gmane.comp.lang.r.fedora http://blog.gmane.org/gmane.comp.lang.r.fedora hourly 1 1901-01-01T00:00+00:00 Gmane http://gmane.org/img/gmane-25t.png http://gmane.org tcktk problem with custom R 2.15.0 build on RHEL5 http://comments.gmane.org/gmane.comp.lang.r.fedora/201 <pre>Hi all, Please bear with me because I'm not all that familiar with R. I manage a research cluster that's running Red Hat 5.6 (64-bit), and we recently installed version 2.15.0 of R for some users. Here's how we built it: ./configure --prefix=/opt/shared/R/2.15.0 --with-tcltk --with-system-zlib --with-system-bzlib --with-system-pcre --with-lapack --enable-R-shlib When we ran "make check-all" it didn't report any obvious problems, and we successfully installed a number of add-on's from CRAN. But when one of our users tries to use R with tcltk he runs into a problem: R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) ... &gt; library("sqldf") Loading required package: DBI Loading required package: gsubfn Loading required package: proto Loading required namespace: tcltk Loading Tcl/Tk interface ... done Loading required package: chron Loading required package: RSQLite Loading required package: RSQLite.extfuns &gt; result&lt;-sqldf("select data.*, meth450part.chromStart as MethChromStart, meth450part.chromEnd as MethChromEnd, meth450part.strand as MethStrand, meth450part.name as MethName, meth450part.score as MethScore from data join meth450part where data.V1=meth450part.chrom and data.V2&lt;=meth450part.chromStart and data.V3&gt;=meth450part.chromEnd") Loading required package: tcltk Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = "tclObj") : [tcl] unknown math function "min". Can anybody tell me why we're getting this tcl error about the function "min" not being found? I've been unable to find anything on the web that relates to this. We're using version 8.14.3 of tcltk (the RedHat supplied packages). Thanks, -Bruce </pre> Bruce Pennypacker 2012-05-21T20:30:52 Paulo Sousa deixou uma mensagem para você... http://comments.gmane.org/gmane.comp.lang.r.fedora/192 <pre>Paulo Sousa deixou uma mensagem para você... Só você pode ler o conteúdo desta mensagem e ver quem a enviou. Delete a qualquer momento ou responda imediatamente com o sistema de troca de mensagens. Para descobrir o que diz a mensagem, siga este link. http://eu1.badoo.com/0278107725/in/XTpafbiaVyU/?lang_id=61&amp;m=63&amp;mid=4f9211a500000000003d00006126f86d Mais gente dessa região que está no Badoo Reis (Porto, Portugal) Diana (Porto, Portugal) Stefania (Porto, Portugal) http://eu1.badoo.com/0278107725/in/XTpafbiaVyU/?lang_id=61&amp;m=63&amp;mid=4f9211a500000000003d00006126f86d Se o link desta mensagem não funcionar, copie e cole-o em seu navegador. Este email faz parte de nosso sistema de entrega para a mensagem enviada por Paulo Sousa. Se recebeu este email por engano, por favor ignore-o. A mensagem será deletada em breve. Divirta-se! A Equipe Badoo Este email foi enviado por Badoo Trading Limited (endereço postal abaixo). http://eu1.badoo.com/impersonation.phtml?lang_id=61&amp;mail_code=63&amp;email=r-sig-fedora%40r-project.org&amp;secret=&amp;action=block&amp;block_code=e0e30f&amp;m=63&amp;mid=4f9211a500000000003d00006126f86d Badoo Trading Limited é uma empresa registrada na Inglaterra e País de Gales com CRN 7540255 e firma registrada no seguinte endereço 12 Red Lion Square, Londres, WC1R 4QD. [[alternative HTML version deleted]] _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora </pre> Badoo 2012-04-21T01:47:19 Installing texlive dependencies http://comments.gmane.org/gmane.comp.lang.r.fedora/188 <pre>Hello ALL! I am running Fedora 16 x86_64. Due to some dubious problems, that i couldn't resolve, with the TeXLive (2007, which is a default), I removed it. That removed R as well, and some other dependent packages. Then, I installed TeXLive 2011 from CTAN. However, when I wanted to install R, from Fedora's repositories, it asks for some TeX dependencies (for example, tex-preview, texinfo-tex, texlive, texlive-dvips etc.). I know that new TeX is installed in other place (/usr/local/texlive/2011/), than the old, default of the Tex 2007 (/usr/share/texmf/). But, I defined PATH properly: PATH=/usr/local/texlive/2011/bin/x86-64-linux:$PATH Also, I have tried with the symbolic link: ln -s /usr/local/texlive/2011 /usr/share/texmf So, I wonder why R asks for those TeX-packages? Can I tell it where to look? In any case, how to fix this mess? Thanks in advance, Petar </pre> Petar Milin 2012-04-18T15:54:51 R-repo.org ? http://comments.gmane.org/gmane.comp.lang.r.fedora/180 <pre> On a totally different topic (or maybe not so different)... I noticed that r-repo.org's first release is also its last release. What's blocking you? Can I help? - Allen S. Rout </pre> Allen S. Rout 2012-03-13T21:04:29 Trying to use current R2spec on RHEL. http://comments.gmane.org/gmane.comp.lang.r.fedora/167 <pre> Is there somewhere a succinct guide to just how much extra crud we need to install on RHEL to make use of EPEL packages? [root&lt; at &gt;troll-1 noarch]# rpm -ivh R2spec-4.1.0-1.el6.noarch.rpm error: Failed dependencies: fedora-packager is needed by R2spec-4.1.0-1.el6.noarch [root&lt; at &gt;troll-1 noarch]# wget