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

piet at bioinf.nl piet at bioinf.nl
Fri Feb 6 17:13:54 CET 2009

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

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. 



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