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

[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]:
> 
> 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