Re: [R-pkg-devel] GPL + other licence

I agree with Brian. This type of license is classified by the Free Software Foundation as "lax" or "permissive" because it does not prevent incorporation of the code into proprietary software. Here is what Richard Stallman has to say: https://www.gnu.org/licenses/ license-compatibility.en.html

Re: [Rd] Makevars CXX_STD variable ignored when no *.cpp files in src/

the C++ compiler is required. In the absence of any such files, the code to set the C++ compiler flags correctly was never run. Martyn On Fri, 2018-03-02 at 09:42 +, Martyn Plummer wrote: > You are not the first person to report this, but last time when I tried > it myself I

Re: [Rd] Makevars CXX_STD variable ignored when no *.cpp files in src/

You are not the first person to report this, but last time when I tried it myself I could not reproduce the bug. Let me try it again. Martyn On Fri, 2018-03-02 at 09:26 +0100, Radosław Piliszek wrote: > Hello! > > I might have found a bug in the way that R handles Makevars file when > building

Re: [Rd] Bug report - duplicate row names with as.data.frame()

On Thu, 2018-03-01 at 09:36 -0500, Ron wrote: > Hello, > > I'd like to report what I think is a bug: using as.data.frame() we can > create duplicate row names in a data frame. R version 3.4.3 (current stable > release). > > Rather than paste code in an email, please see the example formatted

Re: [R-pkg-devel] Package check help: Package required but not available

On Thu, 2018-03-01 at 16:05 +, David Stanley wrote: > Hi Everyone, > > I’m new to this list but hopefully you can help me. > > I’m working on updating my apaTables package (most recent code: https > ://github.com/dstanley4/apaTables) > > However, I’m encountering problems passing the CRAN

Re: [R-pkg-devel] Using C++11 and compilation in sub-directories together

On Wed, 2018-02-07 at 15:17 +0300, Alexander Loboda wrote: > Dear all, > > I'm trying to build a package that uses c++11 code and sub-directories > in src/ according to the "Writing R Extensions" manual, but it seems > like R CMD doesn't want to compile the code with c++11 flags when source >

Re: [R-pkg-devel] Licensing of an R package

that CRAN is legally entitled to distribute Windows and MacOS binaries. In any case, the vast majority of CRAN packages are not problematic as they are licenced under GPL or a GPL-compatible license without linkage to a non-free library. Martyn > Cheers, > > Chris > > >

Re: [R-pkg-devel] Licensing of an R package

On Fri, 2018-01-19 at 20:28 +, Chris Brien wrote: > Hi Dirk & Duncan, > > I too like GPL and I had thought that the situation was as Duncan > outlines. Consequently, I had licensed `foo' as GPL >= 2. > > However, because I have been unable to find a discussion of my case, > in spite of the

Re: [R-pkg-devel] Future location of Rtools?

On Wed, 2017-10-25 at 10:52 +0200, Uwe Ligges wrote: > > On 25.10.2017 10:48, "Jens Oehlschlägel" wrote: > > Good morning, > > > > Duncan has announced that he steps back from the maintenance of Rtools. > > Where will I find the new Rtools toolchain that complements Microsofts > > R-version? >

Re: [Rd] Illegal Logical Values

On Fri, 2017-10-20 at 14:01 +, brodie gaslam via R-devel wrote: > I'm wondering if WRE Section 5.2 should be a little more explicit > about misuse of integer values other than NA, 0, and 1 in LGLSXPs. > I'm thinking of this passage: > > > Logical values are sent as 0 (FALSE), 1 (TRUE) or

Re: [Rd] Duncan's retirement: who's taking over Rtools?

David, I think ideally we want to appoint a single person to take primary responsibility for the Windows builds. We are currently discussing this within R Core. We also recognize that Microsoft is a stakeholder in R for Windows. The same is true of other members of the R Consortium. Going

Re: [R-pkg-devel] loadMethod() not available with Rscript

On Wed, 2017-09-20 at 09:45 -0500, Dirk Eddelbuettel wrote: > Thierry, > > This has always been a considerable puzzle, and the source of some amusement, > to me. It is a clear design bug in Rscript because _code that would > otherwise work_ will not if it happens to rely on library(methods). S4

