Re: [Rd] Failure to load the recommended package Matrix (Was: [R] Can one get a list of recommended packages?)
I'm suffering from hay fever now... from http://sage.math.washington.edu/home/mpatel/trac/8306/r-2.10.1.p2.log | gcc -v | Using built-in specs. | Target: sparc-sun-solaris2.10 | Configured with: ../gcc-4.4.1/configure --prefix=/usr/local/gcc-4.4.1-sun-linker/ --with-as=/usr/ccs/bin/as | --without-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-languages=c,c++,fortran --with- | mpfr-include=/usr/local/include --with-mpfr-lib=/usr/local/lib --with-gmp-include=/usr/local/include --with- | gmp-lib=/usr/local/lib CC=/usr/sfw/bin/gcc CXX=/usr/sfw/bin/g++ | Thread model: posix | gcc version 4.4.1 (GCC) I think that this gcc is `/usr/local/gcc-4.4.1-sun-linker/bin/gcc'. library when gcc compiled it is `/usr/local/gcc-4.4.1-sun-linker/lib/libgcc_s.so'. if it follows the instruction of FAQ(gcc). http://gcc.gnu.org/faq.html#rpath The build is done by using run time directory in LD_RUN_PATH. LD_RUN_PATH=/usr/local/gcc-4.4.1-sun-linker/lib make or You should enumerate the run time directory of gcc in LD_LIBRARY_PATH. LD_LIBRARY_PATH=/usr/local/gcc-4.4.1-sun-linker/lib:$LD_LIBRARY_PATH I think that it is a policy of system administration. It is not a problem of R. There is not the problem in R on Solaris10 which I use. Sorry in advance if I'm wrong. 2010/6/15 Dr. David Kirkby david.kir...@onetel.net: On 06/14/10 10:05 AM, Ei-ji Nakama wrote: And if you look at the other R-help message posted by David Kirby you will find a link to the trouble ticket report in Sage as http://trac.sagemath.org/sage_trac/ticket/9201 From the link,... | kir...@t2:[~] $ echo $LD_LIBRARY_PATH | /usr/local/gcc-4.4.1-sun-linker/lib:/usr/local/gcc-4.4.1-sun-linker/lib/sparcv9:/usr/local/lib `/usr/local/gcc-4.4.1-sun-linker/lib/sparcv9' is 64bit, it is unnecessary. I think that this obstructs it. This is not the reason. If it picked up the wrong library, then there would be a message that there was the wrong ELF class, but no library whatever is being found. I've tried without the 'sparcv9' in LD_LIBRARY_PATH and it makes no difference whatsoever. I've tried on two SPARCs too, running different releases of Solaris 10. Using 'crle' might work, but that is not really a good answer, as it needs root access. It should be possible to install an application like R without being root. There is something wrong if LD_LIBRARY_PATH can't be used to locate libraries. I can build the whole of the Sage source code (around 300 MB) and don't see this failure elsewhere. Instead, there are a number of programs which link to libgcc_s.so.1. I stuck some further information at http://trac.sagemath.org/sage_trac/ticket/9201 but it basically just confirms what I've written above. -- EI-JI Nakama nakama (a) ki.rim.or.jp \u4e2d\u9593\u6804\u6cbb nakama (a) ki.rim.or.jp __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] Prime Numbers Pkgs - Schoolmath is broken
Gavin Simpson wrote: On Mon, 2010-06-14 at 07:16 -0700, Red Roo wrote: primes() and primlist are broken in Schoolmath pkg on CRAN. My analysis can be found here http://j.mp/9BNI9q Not sure what the procedure is for getting things fixed, so I've cross-posted to r-dev as well. Neither place is correct. This has *nothing* to do with R. Address bug reports directly to the package maintainer, details of which can be found here: http://cran.r-project.org/web/packages/schoolmath/index.html which is what is requested in the posting guide... Hmm, well... yes, but: It could be argued that we are a little too closed to discussing items outside of base R. There is something to be said for allowing people to point out to us that we do have a package on CRAN that claims that 133 is a prime! Of course it might be considered more polite first to tell the package maintainder that he has egg on his face... -pd -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] Prime Numbers Pkgs - Schoolmath is broken
On Tue, 2010-06-15 at 13:54 +0200, Peter Dalgaard wrote: Gavin Simpson wrote: On Mon, 2010-06-14 at 07:16 -0700, Red Roo wrote: primes() and primlist are broken in Schoolmath pkg on CRAN. My analysis can be found here http://j.mp/9BNI9q Not sure what the procedure is for getting things fixed, so I've cross-posted to r-dev as well. Neither place is correct. This has *nothing* to do with R. Address bug reports directly to the package maintainer, details of which can be found here: http://cran.r-project.org/web/packages/schoolmath/index.html which is what is requested in the posting guide... Hmm, well... yes, but: It could be argued that we are a little too closed to discussing items outside of base R. There is something to be said for allowing people to point out to us that we do have a package on CRAN that claims that 133 is a prime! Of course it might be considered more polite first to tell the package maintainder that he has egg on his face... -pd Hi Peter, I agree with what you say; on the main R-Help list people are free to answer/ignore questions on contributed packages as they wish so there shouldn't be discouragement of such communications. There was an interesting discussion on R-Help or R-Devel (I forget which) recently where a question was asked about when it was appropriate to send a public email to R-Help/R-Devel notifying the community of problems with a package on CRAN that had gone unacknowledged despite the OP having contacted the package maintainers. That post solicited several interesting and consider replies, and I too would like to be made aware if a package was providing incorrect/erroneous results. As you say, it is good form to give the maintainer an opportunity to fix the problem and/or respond. However, the tone of Neil Gunther's analysis left a sour taste in the mouth and didn't indicate the maintainer had been contacted to correct the problems. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] GUI's and R background processes
