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://permalink.gmane.org/gmane.comp.lang.r.fedora/211 <pre> On May 22, 2012, at 17:13 , Tom Callaway wrote: Yes, I think this is the case. I don't think there are any structural requirements for Tcl 8.5. AFAIR, we use some ABI features not present in at least 8.0, but I have long forgotten what is the last version to break. However, an ABI level issue would prevent building the package at all, which is clearly not the case here. The remaining issue is whether applications/packages could be using new features. That is pretty much impossible to guard against, but I would assume that we'd be hearing about it if they do.... When Tcl 8.6 finally comes chugging along, there is a non-vanishing chance that I'd try using the new canvas features for a demo or maybe even a graphics device driver. I'll try to remember to check the Tcl version number... </pre> peter dalgaard 2012-05-22T15:42:25 http://permalink.gmane.org/gmane.comp.lang.r.fedora/210 <pre> Ah, okay. I do not believe we're packaging sqldf right now. ~tom == Fedora Project </pre> Tom Callaway 2012-05-22T15:13:38 http://permalink.gmane.org/gmane.comp.lang.r.fedora/209 <pre> Hi Tom, Thanks for jumping in. My read, and I would ask Peter to comment as well, is that this requirement seems to be specific to the 'sqldf' package on CRAN and not to "base" R more generally. If Fedora/EPEL are including sqldf as a binary RPM for installation via yum, that might be a different scenario however. If the min function is in fact in the tclx extension package to tcl 8.4 in RHEL 5 and Bruce follows Peter's follow up note on using tclRequire(), then that might satisfy the focused need by Bruce. Additionally, reading the INSTALL file for sqldf: http://cran.r-project.org/web/packages/sqldf/INSTALL it would seem that the tcl requirement is optional, due to its use by Gabor's gsubfn() function. There appears to be an option, which Bruce might want to try within R: options(gsubfn.engine = "R") after loading the sqldf package. This would force the use of R code in place of tcl code. That might be a quick and dirty solution here. Regards, Marc </pre> Marc Schwartz 2012-05-22T15:09:21 http://permalink.gmane.org/gmane.comp.lang.r.fedora/208 <pre> Does R need tcl 8.5 now? ~tom == Fedora Project </pre> Tom Callaway 2012-05-22T14:48:14 http://permalink.gmane.org/gmane.comp.lang.r.fedora/207 <pre> On May 22, 2012, at 8:28 AM, Bruce Pennypacker wrote: Thanks to Peter for the clarifications. There was something about the combination of issues that was bugging me. Looking more closely now at the SQL statement being executed it becomes a bit more clear. Taking a peek at the SRPMS for RHEL 5: http://ftp.redhat.com/pub/redhat/linux/enterprise/5Server/en/os/SRPMS/ it would appear that tcl 8.4 is the latest version available. Checking RHEL 6, it would appear that tcl is 8.5 there so they did upgrade 6's tcl installation. This suggests that you will need to go upstream if you want 8.5 on RHEL 5 to satisfy the need for the 'min' function and you may need to be cautious in mixing versions/dependencies, etc. Regards, Marc </pre> Marc Schwartz 2012-05-22T14:36:30 http://permalink.gmane.org/gmane.comp.lang.r.fedora/206 <pre> On May 22, 2012, at 15:28 , Bruce Pennypacker wrote: Did you try the tclRequire() bit? These things are like R packages, it's not enough to install them; you also need to load them into the running Tcl interpreter. </pre> peter dalgaard 2012-05-22T14:33:36 http://permalink.gmane.org/gmane.comp.lang.r.fedora/205 <pre>Ahh, thanks for the pointers. Yes, I screwed up the version number of tcltk. It's 8.4.13, not 8.14.3... And I do see a separate tclx package in the RHEL5 repo, but after installing it and it's companion -devel package I'm still getting the same unknown function error. Given that this is likely new in Tcl 8.5 I may just bite the bullet and install that then rebuild R. But in any event you've given me some good information to hopefully get me in the right direction. Thanks! -Bruce </pre> Bruce Pennypacker 