Installing texlive dependencies

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