's functionality requires users to supply an access key
| that allows the package to work with the API. I want to display text
| immediately upon loadi
On 14 April 2012 at 20:45, Ben Bolker wrote:
|
| Does anyone have advice on how to instruct R CMD check to use a
| non-standard set of libraries? Here's the situation:
One way around is something like this:
edd@max:~$ tail -5 .R/check.Renviron
# edd Apr 2003 Allow local install in /usr/loc
On 18 April 2012 at 17:40, Nikolaos Bezirgiannidis wrote:
| Hi all,
|
| I am a PhD student and I am working on a C project that involves some
| statistical calculations. So, I tried to embed R into C, in order to
| call R functions from a C program. My program seems to get the correct
| r
On 24 April 2012 at 12:39, Duncan Murdoch wrote:
| On 24/04/2012 12:31 PM, oliver wrote:
| > Hello,
| >
| > what if I want to write a package mixed R/C-extension
| > and want to use code that is provided by other peoples packages?
| >
| > How for example can I use one of the provided wavelet packa
On 4 May 2012 at 00:07, Owe Jessen wrote:
| I am running into a wall getting my system to work with rcpp and inline.
| Following Dirk's advice on stackoverflow, I hope someone is able to help
| me.
There is a dedicated mailing list for Rcpp: rcpp-devel.
Please let us try to continue the di
On 4 May 2012 at 22:31, andre zege wrote:
| Simon, thanks for your comment. I guess there is no problem, i am
| apparently being lazy/busy and wondered if there is ready code that does
| it. You are right, i suppose -- i'll look at the c++ code for bigmatrix and
| will try to hack a solution.
Yo
On 6 May 2012 at 07:53, Duncan Murdoch wrote:
| On 12-05-06 6:43 AM, Duncan Murdoch wrote:
| > On 12-05-05 10:39 PM, Joshua Ulrich wrote:
| >> Hi all,
| >>
| >> I experienced a crash in R-2.15.0 on 32-bit Windows XP (sessionInfo
| >> below) when running the piece of code below. I cannot replicate
On 9 May 2012 at 00:35, Zalan Szakolci wrote:
| Hi there,
|
| I am trying to interface c++ code in R and make a package. With R CMD SHLIB
| the dll was created, but when I try R CMD check, I am getting 'undefined
| reference to..' linkage error messages.
|
| The relevant c++ source from conf-inf
On 26 May 2012 at 14:00, Simon Urbanek wrote:
| [...] the real answer is use .Call() instead.
Maybe Kurt could add something to that extent to the R FAQ ?
Dirk
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| __
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of Rcpp and related packages, you get to keep the pieces.
That said, I'd be interested in supporting it eventually but I guess I want
to first understand better how/if it is supported (on Linux) by R itself.
Dirk
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuette
ybe you did more 'funky' stuff you now need to
consider.
Dirk, who thinks this should have been on r-sig-debian all along
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to read in Java? Why don't you use a format that Java can read
easily - such as JSON?
Or even use something designed for fast, large scale data serialization such
as Google Protocol Buffers.
You get code generated for Java from using the Google library / binaries for
it, and the R package RProtoBuf will provide the other side.
Dirk
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e, just plain C, without external dependencies. If your
package has other languages or dependencies, try to find something that
matches its profile. The compare the setup, and the output created when
running the relevant commands.
Dirk
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.e
#x27;print(search())'
[1] ".GlobalEnv" "package:methods" "Autoloads" "package:base"
edd@max:~$
Dirk
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On 2 July 2012 at 12:00, Dirk Eddelbuettel wrote:
|
| On 2 July 2012 at 09:23, Charlie Friedemann wrote:
| | The error message you are getting makes it rather clear what the problem
is.
| | R is unable to find the function 'hasArg'. As the hasArg function is part
| | of the packag
e/universe amd64 Packages
edd@max:~$
Dirk, one of several volunteers making sure the above "just works"
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| Hadley
|
|
| --
| Assistant Professor / Dobelman Family Junior Chair
| Department of Statistics / Rice University
| http://had.co.nz/
|
| __
| R-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
Dirk Eddelbuettel | e..