Hello, I am new to R and have created an application using R 2.10, with a graphical UI using TclTk 8.5, running on windows 7, quad core machine. The intention of the application is to launch calculations and display results on a graphical dashboard. I've reached a roadblock, and I need to confirm that the following CANNOT be done. I've been trying to find a mechanism for doing the following: 1. From the dashboard, start a huge calculation (i.e. call a function) that take at least 30 seconds to run, but without tying up the other dashboard features 2. Dashboard can detect when the calculation is finished 3. Dashboard can display incremental results as the calculation runs (i.e. status/progress) The requirement is to kickoff 4 calculations (#1), but I don't want the user to wait for the others to finish. The calculations are not dependent. I just need to display results. I've been reading that threading in R is not an option. I tried using the multicore package, but that is still synchronous. I looked at multicore, fork(), addTaskCallback(), and TclTk threading, and none of these seem like an option. Is there a way to launch multiple R scripts from controller that can communicate back and forth? I believe this means that the separate processes are able to communicate. I certainly appreciate any direction you can provide. I really want to find some good news to tell the boss, though, since we went down this path before realizing the limitations. Thanks very much, Anne [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] GUI's and R background processes
Anne George wrote: Hello, I am new to R and have created an application using R 2.10, with a graphical UI using TclTk 8.5, running on windows 7, quad core machine. The intention of the application is to launch calculations and display results on a graphical dashboard. I've reached a roadblock, and I need to confirm that the following CANNOT be done. I've been trying to find a mechanism for doing the following: 1. From the dashboard, start a huge calculation (i.e. call a function) that take at least 30 seconds to run, but without tying up the other dashboard features 2. Dashboard can detect when the calculation is finished 3. Dashboard can display incremental results as the calculation runs (i.e. status/progress) The requirement is to kickoff 4 calculations (#1), but I don't want the user to wait for the others to finish. The calculations are not dependent. I just need to display results. I've been reading that threading in R is not an option. I tried using the multicore package, but that is still synchronous. I looked at multicore, fork(), addTaskCallback(), and TclTk threading, and none of these seem like an option. Is there a way to launch multiple R scripts from controller that can communicate back and forth? I believe this means that the separate processes are able to communicate. I certainly appreciate any direction you can provide. I really want to find some good news to tell the boss, though, since we went down this path before realizing the limitations. This is possible, but not easy. You need to work at the C level. The key is that the long running processes need to periodically tell R to check for user events by calling R_ProcessEvents(); R_CheckUserInterrupt(); at the C level. This works in Windows in current versions, and I believe on all platforms in R-devel. The code should be prepared for R to call it again during R_ProcessEvents, so if it is not re-entrant, it should arrange to signal an error. It should be prepared for the R_CheckUserInterrupt call to never return if the user happened to interrupt the calculation. You probably only want one processor to do this, and let it check on the other cores to see if there are any results ready. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] location of Sweave.sty in R devel (2010-06-15 r52280)
Sorry if I was supposed to file a bug report, but I don't know whether
we're supposed to do that on R devel. I just built R devel from source
(2010-06-15 r52280) and tried to check a package with it and Sweave
failed on the vignette. It puts the line
\usepackage{/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/Sweave}
in the *.tex file but, that's not where Sweave.sty is
oak$ find ~/local/devel -name Sweave.sty
/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/tex/latex/Sweave.sty
All I did was configure; make; make install and the only configure
flags were --prefix=/HOME/faculty/charlie/local/devel
and --with-valgrind-instrumentation=2 Don't see why either would mess
up Sweave.