http://dl.fedoraproject.org/pub/epel/6/x86_64/fedora-packager-0.5.9.4-1.el6.noarch.rpm [...] [root&lt; at &gt;troll-1 noarch]# rpm -ivh fedora-packager-0.5.9.4-1.el6.noarch.rpm error: Failed dependencies: bodhi-client is needed by fedora-packager-0.5.9.4-1.el6.noarch fedora-cert = 0.5.9.4-1.el6 is needed by fedora-packager-0.5.9.4-1.el6.noarch fedpkg &gt;= 1.0 is needed by fedora-packager-0.5.9.4-1.el6.noarch koji is needed by fedora-packager-0.5.9.4-1.el6.noarch mock is needed by fedora-packager-0.5.9.4-1.el6.noarch redhat-rpm-config is needed by fedora-packager-0.5.9.4-1.el6.noarch rpmdevtools is needed by fedora-packager-0.5.9.4-1.el6.noarch rpmlint is needed by fedora-packager-0.5.9.4-1.el6.noarch ykpers is needed by fedora-packager-0.5.9.4-1.el6.noarch Oy. - Allen S. Rout </pre> Allen S. Rout 2012-03-12T20:10:06 install warning on fedora 16 http://comments.gmane.org/gmane.comp.lang.r.fedora/162 <pre>Hi: I am working on some code in a package I'm writing and I'm getting the warning below when I do the install on a newly installed fedora 16 OS. But when I run the same install on windows, I don't get the error. and when I used to run the install on Fedora 14 ( I missed Fedora 15 ), I didn't get the warning there either ? Does anyone know what the problem might be ? Maybe a difference with gcc ? It's only a warning but it scares me a little because the variables should be getting used contrary to what the warning says. Thanks a lot for any hints/suggestions. My session Info is below and the install output is after that. and happy holidays to all also. and #======================================================================= sessionInfo() R version 2.14.0 (2011-10-31) Platform: i386-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] datasets graphics tools grid stats utils grDevices methods base other attached packages: [1] bmod_0.0-10.1 FinTS_0.4-4 numDeriv_2010.11-1 fgui_1.0-2 lmtest_0.9-29 RSQLite_0.10.0 DBI_0.2-5 filehash_2.2 [9] gridExtra_0.8.5 latticeExtra_0.6-19 RColorBrewer_1.0-5 lattice_0.20-0 zoo_1.7-6 chron_2.3-42 loaded via a namespace (and not attached): [1] tcltk_2.14.0 #====================================================================== OUTPUT WHEN INSTALLING THE PACKAGE #========================================================================= :~/research/R/Rlibs/library&gt; R CMD INSTALL -l . bmod_0.0-10.1.tar.gz [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_ TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C" [1] "LOADING MASS LIBRARY" [1] "LOADING LATTICE LIBRARY" * installing *source* package 'bmod' ... ** libs gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ar1_functions.c -o ar1_functions.o ar1_functions.c: In function ‘calc_ar1_hessian’: ar1_functions.c:261:10: warning: variable ‘phigrad’ set but not used [-Wunused-but-set-variable] ar1_functions.c:260:10: warning: variable ‘alphagrad’ set but not used [-Wunused-but-set-variable] ar1_functions.c:259:10: warning: variable ‘betagrad’ set but not used [-Wunused-but-set-variable] ar1_functions.c:258:10: warning: variable ‘rhograd’ set but not used [-Wunused-but-set-variable] gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c ma1_functions.c -o ma1_functions.o ma1_functions.c: In function ‘calc_ma1_hessian’: ma1_functions.c:246:10: warning: variable ‘alphagrad’ set but not used [-Wunused-but-set-variable] ma1_functions.c:245:10: warning: variable ‘betagrad’ set but not used [-Wunused-but-set-variable] ma1_functions.c:244:10: warning: variable ‘rhograd’ set but not used [-Wunused-but-set-variable] gcc -m32 -std=gnu99 -shared -Wl,-z,relro -o bmod.so ar1_functions.o ma1_functions.o -L/usr/lib/R/lib -lR installing to /home/markleeds/research/R/Rlibs/library/bmod/libs ** R ** demo ** inst ** preparing package for lazy loading ** help No man pages found in package 'bmod' *** installing help indices ** building package indices ... ** testing if installed package can be loaded [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C" [1] "LOADING MASS LIBRARY" [1] "LOADING LATTICE LIBRARY" * DONE (bmod) :~/research/R/Rlibs/library&gt; [[alternative HTML version deleted]] _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora </pre> Mark Leeds 2011-12-25T03:39:39 error installing geepack on 64bit fedora 16 http://comments.gmane.org/gmane.comp.lang.r.fedora/159 <pre>Hi Does anyone know how to install geepack on fedora 16 - 64bit - R google only yields a couple of hits with unanswered Q Installation just throws an error with an undefined symbol. Previous version won't load due to lack of NAMESPACE. Sadly, its a show stopper w.r.t. upgrading my work PCs Any hints/suggestions most welcome Thanks Cheers Peter ================================================================ _ platform x86_64-redhat-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 14.0 year 2011 month 10 day 31 svn rev 57496 language R version.string R version 2.14.0 (2011-10-31) Installing package(s) into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) trying URL 'http://cran.csiro.au/src/contrib/geepack_1.1-3.tar.gz' Content type 'application/x-gzip' length 206062 bytes (201 Kb) opened URL ================================================== downloaded 201 Kb * installing *source* package ‘geepack’ ... ** package ‘geepack’ successfully