[R-sig-Debian] plans for lenny-cran? can I help?

[Piet Plomp]

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:
> 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]:
> > 
> > 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 ]
> > 
> > > 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.
> > 
> > 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.
> > 
> > > 
> > > Bioinformatics with R at the high-school level? Neat.
> > 
> > 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.
> > 
> > >  
> > > | 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?
> > 
> > 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.
> > 
> > >  
> > > | With the upcoming release of lenny: is anyone planning a lenny-cran? 
> > 
> > Addition: as this would make upgrades a lot easier, we're talking numbers here.
> > 
> > > | If not, can I help (I've only got amd64/x86_64 systems available)?
> > > 
> > > That's what is typically done -- a new release and the porters roll forward
> > > to it too.
> > >  
> > > | I'll need some help setting things up; currently I've got one system
> > > | running lenny (without R as you'll have understood) 
> > > 
> > > I don't understand either.  
> > 
> > The intention of this is: if you need help compiling "lenny-cran" packages,
> > I have a lenny system to do it.
> > 
> > > 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.
> > 
> > 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!
> > 
> > > 
> > > Dirk
> > > 
> > > -- 
> > > Three out of two people have difficulties with fractions.
> > 
> > Btw, the cran README files (e.g. bin/linux/debian/README{,.html}) are not
> > mirrored, at least not to the Utrecht mirror. 
> > 
> > Thanks,
> > 
> > Piet
> > 
> > _______________________________________________
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> 
> -- 
> Dr. Johannes Ranke                 jranke at uni-bremen.de