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Petar Milin | 18 Apr 2012 17:54
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Installing texlive dependencies

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. That removed R as well, and some other dependent packages. 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.).
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?

Thanks in advance,
Petar
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R P Herrold | 18 Apr 2012 20:02
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Installing texlive dependencies

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
(Continue reading)

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Peter Baker | 25 Apr 2012 15:03
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Re: Installing texlive dependencies

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
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Petar Milin | 25 Apr 2012 16:39
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Re: 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
(Continue reading)

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Peter Baker | 26 Apr 2012 08:15
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Re: Installing texlive dependencies

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@...> 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,
(Continue reading)

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Petar Milin | 26 Apr 2012 10:01
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Re: 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@...> wrote:
(Continue reading)

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Peter Baker | 26 Apr 2012 16:04
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Re: Installing texlive dependencies

Hi Petar

I can only guess that the dependencies for R rpm's aren't quite
specified right for texlive 2011
but if the appropriate texlive 2011 packages are already installed
then there should be no problems

It is difficult to guess exactly what you need on your system but
here's what I have on mine. Collections pull in the actual packages.
Unfortunately I can't remember the exact details but here's what I
think I did

The repo file is

/etc/yum.repos.d/texlive-release.repo
===========================
[texlive]
name=TeX Live
baseurl=http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/
enabled=1
metadata_expire=1d
gpgcheck=0
=======================

which for Fedora 16 you can install with

rpm -i http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/texlive-release.noarch.rpm

see http://fedoraproject.org/wiki/Features/TeXLive for details of how
to upgrade/install etc - the essential line is
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Petar Milin | 27 Apr 2012 13:39
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Re: Installing texlive dependencies

Dear Peter,
Thank you so much! The texlive-collections did the trick! :-)

So, I am making this digested how-to below, from your last message.

PS: I noticed you are using yum to install R-packages. Isn't it better
to use install.packages() and update.packages() from R?

Best,
Petar

On Fri, 2012-04-27 at 00:04 +1000, Peter Baker wrote:
> Hi Petar
> 
> I can only guess that the dependencies for R rpm's aren't quite
> specified right for texlive 2011
> but if the appropriate texlive 2011 packages are already installed
> then there should be no problems
> 
> It is difficult to guess exactly what you need on your system but
> here's what I have on mine. Collections pull in the actual packages.

> For Fedora 16 you can install with
> rpm -i http://jnovy.fedorapeople.org/texlive/2011/packages.fc16/texlive-release.noarch.rpm
> (see http://fedoraproject.org/wiki/Features/TeXLive for details)

> yum clean all
> yum update
> yum install texlive-collection-latex texlive-collection-latexextra
(Continue reading)

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Peter Baker | 28 Apr 2012 03:24
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Re: Installing texlive dependencies

Hi Petar

Glad this worked!

I only install R and R-devel along with the odd R package using yum -
usually I do this so that I know I have the right dependencies are
installed eg graphviz-R. Once installed I often just use
update.packages() which might conflict with 'yum update' if the
versions on CRAN are newer but yum just installs packages over the
top. Strictly speaking I probably should use something like

yum-builddep graphviz-R

to install required dependencies and then in R

> install.packages("Rgraphviz", dep=T)

should work just fine but only for packages already distributed as
RPMs. But I'm lazy. I know there is some talk of an automatic RPM
repository to mirror CRAN which would be great in that packages
wouldn't need to be compiled but just unpacked - which would be much
quicker. Of course thats an awful lot of work and I don't know how far
its got

I doubt it makes much practical difference except that using
'install.packages' may take quite a bit longer when installing many
packages and some dependencies/libraries might be missing so its a bit
more mucking around

Thanks for making a how-to - its a good idea
(Continue reading)

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Petar Milin | 28 Apr 2012 10:52
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Re: Installing texlive dependencies

Hello!
One correction to the how-to below: you probably must add a symbolic
link. Something like this:
ln -s /usr/share/R/texmf/tex/latex /usr/share/texlive/texmf/tex/latex/R

Best,
Petar

On Sat, 2012-04-28 at 11:24 +1000, Peter Baker wrote:

> Thanks for making a how-to - its a good idea
> 
> Cheers
> peter
> 
> On Fri, Apr 27, 2012 at 9:39 PM, Petar Milin <pmilin@...> wrote:
> > Dear Peter,
> > Thank you so much! The texlive-collections did the trick! :-)
> >
> > So, I am making this digested how-to below, from your last message.
> >
> > Best,
> > Petar
> >
> > On Fri, 2012-04-27 at 00:04 +1000, Peter Baker wrote:
> >> Hi Petar
> >>
> >> I can only guess that the dependencies for R rpm's aren't quite
> >> specified right for texlive 2011
> >> but if the appropriate texlive 2011 packages are already installed
(Continue reading)

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