unpacked and MD5 sums checked ** libs g++ -m64 -I/usr/include/R -I../inst/include -DNDEBUG -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c famstr.cc -o famstr.o +++++++++++++++++ stuff deleted - all OK +++++++++++++++++++++ ** building package indices ... *** tangling vignette sources ... ‘geepack-manual.Rnw’ using ‘latin1’ ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib64/R/library/geepack/libs/geepack.so': /usr/lib64/R/library/geepack/libs/geepack.so: undefined symbol: _Z5ValidIiEN3TNT6VectorIT_EERS3_RNS1_IiEE Error: loading failed Execution halted ERROR: loading failed * removing ‘/usr/lib64/R/library/geepack’ * restoring previous ‘/usr/lib64/R/library/geepack’ ++++ startup stuff deleted +++++ Error in library(geepack) :   package ‘geepack’ does not have a NAMESPACE and should be re-installed&gt; a bit of a catch 22 thanks </pre> Peter Baker 2011-12-14T08:08:16 installing R from source on fedora http://comments.gmane.org/gmane.comp.lang.r.fedora/152 <pre>Hello: I've included a txt file ( some day, when I have more time, I'll turn it into latex ) that has the steps for installing R from source on Fedora. It was written only for people like myself who find these tasks difficult. Also, could someone from the R-Sig-Fedora list let me know if the txt file was attached because I don't actually receive emails that I send to the R-Sig-Fedora list. ( not sure why this is ? ). If it doesn't go through, I'll cut and paste and re-send it in the email itself. Thanks. The following are instructions for installing R from source in Fedora Linux. Note that I deleted the previous version of R and any directories associated with it ( except for packages pevious downloadedfrom cran. These packages do not need to be deleted as long as they are in a personal and non R build related directory ) in order to make these instructions for installing R from source rather than for upgrading R. Upgrading requires a slightly different set of instructions and will not be discussed here. Some of the steps in these instructions may not be exactly required and it is possible that there are alternative ways of achieving the same build. They only reflect the way I achieved my build. Many thanks to Gavin Simpson, Marc Schwartz, Pierre-Yves Chibon and Jose Matos for their help in creating these instructions. Most of the instructions resulted from various communications between myself and Gavin Simpson. There are what I view as eight steps when installing R on Fedora from source and these are described below: #========================================================================================================================================================================== Step 1) Create a directory structure right above your home directory called R/2.14/build by going to your home directory and doing mkdir -p R/2.14/build. The 2.14 directory will eventually contain the R source tree and the build directory will contain the various output once the R source tree is configured and built. #============================================================================================================================================ Step 2) Go to the build directory by doing cd ~/R/2.14/build and grab the latest source from the svn repository by issuing the command: svn checkout https://svn.r-project.org/branches/R-2-14-branch ../ This command will install the R source tree in the ~/R/2.14 directory. Note that the step above can be modified by grabbing the the latest release from a cran mirror instead: Go to www.r-project.org and then one of the cran mirrors. Click on the sources icon and download the R.X.tar.gz file to the ~/R/2.14 directory. You can extract the source from the tar.gz fiel by issuing the command t tar xvfz filename.tar.gz This will extract the source tree also. But note that this source will not include any of the latest patches that have occurred since that R release. Note that, if svn is used to checkout the source tree, then Step 4 below is required. If svn is not used and used and tar is used instead, then Step 4 is not necessary. Next we need to configure and build R from the source tree and this is where things can get tricky. The reason it can be tricky is because there are many header and development files that are required to be installed on your machine in order for the build to work correctly. As far as I know, there are two insurance policies that can be taken out in order to try to insure that all of the headers and development packages are on your machine. These policies are described in steps 3A and 3B. I recommend that both policies be used because if 3b) tries to load a dependency that is already installed, it will just stop with a message that the package is already installed. #============================================================================================================================================ Step 3A) Use yum or the Fedora software manager and install the following packages. If they already installed on your machine, you will be notified of this when you try to install them. The RPMs that should be installed are listed below. libX11 libX11-devel libXt libXt-devel readline-devel cairo-devel libtiff-devel libjpeg-turbo-devel libpng-devel tk-devel tcl-devel Note that it does not matter what directory you are in when installing these packages. So, for example, if you are using yum, then do su -c "yum install libX11" to install libX11.