Re: [Rd] hpc r configure not recognizing zlib

You do not need to compile R from source on RHEL 6. If you enable the EPEL repository then you can install the binary RPM via yum. See https://fedoraproject.org/wiki/EPEL Tom Callaway, who maintains the Red Hat binaries of R, statically links up-to-date versions of bzip2, xz, pcre, and curl into

Re: [Rd] Question about R developpment

I would describe MRO as a distribution of R, in the same way that Fedora, Debian, SUSE etc are distributions of Linux. It is not fundamentally different from the version of R that you can download from CRAN but the binary builds offer some specific features: 1) The binary build is linked to

Re: [Rd] Getting an R bugzilla account

Thanks for your help Nathan. I have added a bugzilla account for you. Martyn On Tue, 2017-05-23 at 21:02 +, Nathan Sosnovske via R-devel wrote: > Hi All, > > I have a fix to this bug ( https://bugs.r-project.org/bugzilla3/show_ > bug.cgi?id=16454) and would like to submit a patch to the bug

Re: [Rd] [R] R-3.4.0 fails test

From: Patrick Connolly <p_conno...@slingshot.co.nz> Sent: 19 May 2017 06:13 To: Martin Maechler Cc: peter dalgaard; Martyn Plummer; Joris Meys; R-devel Subject: Re: [Rd] [R] R-3.4.0 fails test On Thu, 18-May-2017 at 05:46PM +0200, Martin Maechler

Re: [Rd] [R] R-3.4.0 fails test

> On 18 May 2017, at 14:51, peter dalgaard wrote: > > >> On 18 May 2017, at 13:47 , Joris Meys wrote: >> >> Correction: Also dlt uses the default timezone, but POSIXlt is not >> recalculated whereas POSIXct is. Reason for that is the different way

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On Thu, 2017-05-11 at 12:23 +, Martyn Plummer wrote: > On Thu, 2017-05-11 at 06:37 -0500, Dirk Eddelbuettel wrote: > > On 11 May 2017 at 10:17, Erwan Le Pennec wrote: > > >  Dear all, > > > > > >  I've stumbled a similar issue with the package clu

Re: [Rd] bug report: nlme model-fitting crashes with R 3.4.0

On Thu, 2017-05-11 at 06:37 -0500, Dirk Eddelbuettel wrote: > On 11 May 2017 at 10:17, Erwan Le Pennec wrote: > >  Dear all, > > > >  I've stumbled a similar issue with the package cluster when  > > compiling the 3.4.0 version with the settings of Fedora RPM specs.  > > Compiling R with

Re: [Rd] prefixed zlib and bzip2 headers

If you are having any trouble compiling R on RHEL or its derivatives, it is worth recalling that a binary distribution of R is provided through the EPEL (Extra Packages for Enterprise Linux) repository: https://fedoraproject.org/wiki/EPEL Install the appropriate epel-release RPM to enable the

Re: [Rd] Default R-3.4.0 RC CXXFLAGS without -O2 on x86_64-linux-gnu with g++-5.4.0 causes WARNING from stl_list.h

This is fixed in R-rc_2017-04-19_r72555.tar.gz If you are affected by this issue then please test the RC tarball. This is the last chance to detect problems (including those created by the last-minute patch) before the release of R 3.4.0. Martyn On Wed, 2017-04-19 at 12:19 +, Neumann,

Re: [Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 16:32 +0200, Angerer, Philipp wrote: > Hi Dirk and Martyn, > > > That looks fine. Can you please give a reproducible example of a > > package > > that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-devel. > > here you go, it’s pretty much the simplest package

Re: [Rd] R 3.4 has broken C++11 support

IFF, NLS, cairo, ICU >   Options enabled:   shared R library, R profiling > >   Capabilities skipped:   >   Options not enabled:   shared BLAS, memory profiling > >   Recommended packages:  yes > > - Ursprüngliche Mail - > Von: "Angerer, Phil

Re: [Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 12:42 +0200, Angerer, Philipp wrote: > Hi! > > Well, my linux distribution has very recent versions > of everything, so a working C++11 compiler exists: > > $ gcc --version | head -n1 > gcc (GCC) 6.3.1 20170306 I am on Fedora 25 which also uses gcc 6.3.1. The default

