http://blog.gmane.org/gmane.comp.lang.r.fedora hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org 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: RSQLi</pre> Bruce Pennypacker 2012-05-21T20:30:52 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</pre> Badoo 2012-04-21T01:47:19 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 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 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 r</pre> Allen S. Rout 2012-03-12T20:10:06 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_ADDR</pre> Mark Leeds 2011-12-25T03:39:39 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 ================================================== downlo</pre> Peter Baker 2011-12-14T08:08:16 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 he</pre> Mark Leeds 2011-11-09T04:47:13 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 KernSm</pre> Mark Leeds 2011-11-07T20:39:59 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 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 #=================================================</pre> Mark Leeds 2011-11-06T23:43:30 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 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</pre> Michael Smith 2011-08-05T14:40:52 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</pre> Wolfgang RAFFELSBERGER 2011-07-18T10:23:24 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 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 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 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</pre> Sean O'Keeffe 2011-03-02T15:46:46 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 def</pre> José Matos 2011-02-01T08:46:05 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 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 the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.fedora