( Note that su -c simulates that you are logged in as root without you having to actually log in as root ). If instead you want to use the software manager rather than yum, then click on System, then Administration then Add/Remove Software and then follow the instructions. They are straightforward. #============================================================================================================================================ Step 3B) Install the yum-utils package by doing yum install yum-utils. This package contains a program called yum-builddep which builds the dependencies that another software package needs. Therefore, once yum-utils is installed, one can issue the command su -c "yum-builddep R" and this should download and install the variious packages that R is dependent on. Again it does not matter what directory you are in when you issue this command. The steps 3A) and 3B) should most likely provide all the header files and development tools that are needed to build R from source. But you won't know until you try it. #============================================================================================================================================ Step 4) Note that, if R was checked out using svn, then the svn repository does not contain th source files for the Recommended R packages and these need to be downloaded seperately using rsync. Therefore, if R was checked out from the svn repo, then, while in the ~R/2.14 directory, issue the command ./tools/rsync-recommended This command will download the sources of the recommended packages like MASS, lattice etc. #============================================================================================================================================ Step 5) Now we can finally run the configure command. Make sure that you are in the directory ~/R/2.14/build and issue the command ../configure The process should complete fairly quickly and the last 10 lines or so of the configure output will indicate whether the configure has run without errors. Hopefully there won't be any errors. If there are errors, then , if they are not obvious, the best thing to do is email the R-Sig-Fedora list. There are many generous and knowledgeable people there who are glad to help. Assuming there are no errors, then proceed to Step 6. #============================================================================================================================================ Step 6) Now we need to build what we configured by issuing the make command. Again make sure that you are in the directory ~/R/2.14/build and issue the command make at the command line. Although the make command will will take a long time to complete, if it goes through completely, that indicates that it worked. If there is an error at any point during the make, the make process will stop and indicate that an error has occurred and provide a brief description of the error. #============================================================================================================================================ Step 7) Now, when in the ~/R/2.14/build directory, issue the command make check to verify that everything was built correctly. You should see a lot of "OK" statements and no "Error" statements. #============================================================================================================================================ Step 8) Finally, although R has been built successfully, we still need to set things up so that, no matter what directory we are in on the machine, we can issue the command R from that directroy and start an R session. Assuming that R was built correctly, then there should exist a directory called ~/R/2.14/build/bin. In this directory reside many bash scripts one of which is called R. R is a bash shell wrapper for the R executable. So, if we can make a link so that, whenever one types R anywhere, this script is run, then this will allow us to run R from any directory by typing R. How to do this : A) Create a directory called bin under your home directory by issuing the command mkdir ~/bin. Also make sure that this directory is on your path by including it in the definition of the PATH variable in your .bashrc file. B) Make a link to the R wrapper in ~R/2.14/build/bin directory by issuing the following command in the bin directory that you made in your home directory: ln -s ~/R/2.14/build/bin/R ~/bin/R This command creates a link so that, whenever you type R anywhere, this will issue the R command in the ~/bin/R directory which is symbolic for the R wrapper in the /build/bin directory. In this manner, whenever R is typed at the command line of any directory, an instance of R will be started. #============================================================================================================================================ Any mistakes in these instructions are due to me and they are subject to change. Again, thanks to eeveryone who helped me install R from source especially Gavin