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

2018-03-02 Thread Martyn Plummer
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 cou

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

2018-03-02 Thread Martyn Plummer
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 a

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

2018-03-01 Thread Martyn Plummer
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 code

Re: [Rd] Illegal Logical Values

2017-10-20 Thread Martyn Plummer
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 INT_

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

2017-09-28 Thread Martyn Plummer
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 forward

Re: [Rd] hpc r configure not recognizing zlib

2017-06-22 Thread Martyn Plummer
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

2017-06-10 Thread Martyn Plummer
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 the

Re: [Rd] Getting an R bugzilla account

2017-05-23 Thread Martyn Plummer
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

2017-05-18 Thread Martyn Plummer
From: Patrick Connolly 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 wrote: |> . |> |> Bei

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

2017-05-18 Thread Martyn Plummer
> 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 values >> are stored (hours, minutes, seco

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

2017-05-11 Thread Martyn Plummer
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 packag

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

2017-05-11 Thread Martyn Plummer
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 th

Re: [Rd] prefixed zlib and bzip2 headers

2017-04-28 Thread Martyn Plummer
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 rep

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

2017-04-20 Thread Martyn Plummer
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, Steffe

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

2017-04-19 Thread Martyn Plummer
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 possib

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

2017-04-19 Thread Martyn Plummer
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, Philipp&q

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

2017-04-19 Thread Martyn Plummer
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 standa

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

2017-04-18 Thread Martyn Plummer
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 def

Re: [Rd] Experimental CXX_STD problem in R 3.4

2017-03-22 Thread Martyn Plummer
On Mon, 2017-03-20 at 16:38 +0100, Jeroen Ooms wrote: > On Sun, Mar 19, 2017 at 9:09 PM, Martyn Plummer > wrote: > > I have just added some code to ensure that the compilation fails > > with an informative error message if a specific C++ standard is > > requested but th

Re: [Rd] Experimental CXX_STD problem in R 3.4

2017-03-19 Thread Martyn Plummer
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 whate

Re: [Rd] Platform dependent native routine registration

2017-03-07 Thread Martyn Plummer
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: > > > > > > .Call("c_non_exis

Re: [Rd] R CMD check error

2017-02-09 Thread Martyn Plummer
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

2017-02-09 Thread Martyn Plummer
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 f

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

2017-01-17 Thread Martyn Plummer
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 that

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

2016-10-25 Thread Martyn Plummer
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 about

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

2016-08-19 Thread Martyn Plummer
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: [Rd] Assignment operator and deep copy for calling C functions

2016-04-07 Thread Martyn Plummer
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

2016-03-10 Thread Martyn Plummer
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 buil

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

2016-02-10 Thread Martyn Plummer
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 t

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

2016-02-09 Thread Martyn Plummer
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: r-devel@r-project.org Subject: [Rd] Typo in C++11 Section of Wri

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

2016-01-15 Thread Martyn Plummer
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 thr

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

2015-11-17 Thread Martyn Plummer
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

2015-10-06 Thread Martyn Plummer
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 question right now, but at

Re: [Rd] Build R with MKL and ICC

2015-09-07 Thread Martyn Plummer
On Sat, 2015-09-05 at 11:53 +0200, arnaud gaboury wrote: > On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer wrote: > > On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: > >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury > >> wrote: > >> > Afte

Re: [Rd] Build R with MKL and ICC

2015-09-04 Thread Martyn Plummer
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 this topic are rather incomple

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

2015-05-15 Thread Martyn Plummer
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

2015-04-22 Thread Martyn Plummer
have > a reference about the syntax and variable names that the Makevars file can > contain...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 comp

Re: [Rd] shlib problems with Intel compiler

2015-04-22 Thread Martyn Plummer
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

Re: [Rd] alternate licensing for package data?

2015-04-22 Thread Martyn Plummer
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: https://svn.r-project.org/R/t

Re: [Rd] vignette checking woes

2015-03-26 Thread Martyn Plummer
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, an

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

2015-03-18 Thread Martyn Plummer
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).

