[R-sig-Fedora] Installing texlive dependencies

Petar Milin pmilin at ff.uns.ac.rs
Thu Apr 26 10:01:25 CEST 2012 

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:
> 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 <pmilin at ff.uns.ac.rs> wrote:
> > 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
> >>
> >>
> >>
> >
> >
> 
> 
>

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