Re: [Rd] R 3.4 has broken C++11 support

A user with the email address flying-sh...@web.de has submitted a bug report on this topic.  https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17260 Assuming that you are the same person, I will address the issue here first. If you get the message “C++11 standard requested but CXX11 is not

Re: [Rd] Experimental CXX_STD problem in R 3.4

On Mon, 2017-03-20 at 16:38 +0100, Jeroen Ooms wrote: > On Sun, Mar 19, 2017 at 9:09 PM, Martyn Plummer <plumm...@iarc.fr> > wrote: > > I have just added some code to ensure that the compilation fails > > with an informative error message if a specific C++ s

Re: [Rd] Experimental CXX_STD problem in R 3.4

C++ support across different platforms is now very heterogeneous. The standard is evolving rapidly but there are also platforms in current use that do not support the recent iterations of the standard. Our goal for R 3.4.0 is to give as much flexibility as possible. The default compiler is

Re: [Rd] Platform dependent native routine registration

On Tue, 2017-03-07 at 14:57 +, Gábor Csárdi wrote: > On Tue, Mar 7, 2017 at 2:51 PM, Dirk Eddelbuettel > wrote: > [...] > > > But I just found that using string literals in .Call() works just > > > fine. Hopefully > > > this will still be allowed in the long run: > > > > > >

Re: [Rd] R CMD check error

system("printenv | grep R_LIBS") > R_LIBS_SITE= > R_LIBS_USER=/people/biostat2/therneau/Rlib > > So, per the manual R CMD check inherits the path.  The question is > why does it ignore it? Hmmm. Perhaps it is being overwritten.  Does this work? $ export R_CHECK_ENVIRON= $

Re: [Rd] R CMD check error

On Wed, 2017-02-08 at 15:51 -0600, Therneau, Terry M., Ph.D. wrote: > I have a local library which depends on the expm library.  The expm library > is loaded into  > my personal space and I have the environment variable R_LIBS_USER set > appropriately.  The  > command "library(expm)" works just

Re: [Rd] strptime("1","%m") returns NA

Hi Frederik, On Mon, 2017-01-16 at 18:20 -0800, frede...@ofb.net wrote: > Hi R Devel, > > I wrote some code which depends on 'strptime' being able to parse an > incomplete date, like this: > > > > > base::strptime("2016","%Y") > [1] "2016-01-14 PST" > > The above works - although it's odd

Re: [Rd] Support for signing R packages with GPG

Thanks Jeroen. The R Foundation has recently formed a working group to look into package authentication. There are basically two models. One is the GPG based model you describe; the other is to use X.509 as implemented in the PKI package. It's not yet clear which way to go but we are thinking

Re: [R-pkg-devel] Validate CRAN package using a linked library

Most people who want to interface to an external library embed the source code of the library in their R package. I see that ginac is a C++ library which creates additional problems. Only a few R packages interface to an external C++ library (e.g. the interfaces to SYMPHONY, gdal, QuantLib,

Re: [Rd] can't build from source: error: template with C linkage

This looks like the result of including a C++ system header inside an extern "C" block. There is no evidence of this happening in the current version 2.22.1. However, it did happen in the previous version 2.22 via the chain of inclusions: MCMCglmmcc.h -> cs.h -> R.h -> various C++ system headers

Re: [R-pkg-devel] What to do when you can't reproduce CRAN R CMD check unit test failures?

On Thu, 2016-05-12 at 01:09 -0500, Kevin Ushey wrote: > Is it possible that `getwd()` is reporting something on the CRAN > build > servers that your `decompose_path()` doesn't handle? For example, > your > tests fail for me if I run them while in the root directory (on OS > X). It does not work

Re: [R-pkg-devel] Compiling error with the new R.h header (R-devel 3.3.0 for Windows) when using the C++ function isnan() of

Short answer: use the R macro ISNAN instead. See the Writing R Extensions manual for details. Long answer: The default standard for C++ code in R packages is C++98, which does not define a function "isnan". The C++11 standard introduced a std::isnan function to C++. What you were previously

Re: [Rd] Assignment operator and deep copy for calling C functions

This is discussed in the "Writing R Extensions" manual section 5.9.10: Named objects and copying. .Call does not copy its arguments and it is not safe to modify them, as you have found, since multiple symbols may refer to the same object. If you are going to modify an argument to .Call you should

