Re: [Rd] [R-sig-Debian] bug in r-base (PR#10521)
I had the same problem, but thanks to help of R-help list I solved it. I'm far from an expert user in Linux, but i solved my problems as follows. sudo apt-get install build-essential g77 sudo apt-get install refblas3 refblas3-dev sudo apt-get install r-base-core r-base-dev r-recommended I really do not know "exactly" what I did with the above commands, but now I can work with R 2.5.1. Vincent Goulet ha scritto: > [Moved from r-devel] > > Le mar. 18 déc. à 10:35, [EMAIL PROTECTED] a écrit : > > >> Full_Name: marco zamboni >> Version: no R version >> OS: ubuntu gusty >> Submission from: (NULL) (87.9.174.188) >> >> >> I have just finish to install gusty ubuntu on my AMD sempron. >> I would like to: >> $ sudo apt-get install r-base >> >> but >> ... >> I seguenti pacchetti hanno dipendenze non soddisfatte: >> r-base: Dipende: r-base-core (>= 2.6.1-1gutsy0) ma 2.5.1-1 sta per >> essere >> installato >> Dipende: r-recommended (= 2.6.1-1gutsy0) ma non sta per >> essere >> installato >> E: Pacchetto non integro >> > > First, this is not a bug with R at all; only a difficulty you have > with installing the r-base package. > > Second, this does not belong to r-devel, but to r-sig-debian. Hence > the discussion is moved to the latter forum. > > Now, did you follow the instructions in the Ubuntu README at > > http://cran.r-project.org/bin/linux/ubuntu/ > > ? What is the result of > > apt-cache policy r-base > > ? > > We should be able to help you with this information. > > Best, > > --- >Vincent Goulet, Associate Professor >École d'actuariat >Université Laval, Québec >[EMAIL PROTECTED] http://vgoulet.act.ulaval.ca > > ___ > R-SIG-Debian mailing list > [EMAIL PROTECTED] > https://stat.ethz.ch/mailman/listinfo/r-sig-debian > > -- Ottorino-Luca Pantani, Università di Firenze Dip. Scienza del Suolo e Nutrizione della Pianta P.zle Cascine 28 50144 Firenze Italia Tel 39 055 3288 202 (348 lab) Fax 39 055 333 273 [EMAIL PROTECTED] http://www4.unifi.it/dssnp/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem compiling R 2.6.1 on POWER 570 system
Cookies all around for the rapid and accurate help! I wound up using a variation of the below (the non-quoted part is what I changed): On 12/19/2007 04:15 PM, Andrew Ferris wrote: > Hello Mark, > > Here's the full configure that I used to get 2.4.1 to work on 64bit SLES on a > 570: > > ./configure CC="gcc -m64" / > CXX="gxx -m64" / CXX="g++ -m64" > F77="gfortran -m64" / > FC="gfortran -m64" / > CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" / > FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" / > LDFLAGS=-L/usr/lib64 / > --without-x This did indeed create a 64-bit executable. Alas, I won the battle but may still lose the war. Red Hat did not include many PPC64 versions of their development libraries (libxml2-devel for example) that I need to install things like AnnBuilder. It looks like RHEL 5 has these available, so I'll need to upgrade this partition and see if I can get this working. Again, thanks for the help! -Mark -- Mark Komarinski [EMAIL PROTECTED] Sr. Research Systems Architect http://ritg.med.harvard.edu Research IT Group Harvard Medical School __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] bug in by.data.frame, R-2.6.1 (PR#10506)
On Wed, 19 Dec 2007, Prof Brian Ripley wrote: > It transpires that package survey relies on the current behaviour (which is > not new in 2.6.1: R 2.0.0 did it). > > The suggested fix is reasonable if 'data' was originally a data frame, but > the default method promotes vectors to data frames, and the data frame method > used to drop them back to vectors. > > I've backed the fix out of R-patched. > > I am not sure if the current undocumented behaviour on vectors is 100% > desirable, but will amend by.default in R-devel to preserve it. > > Thomas: I think svymean() needs not to assume that 1-column data frames will > be dropped. Ok. I think that actually simplifies some things. I hope to have some time next week to catch up on a number of package issues. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] SHLIB steps on a Makefile