On 25 July 2012 at 18:46, Dirk Eddelbuettel wrote:
|
| On 25 July 2012 at 15:56, Hadley Wickham wrote:
| | Hi all,
| |
| | Recently, when compiling R packages containing C code, I've started
| | getting the following error:
| |
| | * installing to library ‘/Users/hadley/R’
| | * insta
illage
from code under development. To keep abreast of these changes, I follow the
RSS feed Duncan set up a few years ago -- it is also as html at
http://developer.r-project.org/blosxom.cgi/R-devel
and summarizes changes committed to the NEWS file, ie high-level changes
worth knowing about
cases.
Alternatively, you just depend on the GSL. Many packages on CRAN do, and the
Windows build infrastructure provides it.
Dirk
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https://stat.et
http://cran.r-project.org";)); print(dim(AP)[1])'
[1] 3988
edd@max:~$
There is a bug somewhere if another count gives 4001.
Dirk
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On 23 August 2012 at 20:42, Prof Brian Ripley wrote:
| On 23/08/2012 20:30, Dirk Eddelbuettel wrote:
| >
| > R-release:
| >
| > edd@max:~$ r -e 'AP <-
available.packages(contrib.url("http://cran.r-project.org";)); print(dim(AP)[1])'
| > [1] 3988
| > ed
packages lacking the DLLs and instruct
the users to get them from somewhere else, but that is at the same rather
error prone (as you will lack all the built-time checks you would have with
source code, as well as a better assurrance that compatible tools are used)
and distasteful as CRAN is
list of exclude patterns in file `.Rinstignore' in the top-level source
directory. These patterns should be Perl-like regular expressions (see
the help for `regexp' in R for the precise details), one per line, to
be matched(10) against the file and directory paths, e.g.
rm" "apropos"
| [6] "aregexec"
|
| Is this a temporary glitch, or is there something new and specific to
| "datasets" ?
Seems to be on purpose -- here is its NAMESPACE file
# This package exports nothing (it uses lazydata)
# exportPattern(".&qu
sed that at the time. Something like this ought
be to implemented in R proper.
In Rcpp, I am now using a similar environment-variable-based approach, and it
doesn't scale particularly well if every (large) package does its own thing.
Dirk
| /Henrik
--
Dirk Eddelbuettel
if()}.
+This is the function used by @R{}'s @code{round()}.
@end deftypefun
@deftypefun double ftrunc (double @var{x})
edd@max:/tmp$
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eally is CRAN, and as it is already being
accounted for, we may as well add a hook we all can use to disable some tests
so that the runtime at CRAN remains within desired bounds. But that is the
special case, and --as-cran should enable it (unless overridden).
Dirk
--
Dirk Eddelbuettel | e...@debian
On 4 September 2012 at 17:26, Duncan Murdoch wrote:
| On 04/09/2012 5:14 PM, Dirk Eddelbuettel wrote:
| > An add-on argument to the already established option --as-cran may be the
| > best.
| >
| > And to iterate, what bugs me is that for _me_ on _my_ machine developing
_my_
| >
[ Email resend 1 of 3 ]
From: Dirk Eddelbuettel
To: R-core
CC: Philip Johnson , e...@debian.org
Subject: The X11 device patch
Date: Wed, 27 Jun 2012 11:53:13 -0500
R Core,
*Great* to see this bubble up in the NEWS aggregation:
2.15.1 patched NEW FEATURES
[ Email repost 2 of 3 ]
From: Dirk Eddelbuettel
To: R-core , Prof Brian D Ripley
Subject: Why fix all.equal for POSIXct at 1 msec?
Date: Sat, 28 Jul 2012 10:29:52 -0500
In R-devel as of today, the following simple loop
edd@max:~/svn/r-devel$ ~/bin/R-devel.sh
R Under
ponders similar questions at a different point in time.
Thanks, Dirk
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[ Email repost 3 of 3 ]
From: Dirk Eddelbuettel
To: R-devel org
Subject: [Patch] Minor glitch in 'Writing R Extensions'
Date: Mon, 3 Sep 2012 10:58:32 -0500
The (marked up in info mode) manual Writing R Extensions says in 6.1.3
-- Function: double fprec (double
s" as
you imply.
Now, if would of course help if CRAN could specify what "significant notes"
were ...
Dirk
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27;make one
initial upload' as you seem to read it. So I say go for it.
Quite a few people seem to push from R-Forge if I read another field in
the DESCRIPTION file (once on CRAN) correctly.
Dirk
--
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_
"R CMD check" for me as I prefer NOT to install packages in a
versioned path.
FWIW, defaulting to a versioned path is (to this no-longer-bemused user) as
much a permenent R bug (on Windoze) as the default installation into a path
with spaces.