Simpson. _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora </pre> Mark Leeds 2011-11-09T04:47:13 close but no cigar http://comments.gmane.org/gmane.comp.lang.r.fedora/150 <pre>Hi Everyone: It turns out that there's still a small ( I hope ) problem. I'm close but that only counts in horse shoes and hand grenades. Here's my problem: When trying to load a package that I am writing, the load is looking for the packageDescription function in the utils package but not finding the utils package. I looked on cran and utils is not there which makes me think that it should have been part of the build. But then I went to my recommended packages directory and it's not there ? (See below ). Is that an error by me that it's not there ? I definitely don't know how to tell R that it needs to load the utils package since I don't seem to have access to the package myself. Thanks for any enlightenment and my apologies for the false SUCCESS earlier. Mark :~/R/2.14/src/library/Recommended&gt; dir total 6748 -rw-rw-r--. 1 markleeds markleeds 3574 Nov 7 10:11 Makefile.in -rw-rw-r--. 1 markleeds markleeds 1661 Nov 7 10:11 Makefile.win -rw-rw-r--. 1 markleeds markleeds 30402 Nov 7 10:20 KernSmooth_2.23-6.tar.gz -rw-rw-r--. 1 markleeds markleeds 466772 Nov 7 10:20 MASS_7.3-16.tar.gz -rw-rw-r--. 1 markleeds markleeds 2513797 Nov 7 10:20 Matrix_1.0-1.tar.gz -rw-rw-r--. 1 markleeds markleeds 225195 Nov 7 10:20 boot_1.3-3.tar.gz -rw-rw-r--. 1 markleeds markleeds 20128 Nov 7 10:20 class_7.3-3.tar.gz -rw-rw-r--. 1 markleeds markleeds 246438 Nov 7 10:20 cluster_1.14.1.tar.gz -rw-rw-r--. 1 markleeds markleeds 12392 Nov 7 10:20 codetools_0.2-8.tar.gz -rw-rw-r--. 1 markleeds markleeds 339028 Nov 7 10:20 foreign_0.8-46.tar.gz -rw-rw-r--. 1 markleeds markleeds 358849 Nov 7 10:20 lattice_0.20-0.tar.gz -rw-rw-r--. 1 markleeds markleeds 510979 Nov 7 10:20 mgcv_1.7-10.tar.gz -rw-rw-r--. 1 markleeds markleeds 705660 Nov 7 10:20 nlme_3.1-102.tar.gz -rw-rw-r--. 1 markleeds markleeds 23418 Nov 7 10:20 nnet_7.3-1.tar.gz -rw-rw-r--. 1 markleeds markleeds 135545 Nov 7 10:20 rpart_3.1-50.tar.gz -rw-rw-r--. 1 markleeds markleeds 40627 Nov 7 10:20 spatial_7.3-3.tar.gz -rw-rw-r--. 1 markleeds markleeds 1248288 Nov 7 10:20 survival_2.36-10.tar.gz lrwxrwxrwx. 1 markleeds markleeds 18 Nov 7 10:20 MASS.tgz -&gt; MASS_7.3-16.tar.gz lrwxrwxrwx. 1 markleeds markleeds 21 Nov 7 10:20 lattice.tgz -&gt; lattice_0.20-0.tar.gz lrwxrwxrwx. 1 markleeds markleeds 19 Nov 7 10:20 Matrix.tgz -&gt; Matrix_1.0-1.tar.gz lrwxrwxrwx. 1 markleeds markleeds 19 Nov 7 10:20 nlme.tgz -&gt; nlme_3.1-102.tar.gz lrwxrwxrwx. 1 markleeds markleeds 23 Nov 7 10:20 survival.tgz -&gt; survival_2.36-10.tar.gz lrwxrwxrwx. 1 markleeds markleeds 17 Nov 7 10:20 boot.tgz -&gt; boot_1.3-3.tar.gz lrwxrwxrwx. 1 markleeds markleeds 21 Nov 7 10:20 cluster.tgz -&gt; cluster_1.14.1.tar.gz lrwxrwxrwx. 1 markleeds markleeds 22 Nov 7 10:20 codetools.tgz -&gt; codetools_0.2-8.tar.gz lrwxrwxrwx. 1 markleeds markleeds 21 Nov 7 10:20 foreign.tgz -&gt; foreign_0.8-46.tar.gz lrwxrwxrwx. 1 markleeds markleeds 24 Nov 7 10:20 KernSmooth.tgz -&gt; KernSmooth_2.23-6.tar.gz lrwxrwxrwx. 1 markleeds markleeds 19 Nov 7 10:20 rpart.tgz -&gt; rpart_3.1-50.tar.gz lrwxrwxrwx. 1 markleeds markleeds 18 Nov 7 10:20 class.tgz -&gt; class_7.3-3.tar.gz lrwxrwxrwx. 1 markleeds markleeds 17 Nov 7 10:20 nnet.tgz -&gt; nnet_7.3-1.tar.gz lrwxrwxrwx. 1 markleeds markleeds 20 Nov 7 10:20 spatial.tgz -&gt; spatial_7.3-3.tar.gz lrwxrwxrwx. 1 markleeds markleeds 18 Nov 7 10:20 mgcv.tgz -&gt; mgcv_1.7-10.tar.gz :~/R/2.14/src/library/Recommended&gt; [[alternative HTML version deleted]] </pre> Mark Leeds 2011-11-07T20:39:59 SUCCESS http://comments.gmane.org/gmane.comp.lang.r.fedora/149 <pre>finally R 2.14 runs for me on fedora linux !!!!!! thanks to gavin, marc, jose and pierre for helping me. but especially gavin. I still have to clean things up and make install instructions so I can send it to this list. But first I need to sleep. I will send the instructions later today since that's absolutely THE LEAST i can do. I haven't gotten much sleep the last couple of days and my head hurts so I'd rather make them with a non-hurting head. this way, I won't skip key details like rsync-recommended for example :). thanks again to everyone. On Mon, Nov 7, 2011 at 3:19 PM, Gavin Simpson &lt;ucfagls-hclig2XLE9Zaa/9Udqfwiw&lt; at &gt;public.gmane.org&gt; wrote: [[alternative HTML version deleted]] </pre> Mark Leeds 2011-11-07T16:18:31 still working on building R from source http://comments.gmane.org/gmane.comp.lang.r.fedora/141 <pre>Hi Everyone: Gavin's been so generous and patient that I figured I'd give him a break and send this snag to the list. When I do get this working, I will send an "How to build R from the tarball " instructions message to this list for posterity's sake ( and myself and anyone else who doesn't know how to build R from the tarball ). So, here's my latest snag: Gavin got me through the configure and the make. So, then I did make check and I get below. But, since that error didn't seem that serious, I figured I'd see whether R would run anyway. The output of the R command is below what's below. It's expecting a file in /usr/lib/R I think ? But maybe the fact that the tests don't complete successfully causes