Re: [Rd] Problem building R-3.2.4

This was reported as a bug earlier today and has been fixed in R- patched: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16755 Martyn On Thu, 2016-03-10 at 08:51 -0800, Mick Jordan wrote: > I am trying to build R-3.2.4 on an Oracle Enterprise Linux system, > where  > I have previously

Re: [R-pkg-devel] Namespace problem with pre-R 3.0.0 package

On Thu, 2016-03-03 at 16:42 +0100, Uwe Ligges wrote: > > On 03.03.2016 16:08, Martyn Plummer wrote: > > On Thu, 2016-03-03 at 15:45 +0100, Sebastien Moretti wrote: > > > I have just found that R 2 filled by itself the NAMESPACE file > > > with > > >

Re: [R-pkg-devel] Namespace problem with pre-R 3.0.0 package

On Thu, 2016-03-03 at 15:45 +0100, Sebastien Moretti wrote: > I have just found that R 2 filled by itself the NAMESPACE file with > # Export all names > exportPattern(".") > > # Import all packages listed as Imports or Depends > import( >    cluster > ) > > > So I filled the NAMESPACE file with

Re: [Rd] problem plotting "ts" in a data.frame

On Tue, 2016-02-09 at 16:56 -0600, Spencer Graves wrote: > Hello: > > >I'm having trouble plotting an object of class "ts" that is in a > data.frame. I can do it with(data.frame, plot(...)) but not with > plot(..., data.frame); see the example below. The plot function is generic so

Re: [Rd] Typo in C++11 Section of Writing R Extensions

Yes you are quite correct and this is the right place for reporting errors in the manuals. I have fixed it. Martyn From: R-devel on behalf of Jonathan Lisic Sent: 09 February 2016 20:31 To:

Re: [Rd] Multiple cores are used in simple for loop

On Fri, 2016-01-15 at 15:03 +0100, Daniel Kaschek wrote: > Dear all, > > I run different R versions (3.2.1, 3.2.2 and 3.2.3) on different > platforms (Arch, Ubuntu, Debian) with a different number of available > cores (24, 4, 24). The following line produces very different behavior > on the

Re: [Rd] Small request of a feature improvement in the next version of R

On Mon, 2015-11-16 at 20:11 -0500, Paul Grosu wrote: > Hi Everyone, > > Sorry to bother the list with this small request, but I've run into this > issue and was wondering if it could be fixed in the next version of R. > Sorry if it was raised in a previous thread: > > So when I try the following

Re: [Rd] authorship and citation

On 06 Oct 2015, at 14:09, S Ellison wrote: >> The former co-author contributed, so he is still author and probably >> copyright >> holder and has to be listed among the authors, otherwise it would be a CRAN >> policy violation ... > > It's a bit of a philosophical

Re: [Rd] Build R with MKL and ICC

On Sat, 2015-09-05 at 11:53 +0200, arnaud gaboury wrote: > On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer <plumm...@iarc.fr> wrote: > > On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: > >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gabo...@gmail.com

Re: [Rd] Build R with MKL and ICC

On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: > On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury > wrote: > > After a few days of reading and headache, I finally gave a try at > > building R from source with Intel MKL and ICC. Documentation and posts > > on

Re: [R-pkg-devel] Note about No repository set, so cyclic dependency check skipped

On Mon, 2015-07-20 at 07:36 +0200, Antonio José Saez Castillo wrote: When checking a package I am getting * checking package dependencies ... NOTE No repository set, so cyclic dependency check skipped This is an old source of discussion and I've found a lot of suggestions, but none of

Re: [R-pkg-devel] FW: CRAN submission berryFunctions 1.8.0

On Wed, 2015-06-03 at 09:51 +0200, Uwe Ligges wrote: On 03.06.2015 09:48, Berry Boessenkool wrote: Hi, after submitting my package update, CRAN (Brian Ripley) found a couple of warnings / messages. URLs that are not longer existent, a non-ASCII character from copypasting,

Re: [Rd] example fails during R CMD CHECK but works interactively?