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

2015-03-18 Thread Martyn Plummer
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 .f9

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

2015-02-10 Thread Martyn Plummer
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, PVM

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

2015-01-14 Thread Martyn Plummer
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 "p

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

2014-12-11 Thread Martyn Plummer
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 > lib

Re: [Rd] Cursor not behaving properly

2014-11-20 Thread Martyn Plummer
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, Larissa

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

2014-11-05 Thread Martyn Plummer
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 one

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

2014-10-31 Thread Martyn Plummer
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 alw

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

2014-10-23 Thread Martyn Plummer
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

2014-09-23 Thread Martyn Plummer
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' an

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

2014-09-23 Thread Martyn Plummer
On Tue, 2014-09-23 at 07:43 +0200, Berend Hasselman wrote: > On 23-09-2014, at 00:33, 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 a

Re: [Rd] blas test problem

2014-07-07 Thread Martyn Plummer
I can reproduce this. It is a bug in reference BLAS. With the R 3.1.0 release, Fedora changed from using the internal BLAS that comes with R to using external BLAS. But reference BLAS does not handle missing values correctly. I expect this has been true since at least 2010, when Brian patched the

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

2014-06-20 Thread Martyn Plummer
ng the non-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

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

2014-06-20 Thread Martyn Plummer
> > > On Fri, Jun 20, 2014 at 12:19 AM, Winston Chang > wrote: > > On Thu, Jun 19, 2014 at 3:15 PM, Martyn Plummer wrote: > > > >> Export filter in the NAMESPACE file *without copying it* in the R source > >> code. > >> > >> > >

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

2014-06-19 Thread Martyn Plummer
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 to

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

2014-06-19 Thread Martyn Plummer
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 pac

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

2014-06-18 Thread Martyn Plummer
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 i

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

2014-06-11 Thread Martyn Plummer
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

Re: [Rd] large integer values

2014-05-14 Thread Martyn Plummer
On Wed, 2014-05-14 at 18:17 +0300, Adrian Dușa wrote: > On Wed, May 14, 2014 at 5:35 PM, Simon Urbanek > wrote: > > > [...] > > > > 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 Rprintf(): > >

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

2014-04-10 Thread Martyn Plummer
On Thu, 2014-04-10 at 11:14 -0400, Gabor Grothendieck wrote: > On Tue, Oct 29, 2013 at 1:58 AM, 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 development. Now c++1

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

2014-04-10 Thread Martyn Plummer
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 INSTAL

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

2014-03-31 Thread Martyn Plummer
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`

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

2014-03-31 Thread Martyn Plummer
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 in

Re: [Rd] valgrind and C++

2014-03-18 Thread Martyn Plummer
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 > q

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

2013-10-25 Thread Martyn Plummer
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 li

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

2013-10-07 Thread Martyn Plummer
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 a

Re: [Rd] C++ debugging help needed

2013-10-07 Thread Martyn Plummer
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 e

Re: [Rd] version comparison puzzle

2013-10-03 Thread Martyn Plummer
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

2013-10-02 Thread Martyn Plummer
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 us

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

2013-08-26 Thread Martyn Plummer
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 p

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

2013-07-17 Thread Martyn Plummer
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) ifels

Re: [Rd] GPL and R Community Policies (Rcpp)

2010-12-02 Thread Martyn Plummer
Dear Dominick, The R community does not have a conflict resolution mechanism. We are quite used to disputes that end with one party, usually a recognized authority, saying "No, you are objectively, verifiably wrong". We cannot, as a group, deal with anything else. Everybody knows that you have

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

2010-09-16 Thread Martyn Plummer
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, 2010-0

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

2010-02-26 Thread Martyn Plummer
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 was

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

2010-02-23 Thread Martyn Plummer
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 Linu

Re: [Rd] [R] R with MKL

2009-03-17 Thread Martyn Plummer
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.

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

2008-12-18 Thread Martyn Plummer
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. > > &

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

2008-12-18 Thread Martyn Plummer
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] typo in ?pie

2008-11-10 Thread plummer
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 cor

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

2008-11-05 Thread plummer
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 ("checkin

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

2008-11-05 Thread Martyn Plummer
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] HAVE_BZLIB_H not set

2008-10-27 Thread Martyn Plummer
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)

2008-10-15 Thread Martyn Plummer
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

2008-09-23 Thread Martyn Plummer
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, > > attemp

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

2008-09-22 Thread Martyn Plummer
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: inlin

Re: [Rd] [R] Date Format

2006-07-12 Thread Martyn Plummer
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

Re: [Rd] [R] Date Format

2006-07-11 Thread Martyn Plummer
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] Provide both shlib and standard versions of R?

2006-01-16 Thread Martyn Plummer
On Mon, 2006-01-16 at 00:45 -0600, Bo Peng wrote: > > then either build your own with correct options or talk to your > > distribution's packaging team. > > It seems that my knowledge about this option is outdated. When I > first encountered this problem two years ago, the R/rpm distribution > ca

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

2006-01-12 Thread Martyn Plummer
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

Re: [Rd] Post processing need for installing packages in rpms.