Dirk
--
Dirk Eddelbuettel | e...@debian
(defining library paths) in
| $R_HOME/etc/Renviron.site
|
| Is it correct to directly edit Rcmd_environ or should it be modified
| only via other files? (A genuine question).
|
| On 17/10/2012 15:59, Dirk Eddelbuettel wrote:
| >
| > Is there a fundamental reason why I cannot set either
, which still fails in my setup as it doesn't
find the package -- whereas any normal R session does.
Dirk
|
| Kasper
|
| On Thu, Oct 18, 2012 at 10:12 AM, Dirk Eddelbuettel wrote:
| >
| > Keith,
| >
| > On 18 October 2012 at 09:14, Keith Jewell wrote:
| > | No reply in a
On 19 October 2012 at 12:39, Gavin Simpson wrote:
| On Thu, 2012-10-18 at 10:18 -0500, Dirk Eddelbuettel wrote:
| > Kasper,
| >
| > On 18 October 2012 at 10:41, Kasper Daniel Hansen wrote:
| > | I set my user libraries in .Rprofile for this very reason. I agree it
| > | is weird
packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
R> library(foo)
library(foo)
Loading required package: Rcpp
Loading required package: xts
Loading
o-examples' then R CMD check passes fine. So
the package seems fine.
e) No issues whatsoever on Linux.
More on Monday or Tuesday.
Thanks, Dirk
| Uwe
|
|
|
|
|
|
|
| On 19.10.2012 23:58, Dirk Eddelbuettel wrote:
| >
| > Hi Uwe,
| >
| > On 19 October 2012 at 19:
, no matter the Linux or X11 flavour. And that is what
Phil's patch does this: adds the feature no matter the X11 GUI or desktop
environment.
Dirk
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ailable information?
"Sort of" --- quoting from the top of the 'CRAN Repository Policy' page:
CRAN is maintained by the efforts of volunteers (the “CRAN team”) and
the resources of the R Foundation and the employers of those volunteers
(WU Wien, TU Dortmund, U
the differences between
-I
-L
-l
They may look the same, especially with a typewriter font, but trust me that
they are not.
Dirk
--
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() and .Call()
arguments. You are mixing both approaches here, which usually ends badly.
Do some more reading, and maybe study some existing (simpler) examples /
packages. You really do not need to engage OpenCV headers and libraries
before you understand the basics better.
Dirk
--
Dirk
More
involved schemes are of course possible too.
Naturally, I would be happy to work on patch if there was any indication that
the patch would be reviewed and possibly included.
With that: comments, please. Is this seen as sensible or deemed nutty and
off-limits?
Thanks, Dirk
--
Dirk Eddel
to do this with MPI, Qt, Wt, and (in SVN)
Boost.
Dirk
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fer for help from Elijah which should a)
be commended ("nice job!") and used but b) we should maybe try to think about
what other resources would help.
Dirk
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uble
vector.
Hope this helps, Dirk
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bout missing files? There does not
seem to be a limit on the disdain for svn among git users. Fascinating.
Dirk
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/13#n2012-12-13
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On 14 December 2012 at 18:07, Uwe Ligges wrote:
| without overhead of packages. The CRAN check times of > 4000 packages
| are typically a good indicator, and they are a bit slower for R-2.15.2
And sadly less so when you force us to turn tests off.
Dirk
--
Dirk Eddelbuettel | e...@debian.
On 14 December 2012 at 18:19, Uwe Ligges wrote:
|
|
| On 14.12.2012 18:11, Dirk Eddelbuettel wrote:
| >
| > On 14 December 2012 at 18:07, Uwe Ligges wrote:
| > | without overhead of packages. The CRAN check times of > 4000 packages
| > | are typically a good indicator, and they a
es up to
speed a while back when I needed to.
Not sure what to do about the CRAN docs though apart from pleading with
Martyn or whoever looks after the meta-information there.
Hth, Dirk
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuette
Jeroen has a package devoted to the sandboxing approach in conjunction with
the system-level AppArmor facility: RAppArmor. See
http://cran.r-project.org/web/packages/RAppArmor/index.html
and more details at
https://github.com/jeroenooms/RAppArmor#readme
Dirk
--
Dirk Eddelbuettel | e
no symbols!
|
| How can I compile a Windows package with "-O2 -g"?
a) [long way] By locally building R with such a configure flag
b) [shortcut] By editing the Makeconf file of the R installation used for
compiling, eg in $R_HOME/etc/Makeconf (or maybe Makeconf.win)
Dirk
--
D
n creating _stale_ and (even
worse) _disconnected_ copies which will never receive updates or fixes from
the _original author_ of that code.