The error can be reproduced by running the bigmemory-Ex.R script which you can find in the bigmemory.Rcheck directory, either in batch mode or via source() in an interactive session. It seems that you have underlying memory allocation problems. I can get the script to running by adding gc() calls

Re: [Rd] shlib problems with Intel compiler

On Tue, 2015-04-21 at 11:46 -0600, Andy Jacobson (NOAA Affiliate) wrote: Hi, I'm encountering trouble compiling caTools_1.17.1.tar.gz and e1071_1.6-4.tar.gz on a Linux system using the Intel compiler suite. 14 other packages I generally use installed without any trouble. I notice both of

Re: [Rd] shlib problems with Intel compiler

...is that documented somewhere?) I wonder if the recommendation for -lR is correct. None of the other packages are compiled with that flag, and everything seems to compile and load OK in R without using that. Best Regards, Andy On Apr 22, 2015, at 9:30 AM, Martyn Plummer plumm...@iarc.fr wrote

Re: [Rd] alternate licensing for package data?

I think this is covered well by the CRAN repository policy: http://cran.r-project.org/web/packages/policies.html The two key license requirements are that: 1) CRAN must have a perpetual license to distribute the package 2) The package license should be listed here:

Re: [Rd] vignette checking woes

On Wed, 2015-03-25 at 15:12 -0500, Roger Koenker wrote: Thierry, I have this: if (require(MatrixModels) require(Matrix)) { X - model.Matrix(Terms, m, contrasts, sparse = TRUE) You have this in the current release, which does not show this problem in the CRAN tests. This, and the

Re: [Rd] Using Fortran 90 code in packages for CRAN

Everything you need to know is in the Writing R Extensions manual, and section 1.2.3 in particular. There are restrictions on Fortran 90/95 use due to portability issues. Make sure you are following all of the advice in the manual, e.g.: - Files containing Fortran 90 code should have extension

Re: [Rd] [Rcpp-devel] Windows gcc toolchain for R 3.2.0

On Wed, 2015-03-18 at 07:55 -0700, Dan Tenenbaum wrote: Is it not considered a known problem that C++ libraries linked against by R packages need to be rebuilt with g++ 4.9.2 in order for the R packages to install/load? This could well be due to incompatible thread models (win32 vs posix). See

Re: [Rd] R CMD check: Uses the superseded package: ‘doSNOW’

The CRAN package snow is superseded by the parallel package which is distributed with R since version 2.14.0. Here are the release notes \item There is a new package \pkg{parallel}. It incorporates (slightly revised) copies of packages \CRANpkg{multicore} and \CRANpkg{snow} (excluding MPI,

Re: [Rd] Request for help with UBSAN and total absense of CRAN response

On Tue, 2015-01-13 at 10:34 -0600, Dirk Eddelbuettel wrote: On 13 January 2015 at 08:21, Dan Tenenbaum wrote: | Where should the package source be downloaded from? I see it in CRAN (but presumably the latest version that causes the issue is not yet downloadable) and in github. The

Re: [Rd] Fwd: No source view when using gdb

On Thu, 2014-12-11 at 14:00 +0100, Pierrick Bruneau wrote: Dear R contributors, Say I want to debug some C code invoked through .Call() - say varbayes in the VBmix package. following the instructions in Writing R Extensions, I perform the following actions : R -d gdb run library(VBmix)

Re: [Rd] Cursor not behaving properly

I can't reproduce this on Fedora 20, so I think it is an Ubuntu bug. If anyone not on Ubuntu can reproduce this then please add a comment in the bug repository. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16077 If not then I'll close it. Martyn On Thu, 2014-11-20 at 10:27 +0100,

Re: [Rd] [R] Calculation of cross-correlation in ccf

The acf and ccf functions assume that time series are stationary, but yours are not. I think that your alternative function is not well founded. You take a separate mean for each sub-series, which implicitly allows the mean of the series to vary arbitrarily with time. However, you only have

Re: [Rd] 'library' or 'require' call not declared from: 'rgl'

On Thu, 2014-10-30 at 17:18 -0400, Michael Friendly wrote: On 10/30/2014 4:19 PM, Simon Urbanek wrote: Did you intend rgl to be optional? If so, then you should use Suggests: instead. When you use Imports: it will load rgl automatically so require() does't make sense (since it will be always

Re: [Rd] make check fails on lapack.R and stats-Ex.R

On Thu, 2014-10-23 at 08:19 +, Pacey, Mike wrote: As my attachment doesn't seem to have survived transit, I'm cut'n'pasting the relevant failures here: Testing examples for package 'stats' comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ... 6466c6466 Grand Mean: 291.5937 ---

Re: [Rd] Replace isnan and lgamma in Fortran subroutine in R package

On Tue, 2014-09-23 at 07:43 +0200, Berend Hasselman wrote: On 23-09-2014, at 00:33, Wang, Zhu zw...@connecticutchildrens.org wrote: Hello, I submitted a package which used Fortran functions isnan and lgamma. However, I was told that: isnan and lgamma are not Fortran 95 functions.