that. I looked to see if I have an ENVIRONMENT variable for R in my .bashrc but it doesn't have one. Thanks for all the help. From past experiences, I knew it was going to be a long road and it has been but I'm getting close. Mark END OF make check OUTPUT #========================================================================================================= make[2]: Entering directory `/home/markleeds/R/2.14/build/tests' running regression tests ... make[3]: Entering directory `/home/markleeds/R/2.14/build/tests' running code in '../../tests/reg-tests-1a.R' ... OK running code in '../../tests/reg-tests-1b.R' ... OK running code in '../../tests/reg-tests-2.R' ... OK comparing 'reg-tests-2.Rout' to '../../tests/reg-tests-2.Rout.save' ... OK running code in '../../tests/reg-examples1.R' ... OK running code in '../../tests/reg-examples2.R' ... OK running code in '../../tests/reg-packages.R' ...make[3]: *** [reg-packages.Rout] Error 1 make[3]: Leaving directory `/home/markleeds/R/2.14/build/tests' make[2]: *** [test-Reg] Error 2 make[2]: Leaving directory `/home/markleeds/R/2.14/build/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/home/markleeds/R/2.14/build/tests' make: *** [check] Error 2 # THEN TRY TO RUN R #================================================================================================== :~/R/2.14/build&gt; R /usr/bin/R: line 229: /usr/lib/R/etc/ldpaths: No such file or directory :~/R/2.14/build&gt; ^C :~/R/2.14/build&gt; [[alternative HTML version deleted]] </pre> Mark Leeds 2011-11-06T23:43:30 installing 2.14.0 on fedora http://comments.gmane.org/gmane.comp.lang.r.fedora/135 <pre>Hi: Does anyone know of instructions for installing R.2.14.0 on fedora-linux ( I'm using f14 ) using only the tar.gz file. I don't think it's available at the fedora repo so I can't use yum. I've look at the R-installation instructions but I didn't get very far with that. Even just an internet link is appreciated. Thanks. Mark [[alternative HTML version deleted]] </pre> Mark Leeds 2011-11-05T15:08:42 Scrolling in Help System Doesn't Work http://comments.gmane.org/gmane.comp.lang.r.fedora/126 <pre>UsRs, When accessing help by typing, for example, the up and down keys do no longer scroll the help page. The page-up and page-down keys also do not work any longer. I can scroll down by pressing the d key, but I cannot scroll up by pressing the b key (although it should work according to the text displayed when you press the h key). I'm not sure whether this question is Fedora-specific, but since this list is most close to my configuration I first would like to know if this can be replicated (or maybe I'm missing something obvious). Below is more information on my computer. Thanks, Michael I'm running F15 and R is from the Fedora repos. R version 2.13.1 (2011-07-08) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.1 [1] "LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION=C" </pre> Michael Smith 2011-08-05T14:40:52 multiple installations of R (in Fedora) http://comments.gmane.org/gmane.comp.lang.r.fedora/125 <pre>Dear list, so far I installed new versions of R on top of the old one in default /linux/local/lib64 . For several reasons (mostly compatibility issues) I would like to change this and to keep older versions still functional/available. Furthermore this should allow to perform installing and testing completely independent of any user still using a precedent version of R, and the switch for users just wanting the latest version should work via changing a simple link. I've checked through the documents for installation (http://cran.r-project.org/doc/manuals/R-admin.html#Installation) and the R-FAQ (http://cran.r-project.org/doc/FAQ/R-FAQ.html) and the mailing list archive (http://tolstoy.newcastle.edu.au/R/about.html) for further information on this issue, but somehow I'm not getting this working ... However, I'm sure many of you might be doing somtyhing of this kind, so that's why I'm looking for your advice. I'm not sure if that matters, at this moment I still have fully another functional installation of R in (default) /linux/local/lib64 . So the place I'd like to install (and keep various versions of R) now/in the future is /linux/biolo/R_fedora/ where I have a copy of R-latest.tar (which is the version I'd like to install at this moment, later e.g. developer versions of R might be added as well) Here the steps I tried : tar -xvf R-latest.tar # then I go the directory that has been created : cd /linux/biolo/R_fedora/R-2.13.1/ ./configure --enable-R-shlib --prefix=/linux/biolo/R_fedora/R-2.13.1 # until here everything seems to work fine make here I get : make[1]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/m4' make[1]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tools' make[1]: Nothing to be done for `R'. ... make[1]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' installing parsed Rd make[3]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' WARNING: ignoring environment value of R_HOME base WARNING: ignoring environment value of R_HOME stats WARNING: ignoring environment value of R_HOME utils WARNING: ignoring environment value of R_HOME methods WARNING: ignoring environment value of R_HOME graphics WARNING: ignoring environment