Dirk
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from anyone.
|
| Looking to get a response here.
Wrong list.
GSoC for R has its own list, and this isn't it. AFAIK the GSoC 2013 has not
yet started, it will surely be announced.
Dirk
(past GSoC mentor and admin)
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Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelb
uot; ) )
}
and packages depending on Rcpp can then do this in the vignette header:
RcppBibfile <- sub("\\.bib$", "", Rcpp:::bib())
which gets used towards the end of the Rnw file as
\bibliography{\Sexpr{RcppBibfile}}
I think so far only one package is using
little later and is also current on Ubuntu.
So I suggest to use something like
Note also that for running @LaTeX{}, the Debian @acronym{GNU}/Linux, Fedora
and Solaris check systems on @acronym{CRAN} use current TexLive;
Thanks, Dirk
--
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.
Also look into './configure --help' to learn about different aspects of the
build which you can turn on or off. I keep a little shell script with my
prefered configuration to create a local build of r-devel from SVN.
Dirk
--
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very verboten place
(and no, I've never been bitten but yes I do make distclean too).
Dirk
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e contrib
| packages that need to compile library objects, right?
At the R 3.0.0 juncture I had to as the ABI broke (due to the many changes),
otherwise no. I only keep a handful of packages in the seperately managed
directory for r-devel.
Dirk
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on
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clude files [1]
Dirk
[1] Unless you also register every single C function which is clearly
impractical with a library as large as the GSL. See '5.4 Registering native
routines' and '5.8 Linking to other packages' in the usual "Writing R
Extensions" manual.
--
Dirk Ed
hich other Boost packages. Again, this works for _template_ based
Boost library and excludes eg Boost regex which needs linking. So this may
not help you if not to also link to Boost Graph.
Dirk
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Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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sync to r-recommended and *honestly* have no idea what your issue is.
I just rebuilt two days ago without an issue:
edd@max:~$ ~/bin/R-devel.sh --version|head -1
R Under development (unstable) (2013-03-15 r62262) -- "Unsuffered
Consequences"
Dirk
--
Dirk Eddelbuettel | e...@debia
you-know-what:
The `OS_type' field specifies the OS(es) for which the package is
intended. If present, it should be one of `unix' or `windows', and
indicates that the package can only be installed on a platform with
`.Platform$OS.type' having that value.
Dirk
--
D
rnings.
But in the long run I am happy they are there so that eg my system does not
get polluted with your .hg and .DS_Store files which are of zero use to me.
Warnings are your friends. Be nice to them.
Dirk
--
Dirk Eddelbuettel | e...@debian.org | htt
loads), and so does
OpenBabel. Maybe some wires get crossed. You may well have to dig down with
the debugger and see what assumptions / environment variables / ... are valid
or invalid between the working and non-working case.
Dirk
--
Dirk Eddelbuettel | e...@debian.org
what I think was that very same issue with
Rmpi as the OpenMPI libraries have there symbols split over several shared
libraries. But that was many many years ago and I have forgotten what we did
then ...
Dirk
| Kevin
|
|
| On 03/26/2013 06:54 AM, Dirk Eddelbuettel wrote:
| > On 25 March 2013
kage developers :)
I am also willing to help here as I do not like the fact that the generated
Rd file itself is broken. A hint from R Core that clean patches would be
taken would be welcomed...
[ And I often call package.skeleton() from a fresh session, that is pretty
close to creating an empty
tual machine or live DVD for me.
apt-get could you your friend too. And virtual machines are pretty easy,
like the virtd / kvm variant (on Linux) quite a bit.
Dirk
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Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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thers have done here; the
XML package is popular for it but the whole scheme is fraught with little
pitfalls as html very definitely is not a good format for data-delivery, and
an html page clearly is no API for data access.
Dirk
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Dirk Eddelbuettel | e...@debian.org | htt
n't part of the API you are on your own figuring out how they work
| > (the source code is available for this of course).
| >
| > Hope that helps,
| > ~G
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.1), 2, 3)
[1] 0.0523 0.1808 0.3483 0.5248 0.6875
Dirk
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wer from
C++ as we get when we call solve(X, y) in R.
Dirk
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