Re: [Rd] Replace isnan and lgamma in Fortran subroutine in R package

Try this patch. Martyn On Mon, 2014-09-22 at 22:33 +, Wang, Zhu wrote: Hello, I submitted a package which used Fortran functions isnan and lgamma. However, I was told that: isnan and lgamma are not Fortran 95 functions. I was asked to write 'cross-platform portable code' and so

Re: [Rd] R CMD check warning with S3 method

...@gmail.com wrote: On Thu, Jun 19, 2014 at 3:15 PM, Martyn Plummer plumm...@iarc.fr wrote: Export filter in the NAMESPACE file *without copying it* in the R source code. Ah, it works! Thank you! --- This message and its

Re: [Rd] R CMD check warning with S3 method

-generic filter function when it tries to check that the filter.test (or filter.ggvis) method is working correctly, and that is why you get the warnings. Martyn From: Hadley Wickham [h.wick...@gmail.com] Sent: 20 June 2014 11:33 To: Martyn Plummer Cc

Re: [Rd] R CMD check warning with S3 method

When you provide a method for a generic function imported from another package then the generic must be on the search path. Otherwise if a user types filter the dispatch to filter.test will never occur. What is happening here is worse because filter is a non-generic function in the stats package

Re: [Rd] R CMD check warning with S3 method

Export filter in the NAMESPACE file *without copying it* in the R source code. From: Winston Chang [winstoncha...@gmail.com] Sent: 19 June 2014 21:28 To: Martyn Plummer Cc: r-devel@r-project.org Subject: Re: [Rd] R CMD check warning with S3 method Oh, I forgot

Re: [Rd] Is it possible to make install.packages compile source code on Unix but use shipped binary on Windows?

On Wed, 2014-06-18 at 16:10 +0200, Renaud Gaujoux wrote: Maybe. Read the documentation and sources for yourself (see below). Not working, at least in my hands, as it requires `sh`. Yes, *and documented* True. I overlooked the beginning of the NB point. (including that it should

Re: [Rd] R CMD check and DESCRIPTION file with Authors@R only

You need to run R CMD build on your package, then run R CMD check on the resulting tarball, as recommended in section 1.3.1 of the Writing R Extensions manual. The tarball will contain a version of the DESCRIPTION file with Author and Maintainer fields built from the Authors@R field. Martyn On

Re: [Rd] large integer values

On Wed, 2014-05-14 at 18:17 +0300, Adrian Dușa wrote: On Wed, May 14, 2014 at 5:35 PM, Simon Urbanek simon.urba...@r-project.orgwrote: [...] How do you print them? It seems like you're printing 32-bit value instead ... (powers of 2 are simply shifts of 1). I am simply using

Re: [Rd] R 3.1.0 and C++11

On Thu, 2014-04-10 at 07:22 -0500, Dirk Eddelbuettel wrote: On 2 December 2013 at 07:04, Dirk Eddelbuettel wrote: | | Following up on the thread spawned a while back, I just wanted to say that I | appreciate today's RSS serving of R-devel NEWS: | |CHANGES IN R-devel PACKAGE

Re: [Rd] R 3.1.0 and C++11

On Thu, 2014-04-10 at 11:14 -0400, Gabor Grothendieck wrote: On Tue, Oct 29, 2013 at 1:58 AM, rom...@r-enthusiasts.com wrote: Le 2013-10-29 03:01, Whit Armstrong a écrit : I would love to see optional c++0x support added for R. c++0x was the name given for when this was in

Re: [Rd] CXX_STD and configure.ac in packages

Hi Martin, Thanks for the patch. I have applied it. I also added CXX1X and friends to the list of approved variables for R CMD config. So you can now query the existence of C++11 support with `R CMD config CXX1X` (It is empty if C++11 support is not available) and then take appropriate action