value of R_HOME grDevices WARNING: ignoring environment value of R_HOME datasets WARNING: ignoring environment value of R_HOME grid WARNING: ignoring environment value of R_HOME tools WARNING: ignoring environment value of R_HOME tcltk WARNING: ignoring environment value of R_HOME splines WARNING: ignoring environment value of R_HOME stats4 WARNING: ignoring environment value of R_HOME compiler make[3]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' building/updating package metadata ... make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' writing package indices make[3]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library' WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME WARNING: ignoring environment value of R_HOME make[3]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[1]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library' make[1]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library/Recommended' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/src/library/Recommended' make[2]: `stamp-recommended' is up to date. make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library/Recommended' make[1]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/src/library/Recommended' When I then try to go on with make check this will give : make[1]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tests' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tests' make[3]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tests/Examples' WARNING: ignoring environment value of R_HOME Testing examples for package 'base' ... Testing examples for package 'compiler' comparing 'compiler-Ex.Rout' to 'compiler-Ex.Rout.prev' ... OK make[3]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/tests/Examples' make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/tests' make[2]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tests' running strict specific tests make[3]: Entering directory `/linux/biolo/R_fedora/R-2.13.1/tests' running code in 'eval-etc.R' ... OK comparing 'eval-etc.Rout' to './eval-etc.Rout.save' ...WARNING: ignoring environment value of R_HOME 1d0 &lt; WARNING: ignoring environment value of R_HOME make[3]: *** [eval-etc.Rout] Error 1 make[3]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/tests' make[2]: *** [test-Specific] Error 2 make[2]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/linux/biolo/R_fedora/R-2.13.1/tests' make: *** [check] Error 2 Do you have any ideas what I'm not getting right or what I could try next ? Is there a confusion between R_HOME of the already existing installation of R and how could I make the co-habit without interfering newer installations ? Thank's in advance, Wolfgang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France wolfgang.raffelsberger (a t) igbmc.fr [[alternative HTML version deleted]] </pre> Wolfgang RAFFELSBERGER 2011-07-18T10:23:24 License of the nutshell package http://comments.gmane.org/gmane.comp.lang.r.fedora/121 <pre>Hello, I wish to package the nutshell package. I need help to understand which license is relevant. The upstream page at http://cran.r-project.org/web/packages/nutshell/index.html says that the license is "file LICENSE". This is further explained at http://cran.r-project.org/web/packages/nutshell/LICENSE as [snip] The audioscrobbler data is made avaialable under the following Creative Commons license: http://creativecommons.org/licenses/by-nc-sa/1.0/ All other data files are made available under a Creative Commons Attribution 3.0 United States License: http://creativecommons.org/licenses/by/3.0/us [/snip] So, which version of the creative commons license is appropriate ? Thanks and regards, </pre> Pai 2011-03-16T07:03:19 Latest version RPM for RHEL5 http://comments.gmane.org/gmane.comp.lang.r.fedora/119 <pre>Hello, As of now, the latest version RPM for RHEL5 is 2.10 (http://probability.ca/cran/bin/linux/redhat/el5/x86_64/). I would really like to be able to use some features/fixes in later versions. So can a 2.12.2 RPM for RHEL5 be compiled? Thank you. William NOTICE: Confidential message which may be privileged. Unauthorized use/disclosure prohibited. If received in error, please go to www.td.com/legal for instructions. AVIS : Message confidentiel dont le contenu peut être privilégié. Utilisation/divulgation interdites sans permission. Si reçu par erreur, prière d'aller au www.td.com/francais/avis_juridique pour des instructions. </pre> Fu, Jie Ning 2011-03-15T19:08:19 installing R in Fedora14 with yum http://comments.gmane.org/gmane.comp.lang.r.fedora/114 <pre>Hi, I want to install R with yum. I did yum info R and got the following *Error: Cannot retrieve repository metadata (repomd.xml) for repository: fedora. Please verify its path and try again *Then googled help an followed the instructions in http://digitizor.com/2009/06/17/how-to-fix-the-cannot-retrieve-repository-metadata-repomd-xml-error-in-fedora-11/ but still don't know how to install R in fedora14 using yum. Any help will be very welcome jules [[alternative HTML version deleted]] </pre> jules hernandez 2011-03-07T13:05:48 CentOS 5 install won't make with shared libs enabled http://comments.gmane.org/gmane.comp.lang.r.fedora/110 <pre>Hi, I've been trying to get a shared library version of the R package(version 2.12.1) installed on a CentOS 5 system. (It installs fine without but other packages demand shared libs - namely Rapache). I've tried this with yum but don't know of any flags to set to tell it to installl with shared libs enabled. I then tried a local R install as non-root with source packages: after downloading the latest tarball and unzipping: ./configure --prefix=/opt --enable-R-shlib make make[3]: Entering directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main' gcc -std=gnu99 -shared -L/usr/local/lib64 -o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o gramLatex.o gramRd.