Hi, I need to create a Makefile.win for a given package so as to fiddle slightly with the compilation process. My Makefile works fine in Linux but I am having trouble creating Makefile.win for MinGW. I first looked at the commands that Rcmd SHLIB appeared to be running and copied those onto the Makefile. But one step seems to be missing, the creation of the _res.rc file needed by windres g++-sjlj -I$(RHOME)/include -I../inst/include/ -O2 -Wall -c pkg.cpp -o pkg.o windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I$(RHOME)/include -I../inst/include -i pkg_res.rc -o pkg_res.o g++-sjlj -shared -s -o pkg.dll pkg.def pkg.o FL pkg_res.o -L$(RHOME)/bin -lR This might be fairly obvious, but it is my first attempt at compiling with MinGW and my search has been fruitless. What is it that I need to add to replicate what Rcmd SHLIB does? Many thanks, Iago Mosqueira __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] SHLIB steps on a Makefile
Iago, On Dec 20, 2007, at 4:49 PM, Iago Mosqueira wrote: > I need to create a Makefile.win for a given package so as to fiddle > slightly with the compilation process. My Makefile works fine in > Linux but I am having trouble creating Makefile.win for MinGW. I > first looked at the commands that Rcmd SHLIB appeared to be running > and copied those onto the Makefile. But one step seems to be > missing, the creation of the _res.rc file needed by windres > > g++-sjlj -I$(RHOME)/include -I../inst/include/ -O2 -Wall -c pkg.cpp > -o pkg.o > windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" > -I$(RHOME)/include -I../inst/include -i pkg_res.rc -o pkg_res.o > g++-sjlj -shared -s -o pkg.dll pkg.def pkg.o FL pkg_res.o -L$ > (RHOME)/bin -lR > > This might be fairly obvious, but it is my first attempt at > compiling with MinGW and my search has been fruitless. > > What is it that I need to add to replicate what Rcmd SHLIB does? > If that is the only step you're missing then you have probably missed the res.rc rule from MakeDll when creating your Makefile: $(DLLNAME)_res.rc: @PERL5LIB=$(RHOME)/share/perl $(PERL) $(RHOME)/src/gnuwin32/ makeDllRes.pl $(DLLNAME) > $@ Cheers, Simon PS: Given that you can override any rule, it is usually easier to just write your modifications in Makevars[.win] when fiddling with the compilation than to replicate the whole process. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] SHLIB steps on a Makefile
On Thu, 20 Dec 2007, Iago Mosqueira wrote: > Hi, > > I need to create a Makefile.win for a given package so as to fiddle > slightly with the compilation process. My Makefile works fine in Linux That's rather dangerous: we have had lots of trouble with packages for which the Makefile works on the maintainer's Linux, but not on other people's systems (even Linux ones). Do you really, really need a Makefile.win?: I would be surprised if you did. Only 9 CRAN packages have a Makefile.win, and two of those are dummies and one other we have asked the maintainers to replace by Makevars.win as it is not portable. > but I am having trouble creating Makefile.win for MinGW. I first > looked at the commands that Rcmd SHLIB appeared to be running and > copied those onto the Makefile. But one step seems to be missing, the > creation of the _res.rc file needed by windres > > g++-sjlj -I$(RHOME)/include -I../inst/include/ -O2 -Wall -c pkg.cpp -o > pkg.o > windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" > -I$(RHOME)/include -I../inst/include -i pkg_res.rc -o pkg_res.o > g++-sjlj -shared -s -o pkg.dll pkg.def pkg.o FL pkg_res.o > -L$(RHOME)/bin -lR > > This might be fairly obvious, but it is my first attempt at compiling > with MinGW and my search has been fruitless. > > What is it that I need to add to replicate what Rcmd SHLIB does? Adding the resources is not essential: they add identification to the DLL which can be very useful but are icing on the cake. So I would not try to emulate that step. But the Makefile in use is src/gnuwin32/MakeDll and that contains $(DLLNAME)_res.rc: @PERL5LIB=$(RHOME)/share/perl $(PERL) $(RHOME)/src/gnuwin32/makeDllRes.pl $(DLLNAME) > $@ $(DLLNAME)_res.o: $(DLLNAME)_res.rc $(RHOME)/include/Rversion.h -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] SHLIB steps on a Makefile