Re: [Rd] CXX_STD and configure.ac in packages

On Mon, 2014-03-31 at 07:09 +, Martyn Plummer wrote: Hi Martin, Thanks for the patch. I have applied it. I also added CXX1X and friends to the list of approved variables for R CMD config. So you can now query the existence of C++11 support with `R CMD config CXX1X` (It is empty if C

Re: [Rd] valgrind and C++

I think the server that runs the valgrind checks is still running the old version of your package (2.17) not the new one (2.18). Wait for an update. Martyn On Mon, 2014-03-17 at 17:26 +, Jarrod Hadfield wrote: Hi, I am sorry if this is perceived as a C++ question rather than an R

Re: [Rd] Multivariate time series in R 3 vs R 2

This has nothing to do with changes in base R. It is due to changes in the dependent packages. These changes mean that when you call lapply it does not dispatch the right as.list method. The method you want (as.list.ts) is provided by the zoo package. It splits a multivariate time series into a

Re: [Rd] C++ debugging help needed

Yes, on reflection it's an ABI problem on Linux (use of PIC code in shared libraries means that any symbol can be interposed). Using namespaces isn't really the answer because that's an API issue. I think what you really need to do is control the visibility of your classes and functions so that

Re: [Rd] R 3.1.0 and C++11

I don't see any harm in allowing optional C++11 support, and it is no trouble to update the documentation to acknowledge the existence of C++11 conforming compilers. However, the questions of what is possible, what is recommended, and what is required for CRAN submissions are distinct. I have

Re: [Rd] version comparison puzzle

It's an underflow problem. When comparing versions, a.b.c is converted first to the integer vector c(a,b,c) and then to the double precision value a + b/base + c/base^2 where base is 1 greater than the largest integer component of any of the versions: i.e 99912 in this case. The last term

Re: [Rd] C++ debugging help needed

In C++, everything goes in the global namespace unless the programmer explicitly creates one. So when you dynamically load two dynamic shared libraries with a Shape object they clash. The solution here is to put namespace rgl { ... } around your class definitions in the rglm package, and

Re: [Rd] Correct NAMESPACE approach when writing an S3 method for a generic in another package

I think rgl should be in Depends. You are providing a method for a generic function from another package. In order to use your method, you want the user to be able to call the generic function without scoping (i.e. without calling rgl::plot3d), so the generic should be on the search path, so the

Re: [Rd] Problem following an R bug fix to integrate()

On Tue, 2013-07-16 at 13:55 +0200, Hans W Borchers wrote: I have been told by the CRAN administrators that the following code generated an error on 64-bit Fedora Linux (gcc, clang) and on Solaris machines (sparc, x86), but runs well on all other systems): fn - function(x, y) ifelse(x^2

Re: [Rd] package test failed on Solaris x86 -- help needed for debugging

Dear Thomas, Is this the deSolve package? http://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/deSolve-00check.html I can help you with that. It does pass R CMD check on my OpenSolaris installation, but I am getting some compiler warnings. I will send you details. Martyn On Thu,

Re: [Rd] Compiling R on Linux with SunStudio 12.1: wide-character type problems (rt)

You can work around this by disabling large file support (configure --disable-largefile). This seems to be another glibc bug. In the header glob.h, there are two lines where the pre-processor fails to check that __GNUC__ is defined, and it isn't defined when using Sun Studio. Evidently, glibc

Re: [Rd] Compiling R on Linux with SunStudio 12.1: wide-character type problems

Russ, This is a known issue with Sun Studio on Linux and was fixed by Brian Ripley in January. If you download R-patched.tar.gz from here: ftp://ftp.stat.math.ethz.ch/Software/R/ then it should work for you. Martyn On Mon, 2010-02-22 at 13:11 -0600, rt wrote: I am trying to compile R on

Re: [Rd] [R] R with MKL

On Tue, 2009-03-17 at 12:12 +0900, Ei-ji Nakama wrote: Hi I have seen a lot of problems from people trying to compile R with MKL. So I am writing my experience in case it helps and to ask one question. I installed R-2.8.1.patched in Ubuntu 9.04 (gcc 4.3.3) using MKL 10.1.1.019. Do

