[R-sig-Fedora] Installing texlive dependencies
Peter Baker
baker.peter2009 at gmail.com
Thu Apr 26 16:04:34 CEST 2012
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
yum clean all
otherwise things don't update properly
and so this is probably
$ yum clean all
$ yum update (assuming no texlive 2007 on your system although this
is supposed to work to upgrade to texlive 2011 I'm not quite so sure)
$ yum install texlive-collection-latex texlive-collection-latexextra
etc etc - the texlive collections below (or just keep adding until R
installs)
$ yum install R R-devel etc
[root at clearwell ~]# yum list all texlive*collection*
Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit
Loading mirror speeds from cached hostfile
* fedora: mirror.aarnet.edu.au
* rpmfusion-free: ucmirror.canterbury.ac.nz
* rpmfusion-free-updates: ucmirror.canterbury.ac.nz
* rpmfusion-nonfree: ucmirror.canterbury.ac.nz
* rpmfusion-nonfree-updates: ucmirror.canterbury.ac.nz
* updates: mirror.aarnet.edu.au
Installed Packages
texlive-collection-basic.noarch 2011-5.20120115_r25109.svn20730 @texlive
texlive-collection-bibtexextra.noarch 2011-5.20120115_r25109.svn24610 @texlive
texlive-collection-binextra.noarch 2011-5.20120115_r25109.svn25012 @texlive
texlive-collection-documentation-base.noarch
2011-5.20120115_r25109.svn17091 @texlive
texlive-collection-fontsextra.noarch 2011-5.20120115_r25109.svn25226 @texlive
texlive-collection-fontsrecommended.noarch
2011-5.20120115_r25109.svn22193 @texlive
texlive-collection-fontutils.noarch 2011-5.20120115_r25109.svn24759 @texlive
texlive-collection-formatsextra.noarch 2011-5.20120115_r25109.svn21879 @texlive
texlive-collection-genericrecommended.noarch
2011-5.20120115_r25109.svn19849 @texlive
texlive-collection-htmlxml.noarch 2011-5.20120115_r25109.svn13822 @texlive
texlive-collection-latex.noarch 2011-5.20120115_r25109.svn25030 @texlive
texlive-collection-latexextra.noarch 2011-5.20120115_r25109.svn25184 @texlive
texlive-collection-latexrecommended.noarch
2011-5.20120115_r25109.svn25030 @texlive
texlive-collection-metapost.noarch 2011-5.20120115_r25109.svn23252 @texlive
texlive-collection-music.noarch 2011-5.20120115_r25109.svn25121 @texlive
texlive-collection-pictures.noarch 2011-5.20120115_r25109.svn25031 @texlive
texlive-collection-pstricks.noarch 2011-5.20120115_r25109.svn25142 @texlive
texlive-collection-publishers.noarch 2011-5.20120115_r25109.svn24685 @texlive
texlive-collection-texinfo.noarch 2011-5.20120115_r25109.svn15216 @texlive
texlive-collection-xetex.noarch 2011-5.20120115_r25109.svn24140 @texlive
Available Packages
DELETED
Once these were installed then install R
[root at clearwell ~]# yum list all R-*
Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit
Loading mirror speeds from cached hostfile
* fedora: mirror.optus.net
* rpmfusion-free: ucmirror.canterbury.ac.nz
* rpmfusion-free-updates: ucmirror.canterbury.ac.nz
* rpmfusion-nonfree: ucmirror.canterbury.ac.nz
* rpmfusion-nonfree-updates: ucmirror.canterbury.ac.nz
* updates: mirror.optus.net
Installed Packages
R.x86_64 2.15.0-1.fc16 installed
R-DynDoc.noarch 1.32.0-2.fc16 @updates
R-RCurl.x86_64 1.7.0-2.fc16 @updates
R-RODBC.x86_64 1.3.3-1.fc16 @updates
R-RUnit.noarch 0.4.26-3.fc16 @updates
R-XML.x86_64 3.4.3-2.fc16 @updates
R-bitops.x86_64 1.0.4.1-6.fc16 @updates
R-car.noarch 2.0-9.fc15 installed
R-core.x86_64 2.15.0-1.fc16 @updates
R-devel.x86_64 2.15.0-1.fc16 installed
R-java.x86_64 2.15.0-1.fc16 @updates
R-java-devel.x86_64 2.15.0-1.fc16 @updates
R-tkWidgets.noarch 1.32.0-2.fc16 @updates
R-widgetTools.noarch 1.32.0-2.fc16 @updates
R-xtable.noarch 1.6.0-1.fc16 @updates
R-zoo.x86_64 1.7.6-2.fc16 @updates
Available Packages
DELETED
I've found that things like pdflatex / sweave etc run fine if I use
something like
R CMD Sweave ....
R CMD pdflatex .... etc but I mainly use 'R CMD rubber' which does
all the rerunning of pdflatex and bibtex as required
so I don't worry about putting Sweave.sty in the right place and I
tend to use Makefiles anyway as I'm too lazy to work out what I need
each time
Hope this helps - but it does take quite a long time and lots of downloading
Good luck!
Cheers
peter
On Thu, Apr 26, 2012 at 6:01 PM, Petar Milin <pmilin at ff.uns.ac.rs> wrote:
>
> 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
>> >>
>> >>
>> >>
>> >
>> >
>>
>>
>>
>
>
--
Dr Peter Baker | Senior Lecturer/Statistician | Epidemiology & Biostatistics
Room 416 | School of Population Health |The University of Queensland | Public
Health Building | Herston Rd | Herston Qld 4006 | Australia
Ph: +61 7 3346 4747 | Fax: +61 7 3365 5442 | http://www.sph.uq.edu.au/ |
Email: p.baker1 at uq.edu.au or baker.peter2009 at gmail.com
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