On Dec 20, 2007 11:23 PM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Thu, 20 Dec 2007, Iago Mosqueira wrote: > > > Hi, > > > > I need to create a Makefile.win for a given package so as to fiddle > > slightly with the compilation process. My Makefile works fine in Linux > > That's rather dangerous: we have had lots of trouble with packages for > which the Makefile works on the maintainer's Linux, but not on other > people's systems (even Linux ones). > > Do you really, really need a Makefile.win?: I would be surprised if you > did. Only 9 CRAN packages have a Makefile.win, and two of those are > dummies and one other we have asked the maintainers to replace by > Makevars.win as it is not portable. > > > but I am having trouble creating Makefile.win for MinGW. I first > > looked at the commands that Rcmd SHLIB appeared to be running and > > copied those onto the Makefile. But one step seems to be missing, the > > creation of the _res.rc file needed by windres > > > > g++-sjlj -I$(RHOME)/include -I../inst/include/ -O2 -Wall -c pkg.cpp > > -o pkg.o > > windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" > > -I$(RHOME)/include -I../inst/include -i pkg_res.rc -o pkg_res.o > > g++-sjlj -shared -s -o pkg.dll pkg.def pkg.o FL pkg_res.o > > -L$(RHOME)/bin -lR > > > > This might be fairly obvious, but it is my first attempt at compiling > > with MinGW and my search has been fruitless. > > > > What is it that I need to add to replicate what Rcmd SHLIB does? > > Adding the resources is not essential: they add identification to the > DLL which can be very useful but are icing on the cake. So I would not > try to emulate that step. > > But the Makefile in use is src/gnuwin32/MakeDll and that contains > > $(DLLNAME)_res.rc: > @PERL5LIB=$(RHOME)/share/perl $(PERL) > $(RHOME)/src/gnuwin32/makeDllRes.pl $(DLLNAME) > $@ > > $(DLLNAME)_res.o: $(DLLNAME)_res.rc $(RHOME)/include/Rversion.h > Many thanks for the information. I am trying to make a package C code compile against a DLL already present in another package, so I need to include its location in the call to gcc. I'll see what the most portable system could be and will test widely. Regards, Iago Mosqueira __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] using example() with S4 documentation
Hi list,
Developping a plot method for a S4 class 'foo' (signature being x="foo",
y="missing"), I would like to access the example contained inside the
\examples{} section of the corresponding Rd file. This file contains the
aliases: \alias{plot-methods} and \alias{plot,foo,missing}. There is no
trouble to access the documentation using:
method ? plot("foo")
or
?plot(new("foo"))
Now, is it possible to have example() work as well ? I tried using the
"package" argument of "example" without success...
Thanks in advance.
Cheers,
Thibaut.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://pbil.univ-lyon1.fr/software/adegenet/
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[Rd] typo in cbind help page (PR#10523)
--=_Part_1509_5179695.1198191004146 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit --=_Part_1509_5179695.1198191004146 Content-Type: application/octet-stream; name=R.bug.report Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename=R.bug.report # Your mailer is set to "none" (default on Windows), # hence we cannot send the bug report directly from R. # Please copy the bug report (after finishing it) to # your favorite email program and send it to # # [EMAIL PROTECTED] # ## The bug is that the cbind help should read stringsAsFactors=FALSE ( rather than TRUE ) in the Data Frame Methods section. --please do not edit the information below-- Version: platform = i686-pc-linux-gnu arch = i686 os = linux-gnu system = i686, linux-gnu status = major = 2 minor = 6.0 year = 2007 month = 10 day = 03 svn rev = 43063 language = R version.string = R version 2.6.0 (2007-10-03) Locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:datasets, .Marks.env, package:lattice, package:nnet, package:car, package:filehash, package:reshape, package:zoo, package:chron, package:MASS, package:utils, package:stats, package:graphics, package:grDevices, package:methods, Autoloads, package:base --=_Part_1509_5179695.1198191004146-- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