On a linux box (openSUSE 11.1 (x86_64)).
The day before I built R-2.11.1 the same way and it works fine.
--
Charles Geyer
Professor, School of Statistics
University of Minnesota
char...@stat.umn.edu
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Re: [Rd] location of Sweave.sty in R devel (2010-06-15 r52280)
That is not the default behaviour of Sweave, which is to use
\usepackage{Sweave}. Do you have SWEAVE_STYLEPATH_DEFAULT set, or
some other non-standard setting that would cause this? (That is even
less needed than before, and it may be removed before 2.12.0 is
released.)
All of CRAN and BioC have been checked in the last 24 hours with
standard settings, so this does look like a problem with some
non-standard setup.
If we can reproduce it we can address the problem, but there is
nothing here that I can do more than guess at.
On Tue, 15 Jun 2010, Charles Geyer wrote:
Sorry if I was supposed to file a bug report, but I don't know whether
we're supposed to do that on R devel. I just built R devel from source
(2010-06-15 r52280) and tried to check a package with it and Sweave
failed on the vignette. It puts the line
\usepackage{/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/Sweave}
in the *.tex file but, that's not where Sweave.sty is
oak$ find ~/local/devel -name Sweave.sty
/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/tex/latex/Sweave.sty
All I did was configure; make; make install and the only configure
flags were --prefix=/HOME/faculty/charlie/local/devel
and --with-valgrind-instrumentation=2 Don't see why either would mess
up Sweave.
On a linux box (openSUSE 11.1 (x86_64)).
The day before I built R-2.11.1 the same way and it works fine.
--
Charles Geyer
Professor, School of Statistics
University of Minnesota
char...@stat.umn.edu
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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Re: [Rd] location of Sweave.sty in R devel (2010-06-15 r52280)
Charles
For some time I have had to add R to the tex paths:
export TEXINPUTS=~/texmf/tex/latex:$RHOME/share/texmf:
export BSTINPUTS=~/texmf/bibtex/bst:$RHOME/share/texmf:
to get vignettes to build. Not sure if I am still suppose to need to do
that, but the symptom looks the same.
Paul
-Original Message-
From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-
project.org] On Behalf Of Prof Brian Ripley
Sent: June 15, 2010 6:23 PM
To: Charles Geyer
Cc: r-devel@r-project.org
Subject: Re: [Rd] location of Sweave.sty in R devel (2010-06-15 r52280)
That is not the default behaviour of Sweave, which is to use
\usepackage{Sweave}. Do you have SWEAVE_STYLEPATH_DEFAULT set, or
some other non-standard setting that would cause this? (That is even
less needed than before, and it may be removed before 2.12.0 is
released.)
All of CRAN and BioC have been checked in the last 24 hours with
standard settings, so this does look like a problem with some
non-standard setup.
If we can reproduce it we can address the problem, but there is
nothing here that I can do more than guess at.
On Tue, 15 Jun 2010, Charles Geyer wrote:
Sorry if I was supposed to file a bug report, but I don't know
whether
we're supposed to do that on R devel. I just built R devel from
source
(2010-06-15 r52280) and tried to check a package with it and Sweave
failed on the vignette. It puts the line
\usepackage{/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/Sweav
e
}
in the *.tex file but, that's not where Sweave.sty is
oak$ find ~/local/devel -name Sweave.sty
/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/tex/latex/Sweave.
s
ty
All I did was configure; make; make install and the only configure
flags were --prefix=/HOME/faculty/charlie/local/devel
and --with-valgrind-instrumentation=2 Don't see why either would
mess
up Sweave.
On a linux box (openSUSE 11.1 (x86_64)).
The day before I built R-2.11.1 the same way and it works fine.
--
Charles Geyer
Professor, School of Statistics
University of Minnesota
char...@stat.umn.edu
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Package development process?