Re: [Rd] [R] Error: bad value problem

This has all the hallmarks of a bug I found and fixed in R-devel (r46998). I did not port the patch over to the R release branch because I could not reproduce the bug. In R-devel, I was seeing problems with make test-Segfault. This would occasionally segfault, but most of the time would create

Re: [Rd] [R] Error: bad value problem

On Thu, 2008-12-18 at 10:57 +0100, Peter Dalgaard wrote: Martyn Plummer wrote: This has all the hallmarks of a bug I found and fixed in R-devel (r46998). I did not port the patch over to the R release branch because I could not reproduce the bug. In R-devel, I was seeing problems

Re: [Rd] typo in ?pie

My Concise Oxford Dictionary has both spellings. Quoting Spencer Graves [EMAIL PROTECTED]: Hello: The help page for 'pie' includes judgements; the standard spelling does not include e, as spell checkers have informed me many times. ... in case someone wants to correct that

Re: [Rd] [R] Building with MKL on Ubuntu

It looks like the em64t version of MKL fails the test for the accuracy of zdotu (checking whether double complex BLAS can be used) and is therefore dropped in favour of R's built-in BLAS. I have just tested this on Fedora and get the same result. The 32-bit MKL does work for me. Martyn On Wed,

Re: [Rd] [R] Building with MKL on Ubuntu

Quoting Peter Dalgaard [EMAIL PROTECTED]: Anand Patil wrote: On Wed, Nov 5, 2008 at 5:59 PM, Martyn Plummer [EMAIL PROTECTED] wrote: It looks like the em64t version of MKL fails the test for the accuracy of zdotu (checking whether double complex BLAS can be used) and is therefore

Re: [Rd] HAVE_BZLIB_H not set

That must be a different problem as this one affects both R 2.7.2 and R 2.8.0 on Fedora 9. When the header is not included, the test program that checks the version of bzlib segfaults. We can fix this by using AC_CHECK_HEADERS instead of AC_CHECK_HEADER when looking for bzlib.h, since the former

Re: [Rd] error installing gtools (PR#13168)

Ebi, You need to install the R-devel RPM, which has the header files. If this is a bug (which it arguably is) it is a problem with the Fedora distribution, not with R itself. Martyn On Wed, 2008-10-15 at 15:30 +0200, [EMAIL PROTECTED] wrote: Full_Name: Ebi Hal Version: R-2.7.2-1 OS: Fedora

Re: [Rd] handling spaces in R invocation scripts

Hi Nathan, Do you think you could provide a patch without the formatting and style changes? This would be easier to read. Martyn On Mon, 2008-09-22 at 08:41 -0400, Nathan Coulter wrote: Nathan Coulter wrote: The attached patch, built against the devel snapshot of 2008-09-20, attempts to

Re: [Rd] R spec file change for building on CentOS 5.2 (PR#12939)

Thanks. We are moving away from the one-size-fits-all spec file for R 2.8.0, but you should still be able to rebuild the RedHat 5 source RPM. On Fri, 2008-09-19 at 20:20 +0200, [EMAIL PROTECTED] wrote: --GZVR6ND4mMseVXL/ Content-Type: text/plain; charset=us-ascii Content-Disposition: inline

Re: [Rd] [R] Date Format

On Tue, 2006-07-11 at 20:05 +0200, Peter Dalgaard wrote: Martyn Plummer [EMAIL PROTECTED] writes: I moved this to R-devel because I am wondering why the base package does not allow you to convert from numeric to Date. Could we not have something like this? as.Date.numeric - function

Re: [Rd] [R] Date Format

I moved this to R-devel because I am wondering why the base package does not allow you to convert from numeric to Date. Could we not have something like this? as.Date.numeric - function(x, epoch=1970-01-01, ...) { if (!is.character(epoch) || length(epoch) != 1) stop(invalid epoch)

Re: [Rd] R 2.2.2-1 RPM build problem and solution on RH AS 4 x86_64

On Wed, 2006-01-11 at 17:26 -0500, Dan Lipsitt wrote: I have a dual Xeon x86_64 system running Red Hat AS 4. There are no x86_64 rpms in http://cran.us.r-project.org/bin/linux/redhat/el4/ (the i386 ones are a point release behind anyway) , and the fc4 rpms have a whole web of dependencies I

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