[R-sig-Fedora] Installing texlive dependencies

[R P Herrold]

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