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plans for lenny-cran? can I help?

9 messages · Dirk Eddelbuettel, piet at bioinf.nl, Piet Plomp +1 more

Original
Piet Plomp
# 
Hi,

I'm running a highschool network with Debian etch and the etch-cran
"backports" on top of it. Being bio-informatics, the newest R is essential to
us.

I did some upgrading experiments; switching to ubuntu is not
an option, neither is fetching the sid debs for r.

When trying to upgrade from etch to lenny with etch-cran packages installed
things block on etch-cran dependencies.

With the upcoming release of lenny: is anyone planning a lenny-cran? 
If not, can I help (I've only got amd64/x86_64 systems available)?

I'll need some help setting things up; currenlty I've got one system running
lenny (without R as you'll have understood) on which I could try to compile R
packages.

Yours,

Piet Plomp
Dirk Eddelbuettel
# 
Hi Piet,
On 5 February 2009 at 12:31, Piet Plomp wrote:
| I'm running a highschool network with Debian etch and the etch-cran
| "backports" on top of it. Being bio-informatics, the newest R is essential to
| us.

Bioinformatics with R at the high-school level? Neat.
 
| I did some upgrading experiments; switching to ubuntu is not
| an option, neither is fetching the sid debs for r.

Why?  Many of us use 'apt-pinning' with luck.  My box is 'testing' but I
often install the .deb package I upload into unstable there as well. Works
like a charm most of time.
 
| When trying to upgrade from etch to lenny with etch-cran packages installed
| things block on etch-cran dependencies.

Can you provide details?
 
| With the upcoming release of lenny: is anyone planning a lenny-cran? 
| If not, can I help (I've only got amd64/x86_64 systems available)?

That's what is tyoically done -- a new release and the porters roll forward
to it too.
 
| I'll need some help setting things up; currenlty I've got one system running
| lenny (without R as you'll have understood) 

I don't understand either.  Lenny has its own (now dated) R, it has (current)
R from CRAN (running the stable builds) and it runs the sid build I maintain.

Dirk
1 day later
piet at bioinf.nl
# 
Hi Dirk and people on the list,

[ This is an attempt to recreate a message I accidently sent only to Dirk;
  extended with some recent experiences ]
Addition: with lenny almost (14feb) released I do want to upgrade to lenny,
now or in the weeks to come. 
We're talking 40 or so systems with 24/7 availability.
When you're uning etch-cran, updating to lenny is an issue.
That's where a potential lenny-cran could help.
R is used in teaching and to some extent research. The students apply their
knowledge in their practice year at e.g. a university hospital.
We are the bioinformatics part a highschool, I mean something like the German
Hochschule or "university of applied schience".
I'm the sysadmin running the bioinformatics network.

All systems run etch with etch-cran on top of it. Above, more than 150 R
packages were compiled locally and offered over nfs.
Of course. 

Take 1: lenny with etch-cran

First situation: a new system, lenny installed from scratch,
attempted to install etch-cran packages on top of it.
This requires libgfortran1 which depends on gcc-4.1-base (4.1.1). Lenny
provides a newer version of gcc-4.1-base (4.1.2) which is needed by all
compilers from the Gnu compiler suite. Most of those have newer versions, gpc
does not (yes we come across pascal program now and then). 
I solved this by hand installing (dpkg) the etch packages libgfortran1 and
gcc-4.1-base, not installing gpc, and preventing gcc-4.1-base from upgrading
to 4.1.2.
r-base-dev (etch-cran) depends on refblas3-dev or atlas3-base-dev. Importing
those from etch gave all sorts of trouble I can't reproduce anymore.
I can upgrade my 150+ non-debian R packages without r-base-dev, so that's not a
problem. 

Second situation: an existing etch system with etch-cran packages.
Upgrading Gnu compilers to the 4.3 level and skipping gpc gave the possibility
to leave libgfortran1 and gcc-4.1-base alone. Again, no r-base-dev.

Take 2: lenny with R packages (and some other) from sid.

This solves the libgfortran1 problem of course. gpc (== 4.1) can be installed;
gcc-4.1-base upgrade.
This upgrade needs tcl/tk 8.5 (lenny has 8.4 by default, but provides 8.5) and
the newer pcre (7.8, lenny has 7.6) suite. Lenny keeps the default tclsh
pointing to tclsh 8.4, I may need to change that to 8.5. Same for tk.
python-biopython needs python-tk which needs tk8.4 (or even 8.3) with python
at 2.5.2 (lenny) level. 
To make sure the locally compiled extension packages also use tcl/tk8.5,
I'll try installing tcl/tk8.5-dev but not tcl/tk8.4-dev.
Addition: as this would make upgrades a lot easier, we're talking numbers here.
The intention of this is: if you need help compiling "lenny-cran" packages,
I have a lenny system to do it.
In the meantime I upgraded one system to sid's r-* packages. Spent the rest of
the day recreating our local R extension package repository for use on lenny
systems. All worked well *given the right *-dev packages of course).