2012-05-22T13:28:10 http://permalink.gmane.org/gmane.comp.lang.r.fedora/204 <pre>On 5/21/12 4:54 PM, Marc Schwartz wrote capabilities("tcltk") does return TRUE. capabilities() returns TRUE for everything except for tiff, aqua, and profmem. We do have the -devel RPM's for tcl/tk installed so I would have expected the R config to pick them up. I may go back and re-run it and take a closer look. -Bruce </pre> Bruce Pennypacker 2012-05-22T13:23:46 http://permalink.gmane.org/gmane.comp.lang.r.fedora/203 <pre> On May 21, 2012, at 22:54 , Marc Schwartz wrote: As I read the error message, Tcl as such is working fine. However, the min function seems to be new in Tcl 8.5, and it is unclear which version is in RH 5.6. There's certainly no Tcl 8.14.3. (library(tcltk); tcl("info", "tclversion") will tell you which one is really loaded.) Google suggests that in earlier versions, there was an add-on called "TclX" that defined min and max functions (among other things, I presume). If it is in RH5.6, I would guess that you could load it with tclRequire("TclX") (or however it might be capiTaLized) before trying to do anything with sqldf(). </pre> peter dalgaard 2012-05-22T06:56:11 http://permalink.gmane.org/gmane.comp.lang.r.fedora/202 <pre> What does: capabilities("tcltk") show? It should return TRUE if all is generally well. If it does come back TRUE, check the output of: capabilities() to see if anything else comes back as FALSE. Since you installed from source rather than using the pre-built binary R RPM available for RHEL from the EPEL (http://fedoraproject.org/wiki/EPEL): http://dl.fedoraproject.org/pub/epel/5/x86_64/repoview/R.html you may be missing the required '-devel' RPMs that contain the header files for tcl/tk. I would have thought that you might have gotten errors from 'config' if that were the case, but perhaps they were missed? Regards, Marc Schwartz </pre> Marc Schwartz 2012-05-21T20:54:49 http://permalink.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 http://permalink.gmane.org/gmane.comp.lang.r.fedora/200 <pre>Hello! One correction to the how-to below: you probably must add a symbolic link. Something like this: ln -s /usr/share/R/texmf/tex/latex /usr/share/texlive/texmf/tex/latex/R Best, Petar On Sat, 2012-04-28 at 11:24 +1000, Peter Baker wrote: </pre> Petar Milin 2012-04-28T08:52:15 http://permalink.gmane.org/gmane.comp.lang.r.fedora/199 <pre>Hi Petar Glad this worked! I only install R and R-devel along with the odd R package using yum - usually I do this so that I know I have the right dependencies are installed eg graphviz-R. Once installed I often just use update.packages() which might conflict with 'yum update' if the versions on CRAN are newer but yum just installs packages over the top. Strictly speaking I probably should use something like yum-builddep graphviz-R to install required dependencies and then in R should work just fine but only for packages already distributed as RPMs. But I'm lazy. I know there is some talk of an automatic RPM repository to mirror CRAN which would be great in that packages wouldn't need to be compiled but just unpacked - which would be much quicker. Of course thats an awful lot of work and I don't know how far its got I doubt it makes much practical difference except that using 'install.packages' may take quite a bit longer when installing many packages and some dependencies/libraries might be missing so its a bit more mucking around Thanks for making a how-to - its a good idea Cheers peter On Fri, Apr 27, 2012 at 9:39 PM, Petar Milin &lt;pmilin-FOMHziomoF2c3/pwSr3LOw&lt; at &gt;public.gmane.org&gt; wrote: </pre> Peter Baker 2012-04-28T01:24:20 http://permalink.gmane.org/gmane.comp.lang.r.fedora/198 <pre>Dear Peter, Thank you so much! The texlive-collections did the trick! :-) So, I am making this digested how-to below, from your last message. PS: I noticed you are using yum to install R-packages. Isn't it better to use install.packages() and update.packages() from R? Best, Petar On Fri, 2012-04-27 at 00:04 +1000, Peter Baker wrote: </pre> Petar