Installing texlive dependencies
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:
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 From memory I didn't install the standard texlive2007 first for F16 - 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 <herrold at owlriver.com> wrote:
On Wed, 18 Apr 2012, Petar Milin wrote:
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.
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)
That removed R as well, and some other dependent packages.
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
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.).
Ley me try: on a fresh install of Fedora 16 (64 bit), I ran: [root at 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 at vm049244226 ~]# cat /etc/redhat-release Fedora release 16 (Verne) [root at 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.
example(t.test)
t.test> require(graphics)
t.test> 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> 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> ## Classical example: Student's sleep data
t.test> plot(extra ~ group, data = sleep)
t.test> ## Traditional interface
t.test> 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> ## Formula interface
t.test> 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
q()
Save workspace image? [y/n/c]: n [root at vm049244226 ~]# ... so it _can_ work under Fedora 16 ...
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?
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 ;( -- Russ herrold
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