Thank you for maintaining the R deb packages!
Btw, the cran README files (e.g. bin/linux/debian/README{,.html}) are not
mirrored, at least not to the Utrecht mirror. 

Thanks,

Piet
Dirk Eddelbuettel
# 
Piet,

I think you need to enable the backport archive as the README suggests. 

IIRC that will help with gfortran and tcl/tk 8.5.  Others run that happily,
so we should be able to help you.  I actually don't run etch anywhere myself
so I will defer to others.

Dirk
Johannes Ranke
# 
Hi Piet,

I do plan to keep doing backports, maybe with the help of Tyler, also
for lenny. Thanks for your offer to help - maybe you could compile the
amd64 packages, although I currently use this process to check build
dependencies (I am not using pbuilder for the initial i386 builds).

Best regards,

Johannes


* piet at bioinf.nl <piet at bioinf.nl> [090206 20:20]:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Piet Plomp
    

    

      
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Hi Johannes,

Backports for lenny would be very welcome!

I'd love to compile the amd64 packages; I could do the dependency check for
you, but we need to synchronize the way we build the packages. So I'll need
some help in setting things up.

One decisions to make: depend on tcl and tk 8.4 (default for lenny) or 8.5
(available in lenny). I guess 8.5 is ok unless we need wish/tclsh etc itself.
Lenny's python-tk depends on 8.4.

Best regards,

Piet

        
On Fri, Feb 06, 2009 at 09:50:36PM +0100, Johannes Ranke wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
  


  


      

    

    
5 days later

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Hi Piet,

thanks for your input to this. I have no idea, frankly speaking, if tcl
and tk 8.4 or 8.5 would be the better choice. As upstream (Dirk) uses
8.5, I would try to stick with it, as it is availabe in lenny, as you
pointed out. Is your point that if we would need tclsh or wish, this
would conflict with tcl8.5, as 8.4 is the default on lenny? I am not
ware that tclsh and wish are being used, are you, Dirk?

Johannes

* Piet Plomp <piet at bioinf.nl> [090208 19:20]:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 12 February 2009 at 20:56, Johannes Ranke wrote:

        
| Hi Piet,
| 
| thanks for your input to this. I have no idea, frankly speaking, if tcl
| and tk 8.4 or 8.5 would be the better choice. As upstream (Dirk) uses
| 8.5, I would try to stick with it, as it is availabe in lenny, as you
| pointed out. Is your point that if we would need tclsh or wish, this
| would conflict with tcl8.5, as 8.4 is the default on lenny? I am not
| ware that tclsh and wish are being used, are you, Dirk?

The recommended R package tcltk -- still the only truly cross-platform GUI --
gets to use so-called 'themed' widgets under the 8.5 versions. As these look
a lot prettier, R Core sort-of suggests upgrading.  As there is no pain and
some gain in Debian unstable and testing, it (still) seems like the right
call.

I am not aware of any conflicts within the tcl/tk world, but I am not a heavy
tcl/tk user. I still use Perl/Tk and other things alongside and everybody
seems to get along.  Maybe I missed what was upsetting Piet...

Dirk

  
    

      
      
    

  


  


      

    

    
4 days later

    

      
      

        


  

        

      Johannes Ranke
    

    

      
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Hi Piet,

sorry for not answering in more detail the last time. Let me make a few
additions (I cut some stuff from the thread, in order to avoid noise):

            

      
      
      
    

        
I have just set up the chroot to start building lenny-cran. It might
still take me some time though. In the meantime, I have updated the
pinning guidance in the README.

            

      
      
      
    

        
Great indeed!

            

      
      
      
    

        
As you experienced, this is problematic, as the dependencies in
etch-cran were tailored to etch.

            

      
      
      
    

        
On my lenny systems, tcl/tk 8.5 was not pulled by the sid R packages,
only the pcre from sid. Did you make any progress on the tcl/tk issues?

            

      
      
      
    

        
Is this OK now?

            

      
      
      
    

        
I tried a few other mirrors, and they are OK. I suggest contacting the
admin of the Utrecht mirror, and/or Stefan Theussl
<stefan.theussl at wu-wien.ac.at> from CRAN.

I hope everything is running well at your end meanwhile,

Johannes