Hello, All: What thoughts might you have on The R Software Package Development Process? I'm looking for ideas, materials, references, and / or collaborators for an article on this topic to be submitted to the Communications of the ACM. My limited experience with other languages such as Matlab and Python suggests that R may be fairly unique with CRAN and this accompanying package development process -- and users of other languages might benefit from emulating R in this regard. We have an immediate deadline of Sept. 15, when Sundar and I are scheduled to speak on this topic for the San Francisco Bay Chapter of the Association for Computing Machinery. So far my literature search for comparable capabilities for other languages have produced essentially nothing comparable.(a) Sundar and I added a section on Selected Repositories to the Wikipedia Software repository entry (http://en.wikipedia.org/wiki/Software_repository). Thanks, Spencer Graves ## (a) I have material discussed by Merijn de Jonge, Eindhoven University of Technology on Package-Based Software Development at the 29th Euromicro Conference (EUROMICRO'03), Belek-Antalya, Turkey, September 01-September 06 (http://www.computer.org/portal/web/csdl/doi/10.1109/EURMIC.2003.1231570). I'm also familiar with material by Friedrich Leisch, Sundar and I on Creating R Packages available as contributed documentation from CRAN. -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package development process?
On Tue, Jun 15, 2010 at 9:45 PM, Spencer Graves spencer.gra...@structuremonitoring.com wrote: Hello, All: What thoughts might you have on The R Software Package Development Process? I'm looking for ideas, materials, references, and / or collaborators for an article on this topic to be submitted to the Communications of the ACM. My limited experience with other languages such as Matlab and Python suggests that R may be fairly unique with CRAN and this accompanying package Perl has CPAN and TeX has CTAN. Ruby has RubyGems. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] location of Sweave.sty in R devel (2010-06-15 r52280)
On Tue, Jun 15, 2010 at 11:23:09PM +0100, Prof Brian Ripley wrote:
That is not the default behaviour of Sweave, which is to use
\usepackage{Sweave}. Do you have SWEAVE_STYLEPATH_DEFAULT set, or
some other non-standard setting that would cause this? (That is even
less needed than before, and it may be removed before 2.12.0 is
released.)
oak$ ~/local/devel/bin/R --vanilla --quiet
Sys.getenv()[SWEAVE_STYLEPATH_DEFAULT]
SWEAVE_STYLEPATH_DEFAULT
TRUE
Sorry. I forgot about that.
I should take that out of my .bashrc I suppose? Done.
I apologize for bothering the list about a stupid luser problem.
All of CRAN and BioC have been checked in the last 24 hours with
standard settings, so this does look like a problem with some
non-standard setup.
If we can reproduce it we can address the problem, but there is
nothing here that I can do more than guess at.
On Tue, 15 Jun 2010, Charles Geyer wrote:
Sorry if I was supposed to file a bug report, but I don't know whether
we're supposed to do that on R devel. I just built R devel from source
(2010-06-15 r52280) and tried to check a package with it and Sweave
failed on the vignette. It puts the line
\usepackage{/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/Sweave}
in the *.tex file but, that's not where Sweave.sty is
oak$ find ~/local/devel -name Sweave.sty
/HOME/faculty/charlie/local/devel/lib64/R/share/texmf/tex/latex/Sweave.sty
All I did was configure; make; make install and the only configure
flags were --prefix=/HOME/faculty/charlie/local/devel
and --with-valgrind-instrumentation=2 Don't see why either would mess
up Sweave.
On a linux box (openSUSE 11.1 (x86_64)).
The day before I built R-2.11.1 the same way and it works fine.
--
Charles Geyer
Professor, School of Statistics
University of Minnesota
char...@stat.umn.edu
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
--
Charles Geyer
Professor, School of Statistics
University of Minnesota
char...@stat.umn.edu
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Package development process?
Hi, Gabor: Thanks. I added a row for Ruby and columns for Package manager and Collaborative development platform to the table of Selected Repositories in the Wikipedia entry for Software repository. Please correct me if I'm wrong, but the Wiki page for Ruby suggested to me that RubyGems is a package manager, crudely comparable to the R CMD check process, while the Ruby counterpart for CRAN is the Ruby Application Archive (RAA). In addition, there is RubyForge, which sounds like analogous to R-Forge. If this is incorrect or can otherwise be improved, please either let me know or change the Wiki yourself. Any other suggestions? Thanks again, Spencer On 6/15/2010 6:52 PM, Gabor Grothendieck wrote: On Tue, Jun 15, 2010 at 9:45 PM, Spencer Graves spencer.gra...@structuremonitoring.com wrote: Hello, All: What thoughts might you have on The R Software Package Development Process? I'm looking for ideas, materials, references, and / or collaborators for an article on this topic to be submitted to the Communications of the ACM. My limited experience with other languages such as Matlab and Python suggests that R may be fairly unique with CRAN and this accompanying package Perl has CPAN and TeX has CTAN. Ruby has RubyGems. -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