2005-10-11 Thread Martyn Plummer
On Tue, 2005-10-11 at 13:11 +0100, Prof Brian Ripley wrote: > On Tue, 11 Oct 2005, [UTF-8] José Matos wrote: > > > Hello,I maintain some packages in Fedora Extras for R related > > modules. > >Until R 2.2.0 I used for post processing (both after installing > > andremoving the pac

Re: [Rd] How do I install rbugs ? (PR#8183)

2005-10-06 Thread plummer
On Thu, 2005-10-06 at 11:33 +0200, Roger Bivand wrote: > On Thu, 6 Oct 2005 [EMAIL PROTECTED] wrote: > > > Dear rbugs, > > > > 6 month a ago the homepage of R showed how I could install and do a = > > test-Run of rbugs. This information is not available anymore. I would = > > appreciate if you co

Re: [Rd] How do I install rbugs ? (PR#8183)

2005-10-06 Thread Martyn Plummer
On Thu, 2005-10-06 at 11:33 +0200, Roger Bivand wrote: > On Thu, 6 Oct 2005 [EMAIL PROTECTED] wrote: > > > Dear rbugs, > > > > 6 month a ago the homepage of R showed how I could install and do a = > > test-Run of rbugs. This information is not available anymore. I would = > > appreciate if you co

Re: [Rd] looks in liblapack.a not liblapack.so

2005-09-19 Thread Martyn Plummer
On Mon, 2005-09-19 at 17:10 +0200, Peter Dalgaard wrote: > Martyn Plummer <[EMAIL PROTECTED]> writes: > > > > The 'recompile with -fPIC' is bullsh*t. The problem is that is is looking > > > in /usr/lib64/liblapack.a rather than /usr/lib64/liblapack.so.3

Re: [Rd] looks in liblapack.a not liblapack.so

2005-09-19 Thread Martyn Plummer
On Sat, 2005-09-17 at 17:19 -0500, Charles Geyer wrote: > I can't compile R-alpha on AMD 64. Rather than include a 1400 line script > I have put it on the web > > http://www.stat.umn.edu/~charlie/typescript.txt > > way down near the bottom it fails building lapack.so > > gcc -shared -L/

Re: [Rd] Failed "make check" under Fedora Core 4 (PR#7979)

2005-06-30 Thread Martyn Plummer
On Wed, 2005-06-29 at 19:55 +0200, [EMAIL PROTECTED] wrote: > I downloaded R v2.1.1 earlier this morning to compile under Fedora Core > 4. It compiled without incident, but 'make check' failed. Below is the > relevant part of its report. Is this a known problem? It is known that gcc 4.0.0 is bug

Re: [Rd] a bug in glm.fit() (PR#7947)

2005-06-16 Thread Martyn Plummer
On Thu, 2005-06-16 at 07:06 +0100, Prof Brian Ripley wrote: > What is the bug? > > This is the same model: the `intercept' term affects the null model, not > the actual model. Just look at all the output. I think the documentation is misleading (On a related issue, it still refers to the defunc

Re: [Rd] R 2.1.1 slated for June 20

2005-06-16 Thread Martyn Plummer
On Thu, 2005-06-16 at 12:41 +0100, Prof Brian Ripley wrote: > On Thu, 16 Jun 2005, Martyn Plummer wrote: > > > On Tue, 2005-06-14 at 17:07 -0500, Marc Schwartz wrote: > >> On Tue, 2005-06-14 at 23:52 +0200, Peter Dalgaard wrote: > >>> Marc Schwartz <[EMAIL PRO

Re: [Rd] R 2.1.1 slated for June 20

2005-06-16 Thread Martyn Plummer
On Tue, 2005-06-14 at 17:07 -0500, Marc Schwartz wrote: > On Tue, 2005-06-14 at 23:52 +0200, Peter Dalgaard wrote: > > Marc Schwartz <[EMAIL PROTECTED]> writes: > > > > > On Fri, 2005-06-10 at 14:57 +0100, Prof Brian Ripley wrote: > > > > On Fri, 10 Jun 2005, Peter Dalgaard wrote: > > > > > > > >

Re: [Rd] memory allocation problem under linux

2005-06-13 Thread Martyn Plummer
On Mon, 2005-06-13 at 12:12 +0200, [EMAIL PROTECTED] wrote: > Scrive Prof Brian Ripley : > > > You keep on sending similar messages -- this is at least the third. You > > need to find out where the segfault is occurring using gdb, and you have > > not told us. > > Sorry for the repeated post (

[Rd] attach and object masking

2005-06-10 Thread Martyn Plummer
The library() function prints an information message when objects are masked on the search path by (or from) a newly attached package. The attach() function, however, doesn't. Is there a good reason for this? I have adapted the machinery for checking conflicts used in the library () function to a

  1   2   >