Milin 2012-04-27T11:39:04 http://permalink.gmane.org/gmane.comp.lang.r.fedora/197 <pre>Hi Petar I can only guess that the dependencies for R rpm's aren't quite specified right for texlive 2011 but if the appropriate texlive 2011 packages are already installed then there should be no problems It is difficult to guess exactly what you need on your system but here's what I have on mine. Collections pull in the actual packages. Unfortunately I can't remember the exact details but here's what I think I did The repo file is /etc/yum.repos.d/texlive-release.repo =========================== [texlive] name=TeX Live baseurl=http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/ enabled=1 metadata_expire=1d gpgcheck=0 ======================= which for Fedora 16 you can install with rpm -i http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/texlive-release.noarch.rpm see http://fedoraproject.org/wiki/Features/TeXLive for details of how to upgrade/install etc - the essential line is yum clean all otherwise things don't update properly and so this is probably $ yum clean all $ yum update (assuming no texlive 2007 on your system although this is supposed to work to upgrade to texlive 2011 I'm not quite so sure) $ yum install texlive-collection-latex texlive-collection-latexextra etc etc - the texlive collections below (or just keep adding until R installs) $ yum install R R-devel etc [root&lt; at &gt;clearwell ~]# yum list all texlive*collection* Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit Loading mirror speeds from cached hostfile * fedora: mirror.aarnet.edu.au * rpmfusion-free: ucmirror.canterbury.ac.nz * rpmfusion-free-updates: ucmirror.canterbury.ac.nz * rpmfusion-nonfree: ucmirror.canterbury.ac.nz * rpmfusion-nonfree-updates: ucmirror.canterbury.ac.nz * updates: mirror.aarnet.edu.au Installed Packages texlive-collection-basic.noarch 2011-5.20120115_r25109.svn20730 &lt; at &gt;texlive texlive-collection-bibtexextra.noarch 2011-5.20120115_r25109.svn24610 &lt; at &gt;texlive texlive-collection-binextra.noarch 2011-5.20120115_r25109.svn25012 &lt; at &gt;texlive texlive-collection-documentation-base.noarch 2011-5.20120115_r25109.svn17091 &lt; at &gt;texlive texlive-collection-fontsextra.noarch 2011-5.20120115_r25109.svn25226 &lt; at &gt;texlive texlive-collection-fontsrecommended.noarch 2011-5.20120115_r25109.svn22193 &lt; at &gt;texlive texlive-collection-fontutils.noarch 2011-5.20120115_r25109.svn24759 &lt; at &gt;texlive texlive-collection-formatsextra.noarch 2011-5.20120115_r25109.svn21879 &lt; at &gt;texlive texlive-collection-genericrecommended.noarch 2011-5.20120115_r25109.svn19849 &lt; at &gt;texlive texlive-collection-htmlxml.noarch 2011-5.20120115_r25109.svn13822 &lt; at &gt;texlive texlive-collection-latex.noarch 2011-5.20120115_r25109.svn25030 &lt; at &gt;texlive texlive-collection-latexextra.noarch 2011-5.20120115_r25109.svn25184 &lt; at &gt;texlive texlive-collection-latexrecommended.noarch 2011-5.20120115_r25109.svn25030 &lt; at &gt;texlive texlive-collection-metapost.noarch 2011-5.20120115_r25109.svn23252 &lt; at &gt;texlive texlive-collection-music.noarch 2011-5.20120115_r25109.svn25121 &lt; at &gt;texlive texlive-collection-pictures.noarch 2011-5.20120115_r25109.svn25031 &lt; at &gt;texlive texlive-collection-pstricks.noarch 2011-5.20120115_r25109.svn25142 &lt; at &gt;texlive texlive-collection-publishers.noarch 2011-5.20120115_r25109.svn24685 &lt; at &gt;texlive texlive-collection-texinfo.noarch 2011-5.20120115_r25109.svn15216 &lt; at &gt;texlive texlive-collection-xetex.noarch 2011-5.20120115_r25109.svn24140 &lt; at &gt;texlive Available Packages DELETED Once these were installed then install R [root&lt; at &gt;clearwell ~]# yum list all R-* Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit Loading mirror speeds from cached hostfile * fedora: mirror.optus.net * rpmfusion-free: ucmirror.canterbury.ac.nz * rpmfusion-free-updates: ucmirror.canterbury.ac.nz * rpmfusion-nonfree: ucmirror.canterbury.ac.nz * rpmfusion-nonfree-updates: ucmirror.canterbury.ac.nz * updates: mirror.optus.net Installed Packages R.x86_64 2.15.0-1.fc16 installed R-DynDoc.noarch 1.32.0-2.fc16 &lt; at &gt;updates R-RCurl.x86_64 1.7.0-2.fc16 &lt; at &gt;updates R-RODBC.x86_64 1.3.3-1.fc16 &lt; at &gt;updates R-RUnit.noarch 0.4.26-3.fc16 &lt; at &gt;updates R-XML.x86_64 3.4.3-2.fc16 &lt; at &gt;updates R-bitops.x86_64 1.0.4.1-6.fc16 &lt; at &gt;updates R-car.noarch 2.0-9.fc15 installed R-core.x86_64 2.15.0-1.fc16 &lt; at &gt;updates R-devel.x86_64 2.15.0-1.fc16 installed R-java.x86_64 2.15.0-1.fc16 &lt; at &gt;updates R-java-devel.x86_64 2.15.0-1.fc16 &lt; at &gt;updates R-tkWidgets.noarch 1.32.0-2.fc16 &lt; at &gt;updates R-widgetTools.noarch 1.32.0-2.fc16 &lt; at &gt;updates R-xtable.noarch 1.6.0-1.fc16 &lt; at &gt;updates R-zoo.x86_64 1.7.6-2.fc16 &lt; at &gt;updates Available Packages DELETED I've found that things like pdflatex / sweave etc run fine if I use something like R CMD Sweave .... R CMD pdflatex .... etc but I mainly use 'R CMD rubber' which does all the rerunning of pdflatex and bibtex as required so I don't worry about putting Sweave.sty in the right place and I tend to use Makefiles anyway as I'm too lazy to work out what I need each time Hope this helps - but it does take quite a long time and lots of downloading Good luck! Cheers peter On Thu, Apr 26, 2012 at 6:01 PM, Petar Milin &lt;pmilin-FOMHziomoF2c3/pwSr3LOw&lt; at &gt;public.gmane.org&gt; wrote: </pre> Peter Baker 2012-04-26T14:04:34 http://permalink.gmane.org/gmane.comp.lang.r.fedora/196 <pre> Dear Peter, Please, can you explain how did you make R accept the TeXLive 2011? I would like to give it a try. But, when I install TeXLive 2011, and then R, the later is asking for dependencies (a list of tex-related packages), and it puts them in /usr/share/texmf. Best, Petar On Thu, 2012-04-26 at 16:15 +1000, Peter Baker wrote: </pre> Petar Milin 2012-04-26T08:01:25 http://permalink.gmane.org/gmane.comp.lang.r.fedora/195 <pre>Hi Petar My guess is that you had something else floating around from previous fedora update/install which caused some mismatches as some binaries have been put into texlive that previously weren't in texlive 2007 - five years (2007 to 2012) is quite a time in computing so sadly you'd expect things to change. I have not used texlive 2007 for quite some time (perhaps f13) and not really had much of a problem with R once I got rid of remnants of texlive 2007. I find texlive 2011/12 to be much easier to update once you get it working. Linux mint is still at texlive 2009 and that seems to work perfectly fine too Of course it doesn't really matter as tex seems to change at a glacial pace compared to R - I am glad it is now working for you. Cheers Peter On Thu, Apr 26, 2012 at 12:39 AM, Petar Milin &lt;pmilin-FOMHziomoF2c3/pwSr3LOw&lt; at &gt;public.gmane.org&gt; wrote: </pre> Peter Baker 2012-04-26T06:15:14 http://permalink.gmane.org/gmane.comp.lang.r.fedora/194 <pre>Hello! Finally [ and contrary to Peter :-) ], I have installed TeXLive 2007 from the main repo. My experience was such that R complained about missing LaTeX in /usr/share/texmf/, while TeXLive 2011 is in the /usr/share/texlive/. I even tried to build symbolic links, to cheat R, but it was firm and complained throughout. Thus, I installed TeXLive 2007 from scratch, and R was/is happy. All additional packages for LaTeX, of course, must be included manually. It is a bit of hassle but not too much. Anyway, once you master how-to, it is smooth. Best, Petar On Wed, 2012-04-25 at 23:03 +1000, Peter Baker wrote: </pre> Petar Milin 2012-04-25T14:39:46 http://permalink.gmane.org/gmane.comp.lang.r.fedora/193 <pre>Hi I've been using the F16 TexLive 2011 stable repo for F16 for quite some time baseurl=http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/ (not the F15 repo as that would be asking for trouble) and for F17beta I've been using the F17 TexLive 2012 repo baseurl=http://jnovy.fedorapeople.org/texlive/2012/packages.fc17/ in /etc/yum.repos.d/texlive-release.repo definitely didn't for F17beta this week. I installed the recent