[R-sig-Fedora] Installing texlive dependencies
Petar Milin
pmilin at ff.uns.ac.rs
Wed Apr 25 16:39:46 CEST 2012
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
> >
> >
> > _______________________________________________
> > R-SIG-Fedora mailing list
> > R-SIG-Fedora at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>
>
>
More information about the R-SIG-Fedora
mailing list