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a ../extra/xz/liblzma.a -L../../lib -lRblas -lgfortran -lm -lreadline -lncurses -ldl -lm /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libR.so] Error 1 make[3]: Leaving directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main' make[2]: *** [R] Error 2 make[2]: Leaving directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main' make[1]: *** [R] Error 1 make[1]: Leaving directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src' make: *** [R] Error 1 I then added the -fPIC to the CC line in Makeconf and did a new make but no joy: make[3]: Entering directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main' gcc -std=gnu99 -fPIC -shared -L/usr/local/lib64 -o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o gramLatex.o gramRd.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/Rembedded.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a ../extra/xz/liblzma.a -L../../lib -lRblas -lgfortran -lm -lreadline -lncurses -ldl -lm /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libR.so] Error 1 I've checked all the faq's and been googling this with no joy. I'd be grateful for any help on installing this dependency to get Rapache installed Thanks, Sean. [[alternative HTML version deleted]] </pre> Sean O'Keeffe 2011-03-02T15:46:46 Fwd: [Rd] Warning: you may need to use R-patchedwith recent R distros http://comments.gmane.org/gmane.comp.lang.r.fedora/109 <pre>Hi, I noted this message yesterday in R-devel. I think it would sensible to package a patched version while 2.12.2 is not delivered. ---------- Forwarded Message ---------- Subject: [Rd] Warning: you may need to use R-patched with recent R distros Date: Monday 31 January 2011, 19:48:33 From: Prof Brian Ripley &lt;ripley-+7o2aNKnwVPQzY9nttDBhA&lt; at &gt;public.gmane.org&gt; To: R-devel-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org Two things have emerged in testing on x86_64 Fedora 14 which mean that a recent R-patched is probably needed. 1) That OS uses zlib 1.2.5: that claims to be binary-compatible with zlib 1.2.3 but is not, as we found (painfully) on Windows. The remedy was to remap _all_ the symbols in R's own copy of zlib (not just those zlib arranged to remap). The symptoms were crashes using packages XML and rgoobi (both of which link to zlib) and incorrect results in RJaCGH (which contains a copy of zlib). There may well be other problems .... 2) Fedora 14 uses gcc 4.5.1. With CFLAGS containing the default -O2 or higher, HAVE_C99_COMPLEX was detected as false because there is a (genuine) incompatibility between types Rcomplex and C99's double complex. This means that R's fallback code is used, and regretably that contains a serious bug in an 'optimization' by a colleague, so z^n is incorrect for most complex z and integer n (and has been since 2.10.0). The remedy is to use R-patched or R-devel, or only optimize to -O. We've also seen incorrect results from package mvtnorm when C optimization was -O3. The upshot is that there is likely to be a 2.12.2 to fix these issues. </pre> José Matos 2011-02-01T08:46:05 Ubuntu? http://comments.gmane.org/gmane.comp.lang.r.fedora/107 <pre>Hello, What is your opinion on Ubuntu. I´ve encountered a couple hurdles here. The Keyboard: I have to hit the quote button twice to get a quote or apostrophe! I tried adjusting keyboard settings but nothing changed. And the RKWard GUI won´t recognize quotes from my machines even though they show up on the RKWard text editor. On the other hand, RKWard will quoted material whien I copy and paste material with quotes, such as in a help.search query. Thank you in advance, Matt [[alternative HTML version deleted]] _______________________________________________ R-SIG-Fedora mailing list R-SIG-Fedora-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora </pre> Matthew Bascom 2011-01-28T20:29:58 problems with rpubchem package on fedora http://comments.gmane.org/gmane.comp.lang.r.fedora/105 <pre>Hi, I tried to run rpubchem in R 2-12.0 on Fedora 13, after installing XML and RCurl'. The sequence of commands were , just following the paper by Rajarshi Guha. aids &lt;- find.assay.id("lung+cancer+carcinoma") sapply(aids, function(x) get.assay.desc(x)$assay.desc) After quite a while the following message was returned: Warning message: In download.file(url, destfile = tmpdest, method = "internal", mode = "wb", : RxmlNanoFTPGetConnection: failed to create socket What is the meaning and how to fix it? Thank you Andreas </pre> Andreas 2010-11-28T07:21:01 Search Engine Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.fedora