texlive first (as above) then R installed without a hitch. My only problem with F17beta is that for R 2.15 RBGL from Bioconductor won't compile with GCC4.7 - I can't recall any problems with F16 There is plenty of discussion about getting the current texlive into standard fedora in standard distro but it revolves around licences rather than any technical problems. It certainly seems to work well although I had quite a few problems a year ago (bad dependencies) but it seems to work pretty well these days. It is nicely set up with collections (see http://fedoraproject.org/wiki/Features/TeXLive and http://jnovy.fedorapeople.org/texlive/collections ) and you can install a particular style file with yum directly eg yum install 'tex(epsfig.sty)' Good luck regards Peter On Thu, Apr 19, 2012 at 4:02 AM, R P Herrold &lt;herrold-lD49m8UYmPxWk0Htik3J/w&lt; at &gt;public.gmane.org&gt; wrote: </pre> Peter Baker 2012-04-25T13:03:22 http://permalink.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 http://permalink.gmane.org/gmane.comp.lang.r.fedora/191 <pre> ughhh ---- filing a bug with Fedora would be useful as well, so they could address any systemic issues that may exist (we'll look into this later in this email) Sadly, implying that 'yum' was used for the removal ... that tool is wayyy' too enthusiastic at removing packages; rpm -e ... is more of a scalpel Ley me try: on a fresh install of Fedora 16 (64 bit), I ran: [root&lt; at &gt;vm049244226 ~]# yum install R ... which wanted much TeX goodness ... texlive x86_64 2007-66.fc16 updates 1.6 M texlive-dvips x86_64 2007-66.fc16 updates 192 k texlive-latex x86_64 2007-66.fc16 updates 84 k texlive-texmf noarch 2007-40.fc16 updates 2.8 M texlive-texmf-dvips noarch 2007-40.fc16 updates 238 k texlive-texmf-fonts noarch 2007-40.fc16 updates 48 M texlive-texmf-latex noarch 2007-40.fc16 updates 5.2 M texlive-utils x86_64 2007-66.fc16 updates 251 k ... and R seems to work here: [root&lt; at &gt;vm049244226 ~]# cat /etc/redhat-release Fedora release 16 (Verne) [root&lt; at &gt;vm049244226 ~]# R 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-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. t.test&gt; require(graphics) t.test&gt; t.test(1:10,y=c(7:20)) # P = .00001855 Welch Two Sample t-test data: 1:10 and c(7:20) t = -5.4349, df = 21.982, p-value = 1.855e-05 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -11.052802 -4.947198 sample estimates: mean of x mean of y 5.5 13.5 t.test&gt; t.test(1:10,y=c(7:20, 200)) # P = .1245 -- NOT significant anymore Welch Two Sample t-test data: 1:10 and c(7:20, 200) t = -1.6329, df = 14.165, p-value = 0.1245 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -47.242900 6.376233 sample estimates: mean of x mean of y 5.50000 25.93333 t.test&gt; ## Classical example: Student's sleep data t.test&gt; plot(extra ~ group, data = sleep) t.test&gt; ## Traditional interface t.test&gt; with(sleep, t.test(extra[group == 1], extra[group == 2])) Welch Two Sample t-test data: extra[group == 1] and extra[group == 2] t = -1.8608, df = 17.776, p-value = 0.07939 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates: mean of x mean of y 0.75 2.33 t.test&gt; ## Formula interface t.test&gt; t.test(extra ~ group, data = sleep) Welch Two Sample t-test data: extra by group t = -1.8608, df = 17.776, p-value = 0.07939 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -3.3654832 0.2054832 sample estimates: mean in group 1 mean in group 2 0.75 2.33 Save workspace image? [y/n/c]: n [root&lt; at &gt;vm049244226 ~]# ... so it _can_ work under Fedora 16 ... The packaging decisions behind R included support for the ability to generate postscript, and documentation; that dragged in all the TeX, in part A clean install of Fedora comes to mind, because mixing packaging systems is inherently 'pot luck' and random in nature, just as mixing tarball hand-compiled matter into a package managed system rarely works well sorry to bear that news ;( </pre> R P Herrold 2012-04-18T18:02:52 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.fedora